Allelic Diversity, Structural Analysis, and Genome-Wide Association Study (GWAS) for Yield and Related Traits Using Unexplored Common Bean (Phaseolus vulgaris L.) Germplasm From Western Himalayas
The north-western Indian Himalayas possesses vast diversity in common bean germplasm due to several years of natural adaptation and farmer’s selection. Systematic efforts have been made for the first time for the characterization and use of this huge diversity for the identification of genes/quantit...
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doaj-a5024d99d54c42de85282aca131234622021-01-28T09:27:56ZengFrontiers Media S.A.Frontiers in Genetics1664-80212021-01-011110.3389/fgene.2020.609603609603Allelic Diversity, Structural Analysis, and Genome-Wide Association Study (GWAS) for Yield and Related Traits Using Unexplored Common Bean (Phaseolus vulgaris L.) Germplasm From Western HimalayasReyazul Rouf Mir0Neeraj Choudhary1Vanya Bawa2Sofora Jan3Bikram Singh4Mohd Ashraf Bhat5Rajneesh Paliwal6Ajay Kumar7Annapurna Chitikineni8Mahendar Thudi9Rajeev Kumar Varshney10Division of Genetics and Plant Breeding, Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Sopore, IndiaDivision of Plant Breeding and Genetics, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, IndiaDivision of Plant Breeding and Genetics, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, IndiaDivision of Genetics and Plant Breeding, Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Sopore, IndiaDivision of Plant Breeding and Genetics, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, IndiaDivision of Genetics and Plant Breeding, Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Sopore, IndiaThe International Institute of Tropical Agriculture, Ibadan, NigeriaDepartment of Plant Sciences, North Dakota State University, Fargo, ND, United StatesCenter of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, IndiaCenter of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, IndiaCenter of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, IndiaThe north-western Indian Himalayas possesses vast diversity in common bean germplasm due to several years of natural adaptation and farmer’s selection. Systematic efforts have been made for the first time for the characterization and use of this huge diversity for the identification of genes/quantitative trait loci (QTLs) for yield and yield-contributing traits in common bean in India. A core set of 96 diverse common bean genotypes was characterized using 91 genome-wide genomic and genic simple sequence repeat (SSR) markers. The study of genetic diversity led to the identification of 691 alleles ranging from 2 to 21 with an average of 7.59 alleles/locus. The gene diversity (expected heterozygosity, He) varied from 0.31 to 0.93 with an average of 0.73. As expected, the genic SSR markers detected less allelic diversity than the random genomic SSR markers. The traditional clustering and Bayesian clustering (structural analysis) analyses led to a clear cut separation of a core set of 96 genotypes into two distinct groups based on their gene pools (Mesoamerican and Andean genotypes). Genome-wide association mapping for pods/plant, seeds/pod, seed weight, and yield/plant led to the identification of 39 significant marker–trait associations (MTAs) including 15 major, 15 stable, and 13 both major and stable MTAs. Out of 39 MTAs detected, 29 were new MTAs reported for the first time, whereas the remaining 10 MTAs were already identified in earlier studies and therefore declared as validation of earlier results. A set of seven markers was such, which were found to be associated with multiple (two to four) different traits. The important MTAs will be used for common bean molecular breeding programs worldwide for enhancing common bean yield.https://www.frontiersin.org/articles/10.3389/fgene.2020.609603/fullcommon beannorth-western Himalayasallelic diversitystructural analysisGWASQTLs/genes for yield traits |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Reyazul Rouf Mir Neeraj Choudhary Vanya Bawa Sofora Jan Bikram Singh Mohd Ashraf Bhat Rajneesh Paliwal Ajay Kumar Annapurna Chitikineni Mahendar Thudi Rajeev Kumar Varshney |
spellingShingle |
Reyazul Rouf Mir Neeraj Choudhary Vanya Bawa Sofora Jan Bikram Singh Mohd Ashraf Bhat Rajneesh Paliwal Ajay Kumar Annapurna Chitikineni Mahendar Thudi Rajeev Kumar Varshney Allelic Diversity, Structural Analysis, and Genome-Wide Association Study (GWAS) for Yield and Related Traits Using Unexplored Common Bean (Phaseolus vulgaris L.) Germplasm From Western Himalayas Frontiers in Genetics common bean north-western Himalayas allelic diversity structural analysis GWAS QTLs/genes for yield traits |
author_facet |
Reyazul Rouf Mir Neeraj Choudhary Vanya Bawa Sofora Jan Bikram Singh Mohd Ashraf Bhat Rajneesh Paliwal Ajay Kumar Annapurna Chitikineni Mahendar Thudi Rajeev Kumar Varshney |
author_sort |
Reyazul Rouf Mir |
title |
Allelic Diversity, Structural Analysis, and Genome-Wide Association Study (GWAS) for Yield and Related Traits Using Unexplored Common Bean (Phaseolus vulgaris L.) Germplasm From Western Himalayas |
title_short |
Allelic Diversity, Structural Analysis, and Genome-Wide Association Study (GWAS) for Yield and Related Traits Using Unexplored Common Bean (Phaseolus vulgaris L.) Germplasm From Western Himalayas |
title_full |
Allelic Diversity, Structural Analysis, and Genome-Wide Association Study (GWAS) for Yield and Related Traits Using Unexplored Common Bean (Phaseolus vulgaris L.) Germplasm From Western Himalayas |
title_fullStr |
Allelic Diversity, Structural Analysis, and Genome-Wide Association Study (GWAS) for Yield and Related Traits Using Unexplored Common Bean (Phaseolus vulgaris L.) Germplasm From Western Himalayas |
title_full_unstemmed |
Allelic Diversity, Structural Analysis, and Genome-Wide Association Study (GWAS) for Yield and Related Traits Using Unexplored Common Bean (Phaseolus vulgaris L.) Germplasm From Western Himalayas |
title_sort |
allelic diversity, structural analysis, and genome-wide association study (gwas) for yield and related traits using unexplored common bean (phaseolus vulgaris l.) germplasm from western himalayas |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Genetics |
issn |
1664-8021 |
publishDate |
2021-01-01 |
description |
The north-western Indian Himalayas possesses vast diversity in common bean germplasm due to several years of natural adaptation and farmer’s selection. Systematic efforts have been made for the first time for the characterization and use of this huge diversity for the identification of genes/quantitative trait loci (QTLs) for yield and yield-contributing traits in common bean in India. A core set of 96 diverse common bean genotypes was characterized using 91 genome-wide genomic and genic simple sequence repeat (SSR) markers. The study of genetic diversity led to the identification of 691 alleles ranging from 2 to 21 with an average of 7.59 alleles/locus. The gene diversity (expected heterozygosity, He) varied from 0.31 to 0.93 with an average of 0.73. As expected, the genic SSR markers detected less allelic diversity than the random genomic SSR markers. The traditional clustering and Bayesian clustering (structural analysis) analyses led to a clear cut separation of a core set of 96 genotypes into two distinct groups based on their gene pools (Mesoamerican and Andean genotypes). Genome-wide association mapping for pods/plant, seeds/pod, seed weight, and yield/plant led to the identification of 39 significant marker–trait associations (MTAs) including 15 major, 15 stable, and 13 both major and stable MTAs. Out of 39 MTAs detected, 29 were new MTAs reported for the first time, whereas the remaining 10 MTAs were already identified in earlier studies and therefore declared as validation of earlier results. A set of seven markers was such, which were found to be associated with multiple (two to four) different traits. The important MTAs will be used for common bean molecular breeding programs worldwide for enhancing common bean yield. |
topic |
common bean north-western Himalayas allelic diversity structural analysis GWAS QTLs/genes for yield traits |
url |
https://www.frontiersin.org/articles/10.3389/fgene.2020.609603/full |
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