The USDA Barley Core Collection: Genetic Diversity, Population Structure, and Potential for Genome-Wide Association Studies

Abstract

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.

Genome-wide SNP discovery and population structure analysis in pepper (Capsicum annuum) using genotyping by sequencing

“…In pepper, a small number of core collections are already developed and published based on phenotypic traits and cluster analysis [56, 66]. We have established a collection of cultivated pepper, using GBS data, confirming that genotyping by sequencing can be used to accurately estimate diversity in more diverse sets of germplasm [67]. …”

Development and Genetic Characterization of an Advanced Backcross-Nested Association Mapping (AB-NAM) Population of Wild × Cultivated Barley

“…To determine whether it is appropriate to apply the previously developed genetic maps to this population, we compared the recombination frequency across the genome in the AB-NAM with the iSelect consensus map (Muñoz-Amatriaín et al 2014). When the AB-NAM recombination events were binned in 10-cM intervals, we observed no areas of the genome where recombination frequency was substantially different from the genome-wide average of 67.1 recombination events per 10 cM ( Figure S2).…”

“…When the markers indicated a recombination event, the imputed marker was given a value between 0 and 1, as a function of the genetic distance between the imputed marker and each of the two flanking markers. The iSelect consensus map (Muñoz-Amatriaín et al 2014) and the POPSEQ Morex 3 Barke sequence contig map (Mascher et al 2013b) were used to impute scores for iSelect and exome capture markers, respectively. …”

“…No other regions of the genome show reduced introgression frequency, but regions on chromosomes 1H and 6H show an overrepresentation of wild barley introgression across the population. Notably, vrs3, a known determinant of spike morphology, is located in the region of chromosome 1H that has an overrepresentation of wild barley introgression (Muñoz-Amatriaín et al 2014). The vrs3 phenotype appears six-rowed Figure 4 Manhattan plots of marker-trait associations.…”

HvDep1 Is a Positive Regulator of Culm Elongation and Grain Size in Barley and Impacts Yield in an Environment-Dependent Manner

“…Barley grains are widely used as animal feed and are the major raw material for the malting and brewing industries. In several geographical regions, barley is used for human consumption, and due to its health benefits in human diets, the interest of using barley as food is increasing, especially in the western world [3]. …”