Cultivated Beta vulgaris L. (beet) is a species complex composed of several distinct crop types developed for specific end uses. The crop types include sugar beet, fodder beet, table beet and leaf beet/chard. The evolution of each crop type appears to have resulted from interactions between selection, drift, gene flow, recombination, and the sorting of ancestral variation. Beets are generally heterozygous and contain self-incompatibility mechanisms. Therefore, reproducing and maintaining the genetic constitution of a single individual for genetic and phenotypic analysis is a challenge. Beet populations are the fundamental unit of improvement and contain the evolutionary and adaptive potential of the species. This research used several approaches which explore the utility of pooled population genomic sequencing to survey the organization and distribution of genetic diversity within cultivated B. vulgaris lineages, and give context and clarity to the genetics underlying important agronomic characters.Whole genome sequence data was produced for important varieties and germplasm releases which represent the B. vulgaris crop type lineages. Using population genetic and statistical methods, relationships were determined between populations. Lineage-specific variation, or variation unique to specific crop types, was uncovered and used to quantify the level of support for these groups as discrete units. Allele frequency was able to differentiate between crop types using Principle Components Analysis (PCA), suggesting positive selection for end use was a major driver of crop type divergence. PCA carried out on a chromosome-by-chromosome basis showed the relative contributions of specific chromosomes to crop type diversification. Gene diversity (e.g., expected heterozygosity) and FST proved powerful indicators of selection along the chromosome at nucleotide resolution. In total, 12.13% of loci within the genome were differentiated with respect to crop type. Interestingly, this corresponds to levels of divergence observed in studies of incipient speciation. Differentiated regions, indicated by FST outliers, contained 472 genes, or 1.6% of the 24,255 genes predicted in the reference genome assembly. Respectively, sugar beet, table beet, fodder beet, and chard genomes contained 16, 283, 2, and 171 genes characterized as differentiated between crop types. Cryptic relationships were observed between crop types due to a high degree of genetic variation shared between crop type lineages. Specific instances of common ancestry, sorting of ancestral variation, and admixture and introgression were identified, which explain the degree of substructure observed between specific crop types.The content and organization of diversity in beet genomes reflects a complex history related to B. vulgaris crop type diversification. With the exception of chard, much of the species' historical selection has focused on the improvement of root characters (e.g., root enlargement, biomass, dry matter content, and sucrose concentration). As a result, major differences in root morphology and physiology can be observed between these lineages. Measures of root development and physiology between crop types were compared, and interestingly, much of the phenotypic variation partitioned between crop types corresponds to candidate genes identified from analyses of genome-wide variation using FST and 2pq. Admixture and introgression appear to have shared specific variation involved in the reduction of lateral roots (e.g., Root primordium defective 1), root enlargement (e.g., Brevis radix-like 4, putative NAC domain-containing protein 94, cytokinin dehydrogenase 3), and biomass accumulation (e.g., 6-phosphofructo-2-kinase). High relationship coefficients and high correlations in allele frequency for this variation were observed, indicating the genetic variation influencing these characters may have been derived from a single origin. The development of beet into an economically viable sugar crop required both an enlarged root and an increase sucrose concentration. Genes were identified that may explain these physiological changes within the root (e.g., decrease in water concentration, increase in dry matter content and increase in sucrose concentrations). These genes correspond to shared variation, distributed among crop types, as well as lineage-specific variation, restricted to sugar beet lineages. Integrating selection, drift, and admixture into a putative demographic history of beet provides evidence for the role of specific genes in the development of beet crop types and the expression of novel phenotypic characters.
Read
