Genomic variability and population structure of six Colombian cattle breeds.

Analyses of the genetic diversity of indigenous cattle are essential for implementing conservation programs, promoting their sustainable use and maintaining productive advantages offered by these breeds in local conditions. The aim of this study was to investigate the genetic diversity and population structure of six Colombian cattle breeds: Blanco Orejinegro (BON), Costeño con Cuernos (CCC), Romosinuano (ROM), Sanmartinero (SAM), Casanareño (CAS), and Hartón del Valle (HDV). Two additional breed groups were included for comparison: Zebu (CEB) and a crossbreed of Colombian cattle breeds × Zebu. Genetic diversity within breeds was analyzed using expected heterozygosity (He), inbreeding coefficient (f), and runs of homozygosity (ROH). Population structure was assessed using model-based clustering (ADMIXTURE) and principal components analysis (PCA). Zebu cattle showed the lowest genetic diversity (He = 0.240). Breeds with the highest genetic diversity level were HDV and BON (He = 0.350 and 0.340, respectively). Inbreeding was lower for Colombian cattle breeds ranging between 0.005 and 0.045. Overall, the largest average genetic distance was found among the group of Colombian cattle breeds and Zebu, while the smallest was found between ROM and CCC. Model-based clustering revealed some level of admixture among HDV and CAS cattle which is consistent with their recent history. The results of the present study provide a useful insight on the genetic structure of Colombian cattle breeds.

Prevalence and risk factors of bovine viral diarrhea in Colombian cattle.

BACKGROUND AND AIM: Bovine viral diarrhea virus (BVDV) is present in most cattle-raising countries around the world, and it has a negative economic impact in cattle herds. In Colombia, previous studies have estimated the prevalence of BVDV in specific locations. The aim of this study was to estimate the prevalence of BVDV in cattle herds located at several municipalities across the country and to identify the associated risk and protective factors. MATERIALS AND METHODS: A cross-sectional study was carried out to investigate the prevalence of BVDV in Colombian cattle populations at farm and animal-levels. A total of 387 herds and 8110 animals located in seven different departments were included in this study. RESULTS: An animal- and farm-level prevalence of 36% and 69%, respectively, were estimated. A high variation for the farm-level prevalence was found among the municipalities studied. Moreover, seropositive cattle to the infectious bovine rhinotracheitis virus (odds ratio (OR)=2.38, p=0.0479) and Neospora caninum (OR=3.15, p=0.0122) were more likely to be seropositive for BVDV, while the practice of burning dead animals at the farm was identified as a protective factor (OR=0.17, p=0.014). CONCLUSION: The prevalence of BVDV varied more at farm-level compared to animal-level. Two risk factors and one protective factor were identified. The results of the current study are essential to understand the epidemiology of BVDV in Colombia, and to formulate strategies in the region to mitigate the impact of this virus on the productive and reproductive indicators of cattle farms at the regional level.

Tick burden in Bos taurus cattle and its relationship with heat stress in three agroecological zones in the tropics of Colombia.

BACKGROUND: Ticks have a negative effect on dairy and beef cattle production systems around the world, with the concomitant risk they represent for the transmission of some important infectious diseases. Colombian cattle breeds are distributed across different agroecological regions and are exposed to different environmental challenges. In humid and warmer climates such as those from the tropics, tick burden and heat stress are important factors that can compromise livestock performance. The aim of this study was to characterize tick burden in four Colombian cattle breeds and evaluate the relationship between heat stress and tick burden in Bos taurus cattle under tropical conditions. Tick counting was conducted in 1332 cattle from Romosinuano (ROMO), Costeño con Cuernos (CCC), San Martinero (SM) and Blanco Orejinegro (BON) breeds, located in the Caribbean, Orinoquia and Andean regions. Vital signs and environmental variables were taken to calculate an adaptability index (AI) and a temperature humidity index (THI). An AI < 2 indicates maximum adaptability while an AI ≥ 2 indicates a state of lower adaptability. In beef cattle, productivity starts to be affected by heat stress when environmental conditions allow an estimation of a THI > 75. RESULTS: Results showed a differing distribution of ticks on the body of individuals that varied according to the agroecological region. There was a significant effect of breed, sex, family, age and live weight on cattle tick burden. The lowest tick burden was observed in the ROMO breed (12.8 ± 2.6), while the highest tick burden was observed in CCC (31.8 ± 2.3), which were located in the same agroecological region. SM and ROMO animals with an AI > 2 had a higher tick burden than their counterparts that had an AI < 2. CONCLUSIONS: Cattle breed, sex, age and live weight affect the tick burden in Bos taurus Colombian cattle breeds. The tick burden is higher in cattle with lower adaptability to heat stress. Moreover, it decreases as heat stress levels increase in a tropical environment. The interaction between tick burden and environmental heat stress can be affected by characteristics of the agroecological region itself, the breed and the genetic resistance of the individual tick, as well as the thermal adaptability of cattle.

Linkage disequilibrium levels and allele frequency distribution in Blanco Orejinegro and Romosinuano Creole cattle using medium density SNP chip data.

The linkage disequilibrium (LD) between molecular markers affects the accuracy of genome-wide association studies and genomic selection application. High-density genotyping platforms allow identifying the genotype of thousands of single nucleotide polymorphisms (SNPs) distributed throughout the animal genomes, which increases the resolution of LD evaluations. This study evaluated the distribution of minor allele frequencies (MAF) and the level of LD in the Colombian Creole cattle breeds Blanco Orejinegro (BON) and Romosinuano (ROMO) using a medium density SNP panel (BovineSNP50K_v2). The LD decay in these breeds was lower than those reported for other taurine breeds, achieving optimal LD values (r2 ≥ 0.3) up to a distance of 70 kb in BON and 100 kb in ROMO, which is possibly associated with the conservation status of these cattle populations and their effective population size. The average MAF for both breeds was 0.27 ± 0.14 with a higher SNP proportion having high MAF values (≥ 0.3). The LD levels and distribution of allele frequencies found in this study suggest that it is possible to have adequate coverage throughout the genome of these breeds using the BovineSNP50K_v2, capturing the effect of most QTL related with productive traits, and ensuring an adequate prediction capacity in genomic analysis.