Debnath, S and Tyagi, W and Rai, M and Singh, K and Majumder, S and Duhan, N and Meetei, N T (2024) Discovery of potential haplotypes associated with varying levels of vicine content due to the InDel1.4 and a coding-SNP in the VC1 gene in faba bean (Vicia faba L.). Plant Gene, 41. ISSN 2352-4073
Full text not available from this repository. (Request a copy)Abstract
Faba bean (Vicia faba L.) is a popular legume due to its nutritional, medicinal and environmental benefits. But vicine and convicine (VC) remain as the main threats for “favism” in individuals with genetic deficiency of Glucose-6-phosphate dehydrogenase (G6PDH) enzyme. Re-sequencing-based allele mining involving allele-specific Tetra-ARMS PCR has revealed a 92 bp InDel (Insertion-Deletion), designated as “InDel1.4” in the intron-4 of VC1 gene and a coding-SNP (T/C) at position +1588 in the exon-5. Consequently, three distinct haplotypes (Hap-1, Hap-2 and Hap-3) were identified based on the size of the intron-4 and the allelic status of the SNP in exon-5. LC-MS/MS analysis confirms that the vicine concentration varied between 3.489 and 10.025 g/kg in the entire collection of germplasm. A strong correlation (r = 0.84**) was observed between haplotypes and variation in vicine concentration. Translation of the sequenced fragments revealed that, the coding-SNP doesn't not change the amino acid composition of the VC1 protein. Therefore, the coding-SNP was found to be a synonymous SNP. As the InDel1.4 was located within few hundred base pairs away from the previously reported “AT insertional-mutation”, which was responsible for very low or near-zero VC faba bean, and also shows correlation with vicine content, the InDel could be utilized for a simple, reliable and cost-effective molecular marker assisted selection and crop improvement for developing faba beans with reduced VC. The Hap-1 and Hap-2 have tremendous potential to be utilized in haplotype-based breeding for faba bean improvement to combat favism.
| Item Type: | Article |
|---|---|
| Divisions: | Genebank Global Research Program - Accelerated Crop Improvement |
| CRP: | UNSPECIFIED |
| Uncontrolled Keywords: | faba bean, crop improvement, potential haplotypes, genetic deficiency |
| Subjects: | Others > Genetic Engineering Others > Genetics and Genomics Others > Legume Crops |
| Depositing User: | Mr Nagaraju T |
| Date Deposited: | 13 May 2025 06:02 |
| Last Modified: | 13 May 2025 06:02 |
| URI: | http://oar.icrisat.org/id/eprint/13071 |
| Official URL: | https://www.sciencedirect.com/science/article/abs/... |
| Projects: | UNSPECIFIED |
| Funders: | UNSPECIFIED |
| Acknowledgement: | Authors are thankful to CPGSAS, CAU (Imphal), Umiam, Meghalaya for providing funds and availing necessary facilities and instrumentation. This study was also supported by the Senior Research Fellowship grant awarded by the ICAR, New Delhi, India. We are also highly thankful to ICAR-NBPGR, New Delhi for providing diverse germplasm collections and ICAR-IARI, New Delhi for sharing two very important national varieties. We are highly thankful to European Nucleotide Archive (ENA) for giving free... |
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