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Genetic diversity and structure of the zombi pea (Vigna vexillata (L.) A. Rich) gene pool based on SSR marker analysis

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Abstract

Zombi pea (Vigna vexillata (L.) A. Rich) is an underutilized legume species and a useful gene source for resistance to biotic and abiotic stresses, although there is little understanding on its genetic diversity and structure. In this study, 422 (408 wild and 14 cultivated) accessions of zombi pea from diverse origins (201 from Africa, 126 from America, 85 from Australia, 5 from Asia and 5 from unknown origin) were analyzed with 20 simple sequence repeat (SSR) markers to determine its genetic diversity and genetic structure. The SSR markers detected 273 alleles in total with a mean of 13.6 alleles per locus. Polymorphism information content values of the markers varied from 0.58 to 0.90 with an average of 0.76. Overall gene diversity was 0.715. Gene diversity and average allelic richness was highest in Africa (0.749 and 8.08, respectively) and lowest in America (0.435 and 4.10, respectively). Nei’s genetic distance analysis revealed that the highest distance was between wild Australia and cultivated Africa (0.559), followed by wild West Africa and wild Australia (0.415). STRUCTURE, neighbor-joining (NJ), and principal coordinate analyses consistently showed that these zombi pea accessions were clustered into three major groups, viz. America, Africa and Asia, and Australia. NJ tree also suggested that American and Australian accessions are originated from East African zombi peas, and that the cultivated accessions from Africa and Asia were genetically distinct, while those from America were clustered with some cultivated accessions from Africa. These results suggest that Africa is the center of origin and diversity of zombi pea, and that domestication of this pea took place more than once in different regions.

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Acknowledgements

This research was supported by the Royal Golden Jubilee Ph.D. Scholarship and the TRF Research Career Development Grant (RSA5880051) both of which co-funded by the Thailand Research Fund (TRF) and Kasetsart University to P. Somta and S. Dachapak.

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Authors and Affiliations

  1. Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, 73140, Thailand

    Sujinna Dachapak, Prakit Somta, Tarika Yimram & Peerasak Srinives

  2. Program in Plant Biotechnology, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, 73140, Thailand

    Supalak Poonchaivilaisak

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  1. Sujinna Dachapak
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Correspondence to Prakit Somta.

Electronic supplementary material

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10709_2017_9957_MOESM1_ESM.pdf

Supplementary Figure S1.A neighbor-joining tree constructed from Nei’s genetic distance (D A) showing the genetic relationship among the 422 accessions of Vigna vexillata in relation to their germination habits (epigeal and hypogeal germinations). D A was calculated from allelic data of 20 simple sequence repeat markers. (PDF 405 KB)

10709_2017_9957_MOESM2_ESM.doc

Supplementary Table S1. Name, origin and germination habit of the 422 accessions of Vigna vexillata used in this study. (DOC 497 KB)

Supplementary Table S2.Primer sequences of the 20 SSR markers used in this study (DOC 41 KB)

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Dachapak, S., Somta, P., Poonchaivilaisak, S. et al. Genetic diversity and structure of the zombi pea (Vigna vexillata (L.) A. Rich) gene pool based on SSR marker analysis. Genetica 145, 189–200 (2017). https://doi.org/10.1007/s10709-017-9957-y

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