Genetic Diversity and Demographic History of Cajanus spp. Illustrated from Genome-Wide SNPs

Saxena, R K and von Wettberg, E and Upadhyaya, H D and Sanchez, V and Songok, S and Saxena, K B and Kimurto, P.K. and Varshney, R K (2014) Genetic Diversity and Demographic History of Cajanus spp. Illustrated from Genome-Wide SNPs. PLoS ONE, 9 (2). pp. 1-9. ISSN 1932-6203

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Understanding genetic structure of Cajanus spp. is essential for achieving genetic improvement by quantitative trait loci (QTL) mapping or association studies and use of selected markers through genomic assisted breeding and genomic selection. After developing a comprehensive set of 1,616 single nucleotide polymorphism (SNPs) and their conversion into cost effective KASPar assays for pigeonpea (Cajanus cajan), we studied levels of genetic variability both within and between diverse set of Cajanus lines including 56 breeding lines, 21 landraces and 107 accessions from 18 wild species. These results revealed a high frequency of polymorphic SNPs and relatively high level of cross-species transferability. Indeed, 75.8% of successful SNP assays revealed polymorphism, and more than 95% of these assays could be successfully transferred to related wild species. To show regional patterns of variation, we used STRUCTURE and Analysis of Molecular Variance (AMOVA) to partition variance among hierarchical sets of landraces and wild species at either the continental scale or within India. STRUCTURE separated most of the domesticated germplasm from wild ecotypes, and separates Australian and Asian wild species as has been found previously. Among Indian regions and states within regions, we found 36% of the variation between regions, and 64% within landraces or wilds within states. The highest level of polymorphism in wild relatives and landraces was found in Madhya Pradesh and Andhra Pradesh provinces of India representing the centre of origin and domestication of pigeonpea respectively.

Item Type: Article
Divisions: RP-Grain Legumes
CRP: CGIAR Research Program on Grain Legumes
Uncontrolled Keywords: Genetic Diversity, Demographic History, Cajanus, Genome-Wide SNPs, Pigeonpea
Subjects: Mandate crops > Pigeonpea
Others > Food Legumes
Others > Genetics and Genomics
Depositing User: Mr Sanat Kumar Behera
Date Deposited: 18 Feb 2014 09:11
Last Modified: 19 Aug 2016 08:45
Official URL:
Funders: United States Agency for International Development, Government of India - Ministry of Agriculture - Department of Agriculture and Cooperation, Florida International University, Fairchild Tropical Botanic Garden, USDA-NIFA-NNF
Acknowledgement: We thank United States Agency for International Development (USAID)- India Mission and Department of Agriculture and Co-opeartion, Ministry of Agriculture, Government of India for financial support for the research work to RKV and support from Florida International University and Fairchild Tropical Botanic Garden to EvW. VS is thankful for financial support from USDA-NIFA-NNF 2011-38420-20053. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. This work has been undertaken as part of the CGIAR Research Program on Grain Legumes. ICRISAT is a member of CGIAR Consortium. We thank Doug Cook, Mulualem Kassa and R VermaPenmetsa for helpful discussions.
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