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

Intramuscular fat (IMF) deposition is the primary economic driver of premium beef production, yet conventional phenotypic selection requires costly rearing to slaughter age. Although whole-genome sequencing has repeatedly flagged the KIRREL3 region on BTA29 as a candidate interval for meat quality in beef cattle, whether intronic polymorphisms within this gene are directly associated with carcass or meat-quality traits--and whether such marker effects remain stable across physiological stages--has not been validated. To address these gaps, we genotyped two intronic SNPs in KIRREL3 (g.30324329C>T, 63-bp site; g.30324473C>T, 203-bp site) in two age cohorts of Woking heifers (n = 226 at 36 months; n = 206 at 48 months), together with an independent validation cohort (n = 41) for fatty-acid profiling, meat-quality phenotyping, and multi-tissue expression analysis. Both loci were moderately polymorphic (PIC = 0.37) and in Hardy-Weinberg equilibrium. At 36 months, the TT genotype was associated with significantly higher dressing percentage, rib thickness, and meat grade than CC at both loci. By 48 months, associations at the 63-bp site persisted and the T allele showed complete dominance (CT and TT both exceeded CC in grade and rib thickness), whereas associations at the 203-bp site dissipated with age, showing no significant effect on intermuscular fat thickness or grade. In the validation cohort, palmitic acid (C16:0), linolenic acid (C18:3n3), and arachidonic acid (C20:4) followed a CC > TC >= TT trend (P < 0.05). Notably, CC animals displayed higher IMF and muscle KIRREL3 mRNA levels than TT animals, yet received lower meat grades--a pattern that awaits functional clarification. These findings identify KIRREL3 g.30324329C>T as a robust age-stable marker, providing a concrete target for early marker-assisted selection in Woking cattle.