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Background  Flower color of soybean is primarily controlled by six genes, viz.,  W1 ,  W2 ,  W3 ,  W4 ,  Wm  and  Wp . This study was conducted to investigate the genetic and chemical basis of newly-identified flower color variants including two soybean mutant lines, 222-A-3 (near white flower) and E30-D-1 (light purple flower), a near-isogenic line (Clark- w4 ), flower color variants (T321 and T369) descended from the  w4 -mutable line and kw4 (near white flower,  Glycine soja ).    Results  Complementation tests revealed that the flower color of 222-A-3 and kw4 was controlled by the recessive allele ( w4 ) of the  W4  locus encoding dihydroflavonol 4-reductase 2 (DFR2). In 222-A-3, a single base was deleted in the first exon resulting in a truncated polypeptide consisting of 24 amino acids. In Clark- w4 , base substitution of the first nucleotide of the fourth intron abolished the 5′ splice site, resulting in the retention of the intron. The  DFR2  gene of kw4 was not expressed. The above results suggest that complete loss-of-function of  DFR2  gene leads to near white flowers. Light purple flower of E30-D-1 was controlled by a new allele at the  W4  locus,  w4-lp . The gene symbol was approved by the Soybean Genetics Committee. In E30-D-1, a single-base substitution changed an amino acid at position 39 from arginine to histidine. Pale flowers of T369 had higher expression levels of the  DFR2  gene. These flower petals contained unique dihydroflavonols that have not yet been reported to occur in soybean and  G. soja .    Conclusions  Complete loss-of-function of  DFR2  gene leads to near white flowers. A new allele of the  W4  locus,  w4-lp  regulates light purple flowers. Single amino acid substitution was associated with light purple flowers. Flower petals of T369 had higher levels of  DFR2  gene expression and contained unique dihydroflavonols that are absent in soybean and  G. soja . Thus, mutants of the  DFR2  gene have unique flavonoid compositions and display a wide variety of flower color patterns in soybean, from near white, light purple, dilute purple to pale.

Allelic variation of soybean flower color gene W4 encoding dihydroflavonol 4-reductase 2