Linkage disequilibrium based association mapping of fiber quality traits in G-hirsutum L. variety germplasm
Linkage disequilibrium based association mapping of fiber quality traits in G-hirsutum L. variety germplasm
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DOI：
10.1007/s10709-008-9337-8
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发表时间：
2009-07-01
期刊：
影响因子：
1.5
通讯作者：
Abdukarimov, Abdusattor
中科院分区：
文献类型：
--
作者：
Abdurakhmonov, Ibrokhim Y.;Saha, Sukumar;Abdukarimov, Abdusattor
棉花是世界上主要的经济作物，但由于多态性有限以及历史驯化过程中的遗传瓶颈，它在标记辅助育种方面落后于其他主要作物。这就需要对棉花种质资源中现有的天然多态性进行表征、标记和利用。在这里，我们使用在乌兹别克斯坦和墨西哥两个不同环境中生长的 335 个陆地棉种质中的 202 个微卫星标记引物对，报告了遗传多样性、种群特征、连锁不平衡 (LD) 程度和纤维质量性状的关联图谱。在显着性阈值（r (2) 千分之 0.1）下，在分析的棉花品种种质中，LD 的全基因组平均值延伸至 25 cM 的遗传距离。 r (2) 千分之一 0.2 处的全基因组 LD 降低至大约 5-6 cM，这为棉花农艺重要性状关联作图的潜力提供了证据。结果表明，连锁、选择、近交、群体分层和遗传漂变是棉花中潜在的 LD 产生因素。在两种环境中，使用结合种群结构和亲缘关系的统一混合线性模型 (MLM)，平均有大约 20 个 SSR 标记与每个主要纤维质量性状相关。这些 MLM 衍生的显着关联在一般线性模型和结构化关联测试中得到了证实，考虑了群体结构和基于排列的多重测试。确定了几个共同的标记，显示了乌兹别克斯坦和墨西哥环境中的显着关联。 7% 到 43% 的 MLM 衍生的显着关联得到“中等至强”和“强至非常强”证据水平的最小贝叶斯因子的支持，表明它们对于标记辅助育种计划的有用性以及使用棉花种质资源进行关联作图的整体有效性。
Cotton is the world's leading cash crop, but it lags behind other major crops for marker-assisted breeding due to limited polymorphisms and a genetic bottleneck through historic domestication. This underlies a need for characterization, tagging, and utilization of existing natural polymorphisms in cotton germplasm collections. Here we report genetic diversity, population characteristics, the extent of linkage disequilibrium (LD), and association mapping of fiber quality traits using 202 microsatellite marker primer pairs in 335 G. hirsutum germplasm grown in two diverse environments, Uzbekistan and Mexico. At the significance threshold (r (2) a parts per thousand yen 0.1), a genome-wide average of LD extended up to genetic distance of 25 cM in assayed cotton variety accessions. Genome wide LD at r (2) a parts per thousand yen 0.2 was reduced to similar to 5-6 cM, providing evidence of the potential for association mapping of agronomically important traits in cotton. Results suggest linkage, selection, inbreeding, population stratification, and genetic drift as the potential LD-generating factors in cotton. In two environments, an average of similar to 20 SSR markers was associated with each main fiber quality traits using a unified mixed liner model (MLM) incorporating population structure and kinship. These MLM-derived significant associations were confirmed in general linear model and structured association test, accounting for population structure and permutation-based multiple testing. Several common markers, showing the significant associations in both Uzbekistan and Mexican environments, were determined. Between 7 and 43% of the MLM-derived significant associations were supported by a minimum Bayes factor at 'moderate to strong' and 'strong to very strong' evidence levels, suggesting their usefulness for marker-assisted breeding programs and overall effectiveness of association mapping using cotton germplasm resources.