Use of methane production data for genetic prediction in beef cattle: A review

The objectives of the present study were to estimate the heritability for daily methane emission (CH4) and residual daily methane emission (CH4res) in Nellore cattle, as well as to perform genome-wide association studies (GWAS) to identify genomic regions and candidate genes influencing the genetic variation of CH4 and CH4res. Methane emission phenotypes of 743 Nellore animals belonging to three breeding programs were evaluated. CH4 was measured using the sulfur hexafluoride (SF6) tracer technique (which involves an SF6 permeation tube introduced into the rumen, and an appropriate apparatus on each animal), and CH4res was obtained as the difference between observed CH4 and CH4 adjusted for dry matter intake. A total of 6,252 genotyped individuals were used for genomic analyses. Data were analyzed with a univariate animal model by the single-step GBLUP method using the average information restricted maximum likelihood (AIREML) algorithm. The effects of single nucleotide polymorphisms (SNPs) were obtained using a single-step GWAS approach. Candidate genes were identified based on genomic windows associated with quantitative trait loci (QTLs) related to the two traits. Annotation of QTLs and identification of candidate genes were based on the initial and final coordinates of each genomic window considering the bovine genome ARS-UCD1.2 assembly. Heritability estimates were of moderate to high magnitude, being 0.42 ± 0.09 for CH4 and 0.21 ± 0.09 for CH4res, indicating that these traits will respond rapidly to genetic selection. GWAS revealed 11 and 15 SNPs that were significantly associated (P < 10-6) with genetic variation of CH4 and CH4res, respectively. QTLs associated with feed efficiency, residual feed intake, body weight and height overlapped with significant markers for the traits evaluated. Ten candidate genes were present in the regions of significant SNPs; three were associated with CH4 and seven with CH4res. The identified genes are related to different functions such as modulation of the rumen microbiota, fatty acid production, and lipid metabolism. CH4 and CH4res presented sufficient genetic variation and may respond rapidly to selection. Therefore, these traits can be included in animal breeding programs aimed at reducing enteric methane emissions across generations.

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Exploring putative enteric methanogenesis inhibitors using molecular simulations and a graph neural network

Aryee,

Mohammed,

Dey

et al. 2024

Preprint

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Atmospheric methane (CH4) acts as a key contributor to global warming. As CH4is a short-lived climate forcer (12 years atmospheric lifespan), its mitigation represents the most promising means to address climate change in the short term. Enteric CH4(the biosynthesized CH4from the rumen of ruminants) represents 5.1% of total global greenhouse gas (GHG) emissions, 23% of emissions from agriculture, and 27.2% of global CH4emissions. Therefore, it is imperative to investigate methanogenesis inhibitors and their underlying modes of action. We hereby elucidate the detailed biophysical and thermodynamic interplay between anti-methanogenic molecules and cofactor F430of methyl coenzyme M reductase and interpret the stoichiometric ratios and binding affinities of sixteen inhibitor molecules. We leverage this as prior in a graph neural network to first functionally cluster these sixteen known inhibitors among ∼54,000 bovine metabolites. We subsequently demonstrate a protocol to identify precursors to and putative inhibitors for methanogenesis, based on Tanimoto chemical similarity and membrane permeability predictions. This work lays the foundation for computational andde novodesign of inhibitor molecules that retain/ reject one or more biochemical properties of known inhibitors discussed in this study.COVER ABSTRACT

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Use of methane production data for genetic prediction in beef cattle: A review

Cited by 3 publications

References 98 publications

Inclusion of Lotus tenuis in beef cattle systems in the Argentinian flooding pampa as an enteric methane mitigation strategy

Inclusion of Lotus tenuis in beef cattle systems in the Argentinian flooding pampa as an enteric methane mitigation strategy

Heritability estimates and genome-wide association study of methane emission traits in Nellore cattle

Exploring putative enteric methanogenesis inhibitors using molecular simulations and a graph neural network

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