Analysis of molecular diversity, population structure and linkage disequilibrium in a worldwide survey of cultivated barley germplasm (Hordeum vulgare L.)

Abstract

Background: The goal of our study was a systematic survey of the molecular diversity in barley genetic resources. To this end 953 cultivated barley accessions originating from all inhabited continents except Australia were genotyped with 48 SSR markers. Molecular diversity was evaluated with routine statistics (allelic richness, gene diversity, allele frequency, heterozygosity and unique alleles), Principal Coordinate Analysis (PCoA), and analysis of genome-wide linkage disequilibrium.

Results: A genotyping database for 953 cultivated barley accessions profiled with 48 SSR markers was established. The PCoA revealed structuring of the barley population with regard to (i) geographical regions and (ii) agronomic traits. Geographic origin contributed most to the observed molecular diversity. Genome-wide linkage disequilibrium (LD) was estimated as squared correlation of allele frequencies (r2). The values of LD for barley were comparable to other plant species (conifers, poplar, maize). The pattern of intrachromosomal LD with distances between the genomic loci ranging from 1 to 150 cM revealed that in barley LD extended up to distances as long as 50 cM with r2 > 0.05, or up to 10 cM with r2 > 0.2. Few loci mapping to different chromosomes showed significant LD with r2 > 0.05. The number of loci in significant LD as well as the pattern of LD were clearly dependent on the population structure. The LD in the homogenous group of 207 European 2-rowed spring barleys compared to the highly structured worldwide barley population was increased in the number of loci pairs with r2 > 0.05 and had higher values of r2, although the percentage of intrachromosomal loci pairs in significant LD based on P < 0.001 was 100% in the whole set of varieties, but only 45% in the subgroup of European 2-rowed spring barleys. The value of LD also varied depending on the polymorphism of the loci selected for genotyping. The 17 most polymorphic loci (PIC > 0.80) provided higher LD values as compared to 19 low polymorphic loci (PIC < 0.73) in both structured (all accessions) and non-structured (European 2-rowed spring varieties) barley populations.

Conclusion: A global population of cultivated barley accessions was highly structured. Clustering highlighted the accessions with the same geographic origin, as well as accessions possessing similar agronomic characters. LD in barley extended up to 50 cM, and was strongly dependent on the population structure. The data on LD were summarized as a genome-wide LD map for barley.

Figure 1

Structure of heterogeneity detected in 953 barley accessions. The columns represent heterogeneity in 565 European accessions (in grey) and in 388 accessions from other geographic regions (in white).

Figure 2

Principal Coordinate Analysis of the global population of 953 barley accessions. Each scatterplot presents clustering of the complete set of 953 accessions with highlighted accessions (I) originating from one geographic region, or (II) possessing a defined agronomic trait. Ia – Europe (Eu), Ib – Asia (A), Ic – Africa (F), Id – Near East (E), Ie – America (M), IIa – 2-rowed accessions (2), IIb – 6-rowed accessions (6), IIc – spring accessions (S), IId – winter accessions (W). III – Distinct clusters of European 2-rowed spring accessions (2S), 2-rowed winter accessions (2W), and 6-rowed winter accessions (6W).

Figure 3

Genome-wide map of intrachromosomal linkage disequilibrium in barley evaluated with 48 SSR loci. Each cell represents r²-values for intrachromosomal loci pairs. The loci are arranged on the X- and Y-axis according to their mapping position, the order is the same as in the Table 2. White cells indicate r² < 0.05. Coloured cells indicate r² > 0.05 for the worldwide population (red), European 2-rowed spring barleys (green), and common between the two populations (blue). A yellow frame indicates r² > 0.1.

Figure 4

The pattern of LD for 48 SSR loci in dependence on the population structure. Plots of LD represented by r² against genetic distance (in centiMorgan) in the global population of 953 accesions (a), 565 European accessions (b), 207 European 2-rowed spring accessions (c), and in the random set of 200 accessions (d). Pairs of loci mapped to different chromosomes were assigned to 200 cM.

Figure 5

The pattern of LD evaluated for highly polymorphic and low polymorphic SSR loci. I – Plots of LD represented by r² against genetic distance for 17 highly polymorphic intrachromosomal pairs of loci in the global population of 953 accesions (a), and in 207 European 2-rowed spring accessions (b). II – Plots of LD against genetic distance for 19 low polymorphic pairs of loci in the global population of 953 accesions (a), and in 207 European 2-rowed spring accessions (b).

Figure 6

Dependence of LD on gene diversity (PIC) and population structure. Plots of LD represented by r² against the sum of PIC values in the global population of 953 accesions (blue), and in 207 European 2-rowed spring accessions (pink). Only intrachromosomal pairs of loci with r² > 0.05 at P < 0.001 level were evaluated.

Figure 7

Dynamics of the allelic richness in dependence on the number of investigated accessions. The curves represent: – Near East, – Asia, – Africa, – America, – Europe.

Figure 8

Schematic presentation of the mapped SSR loci on seven barley chromosomes.