SNP genotyping and diversity analysis based on genic-SNPs through high resolution melting (HRM) analysis in blackgram [
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RESEARCH ARTICLE
SNP genotyping and diversity analysis based on genic-SNPs through high resolution melting (HRM) analysis in blackgram [Vigna mungo (L.) Hepper] Avi Raizada . J. Souframanien
Received: 20 March 2020 / Accepted: 5 November 2020 Ó Springer Nature B.V. 2020
Abstract Genetic relatedness among 27 blackgram [Vigna mungo (L.) Hepper] genotypes was analysed using 19 genic-single nucleotide polymorphisms (SNPs) through high resolution melting (HRM) analysis. The scrutiny of normalized HRM curves grouped most of the genotypes with cultivated blackgram. Notably, the SNP markers TWSNP33 and TWSNP 59, clustered all the genotypes with the cultivar TU94-2, while the SNP markers TWSNP40a and TWSNP859 grouped majority of the genotypes with wild accession. A total of 13 genic-SNPs were found to lie in the coding region and the rest were confined to the untranslated regions. Among the 13 genic-SNPs, only 4 were found to have missense substitution. NCBI annotations and Iterative Threading ASSEmbly Refinement (I-TASSER) results on SNPs effects on protein structure and kinetics provided a valuable asset for further discovery of genes, gene variants and
Electronic supplementary material The online version of this article (https://doi.org/10.1007/s10722-020-01064-6) contains supplementary material, which is available to authorized users. A. Raizada J. Souframanien (&) Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India e-mail: [email protected] A. Raizada J. Souframanien Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
development of functional markers. SNP markers TWSNP33, 61 and 73 housed in the genes coding for UDP-glycosyltransferase 89B1, molecular chaperone regulator 7 (BAG family) and WRKY transcription factor 17, respectively, were known to be involved in stress and defense responses. Unweighted pair group method with arithmetic mean clustering placed elite blackgram varieties in 2 major clusters while the wild accession formed a separate operational taxonomic unit. The unravelling of the genetic relatedness is of paramount importance for designing appropriate breeding strategies for developing elite varieties through exploitation of novel/rare alleles of agronomic importance. Keywords Single nucleotide polymorphism High resolution melting Blackgram Genic-SNP markers Germplasm
Introduction Blackgram [Vigna mungo (L.) Hepper], popularly known as urdbean is an important legume crop domesticated from V. mungo var. silvestris. It is extensively cultivated for its proteinaceous seeds which constitute the major dietary component of the predominant vegetarian population in Asian countries. It also assumes significance as a component of several
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Genet Resour Crop Evol
cropping systems and is in high demand by various sprout industries of Thailand and Japan (Somta et al. 2019). Domestication and recurrent usage of genetically related genotypes in hybridi
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