Resumen de Avaluacions genómiques de les races de bestiar boví en climes tropicals
The largest number of cattle heads is concentrated in the so-called tropical and subtropical regions. These are characterized by special and specific environments, so understanding how cattle adapt to this type of ecosystem to survive and produce is important. For many years, several strategies have been implemented to genetically improve cattle in the tropics in order to find the best techniques that efficiently combine adaptation and production. The main objective of this thesis is to evaluate the effects of adaptation and selection in beef cattle in tropical climates, as well as their potential genetic gains through different strategies of genetic improvement.
In a first study, we used the whole-genome sequences of a total of 12 samples from the Chacuba population (CHCU) and 60 samples from six other breeds of taurine, zebu and cross-breeds to estimate the genetic diversity, structure and precise ancestral origin of the CHCU animals. Although these animals were assumed to be a closed population, closeup analysis indicates limited introgression of Bos indicus, probably due to a single, non-continuous introgression event. The extended haplotype homozygosity test (EHH) was used to identify regions that may have played an important role in adaptation to tropical conditions. Regions with a high percentage of zebu were enriched in possible selective events, but only slightly and adaptation cannot be explained by the influence of zebu breeds alone. EHHs revealed signs of possible adaptation that included genes involved in thermogenesis (UCP1, DIO2 and ACSL1) and hair development (BMPR1A, CDSN and FGF7). We also identified variants within these genes that may have a functional impact and could thus explain some of the phenotypic differences observed between the CHCU and the French Charolais breed.
In a second study, we developed a flexible generic advance simulator, called SeqBreed, in order to optimize genomic prediction (GP) or genome-wide association studies, incorporating some of the most popular GP methods such as genomic best linear unbiased prediction (GBLUP), single-step GBLUP, pedigree-based BLUP, and mass selection and including several visualization tools.
Finally, in a third study, we used the SeqBreed software to compare three Bos indicus x Bos taurus cross-breeding programs: F1, grading up or backcrossing and rotational crosses. We simulated, using real SNP data of zebus and taurines, phenotypes of three traits of utmost importance in terms of productivity, mainly in tropical production systems based on cattle breeding: shear force, growth and tolerance. The accuracy of the prediction was compared between three 50k chips that differed in the way the SNPs were chosen: (i) randomly, (ii) with a minimal difference in allele frequency between the breeds, and (iii) with a minimal difference in allele frequency between the breeds as long as the allele frequency was greater than 0.09 on the Bos taurus. We found that the rotational crossing system is the optimal one in terms of predictive accuracy, and that the selection of markers based on the differences in allele frequency between the races does not compensate and is even detrimental.
