Selection of genomic regions and genes associated with adaptation and fertility traits in two Colombian creole cattle breeds

Colombian creole breeds Blanco Orejinegro (BON) and Sanmartinero (SM) are widely used as pure breeds and in crossbreeding programs due to their excellent performance in the double ability of milk and meat production. We examined genomic regions and genes that from generation to generation have been selected by positive natural selection in favor of the adaptability and reproductive performance of these two Colombian creole breeds. Natural selection of genomics region and genes is one of the main evolutive changes resulting in phenotypic adaptations. The selected genomic regions can be detected by comparing differences in regional linkage disequilibrium (LD) between cattle populations with potential adaptations for economic traits. In this study, we used 58,868 single nucleotide polymorphisms (SNPs) from BON and 57482 SNPs from SM, using genotyping data from 1262 BON and 742 SM animals to estimate the variation of genome-wide LD between populations using the VARLD program. The top 0.1 and 0.01th percentiles of standardized VarLD scores were used as a criterion for all comparisons. A total of 10 selection signatures on chromosomes 3, 5, 11, 15, 18, 21, 22, 23, 25 and 29 were identified in all populations. These signatures overlapped with quantitative trait loci for adaptability and reproductive performance in both breeds. Within the signature located between 23,903,882 and 23,955,588 bp on chromosome 18, we identified the SLC6A2 gene involved in the response to high stress. Also, we identified the genes CTDSP2, CES1, CFAP161, CLEC14A, HIPK1, RBM4, SSTR involved in the expressions of economic traits (meat and milk production), KDMID, OLFML3 genes involved in reproductive traits (age at first calving and calving interval), and ATP23, LRRTM1, SLC6A2, DEK, SYT6, KDMID genes involved in cellular stress response and response to important environmental changes such as high temperature. We conclude that these genomic regions seem to point toward a recent selection in BON and SM populations. These regions can be used in selection and conservation programs.