Centre UdL-IRTA, Departament de Producció Vegetal i Ciència Forestal, Universitat de Lleida, Lleida, Spain.
BMC Genomics. 2013 Jun 27;14:424. doi: 10.1186/1471-2164-14-424.
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.
耐霜性是大麦的一个重要经济和农艺性状，因为它是冬季抗寒性的主要组成部分，因此限制了作物的地理分布和春、冬作物类型之间的质量性状的有效转移。已经从双亲子代遗传图谱中鉴定出三个主要的耐霜性 QTL（Fr-H1、Fr-H2 和 Fr-H3），但可以说，那些作图群体仅捕获了该物种遗传多样性的一部分。由 184 个基因型组成的遗传多样性广泛的数据集，代表了地中海盆地在较长时间内种植的大麦基因库，用 1536 个 SNP 标记进行了基因型分析。在两个试验点（西班牙的福拉达达和意大利的菲奥伦佐拉）收集了耐霜性表型评分，并结合基因组广泛关联分析（GWAS）中的基因型数据，使用 Eigenstrat 和亲缘关系方法来解释群体结构。
使用 Eigenstrat 进行 GWAS 分析，在福拉达达和菲奥伦佐拉分别鉴定出 12 个和 7 个阳性 SNP 关联，使用亲缘关系分别鉴定出 6 个和 4 个。对显著 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 SNP 关联与染色体 5H 和 4HL 上的 Fr-H2 和 HvBmy 基因座紧密连锁。其他显著的亲缘关系关联位于以前与冷胁迫无关的基因组区域。
单倍型分析表明，大多数显著 SNP 位点在冬季或兼性类型中是固定的，而在未适应的春大麦基因库中则自由分离。尽管检测新的变异以提高现有冬季和兼性类型的耐霜性具有重要意义，但从 GWAS 的角度来看，在未适应的春大麦种质库中工作是一种有吸引力的替代策略，这将最大限度地减少统计问题，简化数据解释，并确定耐霜性与物候无关的遗传决定因素。
