Host genetic regulation of rumen 6-hydroxymelatonin reduces methane emissions in dairy cattle.

Abstract

The mechanisms linking host genetics to ruminal methane emissions remain unclear. Here, we integrated multiomics data from 304 lactating cows and demonstrated that methane emission per dry matter intake (M/D) exhibitd higher heritability (<i>h²</i> = 0.42) than microbiability (<i>m²</i> = 0.19), highlighting the predominant role of host genetics. Mendelian randomization (MR) analysis identified three heritable <i>Prevotella</i> species (including <i>Prevotella_bryantii</i>) that causally reduce methane emissions. Network suggested that <i>Prevotella_bryantii</i>, which harbors the [NiFe]_Group_1d hydrogenase, exerts this effect by competing with methanogens for H₂. Furthermore, the methane-reducing effect of <i>Prevotella _bryantii</i> was confirmed by in vitro fermentation experiments. To trace the host regulation upstream, the host-derived metabolite 6-hydroxymelatonin was identified as a key regulator that positively influences these <i>Prevotella</i> species by MR analysis, which was further validated by in vitro fermentation and pure bacterial culture experiments. Genome-wide association studies linked ruminal 6-hydroxymelatonin levels to host genetic variants (e.g., 5:106926534) near candidate genes including <i>ITFG</i>2. Functional studies in bovine hepatocytes revealed that <i>ITFG</i>2 knockdown activated the mTORC1 pathway, upregulated <i>CYP</i>1<i>A</i>2 expression, and increased 6-hydroxymelatonin synthesis. Furthermore, cattle carrying the TA genotype at 5:106926534 exhibited significantly lower predicted and measured methane emissions. Collectively, this study unveils a pathway whereby host genetics (via <i>ITFG</i>2/mTORC1) modulate hepatic 6-hydroxymelatonin synthesis, which enriches specific rumen <i>Prevotella</i> that compete with methanogens for hydrogen, thereby reducing methane.