Marker assisted selection using SNP haplotype blocks in dairy cattle

The aim of this thesis was to develop a method for using haplotypes for selection of dairy cattle. The first step was to develop methodology to define haplotype blocks in Granddaughter Design (GDD) families. A Maximum Likelihood (ML) procedure was developed in a simulation study to detect regions of the chromosome where recombination rates are high (known as hotspots), using information from the genotypes of grandsires and their sons. Different scenarios were tested with different numbers of grandsires (5, 10, 20), sons per grandsire (50, 80) and Single Nucleotide Polymorphisms (SNP) on a chromosome (100, 300). The method was able to successfully define haplotype blocks and detect hotspot regions (p<0.05). The second step was to investigate the possibility of using SNP haplotype blocks for mapping Quantitative Trait Loci (QTL). A chromosome with 300 biallelic markers was simulated with 50 blocks of haplotypes with one biallelic QTL in block 11. Likelihood Ratio (LR) test was used to detect the QTL and critical values of the test statistic corresponding to 1% type II error rate were computed empirically. In a scenario with ten grandsires and 50 sons per grandsire, LR could detect (p<0.01) a QTL of 0.2σ p. The proposed method is powerful enough (0.90) to detect QTL larger than 0.2σp which explain 80% of the genotypic variation of a quantitative trait. Third step was to develop methodology for obtaining QTL solutions without inverting the Identity By Descent (IBD) probability matrix and solving large Mixed Model Equations (MME). An averaged gametic relationship IBD matrix was used in this study, so that the polygenic and QTL incidence matrices were equal. Therefore, application of Henderson's shortcut for the non-additive genetic model to obtain QTL solutions without inverting the IBD matrix was possible. An example with five grandsires, 50 sons per grandsire and 50 daughters per son was used to illustrate the methodology. The full model included fixed contemporary groups and random polygenic, QTL and residual terms. Identical solutions were obtained for the full equations and proposed shortcut method.