Allele and Genotype Frequencies of Production Trait SNPs in Crossbred Heifers of the Colombian Caribbean.
- 1CTIE (Centro de Transferencia, Innovación y Emprendimiento of the Universidad de Cartagena), Universidad de Cartagena, Cartagena de Indias 130001, Colombia.
- 2Faculty of Agricultural Sciences, La Salle University, Bogotá 111321, Colombia.
Abstract
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.
Related
- Reef fish assemblages on Acropora patches in the Colombian Caribbean: resistance to reef degradation
- Genotype-by-environment interaction analysis for flowering, maturity time and yield in fonio across traditional and prospective production areas in Northern Benin
- Genotype by environment interaction under two production systems utilizing a random regression model for milk production traits in multiparous South African Holstein dairy cattle.
- Genotype by environment interactions for production and resilience-related traits: the role of management across size-contrasting sheep breeds and pasture qualities
- Assessing the comparative longitudinal immunogenicity of two commercial foot-and-mouth disease vaccines in crossbred dairy calves in Sebeta Hawas, Ethiopia
BibTeX
@article{velasco2026allele,
title = {{Allele and Genotype Frequencies of Production Trait SNPs in Crossbred Heifers of the Colombian Caribbean.}},
author = {Marcos Ahumada Velasco and Andrés Camilo Rodríguez Serrano and Juan David Corrales Álvarez and Jesús María Cárdenas Beltrán and José Morelos Gómez},
journal = {Animals : an open access journal from MDPI},
year = {2026},
month = oct,
doi = {10.3390/ani16203270},
url = {https://europepmc.org/article/MED/42939201},
note = {CC BY},
}
RIS
TY - JOUR
TI - Allele and Genotype Frequencies of Production Trait SNPs in Crossbred Heifers of the Colombian Caribbean.
AU - Marcos Ahumada Velasco
AU - Andrés Camilo Rodríguez Serrano
AU - Juan David Corrales Álvarez
AU - Jesús María Cárdenas Beltrán
AU - José Morelos Gómez
PY - 2026
DA - 2026/10/17
JO - Animals : an open access journal from MDPI
DO - 10.3390/ani16203270
UR - https://europepmc.org/article/MED/42939201
AB - 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.
SN - 2076-2615
ER -