Exploring methane phenotypes and their relationship with productive traits in the Spanish Holstein Population

The goal of this study was to evaluate alternative phenotypes for methane emissions in dairy cattle and to estimate their genetic relationships with productive traits. Methane (CH4) and carbon dioxide (CO2) concentration in exhaled breath and eructation events were measured with sniffers from 2,961 dairy cows across 34 commercial farms in 5 Spanish regions between 2018 and 2023. Records for CO2 concentrations were available for 23 farms. Traits derived included the average of CH4 concentration, area under the curve of CH4 concentration from eructation events, average maximum values of CH4 concentration in eructation events, number of eructation events per minute, average of CO2 concentration, CH4:CO2 ratio from average gas concentrations, and 2 methane production traits (g/d) derived from ratio. A Bayesian approach was used to estimate variance components and genetic correlations. Heritability estimates for methane phenotypes ranged from 0.07 (Highest Posterior Density interval, HPD = 0.03: 0.11) to 0.12 (HPD = 0.06: 0.17), with moderate-to-high repeatability (0.49-0.58). The number of eructation events per minute showed higher heritability (0.30; HPD = 0.24: 0.37) and repeatability (0.75; HPD = 0.73: 0.76). The phenotypic and genetic correlations between methane concentrations traits were high, ranging from 0.78 to 0.99, except for the number of eructation events per minute, which correlated positively with peak-based traits at the phenotypic level, but lowly or even negatively at the genetic level with most methane phenotypes. The phenotypic and genetic correlation between ratio and other methane concentration traits was moderate (0.46; HPD = 0.13: 0.73) to high (0.94; HPD = 0.85: 0.99), while strong and positive (0.92; HPD = 0.84: 0.98, or 0.99; HPD = 0.98: 0.99) with methane production. Methane production traits showed high phenotypic correlation (0.56-0.74) and moderate (0.44; HPD = 0.07: 0.79) to high (0.99; HPD = 0.98: 0.99) genetic correlation with methane concentration traits. The genetic correlation estimates with productive traits were low (0.12; HPD = -0.06: 0.42) to high (0.78; HPD = 0.47: 0.98) for all methane and carbon dioxide traits, with stronger associations observed with fat yield. Sniffer devices provide robust methane phenotypes under commercial conditions, enabling accurate genetic parameter estimation. We show strong correlations among methane traits, positive links with production traits, and highlight a new methane production phenotype that avoids bias in genetic correlation estimates when productive traits are used in the conversion from ppm to g/d. These results support the inclusion of methane traits in breeding programs to balance productivity with environmental sustainability.