DNA fingerprinting, fixation-index (Fst), and admixture mapping of selected Bambara groundnut (Vigna subterranea [L.] Verdc.) accessions using ISSR markers system

Abstract As a new crop in Malaysia, forty-four Bambara groundnut (Vigna subterranea L. verdc.) genotypes were sampled from eleven distinct populations of different origins to explore the genetic structure, genetic inconsistency, and fixation index. The Bambara groundnut, an African underutilized leg...

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Autores principales:	Md Mahmudul Hasan Khan, Mohd Y. Rafii, Shairul Izan Ramlee, Mashitah Jusoh, Md Al Mamun, Jamilu Halidu
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Vigna subterranea [L.] Verdc. DNA fingerprinting Fixation-index (Fst) Admixture mapping ISSR primers and Molecular differentiation Medicine R Science Q
Acceso en línea:	https://doaj.org/article/893af0eef96b47828e3ed9c129c41e3a
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spelling	oai:doaj.org-article:893af0eef96b47828e3ed9c129c41e3a2021-12-02T15:33:00ZDNA fingerprinting, fixation-index (Fst), and admixture mapping of selected Bambara groundnut (Vigna subterranea [L.] Verdc.) accessions using ISSR markers system10.1038/s41598-021-93867-52045-2322https://doaj.org/article/893af0eef96b47828e3ed9c129c41e3a2021-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-93867-5https://doaj.org/toc/2045-2322Abstract As a new crop in Malaysia, forty-four Bambara groundnut (Vigna subterranea L. verdc.) genotypes were sampled from eleven distinct populations of different origins to explore the genetic structure, genetic inconsistency, and fixation index. The Bambara groundnut, an African underutilized legume, has the capacity to boost food and nutrition security while simultaneously addressing environmental sustainability, food availability, and economic inequalities. A set of 32 ISSRs were screened out of 96 primers based on very sharp, clear, and reproducible bands which detected a total of 510 loci with an average of 97.64% polymorphism. The average calculated value of PIC = 0.243, RP = 5.30, H = 0.285, and MI = 0.675 representing the efficiency of primer set for genetic differentiation among the genotypes. The ISSR primers revealed the number of alleles (Na = 1.97), the effective number of alleles (Ne = 1.38), Nei's genetic diversity (h = 0.248), and a moderate level of gene flow (Nm = 2.26) across the genotypes studied. The estimated Shannon’s information index (I = 0.395) indicates a high level of genetic variation exists among the accessions. Based on Nei’s genetic dissimilarity a UPMGA phylogenetic tree was constructed and grouped the entire genotypes into 3 major clusters and 6 subclusters. PCA analysis revealed that first principal component extracted maximum variation (PC1 = 13.92%) than second principal component (PC2 = 12.59%). Bayesian model-based STRUCTURE analysis assembled the genotypes into 3 (best ΔK = 3) genetic groups. The fixation-index (Fst) analysis narrated a very great genetic diversity (Fst = 0.19 to 0.40) exists within the accessions of these 3 clusters. This investigation specifies the effectiveness of the ISSR primers system for the molecular portrayal of V. subterranea genotypes that could be used for genetic diversity valuation, detection, and tagging of potential genotypes with quick, precise, and authentic measures for this crop improvement through effective breeding schemes.Md Mahmudul Hasan KhanMohd Y. RafiiShairul Izan RamleeMashitah JusohMd Al MamunJamilu HaliduNature PortfolioarticleVigna subterranea [L.] Verdc.DNA fingerprintingFixation-index (Fst)Admixture mappingISSR primers and Molecular differentiationMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-23 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Vigna subterranea [L.] Verdc. DNA fingerprinting Fixation-index (Fst) Admixture mapping ISSR primers and Molecular differentiation Medicine R Science Q
spellingShingle	Vigna subterranea [L.] Verdc. DNA fingerprinting Fixation-index (Fst) Admixture mapping ISSR primers and Molecular differentiation Medicine R Science Q Md Mahmudul Hasan Khan Mohd Y. Rafii Shairul Izan Ramlee Mashitah Jusoh Md Al Mamun Jamilu Halidu DNA fingerprinting, fixation-index (Fst), and admixture mapping of selected Bambara groundnut (Vigna subterranea [L.] Verdc.) accessions using ISSR markers system
description	Abstract As a new crop in Malaysia, forty-four Bambara groundnut (Vigna subterranea L. verdc.) genotypes were sampled from eleven distinct populations of different origins to explore the genetic structure, genetic inconsistency, and fixation index. The Bambara groundnut, an African underutilized legume, has the capacity to boost food and nutrition security while simultaneously addressing environmental sustainability, food availability, and economic inequalities. A set of 32 ISSRs were screened out of 96 primers based on very sharp, clear, and reproducible bands which detected a total of 510 loci with an average of 97.64% polymorphism. The average calculated value of PIC = 0.243, RP = 5.30, H = 0.285, and MI = 0.675 representing the efficiency of primer set for genetic differentiation among the genotypes. The ISSR primers revealed the number of alleles (Na = 1.97), the effective number of alleles (Ne = 1.38), Nei's genetic diversity (h = 0.248), and a moderate level of gene flow (Nm = 2.26) across the genotypes studied. The estimated Shannon’s information index (I = 0.395) indicates a high level of genetic variation exists among the accessions. Based on Nei’s genetic dissimilarity a UPMGA phylogenetic tree was constructed and grouped the entire genotypes into 3 major clusters and 6 subclusters. PCA analysis revealed that first principal component extracted maximum variation (PC1 = 13.92%) than second principal component (PC2 = 12.59%). Bayesian model-based STRUCTURE analysis assembled the genotypes into 3 (best ΔK = 3) genetic groups. The fixation-index (Fst) analysis narrated a very great genetic diversity (Fst = 0.19 to 0.40) exists within the accessions of these 3 clusters. This investigation specifies the effectiveness of the ISSR primers system for the molecular portrayal of V. subterranea genotypes that could be used for genetic diversity valuation, detection, and tagging of potential genotypes with quick, precise, and authentic measures for this crop improvement through effective breeding schemes.
format	article
author	Md Mahmudul Hasan Khan Mohd Y. Rafii Shairul Izan Ramlee Mashitah Jusoh Md Al Mamun Jamilu Halidu
author_facet	Md Mahmudul Hasan Khan Mohd Y. Rafii Shairul Izan Ramlee Mashitah Jusoh Md Al Mamun Jamilu Halidu
author_sort	Md Mahmudul Hasan Khan
title	DNA fingerprinting, fixation-index (Fst), and admixture mapping of selected Bambara groundnut (Vigna subterranea [L.] Verdc.) accessions using ISSR markers system
title_short	DNA fingerprinting, fixation-index (Fst), and admixture mapping of selected Bambara groundnut (Vigna subterranea [L.] Verdc.) accessions using ISSR markers system
title_full	DNA fingerprinting, fixation-index (Fst), and admixture mapping of selected Bambara groundnut (Vigna subterranea [L.] Verdc.) accessions using ISSR markers system
title_fullStr	DNA fingerprinting, fixation-index (Fst), and admixture mapping of selected Bambara groundnut (Vigna subterranea [L.] Verdc.) accessions using ISSR markers system
title_full_unstemmed	DNA fingerprinting, fixation-index (Fst), and admixture mapping of selected Bambara groundnut (Vigna subterranea [L.] Verdc.) accessions using ISSR markers system
title_sort	dna fingerprinting, fixation-index (fst), and admixture mapping of selected bambara groundnut (vigna subterranea [l.] verdc.) accessions using issr markers system
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/893af0eef96b47828e3ed9c129c41e3a
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DNA fingerprinting, fixation-index (Fst), and admixture mapping of selected Bambara groundnut (Vigna subterranea [L.] Verdc.) accessions using ISSR markers system

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