Identification of a new fragrance allele in soybean and development of its functional marker

We have previously reported an association between a single nucleotide polymorphism (SNP) in exon 10 of GmBADH2 gene and fragrance in vegetable soybean [Glycine max (L.) Merr.] cultivar Kaori. The SNP causes amino acid substitution in a highly conserved motif of GmBADH2 protein, which is necessary for functional activity of the protein. In this study, we sequenced GmBADH2 in another fragrant soybean cultivar Chamame and discovered a new fragrance allele, which has a 2-bp (TT) deletion in exon 10. The deletion causes a reading frame shift and introduces a premature stop codon, which could abolish protein function and result in fragrance. The old and new fragrance-promoting alleles were designated Gmbadh2-1 and Gmbadh2-2, respectively. A simple and co-dominant functional marker was developed for genotyping Gmbadh2-2. The marker can discriminate between fragrant and non-fragrant soybeans and distinguish the two different fragrant soybeans, and thus is useful for routine genotyping for the fragrance trait in breeding programs. Quantitative trait locus (QTL) mapping in an F-2 population using Chamame as the fragrance donor revealed that the location of the fragrance QTL nearly coincided with that of the functional marker, confirming the association between GmBADH2 and fragrance in Chamame.