Transcriptomic and DNA methylation response to feed intake in the duodenum in high- and low- feed efficiency pig lines
Résumé
Feed efficiency is a complex trait of interest in animal breeding to reduce environmental impact of livestock herding and the cost of animal feed. A divergent selection on feed efficiency was carried out in pigs for more than 10 generations at an INRAE experimental unit, establishing lines of relative high- and low-feed efficiency in large white pigs. The objective of this study was to identify the molecular mechanisms underlying the divergence in feed efficiency between the two pig lines in the duodenum. We focused on the duodenum because of its sensory role in the hunger satiety pathways.
Duodenum mucosal samples were collected in post-weaning pigs from the two divergent lines either after a 12 h period of feed restriction, or with a 10 h period of feed restriction followed by a 2 h period of ad libitum feed access (n = 6 per group and per line). Transcritomes and methylomes were analysed by poly-A RNA sequencing (RNA-seq) and by methylated DNA precipitation followed by sequencing (MeDP-seq), respectively. Transcriptomic reads were analysed with nf-core/rnaseq and limma-voom. MeDP-seq reads were analysed with nf-core/chipseq and the BayMeth method.
A total of 962 genes were differentially expressed in the duodenum mucosa between the conditions (fasted vs fed), in contrast with 318 differentially expressed genes when comparing the divergent lines. The DNA methylome of the duodenum mucosa was unaffected by short term feed intake, but was distinct between the lines. More transcripts were affected by short term feed intake in the feed-efficient line than in the other line, including genes of the incretine secretion pathways involved in the production of GIP and GLP-1.
Thus the duodenum transcriptomic response to short term feed intake was distinct in feed efficient and less efficient pig lines. These differences might in part be due to differences in DNA methylation profiles.
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