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The wide range of flower colors in soybean is controlled by six independent loci ( W1 ,  W2 ,  W3 ,  W4 ,  Wm , and  Wp ). Among these loci, mutations in the  W3  locus under the  w4  allelic background (i.e.,  w3w4 ) produce near-white flowers, while the  W3w4  genotype produces purple throat flowers. Although a gene encoding dihydroflavonol 4-reductase,  DFR1 , has been known to be closely associated with the  W3  locus, its molecular identity has not yet been characterized. In the present study, we aimed to determine whether  DFR1  is responsible for allelic variations in the  W3  locus. On the basis of the sequence of a  DFR  probe,  Glyma . 14G072700  was identified as a candidate gene for  DFR1 , and nucleotide sequences of  Glyma . 14G072700  from cultivars with previously validated genotypes for the  W3  locus were determined. As a result, a number of nucleotide polymorphisms, mainly single-base substitutions, between both coding and 5′-upstream region sequences of the  W3  and  w3  alleles were identified. Among them, an  indel  of 311-bp in the 5′-upstream region was noteworthy, since the  Glyma . 14G072700  in all the  w3  alleles examined contained the  indel , whereas that in all the  W3  alleles did not; the former was barely expressed, but the latter was well expressed. These results suggest that  Glyma . 14G072700  is likely to correspond to  DFR1  for the  W3  locus and that its expression patterns may lead to allelic color phenotypes of  W3  and  w3  alleles under the  w4  allelic background.

Elucidation of Molecular Identity of the W3 Locus and Its Implication in Determination of Flower Colors in Soybean