Genomic Differences Between Pre-weaning Survival and Mortality of Piglets Following PEDv Outbreaks

PED (Porcine Epidemic Diarrhea) is a disease caused by PED virus, which belongs to the Coronavirus family and affects pigs of all ages, but can cause 100% mortality in suckling piglets in the acute phase of the disease. This disease has been relatively common in Asia and Europe since the 1970s, while the USA experienced a widespread epidemic of PED beginning in 2013. In this research, 156 dead and 106 surviving pigs from five PED outbreak farms located in USA, Canada or Germany were genotyped with the 80K SNP chip. Sampling occurred within 3 weeks of the initial onset of PED, prior to the development of maternal immunity. Surviving piglets experienced PED diarrhea but did not succumb to the disease during lactation. After filtering the marker data 60,969 SNPs were used in an Fst analysis comparing dead and surviving pigs using non-overlapping 1Mb windows (using the average Fst of all the SNPs in each window). Results were then normalized to find regions that diverged more than others within the comparison. Significant regions associated with survival were found on chromosomes 2, 4 and 15 and contained 162 genes. Analysis with EnriChr showed that several genes were under or over expressed in several coronavirus infections in humans. Analysis with GOrilla revealed enrichment for genes that belong to the Golgi apparatus and membrane, together with genes involved in ion transporter, metabolism, and ATPase activity.