Maternal effects and recessive epistasis govern green, yellow and brown seed coat color inheritance in soybean [Glycine max (L.) Merr.]

Seed coat color is crucial for consumer preference in soybeans. This study explores the genetic mechanisms underlying yellow, green, and brown seed coats through reciprocal crosses, revealing that seed coat color is maternally inherited, with F₁ seeds matching the female parental phenotype. In the F₂ generation, all seeds had green coats, while F₃ segregation patterns followed a two-gene epistatic model. The yellow (SKAF148) x brown (AGS457) cross segregated in a 9:3:4 ratio (green: yellow: brown), while yellow x green (SKAF148 x AGS346) segregated in a 3:1 ratio (green: yellow). Here, we report that two loci, G1 and G2, govern color expression. Dominant alleles at both loci (G1_G2_) produced green seed coats, while yellow required G1_g2g2 and brown required homozygous recessive g1g1 alleles, demonstrating recessive epistasis where g1g1 masked G2 effects. This research establishes a genetic pathway from brown to yellow to green, offering key insights into the digenic inheritance of seed coat color. The parental genotypes were inferred as G1G1g2g2 (yellow), G1G1G2G2 (green), and g1g1G2G2 (brown). These findings provide valuable guidance for breeding programs targeting consumer-preferred seed coat colors in soybeans.