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

Abstract

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.

Color Variation in a Novel Glycine soja Mutant W4‐S1 with Pinkish‐White Flowers Is Controlled by a Single Recessive Allele at the W4 Locus

“…In our previous study, we reported that a 311‐bp indel in the 5′‐upstream region of G . max DFR1 distinguished W3 from w3 (Park et al, 2015). In brief, the w3 allele had the indel and was associated with the disruption of DFR1 expression, whereas the W3 allele did not and was accompanied by a high level of DFR1 expression.…”

“…W1 , W2 , Wm , and Wp encode flavonoid 3′5′‐hydroxylase (F3′5′H), myeloblastosis (MYB) transcription factor, flavonol synthase, and flavanone 3‐hydroxylase, respectively (Takahashi et al, 2007, 2013; Zabala and Vodkin, 2005, 2007). W3 and W4 encode dihydroflavonol 4‐reductase (DFR) (Fasoula et al, 1995; Park et al, 2015; Xu et al, 2010).…”

“…Double mutations in W3 and W4 (i.e., W1w3w4 ) invariably lead to the production of near‐white flowers in G . max (Hartwig and Hinson, 1962; Park et al, 2015). Park et al (2015) demonstrated that the W3 locus probably encodes DFR1.…”

“…max (Hartwig and Hinson, 1962; Park et al, 2015). Park et al (2015) demonstrated that the W3 locus probably encodes DFR1. These authors found that DFR1 is highly expressed in a W3 allelic background but is barely expressed in w3 and also proposed that, among several polymorphisms detected in the genomic sequence of the w3 allele, a noteworthy insertion and deletion (indel) of 311 bp in the 5′‐upstream region might cause the disruption of DFR1 expression.…”

Genetic and Chemical Analysis of Deep Purple Flower in Soybean

“…The F 2 population segregated into 86 plants with purple flowers and 24 plants with deep purple flowers. gene) in Chr 17, and DFR3 in Chr 2 (Xu and Palmer, 2005;Yang et al, 2010;Park et al, 2015). All of the 10 F 3 families derived from F 2 plants with deep purple flowers were fixed for deep purple flowers (Table 2).…”