Genome-wide association study of methane emissions, feed intake, residual feed intake, and body weight in Merino sheep

Improving feed efficiency and reducing enteric methane emissions are key priorities for enhancing the sustainability of ruminant production systems. This study examined the genetic architecture of dry matter intake (DMI), residual feed intake (RFI), methane emissions (ME), and BW in Merino sheep using weighted single-step genome-wide association studies (WssGWAS). Phenotypic records were collected from 1 247 Merino sheep for DMI, 1 231 for RFI, 1 219 for ME, all of which were genotyped using the GeneSeek® Genomic Profiler™ 50K single-nucleotide polymorphism (SNP) array, as well as BW records from 78 466 animals, of which 1 626 were genotyped. Genomic regions explaining at least 0.5% of the additive genetic variance were identified for all traits, with several regions shared by at least two traits. Shared regions on chromosomes 5, 6, 10, 19, and 21 were further evaluated using the Close Linkage versus Pleiotropism (CLIP) test to distinguish pleiotropy from close linkage, revealing pleiotropic loci (chromosome 10 shared between DMI and RFI; chromosome 19 shared between DMI and ME) and closely linked loci influencing multiple traits. Candidate genes located within these regions include RXFP2 , members of the ITIH gene family, and FADS1–2 , which have been previously associated with growth, metabolism, and tissue development, reflecting potential biological mechanisms underlying feed intake, growth, and methane production. No single genomic window exceeded 6.73% of the additive genetic variance, and even within regions showing the strongest window-based signals, the combined effect of the five most informative SNPs accounted for less than 0.23% of the genetic variance, supporting a highly polygenic architecture across all traits, with ME exhibiting the most pronounced polygenic pattern. Several of the candidate genes identified here have also been reported in other ruminant and non-ruminant species, suggesting partially conserved biological mechanisms of potential relevance beyond Merino sheep. These findings provide a foundation for future studies aimed at refining genomic prediction models and support the use of multi-trait evaluations and Bayesian approaches incorporating GWAS-derived priors for traits that are difficult and expensive to measure, such as feed efficiency and methane emissions.