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. 2025 May 30;16(6):677.
doi: 10.3390/genes16060677.

Assessment of Genetic Diversity and Productive Traits in Crossbreed Cattle in the Caribbean Region, Colombia

Andrés Rodríguez-Serrano  1 , Marcos Ahumada-Velasco  1 , Jesús María Cárdenas Beltrán  1
Affiliations

Assessment of Genetic Diversity and Productive Traits in Crossbreed Cattle in the Caribbean Region, Colombia

Andrés Rodríguez-Serrano et al. Genes (Basel). .

Abstract

Objectives: Evaluate the genetic diversity and productive traits of crossbred cattle in the Caribbean region of Colombia, through analyses derived from the assessment of the genome-wide single-nucleotide polymorphism (SNP).

Methods: A total of 590 individuals and 66,098 SNPs were analyzed by principal components analysis (PCA) and detection of runs of homozygosity (ROH). The population was composed of 531 heifers marked as crossbreed and a group of 59 heifers marked as purebred Gyr. Additionally, allele frequencies were calculated for commercially important traits (CSN2, CSN3, LGB, DGAT1, GH1, CAPN1_316, CAPN1_350, CAPN1_4751, CAST_282, CAST_2870, and CAST_2959).

Results: Global differences in PCA were 7.35%, and principal components explained 1.94% and 5.41% of the variation. Five ROH islands were identified in crossbred animals on chromosomes 2, 5, 7, 8, and 12. The majority of observed ROH classes were shorter than 2 Mb, 54% in crossbreed cattle and 47% in Gyr cattle. Individual inbreeding was 5.2% in crossbreed and 12% in Gyr cattle. Both groups had similar allelic and genotypic frequencies for most of the evaluated commercial traits. Only a wide variation was observed in the genes related to growth hormone (GH1) and Calpastatin (CAST_2870 and CAST_22959). Crossbreed heifers had desired allele frequencies for better milk production and quality in the genes CSN2, LGB, DGAT1, and GH1, as well as in the genes CAST_2870 and CAST_2959.

Conclusions: Crossbreed cattle in the Colombian Caribbean region possess high genetic diversity and desirable allele frequencies to implement breeding and intense selection programs aimed at improving production yields.

Keywords: Gyr cattle; SNPs; dual-purpose systems; genomic analysis; homozygosity; inbreeding.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
Population groups according to principal component analysis (PCA).
Figure 2
Figure 2
SNP frequency within run of homozygosity in the autosome of crossbreed and Gyr cattle in the Caribbean region of Colombia.
Figure 3
Figure 3
Inbreeding based on ROH among the autosome of crossbreed and Gyr cattle from the Colombian Caribbean region.
See this image and copyright information in PMC

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