Yadav, A K and Singh, C K and Kalia, R K and Mittal, S and Wankhede, D P and Kakani, R K and Ujjainwal, S and Aakash, . and Saroha, A and Nathawat, N S and Rani, R and Panchariya, P and Choudhary, M and Solanki, K and Chaturvedi, K K and Archak, S and Singh, K and Singh, G P and Singh, A K (2023) 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. BMC Plant Biology (TSI), 23. pp. 1-17. ISSN 1471-2229
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Abstract
Background Moth bean (Vigna aconitifolia) is an underutilized, protein-rich legume that is grown in arid and semiarid 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.
| Item Type: | Article |
|---|---|
| Divisions: | Genebank |
| CRP: | UNSPECIFIED |
| Uncontrolled Keywords: | Flowering time, GBS, GWAS, Multi-locus association, Moth bean, SNPs |
| Subjects: | Others > Genetics and Genomics Others > Legume Crops |
| Depositing User: | Mr Nagaraju T |
| Date Deposited: | 04 Oct 2023 09:53 |
| Last Modified: | 04 Oct 2023 09:53 |
| URI: | http://oar.icrisat.org/id/eprint/12212 |
| Official URL: | https://bmcplantbiol.biomedcentral.com/articles/10... |
| Projects: | BT/Ag/Network/Pulses-1/2017–18 |
| Funders: | Government of India - Department of Biotechnology |
| Acknowledgement: | The authors are thankful to Director, Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources (NBPGR), New Delhi, India, and ICAR-Central Arid Zone Research Institute for extending laboratory and field facilities for undertaking this work |
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