FRANCISCO ROSA.pdf'

To achieve the livestock products demand, the milk productive chain has been changed constantly over the last 20 years. For instance, dairy cattle’s breeding has been improving many milk quality and productivity traits. But, the heavy use of a small number of sires and the artificial insemination practice on breeding programs has been increasing the dairy cattle inbreeding. Besides that, these high levels have been related to reduced fitness and reproductive performance. In Holstein dairy cattle it is almost impossible to find individuals without some level of inbreeding. The interest to estimate inbreeding coefficients with genomic information appears with the advent of high throughput genotyping technologies. For instance, was applied in dairy cattle the estimation of inbreeding coefficient with runs of homozygosity (ROH). Therefore, the aim of this study was to evaluate the effect of selection with assortative positive mating on inbreeding depression considering simulated dairy cattle populations distinguished by linkage disequilibrium (LD). In addition, this thesis evaluated the use of genomic simulated data to investigate many aspects and scenarios of inbreeding and autozygosity under dairy cattle populations. Thus, also the aim of was to evaluate the ability of sliding and consecutive ROH approach to detect and express autozygosity and genomic inbreeding coefficient (FROH) in taurine and indicine simulated populations with twenty generations of assortative positive mating. The evaluation was applied in dairy cattle populations distinguished by linkage disequilibrium (LD). Using the QMSim software, the populations were simulated based on forward-in-time process. The parameters were chosen to try and generate a population with similar characteristics of taurine and indicine dairy cattle. Were simulated 93 milk yield QTLs randomly distributed on 29 autosomal chromosomes of Bos taurus. To create a high and low level of initial linkage disequilibrium were made a bottleneck in the historical population, 1,020 or 2,020 generations were simulated starting from an effective population of 1,000 to 200 animals at the end of the cycle. To found 20 generations of five different scenarios for each level of LD, the populations were simulated with a different mating system and selection criteria. The selection was based on breeding values estimated with BLUP method or, the true breeding value estimated with the effect of QTLs. Each generation inbreeding mean was estimated by QMSim and associated with the level of inbreeding depression of milk yield found in the literature. From the last generation of the historical population, to generate genotypic data for the selection, the individuals were randomly selected with a total of 50,000 markers (MAF ≥ 0.02), these data mimicked the commonly SNP panel used to genotype cattle. The runs of homozygosity were obtained by two different methodologies in the detectRUNS package of R software for 1,000 individuals of generations 1, 5, 10, 15, and 20. At first, the sliding window method scans along everyone’s genotype, at each SNP marker position, for detection of homozygous segments with a specified length or number of homozygous SNPs. At second, the consecutive method does not use the sliding windows to avoid the introduction of artificial ROH that are shorter than the window. Inbreeding coefficient based on ROH (FROH) is a genomic portion of individual autozygosity and defined it as the proportion of the autosomal genome lying in ROH of certain minimal length relative to the overall genome in interest. The highest inbreeding levels, varying from 0.2 to 0.36, in the twentieth generation were obtained for positive assortative mating systems. The intense use of a few numbers of sires in twenty generations of selection may cause a loss between 6.98 and 7.20% on milk yield in the worst scenarios. In general, for minimizing inbreeding scenarios, the average level inbreeding increasing of ~3 and ~8% in the twenty generations of selection decreases ~0.6 and ~1.8% the milk yield at 305 days respectively. The intensive selection for one trait could rapidly increase the average inbreeding coefficient on critical levels in populations with high and low initial LD. Non-random mating systems must be applied to control inbreeding levels and consequently inbreeding depression. In general, the class of 1-2 Mb length size has the highest number of ROH across all evaluations on generations 1, 5, 10 and 20. The percentage of ROH class 1-2 Mb decreases from generation 1 to 20. Nevertheless, the percentage of ROH class >8 increase across the twenty generations of selection in the distinguished populations and ROH detection methodologies. The mean ROH length in the class 1-2 Mb is higher for taurine than to indicine simulated population. Otherwise, for the class >8 Mb the indicine generally has higher mean ROH length. The inbreeding coefficient level based on pedigree (FPED) increases across the twenty simulated generations for taurine and indicine populations. But, genomic inbreeding coefficients based on ROH detected by sliding approach (FROHs) and ROH detected with the consecutive approach (FROHc) are different among these two populations. These results suggest that FROH from both methods to access ROH can detect ancient and recent autozygosity. Genomic inbreeding estimates based on ROH segments can represent and evolutionary events which distinguish some breeds. Key-words: Holstein, Linkage, Disequilibrium, QMSim, Simulation, Selection, ROH, homozygosity, SNP