Proxies in practice: Implementing rumen metagenomic profiles for genomic selection of methane emissions

Selective breeding for low-methane ruminants is a viable solution for reducing agricultural greenhouse emissions, but requires phenotypic measures of methane. Methods for obtaining on-farm methane emission measurements are available but are expensive and laborious, whereas proxy traits may provide a more efficient and cheaper alternative. A rumen metagenomic profile (RMP) has recently been shown to be one suitable proxy for methane, as it is both predictive of, and genetically correlated with, methane-related traits. We describe a two-step approach for using RMP as a proxy trait to generate genomic breeding values of methane related traits from portable accumulation chambers (PAC). We illustrate the utility of this approach on a commercially reared sheep flock. Our sequence-based, low-cost approach is extremely robust and could be extended to other ruminants (i.e., cattle) and would have greater utility for large ruminants where measuring methane emissions is more difficult compared to sheep.