Large deletions including inverted repeats of the pseudo<i>CHS</i> gene in seed-coat-pigmented mutants derived from Japanese yellow soybean cultivars

In many yellow soybean (Glycine max) cultivars grown in Japan, pigmentation is suppressed throughout the seed coat, including the hilum region. This phenomenon is due to naturally occurring RNA silencing of chalcone synthase (CHS) genes, which is induced by the I allele of the I locus. A candidate for the I allele, designated GmIRCHS, includes inverted repeats of the pseudoCHS gene and is clustered with the ICHS1 gene. Fully pigmented seeds are sometimes produced by yellow soybean cultivars as a result of a spontaneous mu‍tation. The causal DNA changes are deletions that involve GmIRCHS. While small deletions of 0.8–3.3 kb have been previously characterized, the details for larger deletions remain unknown. Here, we characterized these large deletions using a recently released whole-genome sequence for the Japanese yellow soybean cultivar ‘Enrei’. The deletions encompass 17- to 38-kb DNA regions, which involve GmIRCHS and some or all of the neighboring genes GmJ1, P450, Transferase, and ICHS1. These data suggest that the DNA region surrounding GmIRCHS is prone to large structural changes, leading to reversion to pigmentation of the seed coat.