Genome-Wide Association Studies of Body Weight, Body Conformation Traits and Coat Color in Gamba Sheep

Elucidating the genetic architecture of body weight (BW), body conformation, and coat color (CC) is vital for the precision breeding of Gamba sheep, a unique high-altitude indigenous breed. While previous studies focused primarily on general plateau adaptation, the specific genetic drivers regulating economic traits in this extreme-altitude population remain poorly understood. In this study, we characterized six key phenotypic traits and conducted genome-wide association studies (GWAS) leveraging whole-genome resequencing data from 296 individuals. To ensure the robustness of our findings, we systematically evaluated five statistical models (GLM, MLM, CMLM, MLMM, and the SUPER model) across different trait categories. The SUPER model was ultimately selected for growth-related traits due to its superior power in balancing signal sensitivity and false-positive control, whereas the MLMM model demonstrated the optimal fitting performance for the binary coat color phenotype, with both models consistently yielding genomic inflation factors ( λ ) close to the theoretical expectation ( 1.0). Phenotypic investigation revealed distinct sexual dimorphism in growth determinants: cannon bone circumference was the primary driver of body weight in rams, whereas body height and heart girth dominated in ewes. The GWAS identified 82 genome-wide significant SNPs, leading to the mapping of a prominent novel genomic region on chromosome 5 associated with body height. Functional annotation highlighted PRKCE and SGIP1 as plausible positional candidate genes for growth characteristics, while SPIRE2 was pinpointed as a primary genomic driver regulating coat color variation. These findings provide novel insights into the genetic blueprint governing growth and pigmentation in this unique livestock, offering precise molecular targets for future marker-assisted selection.