Using rumen microbial predictors for genomic prediction of feed efficiency

Obtaining phenotypic measures of feed efficiency requires measuring intake levels and growth rates over a period of approximately 8 weeks (2 weeks of adaption and 6 of measurement), which is expensive and low-throughput. Rumen microbial community (RMC) profiles have shown to be associated with feed efficiency traits in ruminants and so may be a suitable proxy. Using a dataset of 1298 animals across 4 genetically linked flocks that were measured through a feed intake facility (FIF), we predicted feed efficiency from RMC profiles and obtained higher prediction accuracies compared to host genomic prediction. The genetic and phenotypic correlations between feed efficiency traits measured from the FIF and predicted from RMC profiles were estimated as 0.64 and 0.33 for mid-trial intake and 0.47 and 0.30 for residual feed intake (RFI). These results suggest RMC profiles have the potential to be used as a proxy for feed efficiency traits in ruminants.