Differential Gene Expression in Peripheral Mononuclear Cells of Pigs Exposed to Topsoil in Early Life

The objective of this study was to evaluate the effect of exposure to topsoil in early life on gene expression in peripheral mononuclear cells in an attempt to explain improved post-weaning performance as observed in previous studies. Litters (n = 12; PIC 29 x 380) delivered within 24 h were selected and blocked by sows’ farrowing body weight (BW) and parity, and then randomly assigned to: 1) control/ no topsoil and 2) free access to topsoil from d 4 to d 21 of lactation. Upon weaning, piglets (5 per litter) were transferred to a nursery facility, and housed in the same pen throughout the nursery period. Nursery diets were devoid of antibiotics and formulated to meet or exceed nutrient requirements recommended by PIC. Blood was collected through venipuncture via jugular vena cava into EDTA tubes from piglets with median BW at d 11 in each litter when they were 11, 20 (weaning), and 56 (the end of nursery) days old. Peripheral blood mononuclear cells (PBMC) were isolated using Histopaque®-1077 gradient centrifugation and total RNA was extracted using TRIzol®. Total RNA that passed quantity and quality criteria (RQI= 5.1-9.8) were sequenced using Illumina chemistry with samples blocked by treatment and age within each sequencing lane. Sequencing reads were quality-checked with FASTQC/0.11.1 and aligned with the Sscrofa 10.2.84 reference genome using Tophat/Bowtie 2. HTseq analysis was performed to assess the number of unique read per gene. Read counts were analyzed using PROC Glimmix of SAS with treatment, lane, RQI, parity of sows, age, sex, and treatment by age interaction fit as fixed effects and pig fit as a random effect. The q-values were calculated in R using the q-value package to control the false discovery rate (FDR) at 0.10. A total of 420 transcripts were differentially expressed for the treatment by age interaction (P < 0.01, q < 0.10) with 320 genes annotated by DAVID (v6.8). Significantly over-represented pathways and biological processes (FDR < 0.10) included acetylation, ubiquitin-like conjugation, serine/threonine protein kinase, phosphoprotein, carbohydrate metabolism, platelet activation, aminoacyl-tRNA biosynthesis, PI3K-AKt, insulin, and HIF-1 signaling pathway. Changes in gene expression in these biological processes may be related to previously observed differences in growth and immune system maturation in pigs exposed to topsoil.