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 F 2 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.