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


Difford, G.F., Plichta, D.R., Løvendahl, P., Lassen, J., Noel, S.J., Højberg, O., Wright, A.-D.G., Zhu, Z., Kristensen, L., Nielsen, H.B., Guldbrandtsen, B., Sahana, G. (2018). Host genetics and the rumen microbiome jointly associate with methane emissions in dairy cows, 14(10),

Plain language summary

In beef cattle, rumen microbiota is essential for the digestion of plant fibers, and contributes to the variation of production and health traits. However, it is largely unknown on how genetics of the host animals affect their rumen microbial features. This study aimed to characterize rumen microbial features and to determine how heritable of the rumen microbiota to the host genetics. The study assessed rumen microbiota from a cohort of 709 beef cattle and the results showed that multiple factors including breed, gender, and diet drove the variation of rumen microbiota among animals. The diversity indices, the relative abundance of some microbial taxa (59 out of 174), and the copy number of total bacteria are low to moderately inheritable with a heritability estimate (h2) ≥ 0.15, suggesting that they are affected in part by host genetics. These rumen microbial features were also found to be associated with host feed efficiency traits. Moreover, 19 single nucleotide polymorphism (SNP) DNA markers of the hos animals located on 12 bovine chromosomes were found to be associated with 14 rumen microbial taxa, and five of these SNPs were known quantitative trait loci for feed efficiency in cattle. These findings suggest that some rumen microbial features are heritable and are influenced by host genetics. The results indicate a potential for the beef industry to manipulate and obtain a desirable and efficient rumen microbiota using genetic selection and breeding and to improve feed efficiency and optimize rumen fermentation through targeting both cattle and their rumen microbiota.


© 2018 Difford et al. 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 (CH4) is a natural by-product of gastro-enteric microbial fermentation of feedstuffs in the rumen and contributes to 6% of total CH4 emissions from anthropogenic-related sources. The extent to which the host genome and rumen microbiome influence CH4 emission is not yet well known. This study confirms individual variation in CH4 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 CH4 emissions. However, the cumulative effect of all bacteria and archaea on CH4 production was 13%, the host genetics (heritability) was 21% and the two are largely independent. This study demonstrates variation in CH4 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 CH4 emissions in the cattle industry.

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