Genetics, Scottish Crop Research Institute, Invergowrie, Dundee, Scotland DD2 5DA, UK.
Genome. 2010 Nov;53(11):967-72. doi: 10.1139/G10-078.
We have previously shown that linkage disequilibrium (LD) in the elite cultivated barley (Hordeum vulgare) gene pool extends, on average, for <1-5 cM. Based on this information, we have developed a platform for whole genome association studies that comprises a collection of elite lines that we have characterized at 3060 genome-wide single nucleotide polymorphism (SNP) marker loci. Interrogating this data set shows that significant population substructure is present within the elite gene pool and that diversity and LD vary considerably across each of the seven barley chromosomes. However, we also show that a subpopulation comprised of only the two-rowed spring germplasm is less structured and well suited to whole genome association studies without the need for extensive statistical intervention to account for structure. At the current marker density, the two-rowed spring population is suited for fine mapping simple traits that are located outside of the genetic centromeres with a resolution that is sufficient for candidate gene identification by exploiting conservation of synteny with fully sequenced model genomes and the emerging barley physical map.
我们之前的研究表明，优良栽培大麦（Hordeum vulgare）基因库中的连锁不平衡（LD）平均延伸<1-5cM。基于这一信息，我们开发了一个全基因组关联研究平台，该平台由我们在 3060 个全基因组单核苷酸多态性（SNP）标记位点上进行了特征分析的优良品系组成。对该数据集的分析表明，优良基因库内存在显著的群体结构，并且多样性和 LD 在每个大麦染色体上都有很大的差异。然而，我们还表明，仅由二棱春种质组成的亚群结构较少，非常适合全基因组关联研究，而无需进行广泛的统计干预来解释结构。在当前的标记密度下，二棱春种群适合精细定位位于遗传着丝粒之外的简单性状，分辨率足以通过利用与完全测序的模式基因组和新兴的大麦物理图谱的同线性保守性来鉴定候选基因。
