Genome-Wide Methylation Profile and Methylation-Associated SNP Analysis Following Prenatal and Postnatal Dietary n-3 Fatty Acid Supplementation in Pigs

We have demonstrated feeding n-3 fatty acids to sows during gestation attenuated the innate immune response of their offspring. The objective of this study was to determine the effect of prenatal and postnatal dietary enrichment of n-3 fatty acids on buffy coat DNA methylation profiles.  Fifteen gilts (n=5 per treatment) were selected from one of three dietary treatments: 1) control diet throughout gestation, lactation, and nursery phase (CCC); 2) n-3 fatty acid supplementation in the form of Gromega™ fed throughout gestation, lactation and nursery phase (GGG); or 3) Gromega™ supplementation only during gestation and lactation, and a control diet devoid of DHA and EPA during the nursery phase (GGC).  At 11 weeks of age and after 8 weeks of nursery feeding, buffy coat genomic DNA was isolated and subjected to methyl CpG binding protein sequencing (MBD-seq) using the Illumina Hi-Seq platform. The methylation profile mapped to 26% of the porcine genome build 10.2 and was highly conserved between animals. Across the genome, twelve differentially methylated regions (DMRs, q <0.05) were identified overlapping intergenic and coding regions. On chromosome 4, a 27.7 kb region overlapping RUNX1T1 was hypomethylated in GGC and GGG groups compared to CCC pigs. Conversely, hypermethylation was detected in intergenic regions of chromosomes 4 and 12 in response to prenatal and postnatal n-3 fatty acid dietary enrichment. Further, 2,031,859 unique SNPs were identified in the sequenced methylome. Of these, 72 SNPs overlapped with DMRs. This work was supported by USDA and Iowa State Experiment Station Animal Health Funds.