Gene network analysis identifies rumen epithelial processes perturbed by diet and correlated with methane production and yield

Ruminants are major contributors to the greenhouse gas, methane (CH4), contributing up to 14% of the anthropogenic contribution to global methane. Since CH4 is produced by the rumen Archaea from H2 and CO2 from bacterial fermentation of ingested feed, studies for mitigating CH4 have focused on suppressing rumen microbial methanogenesis. However, CH4 yield (CH4 production per unit of dry matter intake) has a heritable component; one possible mechanism is host-mediated changes in rumen flow rate. To identify signals of the genetic mechanism for variation in CH4 yield in the rumen wall, we sequenced mRNAs of full-depth rumen wall tissue from 24 female sheep from an experiment conducted at AgResearch, New Zealand. These sheep had high and low genetic potential to produce methane and were offered different amounts and quality of feed. Feed quality and amount and volatile fatty acid (VFA) concentrations are correlated with total CH4 production, which are all highly correlated with the expression of rumen cell cycle genes. This suggests that the turnover of the rumen epithelium is influenced by the level of energy intake. VFA concentrations and total methane production are also positively correlated with the expression of a gene module with enrichment for metabolism of keto-acids. To increase the signal to noise ratio of the analysis, the NZ gene expression data was combined with an independent experiment undertaken in Australia. The Australian study was on gene expression of full-depth ventral rumen wall tissue of 62 female sheep phenotyped extensively for CH4 and associated traits. The small set of genes correlated with methane yield (albeit weakly) in both experiments included those encoding key enzymes in the ketone body synthesis pathway: ACADS, HMGCL and BHD1. Ketone body metabolism is a critical process in energy transactions for ruminants, in particular capturing butyrate from the rumen contents. The positive correlation between CH4 yield and expression of these genes suggests that ketone body synthesis is downstream of the genetic control of methane production. No significant correlation between rumen wall muscle gene expression and CH4 yield was detected. Further analysis of the relationships between gene expression and CH4 yield are underway to identify drivers of the genetically determined differences in methane production in sheep. These analyses may identify potential pathways for host regulation of methane production and elucidate some of the down-