Genetic Diversity, Linkage Disequilibrium and Population Structure of Bulgarian Bread Wheat Assessed by Genome-Wide Distributed SNP Markers: From Old Germplasm to Semi-Dwarf Cultivars

Abstract

Genetic diversity and population structure are key resources for breeding purposes and genetic studies of important agronomic traits in crops. In this study, we described SNP-based genetic diversity, linkage disequilibrium and population structure in a panel of 179 bread wheat advanced cultivars and old accessions from Bulgaria, using an optimized wheat 25K Infinium iSelect array. Out of 19,019 polymorphic SNPs, 17,968 had а known chromosome position on the A (41%), B (42%) and D (11%) genome, and 6% were not assigned to any chromosome. Homoeologous group 4, in particular chromosome 4D, was the least polymorphic. In the total population, the Nei's gene diversity was within the range 0.1-0.5, and the polymorphism information content ranged from 0.1 to 0.4. Significant differences between the old and modern collections were revealed with respect to the linkage disequilibrium (LD): the average values for LD (r²), the percentage of the locus pairs in LD and the LD decay were 0.64, 16% and 3.3 for the old germplasm, and 0.43, 30% and 4.1 for the modern releases, respectively. Structure and k-means clustering algorithm divided the panel into three groups. The old accessions formed a distinct subpopulation. The cluster analysis further distinguished the modern releases according to the geographic region and genealogy. Gene exchange was evidenced mainly between the subpopulations of contemporary cultivars. The achieved understanding of the genetic diversity and structure of the Bulgarian wheat population and distinctiveness of the old germplasm could be of interest for breeders developing cultivars with improved characteristics. The obtained knowledge about SNP informativeness and the LD estimation are worthwhile for selecting markers and for considering the composition of a population in association mapping studies of traits of interest.

Keywords: SNP markers; bread wheat; genetic diversity; linkage disequilibrium; modern cultivars; old germplasm; population structure.

Figure 1

Distribution of Nei’s gene diversity (GD) (A) and polymorphism information content (PIC) (B) for 19,019 polymorphic SNP markers within a population of 179 old and modern Bulgarian bread wheat accessions.

Figure 2

Distribution of SNP markers along the A, B and D genomes within a population of 179 old and modern Bulgarian bread wheat accessions.

Figure 3

Distribution (A) and density (B) of SNP markers along the wheat chromosomes within a population of 179 old and modern Bulgarian bread wheat accessions.

Figure 4

Genetic structure of Bulgarian old and modern bread wheat accessions. (A) Estimation of the optimal number of clusters, defined by the Evanno method. (B) Inferred structure of a panel of 179 accessions. Each individual is represented by a colored bar with a length proportional to the estimated membership to each of the three clusters. (C) Plots in right depict the clusters as separate subpopulations (SPs): SP1 (109 accessions); SP2 (49 accessions); SP3 (16 accessions) and 5 were admixed.

Figure 5

A neighbor-joining dendrogram is inferred by the k-means clustering algorithm. Correspondence with SPs, obtained by STRUCTURE: the largest cluster (blue) corresponds to SP1; the green cluster corresponds to SP2 and the red cluster corresponds to SP3.

Figure 6

Distribution of old (A) and modern (B) accessions depending on their assignment to the STRUCTURE subpopulations (SPs). Distribution of old (C) and modern (D) accessions according to the geographic origin—breeding centre/collection site (N, Northern; S, Southern; W, Western part of Bulgaria).

Figure 7

Principal component analysis (PCA) of 179 Bulgarian bread wheat accessions. (A) Differentiation between old and modern accessions; (B) Differentiation between accessions according to the region of breeding or collection site.