MutMap Reveals a Structural Deletion at the Chalcone Synthase Locus Controlling Black Seed Coat in a Gamma-Irradiated Vietnamese Soybean Mutant

Abstract

Black soybean is an important functional crop valued for its high anthocyanin content and associated health benefits, attracting increasing interest in plant breeding and mutation-based approaches to enhance its nutritional and agronomic traits. Here, we investigated a DT26 black seed-coat mutant (DT26BS) derived from the Vietnamese cultivar DT26 following gamma irradiation. Genetic analysis of F2 populations indicated that the phenotype is controlled by a single recessive mutation, with additional epistatic interactions observed in other genetic backgrounds. MutMap analysis based on whole-genome sequencing of pooled F2 individuals identified a candidate region on chromosome 8 corresponding to the I locus. A large deletion (~176 kb) was identified in this region, affecting multiple Chalcone Synthase (CHS) gene repeats, and which may disrupt RNAi-mediated silencing of CHS, thereby triggering anthocyanin restoration in the seed coat. PCR-based markers confirmed tight linkage between this deletion and the black seed-coat phenotype. Crosses with elite lines and further selection until F7 generations showed that the mutation has no adverse effects on major agronomic traits and is useful as a donor for developing improved lines with black seed coat, shorter maturity, high yield, and enhanced anthocyanin content for nutritional improvement. These results demonstrate the utility of MutMap for detecting irradiation-induced structural variants and extend its application to a non-reference elite tropical soybean background, providing a useful genetic resource for black soybean breeding.