SNP genotyping and diversity analysis based on genic-SNPs through high resolution melting (HRM) analysis in blackgram [Vigna mungo (L.) Hepper]

Publication Overview
TitleSNP genotyping and diversity analysis based on genic-SNPs through high resolution melting (HRM) analysis in blackgram [Vigna mungo (L.) Hepper]
AuthorsRaizada A, Souframanien J
TypeJournal Article
Journal NameGenetic resources and crop evolution
Volume68
Issue4
Year2021
Page(s)1331-1343
CitationRaizada A, Souframanien J. SNP genotyping and diversity analysis based on genic-SNPs through high resolution melting (HRM) analysis in blackgram [Vigna mungo (L.) Hepper]. Genetic resources and crop evolution. 2021; 68(4):1331-1343.

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 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.
Features
This publication contains information about 19 features:
Feature NameUniquenameType
TWSNP_0033TWSNP_0033genetic_marker
TWSNP_0040TWSNP_0040genetic_marker
TWSNP_0058TWSNP_0058genetic_marker
TWSNP_0059TWSNP_0059genetic_marker
TWSNP_0061TWSNP_0061genetic_marker
TWSNP_0073TWSNP_0073genetic_marker
TWSNP_0078TWSNP_0078genetic_marker
TWSNP_0093TWSNP_0093genetic_marker
TWSNP_0138TWSNP_0138genetic_marker
TWSNP_0859TWSNP_0859genetic_marker
TWSNP_0904TWSNP_0904genetic_marker
TWSNP_1304.1TWSNP_1304.1genetic_marker
TWSNP_1304.2TWSNP_1304.2genetic_marker
TWSNP_1559TWSNP_1559genetic_marker
TWSNP_1771TWSNP_1771genetic_marker
TWSNP_2931TWSNP_2931genetic_marker
TWSNP_4407TWSNP_4407genetic_marker
TWSNP_5816TWSNP_5816genetic_marker
TWSNP_5835TWSNP_5835genetic_marker
Properties
Additional details for this publication include:
Property NameValue
Publication TypeJournal Article
Publication Date2021
Language Abbreng
URLhttp://dx.doi.org/10.1007/s10722-020-01064-6
KeywordsVigna mungo, assets, black gram, cultivars, evolution, genetic relationships, genotyping, molecular chaperones, protein structure, transcription factors
Cross References
This publication is also available in the following databases:
DatabaseAccession
AGL: USDA National Agricultural LibraryAGL:7070971