Selection for reduced methane emissions based on the genetic associations between abundances of microbial genes and metabolites in the rumen

Short-chain fatty acids (SCFAs) are the primary energy source of ruminants and dietary interventions that alter the ratio of acetate-to-propionate are known to be related to methane (CH4) emissions. However, there is a lack of knowledge of the role of animal genetics in these metabolisms. Additionally, the genetic associations between SCFAs metabolism and functional microbial genes identified using the KEGG database need to be studied, as they could enhance microbiome-driven breeding for reduced CH4 emissions. Therefore, we tested the hypothesis that animal genomics influence the abundance of microbial genes favourably associated with propionate production and reduces CH4 emissions. In a Bayesian analysis, we used data from 363 beef cattle genotyped with the 50k SNP chip, measured for CH4 emissions in respiration chambers and analysed for ruminal whole metagenomics and SCFAs profiles. Heritability estimates for molar proportions of acetate and propionate were 0.22 (±0.18) and 0.34 (±0.24), respectively. These SCFAs showed genetic correlations with CH4 production (g/day) at 0.51 (prob. ≠ 0, Po=0.84) and -0.57 (Po=0.88), respectively. The microbial gene of anaerobic sulphite reductase (asr) subunit C exhibited strong genetic correlations with acetate (-0.74, Po=0.95) and propionate (0.87, Po=0.99) concentration and was negatively genetically correlated with CH4 production. These findings indicate that including the asr gene abundances as an additional trait in microbiome-driven breeding would contribute to reduce CH4 emissions by shifting ruminal metabolism toward higher propionate production relative to acetate. Further analyses will explore whether other identified microbial genes are associated with both SCFAs and reduction in CH4 emissions to improve our understanding of how animal genomics is linked to functional microbial regulation of SCFAs metabolism. Overall, our results provide evidence supporting the hypothesis that there are animal genetic effects on the abundances of microbial KEGG genes affecting the concentration of SCFAs in the rumen, which are genetically correlated with CH4 production.