Omics & gene networks

Single-step genome-wide association study for fecal metabolites in Nellore Cattle

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Abstract

The integration of genomics and metabolomics enables analyses using metabolite profiles as phenotypes to identify candidate genes, uncover functional genes linked to metabolic physiology, and elucidate underlying molecular mechanisms and metabolic pathways. Objective of this study was to identify genomic regions and genes related to fecal metabolites in Nellore cattle. A total of 3862 animals were genotyped and imputed to the high-density chip (700 k), and pedigree file contained information on 4962 animals. Fecal bio samples from 265 males, aged 415 ± 74 days, participating in feed efficiency tests were used and all animals were fed the same diet. Metabolomics analyses were performed by Nuclear Magnetic Resonance (1H NMR). The 1H NMR spectra were analyzed for identification and quantification of metabolites. Forty-five metabolites were identified and quantified in mg/dL and the fecal metabolome comprised metabolites mainly related to short-chain fatty acids, amino acid metabolism, organic acids involved in energy pathways, nitrogen-containing compounds, lipid metabolism, and microbial-derived aromatic compounds. For each metabolite, values were centered by its mean and scaled by its standard deviation. To estimate variance components and heritability of each metabolite, a single-trait animal model was fitted, including fixed effects of bio sample collection date, animal's age at collection (linear effect) as a covariate, random additive genetic effect of animal, including additive relationship matrix genotypes. A single-step genome-wide association study (ssGWAS) approach was performed for metabolite butyrate that showed highest heritability estimate (0,34±0,15). The mGWAS results were represented as the proportion of variance explained by a genomic window of 100 adjacent single nucleotide polymorphisms (SNPs). Although fecal metabolites reflect animal and microbial metabolism, the observed variation showed a detectable genetic component. Eight genomic windows that explained more than 1.0% of additive genetic variance were identified. Several genes were identified within those genomic regions located on 28:1.13-1.44, 13:53.80-54.80, 10:91.77-92.58, 17:32.81-33.43, 10:90.30-90.58, 28:5.03-5.37, 7:3.62-4.03, 13:38.09-38.91 Mb. Functional enrichment analysis was performed by DAVID tool and revealed several (p CCSAP, TM6SF2, NCAN, SUGP1 and COL9A3, are involved in important traits for livestock production, such as feed efficiency, dry matter intake, weight gain, fatty acid profile, and lipid metabolism. Key metabolic pathways, such as protein processing in the endoplasmic reticulum and pyrimidine metabolism, reflect important roles in nutrient utilization and cellular metabolism. Pathways related to endocytosis, nucleocytoplasmic transport, and regulation of the actin cytoskeleton highlight mechanisms involved in cellular organization and energy regulation. Immune-related functions, including the cytosolic DNA-sensing pathway, point to mechanisms associated with disease resistance. These results contribute to improving knowledge of genetic architecture of metabolites in Nellore beef cattle and may contribute to improving genetic evaluations.

Keywords: 2026

How to Cite:

Pinto, K., Malheiros, J., Feitosa, F., Valente, L., Soares, T., Ligori, V., David, B. & Mercadante, M., (2026) “Single-step genome-wide association study for fecal metabolites in Nellore Cattle”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2295751. doi: https://doi.org/10.31274/wcgalp.24369

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