Rumen metagenome profiles are heritable and predict enteric methane emissions across the New Zealand national sheep flock

Global targets to reduce greenhouse-gas emissions to meet international climate change commitments have driven the livestock industry to develop solutions to reduce methane emission in ruminants while maintaining production. Research has shown that selective breeding for low methane emitting ruminants using genomic selection is one viable solution to meet methane targets at a national level. However, this requires obtaining sufficient measures of methane production on individual animals across the national herd. In sheep, one affordable method for measuring methane on farm is portable accumulation chambers (PAC), although this method is not without its challenges. An alternative approach is to use a proxy trait that is genetically correlated with direct methane measures. One such trait that has shown promise is rumen metagenome community (RMC) profiles. In this study, we investigate the potential of using RMC profiles as a proxy trait for methane emissions in sheep using a large dataset consisting of 4,585 mixed-sex lambs from several flocks and years across New Zealand. RMC profiles were generated from rumen samples collected on the animals immediately after being measured through PAC using restriction enzyme-reduced representational sequencing (RE-RRS). The prediction ability of the RMC profiles to predict methane traits was examined and the heritability and genetic and phenotypic correlations with PAC methane data was estimated from the data.