Sustainability & efficiency

Novel microbiome-driven breeding strategies to reduce methane production while avoiding adverse effects on growth

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Abstract

Microbiome‑driven breeding (MDB), which is based on the abundances of the most informative ruminal microbial genes that are heritable and genetically correlated with methane production (CH4P), represents a cost‑effective strategy for methane mitigation in beef cattle by avoiding direct CH4P measurements. Our previous study showed that CH4P is highly heritable (h2 = 0.56) but unfavorably genetically correlated (rg = 0.58) with average daily gain (ADG). To counteract that selection to reduce CH4P compromises ADG, we developed one MDB strategy selecting for microbial genes, whose abundances were favorably (negative/positive) correlated with CH4P and ADG (MDB.FOR) and another strategy selecting against those unfavorably (positive/negative) correlated (MDB.AGAINST) and compared these to a scenario without such restrictions (MDB.CH4P).Data included CH4P measurements (n = 287) obtained in respiration chambers and ADG (n = 352) from 359 beef steers, balanced for breed and diet, collected under experimentally controlled conditions. Host genotypes and whole metagenomic sequences of ruminal microbial DNA were available. Bivariate Bayesian analyses including the genomic relationship matrix (37K SNPs) were performed between the abundances of each microbial gene (n = 3361) and CH4P or ADG. Based on these results, we identified the 35 most informative microbial genes for each MDB strategy. A multiple-trait model including the abundances of these microbial genes, their genetic and residual (co)variances among each other and with CH4P and ADG, was used to estimate genomic breeding values (GEBVs) for methane and growth, in which direct measurements were treated as missing.Selection of the 10% best animals based on CH4P GEBVs using MDB.CH4P resulted in a successful reduction in CH4P of ‑17% of its mean (GEBV accuracy = 0.71; HPD95%: ‑21% to -14%), but also in an undesirable significant decrease of -8% in ADG (0.69; ‑12% to ‑5%). In contrast, selection at the same intensity using MDB.FOR and MDB.AGAINST led to lower CH4P reductions of ‑14% (0.59; ‑19% to ‑10%) and ‑11% (0.50; ‑15% to ‑6%), respectively, without any significant adverse effects on ADG, at +2% (0.55; ‑2% to 6%) and +0.4% (0.49; ‑4% to 5%), respectively. The functions of microbial genes included in MDB.FOR support efficient fermentation processes, including amino acid/vitamin biosynthesis (serC, hisD, cobT) and polysaccharide/starch degradation (kduI, abfA, amyA), whereas MDB.AGAINST microbial genes are linked to oxidoreductase activity and redox states needed for methane biosynthesis.MDB successfully mitigated CH4P without compromising growth by targeting microbial genes, either through enhancing ruminal fermentation efficiency (MDB.FOR) or by selecting against gene abundances involved in methane biosynthesis (MDB.AGAINST). Of these strategies, MDB.FOR was more effective in reducing CH4P, indicating that selecting for beneficial pathways that enhance ruminal microbial fermentation efficiency and thereby limit substrate availability for methanogenesis is more successful than directly targeting the methane production pathways.

Keywords: 2026

How to Cite:

Cleveland, M., Lima, J., Martà­nez‐Álvaro, M., Nguyen, T. & Roehe, R., (2026) “Novel microbiome-driven breeding strategies to reduce methane production while avoiding adverse effects on growth”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2283862. doi: https://doi.org/10.31274/wcgalp.23530

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