Allele and Genotype Frequencies of Production Trait SNPs in Crossbred Heifers of the Colombian Caribbean

The Colombian Caribbean dual-purpose livestock system (Bos taurus × Bos indicus) is an important source of milk and beef, yet molecular characterization of trait-associated markers remains limited. This study characterized allele and genotype frequencies of 29 single-nucleotide polymorphisms (SNPs) associated with meat quality and milk production traits in 1585 crossbred heifers from five departments of the Colombian Caribbean. DNA was extracted from hair follicles and genotyped with the Axiom™ Bovine 100K Array. Markers spanned genes for muscle growth and proteolysis (CAPN1, CAST, MSTN), energy metabolism (LEP, DGAT1), and milk protein composition (CSN2, CSN3, PAEP, GH1, GHR, ABCG2). Hardy–Weinberg equilibrium (HWE) was assessed by chi-squared test. Of the 29 markers, 21 were polymorphic and testable: 19 conformed to HWE and 2 deviated (PAEP_239, PAEP_312). The remaining 8 were monomorphic. Approximately 48% of loci showed very high favorable allele frequencies (q > 0.99 or p > 0.99), whereas 52% maintained intermediate heterozygosity. CSN3_526 reached near-fixation of the favorable B allele (q = 0.996), consistent with selection for cheese yield, whereas CAST_282 and CAST_2870 showed high heterozygosity (f(AB) ≈ 0.47–0.48), indicating substantial remaining variation at these loci. These findings provide the first descriptive dual meat-and-milk SNP frequency profile for these crossbred heifers and a molecular baseline for the future development of bioeconomic selection indices in tropical dual-purpose systems. Frequencies are reported at the pooled and department-stratified levels; the results are descriptive and require phenotypic validation before any inference on marker effects or suitability for selection.