Effect of polymorphisms in four candidate genes for fertility on litter size in a German pig line

We carried out an SNP discovery project in pigs for candidate genes playing potentially important roles in embryonic development. Using eight pigs one each from eight breeds (Meishan, Mangalitza, Duroc, Pietrain, German Landrace, Hampshire, Husum Red Pied, German Large White), 36 SNPs were identified in intronic sequences of 21 porcine candidate genes based on sequencing of PCR products. The primer pairs were designed using porcine EST sequences allowing amplification of introns. These SNPs were tested for their association with the number of piglets born alive in German Large White sows using a discordant approach. Significant effects (p < 0.001 and p < 0.05, respectively) of intronic SNPs on litter size were found for four genes: mitogen-activated protein kinase kinase kinase 3 (MAP3K3), vascular endothelial growth factor receptor (KDR), erbb2 interacting protein (ERBB2IP) and peroxisome proliferator-activated receptor delta (PPARD). These SNPs can be further tested in upcoming association studies for their influence on litter size in different breeds using larger sample sizes.