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Genetic diversity, population structure, and genome-wide association study for the flowering trait in a diverse panel of 428 moth bean (Vigna aconitifolia) accessions using genotyping by sequencing
BACKGROUND: Moth bean (Vigna aconitifolia) is an underutilized, protein-rich legume that is grown in arid and semi-arid areas of south Asia and is highly resistant to abiotic stresses such as heat and drought. Despite its economic importance, the crop remains unexplored at the genomic level for gene...
Autores principales: | , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10148550/ https://www.ncbi.nlm.nih.gov/pubmed/37120525 http://dx.doi.org/10.1186/s12870-023-04215-w |
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author | Yadav, Arvind Kumar Singh, Chandan Kumar Kalia, Rajwant K. Mittal, Shikha Wankhede, Dhammaprakash P. Kakani, Rajesh K. Ujjainwal, Shraddha Aakash Saroha, Ankit Nathawat, N. S. Rani, Reena Panchariya, Pooja Choudhary, Manoj Solanki, Kantilal Chaturvedi, K. K. Archak, Sunil Singh, Kuldeep Singh, Gyanendra Pratap Singh, Amit Kumar |
author_facet | Yadav, Arvind Kumar Singh, Chandan Kumar Kalia, Rajwant K. Mittal, Shikha Wankhede, Dhammaprakash P. Kakani, Rajesh K. Ujjainwal, Shraddha Aakash Saroha, Ankit Nathawat, N. S. Rani, Reena Panchariya, Pooja Choudhary, Manoj Solanki, Kantilal Chaturvedi, K. K. Archak, Sunil Singh, Kuldeep Singh, Gyanendra Pratap Singh, Amit Kumar |
author_sort | Yadav, Arvind Kumar |
collection | PubMed |
description | BACKGROUND: Moth bean (Vigna aconitifolia) is an underutilized, protein-rich legume that is grown in arid and semi-arid areas of south Asia and is highly resistant to abiotic stresses such as heat and drought. Despite its economic importance, the crop remains unexplored at the genomic level for genetic diversity and trait mapping studies. To date, there is no report of SNP marker discovery and association mapping of any trait in this crop. Therefore, this study aimed to dissect the genetic diversity, population structure and marker-trait association for the flowering trait in a diversity panel of 428 moth bean accessions using genotyping by sequencing (GBS) approach. RESULTS: A total of 9078 high-quality single nucleotide polymorphisms (SNPs) were discovered by genotyping of 428 moth bean accessions. Model-based structure analysis and PCA grouped the moth bean accessions into two subpopulations. Cluster analysis revealed accessions belonging to the Northwestern region of India had higher variability than accessions from the other regions suggesting that this region represents its center of diversity. AMOVA revealed more variations within individuals (74%) and among the individuals (24%) than among the populations (2%). Marker-trait association analysis using seven multi-locus models including mrMLM, FASTmrEMMA FASTmrEMMA, ISIS EM-BLASSO, MLMM, BLINK and FarmCPU revealed 29 potential genomic regions for the trait days to 50% flowering, which were consistently detected in three or more models. Analysis of the allelic effect of the major genomic regions explaining phenotypic variance of more than 10% and those detected in at least 2 environments showed 4 genomic regions with significant phenotypic effect on this trait. Further, we also analyzed genetic relationships among the Vigna species using SNP markers. The genomic localization of moth bean SNPs on genomes of closely related Vigna species demonstrated that maximum numbers of SNPs were getting localized on Vigna mungo. This suggested that the moth bean is most closely related to V. mungo. CONCLUSION: Our study shows that the north-western regions of India represent the center of diversity of the moth bean. Further, the study revealed flowering-related genomic regions/candidate genes which can be potentially exploited in breeding programs to develop early-maturity moth bean varieties. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-023-04215-w. |
format | Online Article Text |
id | pubmed-10148550 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-101485502023-04-30 Genetic diversity, population structure, and genome-wide association study for the flowering trait in a diverse panel of 428 moth bean (Vigna aconitifolia) accessions using genotyping by sequencing Yadav, Arvind Kumar Singh, Chandan Kumar Kalia, Rajwant K. Mittal, Shikha Wankhede, Dhammaprakash P. Kakani, Rajesh K. Ujjainwal, Shraddha Aakash Saroha, Ankit Nathawat, N. S. Rani, Reena Panchariya, Pooja Choudhary, Manoj Solanki, Kantilal Chaturvedi, K. K. Archak, Sunil Singh, Kuldeep Singh, Gyanendra Pratap Singh, Amit Kumar BMC Plant Biol Research BACKGROUND: Moth bean (Vigna aconitifolia) is an underutilized, protein-rich legume that is grown in arid and semi-arid areas of south Asia and is highly resistant to abiotic stresses such as heat and drought. Despite its economic importance, the crop remains unexplored at the genomic level for genetic diversity and trait mapping studies. To date, there is no report of SNP marker discovery and association mapping of any trait in this crop. Therefore, this study aimed to dissect the genetic diversity, population structure and marker-trait association for the flowering trait in a diversity panel of 428 moth bean accessions using genotyping by sequencing (GBS) approach. RESULTS: A total of 9078 high-quality single nucleotide polymorphisms (SNPs) were discovered by genotyping of 428 moth bean accessions. Model-based structure analysis and PCA grouped the moth bean accessions into two subpopulations. Cluster analysis revealed accessions belonging to the Northwestern region of India had higher variability than accessions from the other regions suggesting that this region represents its center of diversity. AMOVA revealed more variations within individuals (74%) and among the individuals (24%) than among the populations (2%). Marker-trait association analysis using seven multi-locus models including mrMLM, FASTmrEMMA FASTmrEMMA, ISIS EM-BLASSO, MLMM, BLINK and FarmCPU revealed 29 potential genomic regions for the trait days to 50% flowering, which were consistently detected in three or more models. Analysis of the allelic effect of the major genomic regions explaining phenotypic variance of more than 10% and those detected in at least 2 environments showed 4 genomic regions with significant phenotypic effect on this trait. Further, we also analyzed genetic relationships among the Vigna species using SNP markers. The genomic localization of moth bean SNPs on genomes of closely related Vigna species demonstrated that maximum numbers of SNPs were getting localized on Vigna mungo. This suggested that the moth bean is most closely related to V. mungo. CONCLUSION: Our study shows that the north-western regions of India represent the center of diversity of the moth bean. Further, the study revealed flowering-related genomic regions/candidate genes which can be potentially exploited in breeding programs to develop early-maturity moth bean varieties. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-023-04215-w. BioMed Central 2023-04-29 /pmc/articles/PMC10148550/ /pubmed/37120525 http://dx.doi.org/10.1186/s12870-023-04215-w Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Yadav, Arvind Kumar Singh, Chandan Kumar Kalia, Rajwant K. Mittal, Shikha Wankhede, Dhammaprakash P. Kakani, Rajesh K. Ujjainwal, Shraddha Aakash Saroha, Ankit Nathawat, N. S. Rani, Reena Panchariya, Pooja Choudhary, Manoj Solanki, Kantilal Chaturvedi, K. K. Archak, Sunil Singh, Kuldeep Singh, Gyanendra Pratap Singh, Amit Kumar Genetic diversity, population structure, and genome-wide association study for the flowering trait in a diverse panel of 428 moth bean (Vigna aconitifolia) accessions using genotyping by sequencing |
title | Genetic diversity, population structure, and genome-wide association study for the flowering trait in a diverse panel of 428 moth bean (Vigna aconitifolia) accessions using genotyping by sequencing |
title_full | Genetic diversity, population structure, and genome-wide association study for the flowering trait in a diverse panel of 428 moth bean (Vigna aconitifolia) accessions using genotyping by sequencing |
title_fullStr | Genetic diversity, population structure, and genome-wide association study for the flowering trait in a diverse panel of 428 moth bean (Vigna aconitifolia) accessions using genotyping by sequencing |
title_full_unstemmed | Genetic diversity, population structure, and genome-wide association study for the flowering trait in a diverse panel of 428 moth bean (Vigna aconitifolia) accessions using genotyping by sequencing |
title_short | Genetic diversity, population structure, and genome-wide association study for the flowering trait in a diverse panel of 428 moth bean (Vigna aconitifolia) accessions using genotyping by sequencing |
title_sort | genetic diversity, population structure, and genome-wide association study for the flowering trait in a diverse panel of 428 moth bean (vigna aconitifolia) accessions using genotyping by sequencing |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10148550/ https://www.ncbi.nlm.nih.gov/pubmed/37120525 http://dx.doi.org/10.1186/s12870-023-04215-w |
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