A genome wide association analysis identifying SNPs for PRRS tolerance on a commercial pig farm

Porcine reproductive and respiratory syndrome (PRRS) is currently the most economically important viral disease affecting pig production outside Australia. This study utilised commercial data to perform a genome wide association study looking for single nucleotide polymorphism (SNP) markers associated with PRRS resistance or tolerance, as assessed indirectly from reproductive traits. In total, phenotypes were measured on 1,545 sows, with the data split according to whether the trait was measured during a healthy PRRS-free phase on the farm (4,378 litters from 1,019 sows) or a diseased phase (1,977 litters from 1,526 sows). All animals were genotyped using the Illumina porcine 7k SNP chip. Associations between each individual SNP and reproductive outcomes were assessed using the residual values from a linear mixed (animal) model analysis of each trait in a series of single SNP analyses. Significant SNP associations were only observed for reproductive traits recorded during the disease phase, implying specificity of identified SNPs to a PRRS active phase. After correction for false positives, six significant SNP markers were identified for piglets born alive, piglets born dead and mummified piglets born per litter. SNP effects were then re-estimated from linear mixed model analyses of the data in which the significant SNPs were fitted as additional fixed effects. The SNPs are generally additive in their mode of action and on average the significant SNPs explain 4.7% of the genetic variation for born alive, 1.6% for born dead and 2.2% for born mummified. After further validation and research, these SNPs may allow breeding of pigs that are more robust in the face of PRRSV infection.