Gaspa, Giustino (2011) Use of genomic information in genetic evaluation of livestock. Doctoral Thesis.
The imprecise location of Quantitative Trait Loci (QTL) in the genome of livestock species has represented a relevant constraint for commercial application of Marker Assisted Selection (MAS) in the past. Nowadays, thanks to chip DNA technology, thousands of markers can be used in genomic selection of livestock. The overall objective of the thesis was to investigate on the use of genetic markers in animal breeding. Specific objectives were: i) a meta-analysis study of QTL data through factor analysis (FA); ii) to study factors affecting direct genomic value (DGV) accuracy; iii) to reduce the dimensionality of marker data through Principal Component Analysis (PCA) FA extracted three factor (F). F1 was associated (0.98) to marker location (marker map index); the F2 was correlated with population size (0.74) and the year (0.84) (dimension of the study); F3 was correlated to the significance level (0.78), the number of families (0.63) and, the marker density (-0.43) (power of the experiment index). The score that each QTL got on each factor may be used to classify the original QTL. The DGV accuracy increased with the heritability, marker density and number of daughters per bull. Whereas, the number of QTLs and generation of random mating did not show any relevant effect. The PC approach yielded the same accuracy of predicted DGV obtained with the regression using SNP genotypes directly, with a reduction in the number of predictors of about 96% and computation time by 99%.
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