PSXII-12 - Partitioning direct and maternal genetic effects into additive and non-additive components for growth and maternal traits in Yorkshire pigs

This study investigates how much direct and maternal non-additive genetic effects contribute to growth and maternal traits in swine. We analyzed a sample of 19,475 genotyped Yorkshire pigs from Acuity Ag Solutions, LLC (Carlyle, IL). Approximately 50K SNPs were kept after quality control, and missing genotypes were then imputed using findhap.f90. The genotypes were used to construct genomic relationship matrices (GRMs) corresponding to additive (A), dominance (D), and additive-by-additive epistasis (E) effects for both direct and maternal effects. The GRMs were subsequently employed as covariance structure matrices in a linear mixed model consisting of eight random components, namely three direct genetic effects (A_d, D_d, and E_d), three maternal genetic effects (A_m, D_m, and E_m), maternal environmental effect, and common litter environmental effect. We estimated these variance components (VCs) for six growth traits (birth weight, average daily gain, back fat, and loin area) and six maternal traits of a sow (total number of piglets born, number of piglets born alive, average weight of piglets at birth, average weight of piglets weaned) using REML in MMAP (https://mmap.github.io/). As shown in Table 1, we found significant (P < 0.05) direct dominance and epistasis VCs for all six growth traits. Additionally, direct epistasis effects explained a larger proportion of phenotypic variation than direct dominance for all growth traits (0.04-0.12 vs. 0.01-0.04). In contrast, direct non-additive VCs were not significant for any maternal trait except for epistasis in average weight of piglets weaned. As for maternal non-additive effects, we only discovered significant additive VC in birth weight and average daily gain and significant epistasis VC in back fat (P < 0.05). Other maternal genetic VCs were largely negligible. In summary, direct dominance and epistasis effects play a prominent role in growth traits of Yorkshire pigs.