Population structure and association mapping of yield contributing agronomic traits in foxtail millet
Population structure and association mapping of yield contributing agronomic traits in foxtail millet
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DOI：
10.1007/s00299-014-1564-0
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发表时间：
2014-06-01
影响因子：
6.2
通讯作者：
Prasad, Manoj
中科院分区：
文献类型：
--
作者：
Gupta, Sarika;Kumari, Kajal;Prasad, Manoj
通过群体结构和亲缘关系的关联分析，筛选出8个SSR标记（p < 0.01）与谷子的9个农艺性状显著关联（R（2）= 18%），表明关联作图是鉴定复杂性状基因的有效工具。虽然利用基因组简单重复序列（SSR）标记进行关联作图已在许多重要农作物中得到成功应用，但在谷子中进行标记-性状关联分析的报道很少。在本研究中，来自不同地理位置的184个谷子种质，使用代表谷子9条染色体的50个SSR标记进行基因分型。这些加入内的遗传多样性进行了研究，使用遗传距离为基础的和一般的基于模型的聚类方法。基于模型的分析，使用50个SSR标记确定了一个潜在的人口结构，包括五个亚群，以及对应的距离为基础的分组。连续三年在田间对20个产量贡献农艺性状进行植物表型分析。结合群体结构和亲缘关系的连锁不平衡分析，在不同染色体上共鉴定出8个SSR标记（p < 0.01），它们与9个农艺性状显著相关（R（2）= 18%）。其中4个标记与多个性状相关。将8个SSR标记的遗传图谱和物理图谱信息与功能注释相结合，发现位于同一染色体（5）上的两个编码磷脂酰基转移酶和泛素羧基末端水解酶的标记分别与旗叶宽和籽粒产量有很强的关联。我们的关联作图的研究结果是第一次报告印度谷子种质，这可以有效地应用于谷子育种，以进一步揭示标记性状与大量的标记。
Association analyses accounting for population structure and relative kinship identified eight SSR markers ( p < 0.01) showing significant association ( R (2) = 18 %) with nine agronomic traits in foxtail millet.Association mapping is an efficient tool for identifying genes regulating complex traits. Although association mapping using genomic simple sequence repeat (SSR) markers has been successfully demonstrated in many agronomically important crops, very few reports are available on marker-trait association analysis in foxtail millet. In the present study, 184 foxtail millet accessions from diverse geographical locations were genotyped using 50 SSR markers representing the nine chromosomes of foxtail millet. The genetic diversity within these accessions was examined using a genetic distance-based and a general model-based clustering method. The model-based analysis using 50 SSR markers identified an underlying population structure comprising five sub-populations which corresponded well with distance-based groupings. The phenotyping of plants was carried out in the field for three consecutive years for 20 yield contributing agronomic traits. The linkage disequilibrium analysis considering population structure and relative kinship identified eight SSR markers (p < 0.01) on different chromosomes showing significant association (R (2) = 18 %) with nine agronomic traits. Four of these markers were associated with multiple traits. The integration of genetic and physical map information of eight SSR markers with their functional annotation revealed strong association of two markers encoding for phospholipid acyltransferase and ubiquitin carboxyl-terminal hydrolase located on the same chromosome (5) with flag leaf width and grain yield, respectively. Our findings on association mapping is the first report on Indian foxtail millet germplasm and this could be effectively applied in foxtail millet breeding to further uncover marker-trait associations with a large number of markers.