Inverted Repeat of Chalcone Synthase 3 Pseudogene Is Associated with Seed Coat Discoloration in Soybean

The dominant T allele for tawny pubescence is associated with chilling tolerance in soybean [Glycine max (L.) Merr.]. Yellow hilum cultivars with dominant I allele are preferred in Japan because of superior external seed appearance. The allelic combination of IITT darkens the entire seed coat, giving a dirty appearance to seeds. Previous studies revealed a quantitative trait locus (QTL) for seed coat discoloration in the vicinity of the I locus. This study was conducted to identify a candidate gene for this QTL. A breeding line 0734BW-1 (IITT) with severe discoloration had an inverted repeat of chalcone synthase 3 pseudogenes (pCHS3s), whereas the 5' copy of pCHS3 was replaced by a fragment of a DnaJ-like protein gene in a breeding line 0518BW-8 (IITT) showing slight discoloration. A marker discriminating this structural polymorphism was mapped at the peak of the QTL, suggesting that pCHS3s might be responsible for seed coat discoloration. The gene structure of 0518BW-8 was identical to that of a gray pubescent cultivar Toyoharuka (IItt) that is tolerant to seed coat browning induced by low temperatures. These results suggest that pCHS3s may control the intensity of seed coat discoloration in tawny pubescent cultivars (TT) and browning in gray pubescent cultivars (tt). Regardless of pubescence color, the allele may be useful for breeding cultivars producing seeds with acceptable external appearance in high-latitude regions where low temperatures frequently prevail.