Observed frequencies and qualitative analysis

Pigmentation did not segregate on the ear of the inbred lines so all kernels on the ear displayed pigmentation (Fig. 2a) which is consistent with pigmented pericarp (Fig. 2b) being a maternal tissue (Wright and Neuffer 1989). This allowed us to give each inbred line a binary rating for the presence (1) or absence (0) of pericarp pigmentation by visually inspecting the RGB TIFF files of the maize kernels. Examples of the variation in pigmentation among transgressive segregants are shown in Supplementary Fig. 2. After visual inspection of the maize kernel images, the observed number of inbred lines with pericarp pigmentation was tabulated per population, and the frequency of inbreds displaying pericarp pigmentation per population was calculated by dividing the number of pigmented progenies by the total population size.

Maize kernels from an inbred line with a) pigmented pericarp and from an inbred line with d) nonpigmented pericarp. b, e) The pericarp tissue is removed from the kernel of both inbred lines. The maize kernels following pericarp excision from the inbred line with c) pigmented pericarp and from the f) inbred line with nonpigmented pericarp.

A chi-square analysis was conducted to test 6 different genetic models to explain the observed inheritance pattern in pigmentation per population. Genetic models ranged from simple single-gene Mendelian inheritance assuming independent assortment to multigene models including epistasis without linkage (Table 2). All genetic models were tested in R software version 4.1 (R Core Team 2021) using the function chisq.test().

Expected segregation ratios associated with 6 different genetic models that assumed independent assortment or epistasis without linkage.