Genomewide association study of methane emissions in Angus beef cattle with validation in dairy cattle1

Abstract

Methane (CH) is a product of enteric fermentation in ruminants, and it represents around 17% of global CH 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 CH traits are required. Therefore, the objectives of this study were 1) to perform a genomewide association study to identify SNP associated with several CH 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 CH traits and determine if the genes associated with CH also control residual CH traits. Phenotypes calculated for the genotyped Angus population included CH production (MeP), CH yield (MeY), CH intensity (MI), DMI, and WT. The Holstein population (POP1) was multiparous, with phenotypes on CH traits (MeP, MeY, and MI) plus genotypes. Additionally, 2 CH traits, residual genetic CH (RGM) and residual phenotypic CH (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 < 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 < 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.

Invited review: Phenotypes to genetically reduce greenhouse gas emissions in dairying

“…Another option, then, is to look at methane intensity, defined as liters of CH 4 related to output [e.g., kg milk (for dairy) or meat (for sheep or beef) produced], or at methane yield, defined as liters of CH 4 related to input (e.g., per kg of DMI). Residual methane production, defined as observed minus predicted CH 4 production, has also been suggested for use (Herd et al, 2014;Berry et al, 2015;Manzanilla Pech et al, 2016). Residual methane production is based on the same concept as residual feed intake (RFI), where the phenotype of interest is regressed for each factor that influences this phenotype.…”

Genome-wide association studies for methane emission and ruminal volatile fatty acids using Holstein cattle sequence data

“…De Haas et al [7] reported that the estimated heritability of predicted methane emission (PME) per milk production and PME per milk production corrected for fat and protein content were 0.35 and 0.58, respectively. Moreover, genome-wide association studies (GWAS) have identified several single nucleotide polymorphisms (SNPs) associated with the measured or predicted rate of methane emission in Holstein cattle [7] and Angus cattle [8]. Thus, genetic selection can be employed to reduce PME per unit of milk production.…”

“…Cattle have a considerable ability to produce high-quality proteins from non-edible plant cell wall components for human consumption [16]. However, it is well established that gastrointestinal microbiota contributes to feed digestion and enteric methane emission in ruminants [17][18][19][20], as approximately 17% of global methane emissions generated through ruminants [8]. Methane emission is a difficult and expensive trait to measure and is not routinely measured in dairy cattle.…”

“…However, they reported that seven SNPs associated with PME in Holstein cattle could explain only 0.2% of the total genetic variance [7]. In another GWAS, 3,304 significant SNPs were identified for PME (p < 0.005) in which 630 of them were also associated with weight-at-test and dry-matter intake [8]. It has been estimated that 19% to 23% of methane emissions per kg of milk can be reduced and converted to production when cows are selected based on milk fat plus protein (19%), or based on the average genetic merit of milk fat plus protein yield (23%) [22].…”

The genetic background of methane emission by dairy cows

“…The genetic background of CH4 emission has been studied before in beef and dairy cattle Manzanilla-Pech et al, 2016). No specific regions of the genome were found to be significantly associated in the GWAS on CH4 emission predicted with feed intake in 665 dairy cows .…”