New allelic variant discovered at soybean flower color locus W1 encoding flavonoid 3′5′-hydroxylase

A soybean line producing light purple flowers (E023-H-12) was developed from an ethyl methanesulfonate (EMS)-treated population of cultivar Bay. The objective of this study was to investigate the genetic and molecular basis of flower color variation in E023-H-12. Genetic analysis suggested that the W1 gene encoding a flavonoid 3′5′-hydroxylase (F3′5′H) controls light purple flower color. A single plant with purple flowers was generated in an F₂ population derived from a cross between E023-H-12 and Clark-w1 with white flowers, probably because of intragenic recombination of the F3′5′H gene. The allele for light purple flower was designated as w1-lp2. The dominance relationships of the locus were W1 > w1-lp2 > w1. Flower petals of E023-H-12 had similar expression levels of the F3′5′H gene but they had 42% less anthocyanins compared with Bay. The lower anthocyanin content may account for the light purple color of this mutant line. The nucleotide sequence of the F3′5′H gene of E023-H-12 had a single nucleotide polymorphism (SNP) resulting in alteration of an amino acid (H137L). A derived cleaved amplified polymorphic sequence (dCAPS) marker to discriminate the SNP co-segregated with flower color. Thus, the amino acid substitution may be responsible for the lower anthocyanin content, and, consequently, light purple flower color.