Gupta Sarika, Kumari Kajal, Muthamilarasan Mehanathan, Parida Swarup Kumar, Prasad Manoj
National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, JNU Campus, New Delhi, 110 067, India.
Plant Cell Rep. 2014 Jun;33(6):881-93. doi: 10.1007/s00299-014-1564-0. Epub 2014 Jan 12.
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.
考虑群体结构和相对亲缘关系的关联分析鉴定出8个SSR标记（p < 0.01）与谷子的9个农艺性状显著关联（R² = 18%）。关联作图是鉴定调控复杂性状基因的有效工具。尽管利用基因组简单序列重复（SSR）标记进行关联作图已在许多重要农作物中成功得到验证，但关于谷子标记-性状关联分析的报道却非常少。在本研究中，利用代表谷子9条染色体的50个SSR标记对来自不同地理位置的184份谷子种质进行了基因分型。使用基于遗传距离和基于通用模型的聚类方法对这些种质内的遗传多样性进行了检测。利用50个SSR标记进行的基于模型的分析确定了一个由5个亚群组成的潜在群体结构，这与基于距离的分组结果吻合良好。连续三年在田间对20个产量相关农艺性状进行了植株表型分析。考虑群体结构和相对亲缘关系的连锁不平衡分析鉴定出不同染色体上的8个SSR标记（p < 0.01）与9个农艺性状显著关联（R² = 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及其功能注释整合后发现，位于同一染色体（5）上的两个分别编码磷脂酰转移酶和泛素羧基末端水解酶的标记，分别与旗叶宽度和籽粒产量强烈关联。我们关于关联作图的研究结果是关于印度谷子种质的首篇报道，这可有效应用于谷子育种，以进一步揭示大量标记与性状之间的关联。
