Exploring different definitions of methane phenotypes in Dutch Holstein cattle

One of the most promising strategies to permanently reduce methane emissions in dairy cattle is through genomic selection, where the primary goal is to identify and selectively breed low-emitting ruminants. An important step is to define which trait definition to use. Several methane phenotypes have been proposed in recent years. When measuring methane using breath analyzers (sniffers), 2 commonly used phenotypes are methane concentration (CH₄c; ppm) and methane production (CH₄p; g/d). However, different definitions exist for both phenotypes. For example, for CH₄c, the average per visit is commonly used, but other phenotypes involving the identification of eructation peaks have been suggested. Several formulas are available to calculate CH₄p, using CH₄c or the ratio between CH₄c and CO₂ concentrations as input, together with other production traits. Additionally, methane intensity (MeI), another phenotype of interest, is the amount of methane produced per milk unit (kg). Therefore, the aims of this study were (1) to estimate genetic parameters for 11 distinct phenotypes, including 3 CH₄c definitions, carbon dioxide concentration per visit (CO₂c), the ratio between CH₄c and CO₂c, 5 phenotypes for CH₄p based on different formulas (Madsen, Chagunda, 2 of Kjeldsen, and IPCC Tier2 as a benchmark), and MeI; and (2) to estimate genetic correlations between these methane phenotypes and milk yield (MY) and BW. A total of 149,726 sniffer (CH₄c and CO₂c) records were available from 7,600 Dutch Holstein cows measured between 2019 and 2024 on 68 farms. Data were analyzed with an animal repeatability model with fixed effects, including herd-year-season, week of lactation, and lactation number with age of cow at calving nested. Estimated heritability values ranged from 0.16 to 0.30 for CH₄c phenotypes, with the number of eructation peaks having the highest heritability. For CH₄p, heritabilities ranged from 0.03 to 0.27, with Tier2 having the highest value. Heritabilities for the CH₄c/CO₂c ratio and CO₂c were 0.08 and 0.13, respectively. Genetic correlations between CH₄c phenotypes were moderate to highly positive, ranging between 0.49 and 0.85. Likewise, highly positive genetic correlations (between 0.89 and 1) were estimated for CH₄p phenotypes, except for Tier2, which presented correlations between 0.04 and 0.37 with the other CH₄p phenotypes. Average CH₄c (avg) per visit and sum of maximum peaks of CH₄c (speaks) had moderate to high positive correlations (0.36-0.95) with the majority of the CH₄p phenotypes (except Tier2). Methane intensity had moderate to high positive genetic correlations (0.38 to 0.80) with the majority of the phenotypes except for Kjeldsen2 (0.03) and Tier2 (-0.90). Milk yield had positive genetic correlations with all the methane phenotypes (0.04 to 0.94) except for MeI (-0.66) and Kjeldsen2 (-0.69). Body weight had close to zero genetic correlations with CH₄c phenotypes (-0.09 to 0.07), and a moderate positive to moderate negative correlation (-0.72 to 0.57) for CH₄p phenotypes. Given their strong correlations with the other methane phenotypes, close to zero correlation with body weight, and no induced dependencies with BW and MY, as seen with the CH₄p phenotypes, avg and speaks appear to suitable proxies for methane emissions when using sniffers.