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Background   Glycine soja  is a wild relative of soybean that has purple flowers. No flower color variant of  Glycine soja  has been found in the natural habitat.    Results  B09121, an accession with light purple flowers, was discovered in southern Japan. Genetic analysis revealed that the gene responsible for the light purple flowers was allelic to the  W1  locus encoding flavonoid 3'5'-hydroxylase (F3'5'H). The new allele was designated as  w1-lp . The dominance relationship of the locus was  W1  > w1-lp  > w1 . One F 2  plant and four F 3  plants with purple flowers were generated in the cross between B09121 and a Clark near-isogenic line with  w1  allele. Flower petals of B09121 contained lower amounts of four major anthocyanins (malvidin 3,5-di- O -glucoside, petunidin 3,5-di- O -glucoside, delphinidin 3,5-di- O -glucoside and delphinidin 3- O -glucoside) common in purple flowers and contained small amounts of the 5'-unsubstituted versions of the above anthocyanins, peonidin 3,5-di- O -glucoside, cyanidin 3,5-di- O -glucoside and cyanidin 3- O -glucoside, suggesting that F3'5'H activity was reduced and flavonoid 3'-hydroxylase activity was increased. F3'5'H cDNAs were cloned from Clark and B09121 by RT-PCR. The cDNA of B09121 had a unique base substitution resulting in the substitution of valine with methionine at amino acid position 210. The base substitution was ascertained by dCAPS analysis. The polymorphism associated with the dCAPS markers co-segregated with flower color in the F 2  population. F 3  progeny test, and dCAPS and indel analyses suggested that the plants with purple flowers might be due to intragenic recombination and that the 65 bp insertion responsible for gene dysfunction might have been eliminated in such plants.    Conclusions  B09121 may be the first example of a flower color variant found in nature. The light purple flower was controlled by a new allele of the  W1  locus encoding F3'5'H. The flower petals contained unique anthocyanins not found in soybean and  G. soja . B09121 may be a useful tool for studies of the structural and functional properties of F3'5'H genes as well as investigations on the role of flower color in relation to adaptation of  G. soja  to natural habitats.

A new allele of flower color gene W1 encoding flavonoid 3'5'-hydroxylase is responsible for light purple flowers in wild soybean Glycine soja