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.)

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.