Six genes (W1, W2, W3, W4, Wm and Wp) primarily control flower color in soybean. The recessive alleles at the W1 locus (white flower) or the W4 locus (near white flower) substantially reduced the amount of anthocyanins without affecting the contents of flavonol glycosides or dihydroflavonols. The recessive allele at the Wp locus (pink flower) reduced anthocyanins, flavonol glycosides, and dihydroflavonols. The recessive allele of the Wm locus (magenta flower) substantially reduced the amount of flavonol glycosides and increased dihydroflavonols without affecting the amount of anthocyanins. The recessive allele of the W2 locus (purple-blue flower) did not affect amount of flavonoids, but it increased vacuolar pH of flower petals, suggesting that W2 is responsible for vacuolar acidification in flower petals.
A new flower color phenotype (light purple) was discovered in a Japanese accession of a wild relative of soybean (Glycine soja Sieb. & Zucc.). Complementation analysis suggested that a new allele at the W1 locus is responsible for light purple flowers. HPLC analysis revealed that light purple flowers contained three novel anthocyanins together with lower amounts of the four anthocyanins present in purple flowers.