title: 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.
authors.affiliation: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, United States of America.
authors.forename: María
authors.initials: M
authors.lastname: Muñoz-Amatriaín
authors.affiliation: Department of Crop and Soil Science, Oregon State University, Corvallis, Oregon, United States of America.
authors.forename: Alfonso
authors.initials: A
authors.lastname: Cuesta-Marcos
authors.affiliation: Department of Horticulture, University of Wisconsin, Madison, Wisconsin, United States of America.
authors.forename: Jeffrey B
authors.initials: JB
authors.lastname: Endelman
authors.affiliation: The James Hutton Institute, Invergowrie, Dundee, United Kingdom.
authors.forename: Jordi
authors.initials: J
authors.lastname: Comadran
authors.affiliation: USDA-ARS, Small Grains and Potato Germplasm Research Unit, Aberdeen, Idaho, United States of America.
authors.forename: John M
authors.initials: JM
authors.lastname: Bonman
authors.affiliation: USDA-ARS, Small Grains and Potato Germplasm Research Unit, Aberdeen, Idaho, United States of America.
authors.forename: Harold E
authors.initials: HE
authors.lastname: Bockelman
authors.affiliation: USDA-ARS, Biosciences Research Lab, Fargo, North Dakota, United States of America.
authors.forename: Shiaoman
authors.initials: S
authors.lastname: Chao
authors.affiliation: The James Hutton Institute, Invergowrie, Dundee, United Kingdom.
authors.forename: Joanne
authors.initials: J
authors.lastname: Russell
authors.affiliation: The James Hutton Institute, Invergowrie, Dundee, United Kingdom.
authors.forename: Robbie
authors.initials: R
authors.lastname: Waugh
authors.affiliation: Department of Crop and Soil Science, Oregon State University, Corvallis, Oregon, United States of America.
authors.forename: Patrick M
authors.initials: PM
authors.lastname: Hayes
authors.affiliation: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, United States of America; Department of Plant Biology, University of Minnesota, St. Paul, Minnesota, United States of America.
authors.forename: Gary J
authors.initials: GJ
authors.lastname: Muehlbauer
mesh_terms: D000383:Agriculture / Q000379:methods; D000483:Alleles; D002874:Chromosome Mapping; D017343:Genes, Plant; D056726:Genetic Association Studies; D014644:Genetic Variation; D005838:Genotype; D005843:Geography; D001467:Hordeum / Q000235:genetics*; D015810:Linkage Disequilibrium; D015233:Models, Statistical; D005810:Multigene Family; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D025341:Principal Component Analysis; D014481:United States; D016885:United States Department of Agriculture
references.citation: BMC Genomics. 2009 Dec 04;10:582
references.pmid: 19961604
references.citation: Mol Ecol. 2005 Jul;14(8):2611-20
references.pmid: 15969739
references.citation: BMC Genomics. 2010 Dec 15;11:707
references.pmid: 21159198
references.citation: PLoS One. 2012;7(2):e32253
references.pmid: 22389690
references.citation: Bioinformatics. 2014 Jun 1;30(11):1623-4
references.pmid: 24532720
references.citation: Plant Physiol. 2008 May;147(1):355-66
references.pmid: 18359843
references.citation: Proc Natl Acad Sci U S A. 2003 May 13;100(10):6263-8
references.pmid: 12730378
references.citation: Mol Biol Evol. 2000 Apr;17(4):499-510
references.pmid: 10742042
references.citation: Nat Genet. 2011 Feb;43(2):169-72
references.pmid: 21217754
references.citation: Curr Opin Plant Biol. 2010 Apr;13(2):167-73
references.pmid: 20167531
references.citation: J Zhejiang Univ Sci B. 2012 Jun;13(6):438-51
references.pmid: 22661207
references.citation: BMC Plant Biol. 2011 Nov 18;11:164
references.pmid: 22098798
references.citation: Genome. 1995 Jun;38(3):575-85
references.pmid: 18470191
references.citation: Theor Appl Genet. 2007 Apr;114(6):1117-27
references.pmid: 17279366
references.citation: Brief Funct Genomics. 2012 Jan;11(1):38-50
references.pmid: 22257472
references.citation: Proc Natl Acad Sci U S A. 2007 Jan 23;104(4):1424-9
references.pmid: 17220272
references.citation: Mol Genet Genomics. 2005 Dec;274(5):515-27
references.pmid: 16244872
references.citation: Science. 2010 Feb 12;327(5967):818-22
references.pmid: 20150489
references.citation: Theor Appl Genet. 2013 Sep;126(9):2335-51
references.pmid: 23771136
references.citation: Eur J Clin Nutr. 2010 Dec;64(12):1472-80
references.pmid: 20924392
references.citation: Proc Natl Acad Sci U S A. 2008 Sep 30;105(39):14970-5
references.pmid: 18812501
references.citation: Genetics. 2007 Mar;175(3):1395-406
references.pmid: 17194788
references.citation: Trends Genet. 2008 Jan;24(1):24-32
references.pmid: 18054117
references.citation: Genetics. 2007 May;176(1):599-609
references.pmid: 17339225
references.citation: Bioinformatics. 2007 Oct 1;23(19):2633-5
references.pmid: 17586829
references.citation: Theor Appl Genet. 2013 Mar;126(3):693-710
references.pmid: 23139143
references.citation: Trends Genet. 2011 Mar;27(3):98-106
references.pmid: 21227531
references.citation: Nature. 2012 Nov 29;491(7426):711-6
references.pmid: 23075845
references.citation: Nat Genet. 2012 Dec;44(12):1388-92
references.pmid: 23160098
references.citation: Science. 1997 Aug 22;277(5329):1063-6
references.pmid: 9262467
references.citation: Science. 2005 Nov 11;310(5750):1031-4
references.pmid: 16284181
references.citation: Proc Natl Acad Sci U S A. 2008 Mar 11;105(10):4062-7
references.pmid: 18316719
references.citation: Am J Bot. 2012 Feb;99(2):407-23
references.pmid: 22314574
references.citation: Theor Appl Genet. 2007 Nov;115(7):993-1001
references.pmid: 17713756
references.citation: Genetics. 2008 Mar;178(3):1709-23
references.pmid: 18385116
references.citation: Theor Appl Genet. 2010 May;120(8):1525-34
references.pmid: 20157694
references.citation: Genetics. 2000 Jun;155(2):945-59
references.pmid: 10835412
references.citation: Eur J Nutr. 2013 Oct;52(7):1743-53
references.pmid: 23229409
references.citation: Theor Appl Genet. 2012 Jan;124(1):111-24
references.pmid: 21898052
references.citation: Brief Funct Genomics. 2014 Jul;13(4):341-50
references.pmid: 24658880
references.citation: Nat Genet. 2010 Apr;42(4):355-60
references.pmid: 20208535
references.citation: Curr Opin Plant Biol. 2009 Apr;12(2):218-22
references.pmid: 19185530
references.citation: Genetics. 2006 Jan;172(1):557-67
references.pmid: 16219791
references.citation: J Exp Bot. 2000 Jan;51(342):9-17
references.pmid: 10938791