Bohra Abhishek, Jha Rintu, Pandey Gaurav, Patil Prakash G, Saxena Rachit K, Singh Indra P, Singh D, Mishra R K, Mishra Ankita, Singh F, Varshney Rajeev K, Singh N P
ICAR-Indian Institute of Pulses Research (IIPR)Kanpur, India.
International Crops Research Institute for the Semi-Arid TropicsHyderabad, India.
Front Plant Sci. 2017 Mar 31;8:377. doi: 10.3389/fpls.2017.00377. eCollection 2017.
Draft genome sequence in pigeonpea offers unprecedented opportunities for genomics assisted crop improvement enabling access to genome-wide genetic markers. In the present study, 421 hypervariable simple sequence repeat (SSR) markers from the pigeonpea genome were screened on a panel of eight pigeonpea genotypes yielding marker validation and polymorphism percentages of 95.24 and 54.11%, respectively. The SSR marker assay uncovered a total of 570 alleles with three as an average number of alleles per marker. Similarly, the mean values for gene diversity and PIC were 0.44 and 0.37, respectively. The number of polymorphic markers ranged from 39 to 89 for different parental combinations. Further, 60 of these SSRs were assayed on 94 genotypes, and model based clustering using STRUCTURE resulted in the identification of the two subpopulations ( = 2). This remained in close agreement with the clustering patterns inferred from genetic distance (GD)-based approaches i.e., dendrogram, factorial and principal coordinate analysis (PCoA). The AMOVA accounted majority of the genetic variation within groups (89%) in comparison to the variation existing between the groups (11%). A subset of these markers was implicated for hybrid purity testing. We also demonstrated utility of these SSR markers in trait mapping through association and bi-parental linkage analyses. The general linear (GLM) and mixed linear (MLM) models both detected a single SSR marker (CcGM03681) with = 16.4 as associated with the resistance to wilt variant 2. Similarly, by using SSR data in a segregating backcross population, the corresponding restorer-of-fertility () locus was putatively mapped at 39 cM with the marker CcGM08896. However, The marker-trait associations (MTAs) detected here represent a very preliminary type and hence demand deeper investigations for conclusive evidence. Given their ability to reveal polymorphism in simple agarose gels, the hypervariable SSRs are valuable genomic resource for pigeonpea research community, particularly in South Asia and East Africa where pigeonpea is primarily grown.
木豆的基因组序列草图为基因组辅助作物改良提供了前所未有的机会，使人们能够获取全基因组遗传标记。在本研究中，对一组8个木豆基因型筛选了来自木豆基因组的421个高变简单序列重复（SSR）标记，标记验证率和多态性百分比分别为95.24%和54.11%。SSR标记分析共发现570个等位基因，每个标记平均有3个等位基因。同样，基因多样性和PIC的平均值分别为0.44和0.37。不同亲本组合的多态性标记数量在39至89之间。此外，对其中60个SSR在94个基因型上进行了分析，使用STRUCTURE基于模型的聚类结果鉴定出两个亚群（K = 2）。这与基于遗传距离（GD）的方法（即树状图、因子分析和主坐标分析（PCoA））推断的聚类模式密切一致。分子方差分析（AMOVA）表明，组内遗传变异占大部分（89%），而组间变异占11%。这些标记的一个子集被用于杂交纯度检测。我们还通过关联分析和双亲连锁分析证明了这些SSR标记在性状定位中的实用性。一般线性（GLM）模型和混合线性（MLM）模型均检测到一个与抗枯萎病变种2相关的SSR标记（CcGM03681），其LOD = 16.4。同样，通过在一个分离回交群体中使用SSR数据，相应的育性恢复（Rf）位点被推定位于39 cM处，标记为CcGM08896。然而，这里检测到的标记-性状关联（MTA）代表了一种非常初步的类型，因此需要更深入的研究以获得确凿证据。鉴于其在简单琼脂糖凝胶中揭示多态性的能力，高变SSR是木豆研究群体的宝贵基因组资源，特别是在木豆主要种植的南亚和东非地区。
