Sustainability & efficiency

Genetic Dissection of Residual Feed Intake and Methane Production in Dairy Cattle Using a Large-Scale Single-Step GWAS

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Abstract

Improving feed efficiency and reducing methane emissions are critical for sustainable dairy production. Residual feed intake (RFI) and residual methane production (RMet) are key traits for genetic selection, as they reflect variation in feed consumption and methane output independent of production traits. This study applied a large-scale, single-step genome-wide association study (ssGWAS) using the algorithm for proven and young (APY) to identify genomic regions associated with RFI and RMet in Holstein cattle. Phenotypic data were collected in 5 commercial herds across the United States using the SmartFeed and GreenFeed equipment for RFI and RMet, respectively. RFI (kg/day) was defined as the residual of a linear regression of dry matter intake (DMI; kg/day) for each herd on energy-corrected milk, metabolic body weight, parity (primiparous or multiparous), age at calving in class (4 levels), including the random effect of the week of experiment. RMet was estimated by regressing methane production (g/day) on the previously mentioned energy sinks, including herd-year as a random effect. Weekly averages of daily RFI and RMet were available for more than 5,000 genotyped Holstein cows, resulting in 72,301 feed intake records and 42,273 methane emission measurements. Genomic data for almost 900,000 animals was used in the analysis, with a core set of 25,000 genotyped animals randomly selected for the APY method. Significant genomic regions were identified for both traits, with several harboring candidate genes implicated in relevant biological processes. For RFI, regions on chromosomes 10, 16, 26, and 29 each explained more than 0.5% of the genetic variance, with candidate genes involved in metabolism, energy regulation, and immune response. For RMet, regions on BTA 1, 9, 19, and 23 explained more than 0.5% of the genetic variance, with candidate genes involved in immune regulation, metabolism, gene expression, and cellular signaling, which are processes that might affect microbial activity and rumen fermentation. Integrating candidate gene information with ssGWAS results improves biological understanding and supports more precise genomic selection. These findings contribute to the understanding of feed efficiency and methane emissions in dairy cattle and provide practical targets for breeding programs focused on environmental sustainability.

Keywords: 2026

How to Cite:

Gonzalez-Peà±a, D., Oliveira Jr., G., Pacheco, H., Vargas, G. & Vukasinovic, N., (2026) “Genetic Dissection of Residual Feed Intake and Methane Production in Dairy Cattle Using a Large-Scale Single-Step GWAS”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2285645. doi: https://doi.org/10.31274/wcgalp.23765

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