GENOME BIOLOGY OF THE CULTIVATED POTATO, SOLANUM TUBEROSUM
Cultivated potato is a highly heterozygous, clonally propagated autotetraploid. These traits make it a difficult crop to study and make genetic improvements. In the following dissertation, I present studies that aim to improve our knowledge of genetic complexity in potato and potato breeding strategies. First, I show that several thousand genes in cultivated potato varieties show evidence of preferential allele expression, a characteristic not expected for autotetraploids. This trend was observed in evolutionarily conserved genes, suggesting that cultivated potato may have preferential expression of functional alleles. Cultivated potato also has excessive copy number variation. The results indicate that ~16-18,000 genes are copy number variable, and are evolutionarily recent and related to adaptation to biotic and abiotic stress. They are also lowly expressed, with only 528 genes showing correlation between copy number and gene expression. Second, a common method of genome reduction in potato, interspecific crossing, is explored to determine possible mechanisms by which genome elimination occurs and somaclonal variation which arises during the process. The results show that haploid inducer line, IVP101, produces <1% somatic translocation event frequency in the Superior dihaploid population studied. The translocation events occurred in regions of open chromatin, suggesting that they may be driven by transcription-coupled DNA repair. Finally, I present an improved potato genome assembly and annotation using a combination of long-read sequencing methods. The new assembly, DM v.5, is 727 Mb, of which 91% is contained in 12 chromosome-scale scaffolds. DM v.5 presents a new opportunity for studies in comparative genomics and potato biology.
Read
- In Collections
-
Electronic Theses & Dissertations
- Copyright Status
- In Copyright
- Material Type
-
Theses
- Authors
-
Pham, Gina Mai
- Thesis Advisors
-
Buell, Carol R.
- Committee Members
-
Douches, David S.
Jiang, Ning
Shiu, Shin-Han
- Date
- 2019
- Program of Study
-
Plant Biology - Doctor of Philosophy
- Degree Level
-
Doctoral
- Language
-
English
- Pages
- 58 pages