MOLECULAR MAPPING OF RUST RESISTANT QTLS IN A SYNTHETIC
HEXAPLOID WHEAT POPULATION
By
Jeffrey David Kovach

A THESIS
Submitted to
Michigan State University
in partial fulfillment of the requirements
for the degree of
Plant Breeding, Genetics, and Biotechnology-Plant Biology- Master of Science
2017

ABSTRACT
MOLECULAR MAPPING OF RUST RESISTANT QTLS IN A SYNTHETIC
HEXAPLOID WHEAT POPULATION
By
Jeffrey David Kovach

Triticum aestivum, common wheat, is a widely grown crop that is responsible for a large
portion of worldwide consumed calories. Bread wheat is an allohexaploid derived from a series
of hybridization and polyploidization events between three diploid progenitor species. Due to its
origin, genetic diversity across the hexaploid wheat genome is lacking, especially in the D
genome. Ae. tauschii, the D genome diploid progenitor, is an important source of D genome
variation and has been used to identify novel genes for multiple traits including disease
resistance. The evolution and spread of new pathogenic Puccinia races highlight the need to
identify and utilize novel sources of disease resistance. A recombinant inbred line population
was derived from a cross between the synthetic 9.131.15(tetraPrelude/TA2474) and KS05HW14,
a hard white winter wheat. This population was phenotyped for resistance to stem, stripe and leaf
rust. All-stage resistance to stem and stripe rust was mapped on 5BL and 4DS originating from
9.131.15 and TA2474, respectively. Leaf rust resistance was mapped to 3BL and adult plant
resistance QTLs were mapped to the 6D and 7D chromosomes for leaf and stem rust resistance
in Mason, MI in 2017. This study identifies resistance to all three Puccinia rust species in this
RIL population. However, further work is needed to determine if the 4DS and 5BL loci are novel
and the identified adult plant resistance QTLs can be repeatedly observed. A single RIL was
phenotyped as resistant to all three Puccinia fungal pathogens in all tested environments. This
line can be used as a useful source of disease resistance to these fungal pathogens.

Copyright by
JEFFREY DAVID KOVACH
2017

This thesis is dedicated to my family, friends, and loving fiancée. Thank you for all your support
over the years. This would not be possible without you.

iv

ACKNOWLEDGMENTS

I would like to acknowledge the members of my committee Dr. Amy Iezzoni, Dr. C.
Robin Buell, and Dr. Eric Olson for their feedback and guidance during my time as a Master
student. Particularly, Dr. Eric Olson who helped mentor and guide me throughout my research as
a member of his lab. I would like to acknowledge my colleagues Dr. Amber Hoffstetter, Dr.
Andrew Wiersma, Linda Brown, Kyle McCarthy, and Jon Turkus for their insights, help with
statistical analysis, and interesting times in both the lab and field. Lee Siler, Matt Graham, and
countless undergraduate workers were all instrumental in helping with field work and expanding
my knowledge about agriculture in general.

v

TABLE OF CONTENTS
LIST OF TABLES ....................................................................................................................... viii
LIST OF FIGURES ....................................................................................................................... ix
KEY TO ABBREVIATIONS ........................................................................................................ xi
CHAPTER 1: Introduction ..............................................................................................................1
Wheat’s Importance, Evolution, and Origin ...................................................................1
Wheat’s Importance in Agriculture .........................................................................1
Evolution and Origin of Hexaploid Wheat ..............................................................1
Genetic Diversity in Hexaploid Wheat .............................................................................3
Genetic Diversity within the Hexaploid Subgenomes ..............................................3
Identification and Utilization of Ae. tauschii Genetic Diversity ..............................4
Overview of the Puccinia Genus .......................................................................................7
Life Cycle .................................................................................................................7
Puccinia graminis as a Pathogen .......................................................................................8
Highly Virulent Races are Capable of Overcoming a Majority of Current
Resistance ................................................................................................................9
Stem Rust Resistance Genes from Ae. tauschii ........................................................9
Puccinia striiformis as a Pathogen ..................................................................................10
Aggressive Virulent Stripe Rust Races are becoming Widespread ........................10
Stripe Rust Resistance Genes from Ae. tauschii ....................................................11
Puccinia triticina as a Pathogen ......................................................................................12
Leaf Rust ................................................................................................................12
Leaf Rust Resistance Genes from Ae. tauschii .......................................................12
Breeding for Disease Resistance .....................................................................................13
Types of Genetic Resistance...................................................................................13
Apparent Association between the Origin of Ae. tauschii Accessions and
Disease Resistance .................................................................................................15
Problem Statement...........................................................................................................16
APPENDIX .......................................................................................................................17
BIBLIOGRAPHY ............................................................................................................21
CHAPTER 2: Mapping Rust Resistance in a Synthetic (tetraPrelude/TA2474) Hexaploid Wheat
Population ......................................................................................................................................33
Abstract .............................................................................................................................33
Introduction ......................................................................................................................33
Materials and Methods ....................................................................................................38
Plant Materials ......................................................................................................38
Stem Rust Phenotyping ..........................................................................................39

vi

Stripe Rust Phenotyping .........................................................................................40
Adult Plant Leaf Rust Phenotyping ........................................................................41
Phenotypic Data Analysis ......................................................................................42
Genotyping-by-sequencing ....................................................................................43
Linkage Map Construction ....................................................................................43
QTL Analysis..........................................................................................................44
Results ...............................................................................................................................44
Linkage Map Construction ....................................................................................44
Screening for Stripe Rust Seedling Resistance ......................................................45
Screening for Stem Rust Seedling Resistance ........................................................45
Greenhouse Screening of Adult Plants for Stem and Stripe Rust Resistance ........46
Field Analysis of Stem Rust....................................................................................47
Adult Plant Reaction to Leaf Rust in Mason, Michigan 2017 ...............................48
Discussion..........................................................................................................................48
Stripe Rust Resistance from TA2474......................................................................48
Stem Rust Resistance from the Synthetic 9.131.15x...............................................49
Alignment of YrAS2388 and Sr49 Markers to the Reference Genome ..................51
Adult Plant Reaction to Leaf Rust Segregating in the U6708 Population .............51
Phenotyping of Adult Plant Resistance ..................................................................53
Summary ................................................................................................................54
APPENDIX .......................................................................................................................56
BIBLIOGRAPHY ............................................................................................................78
CHAPTER 3: Conclusions ............................................................................................................87
Conclusions of Current Research ...................................................................................87
Future Directions .............................................................................................................89
APPENDIX .......................................................................................................................91
BIBLIOGRAPHY ............................................................................................................95

vii

LIST OF TABLES

Table 2.1. Quantitative trait loci for resistance to stem, stripe, and leaf rust .................................57
Sup Table 2.1. Genomewide threshold values generated for each trait individually using 1000
permutations at α=0.05 .....................................................................................................................58
Sup Table 2.2. Polymorphic segregating on each chromosome in the U6708-03 and U6708-04
families. ..............................................................................................................................................63
Table 3.1. A U6708-03 line that displays disease resistance to all three Puccinia species tested
in all environments. ............................................................................................................................92

viii

LIST OF FIGURES

Figure 1.1. Hybridization and polyploidization events that result in the formation of hexaploid
wheat. .................................................................................................................................................18
Figure 1.2. The gene pools of T. aestivum ........................................................................................19
Figure 1.3. Development of extracted tetraploid from a hexaploid parent......................................20
Figure 2.1. Flow through of the population development of the U6708-03 and U6708-04
families ...............................................................................................................................................58
Figure 2.2. QTL analysis of the U6708-03 family using composite interval mapping for stem,
stripe, and leaf rust resistance QTL ...................................................................................................59
Figure 2.3. QTL analysis of the U6708-04 family using composite interval mapping for stem
and leaf rust resistance QTL ..............................................................................................................60
Figure 2.4. Examples of Pst seedling reactions to Pst-37 in the U6523 F2:3 population .................61
Figure 2.5. Examples of adult plant reactions to leaf rust in the U6708 population in Mason,
Michigan 2017 ...................................................................................................................................61
Figure 2.6. Examples of Pgt seedling reactions to Pgt-QFCSC in the U6708 population ...............62
Sup Fig. 2.1A. U6708-04 linkage groups for group 1 aligned to the respective representative
chromosomes of the reference genome based on aligned marker positions. .....................................64
Sup Fig. 2.1B. U6708-03 linkage groups for group 1 aligned to the respective representative
chromosomes of the reference genome based on aligned marker positions. .....................................64
Sup Fig. 2.2A. U6708-04 linkage groups for group 2 aligned to the respective representative
chromosomes of the reference genome based on aligned marker positions.. ....................................65
Sup Fig. 2.2B. U6708-03 linkage groups for group 2 aligned to the respective representative
chromosomes of the reference genome based on aligned marker positions.. ....................................66

ix

Sup Fig. 2.3A. U6708-04 linkage groups for group 3 aligned to the respective representative
chromosomes of the reference genome based on aligned marker positions.. ....................................67
Sup Fig. 2.3B. U6708-03 linkage groups for group 3 aligned to the respective representative
chromosomes of the reference genome based on aligned marker positions.. ....................................68
Sup Fig. 2.4A. U6708-04 linkage groups for group 4 aligned to the respective representative
chromosomes of the reference genome based on aligned marker positions.. ....................................69
Sup Fig. 2.4B. U6708-03 linkage groups for group 4 aligned to the respective representative
chromosomes of the reference genome based on aligned marker positions.. ....................................70
Sup Fig. 2.5A. U6708-04 linkage groups for group 5 aligned to the respective representative
chromosomes of the reference genome based on aligned marker positions.. ....................................71
Sup Fig. 2.5B. U6708-03 linkage groups for group 5 aligned to the respective representative
chromosomes of the reference genome based on aligned marker positions.. ....................................72
Sup Fig. 2.6A. U6708-04 linkage groups for group 6 aligned to the respective representative
chromosomes of the reference genome based on aligned marker positions.. ....................................73
Sup Fig. 2.6B. U6708-03 linkage groups for group 6 aligned to the respective representative
chromosomes of the reference genome based on aligned marker positions.. ....................................74
Sup Fig. 2.7A. U6708-04 linkage groups for group 7 aligned to the respective representative
chromosomes of the reference genome based on aligned marker positions.. ....................................75
Sup Fig. 2.7B. U6708-03 linkage groups for group 7 aligned to the respective representative
chromosomes of the reference genome based on aligned marker positions.. ....................................76
Sup Fig. 2.8. Histograms of both IT and severity scores recorded for the U6708 population in
response to Puccinia inoculation .......................................................................................................77
Sup Fig. 3.1. Graphical genotypes of linkage groups containing resistance QTLs in
U6708-03-028 ....................................................................................................................................93

x

KEY TO ABBREVIATIONS

APR Adult plant resistance
CIM Composite interval mapping
GBS Genotyping-by-sequencing
GH Greenhouse
HTAPR High temperature adult plant resistance
LOD Logarithm of the odds
MM Mason, MI
MYA Million years ago
Pt Puccinia triticina
Pgt Puccinia graminis f. sp. tritici
Pst Puccinia striiformis f. sp. tritici
QTL Quantitative trait loci
RIL Recombinant inbred line
RH Relative humidity
SHW Synthetic hexaploid wheat

xi

CHAPTER 1: Introduction
Wheat’s Importance, Evolution and Origin
Wheat’s Importance in Agriculture
Wheat is one of the most important row crops grown worldwide and a common sight
when traveling through agricultural regions. However, a field full of amber wheat spikes can
quickly transform into shriveled diseased heads attached to broken stems due to the presence of
evolving virulent pathogens. In 2016, wheat was planted on over 50 million acres in the United
States alone (USDA, 2016). Flour from wheat is used to produce a wide range of food products
ranging from crackers to bread. Around nineteen percent of calories consumed by humans are
from wheat (Braun et al. 2010). Since wheat is widely grown and an important food source there
is a considerable world wide effort to continually improve yields. However, wheat yields are
affected by both the environment they are grown in and the diseases present in their
environment. The Puccinia fungal species are treacherous wheat pathogens because of their
capability to evolve new aggressive and virulent races to overcome presently deployed resistance
genes (Milus et al., 2009; Singh et al., 2011b; Hovmøller et al., 2016; Bhattacharya, 2017). In
order to better understand methods to improve hexaploid wheat, it is important to understand the
origin of hexaploid wheat to more effectively utilize available wild germplasm.
Evolution and Origin of Hexaploid Wheat
The evolution of hexaploid wheat began over 10,000 years ago with the domestication of
cereals beginning where present day Turkey and Syria are located and is tied with the
development of agriculture (Lev-Yadun et al., 2000; Tanno, 2006). Wheat is a member of the
grass family Poaceae and the tribe Tritceae which include barley and rye. Divergence between

1

wheat and these other members of Tritceae occurred 11 to 7 MYA respectively (Huang et al.,
2002). Common wheat, Triticum aestivum (AABBDD, 2n=6x=42), is the most widely cultivated
wheat worldwide. Common wheat is an allohexaploid which consists of the independently
segregating A, B, and D genomes. The grouping of these genomes during the evolution of
common wheat involved a series of interspecific hybridizations, followed by subsequent
polyplodization, between three different diploid progenitor species. The first in this series of
hybridizations occurred between the A genome progenitor and the B genome progenitor species
which, when followed by spontaneous chromosome doubling, generated the wild tetraploid
emmer species T. turgidum ssp. dicoccoides (AABB, 2n=4x=28) (Feuillet et al., 2008). The A
genome progenitor species that produced this wild tetraploid has been demonstrated to be, T.
uratru (AA, 2n=2x=14) (Chapman et al., 1976; Dvorák et al., 1993). The identification of the B
genome progenitor species has been difficult. It was originally speculated to be the wild goat
grass species Ae. speltoides (SS, 2n=2x=14),(Sarkar and Stebbins, 1956). However, current
research supports the theory that Ae. speltoides is instead a closely related relative of the B
genome progenitor species (Salse et al., 2008). This wild emmer species was subsequently
cultivated resulting in the formation of T. turgidum ssp. dicoccum (Peng et al., 2011).
The second interspecific hybridization and spontaneous chromosome doubling occurred
between cultivated emmer T. dicoccum (AABB, 2n=4x=28) and the D genome progenitor
species resulting in the formation of hexaploid wheat (McFadden and Sears, 1946). The D
genome of hexaploid wheat originated from the wild goat grass species Ae. tauschii ssp.
strangulata (DD, 2n=2x=14) (Kihara, 1944; McFadden and Sears, 1946). It is thought that
cultivated emmer, and not wild emmer, hybridized with Ae. tauschii to generate common wheat
due to the shared geographical distribution of T. dicoccum with Ae. tauschii (Zohary et al., 1969;

2

Cox, 1997). Ae. tauschii itself is hypothesized to have arisen from a homoploid hybridization
between the A and B genome progenitor species (Marcussen et al., 2014). However, taking into
account the presence of additional genomes in the Aegilops-Triticum complex and using both
nuclear and chloroplast DNA, evidence supports a hybrid origin of Ae. tauschii but further work
is needed to determine the correct model describing its origins (Li et al., 2015). The origin of
common wheat helps to explain the amount of genetic diversity present in current breeding
populations and identify potential sources to improve it.
Genetic Diversity in Hexaploid Wheat
Genetic Diversity within the Hexaploid Subgenomes
The recent polyploidization of common wheat has resulted in a narrow genetic base
(Feuillet et al., 2008; Peng et al., 2011). However, this lack of genetic diversity is not consistent
between the three subgenomes. The A and B genomes contain a higher amount of
polymorphisms compared to the D genome (Poland et al., 2012; Cavanagh et al., 2013; Wang et
al., 2014). An explanation for the increased diversity in the A and B genomes present in
hexaploid wheat is the potential formation of female fertile hybrids by tetraploid and hexaploid
wheat crossing (Cox, 1997; Dvorak et al., 2006). These fertile hybrids would enable
hybridization between tetraploids and the hexaploid population increasing genetic diversity of
the shared genomes (Figure 1.1). However, in the case of the D genome, the recent
polyplodization event between Ae. tauschii and T. turgidum created a genetic bottleneck,
reducing the genetic diversity present in the D genome of T. aestivum compared to the diploid
progenitor species (Dvorak et al., 1998; Caldwell et al., 2004; Reif et al., 2005).

3

It is widely thought that the Green Revolution, while significant in increasing wheat
production, has reduced the genetic diversity in breeding populations (Trethowan et al., 2007).
There was an initial decrease in genetic diversity after the Green Revolution where intense
selection for high yielding and disease resistant varieties was undertaken (Warburton et al.,
2006). In efforts to introduce a greater amount of genetic diversity, specifically in the D genome,
breeders can use available landraces or wild relatives in their programs. The use of wild species
has increased the genetic diversity of both spring hexaploid and durum wheat varieties since the
Green Revolution (~1980s to present) (Reif et al., 2005; Ren et al., 2013). However, the
difference in genomewide genetic diversity between land races and modern cultivars is minor,
which is speculated to be because selection from breeding acts on only a subset of the genome
(Cavanagh et al., 2013). In contrast, Ae. tauschii accessions have greater D genome variation
compared to both landraces and modern bred cultivars (Reif et al., 2005). The introduction of
novel variation from wild species, such as Ae. tauschii, is paramount to continue the
improvement of modern wheat varieties.
Identification and Utilization of Ae. tauschii Genetic Diversity
As modern breeding practices are used to develop new elite wheat varieties, there is an
ever increasing emphasis to identify new sources of beneficial alleles to enhance current
germplasm. Novel genetic variation that is available for use can be separated into different gene
pools based on observed meiotic pairing and production of fertile hybrids with the primary gene
pool allowing for recombination and fertile hybrids to be generated through hybridization
(Figure 1.2) (Cox, 1997; Feuillet et al., 2008). Those species that are included in this primary
gene pool include T. turgidum, and the progenitor diploid species (Harlan and de Wet, 1971;
Cox, 1997). The low genetic diversity of the D genome can potentially be improved through the

4

introduction of novel alleles from Ae. tauschii. The lineage of Ae. tauschii accessions and the
method of introgression can impact the successful introgression of beneficial alleles to common
wheat. The Ae. tauschii gene pool itself can be split into two separate lineages based on DNA
marker data (Dvorak et al., 1998; Wang et al., 2013). While it is unknown the specific number of
hybridizations that occurred between Ae. tauschii and T. dicoccum to form hexaploid wheat, it
has been demonstrated that a single Ae. tauschii sublineage is the most related to the original D
genome progenitor ancestor (Wang et al., 2013). Therefore, Ae. tauschii accessions that are not
genetically similar to this sublineage may be of additional interest to use to introduce novel
genetic variation. The introduction of novel variation from wild species into cultivated wheat has
several key problems that need to be addressed including: (1) the phenotyping of wild and alien
species for desired traits, (2) the introduction of genetic information from donor species into an
adapted variety.
Identification of Ae. tauschii accessions that contain desirable alleles can be performed in
a straightforward manner for those qualitative traits that are controlled by a few major effect
genes. One example is disease resistance, especially major gene resistance, which can be
evaluated directly in wild species. Examples of this include Septoria tritici blotch (McKendry
and Henke, 1994) and the rusts (Zaharieva et al., 2001; Assefa and Fehrmann, 2004; Liu et al.,
2010; Rouse et al., 2011). Thus, the identification of novel genetic variation that contributes to
highly heritable traits can be done before the introgression of wild relatives into a common wheat
background. However, identifying wild germplasm with desirable alleles that affect quantitative
traits controlled by many minor effect QTLs, such as grain yield, can be difficult due to the
presence of several negative alleles in the background of these un-adapted varieties (Cox, 1997).
In order to identify genomic regions that confer positive alleles from wild germplasm it is often

5

necessary to evaluate wild material in an adapted background and use backcross methods to
reduce linkage drag to eliminate negative alleles (Tanksley and Nelson, 1996).
Introduction of genetic variation from Ae. tauschii can be done through either direct
crossing or the production of synthetic hexaploids. Direct crossing between hexaploid and
diploid Ae. tauschii creates an F1 hybrid that has an AABBD genome. However, endosperm
development of the F1 hybrids is halted and requires embryo rescue to successfully produce a
plant (Gill and Raupp, 1987). These F1 hybrids are male sterile and are backcrossed twice to the
recurrent parent to return to a normal ploidy level (Olson et al., 2013a). It has been previously
demonstrated that the genotype of wild relatives other than Ae. tauschii has an impact on the
number of F1 hybrids recovered during direct crosses (Sharma and Ohm, 1990; Valkoun et al.,
1990; Tixier et al., 1998; Fedak, 1999). Differences in the number of F1 embryos per direct cross
produced has been observed between white and red winter wheat and different Ae. tauschii
accessions (E. Olson, Personal Communication). However, there are no known reasons for this
genotypic effect in direct hexaploid wheat x Ae. tauschii crosses. Synthetic wheat is produced
through the direct hybridization of tetraploid wheat (AABB) with Ae. tauschii (DD) to create a
triploid (ABD), which, through chromosome doubling, produces a hexaploid wheat line
(AABBDD) (McFadden and Sears, 1946). Production of direct hybrids can be technically
challenging in comparison to the production of synthetic lines. However, it can allow for an
accelerated return to an adapted background after the initial direct cross.
The tetraploid parent in a synthetic cross can be a T. turgidum line or an extracted
tetraploid. Extracted tetraploids are made through the crossing of a hexaploid line to a tetraploid
line to create a pentaploid F1 hybrid which is then backcrossed for several generations to create
an AABB extracted tetraploid (Kerber, 1964). These extracted tetraploids retain the A and B

6

genomes from their hexaploid form. The extracted tetraploids have less vigor than their
hexaploid counterparts owing to the elimination of a third of their genome, though differences in
vigor may be impacted by the tetraploid accession and the number of backcrosses used to
produce the extracted tetraploid (Figure 1.3) (Kerber, 1964; Kaltsikes, P. J. , Evans, L.E. , Larter,
1969; Yang et al., 1999).
Overview of the Puccinia Genus
A major group of pathogens that affect wheat and other grass species are the fungi that
are members of the Puccinia genus. The fungi in this genus can be delineated into multiple
species dependent on the host plants they are capable of infecting. Puccinia striiformis f.sp.
tritici (wheat stripe rust), Puccinia graminis f. sp. tritici (wheat stem rust) and Puccinia triticina
f. sp. tritici (leaf rust) being among the rust fungi that infect wheat. These species can be further
delineated into “races” which describes a specific virulence/avirulence to a specific set of
resistance genes (Roelfs, 1984).
Life Cycle
The life cycle of the members of the Puccinia genus is well understood (Chen, 2005;
Leonard and Szabo, 2005; Chen et al., 2014). Briefly, the asexual uredinospores (n+n) germinate
and fungal hyphae enter through the stomata. After the fungus has developed, hyphae burst
through the epidermis and produce new uredinospores asexually. As the wheat plant begins to go
through senescence, diploid teliaspores form through the fusion of the haploid genomes of the
uredinospores. These teliospores undergo meiosis to produce haploid basidospores which infect
the alternative host. After successful germination and proliferation, basidospores develop pycinia
which produce spermagonia that fuse with other spermagonia to produce dikaryotic mycelium.

7

These mycelium develop and produce aecia which release aceiospores that infect wheat. The
asexual uredinospores that are subsequently produced are capable of spreading over thousands of
miles and can cause multiple cycles of infection over a single growing season (Roelfs and
Bushnell, 1984).
Stem, stripe, and leaf rust are examples of heterocious biotrophic fungal pathogens that
complete their life cycle on two different hosts. Asexual propagation occurs on the primary host
while an alternative host is required for the successful completion of sexual reproduction. The
alternative host for stem rust has been known to be barberry but it has not been demonstrated
until recently that stripe rust can develop on both barberry species and Mahonia aquifolium,
Oregon grape (Jin, 2011; M.N, 2013; Zhao et al., 2013). Unlike stem and stripe rust, leaf rust’s
alternative host is Thalictrum speciosissimum (Bolton et al., 2008; Kolmer, 2013). The presence
of this mixed reproduction in the rusts creates a situation where new virulent races are capable of
being produced at a high rate (McDonald and Linde, 2002; Jin, 2011). Two factors that can
influence the impact of these spores are the environment a wheat crop is grown in and the
deployment of resistant varieties. Rust spores are sensitive to both humidity and temperature,
which can affect spore germination and limits the initial presence of spores at the beginning of
the growing season in more temperate growing zones (McGregor and Manners, 1985; Kramer
and Eversmeyer, 1992; Chen, 2005). The evolution of new rust races that are more aggressive
and are virulent to currently deployed resistance genes can have a potentially devastating effect
on wheat yield. Thus, it is necessary for new novel sources of rust resistance to be identified.

8

Puccinia graminis as a Pathogen
Highly Virulent Races are Capable of Overcoming a Majority of Current Resistance
The overwintering of stem rust on the alternative host, Berberis vulgaris L, or what is
known commonly as Common Barberry, allows for both sexual recombination and earlier
infection to occur in these regions where it is grown (Jin, 2011). In the early 20th century, there
was a concerted effort to eliminate the common barberry from the United States and this
program was a success with only occasional sightings of common barberry in non-grain growing
areas (Roelfs, 1982). This “elimination” of the sexual recombination step in the stem rust’s life
cycle can negatively impact its ability to adapt and overcome deployed resistance genes.
However, the elimination of the alternative host does not completely eliminate the potential for
new aggressive races. The proliferation of clonally propagated uredinospores and the
accumulation of spontaneous mutations can lead to the formation of new virulent races (Jin,
2011). Several new stem rust races have been identified including Pgt-TTKSK, also known as
Ug99, and Pgt-TTTTF that are virulent against a large number of stem rust resistance genes that
are currently used, with Ug99 being capable of successfully infecting over 80% of wheat
cultivars (Singh et al., 2011b; Bhattacharya, 2017). There is a need to identify new sources of
genetic variation in current wheat breeding germplasm and wild relatives that can be used to
identify sources of resistant to these constantly evolving pathogens.
Stem Rust Resistance Genes from Ae. tauschii
Stem rust resistance genes have been identified on all three genomes. The diploid
progenitor for the D genome Ae. tauschii has served as a useful source of resistant genes. Efforts
have been directed towards identifying these disease resistance genes with 42 stem rust genes

9

officially designated(McIntosh et al., 2014). Currently designated stem rust genes successfully
introgressed from Ae. tauschii into common wheat include Sr33, Sr45, Sr46, SrTA1662,
SrTA10171, and SrTA10187 (Kerber and Dyck, 1979; Marais et al., 1998; McIntosh et al., 2013;
Olson et al., 2013a; b). Sr33 and Sr45 are located on the 1D chromosome and originated from
Ae. tauschii accessions RL5288 and RL5289, respectively (Marais et al., 1998). Sr46 is located
on the 2D chromosome and is from the Ae. tauschii accession TA1703 (Rouse et al., 2011).
SrTA1662, from the Ae. tauschii accession TA1662, is located on the 1D chromosome (Olson et
al., 2013a). SrTA10171 and SrTA10187, from Ae. tauschii accessions TA10171 and TA10187,
are located on the 7D and 6D chromosomes, respectively (Olson et al., 2013b). All six of these
genes are all-stage resistance genes that are effective against Ug99 (Rouse et al., 2011; Olson et
al., 2013a; b). However, Sr33, Sr45, and Sr46 were susceptible to Pgt-TTTTF based on seedling
tests (Rouse et al., 2011).
Puccinia striiformis as a Pathogen
Aggressive Virulent Stripe Rust Races are becoming Widespread
Historically, the temperature sensitivity of stripe rust has limited its primary range to
where local inoculum can survive until it is spread by wind into more temperate regions. The
potential for stripe rust to develop adaptations to survive at a wider range of temperatures as well
as the changing climate could be disastrous for wheat growing regions that had previously been
mostly unaffected by stripe rust (Milus et al., 2009; Chakraborty et al., 2011; Hovmøller et al.,
2011). There has been a massive shift in the worldwide stripe rust population in the 2000s with
high temperature adapted strains, such as PstS1, PstS2, and Pst-Warrior currently widespread
(Hovmøller et al., 2016; Walter et al., 2016; Ali et al., 2017). In addition to temperature
adaptation, stripe rust populations have developed virulence to a significant number of resistance

10

QTLs. In a survey of the global yellow rust population, only Yr5 and Yr15 displayed resistance to
all tested races out of all of the tested QTLs, Yr1, Yr2, Yr3, Yr4, Yr5, Yr6, Yr7, Yr8, Yr9, Yr10,
Yr15, Yr17, Yr24, Yr25, Yr27, Yr32 (Ali et al., 2017). Evidence has demonstrated that the PstWarrior rust races, that has replaced the pre-2011 population of stripe rust in the United
Kingdom, is more genetically diverse than the previous population (Hovmøller et al., 2016).
Both the adaptation to a wider temperature range and the presence of genetically diverse virulent
strains of stripe rust increases the need for the identification of novel stripe rust genes.
Stripe Rust Resistance Genes from Ae. tauschii
Major efforts have focused on identifying stripe rust resistance with 61 resistance genes
officially designated (McIntosh et al., 2014). The current officially identified stripe rust genes
successfully introgressed from Ae. tauschii include Yr28 and YrAS2388 (Singh et al., 2000;
Huang et al., 2011). Both of these genes were introgressed into hexaploid wheat through the use
of synthetic lines. The diploid source of YrAS2388 has a highly resistant infection type (0-1)
based on inoculation with a mixture of stripe rust races native to China (Huang et al., 2011).
However, the AS2388 accession displays a higher resistance in the diploid background compared
to the synthetic indicating that there may be interactions suppressing resistance from Ae. tauschii
(Huang et al., 2011). YrAS2388 is present on the distal end of the 4DS chromosome and
originates from AS2388 (Huang et al., 2011). Yr28 has a resistant infection type (2-4) as a
synthetic and screening was not performed on the diploid parent (Singh et al., 2000). Yr28
originated from the W-219 Ae. tauschii accession and is located on the distal end of 4DS (Singh
et al., 2000). These genes are both all-stage resistance genes and have similar infection types in
the synthetic background. Presently, it is unknown if Yr28 and YrAS2388 are the same or

11

different loci though Huang et. al. 2011 claims a difference based on differing IT reactions of
Yr28 and YrAS2388 to the same rust race in separate studies.
Puccinia triticina as a Pathogen
Leaf Rust
Recently, attention has been focused on new highly virulent stem and stripe rust races.
However, leaf rust is still a threat that, like stem and stripe rust, has the ability to quickly develop
virulent races that can overcome widely deployed resistant genes. In 1977, the presence of
virulent races to J73, a widely grown variety of wheat in northwest Mexico, resulted in yield
losses of over 40% and required government backed fungicide applications to protect the
affected wheat in the region (Dubin, 1981). Leaf rust is more amiable to a wider range of
temperatures compared to stripe and stem rust allowing it to spread across a greater number of
geographical regions (Bolton et al., 2008). Leaf rust can cause around 7-50% yield loss
dependent on stage of growth infection occurs (Singh et al., 2011a). Leaf rust not only can affect
the yield of a wheat line but also may have an impact on its quality (Everts et al., 2001). Leaf
rust is a highly diverse pathogen with new races identified annually from multiple countries
(Bolton et al., 2008). A survey of North American leaf rust races demonstrated races are
geographically localized with virulence to wheat cultivars resistance genes (Kolmer and Hughes,
2015). Identifying novel sources of resistance to leaf rust will help protect cultivars from this
diverse widespread rust pathogen.
Leaf Rust Resistance Genes from Ae. tauschii
Over 55 leaf rust resistance genes have been officially designated (McIntosh et al., 2014).
Those official leaf rust genes that originate from Ae. tauschii include Lr21, Lr22a, Lr32, Lr39

12

Lr41, and Lr42 (Kerber, 1987; Cox et al., 1994; Raupp et al., 2001; Hiebert et al., 2007; Sun et
al., 2009). Lr21 is seedling resistance gene present on the 1DS chromosome and originated from
the RL5289 Ae. tauschii accession(Cox et al., 1994). Lr22a is the only adult plant resistance
gene from Ae. tauschii that has been officially identified and is present on the 2DS chromosome
(Hiebert et al., 2007). Lr32 is a seedling resistance gene (IT 0;-1) that originated from RL5497-1
and is located on the 3D chromosome (Kerber, 1987). The location of Lr43 is unknown (Cox et
al., 1994). Lr41and Lr42 are seedling resistance genes located on the 1D chromosome and
originated from TA2460 and TA2450, respectively (Cox et al., 1994). Recently, Lr39 was
determined to be allelic with Lr41, which is actually located on 2DS (Singh et al., 2004). Lr39 is
located on 2DS and originated from multiple tested germplasm lines (Raupp et al., 2001; Singh
et al., 2004).
Breeding for Disease Resistance
Types of Genetic Resistance
The original hypothesis concerning gene-for-gene interactions was first identified by Flor
concerning resistance of flax to rust (Flor, 1955). This hypothesis states that an interaction
between a substrate from a pathogen is recognized by the host organism resulting in a resistant
phenotype. These gene-for-gene interactions in terms of rust resistance are exemplified by
seedling resistance genes. Seedling resistance is characterized by a qualitative hypersensitive
response to infection that is present throughout all growth stages of the plant and tends to be race
specific (Leonard and Szabo, 2005; Chen et al., 2014). This hypersensitive response typically
entails necrosis occurring around the point of infection which prevents the spread of this
biotrophic pathogen past the point of infection (Stakman, 1915). Adult plant resistance (APR) is
typically quantitative, is present in the adult growth stages and tends to be non-race specific.

13

APR does not prevent initial infection but lessens its proliferation (Singh et al., 2011c). While
APR tends to be non-race specific, there are examples of stripe rust race specific APR genes
(Milus et al., 2015). Rust resistance can be influenced by the environment with some
environments decreasing the effectiveness and others increasing the effectiveness of certain APR
genes (Chakraborty et al., 2011). An example of environment being a positive influence on rust
resistance is high temperature adult plant resistance (HTAPR) (Qayoum and Line, 1985; Chen,
2005; Lin and Chen, 2007). HTAPR is characterized by the susceptibility of a variety at the
seedling stage but as the plant develops and the temperature increases, host resistance increases
as well.
In addition to the environment affecting the expression of resistance QTLs, epistatic
interactions have been identified between these QTLs and genomic regions present in different
genetic backgrounds. These regions are capable of reducing the effect of a resistance QTL and
termed as suppressors. Examples of suppressors are present on all three wheat subgenomes and
lessen the impact of introgressed resistance QTLs for stem (Kerber and Green, 1980; Dyck,
1987; Bai and Knott, 1992), stripe (Ma and Singh, 1995), as well as leaf rust (Bai and Knott,
1992). Thus, the background of the recurrent parent needs to be taken into account when
determining the effectiveness of resistance QTL.
Due to its phenotype, all-stage resistance genes are relatively easy and inexpensive to
screen for. However, these seedling resistance genes when deployed can be quickly overcome by
increased selective pressure to produce virulent stripe rust races through random mutations
(Poland et al., 2009; Hulbert and Pumphrey, 2014). Thus, a common method that can be used to
increase the durability of newly identified seedling resistance genes, called gene pyramiding, is
to combine multiple seedling resistance genes together in one cultivar (St.Clair, 2010; Mundt,

14

2014). This reduces the chances that races will become virulent when compared to deployment
of a single seedling resistance gene (Mundt, 2014; Bourget et al., 2015). In addition to the use of
seedling resistance genes in breeding program, there is an increased effort to identify and use
quantitative APR resistance. APR is thought to be the more durable resistance compared to
seedling resistance. However, even when pathogens develop virulence to major gene resistance,
these “defeated” genes can still have a residual effect on resistance (Bodny et al., 1986; Li et al.,
1999). Enough of these defeated QTLs together can potentially provide a durable resistance to
disease (Li et al., 1999). Screening for APR typically requires more time, a greater amount of
space, and a greater risk of environmental variation and contamination from other field diseases
when compared to seedling assays, which occur in a controlled environment. However, work has
been done that attempts to measure APR in artificially inoculated and controlled setting in the
greenhouse for both stripe (Pretorius et al., 2007) and stem rust (Bender and Pretorius, 2016).
Apparent Association between the Origins of Ae. tauschii Accessions and Disease Resistance
Ae. tauschii is a useful source for disease resistance QTL for breeders but it’s necessary
to be able to identify potentially useful accessions before undergoing the process of creating
direct crosses or synthetic lines for greater efficiency. As discussed earlier in the chapter, genetic
analysis and screening for disease resistance has been performed previously on the Ae. tauschii
accessions themselves before their introduction into a hexaploid genetic background. In order to
identify those accessions useful for screening, a breeder may select lines that originate from
certain geographical regions. The geographic origin of a line has been demonstrated to be
associated with resistance to stem rust (Cox et al., 1992), stripe rust (Liu et al., 2010), and
fusarium head blight (Brisco et al., 2017). Those environments that are favorable to disease tend
to contain more resistant accessions as these environments would exhibit a higher disease

15

pressure to drive R gene evolution and selection (Cox et al., 1992). Breeders can use associations
between environments conducive to disease development and resistance to more effectively
identify Ae. tauschii accessions more likely to contain disease resistance QTLs in order to
introgress them into their breeding germplasm.
Problem Statement
Common wheat is a widely grown row crop that first originated in the Middle East and
evolved through a series of interspecific hybridizations between three diploid progenitor species.
These recent hybridizations resulted in a diminished genetic diversity in common wheat,
specifically in the D genome. Ae. tauschii, the D genome progenitor, has been used to increase
the novel genic variation in hexaploid wheat. This progenitor species has been shown to harbor
numerous QTLs for disease resistance to all three rust species. New races of rust have been
observed that have increased aggressiveness and virulence to currently utilized resistance. In the
study described in this thesis, a synthetic RIL population was used to identify novel genes
conferring resistance to stem, stripe, and leaf rust. This RIL population was created by crossing
9.131.15x (tetraPrelude/TA2474) with KS05HW14 and tested for all-stage resistance and APR
in the field and greenhouse. QTL analysis allowed for the identification of disease resistance in
this population that can be used to improve current wheat varieties.

16

APPENDIX

17

APPENDIX
Figure 1.1. Hybridization and polyploidization events that result in the formation of hexaploid
wheat. Dash lines indicate potential hybridizations that can occur between domesticated and
cultivated tetraploid wheat and between tetraploid wheat and hexaploid wheat. Figure adapted
from Feuillet et al., (2008).

18

Figure 1.2. The gene pools of T. aestivum. Gene pools are determined by F1 fertility and meiotic
pairing. Ae. tauschii is a part of the primary gene pool due to its homology to the D genome
regardless of its ploidy difference with bread wheat. Figure adapted from Cox, (1997) and
Feuillet et al., (2008).

Tertiary
Ex. Rye, Thinopyrum

Secondary

Ex. T. timopheevii

Primary
Ex. Ae. tauschii,
T. turgidum,
landraces, elite
cultivars

19

Figure 1.3. Development of an extracted tetraploid from a hexaploid parent. Briefly, the
hexaploid parent is crossed to a tetraploid variety and pentaploid F1 plants are backcrossed back
to the hexaploid parent. Pentaploid progeny are selected in each generation and backcrossed
multiple times. Pentaploid progeny from the last backcross were selfed and tetraploid progeny
were retained. The size and vigor of the extracted tetraploid is stunted compared to the
hexaploid. Flow through adapted from and photograph from Zhang et al., (2014). Extracted
tetraploid procedure originates from Kerber, (1964.

Hexaploid
parent

X

Pentaploid

Tetraploid
parent
X
(x7)

Hexaploid
parent

Extracted
tetraploid

Hexaploid Extracted tetraploid
(AABBDD)
(AABB)

20

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CHAPTER 2: Mapping Rust Resistance in a Synthetic (tetraPrelude/TA2474)
Hexaploid Wheat Population

Abstract
New pathogenic Puccinia races highlight the need to identify new sources of disease
resistance. Disease resistance from the D genome progenitor of common wheat, Ae. tauschii, can
be introgressed into hexaploid wheat. Two BC1F5:6 RIL families (n = 70) were derived from a
cross between synthetic hexaploid 9.131.15x (tetraPrelude/TA2474) and a hard white winter
wheat line, KS05HW14. All-stage and adult plant resistance to stripe, stem, and leaf rust were
evaluated in the growth chamber, greenhouse and field environments. Both families segregated
for stem rust resistance in all environments tested and only one family segregated for stripe rust
resistance. Using composite interval mapping, a region on 4DS was identified that confers allstage resistance to stripe rust and a region on 5BL confers all-stage resistance to stem rust. The
4DS region is inherited from the Ae. tauschii donor TA2474 and the 5BL region is from
9.131.15x. Resistance to leaf rust, originating from KS05HW14, segregated in both families on
3BL. Adult plant resistance to leaf and stem rust, on 6D and 7D respectively, segregated in
U6708-03 and originated from TA2474. Currently, there are no officially designated adult plant
resistance genes on either 6D or 7D from Ae. tauschii. This study identifies potentially novel
resistance to all three Puccinia rust species and can be used to develop rust resistant varieties.
Introduction
There is a constant need to identify new effective sources of resistance as new highly
pathogenic diseases emerge throughout the world and threaten the yield of common wheat. The
need to ensure crop productivity worldwide is becoming increasingly important as the climate

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shifts and the world population continues to increase (Lobell et al., 2008; Godfray et al., 2010).
Over 224 million bushels of wheat were produced in 2016 and provide about a fifth of human
consumed calories worldwide (Shiferaw et al., 2013; FAO, 2015). In consequence, there has
been a continued focus by plant breeders both to improve the yield of new varieties and to
protect against wheat fungal pathogens.
Identifying new sources of genetic diversity and disease resistance allows breeders to
respond to newly evolved pathogen races. The potential for a pathogen to evolve highly virulent
races is exemplified by stripe rust (Puccinia striiformis f. sp. tritici, Pst), stem (Puccinia
graminis f. sp. tritici, Pgt) and leaf rust (Puccinia triticina, Pt), all members of the Puccinia
genus. These rusts are heteroecious biotrophic fungi which are capable of both asexual and
sexual propagation. Infection of susceptible plants by these pathogens can affect yield by
reducing quantity and quality of produced grain (Leonard and Szabo, 2005; Chen et al., 2014).
Despite the extensive efforts by breeders to find and utilize effective resistance genes,
new Pst and Pgt races have developed new virulence patterns (Milus et al., 2009; Singh et al.,
2011b). The Ug99 Pgt race, Pgt-TTKSK, is capable of overcoming a majority of known
resistance genes that are currently deployed in cultivated wheat (Singh et al., 2011b). While
Ug99 is currently contained in Africa and parts of the Middle East, the potential for its spread is
concerning. The emergence of new Pgt races such as Pgt-TTTTF with similar virulence patterns
to Ug99 raises the concern that currently grown cultivars are inadequate in their protection
(Bhattacharya, 2017). Pst races, like Pst-Warrior and PstS2, are spreading quickly worldwide
and are virulent to many resistance genes (Hovmøller et al., 2016; Ali et al., 2017). While there
are currently no widespread hyper-virulent Pt races similar to PstS2 and Ug99, this pathogen is
capable of evolving new virulent races like Pgt and Pst. Mexico experienced a widespread leaf

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rust epidemic in 1977 which resulted in yield losses of over 40% and required government
backed fungicide applications to control the spread of an aggressive Pt race (Dubin, 1981). Also,
Pt is capable of tolerating a wider temperature range compared to either Pgt or Pst and is a
highly diverse pathogen with multiple new races identified annually in different countries
(Bolton et al., 2008). A survey of North American leaf rust races demonstrated that races are
geographically localized with virulence to wheat cultivars resistance genes (Kolmer and Hughes,
2015).Thus, the identification of new rust resistance genes and their introgression into hexaploid
wheat is necessary to counter the proliferation of new rust races.
There is concern that intense selection by plant breeders has decreased the amount of
genetic diversity present in modern cultivars (Warburton et al., 2006; Trethowan et al., 2007).
This loss in genetic diversity is not consistent across the three subgenomes of wheat. The D
genome has the least amount of genetic diversity compared to both the A and B genomes based
on the presence of significantly fewer polymorphisms (Poland et al., 2012; Cavanagh et al.,
2013; Wang et al., 2014). The lack of genetic diversity in hexaploid wheat, particularly in the D
genome, is also a consequence of the evolutionary history of hexaploid wheat which resulted in
severe genetic bottleneck (Dvorak et al., 1998; Caldwell et al., 2004; Reif et al., 2005).
Hexaploid wheat is an allohexaploid composed of three subgenomes: A, B, and D. This
allohexaploid is derived from the hybridization between T. turgidum (AABB, n=14) with the D
genome progenitor Ae. tauschii (DD, n=7) followed by spontaneous chromosome doubling
(Kihara, 1944; McFadden and Sears, 1946).
Wheat breeders use a wide range of gene pools composed of diploid and polypoid wheat
progenitor species and wild relatives to improve genetic diversity and identify novel variation.
The use of wild relatives introduces challenges to breeders based on differences in ploidy, lack of

35

homology, infertile offspring, and linkage drag (Cox, 1997; Feuillet et al., 2008). One relative
that has been extensively used to improve hexaploid wheat is Ae. tauschii. Ae. tauschii contains
a greater amount of genetic polymorphisms in its genome compared to the D genome of both
elite and landrace hexaploid wheat (Reif et al., 2005). Thus, Ae. tauschii can be used as a source
of novel alleles by plant breeders to increase D genome variation. One common method used to
introgress novel variation from Ae. tauschii into common wheat is the production of synthetic
hexaploid wheat (SHW) lines. SHW is produced by the same process that originally resulted in
the formation of hexaploid wheat. A tetraploid parent is crossed to an Ae. tauschii accession
resulting in an F1 triploid. This F1 triploid has its genome doubled by a doubling agent which
results in the formation of a hexaploid plant (Ogbonnaya et al., 2013). Ae. tauschii has been used
to improve multiple traits including quality (Hsam et al., 2001; Kunert et al., 2007) and disease
resistance (Liu et al., 2010; Rouse et al., 2011; Brisco et al., 2017). Utilizing these genetic
resources is critical when it comes to disease resistance as continued evolution of pathogens can
render currently utilized resistance genes ineffective.
Resistance to rust can be categorized as seedling resistance or adult plant resistance.
Seedling resistance tends to be race-specific and confers resistance throughout all growth stages
while adult plant resistance (APR) is typically non race-specific and is only effective during the
adult stages of development (Leonard and Szabo, 2005; Singh et al., 2011c). It has been
demonstrated in Pst that infection type decreases and latency period increases as wheat continues
to develop with resistance greatest during anthesis (Ma and Singh, 1996). Some APR genes have
been identified that provide protection against multiple diseases either through a pleiotropic
effect of a single gene or a haplotype of tightly linked genes. Two examples of pleiotropy
include Sr2 and Lr67/Yr46. Sr2 is a Pgt APR gene that is either tightly linked with other

36

resistance genes or confers by itself, resistance to Pt and powdery mildew (Mago et al., 2011).
Lr67/Yr46, located on chromosome 4DL, is associated with powdery mildew, Pgt, Pst, and Pt
resistance (Herrera-Foessel et al., 2011, 2014). Although APR is commonly viewed as more
durable than seedling resistance, proper utilization of seedling resistance can help mitigate the
potential for virulent populations to evolve. Deployment of seedling resistance in gene pyramids
or use of different resistance genes in back-to-back seasons can reduce the likelihood of
pathogen races developing the necessary mutations to bypass deployed resistance genes.
Currently two Pst, eight Pgt, and five Pt resistance genes originating from Ae. tauschii
have been officially designated (McIntosh et al., 2014). Yr28 and YrAS2388 on chromosome 4D,
Sr46 on chromosome 2D, and SrTA10187 on chromosome 6D are four examples of known rust
resistance genes derived from Ae. tauschii (Singh et al., 2000; Huang et al., 2011; Rouse et al.,
2011; Olson et al., 2013b). Both Yr28 and YrAS2388 were derived from SHW lines developed
from Ae. tauschii accessions, W-219 and AS2388 respectively and are seedling resistance genes
(Singh et al., 2000; Huang et al., 2011). Sr46 is an seedling resistance gene effective against
several Pgt races including Ug99 but is susceptible to Pgt-TTTTF (Rouse et al., 2011).
SrTA10187 is an seedling resistance gene that is resistant to multiple Pgt races such as PgtTTKSK, Pgt-QFCSC and Pgt-RKQQC (Olson et al., 2013b; Wiersma et al., 2016). Pt resistance
genes that originate from Ae. tauschii include Lr21, Lr22a, Lr32, Lr39, Lr41, and Lr42 (Cox et
al., 1994; Raupp et al., 2001; Hiebert et al., 2007; Sun et al., 2009). Currently, Lr22a is the only
identified Pt APR gene from Ae. tauschii (Hiebert et al., 2007). Wheat breeders have been able
to use other wheat relatives, landraces, and elite varieties to identify novel disease resistance
genes located on the A and B genomes. On chromosome 5BL there are two officially designated

37

Pgt resistance genes, Sr49 and Sr56. Both of these genes originate from common wheat (Bansal
et al., 2014, 2015). Sr49 is a seedling resistance gene and Sr56 is an APR gene.
Due to the evolution of more aggressive and virulent races of Pst, Pgt, and Pt there is a
need to identify new sources of disease resistance. The SHW accession 9.131.15x
(tetraPrelude/TA2474) is resistant to Pst-37 and Pgt-QFCSC. The objective of this study was to
identify and map sources of Pst and Pgt resistance in two RIL families derived from a cross
between 9.131.15x (tetraPrelude/TA2474) and KS05HW14. Regions were identified that
confirm seedling resistance to Pst on 4D and to Pgt on 5B. Additionally, Pt resistance was
phenotyped in both families in response to an endemic population of leaf rust in Mason, MI, in
2017.
Materials and Methods
Plant Materials
The SHW, 9.131.15x, was derived from a direct cross between the Ae. tauschii accession
TA2474 and an extracted tetraploid of the hexaploid wheat variety ‘Prelude’, tetraPrelude
(Kerber, 1964), followed by colchicine treatment as described in Kalia (2015). TA2474, was
confirmed to be resistant to Pgt-TTKSK (Rouse et al., 2011) and seedling susceptible to a
number of leaf rust races (Kalia et al., 2017). 9.131.15x was crossed with KS05HW14 and the
resulting F1 progeny was self-pollinated to produce the F2 population herein referred to as U6523
(Figure 2.1). A single F2 plant from this population, U6523-1-156, was identified as resistant to
Pgt-RKQQC and backcrossed with KS05HW14. Two BC1F1 individuals were self-pollinated
and the resulting BC1F2 progeny from each population were advanced by single seed descent to
generate the RIL families U6708-03 (n=71) and U6708-04 (n=73) (Figure 2.1).

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Stem Rust Phenotyping
Stem rust phenotyping was performed on U6708-03 and U6708-04 at the seedling stage
using Pgt-QFCSC. Ten to twenty seeds per pot were planted for each RIL, ten to fifteen seeds
per pot for KS05HW14 and five seeds per pot for each inbred parent using a standard
Arabidopsis thaliana potting soil media. Each inoculated tray contained one check of
KS05HW14. Seeds were cold-imbibed (4⁰C) to promote even germination. After cold-imbibing,
plants were placed into a growth chamber (20 ±0.5⁰C). Lines were inoculated with Pgt-QFCSC
spores suspended in Solitrol using an atomizer after the emergence of the second leaf. After
inoculation, the seedlings were incubated in a dew chamber for 16h (20⁰C, 100% RH). Seedlings
were then returned to the growth chamber. Disease measurements for infection type were based
on a 0-4 scale (Stakman et al., 1962). The Pgt seedling phenotypic scores for the U6708
populations were subsequently converted to a quantitative 1-5 scale from the 0-4 scale (Dunckel
et al., 2015).
Stem rust phenotyping was performed on U6708-03 and U6708-04 families at the adult
plant stage under greenhouse conditions using Pgt-QFCSC. Lines from the U6708-03 and
U6708-04 families were planted in SureMix plant media in 4” pots. Lines were unreplicated and
1-6 seeds were planted per line. Pots were assigned randomly to trays and placed into a
greenhouse (70±2⁰C) on a 16/8 h day/night cycle. Lines were inoculated at anthesis with an
atomizer using Pgt-QFCSC spores suspended in Solitrol. These plants were incubated in a dew
chamber for 16h (20⁰C, 100% RH). Plants were returned to the greenhouse and individual
inoculated plants were scored for infection type and severity. Infection type was scored resistant
(R), moderately resistant (MR), intermediate (M), moderately susceptible (MS), or susceptible
(S) (Roelfs et al., 1992). This APR infection type score was converted to a 1-5 quantitative scale

39

to allow QTL mapping. Rust severity on the flag leaf was measure on a scale of 0-100% based
on the Cobb scale (Peterson et al., 1948). Scores within pots for the adult plant screening in the
greenhouse were averaged together.
Stem rust phenotyping was performed on U6708-03 and U6708-04 at the adult plant
stage under inoculated field conditions using Pgt-QFCSC. Lines from both U6708 families were
planted in the field using 1.5m single row plots in April 2017. Lines were replicated twice.
However, twenty-six lines out of a total of 132 lines for both families had only a single replicate
due to seed availability and plant survival. ‘Morocco’ was planted around and within the trial to
serve as spreader row as well as a susceptible check. The entire trial was inoculated with PgtQFCSC spores suspended in Solitrol using a commercial RoundUp® H-style sprayer. The trial
was inoculated three times, with around 0.5 g of spores per inoculation, at growth stages 5, 9,
and 12 based on the feekes scale. Lines were phenotyped for both infection type and severity in
the same manner as performed in the greenhouse.
Stripe Rust Phenotyping
Stripe rust phenotyping was performed on U6708-03 and U6708-04 at the seedling stage
using Pst-37. Ten to twenty seeds per pot were planted for each RIL, ten to fifteen seeds per pot
for KS05HW14 and five seeds per pot for each inbred parent. Each inoculated tray contained one
check of KS05HW14. Planting and imbibing was performed using the same previously described
procedure for seedling screens. After cold-imbibing, these plants were placed into the growth
chamber (14±0.5⁰C). Lines were inoculated with Pst-37 suspended in Solitrol using an atomizer
after the emergence of the second leaf. After inoculation, the seedlings were incubated in a dew
chamber for 16h (14⁰C, 100% RH). Seedlings were then returned to the growth chamber. Disease

40

measurements for infection type were based on a 0-9 infection type (IT) scale (McNeal et al.,
1971).
Stripe rust phenotyping was performed on U6708-03 at the adult plant stage under
greenhouse conditions using Pst-37. Lines from the U6708-03 family were planted in two
replicates in 4” square pots using SureMix plant media. Each pot consisted of 1-6 seeds. Pots
were randomly assigned to a tray and were placed into a greenhouse (65±2⁰C) on a 16/8 h
day/night cycle. Plants were inoculated using an atomizer with Pst-37 spores suspended in
Solitrol at approximately Feekes 10. After inoculation, plants were incubated in a dew chamber
for 16h (14⁰C, 100% RH). Plants were then returned to the greenhouse. Individual flag leaves,
or lower leaves if the flag leaf could not be scored, were scored for infection type using the 0-9
IT scale and severity based on the Cobb scale (Peterson et al., 1948; McNeal et al., 1971).
Scores within pots for the adult plant screening in the greenhouse were averaged together.
Adult Plant Leaf Rust Phenotyping
Leaf rust phenotyping was performed on U6708-03 and U6708-04 at the adult plant stage
under endemic leaf rust inoculation at Mason, MI, for the 2017 growing season. The U6708
families were planted in 1.5m single row plots in April 2017 in two separate trials with lines
replicated twice per trial with U6708-03 lines replicated a total of four times. However, due to
seed availability and plant survival, six lines out of a total of 143 lines for both families had only
a single replicate. Morocco was planted on the borders of each trial and within each trial to serve
as a susceptible check and spreader. Lines were naturally inoculated with leaf rust endemic to
Mason, MI, during the summer of 2017. Plant flag leaves were scored for infection type using a
categorical system (R: resistant, MR: moderately resistant, M: intermediate, MS: moderately
susceptible, S: susceptible) (Roelfs et al., 1992). This APR infection type score was converted to

41

a quantitative 1-5 scale to allow QTL mapping. Severity was measured and was based on the
Cobb scale (Peterson et al., 1948).
Phenotypic Data Analysis
Mean Pst and Pgt seedling scores were obtained for each genotype. Using Proc GLM in
SAS® 9.4 (SAS Institute Inc, Cary, NC, USA), a mixed model was developed for Pst infection
type. Genotype was considered a fixed factor while inoculation group and leaf scored were
treated as random factors. An AUDPC was generated for each line from severity scores.
In order to account for field effect in Mason, MI, in 2017, both infection type and
severity for Pgt and Pt ratings were adjusted using the susceptible check Morocco. For Pgt rating
adjustments, the stem rust nursery was split into two separate replications with each replication
consisting of two incomplete blocks. The grand mean of Morocco for infection type and severity
was calculated for each replication and was compared to the mean of Morocco within the
respective incomplete blocks. The phenotypes of the lines were adjusted based on these
differences between incomplete blocks nested within replicates. SAS® 9.4 (SAS Institute Inc,
Cary, NC, USA) was used to perform an ANOVA with genotype as a fixed factor and replication
as a random factor. LSMeans for both severity and infection type were generated using this
mixed model for Pgt APR. Pt rating adjustments were performed in a similar manner, however
both the Pgt-inoculated nursery and a second nursery inoculated with Pst were included (note:
Pst disease development was not observed). Effect of replication and nursery were ANOVA
tested with SAS® 9.4 (SAS Institute Inc, Cary, NC, USA). A mixed model with replication as a
random effect and line as a fixed effect was used to calculate LSMeans for Pt adult plant
phenotypes.

42

Genotyping-by-sequencing
Leaf tissue of BC1F5 seedlings from each line (U6708-03, n=71; and U6708-04, n=73)
were collected in a 96-well format and stored at -80⁰C. DNA was extracted, quantified, and
normalized according to Wiersma et al., (2016). Genotyping-by-sequencing (GBS) libraries were
prepared using a two enzyme protocol as performed by Poland et al., (2012). Briefly, DNA was
normalized to 20 ng/µL, samples were digested using PstI and MspI restriction enzymes,
adapters and barcode sequences were ligated to digested genomic fragments, and pooled libraries
were PCR amplified and confirmed using gel electrophoresis.
Pooled libraries were sequenced at the MSU sequencing facility on an Illumina HiSeq
2500 platform. Tags were called using the TASSEL 5.0-GBS pipeline (Bradbury et al., 2007;
Glaubitz et al., 2014). Tags were then aligned to the IWGSC (2014) Chinese Spring v1.0
reference genome and filtered using TASSEL 5 for greater than 0.05 MAF and less than 70%
missing data (Bradbury et al., 2007; Poland et al., 2012; Glaubitz et al., 2014). GBS tags were
retained if they were polymorphic between the recurrent parent KS05HW14 and 9.131.15x
resulting in 3,554 unique tags.
Linkage Map Construction
Using JoinMap 4.0 (Van Ooijen, 2006), separate linkage maps for the U6708-03 and the
U6708-04 families with the 3554 retained GBS markers were constructed. Markers were
grouped together based on independent LOD scores with a minimum of LOD score of 3.0.
Markers were sorted in each group using the “fixed” and “start” order options. Map distances
were calculated using the Kosambi’s mapping function with default parameters (Kosambi,

43

1943). Comparisons between these linkage maps to the IWGSC (2014) Chinese Spring v1.0
reference genome were visualized using MapChart (Supp. Figure 2.1-7A,B) (Voorrips, 2002).
QTL Analysis
QTL analysis was performed using Windows QTL cartographer version 2.5 (WinQTL)
(Wang et al., 2012). Composite interval mapping (CIM) was performed for each trait based on
the following parameters: walk speed=1.0 cM, window size=10.0 cM, control markers=5, and
backwards regression. Genomewide threshold values were generated for each trait individually
using 1000 permutations at α=0.05 (Sup. Table 1). Graphical representations of QTL positions
were generated using MapChart (Voorrips, 2002).
Results
Linkage Map Construction
There were a total of 96,164 GBS raw tags generated using genotyping-by-sequencing.
After filtering, for markers that had a maximum of 30% missing data and 0.05 MAF, and
removing, indels, non bi-allelic, heterozygous and missing markers, a total of 5,831 markers that
were polymorphic or monomorphic between 9.131.15x and KS05HW14 were identified. Out of
those markers, around 39% were monomorphic and fail to segregate in the population. After
selecting for polymorphic markers, a total of 3,554 GBS SNPs were retained for further analysis.
A total of 34 and 32 linkage groups were assembled for U6708-03 and U6708-04 respectively
(Sup. Figure 2.1-7). In total, 1,840 polymorphic markers segregate in the U6708-04 family and
1,967 polymorphic markers segregate in the U6708-03 family. There was an average of 57
markers per linkage group for each family (Sup. Table 2). However, some linkage groups are
composed of a large amount of markers (Sup. Figure 2.3A, B) and others are composed of very

44

few markers (Sup. Figure 2.1A, B) indicating that there is a wide range in the number of markers
per linkage group. No linkage groups were able to be constructed that aligned to chromosome 2B
in U6708-04 and chromosome 3D from U6708-03 due to a lack of polymorphic markers present.
Linkage groups typically aligned to the telomeric ends of the chromosomes with only a few,
notably 6D in both families, capturing regions near the centromere.
Screening for Stripe Rust Seedling Resistance
Both U6708 families were screened for resistance to Pst-37 at the seedling stage,
however, only U6708-03 segregated for Pst resistance while U6708-04 was completely
susceptible. Prelude was susceptible while the synthetic was resistant (Figure 2.5). Infection type
measured at the seedling stage was mapped to two distinct 4D linkage groups. The first
significant association between IT and GBS-SNP markers is located on the short arm of 4D and
originated from TA2474 (Table 2.1) with an R2 of 0.64 and the allelic effect (a) is -1.60 based on
the 0-9 IT scale (Table 2.1). The second significant association between IT and GBS-SNP
markers is located on the long arm of 4D and originates from the recurrent parent KS05HW14
(Table 2.1).
Screening for Stem Rust Seedling Resistance
The U6708-03 and U6708-04 families were screened for resistance to the Pgt-QFCSC
race in a seedling assay and both families segregated for Pgt resistance. An intermediate IT to
Pgt-QFCSC was observed in the synthetic while a highly resistant reaction was observed in
Prelude (Figure 2.6). In the U6708-03 family, the 2D, 4D, and 5B linkage groups contained
significant regions associated with IT measured in the three tested environments (Figure 2.2). In
the U6708-04 family, regions on the 2D and 5B linkage groups were associated with IT

45

measured in the three environments (Figure 2.3). Both significant associations between the IT
phenotype measured in the GC with GBS-SNP markers located on the short arm of chromosome
2D in the U6708-03 family (R2 = 0.12 and a= -0.29) and the U6708-04 family (R2 = 0.17 and a=
-0.38) originated from TA2474 (Table 2.1). Significant associations between the IT phenotype
measured in the GC with GBS-SNP markers located on the long arm of chromosome 5B in the
U6708-03 family (R2 = 0.29 and a= -0.45) and U6708-04 family (R2 = 0.25 and a= -0.56)
originated from 9.131.15x.
Greenhouse Screening of Adult Plants for Stem and Stripe Rust Resistance
The U6708-03 family segregated for Pst resistance at the adult plant stage for both
infection type (IT) and severity in the greenhouse. Significant associations between markers and
adult plant ITs were located on the short arms of chromosome 4D and 3B (Figure 2.2). An
AUDPC score was generated from the Pst severity scores. Both the AUDPC and adult plant IT
phenotype co-localize with the seedling IT phenotype on chromosome 4D (Figure 2.2).
Both U6708-03 and U6708-04 segregated for Pgt resistance at the adult plant stage for
both infection type and severity in the greenhouse. Significant associations between markers on
4B and 5B for infection type in the U6708-03 family were identified (Table 2.1). However, no
significant associations for severity in the U6708-03 family were identified. Infection type
measured in the U6708-03 family in the greenhouse (R2 = 0.29 and a = -0.84) co-localized with
seedling IT (Figure 2.2). Significant markers located on 4B associated with IT in the U6708-03
family are derived from KS05HW14, the recurrent parent (Table 2.1). Adult plant infection type
measured in the U6708-04 family had significant associations with markers on chromosome 5B
and 4B. Additionally, severity measured in the U6708-04 was significantly associated with
markers located on chromosome 5B. Both adult plant infection type (R2 = 0.46 and a= -0.86) and

46

severity (R2=0.16 and a= -7.47) measured in the greenhouse co-localize with the seedling IT
measured in the growth chamber (Figure 2.3). Infection type associated with markers on
chromosome 4B does not co-localize with any other phenotypes identified in the U6708-04
family.
Field Analysis of Stem Rust
Both Prelude and 9.131.15x showed an intermediate infection type in Mason, MI, in
2017. Pgt resistance segregated in both the U6708-03 and U6708-04 families (Figure 2.2, 2.3).
Associated regions for severity and infection type on chromosome 5B co-localized with IT
mapped in the seedling and greenhouse adult plant screen for the presumed major effect Pgt
seedling resistance QTL (Figure 2.2, 2.3). Multiple genomic regions associated with severity,
inherited from KS05HW14, were identified in U6708-04 located on 7D and 3D and, in U670803, on 1B (Table 2.1). Infection type and severity in the U6708-03 family co-localized on the
short arm of chromosome 7D with marker alleles which originated from TA2474 (Figure
2.2).These putative QTLs did not align with any of the previously mapped Pgt phenotypes in
either the seedling or greenhouse experiments. In the U6708-04 family a genomic region
associated with severity, with alleles inherited from 9.131.15x, was mapped to 3BS with
infection type slightly under the genomewide threshold level on the same linkage group (Figure
2.3). Both infection types with significant associations on 4B identified in the greenhouse, and
infection types with significant associations on 2D identified in the growth chamber did not colocalize with any phenotypes that were deemed significant in the 2017 field analysis.

47

Adult Plant Reaction to Leaf Rust in Mason, Michigan 2017
Both the U6708-03 and U6708-04 families segregated for resistance to Pt during the
2017 field season in Mason, MI. Prelude and 9.131.15x were scored as susceptible in the field
with moderately resistant phenotypes occurring in the RILs (Figure 2.5). In the U6708-03 family,
there were two putative resistance QTLs, one identified on 3BL and one on 6DL (Table 2.1).
Both the severity and infection type phenotypes co-localized on the 3B linkage group and
originated from the recurrent parent KS05HW14 (Figure 2.2). The 6DL QTL, associated with
the infection type phenotype, originated from the Ae. tauschii accession TA2474. Both the
severity and infection type phenotypes co-localized to the 3BL linkage group present in the
U6708-04 population and originated from KS05HW14 (Figure 2.3). KS05HW14 was not
included in the study because it is a winter wheat. In 2006, the Regional Germplasm
Observational Nursery (RGON) included KS05HW14 in their field trials. It garnered a 50%
severity and a moderately susceptible IT rating in St. Paul, MN.
Discussion
Stripe Rust Resistance from TA2474
A seedling resistance QTL, QYr.msu-4DS, has been identified in the SHW 9.131.15x on
4D for resistance to Pst. Infection type observed in the seedling stage and co-localized with adult
plant infection type and AUDPC phenotypes measured in the greenhouse environment (Figure
2.2). QYr.msu-4DS is located on the short arm of chromosome 4D and originated from the Ae.
tauschii accession TA2474. Currently, two officially designated Pst seedling genes have been
identified on 4D, Yr28 (Singh et al., 2000)and YrAS2388 (Huang et al., 2011), both at the distal
end of the short arm of chromosome 4D. Yr28 and YrAS2388 are distinct based on their

48

differential resistance and physical position (Huang et al., 2011). These genes originate from
two different Ae. tauschii accessions, W-219 and AS2388, respectively, while QYr.msu-4DS is
from TA2474 (Singh et al., 2000; Huang et al., 2011). Owing to its own distal nature on 4DS,
QYr.msu-4DS is likely either a novel resistance QTL or a potential variant of YrAS2388. Further
tests, like an allelism test, need to be performed to confirm the novelty of QYr.msu-4DS.
Although numerous Ae. tauschii accessions and other wild wheat relatives have been
screened for stripe rust resistance, either in their diploid form or in a synthetic, the designated
stripe rust genes derived from these accessions have only been observed at the proximal end of
4DS (Singh et al., 2000; Huang et al., 2011). A recent survey of Ae. tauschii germplasm has
postulated that YrAS2388 is a common gene present in multiple Ae. tauschii accessions and is
most likely a variant of Yr28 (Liu et al., 2013). This indicates the possibility that common rust
resistance genes are shared among Ae. tauschii germplasm. Further investigation into the
distribution of YrAS2388 in the Ae. tauschii germplasm can provide insight into the evolution of
major gene resistance to Puccinia in natural populations.
Stem Rust Resistance from the Synthetic 9.131.15x
The putative stem rust seedling resistance QTL QSr.msu-5BL

was

identified on

chromosome 5B in both families and with infection type and severity taken in multiple
environments co-localizing. Both of these QTLs were linked to similar markers. Therefore, it is
likely that the 5B Pgt seedling resistance QTL is the same locus in both families (Sup Fig
2.5A,B). The origin of resistance for this QTL is the synthetic parent. There are currently two
officially designated stem rust genes present on 5BL, Sr56 and Sr49. Both of these genes
originated from hexaploid wheat. However, Sr49 is a seedling resistance gene and Sr56 is an
APR gene (Bansal et al., 2014, 2015). Sr49 originated from the land race Mahmoudi (Bansal et

49

al., 2015). The very distal nature of QSr.msu-5BL indicates the potential for it to be a novel Pgt
seedling resistance QTL or a variant of Sr49. Sr49 confers an intermediate resistant phenotype in
Mahmoudi similar to QSr.msu-5BL in 9.131.15x (Bansal et al., 2015). However, the putative
originator of the 5B Pgt seedling resistance QTL, hexaploid Prelude, exhibits a highly resistant
fleck phenotype to both Pgt-QFCSC (Figure 2.4) as well as the Pgt-98-1,2,(3),(5),6 (Hiebert et
al., 2016), a Pgt race from Australia used to map Sr49 (Bansal et al., 2015). This supports the
possibility that QSr.msu-5BL and Sr49 confer different ITs, although only if QSr.msu-5BL is
present in different hexaploid backgrounds. A potential 7D APR QTL originating from TA2474
was identified in the 2017 field trial at Mason, MI. This QTL is a small effect QTL and was not
observed in the greenhouse study. There are currently no officially designated Pgt APR QTLs
located on 7D that originate from Ae. tauschii making this a potential, novel QTL (McIntosh et
al., 2013). However, this will require further testing to confirm that this 7D QTL is repeatable.
The origin of resistance for the QSr.msu-5BL QTL is the synthetic parent and rationally
from tetraPrelude (due to its location in the B genome). This is supported additionally by the
highly resistant phenotype of the hexaploid Prelude. However, sequencing of hexaploid Prelude
revealed significant marker differences present throughout the A and B genome from the
synthetic. It has been observed that the creation of the tetraPrelude may have resulted in
translocation events between the 1D chromosome and the A and B genome (Dronzek et al.,
1970). In order to test this, an LD analysis was performed between SNP markers aligned to the
1D chromosome and SNPs aligned to the A and B genome (data not shown). Our results indicate
that it is unlikely that the tetraploid Prelude used to create this SHW suffered from the same
translocation events that have previously been observed (Dronzek et al., 1970). Further
investigation will be needed to pinpoint the exact origin of the QSr.msu-5BL QTL.

50

Alignment of YrAS2388 and Sr49 Markers to the Reference Genome
In an effort to discover additional evidence on the potential novelty of these identified
QTLs, the recent release of the IWGSC (IWGSC, 2014b) Chinese Spring v1.0 reference genome
was used to align markers linked to Sr49 and YrAS2388 using BLAST (Huang et al., 2011;
Bansal et al., 2015). Both the Sr49 and YrAS2388 markers that were aligned to the reference
were situated in overlapping molecular positions with markers associated with QSr.msu-5BL and
QYr.msu-4DS respectively (data not shown). This additional data supports the hypothesis that
these identified seedling resistance QTLs may be variants of YrAs2388 and Sr49. However, both
the length of DNA sequence associated between flanked markers as well as the propensity for R
genes to be clustered together in the genome, indicates the needs for additional tests. Therefore,
allelism tests should be performed to better determine the novelty of QTLs that may be located
very close together (Bergelson et al., 2001; Leister, 2004).
Adult Plant Reaction to Leaf Rust Segregating in the U6708 Population
The 9.131.15x synthetic (tetraPrelude/TA2474) was originally created at Kansas State
University by Dr. Bhanu Kalia for the purpose of identifying adult plant resistance to leaf rust
isolates present in Kansas (Kalia, 2015). TA2474 and 9.131.15x were phenotyped as susceptible
to a number of leaf rust isolates at the seedling stage (Kalia, 2015; Kalia et al., 2017). A
mapping population was created by crossing 9.131.15x to WL711 which was phenotyped at
several locations, and APR QTLs were identified on 1B, 1A, 2D, 5D, 5A and 6B (Kalia, 2015).
All regions from the D genome were contributions from TA2474.
None of the previously identified leaf rust APR QTLs from 9.131.15x were identified in
the U6708 population. There are a multitude of reasons why this may be the case. First, the

51

populations could have had a differential inheritance of genetic information from the synthetic
parent. This is supported by the extremely small 1A and 1B linkage groups that are present in the
U6708 population, indicating the probability that these previously identified QTLs were not
captured during the creation of this population. Second, the genetic background of this
population is different. The recurrent parent in the U6708 population is KS05HW14, a hard
white winter wheat, and a parent in the other mapping population was W7111, a spring wheat
variety. The genetic background of wheat has been shown to be significant in influencing QTLs
in the case of rust where suppressors can alter the effectiveness of rust resistance QTLs (Bai and
Knott, 1992; Assefa and Fehrmann, 2004). Third, the endemic leaf rust isolates likely differ
between Kansas/CIMMYT disease nurseries compared to Mason, MI. Thus, previously
identified QTLs that are shared between these two populations may be either environmental or
race specific.
The susceptible reaction of Prelude and 9.131.15x compared to the moderately resistant
phenotype that is segregating through the population indicates that either KS05HW14 is the
contributor of Pt resistance or suppression is occurring in the SHW. There were three putative
QTLs identified in these two families, two occurring on 3B and one occurring on 6D. The major
effect QTLs that have been identified in both populations occur on the 3B chromosome with
both originating from KS05HW14, appear to be located near one another, and are likely shared
between the populations (Figure 2.2, 2.3). The 6D QTL originates from TA2474 and was only
observed in a single family (Table 2.1). KS05HW14, a winter wheat, was not rated for leaf rust
during the 2017 field season as the U6708 population is spring type, but it was rated in 2006 in
the RGON and displayed a moderately susceptible infection type and a 50% severity. A follow

52

up study testing KS05HW14 for APR to leaf rust in Mason, MI, will need to be performed to test
if the resistance observed may originate from a race-specific resistance QTL.
The substitution at this genomic region for KS05HW14 alleles providing enhanced leaf
rust resistance is an indication of two possibilities: an unidentified resistance QTL is present in
KS05HW14 on 3B, or this substitution eliminates a suppressor. Phenotyping KS05HW14 for Pt
resistance and testing 9.131.15x for Pt resistance in different hexaploid background could test
these two hypotheses. Only one Pt resistance QTL originating from Ae. tauschii was observed
and it was only present in one family (Table 2.1). The large effect of the 3B QTLs in both
families may make it difficult to identify minor effect QTLs present, especially with the small
number of individuals in this population (Beavis, 1998; Xu, 2003). Thus, resistance may be
originating from multiple TA2474 derived QTLs, but their effect is masked by the presence of a
highly significant suppressor. No QTL that have been identified for stem or stripe rust in the
U6708 population co-localized with the QTL on 3B or on 6D. Thus, the Pt resistance QTLs
identified in this experiment is not currently thought to be either pleiotropic or linked to
previously identified QTLs. Further testing of the population with a single-spore Pt isolate can
help further delineate whether or not the segregating resistance in U6708 is a seedling resistance
gene or an APR loci.
Phenotyping of Adult Plant Resistance
Recent efforts have demonstrated the feasibility of using the greenhouse to both screen
and identify new sources of genetic resistance to stripe and stem rust at the adult plant stage
(Pretorius et al., 2007; Bender and Pretorius, 2016). In this study, greenhouse screening of adult
plants was successful in identifying both major and minor effect QTLs (Table 2.1). However,
greenhouse screening of adult plants failed to identify minor effect seedling resistance QTLs

53

from the seedling assay as well as APR QTLs identified in Mason, MI, for Pgt resistance. Minor
effect QTL for Pst and Pgt resistance originating from the KS05HW14 were identified, which
was rated as susceptible at the seedling stage to both stripe and stem rust. There can be a
multitude of reasons for this lack of repeatability of these minor effect QTLs between
environments. The lack of replication due to space and time constraints in the greenhouse and
loss of replication for some lines in the field may impact the ability to detect QTLs with a low R2
value, especially in the presence of other major QTLs. Also, due to the population size, it is
likely the Beavis effect influenced the ability to detect authentic minor effect QTL and caused
spurious minor effect QTLs to appear (Beavis, 1998; Xu, 2003). While minor seedling QTLs are
more readily identified in controlled assays, the question remains for the breeder if these QTLs
will be effective in the field environment when deployed. Minor seedling QTLs for stem rust that
were detected in the seedling stage and not in the greenhouse were also not detected in the field
environment (Table 2.1). However, the major seedling QTL present on 5BL could be identified
in all three environments and the major seedling QTL present on 4DS could be detected in all Pst
experiments. Those minor effect QTLs that failed to display significance in multiple
environments are thus likely aberrations due to population size limitations and, if they are real
seedling resistance genes, likely not effective in the adult plant stage, making their identification
difficult regardless of the method.
Summary
The SHW 9.131.15x was analyzed using seedling, greenhouse, and field experiments to
identify sources of resistance to both Pst-37 and Pgt-QFCSC. U6708-03 and U6708-04 both
segregated for Pgt resistance while only U6708-03 segregated for Pst resistance. Two seedling
resistance loci, QYr.msu-4DS and QSr.msu-5BL, were identified in the seedling, greenhouse, and

54

field environments. QYr.msu-4DS is located on 4DS and originated from the Ae. tauschii parent
TA2474. It is either a novel stripe rust QTL or a variant of the most distal Pst gene on 4DS,
YrAS2388. QSr.msu-5BL is located on 5BL and originated from 9.131.15x. Due to its distal
nature on 5BL, this is likely a novel Pgt QTL or a variant of Sr49. In addition to Pgt and Pst
resistance, QTLs for Pt resistance are also present in the population. Thus, in addition to
harboring potentially new putative disease resistance QTLs for stem, stripe, and leaf rust, lines
extracted from this population can be used to increase resistance to multiple Puccinia species
when crossed into a breeding program.

55

APPENDIX

56

APPENDIX
Table 2.1. Quantitative trait loci for resistance to stem, stripe, and leaf rust.
a: Sr= Stem rust, Lr=Leaf rust, Yr= Stripe rust, IT was rated based on the 0–9 McNeal scale for Pst resistance at both the seedling
and adult stage. IT for Pgt and Pt resistance were measured using the 0–4 Stakman scale for seedling resistance and were rated as
susceptible (S), moderately susceptible (MS), moderate (M), moderately resistant (MR) or resistant (R) as adult plants. Severity
was rated from 0–100% based on the Cobb scale, AUDPC = area under the disease progression curve. GC = growth chamber
phenotyping environment; GH = greenhouse phenotyping environment; MM = Mason, Michigan, 2017 phenotyping
environment.
b: Most significant marker based on LOD.
c: Additive effect of the alleles.
Disease
Stem
Rust

QTL

Family

Stage

Trait

Location

Chr

Position

LOD

R2

Effectc

Origin

QSr.msu-1BS

U6708-03

Adult

IT

Field

1BS

665,403,509

3.96

0.12

-7.36

KS05HW14

QSr.msu-3BL

U6708-04

Adult

IT

Field

3BL

573,497,145

6.66

0.08

-0.35

Synthetic

QSr.msu-4BL

U6708-03

Adult

IT

GH

4BL

U6708-04

Adult

IT

GH

4BL

619,589,061

4.72

0.13

-0.56

KS05HW14

626,604,202

3.78

0.08

-0.37

KS05HW14

U6708-03

Seedling

IT

GC

U6708-04

Seedling

IT

GC

5BL

699,455,437

10.77

0.29

-0.45

Synthetic

5BL

699,728,464

7.07

0.25

-0.56

Synthetic

U6708-03

Adult

IT

U6708-04

Adult

IT

GH

5BL

693,686,064

8.23

0.29

-0.84

Synthetic

GH

5BL

699,728,464

14.03

0.46

-0.86

Synthetic

U6708-04

Adult

Severity

GH

5BL

697,611,190

4.37

0.16

-7.47

Synthetic

U6708-03
U6708-04

Adult

IT

Field

5BL

699,455,437

15.76

0.52

-0.84

Synthetic

Adult

IT

Field

5BL

699,407,657

25.21

0.69

-1.01

Synthetic

U6708-03

Adult

Severity

Field

5BL

699,422,973

8.83

0.32

-11.81

Synthetic

U6708-04

Adult

Severity

Field

5BL

697,865,267

7.69

0.29

-12.83

Synthetic

U6708-03

Seedling

IT

GC

2DS

7,527,954

6.34

0.12

-0.29

TA2474

U6708-04

Seedling

IT

GC

2DS

13,242,604

5.61

0.17

-0.38

TA2474

QSr.msu-3DL

U6708-04

Adult

IT

Field

3DL

45,015,647

3.87

0.05

-0.26

KS05HW14

QSr.msu7DS.1
QSr.msu7DS.2

U6708-04

Adult

Severity

Field

7DS

1,570,012

5.63

0.16

-9.69

KS05HW14

U6708-03

Adult

IT

Field

7DS

62,120,102

3.81

0.074

-0.33

TA2474

U6708-03

Adult

Severity

Field

7DS

72,699,333

5.25

0.17

-8.90

TA2474

QYr.msu-3BS

U6708-03

Adult

IT

GH

3BS

14,482,106

4.21

0.12

-0.63

KS05HW14

QYr.msu-4DS

U6708-03

Adult

IT

GH

4DS

2,828,876

4.78

0.15

-0.70

TA2474

U6708-03

Adult

AUDPC

GH

4DS

1,704,666

6.72

0.22

-17.17

TA2474

QSr.msu-5BL

QSr.msu-2DS

Stripe
Rust

Leaf
Rust

U6708-03

Seedling

IT

GC

4DS

1,242,429

19.43

0.64

-1.60

TA2474

QYr.msu-4DL

U6708-03

Seedling

IT

GC

4DL

345,415,047

5.85

0.09

-0.62

KS05HW14

QLr.msu-3BL

U6708-03

Adult

IT

Field

3BL

748,448,161

22.83

0.76

-1.06

KS05HW14

U6708-04

Adult

IT

Field

3BL

748,448,161

14.62

0.47

-0.81

KS05HW14

U6708-03

Adult

Severity

Field

3BL

748,448,161

16.63

0.68

-13.75

KS05HW14

U6708-04

Adult

Severity

Field

3BL

748,448,161

10.11

0.38

-11.48

KS05HW14

U6708-03

Adult

IT

Field

6DL

347,713,271

6.73

0.08

-0.37

TA2474

QLr.msu-6DL

57

Sup Table 2.1. Genomewide threshold values generated for each trait individually using 1000
permutations at α=0.05.
U6708-04

U6708-03

Trait
Yr IT GC

LOD
N/A

LOD
3.6

Yr IT GH

N/A

3.51

Yr AUDPC GH

N/A

3.58

Sr IT GC

3.58

3.59

Sr IT GH

3.58

3.7

Sr Severity GH

3.47

6.16

Sr IT Mason,
Michigan 2017

3.67

3.73

Sr Severity Mason,
Michigan 2017

3.66

3.65

Lr IT Mason,
Michigan 2017

3.62

3.78

Lr Severity Mason,
Michigan 2017

3.62

3.62

Figure 2.1. Flow through of the population development of the U6708-03 and U6708-04
families. A single F2 individual from the U6523 population, U6523-1-156, was backcrossed to
KS05HW14 to create the two individual U6708 families.

58

LG12

4B03LG15

LG16

Figure 2.2. QTL analysis of the U6708-03 family using composite interval mapping for stem,
stripe, and leaf rust resistance QTL. Eight linkage groups, of chromosomes 1B, 2D, 3B, 4B, 4D,
5B, 6D, and 7D, were identified that carry rust resistance QTL. Leaf, stripe, and stem rust
resistance QTL are shown in blue, green and black, respectively.
LG3

1B

3B

3D

9

10

8

7

6

5

4

3

2

1

0

9

8

10

7

6

5

4

3

2

Lr/IT/Field

85.1
85.2
85.5
85.6
85.7
85.9
86.3
86.5
86.8
86.9

1

84.6

0

9

8

7

22.1
22.9
24.4
24.5
24.7
24.9
25.0
25.3
25.6
25.9
26.1
26.8
27.5
27.9
28.2
28.3
28.4
28.9
29.5
29.7
29.9
30.1
30.2
30.7
31.0
31.2
31.6
33.0
33.5
34.4
36.1
36.4
37.2
37.3
37.7
38.3
38.7
39.0
39.2
39.7
40.1
40.3
41.0
41.3
41.6
42.4
42.7
43.9
44.8
45.3
45.8
46.7
47.6
47.8
49.2
50.0
50.2
50.7
50.9
51.3
52.1
52.7
52.9
53.2
53.3
53.7
54.1
54.7
56.7
59.8
60.3
61.3
62.1
62.7
63.5
64.8
65.1
65.6
68.2
68.7
68.9
69.3
70.2
70.7
71.7
72.4
72.7
73.4
74.3
75.5
78.1
78.3
79.8
80.0
80.9
81.3
81.6
82.0
82.9
83.0
83.7
84.4
84.5

S6D_12018199
S6D_12019189
S6D_12023993
S6D_12435877
S6D_12358606
S6D_13197345
S6D_13202325
S6D_13206838
S6D_13970695
S6D_13863766
S6D_33926349
S6D_15170081
S6D_14657290
S6D_15256175 S6D_15779113
S6D_15809407
S6D_17446940 S6D_16008076
S6D_16704893
S6D_16706514
S6D_17181122
S6D_19567917
S6D_22766557
S6D_23622322
S6D_80064974
S6D_26002250
S6D_25851509
S6D_26002274
S6D_27859416
S6D_27525812
S6D_28304138
S6D_30744756
S6D_28324147
S6D_29875372
S6D_53640739
S6D_33305189
S6D_34075504
S6D_37228815
S6D_37231315
S6D_36689837
S6D_54695381 S6D_42153457
S6D_53775029
S6D_51732906
S6D_54748293
S6D_351124936
S6D_70772794
S6D_65353137
S6D_67545931
S6D_68098967 S6D_65912199
S6D_81920593 S6D_79864250
S6D_82501332
S6D_77864626 S6D_83223948
S6D_81659451
S6D_101721161
S6D_109485496
S6D_98090181
S6D_98090252
S6D_101758490
S6D_102473339
S6D_121347763
S6D_132054396
S6D_132200523
S6D_137541139
S6D_135112843
S6D_132200911
S6D_173445362 S6D_207934182
S6D_291699332
S6D_291620586
S6D_241296319
S6D_305272917
S6D_351124932
S6D_324565245
S6D_350131401
S6D_347713271
S6D_372432436
S6D_364851010
S6D_381549747
S6D_391693326
S6D_392881561
S6D_397083937
S6D_400080086
S6D_400398852
S6D_411724906
S6D_412622083
S6D_406343375
S6D_406103601 S6D_407829580
S6D_405678645
S6D_415751919
S6D_414403571
S6D_429830688
S6D_429358398
S6D_431108774
S6D_428697773
S6D_429674940
S6D_431173308
S6D_431148615
S6D_432929380
S6D_434207907
S6D_435306317
S6D_435810167
S6D_434751489
S6D_435950336
S6D_435834479
S6D_436673680 S6D_436466074
S6D_436452770
S6D_436816070
S6D_437296228
S6D_436813800
S6D_436722115
S6D_438097245
S6D_438829921
S6D_445337359
S6D_445458196
S6D_446919153
S6D_446477307
S6D_446478084 S6D_445773103
S6D_447845104
S6D_448872056
S6D_449923131
S6D_448872117
S6D_451915018
S6D_452410589
S6D_452405960
S6D_452342253
S6D_452410667
S6D_453174642
S6D_452587154
S6D_455735643
S6D_455718701
S6D_455558727 S6D_455626507
S6D_466738586
S6D_463744870
S6D_460468252
S6D_460468308
S6D_461501885
S6D_462479366
S6D_463079592
S6D_461467572
S6D_456683425 S6D_463547451
S6D_462494601
S6D_464483328
S6D_463051540
S6D_464830674
S6D_467208090
S6D_467861477
S6D_467803310 S6D_467187468
S6D_467198574
S6D_468833640
S6D_469567355
S6D_469583807
S6D_469344492
S6D_469537865
S6D_468113435
S6D_470373596
S6D_471828200
S6D_472404065
S6D_472533683

Sr/IT/Field

10

59

6

S4D_3238232

5

S4D_2828876

13.7

9

12.7

10

S5B_710784650

S4D_1999942

4

S5B_711244784

9.9

11.4

Yr/IT/GC

9.6

S4D_1242429

3

Yr/AUDPC/GH

Sr/Severity/Field

9.7

8

YrIT/GH

Sr/Severity/Field

Yr/IT/GC

Sr/IT/Field

7D
2

Yr/AUDPC/GH

Sr/IT/GH

S7D_59105969
S7D_58491641
S7D_60279204
S7D_60217671
S7D_60459462
S7D_62120178
S7D_61757302
S7D_62120102
S7D_64236500
S7D_61188004
S7D_64379914
S7D_63453715
S7D_63471298
S7D_65592365
S7D_65617305
S7D_65715714
S7D_65752952
S7D_68518279
S7D_68431283
S7D_71569531
S7D_74060422 S7D_72699333
S7D_75136077
S7D_72452170
S7D_75271662
S7D_74963530
S7D_72808182
S7D_73153208
S7D_72699287
S7D_78193178
S7D_80264777
S7D_78672632
S7D_79299360
S7D_83426451
S7D_80294908
S7D_83376988
S7D_83666746
S7D_83666851
S7D_83473595
S7D_80292147
S7D_92604251
S7D_101557747
S7D_504011403
S7D_502232313
S7D_502232988 S7D_505129726
S7D_507848669
S7D_519112634
S7D_576703863
S7D_576735344
S7D_89733085
S7D_393456338
S7D_577782004
S7D_579634283
S7D_580379374
S7D_70048992
S7D_579361833
S7D_579085646
S7D_588085500
S7D_592223121
S7D_592632637
S7D_592632581
S7D_592392427
S7D_595068840
S7D_595528770
S7D_597019065 S7D_595613399
S7D_596434245
S7D_597118932
S7D_600837544
S7D_599115002
S7D_601070723
S7D_601781609
S7D_601904143
S7D_601071069
S7D_601487305
S7D_602197236
S7D_603678242
S7D_605596128
S7D_604869757
S7D_605744448
S7D_611014718
S7D_610740232
S7D_610739554
S7D_623403351
S7D_619996988
S7D_620622222
S7D_620283090
S7D_621951204
S7D_620924768
S7D_621212944
S7D_621155254
S7D_623068416
S7D_626481419
S7D_627295271
S7D_626927234
S7D_626950802
S7D_627411185
S7D_627569993
S7D_629311395
S7D_628521992
S7D_629311461
S7D_630196200
S7D_630440805
S7D_632509242
S7D_631758106
S7D_632648460
S7D_631681105 S7D_631922149
S7D_638440265
S7D_635844631
S7D_632593226
S7D_638208446
S7D_632802365
S7D_638541382
S7D_631978910
S7D_634562548

1

19
18
17
16
15
14
13
12
11
10
9
8
7
6
5
4
3
2
1
0

Sr/IT/GC

YrIT/GH

S5B_703233730
S5B_701519795
S5B_703229470

Sr/IT/Field

4.0
4.2
4.3

S3D_443309864

S7D_5653553

Sr/IT/Field

Lr/IT/Field

Lr/Severity/Field

4D

12.0
12.6
13.1
13.5
13.9
14.4
14.5
14.8
14.9
15.4
15.7
15.9
16.1
16.7
17.0
17.1
17.2
17.4
17.7
17.8
18.2
18.4
18.5
18.6
19.0
19.4
20.1
20.4
21.5
22.0
22.2
22.5
22.7
22.8
23.2
23.3
23.6
23.7
24.2
25.6
27.6
29.8
30.6
30.7
31.2
32.0
32.7
33.2
33.5
34.0
35.0
36.6
38.4
38.5
39.3
40.2
46.2
49.2
49.8
50.4
50.9
51.7
53.0
53.6
54.1
54.2
55.3
55.9
57.3
57.8
58.2
58.4
58.9
59.8
60.5
61.9
62.4
63.4
66.7
68.0
69.4
71.6
76.0
77.4
77.9
78.3
79.0
79.2
79.4
79.8
80.0
80.5
80.7
81.2
81.7
82.2
83.0
83.3
83.5
84.0
84.7
85.2
85.4
85.5
85.8
86.1
86.2
86.6
86.8
88.1
88.6
89.7
90.1

0.0
0.8
1.2
1.8
2.0
2.4
2.6
3.0
3.3
4.1
5.5
7.4
7.6
7.8
8.1
8.4
8.8
9.0
9.2
9.5
10.4
11.2
11.9
12.5
13.1
14.2
15.5
16.0
16.4
16.7
17.3
17.7
19.0
19.9
20.2
20.7
20.8
20.9
21.1

0

0.0

S4D_1704666

Sr/Severity/Field

S5B_699728464 S5B_699407657
S5B_697611190 S5B_699455437

Sr/IT/GC

S5B_697831155

2.8

Sr/IT/GH

S5B_699422973

2.4

7

34.9

S5B_693686064

2.0

6

Lr/Severity/Field

15
14
13
12
11
10
9
8
7
6
5
4
3

0.0

5

Lr/IT/Field

Sr/IT/Field

Yr/IT/GH

LG17

0.0

4

LG33

LG23

5B

3

12.3
12.4
12.8
13.0
13.2
13.5
13.7
14.0
14.2
14.4
14.6
14.8
15.2
15.5
16.7
16.8
17.2
17.6
17.8
18.3
18.7
19.2
19.5
19.8
20.1
20.2
20.4
20.8
21.1
21.3
21.7
22.1
22.4
22.5
22.7
22.8
23.0
23.1
23.4
23.5
23.7
23.8
24.0
24.4
24.6
24.7
25.2

2

12.2

6D

1

9

8

7

S4B_25886179
S4B_32279358
S4B_38624956
S4B_34025485
S4B_191090248
S4B_556069660
S4B_529563719
S4B_526935208
S4B_535089159
S4B_544293087
S4B_544042765
S4B_529563963
S4B_547093363
S4B_554966435
S4B_552833587 S4B_531946700
S4B_558583868
S4B_527979736
S4B_546023632
S4B_557995550
S4B_553915774
S4B_562355380
S4B_536895442
S4B_568709455
S4B_565528122
S4B_567004232
S4B_572558230
S4B_567591085 S4B_573387592
S4B_571049371
S4B_602403716
S4B_577694813
S4B_579313471
S4B_588905418
S4B_588779331
S4B_589181090
S4B_583475648
S4B_601792870
S4B_601934091 S4B_602403655
S4B_610244239
S4B_601774330
S4B_601792322
S4B_613388382
S4B_615562770
S4B_613715043
S4B_615382677
S4B_615383946
S4B_615708070
S4B_616575086
S4B_616932643
S4B_617334542
S4B_619588944
S4B_619589061
S4B_619935881
S4B_625963961
S4B_621446792
S4B_620061711 S4B_621679408
S4B_621679237
S4B_625971498
S4B_626604202 S4B_623099621
S4B_626604971
S4B_629962284 S4B_627319108
S4B_626768439
S4B_629228008
S4B_627811289
S4B_627555294 S4B_629853060
S4B_633755571
S4B_634308810 S4B_635685764
S4B_633768930
S4B_630319525 S4B_631708532
S4B_634322252
S4B_637586849
S4B_635024663
S4B_637289578
S4B_639124617
S4B_638815052
S4B_636499665
S4B_644330895
S4B_647704569
S4B_649471268
S4B_647667811
S4B_650883943
S4B_640532063
S4B_654440068
S4B_660500077
S4B_660591179 S4B_660515583
S4B_660676396
S4B_662565558
S4B_663662540
S4B_662714113
S4B_672116501
S4B_670983327
S4B_670901586

S3D_20233332
S3D_20618963
S3D_20544442
S3D_22223658
S3D_20353646
S3D_26642137
S3D_26654879
S3D_26443648
S3D_28247675
S3D_28247721
S3D_30393736
S3D_38010276
S3D_37970827
S3D_36585107 S3D_33314732
S3D_33296656
S3D_37969605 S3D_35889019
S3D_33388811
S3D_41423982
S3D_42631446
S3D_41141983
S3D_44223324
S3D_45015647
S3D_45587843
S3D_45021010
S3D_48363653
S3D_47539627
S3D_47345231
S3D_47345297
S3D_48442324
S3D_55577045
S3D_56238010
S3D_56438931
S3D_58369980
S3D_58370142
S3D_62117027
S3D_68164115
S3D_66484029
S3D_70259952
S3D_67534715
S3D_62345840
S3D_73446898
S3D_68880849
S3D_70713380
S3D_79428382
S3D_93196771
S3D_184583746
S3D_220863200
S3D_179758809
S3D_149912136
Sr/IT/GH
S3D_225856460
S3D_192058920
S3D_214796069
S3D_250050929
S3D_244970665
S3D_226695276
S3D_289698840
S3D_276911714
S3D_260559779
S3D_251293045
S3D_226198159
S3D_296039573
S3D_277546305

0

S4B_256327967

9

4.0

8

S4B_20679079

7.3
8.9
11.4
12.5
14.5
15.0
18.6
18.8
18.9
19.0
19.1
19.4
19.5
19.7
19.8
19.9
20.0
20.1
20.3
20.4
20.5
20.6
20.7
20.8
20.9
21.0
21.2
21.3
21.4
21.5
21.6
21.9
22.0
22.1
22.3
22.5
22.6
22.9
23.2
23.3
23.5
23.8
23.9
24.1
24.2
24.4
25.1
25.6
25.7
26.2
26.4
26.7
26.8
27.0
27.2
27.3
27.4
27.5
27.7
27.8
27.9
28.0
28.1
28.2
28.3
28.4
28.5
28.7
28.9
29.1
29.2
29.7
30.1
30.4
31.3
32.1
37.4
39.6
40.7
42.8
47.2
52.6
61.8
63.1
66.7
71.9
73.6
74.4
86.8
88.9
92.8

Sr/Severity/Field

10

6

5

4

Sr/IT/GC

S2D_15496601
S2D_2452029
S2D_2201680
S2D_370235
S2D_2452116
S2D_2145981
S2D_2313854
S2D_2877134
S2D_5504248
S2D_5789154
S2D_6899497
S2D_7527954
S2D_7443363
S2D_9106403
S2D_6731847
S2D_7309581
S2D_9882889
S2D_9905362
S2D_10699856
S2D_11545271
S2D_10718874
S2D_11575943
S2D_13242604
S2D_11426549
S2D_11373542 S2D_12304410
S2D_13853778
S2D_14652683
S2D_14408803
S2D_14784910
S2D_16900439
S2D_14942177 S2D_15266667
S2D_17171539 S2D_18377691
S2D_16056873 S2D_15134145
S2D_16910840
S2D_19022196
S2D_17794172 S2D_17044373
S2D_19022113
S2D_16961444
S2D_19646151
S2D_20358129
S2D_20610775
S2D_20188084
S2D_21057222
S2D_20382122
S2D_22502442

3

S2D_8381688

2

5.1

1

0

S2D_273867

7

S1B_687280529

0.0

6

LG9_03

40.1

5

S1B_681077251

4

35.1

3

S1B_671196413
S1B_673581680
S1B_673502523
S1B_676782576
S1B_678479896
S1B_678894369
S1B_679435269

S4B_20568400
S4B_18703228

2.4

Sr/IT/GH

27.9
28.8
29.5
30.5
31.9
32.2
32.8

2

S1B_655342042
S1B_658439169
S1B_656423128
S1B_661641546
S1B_661567261
S1B_665410020
S1B_666812791
S1B_665113216
S1B_665403509
S1B_667911834
S1B_668546008
S1B_667672004
S1B_667050810

1

14.7
15.5
16.1
17.4
17.5
18.9
19.9
20.4
21.5
22.2
22.6
23.3
24.1

0

S1B_670556988

0.0
0.6

Yr/IT/GH

10.1

S3B_14482106
S3B_15802938
S3B_17613580
S3B_16000571
S3B_18393918
S3B_17070378
S3B_16402517
S3B_17802909
S3B_18484734
S3B_17974253
S3B_17866567
S3B_18664529
S3B_17587960
S3B_19396724
S3B_18966637
S3B_19394721
S3B_18253325
S3B_23398620
S3B_23719942
S3B_23021423
S3B_24397727
S3B_25180892
S3B_24940723
S3B_25803185
S3B_31994039
S3B_29498643
S3B_31701487
S3B_31010542
S3B_31995430
S3B_31366808
S3B_30978492
S3B_31306132
S3B_32592979
S3B_34005391
S3B_34284104
S3B_37643852
S3B_65705378
S3B_221532616
S3B_49870546
S3B_44287903
S3B_45197605
S3B_738367733
S3B_65342485
S3B_54294716
S3B_115244542
S3B_59036362
S3B_207795625
S3B_64498113
S3B_126304477
S3B_136095746
S3B_157637296
S3B_241087014
S3B_222247201
S3B_206291972
S3B_241087084
S3B_246145297
S3B_250568343
S3B_561366011
S3B_562272668
S3B_567001229
S3B_565273183
S3B_577639496
S3B_573497145
S3B_566830710 S3B_565725179
S3B_577639587
S3B_580348857
S3B_594745123
S3B_579446416 S3B_580784890
S3B_580521282
S3B_589561483 S3B_589458274
S3B_626712790
S3B_607406113
S3B_590623676
S3B_630398559
S3B_623654517
S3B_581268461 S3B_596232284
S3B_604416993
S3B_708013501
S3B_721046442
S3B_710167869
S3B_709533742
S3B_707906568
S3B_51062266
S3B_732436011
S3B_739510275
S3B_737607726
S3B_738504067 S3B_738504003
S3B_737442426
S3B_738110120
S3B_737639274
S3B_740106816
S3B_740547573
S3B_740133519
S3B_766364455
S3B_748448161
S3B_769535066
S3B_739923181
S3B_772467523
S3B_773565617
S3B_775659912

22
21
20
19
18
17
16
15
14
13
12
11
10
9
8
7
6
5
4
3
2
1
0

S1B_666920908

Sr/Severity/Field

8.0

0.0
0.5
1.5
1.9
2.6
3.5
4.0
4.3
4.6
4.9
5.1
5.3
5.5
5.7
6.1
6.3
6.9
7.8
8.1
8.3
9.4
9.9
10.1
10.8
17.3
17.9
18.5
19.1
19.4
19.9
20.0
20.6
21.1
21.3
22.3
22.8
23.9
24.3
24.6
25.8
26.0
26.7
28.4
28.6
29.0
29.2
30.0
31.3
31.7
32.4
33.2
33.7
34.5
35.2
35.5
35.7
36.0
38.6
38.7
38.8
39.0
39.2
39.3
39.5
39.6
39.8
40.0
40.1
40.3
40.4
40.5
40.6
40.9
41.1
41.2
41.4
42.0
45.4
45.9
46.5
46.9
47.1
48.4
48.8
49.7
50.7
51.3
51.6
51.9
52.3
52.6
53.1
53.6
54.0
54.4
55.6
56.6
58.2
58.5
61.4

0.0
0.7
1.6
2.1
3.1
7.4
8.0
8.4
9.1
9.6
11.6
12.0
12.1

10

S1B_660283102

0.0

10.2
10.7
10.8
11.6
12.0
12.3
13.2
14.1
14.5
14.9
15.4
15.9
16.2
16.9
17.0
17.2
17.9
18.2
18.5
18.6
18.8
18.9
19.1
19.6
19.8
20.1
20.5
21.1
21.4
21.6
21.8
22.0
22.1
22.3
22.4
22.6
22.9
23.1
23.7
23.9
24.3
24.5
24.9
25.8
28.2

4B

Sr/Severity/Field
Sr/IT/Field

100.3

S6D_472369559

104.4

S6D_471330647

105.3

S6D_472103008

107.6

S6D_472073634

Lr/IT/Field

4B04LG19
LG23

Figure 2.3. QTL analysis of the U6708-04 family using composite interval mapping for stem
and leaf rust resistance QTL. Seven linkage groups, of chromosomes 2D, 3B, 3D, 4B, 5B, and
7D were identified that
carry rust resistance QTL. Leaf and stem rust resistance QTL are shown
3BLg1504
in blue
and black, respectively.
LG9_04

28.6
28.7
28.9
29.0
29.1
29.2
29.3
29.4
29.5
29.7
29.8
30.0
30.2
30.3
30.5
30.9
34.4
39.5
40.7
41.4
42.6
45.9
47.5
53.4
53.6
54.6
55.5
57.6
58.4
59.3
64.6
66.1
68.0

9

9

8

QSr.msu-7DS.1

10

7

6

Sr/IT/Field

5

60

Sr/Severity/Field

S7D_1570012
S7D_4246387
S7D_4188276
S7D_5671117
S7D_6772594
S7D_6136243
S7D_10726785
S7D_10726864
S7D_9928472
S7D_9096883
S7D_10804279
S7D_12151885
S7D_12549816
S7D_12558018
S7D_13925669
S7D_14175649
S7D_14176788
S7D_14025943
S7D_14426487
S7D_14251853
S7D_13894806
S7D_17753962
S7D_18682792
S7D_17905353
S7D_18590915
S7D_18679585
S7D_17891069
S7D_19927998
S7D_20115523
S7D_20237471
S7D_22575972
S7D_24826665
S7D_24519265
S7D_22719681
S7D_24977929
S7D_25356570
S7D_27486623
S7D_28043357
S7D_28248589
S7D_28839483
S7D_29262723
S7D_28880153
S7D_29958815
S7D_29408544
S7D_29217976
S7D_29534136
S7D_29075566
S7D_30956741
S7D_36275099
S7D_635517741

4

S7D_8333685

3

5.3
10.8
13.0
13.8
14.3
14.6
15.0
15.1
15.5
15.7
15.8
16.3
16.6
17.2
17.5
18.0
18.2
18.4
18.6
19.0
19.3
19.9
21.7
21.9
22.1
22.3
22.4
23.2
23.5
23.8
24.9
26.4
26.9
27.3
27.6
27.8
28.2
29.3
29.9
30.5
31.3
31.7
32.1
32.3
32.5
32.9
33.4
33.7
35.1
37.8
37.9

2

S7D_1537886

1

0.0

28.4

S4B_18703228

S4B_34025485
S4B_32279358
S4B_38624956
S4B_191090248
S4B_556069660
S4B_529563963
S4B_529563719
S4B_531946700
S4B_526935208
S4B_527979736
S4B_536895442
S4B_557995550
S4B_544042765
S4B_546023632
S4B_547093363
S4B_554966435
S4B_535089159 S4B_553915774
S4B_552833587
S4B_558583868
S4B_562355380 S4B_544293087
S4B_568709455 S4B_565528122
S4B_571049371
S4B_572558230
S4B_567591085
S4B_573387592
S4B_567004232
S4B_579313471
S4B_577694813
S4B_588779331 S4B_588905418
S4B_589181090 S4B_583475648
S4B_601934091
S4B_601792322
S4B_602403655
S4B_602403716
S4B_601774330 S4B_610244239
S4B_601792870
S4B_613388382
S4B_615562770
S4B_616575086 S4B_613715043
S4B_616932643 S4B_615382677
S4B_615383946 S4B_615708070
S4B_620061711
S4B_621446792
S4B_621679237 S4B_619935881
S4B_625963961
S4B_625971498
S4B_617334542
S4B_619589061 S4B_619588944
S4B_626768439
S4B_623099621 S4B_634308810
S4B_621679408
S4B_631708532
S4B_626604971
S4B_627811289 S4B_627555294
S4B_629853060 S4B_630319525
S4B_637289578
S4B_629228008
S4B_629962284
S4B_634322252
S4B_627319108
S4B_633755571 S4B_626604202
S4B_635685764
S4B_635024663
S4B_633768930
S4B_636499665
S4B_639124617 S4B_638815052
S4B_637586849
S4B_644330895
S4B_647704569
S4B_647667811
S4B_649471268
S4B_650883943
S4B_654440068
S4B_640532063
S4B_660515583
S4B_660676396
S4B_660591179
S4B_660500077
S4B_662714113
S4B_663662540
S4B_662565558
S4B_670983327
S4B_670901586
S4B_672116501

Sr/Severity/Field

Sr/IT/GC
Sr/IT/GH
Sr/Severity/GH
Sr/IT/Field
Sr/Severity/Field

Sr/IT/GH

Sr/IT/GH

7D

Sr/IT/Field

Sr/Severity/GH

9

S5B_710784650

8

S5B_711244784

56.2

22.8
22.9
23.4
23.8
23.9
24.0
24.1
24.3
24.4
24.8
25.2
25.3
25.6
25.7
25.8
26.1
26.2
26.5
27.0
27.1
27.2
27.3
27.4
27.6
27.7
27.8
27.9
28.0
28.1
28.2
28.3

10

54.2
7

6

5

4

3

Sr/IT/Field

Lr/Severity/Field

2

1

Lr/IT/Field

S5B_693686064
S5B_697611190
S5B_699407657
S5B_699728464
S5B_699422973
S5B_697831155
S5B_699455437
S5B_701519795
S5B_703233730
S5B_703229470

0

3D
0

14

S3D_443309864

12.2

13

34.9

12

9

12.3
12.4
12.8
13.0
13.2
13.5
13.7
14.0
14.2
14.4
14.6
14.8
15.2
15.5
16.7
16.8
17.2
17.6
17.8
18.3
18.7
19.2
19.5
19.8
20.1
20.2
20.4
20.8
21.1
21.3
21.7
22.1
22.4
22.5
22.7
22.8
23.0
23.1
23.4
23.5
23.7
23.8
24.0
24.4
24.6
24.7
25.2

S3D_20233332
S3D_20618963
S3D_20544442
S3D_22223658
S3D_20353646
S3D_26642137
S3D_26654879
S3D_26443648
S3D_28247675
S3D_28247721
S3D_30393736
S3D_38010276
S3D_37970827
S3D_36585107 S3D_33314732
S3D_33296656
S3D_37969605 S3D_35889019
S3D_33388811
S3D_41423982
S3D_42631446
S3D_41141983
S3D_44223324
S3D_45015647
S3D_45587843
S3D_45021010
S3D_48363653
S3D_47539627
S3D_47345231
S3D_47345297
S3D_48442324
S3D_55577045
S3D_56238010
S3D_56438931
S3D_58369980
S3D_58370142
S3D_62117027
S3D_68164115
S3D_66484029
S3D_70259952
S3D_67534715
S3D_62345840
S3D_73446898
S3D_68880849
S3D_70713380
S3D_79428382
S3D_93196771
S3D_184583746
S3D_220863200
S3D_179758809
S3D_149912136
S3D_225856460
S3D_192058920
S3D_214796069
S3D_250050929
S3D_244970665
S3D_226695276
S3D_289698840
S3D_276911714
S3D_260559779
S3D_251293045
S3D_226198159
S3D_296039573
S3D_277546305

0.0
0.7
1.6
2.1
3.1
7.4
8.0
8.4
9.1
9.6
11.6
12.0
12.1

40.0
41.5
42.6
43.1
43.3
44.1
44.5
45.4
46.0
46.5

22.7

Sr/IT/GH

S3B_604416993

Sr/IT/Field

8

S3B_630398559

LG33

10

9.2

10.5
12.4
13.0
15.9
17.3
19.9
20.9
21.0
21.2
21.6
21.7
21.9
22.0
22.1
22.4
22.5

Sr/Severity/Field

S3B_594745123
S3B_596232284
S3B_580784890
S3B_607406113
S3B_623654517
S3B_626712790

S5B_635470596
S5B_639966513
S5B_634442465
S5B_641840292
S5B_642840568
S5B_641559958
S5B_641429270
S5B_642596620
S5B_647387627
S5B_648176891
S5B_688709062
S5B_653428552
S5B_652866604
S5B_655150714
S5B_659749112
S5B_662024958
S5B_662010281
S5B_666129720
S5B_665685805
S5B_667955149
S5B_669191995
S5B_667493428
S5B_454870430
S5B_661902755
S5B_666300492
S5B_684618096
S5B_682375605
S5B_681773457
S5B_688967393
S5B_687326022
S5B_697865267

Sr/IT/GC

7.4
7.6
7.9
8.2
8.4
8.7

10.8
12.7
13.4
14.1
14.7
15.0
15.1
15.5
15.8
16.2
16.3
17.3
18.2
18.8
19.9
20.8
21.3
22.0
22.9
23.4
24.5
25.2
25.8
26.0
29.0
29.7
30.7
31.5
32.7
33.4
36.4

7

LG16

S5B_642594088

6

S3B_562272668
S3B_573497145
S3B_561366011
S3B_565273183
S3B_566830710
S3B_565725179
S3B_567001229
S3B_579446416
S3B_577639587
S3B_580521282
S3B_577639496
S3B_580348857
S3B_590623676
S3B_581268461
S3B_589561483
S3B_589458274

S5B_546722917

5.7

5

3.2
3.5
3.9
4.2
4.5
4.7
5.0
5.4
5.6
5.8
6.0
6.1
6.2
6.3
6.5
6.8

S5B_595132460

4.4

4

S3B_501653695
S3B_550791112
S3B_554549234

3.1

4B

0.0

3

2.2
2.4
2.6

S5B_595052159

2

S3B_554586301

0.0

1
25
0
24
23
22
21
20
19
18
17
16
15
14
13
12
11
10
9
8
7
6
5
4
3
2
1
0

1.6

Sr/IT/Field

S3B_545012683

5B

10

9

8

7

6

5

4

10

3

3B
S3B_512743315

0.8

11

S3B_773565617

8

10.1

7

S3B_772467523

6

8.4

5

S3B_775659912

4

3

Lr/IT/Field

7.7

Lr/Severity/Field

5.0

S3B_769535066

10

3B

S3B_766364455

0.0

10.6

S3B_748448161

4.2

9

S2D_8381688
S2D_2145981
S2D_370235
S2D_2201680
S2D_2313854
S2D_6731847
S2D_7527954
S2D_7309581
S2D_7443363
S2D_6899497
S2D_9905362
S2D_10718874
S2D_10699856
S2D_9882889
S2D_11426549
S2D_9106403
S2D_11373542
S2D_11545271
S2D_11575943
S2D_12304410
S2D_13242604
S2D_13853778
S2D_14942177
S2D_14652683
S2D_15266667
S2D_14408803
S2D_15134145
S2D_14784910
S2D_16056873
S2D_16961444
S2D_17171539
S2D_16910840
S2D_17044373
S2D_16900439
S2D_17794172
S2D_19022196
S2D_19022113
S2D_18377691
S2D_19646151
S2D_20188084
S2D_20610775
S2D_20382122
S2D_21057222
S2D_20358129
S2D_22502442
S2D_15496601

Sr/IT/GC

LG14

0.0

8

7

6

5

4

3

2

1

0

9.6
10.8
11.2
12.5
13.8
17.9
18.7
19.3
19.6
20.4
21.0
21.6
22.1
22.3
22.6
22.7
22.9
23.5
23.9
24.4
25.0
25.6
26.2
26.4
26.6
26.8
27.2
27.6
28.0
28.1
28.3
28.5
28.7
29.0
29.8
30.3
30.5
30.8
31.6
32.1
32.7
33.0
33.7
34.4
37.1
42.6

2D

S2D_273867

0.0

Figure 2.4. Examples of Pst seedling reactions to Pst-37 in the U6523 F2:3 population: A.
Prelude displays a susceptible reaction. B. 9.131.15x exhibits a resistant reaction with a
hypersensitive response seen by necrosis and low sporulation. C. U6523-1-87 is a susceptible
line in the population with abundant sporulation. D. U6523-1-90 is resistant, displaying an
infection type similar to 9.131.15x. The U6708 population has the same infection types
segregating as the U6523 population.

Figure 2.5. Examples of adult plant reactions to leaf rust in the U6708 population in Mason,
Michigan 2017: A. Prelude displays a susceptible reaction with abundant sporulation and no
chlorosis. B. 9.131.15x displays a susceptible to moderately susceptible reaction with abundant
sporulation and slight chlorosis. C. A moderately resistant line with necrosis and small uredinia.
KS05HW14, the recurrent parent, was not measured in the field as it was a winter wheat and not
available to rate.

61

Figure 2.6. Examples of Pgt seedling reactions to Pgt-QFCSC in the U6708 population: A.
Morocco serves as a susceptible check. B. KS05HW14 is the susceptible recurrent parent. C.
Prelude displays a highly resistant fleck phenotype with no uredinia present and necrosis is
evident. D. 9.131.15x displays an intermediate resistant phenoytpe. E. U6708-03-025 D. U670803-044 G. U6708-03-073 H. U6708-03-08. E and D are examples of the intermediate resistance
segregating in the U6708 population. G and H are examples of susceptible reactions in the
population. The same infection types for resistant and susceptible RILs were observed in both
families.

A
B
C
D
E
F

G
H

62

Sup Table 2.2. Polymorphic segregating on each chromosome in the U6708-03 and U6708-04
families.

Chromosome
1A
1B
1D
2A
2B
2D
3A
3B
3D
4A
4B
4D
5A
5B
5D
6A
6B
6D
7A
7B
7D

U6708-04
Number of
markers
21
26
9
140
N/A
132
133
92
65
59
103
49
141
48
76
5
92
173
200
215
63

63

U6708-03
Number of
markers
26
25
3
113
100
191
134
105
N/A
50
105
98
113
86
75
76
5
172
163
170
157

Sup Fig. 2.1A. U6708-04 linkage groups for group 1 aligned to the respective representative
chromosomes of the reference genome based on aligned marker positions.

1B

1D

1A

Sup Fig. 2.1B. U6708-03 linkage groups for group 1 aligned to the respective representative
chromosomes of the reference genome based on aligned marker positions.

1B

1A

64

1D

Sup Fig. 2.2A. U6708-04 linkage groups for group 2 aligned to the respective representative
chromosomes of the reference genome based on aligned marker positions.

2A

2D

65

Sup Fig. 2.2B. U6708-03 linkage groups for group 2 aligned to the respective representative
chromosomes of the reference genome based on aligned marker positions.

2A

2B

2A

66

2D

3B

3BLG1

3BLG2

3BLG3

3BLG4

3BLG5

Sup Fig. 2.3A. U6708-04 linkage groups for group 3 aligned to the respective representative
chromosomes of the reference genome based on aligned marker positions.
3A
2A

0
67780712
69503729
71777176 71785281
74544791
76558920
77970310
78729102
80219148
99588532
114713700
136428481
144157542
231686396
251368130
297838205
440081272
456437110
459865181
465575249
468520839
471285948
472790215
474447249
474554821 474564407
476383953
478166110
479775420 480154233
486929784
503145562 503348227
504034310
512321079
512556966
513927792
533130965
534992821
535811562
539198714
541246438 541482881
542688101
572745436
594291711
595935088
596365858
598283263
598947516
602859696
603824986
604572371
605002080 605167769
605990866
606055439 606435120
613343831
615938108
620208293
625237531
633055347
635484966
645105608
652024317 652024527
653303594 653925713
654806031
658048785 658239559
658244430 658598014
658731939
662902742
667794614 667795556
674402235
683543035
685289392
686179591 686200893
687619903
688594252 688621935
691124368
694947647
701735393 701767703
707911795 708000759
708005198 708005281
709223143 709379403
709595149
709953875 710274467
710298707
710461601
711364406 711420588
716528073 716615669
717425759
720487803
721301834
722446579
723655432 723657938
727294844 727485286
727485335
728321064
729723306
733755794
734515896
740027681
742886658
744843309 745319069
746309192 746378992
746565332
747301890 747301972
747932453 747936294
749189328 749241987
749402319
750538937 750843639

3A

3B

3ALG1

S3A_69503729
S3A_74544791
S3A_71785281 S3A_67780712
S3A_77970310
S3A_80219148 S3A_71777176
S3A_99588532
S3A_78729102
S3A_76558920
S3A_114713700
S3A_251368130 S3A_144157542
S3A_136428481
S3A_231686396
S3A_465575249
S3A_476383953
S3A_471285948
S3A_440081272
S3A_456437110
S3A_474447249
S3A_459865181
S3A_479775420
S3A_472790215
S3A_474564407
S3A_468520839
S3A_478166110
S3A_480154233
S3A_486929784
S3A_474554821
S3A_503145562
S3A_503348227
S3A_504034310
S3A_535811562
S3A_533130965
S3A_512556966
S3A_539198714
S3A_534992821
S3A_541482881
S3A_512321079
S3A_513927792
S3A_542688101
S3A_595935088
S3A_541246438
S3A_598283263
S3A_594291711
S3A_572745436
S3A_596365858
S3A_603824986
S3A_598947516
S3A_605990866
S3A_620208293
S3A_606055439 S3A_606435120
S3A_613343831
S3A_605167769
S3A_625237531
S3A_602859696
S3A_615938108
S3A_605002080
S3A_633055347
S3A_645105608
S3A_653303594
S3A_635484966
S3A_652024317
S3A_658048785
S3A_653925713
S3A_652024527
S3A_658244430
S3A_658731939
S3A_662902742
S3A_604572371 S3A_658598014
S3A_667795556
S3A_667794614
S3A_654806031
S3A_674402235
S3A_297838205
S3A_691124368
S3A_685289392
S3A_686200893
S3A_686179591
S3A_658239559
S3A_687619903
S3A_688594252
S3A_683543035
S3A_694947647
S3A_688621935
S3A_701735393
S3A_701767703 S3A_720487803
S3A_723655432
S3A_709223143
S3A_722446579
S3A_710274467
S3A_709953875
S3A_709379403
S3A_723657938
S3A_709595149
S3A_742886658
S3A_710298707
S3A_727294844
S3A_734515896
S3A_729723306
S3A_721301834
S3A_711420588
S3A_733755794
S3A_745319069
S3A_716528073
S3A_717425759
S3A_727485286
S3A_710461601
S3A_746309192
S3A_711364406 S3A_728321064
S3A_746565332
S3A_727485335
S3A_744843309 S3A_716615669
S3A_747301890
S3A_740027681
S3A_749189328
S3A_708005198
S3A_747301972
S3A_750538937
S3A_749402319
S3A_746378992
S3A_708005281
S3A_749241987
S3A_747932453
S3A_708000759
S3A_707911795
S3A_747936294

0
2191035 2222629
2259598
4553446 5075908
5973360 6071559
6181603 6418150
7236962
11165931
11466496 11562465
11601797
12180005
14482106
15802938 16000571
16402517
17070378 17587960
17613580
17802909 17866567
17974253 18253325
18393918 18484734
18664529 18966637
19394721 19396724
23021423
23398620 23719942
24397727
24940723 25180892
25803185
501653695
512743315
545012683
550791112
554549234 554586301
561366011
562272668
565273183
565725179
566830710 567001229
573497145
577639496 577639587
579446416
580348857 580521282
580784890
581268461
589458274 589561483
590623676
594745123
596232284
604416993
607406113
623654517
626712790
630398559
748448161
766364455
769535066
772467523
773565617
775659912
794315875
794765685
798251954 798346341
798497287
798641579
799723126
802872369 802921213
815364467 815463878
817459692 817595966
818513872
818773941
820674710
823167758
829318278

S3B_2259598
S3B_2222629
S3B_2191035
S3B_4553446
S3B_5075908
S3B_5973360
S3B_6418150
S3B_6181603
S3B_6071559
S3B_7236962
S3B_11165931
S3B_11562465
S3B_11601797
S3B_12180005
S3B_14482106
S3B_11466496
S3B_16000571
S3B_15802938
S3B_17613580
S3B_16402517
S3B_17070378
S3B_17866567 S3B_17587960
S3B_17974253
S3B_17802909
S3B_18253325
S3B_18393918
S3B_18664529
S3B_19396724
S3B_18484734
S3B_19394721
S3B_18966637
S3B_23021423
S3B_23719942
S3B_24397727
S3B_23398620
S3B_25180892
S3B_25803185
S3B_24940723

S3B_512743315
S3B_545012683
S3B_554586301
S3B_501653695
S3B_550791112
S3B_554549234
S3B_562272668
S3B_573497145
S3B_561366011
S3B_565273183
S3B_566830710
S3B_565725179
S3B_567001229
S3B_579446416
S3B_577639587
S3B_580521282
S3B_577639496
S3B_580348857
S3B_590623676
S3B_581268461
S3B_589561483
S3B_589458274
S3B_594745123
S3B_596232284
S3B_580784890
S3B_607406113
S3B_623654517
S3B_626712790
S3B_630398559
S3B_604416993

S3B_748448161
S3B_766364455
S3B_769535066
S3B_775659912
S3B_772467523
S3B_773565617

S3B_794765685
S3B_794315875
S3B_798251954
S3B_798346341
S3B_798497287 S3B_798641579
S3B_799723126
S3B_802921213 S3B_802872369

S3B_815463878
S3B_815364467
S3B_817595966
S3B_817459692
S3B_818773941
S3B_818513872
S3B_820674710
S3B_823167758

3D

67

Sup Fig. 2.3B. U6708-03 linkage groups for group 3 aligned to the respective representative
chromosomes of the reference genome based on aligned marker positions.

3A

3B

68

Sup Fig. 2.4A. U6708-04 linkage groups for group 4 aligned to the respective representative
chromosomes of the reference genome based on aligned marker positions.
4A

4B

4D

69

Sup Fig. 2.4B. U6708-03 linkage groups for group 4 aligned to the respective representative
chromosomes of the reference genome based on aligned marker positions.
4D

4A

0
5021186
7176912
11258209
11986495 12152216
13746274
15148625
17023830 17252870
17889491
45140369 45144499

555878546
556308536 556604064
556604095
557798455
558649775
574539217
583751187
583968718 584046342
584515096
597862222
598226912 598418786
598434395
599486123 599647431
600929422 601140099
602188240 602753700
603030938
604952772
606397602 606526706
610841005
738540763
738961197 739129602
739415724
739596257
741159110
742312913 742566394
742606343 742608370
742751446
744522297 744588157

S4A_738540763
S4A_742312913
S4A_739129602
S4A_741159110
S4A_739415724
S4A_738961197
S4A_742566394
S4A_742608370
S4A_739596257
S4A_742751446
S4A_744522297
S4A_742606343

S4A_5021186
S4A_7176912
S4A_11258209
S4A_12152216
S4A_11986495
S4A_13746274
S4A_15148625
S4A_17889491
S4A_17023830
S4A_557798455
S4A_17252870
S4A_45144499
S4A_45140369
S4A_556604095
S4A_558649775
S4A_556604064
S4A_556308536
S4A_555878546
S4A_574539217
S4A_583751187
S4A_583968718
S4A_584046342
S4A_584515096
S4A_597862222
S4A_598226912
S4A_598418786
S4A_600929422
S4A_601140099 S4A_599647431
S4A_599486123
S4A_603030938
S4A_598434395
S4A_602188240
S4A_602753700
S4A_604952772
S4A_606397602
S4A_606526706
S4A_615180638
S4A_610841005
S4A_615181084
S4A_615197801
S4A_616935053
S4A_617359000
S4A_618843280
S4A_615197597
S4A_620342297
S4A_617487102

4B
N
0
18703228
20568400 20679079
25886179
32279358
34025485
38624956
191090248
256327967
526935208
527979736
529563719 529563963
531946700
535089159
536895442
544042765 544293087
546023632
547093363
552833587
553915774
554966435
556069660
557995550
558583868
562355380
565528122
567004232
567591085
568709455
571049371
572558230
573387592
577694813
579313471
583475648
588779331 588905418
589181090
601774330 601792322
601792870
601934091 602403655
602403716
610244239
613388382 613715043
615382677 615383946
615562770 615708070
616575086
616932643 617334542
619588944 619589061
619935881 620061711
621446792 621679237
621679408
623099621
625963961 625971498
626604202 626604971
626768439
627319108
627555294 627811289
629228008
629853060 629962284
630319525
631708532
633755571 633768930
634308810 634322252
635024663
635685764
636499665
637289578
637586849
638815052
639124617
640532063
644330895
647667811
647704569
649471268
650883943
654440068
660500077 660515583
660591179 660676396
662565558 662714113
663662540
670901586 670983327
672116501
673617499

4DU670803LG1

4DU670803LG2

4D
S4B_18703228
S4B_34025485
S4B_32279358
S4B_38624956
S4B_191090248
S4B_556069660
S4B_529563963
S4B_529563719
S4B_531946700
S4B_526935208
S4B_527979736
S4B_536895442
S4B_557995550
S4B_544042765
S4B_546023632
S4B_547093363
S4B_554966435
S4B_535089159 S4B_553915774
S4B_552833587
S4B_558583868
S4B_562355380 S4B_544293087
S4B_568709455 S4B_565528122
S4B_571049371
S4B_572558230
S4B_567591085
S4B_573387592
S4B_567004232
S4B_579313471
S4B_577694813
S4B_588779331 S4B_588905418
S4B_589181090 S4B_583475648
S4B_601934091
S4B_601792322
S4B_602403655
S4B_602403716
S4B_601774330 S4B_610244239
S4B_601792870
S4B_613388382
S4B_615562770
S4B_616575086 S4B_613715043
S4B_616932643 S4B_615382677
S4B_615383946 S4B_615708070
S4B_620061711
S4B_621446792
S4B_621679237 S4B_619935881
S4B_625963961
S4B_625971498
S4B_617334542
S4B_619589061 S4B_619588944
S4B_626768439
S4B_623099621 S4B_634308810
S4B_621679408
S4B_631708532
S4B_626604971
S4B_627811289 S4B_627555294
S4B_629853060 S4B_630319525
S4B_637289578
S4B_629228008
S4B_629962284
S4B_634322252
S4B_627319108
S4B_633755571 S4B_626604202
S4B_635685764
S4B_635024663
S4B_633768930
S4B_636499665
S4B_639124617 S4B_638815052
S4B_637586849
S4B_644330895
S4B_647704569
S4B_647667811
S4B_649471268
S4B_650883943
S4B_654440068
S4B_640532063
S4B_660515583
S4B_660676396
S4B_660591179
S4B_660500077
S4B_662714113
S4B_663662540
S4B_662565558
S4B_670983327
S4B_670901586
S4B_672116501

70

0
1242429 1704666
1999942
2828876 3238232
7283672.386
14567344.77
20677451
27961123.39
22950237
26245047
26926611
27556679
34840351.39
35621966 35622015
42905687.39
37263274
44546946.39
46632606
53916278.39
61199950.77
68483623.16
75767295.54
73317877
80601549.39
82148169
84753003
92036675.39
88509181
95792853.39
100355830 100569592
107853264.4
105889938
113173610.4
120457282.8
127740955.2
135024627.5
142308299.9
149591972.3
156875644.7
164159317.1
163806933
166941711
174225383.4
181509055.8
188792728.2
196076400.5
203360072.9
210643745.3
217927417.7
225211090.1
232494762.5
239778434.9
247062107.2
254345779.6
261629452
268913124.4
276196796.8
283480469.2
290764141.6
298047813.9
305331486.3
312615158.7
310468098
317751770.4
325035442.8
332319115.2
333101590
340385262.4
347668934.8
345415047
352698719.4
359982391.8
367266064.2
368501531
370674111
377957783.4
372992071
380275743.4
385650316
392933988.4
400217660.8
394111380
401395052.4
408678724.8
413036160
420319832.4
427603504.8
434887177.2
434175179
441458851.4
438155104
440276529
441064724
442739574
443405578
450689250.4
446976026
454259698.4
455479092
455618800
462902472.4
459686868
461573496
465955139 473238811.4
466293054
467616597
474900269.4
474561328
476332925
477016556
480310343
487594015.4
481554491
481893274 482360873
486928774
494212446.4
490012318 490087380
490394561
493548857 493749368
493907811 494025693
494110724 494123603
501407275.4
497091222
497126718 497184136
497914471 498380884
498573203 498583417
499252536 499256380
499594567
500929111
502033625 502054878
502065892
502546928 509830600.4
502633511 502642017
502648830 502653803
502757895 502783808
503444492 503511744
503596098 503617408
503693533
506471233 506496375
506868620 506940249
507006529
509230107 509284007
509356148
509798252 517081924.4

S4D_1704666

S4D_1242429
S4D_1999942
S4D_2828876
S4D_3238232

S4D_20677451
S4D_26926611
S4D_22950237
S4D_27556679
S4D_26245047
S4D_37263274
S4D_35621966
S4D_35622015
S4D_46632606
S4D_82148169
S4D_73317877
S4D_84753003
S4D_88509181
S4D_100569592
S4D_105889938
S4D_100355830
S4D_166941711
S4D_345415047
S4D_163806933
S4D_310468098
S4D_372992071
S4D_333101590
S4D_370674111
S4D_368501531
S4D_394111380
S4D_385650316
S4D_413036160
S4D_434175179
S4D_438155104
S4D_440276529
S4D_441064724
S4D_446976026
S4D_442739574
S4D_443405578
S4D_455479092
S4D_455618800
S4D_459686868
S4D_461573496
S4D_465955139
S4D_467616597
S4D_466293054
S4D_474561328
S4D_477016556
S4D_476332925
S4D_480310343
S4D_482360873
S4D_481554491
S4D_481893274
S4D_486928774
S4D_490087380
S4D_490012318
S4D_493548857
S4D_490394561
S4D_493749368
S4D_497091222
S4D_497126718
S4D_494025693
S4D_494123603
S4D_493907811
S4D_497184136
S4D_494110724
S4D_497914471
S4D_498573203
S4D_498583417
S4D_498380884
S4D_499256380
S4D_499252536
S4D_499594567
S4D_500929111
S4D_502065892
S4D_502546928
S4D_502033625
S4D_502648830
S4D_503693533
S4D_502054878
S4D_502633511
S4D_502642017
S4D_502783808
S4D_502757895
S4D_502653803
S4D_503511744
S4D_503444492
S4D_503596098
S4D_503617408
S4D_506471233
S4D_506496375
S4D_506940249
S4D_507006529
S4D_506868620
S4D_509798252
S4D_509356148
S4D_509230107
S4D_509284007

5A 5ALG2

5ALG1

Sup Fig. 2.5A. U6708-04 linkage groups for group 5 aligned to the respective representative
chromosomes of the reference genome based on aligned marker positions.

5A

5B

0

S5A_30001455

30001455 30060588
31132338

S5A_30060588

51793344

S5A_31132338

110112163

194003504

389166990
389726021
393918785
394754086
402545278
403350768
403905372
427837907
431894177 431894778
432036515
433782314 433935165
436102473
439551041
445256919
454733343 454775722
454808370
456974887
458562272
461003088 461229843
461495592 461899760
461904100
463766599
464470946
465996932
466575980
467370064 467370141
468139726
468931988 469117164
469272174
469516866 469608226
469896515
470186553
514092714 514151246
514260464 514279842
514295962 514296231
514296299
514983554
519892082
522153944
523025526 523437951
525835471
526386144
534063696
535010010
535140011 535519822
535668155
536797385 536896267
537015981
537252134 537662517
538581615 538978700
538979750
539103284
546260057 546389244
548759658 549192141
552747815 552864525
552890813 553168885
556175706
564542127
565398445 565417008
566922135
568234305 568359835
568464107 568491334
569163892
572407329
573787287
577799125
579325262 579358472
580935035
582654201
585202175
586297205
586600382
590316067 590355732
613020548
659313545
661176022
669911707
673682320 674066279
674086589
674541997
675264427 675520254
675566100
675960043
678232488
678556789
680980888 680981403
681251635 681466323
681560690 681649916
683133185
684702984 685068591
685101101 685141655
685792099 685792141
685866260
688359760
698127281 698225912
702491802
705063494 705351694
705365208 705376300
705550787
709773743

S5A_659313545
S5A_661176022
S5A_669911707
S5A_673682320
S5A_674086589
S5A_675960043
S5A_675264427
S5A_674541997
S5A_675520254
S5A_675566100 S5A_674066279
S5A_678232488
S5A_678556789
S5A_680981403
S5A_681466323
S5A_681560690
S5A_684702984
S5A_685101101
S5A_685068591
S5A_681649916
S5A_685792141
S5A_685141655
S5A_681251635
S5A_685866260
S5A_685792099
S5A_680980888
S5A_688359760
S5A_683133185
S5A_698127281
S5A_698225912
S5A_702491802
S5A_705365208
S5A_705351694
S5A_705376300
S5A_705550787
S5A_705063494

S5A_110112163
S5A_194003504
S5A_51793344
S5A_389726021
S5A_394754086
S5A_403905372
S5A_402545278
S5A_389166990
S5A_427837907
S5A_431894177
S5A_403350768
S5A_432036515
S5A_433935165
S5A_433782314
S5A_393918785
S5A_436102473
S5A_431894778
S5A_439551041
S5A_454733343
S5A_445256919
S5A_454775722
S5A_454808370
S5A_456974887
S5A_461899760
S5A_466575980
S5A_463766599
S5A_461904100
S5A_467370141
S5A_461003088
S5A_464470946
S5A_458562272
S5A_469117164
S5A_467370064 S5A_469272174
S5A_465996932
S5A_461229843
S5A_461495592
S5A_468931988
S5A_469896515
S5A_469516866
S5A_469608226
S5A_470186553
S5A_468139726
S5A_514296299
S5A_514260464
S5A_514092714
S5A_514151246
S5A_514279842
S5A_523437951
S5A_514983554
S5A_514296231
S5A_522153944
S5A_514295962
S5A_534063696 S5A_519892082
S5A_525835471
S5A_523025526
S5A_526386144
S5A_535010010
S5A_535519822
S5A_537015981 S5A_535140011
S5A_538581615
S5A_535668155
S5A_536896267
S5A_536797385
S5A_537662517
S5A_538978700
S5A_539103284
S5A_538979750
S5A_537252134
S5A_546260057
S5A_546389244
S5A_549192141
S5A_548759658
S5A_552890813
S5A_552747815
S5A_553168885
S5A_556175706
S5A_552864525
S5A_613020548
S5A_565398445
S5A_564542127
S5A_565417008
S5A_566922135
S5A_568491334
S5A_568234305
S5A_569163892
S5A_572407329
S5A_568464107
S5A_568359835
S5A_573787287
S5A_579358472
S5A_579325262
S5A_582654201
S5A_580935035
S5A_577799125
S5A_590316067
S5A_585202175
S5A_586297205
S5A_590355732
S5A_586600382

5D

0

S5B_595052159
S5B_595132460
S5B_546722917
S5B_642594088
S5B_635470596
S5B_639966513
S5B_634442465
S5B_641840292
S5B_642840568
S5B_641559958
S5B_641429270
S5B_642596620
S5B_647387627
S5B_648176891
S5B_688709062
S5B_653428552
S5B_652866604
S5B_655150714
S5B_659749112
S5B_662024958
S5B_662010281
S5B_666129720
S5B_665685805
S5B_667955149
S5B_669191995
S5B_667493428
S5B_454870430
S5B_661902755
S5B_666300492
S5B_684618096
S5B_682375605
S5B_681773457
S5B_688967393
S5B_687326022
S5B_697865267
S5B_693686064
S5B_697611190
S5B_699407657
S5B_699728464
S5B_699422973
S5B_697831155
S5B_699455437
S5B_701519795
S5B_703233730
S5B_703229470
S5B_711244784
S5B_710784650
S5B_711579204

454870430
546722917
595052159 595132460
634442465
635470596
639966513
641429270
641559958 641840292
642594088 642596620
642840568
647387627
648176891
652866604
653428552
655150714
659749112
661902755 662010281
662024958
665685805
666129720 666300492
667493428 667955149
669191995
681773457
682375605
684618096
687326022
688709062 688967393
693686064
697611190 697831155
697865267
699407657 699422973
699455437 699728464
701519795
703229470 703233730
710784650 711244784
711579204
713149757

71

0
471112589
472276260 472276314
478876879
479757190
487175843
487294974 487432972
487586223 487757143
487982782 488225925
488425641
490439748 490598519
490600350
490937629
498291323
498777942
501116317
507377245
509957297
513545958 513556028
513928523 514025667
514149283 514202261
520055525 520418011
525320991 525379083
526415908 526698027
530301830
531409476
541681051
543253950 543329239
543466442 543534061
543609717
544283587
544532701 544665516
544702678
545451350
545942805 545982657
546022043 546455220
546687949 546819701
547236773
547705132
548844677 548844739
549822051
551401669 551545354
551891970 552043227
552080525
554401646
555357986 555374404
556408254
557667347 557786944
558024570 558307080
562064108
563331517
564295382
564552549
565757897 566080677

S5D_471112589
S5D_472276314
S5D_472276260
S5D_478876879
S5D_479757190
S5D_487586223
S5D_487432972
S5D_487294974
S5D_487757143
S5D_487175843
S5D_487982782
S5D_488425641
S5D_488225925
S5D_490937629
S5D_490600350
S5D_490598519
S5D_490439748
S5D_498291323
S5D_498777942
S5D_501116317
S5D_507377245
S5D_514025667
S5D_509957297
S5D_513556028
S5D_513545958
S5D_514202261
S5D_513928523
S5D_514149283
S5D_520055525
S5D_520418011
S5D_525379083
S5D_526415908
S5D_526698027
S5D_530301830
S5D_525320991
S5D_531409476
S5D_541681051
S5D_543329239
S5D_543534061
S5D_543253950
S5D_543466442
S5D_544532701
S5D_544283587
S5D_544702678
S5D_543609717
S5D_544665516
S5D_545982657
S5D_545451350
S5D_545942805
S5D_546819701
S5D_547705132
S5D_547236773
S5D_546022043
S5D_548844677
S5D_546455220
S5D_548844739
S5D_549822051
S5D_546687949
S5D_551545354
S5D_551401669
S5D_552080525
S5D_551891970
S5D_554401646
S5D_555357986
S5D_555374404
S5D_552043227
S5D_556408254
S5D_558024570
S5D_564295382
S5D_557667347
S5D_564552549
S5D_563331517
S5D_565757897
S5D_557786944
S5D_558307080
S5D_562064108

Sup Fig. 2.5B. U6708-03 linkage groups for group 5 aligned to the respective representative
chromosomes of the reference genome based on aligned marker positions.
5D

5DLG1

5A

0
1532096
3648497
5295116 5650487
5971613
30001455 30060588
31132338
51793344
110112163
194003504
389166990
389726021
393918785
394754086
402545278
403350768
403905372
427837907
431894177 431894778
432036515
433782314 433935165
436102473
514092714 514151246
514260464 514279842
514295962 514296231
514296299
514983554
519892082
522153944
523025526 523437951
525835471
526386144
534063696
535010010
535140011 535519822
535668155
536797385 536896267
537015981
537252134 537662517
538581615 538978700
538979750
539103284
546260057 546389244
548759658 549192141
552747815 552864525
552890813 553168885
556175706
564542127
565398445 565417008
566922135
568234305 568359835
568464107 568491334
568799448
569163892
572407329
573787287
577799125
579325262 579358472
580935035
582654201
585202175
586297205
586600382
590316067 590355732
659313545
661176022
669911707
673682320 674066279
674086589
674541997 674775567
675264427 675520254
675566100
675960043
678232488
678556789
680980888 680981403
681251635 681466323
681560690 681649916
683133185
684702984 685068591
685101101 685141655
685792099 685792141
685866260
688359760
709773743

5B

S5A_1532096
S5A_3648497
S5A_5650487
S5A_5971613
S5A_5295116

S5A_31132338
S5A_30001455
S5A_30060588
S5A_51793344
S5A_110112163
S5A_393918785
S5A_194003504
S5A_403905372
S5A_389726021
S5A_403350768
S5A_431894778
S5A_402545278 S5A_389166990
S5A_427837907 S5A_394754086
S5A_431894177
S5A_433935165
S5A_433782314
S5A_432036515
S5A_436102473

S5A_661176022
S5A_659313545
S5A_674775567
S5A_669911707
S5A_673682320
S5A_675264427
S5A_674086589
S5A_674541997
S5A_674066279
S5A_675566100
S5A_675960043
S5A_675520254
S5A_678232488
S5A_678556789
S5A_680980888
S5A_681251635
S5A_681649916
S5A_685101101
S5A_681466323 S5A_680981403
S5A_685068591
S5A_681560690
S5A_685792141
S5A_685141655 S5A_684702984
S5A_683133185 S5A_685792099
S5A_688359760 S5A_685866260

0
471112589
472276314
478876879
479757190
487175843
487294974 487432972
487586223 487757143
487982782 488225925
488425641
490439748 490598519
490600350
490937629
498291323
498777942
501116317
507377245
509957297
513545958 513556028
513928523 514025667
514149283 514202261
520055525 520418011
525320991 525379083
526415908 526698027
530301830
531409476
541681051
543253950 543329239
543466442 543534061
543609717
544283587
544532701 544665516
544702678
545451350
545942805 545982657
546022043 546455220
546687949 546819701
547236773
547705132
548844677 548844739
549822051
551401669 551545354
551891970 552043227
552080525
554401646
555357986 555374404
556408254
557667347 557786944
558024570 558307080
562064108
563331517
564295382
564552549
565757897 566080677

S5A_514296299
S5A_514092714
S5A_514151246
S5A_514279842
S5A_535010010
S5A_523437951
S5A_522153944 S5A_514295962
S5A_514260464
S5A_535519822 S5A_514983554
S5A_534063696
S5A_535140011
S5A_526386144 S5A_519892082
S5A_514296231
S5A_536797385
S5A_535668155
S5A_537015981
S5A_525835471
S5A_523025526
S5A_536896267
S5A_537662517
S5A_537252134
S5A_539103284
S5A_538978700
S5A_538979750
S5A_538581615
S5A_546260057
S5A_548759658
S5A_546389244
S5A_549192141
S5A_553168885
S5A_552747815
S5A_552864525
S5A_556175706
S5A_552890813
S5A_565417008
S5A_565398445
S5A_564542127
S5A_566922135
S5A_568359835
S5A_568464107
S5A_568234305
S5A_569163892
S5A_568491334
S5A_572407329
S5A_573787287
S5A_579325262
S5A_582654201
S5A_577799125
S5A_580935035
S5A_579358472
S5A_586297205
S5A_585202175
S5A_586600382
S5A_590316067
S5A_590355732
S5A_568799448

S5D_472276314
S5D_471112589
S5D_478876879
S5D_479757190
S5D_487294974
S5D_487757143
S5D_487586223
S5D_487432972
S5D_487175843
S5D_488225925
S5D_488425641
S5D_487982782
S5D_490598519
S5D_490439748
S5D_490600350
S5D_490937629
S5D_498777942
S5D_498291323
S5D_501116317
S5D_507377245
S5D_509957297
S5D_513545958
S5D_514025667
S5D_513556028
S5D_520055525
S5D_514202261
S5D_514149283
S5D_513928523
S5D_520418011
S5D_525379083
S5D_526698027
S5D_526415908
S5D_530301830
S5D_531409476
S5D_543253950
S5D_541681051
S5D_525320991
S5D_543329239
S5D_543466442
S5D_543534061
S5D_543609717
S5D_544283587
S5D_544665516
S5D_544702678 S5D_544532701
S5D_546819701
S5D_545982657
S5D_545942805 S5D_545451350
S5D_546455220
S5D_547236773
S5D_546022043
S5D_546687949
S5D_547705132
S5D_548844739
S5D_548844677
S5D_549822051
S5D_552043227
S5D_552080525
S5D_551401669
S5D_551891970
S5D_551545354
S5D_555357986
S5D_554401646
S5D_555374404
S5D_556408254
S5D_558024570
S5D_557786944
S5D_557667347
S5D_558307080
S5D_564552549
S5D_564295382
S5D_565757897
S5D_563331517
S5D_562064108

0
8071663
13171650
13448628
14370461
345520452
516538217
518077844 518232524
527181268
529046306 529048335
531194957 531358314
531530720 531590087
531600857 531853869
532604555
532855491 532858075
532933742
533748253
534316754
535702924
536588237 536592571
541284267 541502928
546780974 546781208
546831391
548045733 548060633
548060802 548435543
548983250 549082730
549546263 549562705
549587540 549669255
549953533
553933522
556185926
558270478
559726088 559839493
561981647
562453115
563463598 563544735
563547266 563878522
563883212 563910613
564205223 564461674
564477647
565154441
571635082 571861468
576916265
577229458 577524288
578827707
580847795
581828063
584851722
586531776 586711100
586715328
587342325
595052159 595132460
693686064
697611190 697831155
699407657 699422973
699455437 699728464
701519795
703229470 703233730
710784650 711244784
713149757

5D

72

S5B_8071663
S5B_13171650
S5B_13448628

S5B_14370461

S5B_693686064
S5B_699422973
S5B_697831155
S5B_699728464 S5B_699407657
S5B_697611190 S5B_699455437
S5B_703233730
S5B_701519795
S5B_703229470
S5B_711244784
S5B_710784650

S5B_516538217
S5B_518077844
S5B_518232524
S5B_345520452
S5B_527181268
S5B_531194957
S5B_529046306 S5B_529048335
S5B_532933742 S5B_531853869
S5B_532604555 S5B_532855491
S5B_531358314 S5B_532858075
S5B_531600857 S5B_531530720
S5B_531590087
S5B_534316754 S5B_533748253
S5B_535702924
S5B_536592571
S5B_536588237
S5B_541502928
S5B_541284267
S5B_546781208
S5B_546780974
S5B_546831391
S5B_548435543
S5B_548060633
S5B_548983250
S5B_548060802
S5B_549546263
S5B_548045733
S5B_549669255
S5B_549562705
S5B_549082730
S5B_549587540
S5B_549953533
S5B_561981647
S5B_553933522
S5B_559839493
S5B_563544735
S5B_556185926
S5B_563910613 S5B_563883212
S5B_564205223
S5B_558270478 S5B_563463598
S5B_559726088 S5B_563878522
S5B_571635082 S5B_564477647
S5B_563547266
S5B_571861468 S5B_565154441
S5B_562453115
S5B_564461674
S5B_576916265
S5B_577524288
S5B_578827707
S5B_577229458
S5B_580847795
S5B_581828063
S5B_586711100
S5B_586531776
S5B_587342325
S5B_584851722
S5B_586715328
S5B_595052159
S5B_595132460

Sup Fig. 2.6A. U6708-04 linkage groups for group 6 aligned to the respective representative
chromosomes of the reference genome based on aligned marker positions.
6B

6A

6B

6A 6ALG1

0

581457113
582252800
584522646 584947253
591218736
618079260

S6A_581457113
S6A_582252800
S6A_584522646
S6A_584947253
S6A_591218736

0
45559153
116332183
116749984
117791265
129858790
132407971
133744491
141656091
149018318
149157187
150278330
157860059 157864381
162606013 162606061
162710951
178019409
179038330
179266622 179660119
188684286
189297186
190376868
191521052
216629042 216875221
290183114
310779386
369032062 369032332
435306949
439356897
439480719
444919233
448366419
451678072
486334942
492857027
540771175
549715775
559513097
561689670
568576952
569389830
573801218
576042280 576268701
576833154 576856920
577416768 577431059
613628843
616781941
617641128
633859145
634330566 634580195
643574058
646169463
647690929
648631459 648802472
650990416
655272662
655892937 656203174
657153861
661035114 661042994
663094605
663750758 663760713
663767352
664396646
668517613
669493587
670533014
673624646
675620435
676372403
677338037
678217457 678286151
678531167
679278115 679343802
679545497
680313575 680472324
680898285 681082967
704012175
720987604

S6B_45559153
S6B_117791265
S6B_116332183
S6B_133744491
S6B_116749984
S6B_129858790
S6B_141656091
S6B_486334942
S6B_150278330
S6B_132407971
S6B_149018318
S6B_149157187
S6B_162606061
S6B_178019409
S6B_664396646
S6B_179266622
S6B_157860059
S6B_162606013
S6B_162710951
S6B_157864381 S6B_179660119
S6B_179038330 S6B_191521052
S6B_216629042
S6B_216875221
S6B_188684286
S6B_310779386
S6B_290183114
S6B_435306949
S6B_439480719
S6B_439356897
S6B_189297186
S6B_190376868
S6B_369032062
S6B_369032332
S6B_451678072 S6B_444919233
S6B_448366419
S6B_492857027
S6B_573801218
S6B_540771175
S6B_576042280
S6B_559513097
S6B_568576952
S6B_576268701
S6B_576833154
S6B_576856920
S6B_569389830
S6B_549715775
S6B_577431059
S6B_561689670
S6B_616781941
S6B_613628843
S6B_577416768
S6B_617641128
S6B_633859145
S6B_634330566
S6B_634580195
S6B_647690929
S6B_648802472
S6B_650990416
S6B_656203174
S6B_657153861
S6B_655272662
S6B_648631459
S6B_655892937
S6B_661042994
S6B_646169463
S6B_663750758
S6B_663094605
S6B_663760713
S6B_663767352
S6B_643574058
S6B_661035114
S6B_668517613
S6B_673624646
S6B_679278115
S6B_670533014
S6B_669493587
S6B_676372403
S6B_677338037
S6B_680313575 S6B_675620435
S6B_679343802
S6B_680472324
S6B_681082967
S6B_678286151
S6B_679545497 S6B_678217457
S6B_680898285
S6B_678531167
S6B_704012175

73

6D
0
12018199 12019189
12023993 12358606
12435877
13197345 13202325
13206838 13863766
13970695
14657290 15170081
15256175 15779113
15809407
16008076
16704893 16706514
17181122
17446940
19567917
22766557
23622322
25851509 26002250
26002274
27525812 27859416
28304138 28324147
29875372
30744756
33305189
33926349 34075504
36689837
37228815 37231315
42153457
51732906
53640739 53775029
54695381 54748293
65353137 65912199
67545931
68098967
70772794
77864626
79864250 80064974
81659451 81920593
82501332
83223948 83426668
98090181 98090252
101721161 101758490
102473339
109485496
121347763
132054396 132200523
132200911
135112843
137541139
173445362
207934182
241296319
291620586 291699332
305272917
324565245
347713271
350131401
351124932 351124936
364851010
372432436
381549747
391693326
392881561
397083937
400080086
400398852
405678645 406103601
406343375
407829580
411724906
412622083
414403571
415751919
428697773
429358398 429674940
429830688
431108774 431148615
431173308
432929380
434207907
434751489 435306317
435810167 435834479
435950336
436452770 436466074
436673680
436722115 436813800
436816070 437296228
438097245
438829921
445337359 445458196
445773103
446477307 446478084
446919153
447845104
448872056 448872117
449923131
451915018
452342253 452405960
452410589 452410667
452587154
453174642
455558727 455626507
455718701 455735643
456683425
460468252 460468308
461467572 461501885
462479366 462494601
463051540 463079592
463547451 463744870
464483328 464830674
466738586
467187468 467198574
467208090 467803310
467861477 468113435
468833640
469344492 469537865
469567355 469583807
470373596
471330647 471828200
472073634 472103008
472369559 472404065
472533683
473592718

6DLG1

S6D_12435877
S6D_12019189
S6D_12358606
S6D_12023993
S6D_12018199
S6D_13197345
S6D_13202325
S6D_13206838
S6D_13970695
S6D_13863766
S6D_15170081
S6D_14657290
S6D_15256175
S6D_15809407
S6D_16008076
S6D_15779113
S6D_17181122
S6D_16706514
S6D_17446940
S6D_16704893
S6D_19567917
S6D_23622322
S6D_22766557
S6D_33926349
S6D_26002250
S6D_26002274 S6D_25851509
S6D_80064974
S6D_28304138
S6D_30744756
S6D_28324147
S6D_27525812
S6D_29875372
S6D_27859416
S6D_34075504
S6D_33305189
S6D_42153457
S6D_37228815
S6D_51732906
S6D_54748293
S6D_37231315
S6D_53775029
S6D_36689837
S6D_54695381
S6D_53640739
S6D_65353137
S6D_65912199
S6D_67545931
S6D_77864626
S6D_70772794
S6D_68098967
S6D_79864250
S6D_81920593
S6D_82501332
S6D_83223948
S6D_81659451
S6D_83426668
S6D_101758490
S6D_102473339
S6D_98090252
S6D_135112843
S6D_121347763 S6D_101721161
S6D_109485496
S6D_132200911
S6D_173445362
S6D_207934182
S6D_132200523 S6D_137541139
S6D_241296319
S6D_132054396
S6D_98090181
S6D_291699332
S6D_305272917
S6D_291620586
S6D_324565245
S6D_351124932
S6D_350131401
S6D_347713271
S6D_364851010
S6D_400398852
S6D_400080086
S6D_391693326
S6D_381549747 S6D_372432436
S6D_397083937
S6D_392881561
S6D_406343375
S6D_407829580 S6D_405678645
S6D_406103601
S6D_415751919
S6D_411724906
S6D_412622083
S6D_414403571
S6D_428697773
S6D_429358398
S6D_431148615
S6D_431173308
S6D_431108774
S6D_429674940
S6D_351124936
S6D_432929380
S6D_429830688
S6D_434207907
S6D_435810167
S6D_435306317
S6D_435834479
S6D_434751489
S6D_435950336
S6D_436673680
S6D_436452770
S6D_436722115
S6D_436466074
S6D_436813800
S6D_436816070
S6D_438097245
S6D_437296228
S6D_438829921
S6D_445337359
S6D_445773103
S6D_445458196
S6D_446477307
S6D_446478084
S6D_446919153
S6D_448872117
S6D_448872056
S6D_447845104
S6D_449923131
S6D_452342253
S6D_452410667
S6D_452410589
S6D_452587154
S6D_452405960
S6D_451915018
S6D_455558727
S6D_455626507
S6D_453174642
S6D_455735643
S6D_455718701
S6D_456683425
S6D_466738586
S6D_460468308
S6D_460468252
S6D_461501885
S6D_461467572
S6D_462494601
S6D_464483328
S6D_463547451
S6D_463051540
S6D_462479366
S6D_463079592
S6D_463744870
S6D_464830674
S6D_467187468
S6D_467803310
S6D_467198574
S6D_467861477 S6D_467208090
S6D_468113435
S6D_469567355
S6D_469583807
S6D_468833640 S6D_469537865
S6D_471828200
S6D_472404065
S6D_469344492
S6D_470373596
S6D_472533683
S6D_472369559
S6D_472073634
S6D_471330647
S6D_472103008

6D

6DLG1

Sup Fig. 2.6B. U6708-03 linkage groups for group 6 aligned to the respective representative
chromosomes of the reference genome based on aligned marker positions.
6A

0
50345873
51375303
55357294
57957359 57957452
59900885
61212031 61215999
62636804
63177063 63193128
64317708 64351211
66262487 66267889
66302437 66423413
67125288
68605608
69639591
71546814
74106770
76625816
86406306
87911429
98982893 99129219
105361547
106479262
106663990
112907140
113174471
114362144
115348315
123541747
135562761
151492080
402260505
405694216
412848068
416649831
420391165
429512775 429939115
431192976 431196234
433962955
435310153 435773114
442087078
449964357 450089405
450448242
453948996 453949039
454675620
498954585
499197587
521587282
522199048
524836385 525029970
525799739
526122132
541404429
542386105
546043162
546620773
549174392
549400546
551108311
551643722 551734300
552483090
554509140 555108940
618079260

6B

6D
S6B_117791265
S6B_116332183
S6B_133744491
S6B_116749984
S6B_129858790
S6B_141656091
0
12018199 12019189
S6B_486334942
12023993 12358606
S6B_150278330
12435877
13197345 13202325
S6B_132407971
13206838 13863766
13970695
S6B_149018318
14657290 15170081
15256175 15779113
S6B_149157187
15809407
S6B_162606061
16008076
16704893 16706514
S6B_178019409
17181122
17446940
S6B_664396646
19567917
S6B_179266622
22766557
23622322
S6B_157860059
25851509 26002250
26002274
S6B_162606013
27525812 27859416
28304138 28324147
S6B_162710951
29875372
S6B_157864381 S6B_179660119
30744756
S6B_179038330 S6B_191521052 33926349 33305189
34075504
36689837
S6B_216629042
37228815 37231315
S6B_216875221
42153457
51732906
S6B_188684286
53640739 53775029
54695381 54748293
S6B_310779386
65353137 65912199
67545931
S6B_290183114
68098967
S6B_435306949
70772794
77864626
S6B_439480719
79864250 80064974
81659451 81920593
S6B_439356897
82501332
S6B_189297186
83223948
98090181 98090252
S6B_190376868
101721161 101758490
102473339
S6B_369032062
109485496
121347763
S6B_369032332
S6B_451678072 S6B_444919233 132054396 132200523
132200911
135112843
S6B_448366419
137541139
173445362
S6B_492857027
207934182
S6B_573801218
241296319
291620586 291699332
S6B_540771175
305272917
324565245
S6B_576042280
347713271
350131401
S6B_559513097
351124932 351124936
S6B_568576952
364851010
372432436
S6B_576268701
381549747
391693326
S6B_576833154
392881561
S6B_576856920
397083937
400080086
S6B_569389830
400398852
405678645 406103601
S6B_549715775
406343375
407829580
S6B_577431059
411724906
S6B_561689670
412622083
414403571
S6B_616781941
415751919
428697773
S6B_613628843
429358398 429674940
S6B_577416768
429830688
431108774 431148615
S6B_617641128
431173308
432929380
S6B_633859145
434207907
434751489 435306317
S6B_634330566
435810167 435834479
S6B_634580195
435950336
436452770 436466074
S6B_647690929
436673680
436722115 436813800
S6B_648802472
436816070 437296228
S6B_650990416
438097245
438829921
S6B_656203174
445337359 445458196
445773103
S6B_657153861
446477307 446478084
446919153
S6B_655272662
447845104
S6B_648631459
448872056 448872117
449923131
S6B_655892937
451915018
452342253 452405960
S6B_661042994
452410589 452410667
S6B_646169463
452587154
453174642
S6B_663750758
455558727 455626507
455718701 455735643
S6B_663094605
456683425
460468252 460468308
S6B_663760713
461467572 461501885
S6B_663767352
462479366 462494601
463051540 463079592
S6B_643574058
463547451 463744870
464483328 464830674
S6B_661035114
466738586
S6B_668517613
467187468 467198574
467208090 467803310
S6B_673624646
467861477 468113435
468833640
S6B_679278115
469344492 469537865
469567355 469583807
S6B_670533014
470373596
S6B_669493587
471330647 471828200
472073634 472103008
S6B_676372403
472369559 472404065
472533683
S6B_677338037
473592718
S6B_680313575 S6B_675620435
S6B_679343802
S6B_680472324
S6B_681082967
S6B_678286151
S6B_679545497 S6B_678217457
S6B_680898285
S6B_678531167
S6B_704012175

S6A_51375303
S6A_50345873
S6A_105361547
S6A_57957359
S6A_59900885
S6A_57957452
S6A_55357294
0
S6A_66267889
116332183
116749984
S6A_63177063
117791265
S6A_63193128
129858790
S6A_61212031
132407971
S6A_61215999
133744491
S6A_62636804
141656091
S6A_64317708
149018318
S6A_66262487
149157187
S6A_68605608
150278330
157860059 157864381
S6A_66302437
162606013 162606061
S6A_64351211
162710951
S6A_67125288
178019409
S6A_76625816
179038330
S6A_86406306
179266622 179660119
S6A_71546814
188684286
S6A_74106770
189297186
190376868
S6A_66423413
191521052
S6A_69639591
216629042 216875221
S6A_98982893
290183114
S6A_99129219
310779386
S6A_87911429
369032062 369032332
S6A_114362144
435306949
S6A_405694216
439356897
439480719
S6A_402260505
444919233
S6A_106479262
448366419
S6A_112907140
451678072
S6A_113174471
486334942
S6A_106663990
492857027
S6A_123541747
540771175
S6A_135562761
549715775
S6A_416649831
559513097
561689670
S6A_115348315
568576952
S6A_431192976
569389830
S6A_412848068
573801218
S6A_151492080
576042280 576268701
S6A_420391165 S6A_429939115 576833154 576856920
S6A_431196234
577416768 577431059
S6A_435773114
613628843
616781941
S6A_433962955
617641128
S6A_442087078
633859145
S6A_429512775
634330566 634580195
S6A_435310153
643574058
S6A_450089405
646169463
S6A_449964357
647690929
S6A_450448242
648631459 648802472
S6A_453948996
650990416
655272662
S6A_453949039
655892937 656203174
S6A_454675620
657153861
S6A_498954585
661035114 661042994
S6A_521587282
663094605
S6A_499197587
663750758 663760713
S6A_522199048
663767352
S6A_549400546
664396646
668517613
S6A_525029970
669493587
S6A_524836385
670533014
S6A_542386105
673624646
S6A_525799739
675620435
S6A_526122132
676372403
S6A_552483090
677338037
S6A_541404429
678217457 678286151
S6A_551643722
678531167
679278115 679343802
S6A_554509140
679545497
S6A_551108311
680313575 680472324
S6A_549174392
680898285 681082967
S6A_551734300
704012175
S6A_546620773
720987604
S6A_555108940
S6A_546043162

74

S6D_12018199
S6D_12019189
S6D_12023993
S6D_12435877
S6D_12358606
S6D_13197345
S6D_13202325
S6D_13206838
S6D_13970695
S6D_13863766
S6D_33926349
S6D_15170081
S6D_14657290
S6D_15256175 S6D_15779113
S6D_15809407
S6D_17446940 S6D_16008076
S6D_16704893
S6D_16706514
S6D_17181122
S6D_19567917
S6D_22766557
S6D_23622322
S6D_80064974
S6D_26002250
S6D_25851509
S6D_26002274
S6D_27859416
S6D_27525812
S6D_28304138
S6D_30744756
S6D_28324147
S6D_29875372
S6D_53640739
S6D_33305189
S6D_34075504
S6D_37228815
S6D_37231315
S6D_36689837
S6D_54695381 S6D_42153457
S6D_53775029
S6D_51732906
S6D_54748293
S6D_351124936
S6D_70772794
S6D_65353137
S6D_67545931
S6D_68098967 S6D_65912199
S6D_81920593 S6D_79864250
S6D_82501332
S6D_77864626 S6D_83223948
S6D_81659451
S6D_101721161
S6D_109485496
S6D_98090181
S6D_98090252
S6D_101758490
S6D_102473339
S6D_121347763
S6D_132054396
S6D_132200523
S6D_137541139
S6D_135112843
S6D_132200911
S6D_173445362 S6D_207934182
S6D_291699332
S6D_291620586
S6D_241296319
S6D_305272917
S6D_351124932
S6D_324565245
S6D_350131401
S6D_347713271
S6D_372432436
S6D_364851010
S6D_381549747
S6D_391693326
S6D_392881561
S6D_397083937
S6D_400080086
S6D_400398852
S6D_411724906
S6D_412622083
S6D_406343375
S6D_406103601 S6D_407829580
S6D_405678645
S6D_415751919
S6D_414403571
S6D_429830688
S6D_429358398
S6D_431108774
S6D_428697773
S6D_429674940
S6D_431173308
S6D_431148615
S6D_432929380
S6D_434207907
S6D_435306317
S6D_435810167
S6D_434751489
S6D_435950336
S6D_435834479
S6D_436673680 S6D_436466074
S6D_436452770
S6D_436816070
S6D_437296228
S6D_436813800
S6D_436722115
S6D_438097245
S6D_438829921
S6D_445337359
S6D_445458196
S6D_446919153
S6D_446477307
S6D_446478084 S6D_445773103
S6D_447845104
S6D_448872056
S6D_449923131
S6D_448872117
S6D_451915018
S6D_452410589
S6D_452405960
S6D_452342253
S6D_452410667
S6D_453174642
S6D_452587154
S6D_455735643
S6D_455718701
S6D_455558727 S6D_455626507
S6D_466738586
S6D_463744870
S6D_460468252
S6D_460468308
S6D_461501885
S6D_462479366
S6D_463079592
S6D_461467572
S6D_456683425 S6D_463547451
S6D_462494601
S6D_464483328
S6D_463051540
S6D_464830674
S6D_467208090
S6D_467861477
S6D_467803310 S6D_467187468
S6D_467198574
S6D_468833640
S6D_469567355
S6D_469583807
S6D_469344492
S6D_469537865
S6D_468113435
S6D_470373596
S6D_471828200
S6D_472404065
S6D_472533683
S6D_472369559
S6D_471330647
S6D_472103008
S6D_472073634

7A

7ALG2

7ALG1

7B

7BLG1

Sup Fig. 2.7A. U6708-04 linkage groups for group 7 aligned to the respective representative
chromosomes of the reference genome based on aligned marker positions.
0
34099753 34450899
34520468
37728390
37923130 38234502
38238713 38241595
38326910 38327857
38666029 38951126
47709202 47772022
48013489 48061983
48626171 49052057
49184643
49560773 49592884
49592941
51497762
52666927
55205096
55362403
62187944
74151919
77533325
80428696
81124969
82946533 83085753
83158966
85074287
89593435
92419590
97402815
99804435 99904293
100724626
116487416 116544032
117484054
118710182
122751133
122984859 123279067
124069496
124224022 124763424
126783900 126871483
127910397
128894961
129060913
129879691 130233836
130302731
133045097
134020144
134571333 134621808
134621832 134732351
136342810
137918755
143143364
143973513
148170518
148411596
149415943 149426415
152084396
158398626 158596870
158599412 158618800
162453333 162595211
162734424 162775292
163353525
167678916
169036120
170685295
172207184
172954069
184174817
186542045
189437949
191698642
192633169
193618317
194006195
201989719
202740195
234522973
234855696
244406809
286518685
299506725
373469763
449335806 449450305
466885821
467849015
471547991
475166035
482490153 482492319
487636684
511714171
522996431
529437855 529453972
533059303
536976297 536976495
536989010
550315701
552991007
555468225
560990618
561870792
563604715
566128405
567030080 567030462
572138335
642093475
644108293
644620616 644848740
648366734
648577609 648674682
648674685
652231224 652539633
652615891
653581685 653597598
660454106
660936870
670917971
675528073
676422794
681696004 681716864
685094932
688948979
690492403 690505874
692469595
695624128 695840163
700824770 700849984
702412677
703895027
704843661 705365587
705556719 705593667
705593710
706402648
709765148 709815078
709816061 709858877
709893810
710958702 710959180
711611176 711824254
712051217
713757590 713773221
714316889 714662345
714762188
715781215
716611061
717175385 717437125
720319330 720319399
720347056 720348470
720585903 720587273
720912697
722322649
724504044
725050709 725165320
725440558 725448123
725637261
736633129

7A

S7A_700849984
S7A_700824770
S7A_704843661
S7A_703895027
S7A_702412677
S7A_705365587
S7A_705593710
S7A_705593667
S7A_705556719
S7A_706402648
S7A_709816061
S7A_709815078
S7A_709858877
S7A_709765148
S7A_711611176
S7A_710959180
S7A_711824254
S7A_712051217
S7A_710958702
S7A_709893810
S7A_713757590
S7A_713773221
S7A_714316889 S7A_717175385
S7A_714662345
S7A_714762188
S7A_715781215
S7A_717437125
S7A_716611061
S7A_720347056
S7A_720319399 S7A_720319330
S7A_720585903
S7A_720912697
S7A_720587273 S7A_720348470
S7A_722322649
S7A_724504044
S7A_725165320
S7A_725448123
S7A_725440558
S7A_725637261
S7A_725050709

S7A_34450899
S7A_34520468 S7A_34099753
S7A_38238713
S7A_37728390
S7A_37923130
S7A_38326910
S7A_38241595 S7A_38234502
S7A_38327857
S7A_38951126
S7A_38666029
S7A_47709202
S7A_47772022
S7A_48061983
S7A_48013489
S7A_48626171
S7A_49052057
S7A_49560773
S7A_49592884 S7A_49184643
S7A_49592941
S7A_51497762
S7A_52666927
S7A_55205096
S7A_55362403
S7A_62187944
S7A_74151919
S7A_77533325
S7A_80428696
S7A_81124969
S7A_83085753
S7A_83158966
S7A_82946533
S7A_85074287
S7A_89593435
S7A_122751133
S7A_143973513
S7A_92419590
S7A_97402815
S7A_99904293
S7A_99804435
S7A_100724626
S7A_123279067
S7A_116544032
S7A_116487416
S7A_124069496
S7A_124763424 S7A_122984859
S7A_124224022
S7A_118710182
S7A_126783900
S7A_117484054
S7A_129879691
S7A_127910397
S7A_130302731
S7A_130233836
S7A_128894961
S7A_133045097
S7A_129060913
S7A_126871483
S7A_134571333
S7A_134621832
S7A_134020144
S7A_134732351 S7A_134621808
S7A_152084396
S7A_137918755 S7A_148170518
S7A_158599412 S7A_136342810
S7A_149426415 S7A_158618800
S7A_162595211 S7A_148411596
S7A_143143364 S7A_163353525
S7A_158596870 S7A_162734424
S7A_162453333 S7A_184174817
S7A_172207184 S7A_162775292
S7A_169036120 S7A_170685295
S7A_149415943
S7A_189437949
S7A_202740195
S7A_172954069
S7A_167678916 S7A_194006195
S7A_193618317
S7A_158398626
S7A_201989719
S7A_186542045
S7A_192633169
S7A_234855696
S7A_234522973
S7A_286518685
S7A_244406809
S7A_373469763
S7A_475166035
S7A_449450305
S7A_299506725
S7A_449335806
S7A_467849015
S7A_482490153
S7A_482492319
S7A_466885821
S7A_487636684
S7A_471547991
S7A_191698642
S7A_533059303
S7A_536989010
S7A_511714171
S7A_529437855
S7A_522996431
S7A_529453972
S7A_536976495
S7A_536976297
S7A_552991007
S7A_550315701
S7A_563604715
S7A_560990618
S7A_676422794
S7A_567030080
S7A_555468225
S7A_567030462
S7A_561870792
S7A_566128405
S7A_572138335
S7A_642093475
S7A_648366734
S7A_648674682
S7A_648577609
S7A_644848740
S7A_644108293
S7A_644620616
S7A_652539633
S7A_652615891
S7A_652231224
S7A_653581685
S7A_653597598
S7A_660454106
S7A_660936870
S7A_648674685
S7A_670917971
S7A_675528073
S7A_681696004
S7A_685094932
S7A_681716864
S7A_688948979
S7A_690505874
S7A_692469595
S7A_695624128
S7A_690492403
S7A_695840163

0
1033544
2327290 2573586
3505031
4826066
11292130
12716393
12952642
14901336
23321402 23321823
23910463
27599492
27783744 28060652
28976027
32346760 32463131
32475870 32548575
33631586 33926268
34050712
35070905
35637403
36483529
37361425
39547351 39617748
41542834
48770176
60863445
61609767
62389381
65165586
66021438
67902749
68246015
73174573
106862456 107095937
158543078
248507719 248509591
254461799
256491492
263724289
271943246
272743417
283360494
285345274
317179762 317179903
317179945
318841318
322389824
352424111
354184874
358496280
373077367
377603990
379728419
382618004
385734315
387149304
389007939
393314447
395591342 395649031
395734415
451485954
452158275 452158662
452496851
458994323 458996011
461241345
474407050
475307777
481310241
481696533
482088585
483759181
498538848 498969589
509576266
510443820 510536323
511927944
513241854
513813110
516450006
527983263
528872079
529147819
529832236
530459507 530804113
538051151 538052460
538124923 538125805
539196288
539879402 539879737
540344806
542989138
556433941
567730519 567884654
568039107
570263282
572578755
580184087 580184684
580884004 580974294
583544321
584193980
587910344 587939545
590283765
590363348 590491608
590815214
592503323 592867997
593639128 594042645
611339740
612331663
617839719
619363563 619664231
620605293 620989090
622525086
624466569
626037289 626043540
646995237
647452299
649097902
650641114
654138445
656960482 657082287
659824932
670583718
672165055
679595509
679817715 680351258
682355609
682378890
683229572
684551382 684948017
695381826
700568716
702555450 702560717
704548773
704739241
705715636
708532377 708673126
709746411
711724505
712775990
714603868
716535045 716958100
717206450 717328803
717371769
719909299
721700995 721736109
725194925
725761307
726400791 726568556
727918743
730150130 730619959
730875437
733461150 733540636
736311125
736871074 736871141
738277862
739275812 739421824
739988762
741535904 741572948
741763059
741881997 742362374
742599439 742665138
742700962 742762324
743417560
744116313 744264948
747988587 747988669
748865742
749122094 749242337
749284801 749525918
750577679

S7B_1033544
S7B_2327290
S7B_2573586
S7B_4826066
S7B_3505031
S7B_11292130
S7B_23910463
S7B_61609767
S7B_14901336
S7B_12952642
S7B_12716393
S7B_23321402
S7B_23321823
S7B_158543078
S7B_28976027
S7B_27783744
S7B_27599492
S7B_28060652
S7B_32463131
S7B_32548575
S7B_32346760
S7B_33926268
S7B_263724289
S7B_34050712
S7B_33631586
S7B_32475870
S7B_39547351
S7B_37361425 S7B_39617748
S7B_36483529
S7B_48770176
S7B_35070905
S7B_41542834
S7B_35637403
S7B_60863445
S7B_67902749
S7B_68246015
S7B_65165586
S7B_62389381
S7B_73174573
S7B_66021438
S7B_107095937
S7B_106862456
S7B_248507719
S7B_254461799
S7B_272743417 S7B_358496280
S7B_317179903
S7B_248509591
S7B_382618004 S7B_352424111
S7B_354184874 S7B_322389824
S7B_317179762
S7B_317179945 S7B_385734315
S7B_393314447 S7B_271943246
S7B_389007939
S7B_373077367
S7B_377603990
S7B_283360494 S7B_285345274
S7B_395649031
S7B_318841318 S7B_395591342
S7B_395734415
S7B_256491492 S7B_513813110
S7B_474407050
S7B_452158275 S7B_461241345
S7B_452158662 S7B_387149304
S7B_475307777 S7B_379728419
S7B_458994323 S7B_498969589
S7B_451485954
S7B_458996011
S7B_498538848
S7B_481696533
S7B_516450006 S7B_509576266
S7B_510536323 S7B_483759181
S7B_511927944
S7B_452496851 S7B_481310241
S7B_513241854
S7B_482088585
S7B_530804113
S7B_529832236
S7B_528872079 S7B_527983263
S7B_539879737 S7B_529147819
S7B_530459507
S7B_538125805
S7B_538124923
S7B_538051151
S7B_538052460
S7B_542989138
S7B_539196288
S7B_539879402
S7B_540344806
S7B_670583718
S7B_567884654
S7B_568039107
S7B_580184087
S7B_567730519
S7B_580184684 S7B_583544321
S7B_556433941
S7B_580974294
S7B_647452299
S7B_570263282
S7B_587910344
S7B_580884004
S7B_572578755
S7B_590283765
S7B_587939545
S7B_584193980
S7B_590491608
S7B_590815214
S7B_590363348
S7B_593639128
S7B_594042645
S7B_592867997
S7B_592503323
S7B_611339740
S7B_612331663
S7B_624466569
S7B_510443820
S7B_620989090
S7B_617839719
S7B_619664231
S7B_622525086
S7B_626037289 S7B_619363563
S7B_620605293
S7B_626043540
S7B_646995237
S7B_649097902
S7B_650641114
S7B_654138445
S7B_656960482
S7B_657082287
S7B_672165055
S7B_704739241
S7B_659824932
S7B_679817715
S7B_682378890
S7B_679595509
S7B_682355609 S7B_683229572
S7B_684551382
S7B_680351258
S7B_700568716
S7B_695381826
S7B_702560717
S7B_684948017 S7B_702555450
S7B_708673126
S7B_704548773
S7B_705715636
S7B_708532377
S7B_736311125
S7B_711724505
S7B_709746411
S7B_712775990
S7B_717206450
S7B_717371769 S7B_719909299
S7B_714603868
S7B_716535045
S7B_716958100
S7B_717328803
S7B_721700995
S7B_726568556
S7B_721736109
S7B_726400791
S7B_725194925
S7B_725761307
S7B_730875437
S7B_741572948 S7B_741763059
S7B_727918743 S7B_730150130
S7B_730619959
S7B_733461150
S7B_742362374
S7B_749284801 S7B_739275812
S7B_741535904
S7B_736871141 S7B_742665138
S7B_738277862 S7B_736871074
S7B_739988762 S7B_747988669
S7B_739421824 S7B_742599439
S7B_741881997 S7B_733540636
S7B_742700962
S7B_747988587
S7B_749122094
S7B_742762324
S7B_748865742
S7B_749242337
S7B_744264948
S7B_744116313
S7B_749525918
S7B_743417560

7B

0
1537886 1570012
4188276 4246387
5671117
6136243
6772594
8333685
9096883
9928472
10726785 10726864
10804279
12151885
12549816 12558018
13894806 13925669
14025943 14175649
14176788 14251853
14426487
17753962 17891069
17905353
18590915 18679585
18682792
19927998 20115523
20237471
22575972 22719681
24519265 24826665
24977929
25356570
27486623
28043357 28248589
28839483 28880153
29075566 29217976
29262723 29408544
29534136 29958815
30956741
36275099

S7D_620283090
620283090
631681105 631758106
631922149 631978910
632509242 632593226
632648460 632802365
634562548
635517741 635844631
638641459

7D

75

S7D_1537886
S7D_8333685
S7D_1570012
S7D_4246387
S7D_4188276
S7D_5671117
S7D_6772594
S7D_6136243
S7D_10726785
S7D_10726864
S7D_9928472
S7D_9096883
S7D_10804279
S7D_12151885
S7D_12549816
S7D_12558018
S7D_13925669
S7D_14175649
S7D_14176788
S7D_14025943
S7D_14426487
S7D_14251853
S7D_13894806
S7D_17753962
S7D_18682792
S7D_17905353
S7D_18590915
S7D_18679585
S7D_17891069
S7D_19927998
S7D_20115523
S7D_20237471
S7D_22575972
S7D_24826665
S7D_24519265
S7D_22719681
S7D_24977929
S7D_25356570
S7D_27486623
S7D_28043357
S7D_28248589
S7D_28839483
S7D_29262723
S7D_28880153
S7D_29958815
S7D_29408544
S7D_29217976
S7D_29534136
S7D_29075566
S7D_30956741
S7D_36275099
S7D_635517741

S7D_631978910
S7D_632509242 S7D_632648460
S7D_631758106 S7D_632593226
S7D_631681105 S7D_631922149
S7D_632802365
S7D_634562548
S7D_635844631

7A 7ALG1

7ALG2

7B 7BLG2

7BLG1

Sup Fig. 2.7B. U6708-03 linkage groups for group 7 aligned to the respective representative
chromosomes of the reference genome based on aligned marker positions.
0
1479446 1480783
2287400
4706457
8530374
10270159
11056233
12098790
13789559 14288986
14896545
15080090 15614042
15639392
16891893 16978949
18503876
24504926 24940330
25877116 26240650
27208690
34099753 34450899
34520468
37728390
37923130 38234502
38238713 38241595
38326910 38327857
38666029 38951126
47709202 47772022
48013489 48061983
48626171 49052057
49184643
49560773 49592884
49592941
51497762
52666927
55205096
55362403
62187944
74151919
77533325
80428696
81124969
82946533 83085753
83158966
85074287
89593435
92419590
97402815
99804435 99904293
100724626
116487416 116544032
117484054
118710182
122751133
122984859 123279067
124069496
124224022 124763424
126783900 126871483
127910397
128894961
129060913
129879691 130233836
130302731
133045097
134020144
134571333 134621808
134621832 134732351
136342810
137918755
143143364
148170518
148411596
149415943 149426415
152084396
158398626 158596870
158599412 158618800
162453333 162595211
162734424 162775292
163353525
167678916
169036120
170685295
172207184
172954069
184174817
186542045
189437949
191698642
192633169
193618317
194006195
201989719
202740195
234522973
234855696
244406809
286518685
299506725
373469763
449335806 449450305
466885821
467849015
471547991
475166035
482490153 482492319
487636684
511714171
522996431
529437855 529453972
533059303
536976297 536976495
536989010
550315701
552991007
555468225
560990618
561870792
563604715
566128405
567030080 567030462
572138335
642093475
644108293
644620616 644848740
648366734
648577609
652231224 652539633
652615891
653581685 653597598
660454106
736633129

S7A_2287400
S7A_1480783
S7A_4706457
S7A_1479446
S7A_8530374
S7A_12098790
S7A_10270159
S7A_11056233
S7A_14288986
S7A_13789559
S7A_14896545
S7A_15614042
S7A_15639392
S7A_15080090
S7A_18503876
S7A_16978949
S7A_24504926
S7A_25877116
S7A_26240650
S7A_24940330
S7A_27208690
S7A_16891893

7A

S7A_34520468
S7A_34450899
S7A_34099753
S7A_38238713
S7A_38241595
S7A_38234502
S7A_37923130
S7A_38327857
S7A_37728390
S7A_38326910
S7A_38951126
S7A_47772022
S7A_48013489
S7A_47709202
S7A_48061983 S7A_38666029
S7A_48626171
S7A_49052057
S7A_49592941
S7A_49592884
S7A_52666927
S7A_49184643
S7A_51497762
S7A_49560773
S7A_55205096
S7A_55362403
S7A_62187944
S7A_74151919
S7A_81124969
S7A_83158966
S7A_80428696
S7A_77533325
S7A_83085753
S7A_82946533
S7A_89593435
S7A_85074287
S7A_122751133
S7A_92419590
S7A_97402815
S7A_99904293
S7A_116544032
S7A_100724626
S7A_99804435
S7A_116487416
S7A_124763424
S7A_117484054
S7A_122984859
S7A_123279067
S7A_124224022
S7A_124069496
S7A_118710182
S7A_126871483
S7A_126783900
S7A_134020144
S7A_129060913
S7A_133045097
S7A_148411596 S7A_127910397
S7A_128894961
S7A_136342810
S7A_143143364
S7A_134571333 S7A_130233836
S7A_130302731
S7A_149415943
S7A_134732351 S7A_137918755
S7A_129879691 S7A_162595211
S7A_134621808 S7A_152084396
S7A_148170518
S7A_158599412 S7A_149426415
S7A_163353525 S7A_134621832
S7A_169036120
S7A_158618800 S7A_158398626
S7A_167678916 S7A_170685295
S7A_172954069 S7A_162775292
S7A_162734424
S7A_186542045
S7A_193618317
S7A_158596870 S7A_189437949
S7A_184174817
S7A_172207184
S7A_194006195
S7A_191698642
S7A_192633169
S7A_201989719
S7A_162453333
S7A_234855696
S7A_511714171
S7A_202740195
S7A_234522973
S7A_449335806 S7A_466885821
S7A_286518685
S7A_299506725
S7A_467849015 S7A_487636684
S7A_482492319
S7A_449450305
S7A_475166035
S7A_244406809
S7A_529453972
S7A_482490153
S7A_471547991
S7A_373469763
S7A_533059303
S7A_522996431
S7A_529437855
S7A_536989010
S7A_536976495
S7A_536976297
S7A_552991007
S7A_555468225
S7A_550315701
S7A_567030462
S7A_560990618
S7A_561870792
S7A_567030080
S7A_566128405
S7A_563604715
S7A_642093475
S7A_644848740
S7A_644108293
S7A_648366734
S7A_652615891
S7A_652231224
S7A_648577609
S7A_644620616
S7A_660454106
S7A_652539633
S7A_653597598
S7A_653581685
S7A_572138335

0
11292130
12716393
23321402 23321823
27599492
27783744 28060652
28976027
32346760 32463131
32475870 32548575
33631586 33926268
34050712
35070905
35637403
36483529
37361425
39547351 39617748
41542834
48770176
60863445
62389381
65165586
66021438
67902749
68246015
73174573
106862456 107095937
158543078
248507719 248509591
254461799
256491492
271943246
272743417
283360494
285345274
317179762 317179903
317179945
318841318
322389824
352424111
354184874
358496280
373077367
377603990
379728419
382618004
385734315
387149304
389007939
393314447
395591342 395649031
395734415
451485954
452158275 452158662
452496851
458994323 458996011
461241345
474407050
475307777
477432771
481310241
481696533
482088585
483759181
498538848 498969589
509576266
510443820 510536323
511927944
513241854
513813110
516450006
527983263
528872079
529147819
529832236
530459507 530804113
538051151 538052460
538124923 538125805
539196288
539879402 539879737
540344806
542989138
556433941
567730519 567884654
568039107
570263282
572578755
580184087 580184684
580884004 580974294
583544321
584193980
587910344 587939545
590283765
590363348 590491608
590815214
592503323 592867997
593639128 594042645
611339740
612331663
617839719
619363563 619664231
620605293 620989090
622525086
624466569
626037289 626043540
646995237
647452299
649097902
650641114
654138445
656960482 657082287
659824932
670583718
672165055
679595509
679817715 680351258
682355609
682378890
683229572
684551382
695381826
700568716
702555450 702560717
704548773
704739241
705715636
708532377 708673126
709746411
711724505
712775990
714603868
716535045 716958100
717206450 717328803
717371769
719909299
721700995 721736109
725194925
750577679

S7B_702560717
S7B_695381826
S7B_702555450
S7B_700568716
S7B_704548773
S7B_708532377
S7B_704739241
S7B_705715636
S7B_708673126
S7B_712775990
S7B_709746411
S7B_711724505
S7B_716535045
S7B_716958100
S7B_717328803
S7B_714603868 S7B_717206450
S7B_717371769
S7B_719909299
S7B_721736109 S7B_721700995
S7B_725194925

7B

S7B_23321402
S7B_23321823
S7B_158543078
S7B_27783744
S7B_27599492
S7B_28060652
S7B_32346760
S7B_28976027
S7B_32475870
S7B_32463131
S7B_32548575
S7B_33631586
S7B_34050712
S7B_33926268
S7B_36483529
S7B_35070905
S7B_39617748
S7B_35637403
S7B_41542834
S7B_39547351
S7B_37361425
S7B_60863445
S7B_48770176
S7B_62389381
S7B_68246015
S7B_65165586
S7B_66021438
S7B_67902749
S7B_73174573
S7B_107095937
S7B_106862456
S7B_11292130
S7B_285345274
S7B_283360494
S7B_248507719
S7B_254461799
S7B_272743417
S7B_256491492
S7B_317179762
S7B_271943246
S7B_352424111
S7B_248509591 S7B_317179903
S7B_373077367
S7B_358496280 S7B_379728419
S7B_322389824 S7B_393314447
S7B_377603990 S7B_385734315
S7B_317179945
S7B_389007939 S7B_354184874
S7B_395734415
S7B_387149304
S7B_318841318 S7B_382618004
S7B_395591342
S7B_395649031
S7B_452496851
S7B_452158275
S7B_452158662
S7B_458996011
S7B_482088585
S7B_12716393
S7B_451485954
S7B_481310241
S7B_461241345
S7B_458994323
S7B_475307777
S7B_477432771
S7B_481696533
S7B_474407050
S7B_483759181
S7B_498969589
S7B_498538848
S7B_509576266
S7B_516450006 S7B_510536323
S7B_513813110
S7B_527983263
S7B_513241854
S7B_529147819
S7B_528872079
S7B_529832236
S7B_530804113 S7B_511927944
S7B_530459507
S7B_538125805
S7B_539879402
S7B_538051151
S7B_538052460
S7B_540344806
S7B_542989138
S7B_539196288 S7B_539879737
S7B_538124923
S7B_510443820
S7B_556433941
S7B_572578755
S7B_567730519 S7B_587939545
S7B_580974294
S7B_580184684
S7B_567884654
S7B_584193980
S7B_568039107
S7B_587910344
S7B_583544321
S7B_570263282
S7B_580184087
S7B_580884004
S7B_590363348
S7B_594042645
S7B_590283765
S7B_593639128
S7B_670583718 S7B_590491608
S7B_592503323
S7B_590815214
S7B_592867997
S7B_612331663
S7B_611339740
S7B_620989090
S7B_619363563
S7B_620605293
S7B_617839719
S7B_622525086
S7B_626037289
S7B_619664231
S7B_624466569
S7B_626043540
S7B_646995237
S7B_649097902
S7B_650641114
S7B_654138445
S7B_656960482
S7B_659824932
S7B_657082287
S7B_672165055
S7B_647452299
S7B_679817715
S7B_679595509
S7B_680351258
S7B_682378890
S7B_682355609
S7B_683229572
S7B_684551382

0
1537886 1570012
4188276 4246387
5653553 5671117
6136243
6772594
8333685
9096883
9928472
10726785 10726864
10804279
12151885
12549816 12558018
13894806 13925669
14025943 14175649
14176788 14251853
14426487
17753962 17891069
17905353
18590915 18679585
18682792
19927998 20115523
20237471
22575972 22719681
24519265 24826665
24977929
25356570
58491641
59105969
60217671 60279204
60459462
61188004
61757302
62120102 62120178
63453715 63471298
64236500 64379914
65592365 65617305
65715714 65752952
68431283
68518279
70048992
71569531
72452170 72699287
72699333
72808182 73153208
74060422
74963530 75136077
75271662
78193178
78672632
79299360
80264777 80292147
80294908
83376988
83426451 83473595
83666746 83666851
89733085
92604251
101557747
393456338
502232313 502232988
504011403
505129726
507848669
519112634
576703863 576735344
577782004
579085646 579361833
579634283
580379374
588085500
592223121 592392427
592632581 592632637
595068840 595528770
595613399
596434245 597019065
597118932
599115002
600837544 601070723
601071069
601487305 601781609
601904143
602197236
603678242
604869757
605596128
605744448
610739554 610740232
611014718
619996988 620283090
620622222 620924768
621155254 621212944
621951204
623068416
623403351
626481419 626927234
626950802 627295271
627411185 627569993
628521992
629311395 629311461
630196200 630440805
631681105 631758106
631922149 631978910
632509242 632593226
632648460 632802365
634562548
635517741 635844631
638208446
638440265 638541382
638641459

S7D_1537886
S7D_1570012
S7D_8333685
S7D_4246387
S7D_5671117
S7D_6136243
S7D_6772594
S7D_10726785
S7D_9928472
S7D_10804279
S7D_4188276
S7D_10726864
S7D_9096883
S7D_12151885
S7D_12549816
S7D_13925669
S7D_14025943
S7D_13894806
S7D_12558018
S7D_14176788
S7D_14426487
S7D_14175649
S7D_14251853
S7D_17905353
S7D_17753962
S7D_18679585
S7D_18682792
S7D_18590915
S7D_19927998
S7D_20237471
S7D_20115523
S7D_17891069
S7D_22575972
S7D_22719681
S7D_24977929
S7D_25356570
S7D_24519265
S7D_24826665
S7D_635517741

7D

76

S7D_5653553
S7D_59105969
S7D_58491641
S7D_60279204
S7D_60217671
S7D_60459462
S7D_62120178
S7D_61757302
S7D_62120102
S7D_64236500
S7D_61188004
S7D_64379914
S7D_63453715
S7D_63471298
S7D_65592365
S7D_65617305
S7D_65715714
S7D_65752952
S7D_68518279
S7D_68431283
S7D_71569531
S7D_74060422 S7D_72699333
S7D_75136077
S7D_72452170
S7D_75271662
S7D_74963530
S7D_72808182
S7D_73153208
S7D_72699287
S7D_78193178
S7D_80264777
S7D_78672632
S7D_79299360
S7D_83426451
S7D_80294908
S7D_83376988
S7D_83666746
S7D_83666851
S7D_83473595
S7D_80292147
S7D_92604251
S7D_101557747
S7D_504011403
S7D_502232313
S7D_502232988 S7D_505129726
S7D_507848669
S7D_519112634
S7D_576703863
S7D_576735344
S7D_89733085
S7D_393456338
S7D_577782004
S7D_579634283
S7D_580379374
S7D_70048992
S7D_579361833
S7D_579085646
S7D_588085500
S7D_592223121
S7D_592632637
S7D_592632581
S7D_592392427
S7D_595068840
S7D_595528770
S7D_597019065 S7D_595613399
S7D_596434245
S7D_597118932
S7D_600837544
S7D_599115002
S7D_601070723
S7D_601781609
S7D_601904143
S7D_601071069
S7D_601487305
S7D_602197236
S7D_603678242
S7D_605596128
S7D_604869757
S7D_605744448
S7D_611014718
S7D_610740232
S7D_610739554
S7D_623403351
S7D_619996988
S7D_620622222
S7D_620283090
S7D_621951204
S7D_620924768
S7D_621212944
S7D_621155254
S7D_623068416
S7D_626481419
S7D_627295271
S7D_626927234
S7D_626950802
S7D_627411185
S7D_627569993
S7D_629311395
S7D_628521992
S7D_629311461
S7D_630196200
S7D_630440805
S7D_632509242
S7D_631758106
S7D_632648460
S7D_631681105 S7D_631922149
S7D_638440265
S7D_635844631
S7D_632593226
S7D_638208446
S7D_632802365
S7D_638541382
S7D_631978910
S7D_634562548

Sup Fig. 2.8. Histograms of both IT and severity scores recorded for the U6708 population in
response to Puccinia inoculation.
Severity was rated from 0–100% based on the Cobb scale, AUDPC = area under the disease progression curve. GC
= growth chamber phenotyping environment; GH = greenhouse phenotyping environment; Field = Mason,
Michigan, 2017 phenotyping environment. IT scores were converted to a 1-5 qualitative scale as described in
materials and methods.

77

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CHAPTER 3: Conclusions
Conclusions of Current Research
A SHW RIL population, consisting of two families (U6708-03 and U6708-04), was
developed from a cross between the synthetic line 9.131.15x (tetraPrelude/TA2474) and
KS05HW14, a hard white winter wheat. The RIL population was genotyped using genotypingby-sequence and GBS-SNP markers were identified using the TASSEL 5.0-GBS pipeline
(Bradbury et al., 2007; Glaubitz et al., 2014). GBS-SNP markers were aligned to the recently
released IWGSC ( 2014) Chinese spring v1.0 reference genome and linkage groups were created
for each family. Twenty of twenty-one chromosomes segregated in each family with a majority
of linkage groups aligning near the telomeres of each respective chromosome. The RIL
population was phenotyped for disease resistance to three different Puccinia species, stripe (P.
striiformis f. sp. tritici, Pst), stem (P. graminis f. sp. tritici, Pgt), and leaf rust (P. triticina, Pt).
Phenotyping was performed at the seedling and adult plant stages with seedling evaluations
performed in the growth chamber and adult plant evaluations performed in both the greenhouse
and field. Greenhouse adult plant evaluations were implemented for additional phenotyping
under a more controlled environment compared to the field. This controlled greenhouse
screening was effective in mapping seedling resistance loci.
Seedling resistance to Pst, conferred by QYr.msu-4DS was mapped to the 4DS
chromosome and originated from TA2474. QYr.msu-4DS was first mapped in a seedling test
conducted in the growth chamber and segregated in only the U6708-03 family. Severity and
infection type phenotypes, scored in a subsequent adult plant greenhouse evaluation, colocalized. Both growth chamber and greenhouse-grown plants were artificially inoculated with

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Pst-37 uredinospores. Two other previously identified Pst seedling resistance genes have been
mapped to chromosome 4DS, Yr28 and YrAS2338 which originated from two different Ae.
tauschii accessions,W-219 and AS2338, respectively (Singh et al., 2000; Huang et al., 2011).
Seedling resistance to Pgt, conferred by QSr.msu-5BL, was mapped to the 5BL
chromosome and segregated in both U6708 families. This seedling resistance locus originated
from 9.131.15x and was associated with the same markers in both families indicating that the
same QTL is present in both families. Phenotyping for Pgt resistance was performed in the
growth chamber, greenhouse, and field environments, which were all artificially inoculated with
Pgt-QFCSC uredinospores. Infection type and severity phenotypes, scored in both the
greenhouse and field environments, co-localized with seedling resistance measured at the
seedling stage. Only one Pgt seedling resistance gene has been previously mapped to 5BL, Sr49,
which originated from the T. aestivum landrace Mahmoudi (Bansal et al., 2015). Further work
will need to be carried out to determine the novelty of QSr.msu-5BL. Potential Pgt APR QTLs
were identified in the greenhouse and field, but these were not repeated between environments.
A putative APR QTL, originating from TA2474, was identified on the 7D chromosome in
Mason, MI. Additional field trials could be performed to determine if the 7D QTL observed in
the field can be observed in a repeatable manner.
Endemic Pt was present in Mason, MI, in 2017 and both families were phenotyped for Pt
disease resistance against local Pt races. In both families, a major effect QTL that originated
from KS05HW14 was mapped to 3BL at GBS-SNP markers shared between families. An
additional Pt resistance QTL was identified on 6D segregating in the U6078-03 family and
originated from TA2474. Previous work on 9.131.15x failed to identify leaf rust resistance on 6D
and there is no currently known Pt QTLs on 6D that have originated from Ae. tauschii (Kalia,

88

2015). A synthetic RIL population consisting of two families U6708-03 and U6708-04
segregated for resistance to three different rust species with all three parents used in the
construction of this U6708 mapping population conferring disease resistance QTL.
Future Directions
The study described previously was successful in mapping seedling resistance to both Pgt
and Pst from 9.131.15x and identifying a Pt resistance QTL from KS05HW14. There are
currently two officially identified Pst seedling resistance genes on 4DS (Huang et al., 2011) and
one Pgt seedling resistance gene on 5BL (Bansal et al., 2015) that are at similar locations as
QYr.msu-4DS and QSr.msu-5BL according to molecular positions based on the IWGSC v1.0
reference genome (2014). Additional testing is required to determine if QYr.msu-4DS and
QSr.msu-5BL are novel resistance loci or variants of previously identified resistance genes.
Future work will involve using an allelism test to better determine the novelty of these QTLs.
Several lines from the U6708 population that are fixed for QSr.msu-5BL will be crossed to the
landrace Mahmoudi, the hexaploid which is the origin of Sr49 (Bansal et al., 2015), and lines
from U6708-03 fixed for QYr.msu-4DS will be crossed with the synthetic harboring the
YrAS2388 gene (Huang et al., 2011). The resulting F1 seeds will be taken to the F2 generation
and subsequently screened at the seedling stage for resistance with either Pst-37 or Pgt-QFCSC.
Segregation for resistance will be analyzed to better characterize the novelty of QYr.msu-4DS
and QSr.msu-5BL with respect to previously identified resistance genes.
The U6708 population was screened against Pst-37 and Pgt-QFCSC. However, with the
emergence of new virulent rust races, it is important to determine if these loci are effective
against the new highly virulent races like Pgt-TTTTF, Pgt-TTKSK, Pst-Warrior, and PstS2
races. RILs will be selected from the population to be sent to St. Paul, MN to be screened for

89

seedling resistance to these rust races in a biocontainment safety level 3 (BSL-3) facility (Jin et
al., 2007). If resistance is observed within the population to Pgt-TTKSK, lines may be sent to
Njoro, Kenya for additional phenotyping for APR in a disease screening nursery.
Additional screening of the U6708 experiment will be required to decipher the
segregating leaf rust resistance in this population. A seedling screen against the previously
identified leaf rust race in Mason, MI, Pt-MCTNB, will be performed to identify if the major
effect 3BL QTL is seedling resistance gene or an APR gene. Screening of KS05HW14 will need
to be performed to confirm that it displays a resistant phenotype to local leaf rust races.
The U6708 population segregated for resistance to three rust species: stem, stripe, and
leaf rust. Resistant lines from this population can be used in the Michigan State University
Wheat breeding program and eventually released as useful germplasm lines for the wheat
breeding community. There is a single RIL in the U6708-03 family that was phenotyped as
resistant to stem, stripe, and leaf rust in all environments (Table 3.1). This RIL contains the
QYr.msu-4DS, QSr.msu-5BL, QSr.msu-7DS.2, QLr.msu-3BL, and QLr.msu-6DL. This line would
be useful to incorporate into wheat breeding programs as a multiple disease resistance donor.

90

APPENDIX

91

APPENDIX

Table 3.1. Disease scores for a U6708-03 line that displays disease resistance to all three
Puccinia species tested in all environments.

92

Sup Fig. 3.1. Graphical genotypes of linkage groups containing resistance QTLs in
U6708-03-028. Blue colored intervals
contain KS05HW14 alleles, red colored intervals contain
LG17
9131.15x alleles, green intervals are heterozygous calls and black intervals are missing marker
data.
3B

0.0
0.5
1.5
1.9
2.6
3.5
4.0
4.3
4.6
4.9
5.1
5.3
5.5
5.7
6.1
6.3
6.9
7.8
8.1
8.3
9.4
9.9
10.1
10.8

S3B_14482106
S3B_15802938
S3B_17613580
S3B_16000571
S3B_18393918
S3B_17070378
S3B_16402517
S3B_17802909
S3B_18484734
S3B_17974253
S3B_17866567
S3B_18664529
S3B_17587960
S3B_19396724
S3B_18966637
S3B_19394721
S3B_18253325
S3B_23398620
S3B_23719942
S3B_23021423
S3B_24397727
S3B_25180892
S3B_24940723
S3B_25803185

17.3
17.9
18.5
19.1
19.4
19.9
20.0
20.6
21.1
21.3
22.3
22.8
23.9
24.3
24.6
25.8
26.0
26.7
28.4
28.6
29.0
29.2
30.0
31.3
31.7
32.4
33.2
33.7
34.5
35.2
35.5
35.7
36.0
38.6
38.7
38.8
39.0
39.2
39.3
39.5
39.6
39.8
40.0
40.1
40.3
40.4
40.5
40.6
40.9
41.1
41.2
41.4
42.0
45.4
45.9
46.5
46.9
47.1
48.4
48.8
49.7
50.7
51.3
51.6
51.9
52.3
52.6
53.1
53.6
54.0
54.4
55.6
56.6
58.2
58.5
61.4

S3B_31994039
S3B_29498643
S3B_31701487
S3B_31010542
S3B_31995430
S3B_31366808
S3B_30978492
S3B_31306132
S3B_32592979
9.7
S3B_34005391
S3B_34284104
S3B_37643852
S3B_65705378
S3B_221532616
S3B_49870546
11.4
S3B_44287903
S3B_45197605
S3B_738367733
S3B_65342485
S3B_54294716
12.7
S3B_115244542
S3B_59036362
S3B_207795625
13.7
S3B_64498113
S3B_126304477
S3B_136095746
S3B_157637296
S3B_241087014
S3B_222247201
0.0
S3B_206291972
S3B_241087084
S3B_246145297
S3B_250568343
S3B_561366011
S3B_562272668
S3B_567001229
S3B_565273183
S3B_577639496
S3B_573497145
2.0
S3B_566830710 S3B_565725179
S3B_577639587
2.4
S3B_580348857

0.0

S4D_1704666

4D

S4D_1242429

21.1

S4D_1999942

LG23 S4D_2828876

S3B_594745123
2.8
S3B_579446416 S3B_580784890
S3B_580521282
S3B_589561483 S3B_589458274
S3B_626712790
S3B_607406113
S3B_590623676
4.0
S3B_630398559
4.2
S3B_623654517
4.3
S3B_581268461 S3B_596232284
S3B_604416993
S3B_708013501
S3B_721046442
S3B_710167869
S3B_709533742
S3B_707906568
S3B_51062266
S3B_732436011
S3B_739510275
S3B_737607726
S3B_738504067 S3B_738504003
S3B_737442426
S3B_738110120
S3B_737639274
S3B_740106816
S3B_740547573
S3B_740133519
S3B_766364455
S3B_748448161
S3B_769535066
S3B_739923181
S3B_772467523
S3B_773565617
S3B_775659912
9.6
9.9

0.0
0.8
1.2
1.8
2.0
2.4
2.6
3.0
3.3
4.1
5.5
7.4
7.6
7.8
8.1
8.4
8.8
9.0
9.2
9.5
10.4
11.2
11.9
12.5
13.1
14.2
15.5
16.0
16.4
16.7
17.3
17.7
19.0
19.9
20.2
20.7
20.8
20.9

S4D_3238232

S5B_693686064

S5B_699422973
S5B_697831155
S5B_699728464 S5B_699407657
S5B_697611190 S5B_699455437

S5B_703233730
S5B_701519795
S5B_703229470

5B

S5B_711244784
S5B_710784650

22.1
22.9
24.4
24.5
24.7
24.9
25.0
25.3
25.6
25.9
26.1
26.8
27.5
27.9
28.2
28.3
28.4
28.9
29.5
29.7
29.9
30.1
30.2
30.7
31.0
31.2
31.6
33.0
33.5
34.4
36.1
36.4
37.2
37.3
37.7
38.3
38.7
39.0
39.2
39.7
40.1
40.3
41.0
41.3
41.6
42.4
42.7
43.9
44.8
45.3
45.8
46.7
47.6
47.8
49.2
50.0
50.2
50.7
50.9
51.3
52.1
52.7
52.9
53.2
53.3
53.7
54.1
54.7
56.7
59.8
60.3
61.3
62.1
62.7
63.5
64.8
65.1
65.6
68.2
68.7
68.9
69.3
70.2
70.7
71.7
72.4
72.7
73.4
74.3
75.5
78.1
78.3
79.8
80.0
80.9
81.3
81.6
82.0
82.9
83.0
83.7
84.4
84.5
84.6
85.1
85.2
85.5
85.6
85.7
85.9
86.3
86.5
86.8
86.9

S6D_12018199
S6D_12019189
S6D_12023993
S6D_12435877
S6D_12358606
S6D_13197345
S6D_13202325
S6D_13206838
S6D_13970695
S6D_13863766
S6D_33926349
S6D_15170081
S6D_14657290
S6D_15256175 S6D_15779113
S6D_15809407
S6D_17446940 S6D_16008076
S6D_16704893
S6D_16706514
S6D_17181122
S6D_19567917
S6D_22766557
S6D_23622322
S6D_80064974
S6D_26002250
S6D_25851509
S6D_26002274
S6D_27859416
S6D_27525812
S6D_28304138
S6D_30744756
S6D_28324147
S6D_29875372
S6D_53640739
S6D_33305189
S6D_34075504
S6D_37228815
S6D_37231315
S6D_36689837
S6D_54695381 S6D_42153457
S6D_53775029
S6D_51732906
S6D_54748293
S6D_351124936
S6D_70772794
S6D_65353137
S6D_67545931
S6D_68098967 S6D_65912199
S6D_81920593 S6D_79864250
S6D_82501332
S6D_77864626 S6D_83223948
S6D_81659451
S6D_101721161
S6D_109485496
S6D_98090181
S6D_98090252
S6D_101758490
S6D_102473339
S6D_121347763
S6D_132054396
S6D_132200523
S6D_137541139
S6D_135112843
S6D_132200911
S6D_173445362 S6D_207934182
S6D_291699332
S6D_291620586
S6D_241296319
S6D_305272917
S6D_351124932
S6D_324565245
S6D_350131401
S6D_347713271
S6D_372432436
S6D_364851010
S6D_381549747
S6D_391693326
S6D_392881561
S6D_397083937
S6D_400080086
S6D_400398852
S6D_411724906
S6D_412622083
S6D_406343375
S6D_406103601 S6D_407829580
S6D_405678645
S6D_415751919
S6D_414403571
S6D_429830688
S6D_429358398
S6D_431108774
S6D_428697773
S6D_429674940
S6D_431173308
S6D_431148615
S6D_432929380
S6D_434207907
S6D_435306317
S6D_435810167
S6D_434751489
S6D_435950336
S6D_435834479
S6D_436673680 S6D_436466074
S6D_436452770
S6D_436816070
S6D_437296228
S6D_436813800
S6D_436722115
S6D_438097245
S6D_438829921
S6D_445337359
S6D_445458196
S6D_446919153
S6D_446477307
S6D_446478084 S6D_445773103
S6D_447845104
S6D_448872056
S6D_449923131
S6D_448872117
S6D_451915018
S6D_452410589
S6D_452405960
S6D_452342253
S6D_452410667
S6D_453174642
S6D_452587154
S6D_455735643
S6D_455718701
S6D_455558727 S6D_455626507
S6D_466738586
S6D_463744870
S6D_460468252
S6D_460468308
S6D_461501885
S6D_462479366
S6D_463079592
S6D_461467572
S6D_456683425 S6D_463547451
S6D_462494601
S6D_464483328
S6D_463051540
S6D_464830674
S6D_467208090
S6D_467861477
S6D_467803310 S6D_467187468
S6D_467198574
S6D_468833640
S6D_469567355
S6D_469583807
S6D_469344492
S6D_469537865
S6D_468113435
S6D_470373596
S6D_471828200
S6D_472404065
S6D_472533683

6D

100.3

S6D_472369559

104.4

S6D_471330647

105.3

S6D_472103008

107.6

S6D_472073634

93

0.0
12.0
12.6
13.1
13.5
13.9
14.4
14.5
14.8
14.9
15.4
15.7
15.9
16.1
16.7
17.0
17.1
17.2
17.4
17.7
17.8
18.2
18.4
18.5
18.6
19.0
19.4
20.1
20.4
21.5
22.0
22.2
22.5
22.7
22.8
23.2
23.3
23.6
23.7
24.2
25.6
27.6
29.8
30.6
30.7
31.2
32.0
32.7
33.2
33.5
34.0
35.0
36.6
38.4
38.5
39.3
40.2
46.2
49.2
49.8
50.4
50.9
51.7
53.0
53.6
54.1
54.2
55.3
55.9
57.3
57.8
58.2
58.4
58.9
59.8
60.5
61.9
62.4
63.4
66.7
68.0
69.4
71.6
76.0
77.4
77.9
78.3
79.0
79.2
79.4
79.8
80.0
80.5
80.7
81.2
81.7
82.2
83.0
83.3
83.5
84.0
84.7
85.2
85.4
85.5
85.8
86.1
86.2
86.6
86.8
88.1
88.6
89.7
90.1

S7D_5653553
S7D_59105969
S7D_58491641
S7D_60279204
S7D_60217671
S7D_60459462
S7D_62120178
S7D_61757302
S7D_62120102
S7D_64236500
S7D_61188004
S7D_64379914
S7D_63453715
S7D_63471298
S7D_65592365
S7D_65617305
S7D_65715714
S7D_65752952
S7D_68518279
S7D_68431283
S7D_71569531
S7D_74060422 S7D_72699333
S7D_75136077
S7D_72452170
S7D_75271662
S7D_74963530
S7D_72808182
S7D_73153208
S7D_72699287
S7D_78193178
S7D_80264777
S7D_78672632
S7D_79299360
S7D_83426451
S7D_80294908
S7D_83376988
S7D_83666746
S7D_83666851
S7D_83473595
S7D_80292147
S7D_92604251
S7D_101557747
S7D_504011403
S7D_502232313
S7D_502232988 S7D_505129726
S7D_507848669
S7D_519112634
S7D_576703863
S7D_576735344
S7D_89733085
S7D_393456338
S7D_577782004
S7D_579634283
S7D_580379374
S7D_70048992
S7D_579361833
S7D_579085646
S7D_588085500
S7D_592223121
S7D_592632637
S7D_592632581
S7D_592392427
S7D_595068840
S7D_595528770
S7D_597019065 S7D_595613399
S7D_596434245
S7D_597118932
S7D_600837544
S7D_599115002
S7D_601070723
S7D_601781609
S7D_601904143
S7D_601071069
S7D_601487305
S7D_602197236
S7D_603678242
S7D_605596128
S7D_604869757
S7D_605744448
S7D_611014718
S7D_610740232
S7D_610739554
S7D_623403351
S7D_619996988
S7D_620622222
S7D_620283090
S7D_621951204
S7D_620924768
S7D_621212944
S7D_621155254
S7D_623068416
S7D_626481419
S7D_627295271
S7D_626927234
S7D_626950802
S7D_627411185
S7D_627569993
S7D_629311395
S7D_628521992
S7D_629311461
S7D_630196200
S7D_630440805
S7D_632509242
S7D_631758106
S7D_632648460
S7D_631681105 S7D_631922149
S7D_638440265
S7D_635844631
S7D_632593226
S7D_638208446
S7D_632802365
S7D_638541382
S7D_631978910
S7D_634562548

7D

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94

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