The Resilient Dairy Genome Project-A general overview of methods and objectives related to feed efficiency and methane emissions.

The Resilient Dairy Genome Project (RDGP) is an international large-scale applied research project that aims to generate genomic tools to breed more resilient dairy cows. In this context, improving feed efficiency and reducing greenhouse gases from dairy is a high priority. The inclusion of traits related to feed efficiency (e.g., dry matter intake [DMI]) or greenhouse gases (e.g., methane emissions [CH4]) relies on available genotypes as well as high quality phenotypes. Currently, 7 countries (i.e., Australia, Canada, Denmark, Germany, Spain, Switzerland, and United States) contribute with genotypes and phenotypes including DMI and CH4. However, combining data are challenging due to differences in recording protocols, measurement technology, genotyping, and animal management across sources. In this study, we provide an overview of how the RDGP partners address these issues to advance international collaboration to generate genomic tools for resilient dairy. Specifically, we describe the current state of the RDGP database, data collection protocols in each country, and the strategies used for managing the shared data. As of February 2022, the database contains 1,289,593 DMI records from 12,687 cows and 17,403 CH4 records from 3,093 cows and continues to grow as countries upload new data over the coming years. No strong genomic differentiation between the populations was identified in this study, which may be beneficial for eventual across-country genomic predictions. Moreover, our results reinforce the need to account for the heterogeneity in the DMI and CH4 phenotypes in genomic analysis.

Estimating breeding values for feed efficiency in dairy cattle by regression on expected feed intake.

The efficiency with which a dairy cow utilises feed for the various physiological and metabolic processes can be evaluated by metrics that contrast realised feed intake with expected feed intake. In this study, we presented a new metric - regression on expected feed intake (ReFI). This metric is based on the idea of regressing DM intake (DMI) on expected DMI using a random regression model, where energy requirement formulations are applied for the calculation of expected DMI covariables. We compared this new metric with the metrics residual feed intake (RFI) and genetic residual feed intake (gRFI), by applying them on 18 581 feed efficiency records from 654 primiparous Nordic Red dairy cows. We estimated variance components for the three metrics and their respective genetic correlations with intake and production traits. In addition, we examined the phenotypes of superior cows. With ReFI, we estimated for feed efficiency a higher genetic variation (4.7%) and heritability (0.23) compared to applying RFI or gRFI. The ReFI metric was genetically uncorrelated with DMI and negatively correlated within energy-corrected milk (ECM), whereas the RFI metric was genetically positively correlated with DMI and metabolic BW. The gRFI metric was genetically positively correlated with DMI and uncorrelated with energy sink traits. Overall, the estimated SE were large. The ReFI metric resulted in a different ranking of cows compared to those based on RFI or gRFI and was superior in selecting the most efficient animals. When the selection was based on ReFI breeding values, then the 10% most efficient cows produced 12.3% more ECM per unit metabolisable energy intake, whereas the corresponding values were only 4.3 or 5.9% when using RFI or gRFI breeding values, respectively. Based on ReFI, superior cows had also higher milk production, whereas based on RFI or gRFI milk production either decreased or was unaffected, respectively. The superiority of the ReFI metric in selecting efficient cows was due to a better modelling of the expected feed intake. The ReFI metric simplified modelling of feed utilisation efficiency in dairy cattle and resulted in breeding values that are equal to percentages of feed saved.