Whole Blood Transcriptomics Is Relevant to Identify Molecular Changes in Response to Genetic Selection for Feed Efficiency and Nutritional Status in the Pig.

The molecular mechanisms underlying feed efficiency need to be better understood to improve animal efficiency, a research priority to support a competitive and sustainable livestock production. This study was undertaken to determine whether pig blood transcriptome was affected by differences in feed efficiency and by ingested nutrients. Growing pigs from two lines divergently selected for residual feed intake (RFI) and fed isoproteic and isocaloric diets contrasted in energy source and nutrients were considered. Between 74 and 132 days of age, pigs (n = 12 by diet and by line) received a regular diet rich in cereals and low in fat (LF) or a diet where cereals where partially substituted by lipids and fibers (HF). At the end of the feeding trial, the total number of white blood cells was not affected by the line or by the diet, whereas the red blood cell number was higher (P<0.001) in low RFI than in high RFI pigs. Analysis of the whole blood transcriptome using a porcine microarray reveals a higher number of probes differentially expressed (DE) between RFI lines than between diets (2,154 versus 92 probes DE, P<0.01). This corresponds to 528 overexpressed genes and 477 underexpressed genes in low RFI pigs compared with high RFI pigs, respectively. Overexpressed genes were predominantly associated with translational elongation. Underexpressed genes were mainly involved in the immune response, regulation of inflammatory response, anti-apoptosis process, and cell organization. These findings suggest that selection for RFI has affected the immune status and defense mechanisms of pigs. Genes DE between diets were mainly related to the immune system and lipid metabolism. Altogether, this study demonstrates the usefulness of the blood transcriptome to identify the main biological processes affected by genetic selection and feeding strategies

Comparison of microarray and qPCR data for eight genes in pigs divergently selected for low or high residual feed intake (RFI).

<p>Transcriptomic differences between the two lines were validated by qPCR at 132 and 74 days of age (onset of the growing period). For values related to microarray, the highest P-value is reported when several probes are differentially expressed for a unique gene (*P < 0.05; **P < 0.01; ***P<0.001). Fold change value is expressed as the expression ratio of low RFI to high RFI samples; ratio was inversed and preceded by a minus sign for value less than 1 (i.e., a ratio of 0.5 is expressed as -2). <i>CD40</i>, tumor necrosis factor receptor superfamily member 5; <i>GPX3</i>, glutathione peroxidase 3; <i>OAZ3</i>, ornithine decarboxylase antizyme 3; <i>DGAT2</i>, diacylglycerol O-acyltransferase 2; <i>NMI</i>, N-myc interactor; <i>TRAF6</i>, TNF receptor-associated factor 6; <i>SLPI</i>, secretory leukocyte peptidase inhibitor; <i>PSEN1</i>, presenilin 1.</p

Comparison of microarray and qPCR data for three genes in pigs fed the HF or LF diet.

<p>For values related to microarray, the highest P-value is reported when several probes are differentially expressed for a unique gene (*P < 0.05; **P < 0.01; ***P < 0.001). Fold change value is expressed as the expression ratio of HF (high fiber high fat, n = 24) to LF (low fiber low fat, n = 24) diets; ratio was inversed and preceded by a minus sign for value less than 1 (i.e., a ratio of 0.5 is expressed as -2). <i>LCN2</i>, lipocalin 2; <i>CPT1A</i>, Carnitine palmitoyltransferase 1A; <i>PSAP</i>, prosaposin.</p