Investigation of the genetic components of maternal infanticide in Sus Scrofa

The aim of this thesis was to investigate the genetic components of maternal infanticide in the domestic pig (Sus scrofa). The killing of piglets by sows by eating them soon after birth is a significant issue for the pig breeding industry because of the impact on animal welfare and the cost in lost revenues. There is evidence that part of this behavior has a genetic basis and this work aims at finding the genes and genome regions linked to this trait. This study focuses on animals from four different breed lines; two have around a 5% incidence of infanticide and two have around a 10% incidence of infanticide. The first half of this work used a genotyping approach using the pig 60K SNP array from Illumina. Two different tests were used to analyse the data: Family Based Association Test (FBAT) and Parent of Origin (PO) test. The FBAT approach uses pedigree information to test for association in the presence of linkage and the PO approach tests for preferential transmission of allele from one parent (this study focused on maternal transmission). The results from the tests, along with previous results generated by our group, were used to design three sequence capture sets in order to study these regions in more detail. The sequencing work was done on a selection of animals grouped in pools, for each line two pools of infanticide animals were selected: animals with an history of infanticide in the pedigree and animals with multiple instances of infanticide. Once sequencing was completed, variants were called on the region of interest, for each pool and the different capture sets, using the Genome Analysis Tool Kit. The variant allele frequencies in the pool was compared between control pools and infanticide pools to select target variants. Some of the variants identified are interesting targets and identify genes of interests.