A Genomic Investigation of Porcine Periweaning Failure to Thrive Syndrome (PFTS)

Porcine Periweaning Failure to Thrive Syndrome (PFTS) affects young pigs around 2-3 weeks post-weaning and it is characterized by anorexia, lethargy and progressive debilitation that frequently leads to death. A genetic basis of this syndrome has been recently hypothesized but until now only one GWAS analysis has been reported, with a moderate suggestive association with the disease. In this experiment, 107 pigs were collected in North America within 2-3 weeks after weaning from commercial farms.

A total of 70 met the PFTS case definition (cases) while 37 were aged-matched penmates (control). Cases and controls were balanced across the farms using a 2:1 ratio. All animals were genotyped with the 80K porcine SNP chip and 53,810 filtered autosomal SNPs were considered for the analyses. Population structure analysis was performed, showing that the samples have a similar genetic background even between cases and controls. Then, three analyses were performed comparing cases and controls. These included Fst analysis, considering single SNPs and the average Fst calculated in 500Kb overlapping windows and logistic regression analysis. Only moderate suggestive associations were found.

A total of four regions not identified previously on chromosome 1, 3 and 11 were concordant for at least two types of analyses and contain some genes that are involved in behavior, energy homeostasis, caloric intake and growth and mature size. With these limited analyses we could not confirm major regions of difference for PFTS but we identified the presence of novel genomic regions that may be moderately associated with this syndrome.