Genome-Wide Association Study Reveals Genetic Loci Associated with Body Measurement Traits in Yanqi Horses

Body measurement traits are a direct production indicator reflecting growth status and guiding genetic selection. Identifying molecular markers associated with body measurement traits could accelerate animal breeding programs. The Yanqi horse, an important indigenous breed in Xinjiang, is primarily distributed in the Bayingolin Mongol Autonomous Prefecture. However, molecular markers linked to body measurement traits in Yanqi horses remain uncharacterized. In the present study, whole-genome resequencing was performed on 183 Yanqi horses, yielding 13,366,672 single-nucleotide polymorphisms (SNPs) after quality control. A genome-wide association study on withers height, body length, heart girth, and cannon bone circumference was conducted using a mixed linear model implemented in GEMMA, with population structure and relatedness controlled using principal components and a genomic kinship matrix. Bonferroni-adjusted thresholds (p < 1 × 10−7 for significant associations; p < 1 × 10−6 for suggestive associations) were applied to minimize false positives. A total of 185 single-nucleotide polymorphisms were significantly associated with body measurement traits and 359 candidate genes were annotated within 200 kb upstream and downstream of the significant loci. Among these, five genes, GABRB1, FIGN, GABRA4, ENSECAG00000051747, and COX7B2, may be implicated in the growth and development of Yanqi horses. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses indicated that these genes are primarily involved in cytoskeletal structures within muscle cells, regulation of the actin cytoskeleton, and neuroactive ligand–receptor interaction pathways. In summary, this study presents novel markers and candidate gene sets associated with body measurement traits in Yanqi horses, offering valuable insights for functional gene investigations and presenting substantial potential for accelerating the breeding of Yanqi horses.