Genetic diversity, population structure and linkage disequilibrium in elite Chinese winter wheat investigated with SSR markers

Abstract

To ascertain genetic diversity, population structure and linkage disequilibrium (LD) among a representative collection of Chinese winter wheat cultivars and lines, 90 winter wheat accessions were analyzed with 269 SSR markers distributed throughout the wheat genome. A total of 1,358 alleles were detected, with 2 to 10 alleles per locus and a mean genetic richness of 5.05. The average genetic diversity index was 0.60, with values ranging from 0.05 to 0.86. Of the three genomes of wheat, ANOVA revealed that the B genome had the highest genetic diversity (0.63) and the D genome the lowest (0.56); significant differences were observed between these two genomes (P<0.01). The 90 Chinese winter wheat accessions could be divided into three subgroups based on STRUCTURE, UPGMA cluster and principal coordinate analyses. The population structure derived from STRUCTURE clustering was positively correlated to some extent with geographic eco-type. LD analysis revealed that there was a shorter LD decay distance in Chinese winter wheat compared with other wheat germplasm collections. The maximum LD decay distance, estimated by curvilinear regression, was 17.4 cM (r(2)>0.1), with a whole genome LD decay distance of approximately 2.2 cM (r(2)>0.1, P<0.001). Evidence from genetic diversity analyses suggest that wheat germplasm from other countries should be introduced into Chinese winter wheat and distant hybridization should be adopted to create new wheat germplasm with increased genetic diversity. The results of this study should provide valuable information for future association mapping using this Chinese winter wheat collection.

Figure 1. Scatter plot of gene diversity vs. number of alleles per locus.

Figure 2. STRUCTURE estimation of the number of populations for K ranging from 1 to 12 by delta K values (

ΔK).

Figure 3. Three subgroups inferred from STRUCTURE analysis.

The vertical coordinate of each subgroup indicates the membership coefficients for each individual, and the digits on the horizontal coordinate represent the accessions corresponding to Table S1. Red zone: SG 1; Green zone: SG 2; Blue zone: SG 3. The colored spots represent the geographic eco-type information of accessions. Red spot: cultivars from northern winter wheat region; Green spot: cultivars from Huang-huai winter wheat region; Blue spot: landraces and introduced germplasm; Purple spot: cultivars from Southwestern winter wheat region; Black spot: cultivars from Yangtze River winter wheat region.

Figure 4. Dendrogram of 90 Chinese winter wheat accessions by UPGMA cluster analysis.

SG 1, SG 2 and SG 3 are the three subgroups identified by STRUCTURE assigned with the maximum membership probability. The different colored lines represent the three subgroups inferred by STRUCTURE analysis. The different colored spots represent the geographic eco-types of accessions.

Figure 5. Principal coordinate analysis of 90 Chinese wheat winter accessions based on 269 SSR markers.

SG 1, SG 2 and SG 3 are the three subgroups identified by STRUCTURE assigned with the maximum membership probability. The different colored spots represent the geographic eco-types of accessions.

Figure 6. Scatter plot of significant r² values and genetic distance (cM) (P<0.001) of locus pairs on A, B, D and whole genomes in Chinese winter wheat.