Integration of quantitative and molecular genetic approaches to improve characteristics associated with pig welfare
Kapell, Dagmar Nicoline Reinhildis Gertrud
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The aims of this thesis were to investigate whether characteristics associated with animal welfare are genetically and genomically determined by using quantitative and molecular genetic approaches and to develop strategies indicating how these traits could be used in breeding programmes. Two traits that are closely related to animal welfare and associated with high socio-economic values are piglet survival at birth and aggressive behaviour in pigs. Piglet survival traits were analysed based on quantitative Bayesian approaches using phenotypic and pedigree information only, while aggressive behaviour was analysed based on molecular genetic approaches such as genome-wide association studies and genomic selection using additionally a dense panel of single nucleotide polymorphisms (SNP). The latter approach was validated using behavioural traits related to welfare characteristics in a welldocumented mouse data set. Selection for piglet survival at birth is expected to be effective, because all lines and breeds in this thesis showed considerable variation for this trait and relatively high heritabilities, particularly in lines with low average birth weight. Maternal heritabilities of individual birth weight were mostly at moderate magnitude and thus of great interest for selection. The genetic correlations between piglet survival and birth weight indicated that selection for either individual or average birth weight or variation of birth weight within litter would indirectly increase survival. The genetic associations of piglet survival with economically important (re)production traits are of great importance for breeding organisations. Undesirable genetic correlations between piglet survival and (re)production traits were generally of low magnitude, so that simultaneous improvement of all traits could be achieved. A comparison of five breeds and lines showed that differences in genetic parameters between breeds and lines can be substantial and no single selection strategy would be optimal for all. A unique study of a sire and a dam line originating from one breed but selected for more than 25 years with different breeding goals demonstrated how selection pressure can alter the genetic parameters over years. Breeding organisations should therefore consider selection strategies per breed or line individually to achieve maximum overall improvement. This study gives new insight into the use of genomic selection for traits associated with animal welfare. It is one of the first to present estimates for linkage disequilibrium in the pig using a new 60K SNP panel and the first to evaluate the efficiency of genomic selection against aggressive behaviour in pigs. Genomic selection showed a high predictive ability in comparison to traditional polygenic selection. It was especially advantageous for traits with lower heritabilities. In particular in situations where little family information was available, the performance of polygenic selection was low and genomic selection increased the performance considerably. Reducing the number of SNPs did not significantly change the performance of genomic selection. The consistently high performance across models indicates that low-density SNP panels may be sufficient to ensure a high efficiency of genomic selection, thus reducing the high costs associated with genotyping in pig breeding with its short generation interval. To summarize, this thesis has shown how to optimise quantitative and genomic approaches to improve animal welfare related characteristics efficiently in pig breeding programmes.