Association of KIRREL3 Intronic Polymorphisms with Carcass Traits, Meat Quality, and Muscle Fatty Acid Composition in Woking Cattle

Intramuscular fat (IMF) deposition drives premium beef value, but phenotypic selection is costly and slow. Although genome-wide studies have linked the KIRREL3 region to meat quality, whether intronic variants directly affect carcass traits and retain predictive power across physiological stages remains unproven. We genotyped two intronic SNPs (g.29756010C>T and g.29756149C>T) in Woking cattle, a high-quality beef breed developed in Jilin Province, China (n = 473; 226 and 206 heifers at 36 and 48 months, respectively, plus an independent validation cohort of n = 41), assessed for fatty acid composition, meat quality, and multi-tissue gene expression. Both loci were polymorphic and in Hardy–Weinberg equilibrium. At 36 months, TT individuals showed higher dressing percentage, rib thickness, and meat grade than CC at both loci. By 48 months, the 63-bp locus retained broader associations with carcass traits, whereas the 203-bp locus effects weakened. In the validation group, CC animals had higher IMF and muscle KIRREL3 expression than TT, yet received lower meat grades. Five fatty acids differed significantly among genotypes after Benjamini–Hochberg correction (q < 0.05), whereas the dominant fatty acids (C16:0, C18:1n9c, C18:0, C18:2n6c) showed no proportional differences. KIRREL3 was most highly expressed in the kidney among eight tissues examined. These findings identify the 63-bp site as a candidate marker for meat quality in local Chinese cattle, with potential for marker-assisted selection pending confirmation in larger cohorts and functional studies.