Identification and characterization of SNPs in released, landrace and wild accessions of mungbean ( Vigna radiata (L.) W
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ORIGINAL RESEARCH
Identification and characterization of SNPs in released, landrace and wild accessions of mungbean (Vigna radiata (L.) Wilczek) using whole genome re‑sequencing Pooja Bangar1,2 · Neetu Tyagi1 · Bhavana Tiwari1 · Sanjay Kumar1 · Paramananda Barman1 · Ratna Kumari1 · Ambika Gaikwad1 · K. V. Bhat1 · Ashok Chaudhury2 Accepted: 26 August 2020 © Korean Society of Crop Science (KSCS) 2020
Abstract Mungbean [Vigna radiata (L.) R. Wilczek var. radiata] is vital grain legume having nutritional and socio-economic importance, especially in the developing countries. We performed whole-genome re-sequencing of three accessions representing the wild progenitor species, released and landrace of mungbean to identify SNPs with relevance to genetic relationships analysis. Approximately 9.3 million raw reads were obtained using Ion Torrent PGM™ platform and more than 92% of the reads were mapped to the reference mungbean genome. We identified a total of 233,799 single-nucleotide polymorphisms in relation to the reference genome (SNPs: 103,341 in wild, 93,078 in released and 37,380 in landrace accessions) and 9544 insertions and deletions (InDels: 4742 in wild, 3608 in released and 1194 in landrace accessions) in the coding and non-coding regions. In all accessions, genomic variants were unevenly distributed within and across the mungbean chromosomes. Among these 5339, 4739 and 1795 SNPs were non-synonymous in 815, 790 and 317 genes of wild, released and landrace accessions, respectively. These polymorphisms might contribute to the variation in important pathways of genes for abiotic and biotic stress tolerance and important agronomic traits, such as seed dormancy, flowering time and seed size in mungbean. Among the randomly selected SNPs, a selected subset was validated using Sanger sequencing technique. The genomic variations among mungbean wild, released and landrace accessions constitute a powerful tool to support genetic research and molecular breeding of mungbean. Keywords Domestication · Insertion/deletion · Mungbean · Single-nucleotide polymorphism · Whole-genome re-sequencing
Electronic supplementary material The online version of this article (https://doi.org/10.1007/s12892-020-00067-0) contains supplementary material, which is available to authorized users. * Ashok Chaudhury [email protected]
Ratna Kumari [email protected]
Pooja Bangar [email protected]
Ambika Gaikwad [email protected]
Neetu Tyagi [email protected]
K. V. Bhat [email protected]
Bhavana Tiwari [email protected]
1
Genomic Resources Division, ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi 110012, India
2
Department of Bio and Nano Technology, Bio and Nano Technology Centre, Guru Jambheshwar University of Science and Technology, Hisar, Haryana 125001, India
Sanjay Kumar [email protected] Paramananda Barman [email protected]
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Introduction Mungbean is a diploid (2n = 22), self-pollinated and fastgrowing ( 2) were removed
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