Genomic evaluation for litter size in Canadian Yorkshire pigs

Maternal traits are expressed only in mature females and generally have low heritability. The reliability of Estimated Breeding Values (EBVs) for maternal traits is therefore very low in young selection candidates. Simulation and empirical studies have shown the potential of genomic information for increasing the reliability of EBVs. The aim of this study was to investigate the impact of using genomic information on the reliability of EBVs for total number of piglets born per litter (NB). A total of 542 Canadian Yorkshire pigs were genotyped using the Illumina PorcineSNP60 BeadChip. Of the 62,163 Single Nucleotide Polymorphisms (SNPs) on the panel, 1,328 SNPs located on sex chromosomes and 9,637 SNPs with minor allele frequency lower than 0.05 were excluded from further analyses. In total, 485 pigs were assigned to the training set and 57 pigs, born after October 2009, to the validation set. The gebv software (Sargolzaei et al, 2009) was used to estimate Genomic EBVs (GEBVs), following VanRaden (2008). GEBVs were based on a combination of parent average EBVs (PAs) of young pigs prior to performance testing and direct GEBV based on estimated 51,198 SNP effects from the training set. PAs and GEBVs were compared to the NB EBVs from the November 2011 national evaluation (EBV2011). The reliabilities, measured as the squared correlations between EBV2011 and both PA and GEBV were 0.55 and 0.66, respectively. Including SNP information increased the accuracy of EBVs, making GEBVs 20% more reliable than PAs. Further studies will include other maternal traits and additional genotyped animals.