The USDA barley core collection: genetic diversity, population structure, and potential for genome-wide association studies

PLoS One. 2014 Apr 14;9(4):e94688. doi: 10.1371/journal.pone.0094688. eCollection 2014.


New sources of genetic diversity must be incorporated into plant breeding programs if they are to continue increasing grain yield and quality, and tolerance to abiotic and biotic stresses. Germplasm collections provide a source of genetic and phenotypic diversity, but characterization of these resources is required to increase their utility for breeding programs. We used a barley SNP iSelect platform with 7,842 SNPs to genotype 2,417 barley accessions sampled from the USDA National Small Grains Collection of 33,176 accessions. Most of the accessions in this core collection are categorized as landraces or cultivars/breeding lines and were obtained from more than 100 countries. Both STRUCTURE and principal component analysis identified five major subpopulations within the core collection, mainly differentiated by geographical origin and spike row number (an inflorescence architecture trait). Different patterns of linkage disequilibrium (LD) were found across the barley genome and many regions of high LD contained traits involved in domestication and breeding selection. The genotype data were used to define 'mini-core' sets of accessions capturing the majority of the allelic diversity present in the core collection. These 'mini-core' sets can be used for evaluating traits that are difficult or expensive to score. Genome-wide association studies (GWAS) of 'hull cover', 'spike row number', and 'heading date' demonstrate the utility of the core collection for locating genetic factors determining important phenotypes. The GWAS results were referenced to a new barley consensus map containing 5,665 SNPs. Our results demonstrate that GWAS and high-density SNP genotyping are effective tools for plant breeders interested in accessing genetic diversity in large germplasm collections.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Agriculture / methods
  • Alleles
  • Chromosome Mapping
  • Genes, Plant
  • Genetic Association Studies
  • Genetic Variation*
  • Genotype
  • Geography
  • Hordeum / genetics*
  • Linkage Disequilibrium
  • Models, Statistical
  • Multigene Family
  • Phenotype
  • Polymorphism, Single Nucleotide
  • Principal Component Analysis
  • United States
  • United States Department of Agriculture