Host genetics and the rumen microbiome jointly associate with methane emissions in dairy cows

Cattle and other ruminants produce large quantities of methane (~110 million metric tonnes per annum), which is a potent greenhouse gas affecting global climate change. Methane (CH(4)) is a natural by-product of gastro-enteric microbial fermentation of feedstuffs in the rumen and contributes to 6% of total CH(4) emissions from anthropogenic-related sources. The extent to which the host genome and rumen microbiome influence CH(4) emission is not yet well known. This study confirms individual variation in CH(4) production was influenced by individual host (cow) genotype, as well as the host’s rumen microbiome composition. Abundance of a small proportion of bacteria and archaea taxa were influenced to a limited extent by the host’s genotype and certain taxa were associated with CH(4) emissions. However, the cumulative effect of all bacteria and archaea on CH(4) production was 13%, the host genetics (heritability) was 21% and the two are largely independent. This study demonstrates variation in CH(4) emission is likely not modulated through cow genetic effects on the rumen microbiome. Therefore, the rumen microbiome and cow genome could be targeted independently, by breeding low methane-emitting cows and in parallel, by investigating possible strategies that target changes in the rumen microbiome to reduce CH(4) emissions in the cattle industry.