Dataset Information

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

ABSTRACT: 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.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.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.

SUBMITTER: Xu Q

PROVIDER: S-EPMC5717800 | biostudies-literature | 2017 Dec

REPOSITORIES: biostudies-literature

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

Xu Qijun Q Zeng Xingquan X Lin Bin B Li Zeqing Z Yuan Hongjun H Wang Yulin Y Zhasang Tashi Nyima N

BMC genetics 20171206 1

<h4>Background</h4>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.<h4>Results</h4>In the present study, we collected 562 hulless barley (Hordeum vulgare L.) accessions with worldwide geographic origins and evaluated their genetic variability and relatedness base ...[more]

PMID: 29207956

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Project description:The entire collection of cultivated barley germplasm accessions conserved in the Indian National Genebank (INGB) was characterized for nine qualitative and 8 quantitative traits to assess the nature and magnitude of prevailing genetic variability and to develop a core set. A wide range of variability was observed for days to spike emergence (51-139 days), days to physiological maturity (100-152 days), plant height (45.96-171.32 cm), spike length (3.44-13.73 cm), grain number/spike (10.48-82.35), and 100-grain weight (1.20-6.86 g). Initially, seven independent core sets were derived using 3 core construction tools- MSTRAT, PowerCore, and Core Hunter 3 by employing the maximization method, heuristic sampling, and optimisation of average genetic distances, respectively. The core set-3 generated by Core Hunter 3 by simultaneous optimisation of diversity and representativeness, captured maximum genetic diversity of the whole collection as evident from the desirable genetic distance, variance difference percentage (VD; 87.5%), coincidence rate of range (CR; 94.27%) and variable rate of coefficient of variance (VR; 113.8%), which were more than threshold value of VD (80%), CR (80%), and VR (100%) required for good core collection. The coefficient of variation and Shannon-Weaver diversity indices were increased in the core set as compared with the whole collection. The low value of Kullback-Leibler distance (0.024-0.071) for all traits and quantile-quantile plots revealed a negligible difference between trait distribution patterns among the core set and entire assembly. Correlogram revealed that trait associations and their magnitude were conserved for most of the traits after sampling of the core set. The extraction of the INGB barley core set and identification of promising accessions for agronomically important traits in different genetic backgrounds will pave the way for expedited access to genetically diverse and agronomically important germplasm for barley breeding.

Project description: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.

Dataset Information

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

Publications

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

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