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Abstract
Skin damage, which includes skin lesions from biting and other types of aggressive behavior, is a trait of economic and welfare importance that results from animal social interaction. Modeling such traits with social interaction models offers the opportunity to increase the total genetic gain and avoid negative responses to selection due to a negative correlation between direct and social genetic effects. Reducing skin damage through selection consists of a comprehensive evaluation of genetic correlations between this trait and other traits of interest, such as the incidence of the swine inflammation and necrosis syndrome (SINS) and pre- and post-weaning production traits under selection. In this dissertation, we showed that modeling skin damage with social interaction models increased the total heritable variation with respect to the total phenotypic variation 3-fold compared with a classical model where social genetic effects were not accounted for. Skin damage was shown to be moderately correlated with SINS, indicating that young piglets presenting SINS signs are more likely to be bitten after weaning. However, skin damage was strongly and unfavorably correlated with carcass backfat thickness and loin depth, suggesting that a selection index is needed for optimally improving welfare and performance traits. Another aspect of pig breeding is that genetic selection is performed on purebred (PB) animals, whereas phenotypic differences are expected to take place on crossbred (CB) animals at the commercial level. Because the environment experienced by PB and CB animals are different, genetic selection for CB performance can be more accurate when CB phenotypic records are included in the genetic evaluation. The incorporation of those CB phenotypes in the genetic evaluation depends on CB pedigree recording, which can be challenging to obtain in commercial environments. As an alternative, CB animals can be genotyped for low-density panels, which could be used for pedigree inference and potentially for genomic prediction, offsetting PB phenotyping. Our results showed that although genotyping CB individuals for low-density panels is a valuable identification tool for linking CB phenotypes to pedigree, that did not benefit genomic predictions for PB individuals or offset CB phenotyping for the two evaluated CB performance traits.