Title: The USDA collection of barley landraces and cultivars: genetic diversity, population structure, and potential for genome-wide association studies Authors
|Munoz-Amatrian, M -|
|Cuesta-Marcos, A -|
|Endelman, J -|
|Comadran, J -|
|Russell, J -|
|Waugh, R -|
|Hayes, P -|
|Muehlbauer, G -|
Submitted to: PLoS One
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: March 18, 2014
Publication Date: April 14, 2014
Citation: Munoz-Amatrian, M., Cuesta-Marcos, A., Endelman, J.B., Comadran, J., Bonman, J.M., Bockelman, H.E., Chao, S., Russell, J., Waugh, R., Hayes, P.M., Muehlbauer, G.J. 2014. The USDA collection of barley landraces and cultivars: genetic diversity, population structure, and potential for genome-wide association studies. PLoS One. 9(4):394688. doi:10.137/journal.pone.0094688. Interpretive Summary: Collections of plant germplasm, such as the National Small Grains Collection (NSGC), are vital sources of genetic diversity for plant breeding. Such diversity is needed to develop new, high quality, high yielding cultivars for US agriculture. Using thousands of newly available molecular markers for barley called ‘SNPs’, we analyzed a subset of the NSGC barley collection. The subset, or Core, was comprised of barley accessions originating from more than 100 countries. We used the SNP results to designate ‘mini-core’ sets of accessions that will be useful for evaluating traits that are difficult or expensive to score. We also demonstrated the utility of the Core for discovering the genetic basis of traits with a technique known as genome wide association mapping (GWAS). Our results will enable plant breeders to more effectively use accessions from the NSGC for barley improvement.
Technical Abstract: New sources of genetic diversity must to 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 the 9K-SNP iSelect platform to genotype 2,417 barley accessions sampled from the USDA National Small Grains Collection of 29,838 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). Distinct patterns of linkage disequilibrium were found in each of the subpopulations. 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.