Sustainability & efficiency

Selection response for reduced methane emissions through microbiome-driven breeding in a divergent selection experiment

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Abstract

Microbiome-driven breeding (MDB), based on simulated selection, has shown strong potential for mitigating methane (CH4) emissions. To validate this approach, the objective of this study was to evaluate the genetic improvement achieved through MDB for reducing methane yield (CH4Y; g CH4/kg dry matter intake; (DMI)) in a practical divergent selection experiment.Four British Blue sires per group were selected for either high or low genomic breeding values (GEBVs) for CH4Y, estimated solely from the rumen microbiome composition (derived from whole-metagenomic sequencing) of their first cohort of progeny (n = 1,421) from crosses with Holstein cows. Microbial genes included in the multiple-trait model of the MDB strategy were selected from 3,631 genes based on their expected selection responses in CH4Y. These responses were predicted from the heritability of the abundances of microbial genes, their genetic correlations with CH4Y and its genetic standard deviation, which were obtained from a previous multi-breed study, since the British Blue crosses were not measured for CH4 emissions.Considering these predicted responses and gene functionality, 33 microbial genes were selected. The abundances of 12 microbial genes were negatively genetically correlated with CH4Y (ranging from -0.20 to -0.37), while 21 were positively genetically correlated (0.20 to 0.37). In general, microbial genes involved in amino acid transport and metabolism exhibited negative associations with CH4Y, whereas those directly related to methanogenesis, such as ferredoxin-type protein (napH), were positively correlated.The British Blue sire GEBVs for CH4Y were estimated in a multiple-trait model including the abundances of the 33 microbial genes and unobserved CH4Y as traits. Genetic and residual (co)variance among the abundances of the 33 microbial genes were estimated based on the first cohort of British Blue crossbreds, while their covariances with CH4Y and its variances were obtained from the previous multi-breed population study. Sires and progeny were linked through their genomic relationship matrix generated based on 68,207 SNPs after quality control and imputation. Fixed effects included batch (test station entry) and sex.Estimated mean GEBVs for LOW and HIGH sires were -1.74 ± 0.55 and 2.54 ± 0.71 g CH4/kg DMI, respectively. Preliminary results from the second cohort of 126 progeny (~50% of the total expected) showed a difference in measured CH4Y using respiration chambers between HIGH and LOW groups of 1.93 g CH4/kg DMI (P = 0.09), equivalent to 8.62% of the mean CH4Y. In one sire comparison, progeny from a HIGH sire produced 3.36 g CH4/kg DMI (P = 0.04; 15% of the mean) more than those from a LOW sire. This difference was associated with 16.3 g more CH4 per day and 0.75 kg less DMI. These preliminary results indicate that MDB can substantially reduce CH4Y without direct CH4 measurements, by specifically targeting ruminal microbial metabolism.

Keywords: 2026

How to Cite:

Cleveland, M., Duthie, C., Lima, J., Martà­nez‐Álvaro, M., Miller, G., Nguyen, T. & Roehe, R., (2026) “Selection response for reduced methane emissions through microbiome-driven breeding in a divergent selection experiment”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2278080. doi: https://doi.org/10.31274/wcgalp.23431

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