Genetic diversity analysis in dairy cows of Nariño, southwestern Colombia

Abstract

In Colombia, different dairy breeds were introduced from Europe and the United States, which underwent different crossing and selection processes that generated specific qualities or differences and which likely have their own genomic structure. To characterize genetic diversity, population structure, and admixture, we used genotypes from 23,182 autosomal single nucleotide polymorphisms (SNPs) of 130 animals representing four dairy cattle breed groups from Nariño. In addition, we merged genotypes from 43,043 autosomal SNPs, from 137 animals from the Decker database (Decker et al., 2014) (DRYAD doi:10.5061/dryad.th092). After the quality control process of pruning the merged dataset, we were left with 7,475 autosomal SNPs shared by both databases of Nariño (127 samples) and Decker (135 samples). Genetic diversity levels were moderate in all breeds (average observed heterozygosity = 0.40). Based on the fixation index values, we conclude that Brahman individuals were more differentiated than the taurine breeds (-0.374 to 0.076 for Brown Swiss). Pairs between taurine breeds showed low genetic differentiation (0.011-0.479). Principal component analysis revealed that in both the Nariño and Decker databases, the taurine formed the most compact cluster compared with other breeds known not to share the same ancestry, and Jersey, Brown Swiss, and Normand individuals exhibited high similarity with Holstein individuals. Hierarchical cluster analysis with Admixture revealed that Brahman, Jersey, Normand, and Holstein from the Decker databases most of which were clustered together with the dairy breeds of the Nariño highland tropics are not able to create different groups, thus having greater similarity with each other. This can be explained by the crosses made by farmers to increase milk production volume, always based on the Holstein breed with semen of bulls from America and Canada. Detrimental impacts due to intensive selection might cause some specific traits from the region to be fixed in the offspring, which can influence their adaptive capacity to the highland tropics.