The USDA barley core collection: genetic diversity, population structure, and potential for genome-wide association studies.
The USDA barley core collection: genetic diversity, population structure, and potential for genome-wide association studies.
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USDA大麦核心收集：遗传多样性，种群结构和全基因组关联研究的潜力。
DOI：
10.1371/journal.pone.0094688
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发表时间：
2014
期刊：
影响因子：
3.7
通讯作者：
Muehlbauer GJ
中科院分区：
文献类型：
--
作者：
Muñoz-Amatriaín M;Cuesta-Marcos A;Endelman JB;Comadran J;Bonman JM;Bockelman HE;Chao S;Russell J;Waugh R;Hayes PM;Muehlbauer GJ
如果要继续提高谷物产量和质量，以及对非生物和生物胁迫的耐受性，就必须将遗传多样性的新来源纳入植物育种计划。种质资源的收集提供了遗传和表型多样性的来源，但这些资源的特性是必需的，以增加其实用性的育种计划。我们使用具有7，842个SNP的大麦SNP iSelect平台对从USDA National Small Grains Collection的33，176个种质中取样的2，417个大麦种质进行基因分型。该核心种质中的大多数种质被归类为地方品种或栽培品种/育种系，来自100多个国家。结构和主成分分析确定了五个主要的亚群内的核心收集，主要区分的地理来源和穗行数（花序结构性状）。不同模式的连锁不平衡（LD）被发现在整个大麦基因组和许多区域的高LD包含的性状参与驯化和育种选择。基因型数据被用来定义“迷你核心”集的加入捕捉大多数的等位基因多样性存在于核心收集。这些“迷你核心”集可用于评估评分困难或昂贵的特征。全基因组关联研究（GWAS）的“船体覆盖”，"穗行数“，和”抽穗期“证明了效用的核心收集定位遗传因素决定重要的表型。GWAS结果参考了包含5，665个SNP的新大麦共有图谱。我们的研究结果表明，GWAS和高密度SNP基因分型是有效的工具，植物育种家有兴趣在大型种质资源收集访问遗传多样性。
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.
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影响因子：
5.8
作者：
Bradbury, Peter J.;Zhang, Zhiwu;Buckler, Edward S.
通讯作者：
Buckler, Edward S.
影响因子：
3.3
作者：
Faure, Sebastien;Higgins, Janet;Laurie, David A.
通讯作者：
Laurie, David A.
影响因子：
5.4
作者：
Cockram, James;Chiapparino, Elena;O'Sullivan, Donal M.
通讯作者：
O'Sullivan, Donal M.
影响因子：
6.9
作者：
Ellis, RP;Forster, BP;Powell, W
通讯作者：
Powell, W
影响因子：
1.2
作者：
AIDUN, VL;HARVEY, BL;ROSSNAGEL, BG
通讯作者：
ROSSNAGEL, BG