Integrative Single- and Multi-Trait GWASs Identify Pleiotropic Loci Affecting Growth and Egg Production in Zhedong Geese

Growth and egg production are the two most economically important traits in goose production systems. However, negative genetic correlations between these traits make it difficult to achieve balanced genetic improvement through selection. In this study, we analyzed whole-genome resequencing data from 1033 Zhedong White Geese to identify genetic variants related to birth weight (BW), body weight at 90 days (BW90), and egg number at 66 weeks of age (EN66). Single-trait genome-wide association studies (GWASs) identified 6, 5, and 5 lead SNPs significantly associated with BW, BW90, and EN66, respectively. By integrating network analysis, PLACO, and multivariate linear mixed models (mvLMMs), we further identified KCNAB2 and KCND3 as potential pleiotropic candidate genes influencing both growth and egg production. Notably, the variant at CHR25: 6006715, located within an intronic region of KCND3, was associated with increased BW (ZscoreBW = 4.44) and decreased EN66 (ZscoreEN66 = −3.55), showing strong pleiotropic significance (P_PLACO = 4.88 × 10−8). Collectively, these findings provide new insights into the genetic architecture underlying the antagonistic relationship between growth and egg production in geese and offer valuable genetic targets for developing breeding strategies that jointly optimize growth performance and reproductive efficiency.