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Abstract：
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 3 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 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 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; 3 were associated with CH4 and 7 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.
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 CH4 and 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 CH4 and 7 for CH4res. The 2 traits possess sufficient genetic variability to be included as selection criteria in breeding programs.
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 CH4 and 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 CH4 and 7 for CH4res. The 2 traits possess sufficient genetic variability to be included as selection criteria in breeding programs.
摘要：
本研究的目的是估计Nellore牛的每日甲烷排放量（CH4）和每日残留甲烷排放量（CH4res）的遗传力，以及进行全基因组关联研究（GWAS）以鉴定影响CH4和CH4res遗传变异的基因组区域和候选基因。评估了属于三个育种计划的743只Nellore动物的甲烷排放表型。CH4是使用六氟化硫（SF6）示踪技术（涉及引入瘤胃的SF6渗透管，和每个动物上的适当设备)，和CH4res作为观察到的CH4和针对干物质摄入量调整的CH4之间的差异获得。总共6,252个基因分型个体用于基因组分析。通过使用平均信息限制最大似然（AIREML）算法的单步GBLUP方法，用单变量动物模型分析数据。使用单步GWAS方法获得了单核苷酸多态性（SNP）的影响。基于与这两个性状相关的数量性状基因座(QTL)相关的基因组窗口来鉴定候选基因。考虑牛基因组ARS-UCD1.2组装，QTL的注释和候选基因的鉴定基于每个基因组窗口的初始和最终坐标。遗传力估计中等到高，CH4为0.42±0.09，CH4res为0.21±0.09，表明这些性状会对遗传选择迅速作出反应。GWAS揭示了11个和15个SNP与CH4和CH4res的遗传变异显著相关(P<10-6)。分别。与饲料效率相关的QTL，残余饲料摄入量，体重和身高与所评估性状的显着标记重叠。十个候选基因存在于重要的SNP区域中；三个与CH4相关，七个与CH4res相关。鉴定的基因与不同的功能有关，例如瘤胃微生物群的调节，脂肪酸生产，和脂质代谢。CH4和CH4res表现出足够的遗传变异，可能对选择反应迅速。因此,这些特征可以包括在动物育种计划中，旨在减少跨代的肠甲烷排放。
