Identifying signatures of recent selection in Holstein cattle in the tropic

Juan C. Rincón; Albeiro López; Julián Echeverri

doi:10.17533/udea.rccp.v31n1a06

Authors

Juan C. Rincón Technological University of Pereira, National University of Colombia
Albeiro López National University of Colombia
Julián Echeverri National University of Colombia

DOI:

https://doi.org/10.17533/udea.rccp.v31n1a06

Keywords:

dairy cattle, genetic mapping, QTLs, selection pressure, single nucleotide polymorphism

Abstract

Background: Holstein cattle have undergone strong selection processes in the world. These selection signatures can be recognized and utilized to identify regions of the genome that are important for milk yield. Objective: To identify recent selection signatures in Holstein from the Province of Antioquia (Colombia), using the integrated haplotype score (iHS) methodology. Methods: Blood or semen was extracted from 150 animals with a commercial kit. The animals were genotyped with the BovineLD chip (6909 SNPs). The editing process was carried out while preserving the loci whose minor allele frequency (MAF) was greater than 0.05. In addition, genotypes with Mendelian errors were discarded using R and PLINK v1.07 software programs. Furthermore, the extended haplotype homozygosity (EHH), iHS and the p-value were determined with the “rehh” package of R language. Results: The minor allele frequencies showed a tendency toward intermediate frequency alleles. In total, 144 focal markers were significant (p < 0.001) for selection signatures. Some chromosomes showed a greater number of signatures than others. Many of the variants were found inside genes, although they were in intronic regions. Some important regions were associated with genes TRAPPC12, PANK3, ZNF16, OPLA and DPYSL4, which are related with cellular transport, excretion or metabolism. Conclusion: Identifying signatures of selection using the iHS method made it possible to determine some important regions for selection in Holstein cattle in the high tropics, some of which had been previously reported to be associated with quantitative traits loci (QTLs).

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Author Biographies

Juan C. Rincón, Technological University of Pereira, National University of Colombia

Zoot, MSc, PhD., Veterinary Medicine and Zootechnics Program, Technological University of Pereira, Risaralda, Pereira, Colombia. Biodiversity and Molecular Genetics Research Group (BIOGEM), Faculty of Agrarian Sciences, Department of Animal Production, National University of Colombia, Medellín, Colombia.

Albeiro López, National University of Colombia

VM, Zoot, MSc, PhD., Biodiversity and Molecular Genetics Research Group (BIOGEM), Faculty of Agrarian Sciences, Department of Animal Production, National University of Colombia, Medellín, Colombia.

Julián Echeverri, National University of Colombia

Zoot, MSc, PhD., Biodiversity and Molecular Genetics Research Group (BIOGEM), Faculty of Agrarian Sciences, Department of Animal Production, National University of Colombia, Medellín, Colombia

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