Genetic Patterns of Domestication in Pigeonpea (Cajanus cajan (L.) Millsp.) and Wild Cajanus Relatives

Kassa, M T and Penmetsa, R V and Carrasquilla-Garcia, N and et al, . (2012) Genetic Patterns of Domestication in Pigeonpea (Cajanus cajan (L.) Millsp.) and Wild Cajanus Relatives. PLoS ONE, 7 (6). pp. 1-13. ISSN 1932-6203

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Pigeonpea (Cajanus cajan) is an annual or short-lived perennial food legume of acute regional importance, providing significant protein to the human diet in less developed regions of Asia and Africa. Due to its narrow genetic base, pigeonpea improvement is increasingly reliant on introgression of valuable traits from wild forms, a practice that would benefit from knowledge of its domestication history and relationships to wild species. Here we use 752 single nucleotide polymorphisms (SNPs) derived from 670 low copy orthologous genes to clarify the evolutionary history of pigeonpea (79 accessions) and its wild relatives (31 accessions). We identified three well-supported lineages that are geographically clustered and congruent with previous nuclear and plastid sequence-based phylogenies. Among all species analyzed Cajanus cajanifolius is the most probable progenitor of cultivated pigeonpea. Multiple lines of evidence suggest recent gene flow between cultivated and non-cultivated forms, as well as historical gene flow between diverged but sympatric species. Evidence supports that primary domestication occurred in India, with a second and more recent nested population bottleneck focused in tropical regions that is the likely consequence of pigeonpea breeding. We find abundant allelic variation and genetic diversity among the wild relatives, with the exception of wild species from Australia for which we report a third bottleneck unrelated to domestication within India. Domesticated C. cajan possess 75% less allelic diversity than the progenitor clade of wild Indian species, indicating a severe ‘‘domestication bottleneck’’ during pigeonpea domestication.

Item Type: Article
Subjects: Mandate crops > Pigeonpea
Others > Genetics and Genomics
Depositing User: Mr Siva Shankar
Date Deposited: 23 Jun 2012 06:22
Last Modified: 23 Jun 2012 06:22
Official URL:
Funders: Indian Council of Agricultural Research under the Indo-US Agricultural Knowledge Initiative
Acknowledgement: The authors acknowledge BOYSCAST fellowships from the Indian Department of Science and Technology to BKS and SD. This paper is contribution number 231 from the Tropical Biology Program of Florida International University, associated with EJBvW. We are grateful to Professor Nigel Barker of Rhodes University Professor Jos van der Maesen of Wageningen University The Netherlands, and Associate Professor David Remington of the University of North Carolina at Greensboro for their helpful comments during preparation of the manuscript, and to Dr Reyazul Rouf Mir and Dr Rachit K Saxena for their valuable assistance with germplasm selection. We also acknowledge the important contributions of certain DNA samples used in this study from Dr Pawan Kulwal of Dr. Panjabrao Deshmukh Agricultural University (PDAU), Akola (India), Dr B Fakrudin University of Agricultural Sciences (UAS)- Bangalore (India), and Dr M Byregowda of UAS-Dharwad (India).
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