A novel pinkish-white flower color variant is caused by a new allele of flower color gene w1 in wild soybean (Glycine soja)

The enzyme flavonoid 3^′,5^′-hydroxylase (F3^′ 5^′H) plays an important role in producing anthocyanin pigments in soybean. Loss of function of the W1 locus encoding F3^′ 5^′H always produces white flowers. However, few color variations have been reported in wild soybean. In the present study, we isolated a new color variant of wild soybean accession (IT261811) with pinkish-white flowers. We found that the flower’s pinkish-white color is caused by w1-s3, a single recessive allele of W1. The SNP detected in the mutant caused amino acid substitution (A₃₀₄S) in a highly conserved SRS4 domain of F3^′ 5^′H proteins. On the basis of the results of the protein variation effect analyzer (PROVEAN) tool, we suggest that this mutation may lead to hypofunctional F3^′ 5^′H activity rather than non-functional activity, which thereby results in its pinkish-white color.