A microsatellite diversity analysis and the development of core-set germplasm in a large hulless barley (Hordeum vulgare L.) collection

Abstract

Background: Clarifying genetic diversity in a large germplasm resource plays important roles in experimental designs that provides flexible utility in fundamental research and breeding in crops. However, the work is limited due to small collections of barley that are insufficient representatives.

Results: In the present study, we collected 562 hulless barley (Hordeum vulgare L.) accessions with worldwide geographic origins and evaluated their genetic variability and relatedness based on 93 simple sequence repeat (SSR) markers. In an integrated analysis of the population structure, analysis of molecular variance (AMOVA) and pairwise F _ST, the 562 barley accessions exhibited a strong stratification that allowed for them to be divided into two major subpopulations (p1 and p2) and an admixture subpopulation, with 93, 408 and 61 accessions, respectively. In a neutral test, considerable proportions of SSR alleles expressed the strong non-neutrality in specific subpopulations (44 and 37), which are probably responsible for population differentiation. To reduce the diversity redundancy in large barley collections, we delicately selected a core set of 200 barley accessions as a tradeoff between diversity and representativeness in an easily handled population. In comparing the 562 barley accessions, the core barley set accounted for 96.2% of allelic diversity and 93% to 95% of phenotypic variability, whereas it exhibited a significant enhancement in minor allelic frequencies, which probably benefit association mapping in the barley core set.

Conclusions: The results provided additional insight into the genetic structure in a large barley germplasm resource, from which an easily manageable barley core set was identified, demonstrating the great potential for discovering key QTLs and ultimately facilitating barley breeding progress.

Keywords: Association mapping; Core germplasm; Genetic diversity; Hulless barley; Population structure.

Fig. 1

Geographic coordinates, phylogenic and principal component analyses of the 562 hulless barley accessions. a Colored dots refer to the sampling regions of the barley accessions, while the color gradient corresponds to the number of accessions sampled in each region. b All 562 barley accessions were clustered into two apparent clades, colored red and blue, based on the structural analysis. c The first two principal components (PC) explained over 10% of the molecular variance and discriminated the whole population into three groups, which is largely consistent with the subpopulations inferred by structural analysis

Fig. 2

Genetic differentiation between the subpopulations was revealed by the neutrality analysis. The number labeled within the different sections of the Venn-plot represent the number of microsatellite alleles that showed significantly non-neutral frequency in specific subpopulations or shared between subpopulations

Fig. 3

Diversity analysis of the assembled barley core set. The barley core set of 200 accessions was mathematically selected from all 562 accessions using the R package ‘corehunter’. a The selected barley core set captured 499 microsatellite alleles accounting for 96.7% of the alleles harbored in the 562 accessions, which is significantly more than the 200 random accessions. b Gene diversity of the core set averaged across the SSR primers. It is significantly higher than the raw 562 accessions and 200 random accessions, which is probably due to the high allele maintenance and balanced allelic frequency in the core set. c Comparison of the Nei1972 distance for accession pairs between the barley core set and raw set; d The alleles captured by accession per se (left panel), gene diversity per SSR (middle panel) and minor allele frequency (MAF) of the alleles (right panel) for each subpopulation and whole population in the core (200 accessions) and raw (562 accessions) sets