Incorporating feed efficiency, methane emissions, and ruminal microbiome into economic selection indices in Spanish...

The main objective of this study was to develop economic selection indices (IM€T) for different dairy production systems (conventional, cheese-oriented, grazing, and organic) by incorporating production, functional, and sustainability-related traits, including enteric methane and feed intake. The potential inclusion of microbiome-derived information was also evaluated in conventional and organic production systems. Relative to a baseline scenario without emphasis on sustainability, the new indices assigned a negative economic weight (1%) to methane emissions. Organic systems, with a larger economic value applied on methane, resulted in a relative weight of 11% for methane production. Feed intake also received a negative economic weight, ranging from 13 to 15% across production systems. The inclusion of sustainability-related traits primarily reduced the economic emphasis on milk and protein yield, with the largest trade-offs observed in organic systems. Longevity also showed a slight reduction in relative economic weight when dry matter intake and methane production were included in the breeding goal. Grazing and organic systems applied a larger weight on longevity, in comparison to IM€T_milk. Predicted genetic responses indicated the greatest expected improvements in reduced methane emissions and enhanced feed efficiency, although these gains were accompanied by lower rates of genetic progress for production traits and longevity. Substituting methane emission and feed intake traits with microbiome-derived information resulted in larger predicted reductions in methane emissions and feed costs, while also improving genetic gain for fat yield. The expected increase in overall genetic gain for profit ranged from 10 to 30% when microbiome information was incorporated. The inclusion of methane emissions and feed intake in selection indices is expected to contribute to shaping the phenotype of future dairy cattle by 2050, emphasizing environmental efficiency alongside traditional productivity traits. Rumen microbiome information showed strong genetic correlations with methane emissions (|r| > 0.74) and feed efficiency (|r| > 0.64), suggesting that it may represent a novel trait for inclusion in dairy breeding programs, although further research is required to validate its utility.