A non-synonymous SNP in homolog of BADH2 gene is associated with fresh pod fragrance in dolichos bean (Lablab purpureus var. lignosus (Prain) Kumari)

Fresh pods are harvestable and marketable economic product in dolichos bean. Fresh pod fragrance is one of the ‘farmers’ and ‘consumers’ preferred traits in dolichos bean varieties. The pods with high fragrance fetch a premium price in the market. In breeding programmes, pod fragrance is routinely assessed by organoleptic (sensory) means, which is highly relative and subjective. Identification of linked DNA markers not only offer an objective means but also enable selection of fragment genotypes at seedling stage itself. Betaine aldehyde dehydrogenase (BADH) is known to be the key gene responsible for fragrance in other legumes such as vegetable soybean and mung bean. Taking cues from highly conserved domains in proteins coded by BADH genes, we isolated dolichos bean homolog (LpBADH2) of soybean GmBADH2 gene using reported degenerate primers designed to conserved domains. Analysis of the translated amino acid sequence of LpBADH2 showed high degree of similarity (97.30%) with those of soybean homolog (GmBADH2). Conserved amino acid sequence of aldehyde dehydrogenase-super family were also identified in LpBADH2. Multiple sequence alignment of nucleotide sequences of LpBADH2 with those of related legumes using “ClustalW” revealed the presence of a single non-synonymous single nucleotide polymorphic (SNPs) and three synonymous SNP sites in LpBADH2. The substitution of the amino acid tyrosine in (fragrant genotypes) with phenyl alanine (non-fragrant genotypes) in protein coded by LpBADH2 appeared to be the cause for switch over from fragrance to non-fragrance in dolichos bean. These results are discussed in relation to strategies to breed dolichos bean cultivars with desired level of pod fragrance.