Patterns of polymorphism and linkage disequilibrium in cultivated barley.
Patterns of polymorphism and linkage disequilibrium in cultivated barley.
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DOI：
10.1007/s00122-010-1466-7
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发表时间：
2011-02
影响因子：
5.4
通讯作者：
Waugh, Robbie
中科院分区：
文献类型：
--
作者：
Comadran, Jordi;Ramsay, Luke;MacKenzie, Katrin;Hayes, Patrick;Close, Timothy J.;Muehlbauer, Gary;Stein, Nils;Waugh, Robbie
我们对多态性进行了全基因组分析（涵盖190个优良栽培品种的4596个单核苷酸多态性位点），这些品种是为了代表当前西北欧和北美优良大麦种质中现有的遗传变异而选取的。在七条大麦染色体上，群体亚结构、多样性模式和连锁不平衡差异很大。富含基因且很少重组的单倍型模块可能占大麦染色体物理长度的60%，它们延伸穿过“遗传着丝粒”。通过关联作图定位2132个双亲图谱单核苷酸多态性标记（其最小等位基因频率高于0.10），87.3%的标记位于其原始遗传图谱位置的5厘摩范围内。我们表明，在当前这种标记密度下，相对较小规模的遗传多样群体足以对简单性状进行精细定位，前提是这些性状在样本中没有强烈分层，位于遗传着丝粒之外，并且在分析中群体亚结构得到有效控制。我们的研究结果对大麦以及其他具有类似基因组和遗传特征的世界主要谷物（包括小麦和黑麦）的关联作图、定位克隆、物理作图和实际植物育种具有重要意义。
本文的网络版（doi:10.1007/s00122 - 2010 - 1466 - 7）包含补充材料，授权用户可获取。
We carried out a genome-wide analysis of polymorphism (4,596 SNP loci across 190 elite cultivated accessions) chosen to represent the available genetic variation in current elite North West European and North American barley germplasm. Population sub-structure, patterns of diversity and linkage disequilibrium varied considerably across the seven barley chromosomes. Gene-rich and rarely recombining haplotype blocks that may represent up to 60% of the physical length of barley chromosomes extended across the ‘genetic centromeres’. By positioning 2,132 bi-parentally mapped SNP markers with minimum allele frequencies higher than 0.10 by association mapping, 87.3% were located to within 5 cM of their original genetic map position. We show that at this current marker density genetically diverse populations of relatively small size are sufficient to fine map simple traits, providing they are not strongly stratified within the sample, fall outside the genetic centromeres and population sub-structure is effectively controlled in the analysis. Our results have important implications for association mapping, positional cloning, physical mapping and practical plant breeding in barley and other major world cereals including wheat and rye that exhibit comparable genome and genetic features. The online version of this article (doi:10.1007/s00122-010-1466-7) contains supplementary material, which is available to authorized users.
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