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Genome scanning of Asiatic Vigna species for discerning population genetic structure based on microsatellite variation

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Abstract

Wild relatives are important genetic resources for crop improvement. However, basic information about their population structure, genetic diversity, species relationships and distribution of variation in a gene pool remains scanty in Vigna species. The level of genetic diversity and population genetic structure of representative accessions of cultivated and wild Asiatic Vigna species collected from diversity-rich endemic areas of India have been investigated using both microsatellite markers and morphological descriptors. Forty-one wild and 12 cultivated accessions of 13 Vigna species were genotyped using 53 polymorphic microsatellite markers. A total of 539 alleles were detected among 53 accessions at all loci with an average 10.16 alleles per locus. The major allele frequency varied from 0.16 to 0.65 (mean = 0.30), while polymorphism information content of polymorphic markers ranged from 0.47 to 0.89 (mean = 0.79). The UPGMA revealed five major clusters accommodating ~96 % of the accessions. The largest cluster accommodated 19 (36 %), while the smallest cluster had only two accessions. Two accessions, JAP/10-5 and JAP/10-9 of V. trilobata, did not group with any other accession. The model-based population structure analysis also showed almost similar pattern and grouped 53 accessions of Vigna into five genetically distinct sub-populations (K = 5) based on maximum ∆K values. Duncan’s multiple range test revealed significant difference between five genetic and one admixture group developed through population structure analysis with 22 morphological descriptors. Analysis of variance for morphological data revealed significant difference in 12 qualitative and quantitative traits including growth habit, terminal leaflet length, colour of petiole base, petiole length, leaf senescence, length of peduncle, raceme position, calyx colour, colour of VSI pod, pod pubescence, pod curvature and 100-seed weight, indicating their significance in distinguishing population groups. The information on genetic diversity and population structure of wild and cultivated accessions of Asiatic Vigna will be tremendously useful to accelerate their use in trait improvement.

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Acknowledgments

We are thankful to National Innovations in Climate Resilient Agriculture (NICRA), ICAR, Govt. of India, for providing financial support to carry out this research. The corresponding author is also thankful to Head, Crop Improvement Division, for providing necessary facilities for carrying out this research.

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Authors and Affiliations

  1. ICAR-Indian Institute of Pulses Research, Kalyanpur, Kanpur, 208024, Uttar Pradesh, India

    Aditya Pratap, Sanjeev Gupta, Nupur Malviya, Rakhi Tomar, Ramanuj Maurya & Narendra Pratap Singh

  2. ICAR-National Bureau of Plant Genetic Resources, Regional Station, Vellanikkara, Thrissur, 680656, Kerala, India

    K. Joseph John & Latha Madhavan

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  1. Aditya Pratap
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Correspondence to Aditya Pratap.

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Pratap, A., Gupta, S., Malviya, N. et al. Genome scanning of Asiatic Vigna species for discerning population genetic structure based on microsatellite variation. Mol Breeding 35, 178 (2015). https://doi.org/10.1007/s11032-015-0355-9

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