A rearrangement resulting in small tandem repeats in the F3′5′H gene of white flower genotypes is associated with the soybean W1 locus

Soybean [Glycine max (L.) Merr.] flower pigmentation is controlled by six loci, W1, W2, W3, W4, Wm, and Wp, of which the functions of only three are known. None of the recessive alleles at those three loci completely abolishes flower pigmentation. On the other hand, the W1 locus is required for flower pigmentotion. Based on genetic and biochemical data, the trihydroxylation reaction to form delphinidin-3-glucoside has been postulated as a likely function of the W1 locus. We report the cloning and sequencing of a flavonoid 3′5′-hydroxylase (F3′5′H) gene from the purple flower soybean line L79-908 (W1) and the recessive allele from the white flower isoline 'Williams' (w1). The mutation is a rearrangement leading to a small (65 bp) insertion of tandem repeats in exon 3 that truncates the translation product prematurely. The presence of this insertion in all-white flower soybean lines examined and in those of a segregating population resulting from a cross between purple and white flower lines presents compelling evidence that the F3′5′H gene isolated is likely encoded by the W1 locus of Glycine max. GmF3′5′H is a single-copy gene, expressed at very low levels in all tissues examined, including flower and seed coats, but sufficient to account for the contribution of the delphinidin-based anthocyanins and/or proanthocyanins in these tissues.