Genome-wide association study identifies candidate genes regulating multi-stage body size traits in Longling yellow goats

• Weaning, sexual maturity, and the yearling period are key goat growth stages. • Genome-wide association studies were performed in Longling yellow goats. • Key loci and genes for three grow and developmental stages were identified. • Biological pathways affecting early-life growth were significantly enriched. • Findings provide insights for improving body size traits in the goat industry. Enhancing growth traits is a key goal in sustainable meat goat production. and is often regarded as a primary objective in breeding programs for meat goats. In this study, whole genome low-depth sequencing data of 300 Longling yellow female goats were used to detected the genome-wide single nucleotide polymorphisms ( SNPs ), and the genome-wide association study ( GWAS ) based on SNPs was performed for the BW, body height ( BH ), body length ( BL ), chest circumference ( CC ), chest depth ( CD ), chest width ( CW ), and cannon circumference ( cc ) at the ages of 3, 9, and 12 months. After genotype imputation and quality control, 6,153,300 SNPs were retained for further analysis. A total of 129 genome-wide significant SNPs were obtained, and these SNPs were annotated to 146 candidate genes associated with body size traits, such as MMP16 , MECOM for BW; SCD5 , LEF1 for BL; and PDE4D , KCND2 for BH. EPHA5 is pleiotropic, associated with BW, BL, BH, CC, and CW. Notably, ADAMTS3 was linked to CD, while GIGYF2 and DGKB were associated with cc. Functional analysis revealed that 13 candidate genes are implicated in pivotal biological processes, including extracellular matrix organization and lipid metabolism. Notably, EPHA5 , ROS1 , and EPHA3 were significantly enriched in molecular function related to growth factor receptor activity. These findings offer valuable genetic markers for genomic selection in goats, thereby providing resources for advancing precision breeding programs.