Flax seed and flower color inheritance is more complicated than once thought.

Flower and seed color are two characteristics of flax (Linum usitatissimum L.) where the mode of inheritance can be obscured by different genetic backgrounds. In this study, eight genetically diverse genotypes of flax with pairwise contrasting seed and flower colors were carefully selected from a large diversity panel and crossed in all directions (56 crosses). The mode of inheritance of seed and flower color was studied in F1, F2, and F3 generations during 2017–2020. Segregation patterns in F1 and F2 generations indicated that seed color is primarily determined by maternal genotype, but parents' genetic constitution finally defines character expression. Segregation analysis in the F3 generation indicated that seed color is governed by three loci designated as G, D, and Y1. Brown seed color was produced by the recessive allele of the Y1 locus and dominant alleles of the G and D loci (GGDDy1y1). The yellow seed color was attributed to the homozygous condition of two recessive genes and one dominant gene (ggDDy1y1 and GGddy1y1) or the homozygous condition of three dominant genes (GGDDY1Y1). Flower color was found to be controlled by three loci assigned as B1, B2, and C′, independent of the ones for seed color. The blue flower is governed by dominant alleles at all three loci, while homozygous recessive at any of the three loci will result in a white flower. Segregating ratios of 3:1, 9:7, 13:3, and 27:37 blue to white flowers suggested different epistatic interactions between these loci, including duplicate‐recessive and dominant‐recessive states. Core Ideas: Seed color is primarily determined by maternal genotype, but parents' genetic constitution determines the final expression of character.Genetic complexity of seed and flower color may be dynamic, transitioning from classical mendelian to epistatic inheritance patterns depending on the genetic background.Seed coat color is governed by three loci designated as G, D, and Y1.Flower color is controlled by three loci assigned as B1, B2, and C.There are epistatic relationships among the genes for seed and flower color traits depending on the genetic background of the parental genotypes. [ABSTRACT FROM AUTHOR]