Sustainability & efficiency

Prediction accuracy of methane production traits from tropically adapted mixed-breed and purebred grazing beef cattle

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Abstract

Enteric fermentation enables cattle and other ruminants to convert otherwise indigestible plant material into usable energy and nutrients. Methane is produced as a byproduct of this digestion process, which results in substantial methane emission being eructated by cattle. Methane production has been shown to be a heritable trait in dairy and beef cattle. This project quantifies methane production from beef cattle grazing tropical and sub-tropical conditions. Cattle in tropical production systems are commonly a mix of both Bos indicus and Bos taurus sub-species as they are adapted to environmental conditions. Phenotypic observations of methane production were recorded utilising the GreenFeed emission monitoring system (GEM), as was pre- and post-trial weight after fasting overnight. Genotype data was collected via tail hair sampling using the Neogen TropBeef 50k SNP array (Neogen, Australasia). In total, 921 cattle were recorded in 16 trials across 5 trial locations in Queensland, Australia, between June 2023 and April 2025. Variance components were estimated for both methane production (MP) and methane intensity (MI) calculated as methane production per kilogram of fasted starting weight Variance components for both traits were calculated using GCTA, with heritabilities estimated as 0.20 ± (0.04, 0.05) for the two traits respectively. Five-fold cross validation was used to test the prediction accuracy of genomic estimated breeding values (GEBV). This involved selecting 20% of the recorded cattle and setting the methane trait to unknown. The remaining 80% of the population were then used as the reference population to predict GEBV. This was than repeated in turn five times until all cattle had GEBV predicted. Three methods were used to test prediction accuracy, firstly cattle were randomly assigned to one of the five validation groups. The second method divided cattle based on principle component 1, which was calculated from genomic relationship matrix (GRM) estimated on the entire reference population. Finally, cattle were divided by trial location, this resulted in uneven sized validation groups being assigned in comparison to the first two methods. The method based on randomly assigned validation groups for both MP and MI resulted in moderate accuracies (0.37, 0.24) with a low bias being observed (1.01, 1.02), respectively. However, prediction of MI based on trial assigned validation groups produced a slightly higher accuracy (0.26) this resulted in a larger bias (0.83), likely due to trial weight being clustered within trial. Genomic prediction of both methane production and methane intensity is moderately accurate utilizing the current reference population recorded, across tropical and sub-tropical regions of northern Australia.

Keywords: 2026

How to Cite:

Hayes, B., McCosker, K., Warburton, C. & Whistler, C., (2026) “Prediction accuracy of methane production traits from tropically adapted mixed-breed and purebred grazing beef cattle”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286154. doi: https://doi.org/10.31274/wcgalp.23863

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