Genetic diversity, population structure, and linkage disequilibrium in elite sugar beet germplasm

Characterization of population structure and genetic diversity of germplasm is of importance for organization of breeding material and association mapping. The objectives of this study were to (i) explore the patterns of population structure, (ii) investigate the genome-wide distribution of genetic diversity, and (iii) assess the extent and genome-wide distribution of linkage disequilibrium (LD) in sugar beet. Two panels with 111 and 178 inbreds from the seed and pollen parent (SP and PP) heterotic pools assessed with SSR markers, and 264 and 238 inbreds from the yield and sugar types of the PP pool assessed with SNP markers, were used in this study. Two distinct subgroups corresponding to the SP and PP pools were detected within the former panel. Moreover, two distinct subgroups corresponding to yield and sugar types were detected within the latter panel. These observations indicated that the artificial selection during the breeding process lead to strongly differentiated populations. MCLUST based on principal components, principal coordinates, or lapvectors had high correspondence with the germplasm type information as well as the assignment by STRUCTURE, indicating that these methods might be alternatives to STRUCTURE for population structure analysis. Signatures of selection were revealed by genome-wide screens of gene diversity and modified Roger’s distance between the yield and sugar type genotypes, suggesting its potential use in identifying candidate genes for the traits under selection. Information about the genome-wide distribution of LD provided the basis for designing SNP genotyping arrays for genome-wide association mapping.