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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 CH4and CH4res. Methane emission phenotypes of 743 Nellore animals belonging to 3 breeding programs were evaluated. CH4was 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 CH4and CH4adjusted 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 2 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 CH4and 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 CH4and 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; 3 were associated with CH4and 7 with CH4res. The identified genes are related to different functions such as modulation of the rumen microbiota, fatty acid production, and lipid metabolism. CH4and CH4respresented 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.The study reports heritability estimates, as well as genomic regions and candidate genes, associated with enteric methane emission traits in Nellore cattle. The results are the first report for Zebu cattle based on phenotyping of the daily methane emission rate of a considerable number of animals. These findings are essential for the inclusion of methane emission traits in the selection indices of beef cattle aiming at reducing greenhouse gas emissions across the beef production chain.Genetic selection designed to reduce the amount of enteric methane emission from livestock is a mitigation strategy to ensure more sustainable production over generations since genetic gains are cumulative. Brazil is a large producer of beef, and the Nellore breed (Bos taurus indicus) plays a very important role in this production. There are a few studies evaluating genetic and genomic aspects of enteric methane emission in Nellore cattle. The objectives of the present study were to estimate the heritability of daily methane emission (CH4) and residual daily methane emission (CH4res) in Nellore cattle, as well as to identify genomic regions and candidate genes associated with genetic variation of these traits. The heritability estimates for CH4and CH4res were of moderate to high magnitude (0.42 ± 0.09 and 0.21 ± 0.09, respectively). Genome-wide association analyses revealed new loci associated with methane emission in Nellore cattle on chromosomes 5, 11, 17, and 20, where 10 candidate genes were identified, 3 for CH4and 7 for CH4res. The 2 traits possess sufficient genetic variability to be included as selection criteria in breeding programs.

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