Mir, R R and Choudhary, N and Bawa, V and Jan, S and Singh, B and Bhat, M A and Paliwal, R and Kumar, A and Chitikineni, A and Thudi, M and Varshney, R K (2021) 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, 11. pp. 1-17. ISSN 1664-8021
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Abstract
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.
| Item Type: | Article |
|---|---|
| Divisions: | Research Program : Genetic Gains |
| CRP: | UNSPECIFIED |
| Uncontrolled Keywords: | Common bean, North-western Himalayas, Allelic diversity, Structural analysis, GWAS, QTLs/genes for yield traits |
| Subjects: | Others > Genetics and Genomics Others > Germplasm Others > Legume Crops |
| Depositing User: | Mr Arun S |
| Date Deposited: | 12 May 2021 09:36 |
| Last Modified: | 12 May 2021 09:36 |
| URI: | http://oar.icrisat.org/id/eprint/11789 |
| Official URL: | https://doi.org/10.3389/fgene.2020.609603 |
| Projects: | UNSPECIFIED |
| Funders: | Science and Engineering Research Board (SERB), Department of Science and Technology (DST), Government of India |
| Acknowledgement: | The authors are highly thankful to the Dean, Faculty of Agriculture, SKUAST-Kashmir for providing different facilities during this study. |
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