Genomic Characterization of Domestication and Genome-Wide LD in Beet

The genetic diversity of a worldwide beet population containing 2035 accessions was analyzed using four different approaches. Three of the methods gave a very coherent picture of the population structure. Fodder beet and sugar beet accessions were grouped together, separated from garden beets and sea beets, reflecting well the origins of beet domestication. Then, linkage disequilibrium (LD) of this worldwide population was compared to the LD of one set of 1338 elite sugar beet lines. The usual measure (r²) was used, and compared with others that correct for population structure and relatedness (r_S², r_V², r_VS²). The LD as measured by r² persisted beyond 10 cM within the elite panel and fell below 0.1 after less than 2 cM in the worldwide population, for almost all chromosomes. With correction for relatedness, LD decreased under 0.1 by 1 cM for almost all chromosomes in both populations, except for chromosomes 3 and 9 within the elite panel. In these regions, the larger extent of LD could be explained by strong selection pressure.