Genomewide association study of methane emissions in Angus beef cattle with validation in dairy cattle

Methane (CH4) is a product of enteric fermentation in ruminants, and it represents around 17% of global CH4 emissions. There has been substantial effort from the livestock scientific community toward tools that can help reduce this percentage. One approach is to select for lower emitting animals. To achieve this, accurate genetic parameters and identification of the genomic basis of CH4 traits are required. Therefore, the objectives of this study were 1) to perform a genomewide association study to identify SNP associated with several CH4 traits in Angus beef cattle (1,020 animals) and validate them in a lactating Holstein population (population 1 [POP1]; 205 animals); 2) to validate significant SNP for DMI and weight at test (WT) from a second Holstein population, from a previous study (population 2 [POP2]; 903 animals), in an Angus population; and 3) to evaluate 2 different residual CH4 traits and determine if the genes associated with CH4 also control residual CH4 traits. Phenotypes calculated for the genotyped Angus population included CH4 production (MeP), CH4 yield (MeY), CH4 intensity (MI), DMI, and WT. The Holstein population (POP1) was multiparous, with phenotypes on CH4 traits (MeP, MeY, and MI) plus genotypes. Additionally, 2 CH4 traits, residual genetic CH4 (RGM) and residual phenotypic CH4 (RPM), were calculated by adjusting MeP for DMI and WT. Estimated heritabilities in the Angus population were 0.30, 0.19, and 0.15 for MeP, RGM, and RPM, respectively, and genetic correlations of MeP with DMI and WT were 0.83 and 0.80, respectively. Estimated heritabilities in Holstein POP1 were 0.23, 0.30, and 0.42 for MeP, MeY, and MI, respectively. Strong associations with MeP were found on chromosomes 4, 12, 14, 20, and 30 at P < 0.001, and those chromosomes also had significant SNP for DMI in Holstein POP1. In the Angus population, the number of significant SNP for MeP at P < 0.005 was 3,304, and approximately 630 of those SNP also were important for DMI and WT. When a set (approximately 3,300) of significant SNP for DMI and WT in the Angus population was used to estimate genetic parameters for MeP and MeY in Holstein POP1, the genetic variance and, consequently, the heritability slightly increased, meaning that most of the genetic variation is largely captured by these SNP. Residual traits could be a good option to include in the breeding goal, as this would facilitate selection for lower emitting animals without compromising DMI and WT.