Genome-wide association mapping of frost tolerance in barley (Hordeum vulgare L.).
Genome-wide association mapping of frost tolerance in barley (Hordeum vulgare L.).
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DOI：
10.1186/1471-2164-14-424
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发表时间：
2013-06-27
期刊：
影响因子：
4.4
通讯作者：
Comadran J
中科院分区：
文献类型：
--
作者：
Visioni A;Tondelli A;Francia E;Pswarayi A;Malosetti M;Russell J;Thomas W;Waugh R;Pecchioni N;Romagosa I;Comadran J
耐霜冻性是大麦中具有经济和农学重要性的关键性状，因为它是抗寒性的主要组成部分，因此限制了作物的地理分布以及春季和冬季作物类型之间质量性状的有效转移。从双亲遗传作图中已鉴定出三个主要的耐霜冻QTL（Fr-H1、Fr-H2和Fr-H3），但可以认为这些作图群体仅捕获了物种遗传多样性的一部分。一个遗传广泛的数据集组成的184个基因型，代表大麦基因库在地中海盆地种植了很长一段时间，基因型与1536 SNP标记。从两个试验地点，Foradada（西班牙）和Fiorenzuola（意大利）收集抗冻性表型评分，并结合基因组全关联分析（GWAS）中的基因型数据，使用Eigenstrat和亲属关系方法来解释种群结构。GWAS分析确定了12个和7个阳性SNP协会在Foradada和Fiorenzuola，分别使用Eigenstrat和6个和4个，分别使用亲属关系。显著SNP关联的连锁不平衡分析表明它们在遗传上是独立的。在亲缘关系分析中，两个显著的SNP关联分别与染色体5 H和4 HL上的Fr-H2和HvBmy位点紧密连锁。其他重要的亲缘关系位于基因组区域，以前没有与冷应激相关。单倍型分析表明，大多数显着的SNP位点是固定在冬季或兼性类型，而他们是自由分离的非适应春大麦基因库。虽然有一个主要的兴趣，在检测新的变化，以提高耐霜冻的可用的冬季和兼性类型，从GWAS的角度来看，在不适应的春季种质库内工作是一个有吸引力的替代策略，这将最大限度地减少统计问题，简化数据的解释，并确定物候独立的耐霜冻的遗传决定因素。
Frost tolerance is a key trait with economic and agronomic importance in barley because it is a major component of winter hardiness, and therefore limits the geographical distribution of the crop and the effective transfer of quality traits between spring and winter crop types. Three main frost tolerance QTL (Fr-H1, Fr-H2 and Fr-H3) have been identified from bi-parental genetic mapping but it can be argued that those mapping populations only capture a portion of the genetic diversity of the species. A genetically broad dataset consisting of 184 genotypes, representative of the barley gene pool cultivated in the Mediterranean basin over an extended time period, was genotyped with 1536 SNP markers. Frost tolerance phenotype scores were collected from two trial sites, Foradada (Spain) and Fiorenzuola (Italy) and combined with the genotypic data in genome wide association analyses (GWAS) using Eigenstrat and kinship approaches to account for population structure. GWAS analyses identified twelve and seven positive SNP associations at Foradada and Fiorenzuola, respectively, using Eigenstrat and six and four, respectively, using kinship. Linkage disequilibrium analyses of the significant SNP associations showed they are genetically independent. In the kinship analysis, two of the significant SNP associations were tightly linked to the Fr-H2 and HvBmy loci on chromosomes 5H and 4HL, respectively. The other significant kinship associations were located in genomic regions that have not previously been associated with cold stress. Haplotype analysis revealed that most of the significant SNP loci are fixed in the winter or facultative types, while they are freely segregating within the un-adapted spring barley genepool. Although there is a major interest in detecting new variation to improve frost tolerance of available winter and facultative types, from a GWAS perspective, working within the un-adapted spring germplasm pool is an attractive alternative strategy which would minimize statistical issues, simplify the interpretation of the data and identify phenology independent genetic determinants of frost tolerance.
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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：
5.3
作者：
Li Y;Böck A;Haseneyer G;Korzun V;Wilde P;Schön CC;Ankerst DP;Bauer E
通讯作者：
Bauer E
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：
7.4
作者：
Kaplan, F;Guy, CL
通讯作者：
Guy, CL