Microbiome

eQTL-based genomic regulation of Leyella and Xylanibacter in pigs identifies candidate targets for breeding

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Abstract

The gut microbiota contributes to nutrient utilization and host performance by fermenting complex carbohydrates into short-chain fatty acids, which influence energy balance and metabolic efficiency in pigs. Among the major fermentative lineages, members of the Prevotellaceae family play central roles in polysaccharide degradation and carbohydrate metabolism, yet their host genetic regulation remains poorly understood. This study investigated the host genetic basis underlying gut microbial abundance related to the recently reclassified genera Leyella and Xylanibacter, aiming to uncover specific host-microbiome regulatory interactions and identify candidate targets for microbiome-informed breeding. Seventy-two immunocastrated Large White pigs fed soybean, fish, or canola oil diets were evaluated. A genome-wide association study (GWAS) was performed using the MLMA-LOCO model (implemented in the GCTA software), adjusted for sire and diet effects. Genotypes from a commercial 50K SNP chip were integrated with microbial profiles obtained by 16S rRNA sequencing of cecal and fecal samples (V3-V4 region, DADA2 pipeline, ASV level ≥10% prevalence, CLR-transformed). Expression quantitative trait loci (eQTL) were derived from RNA-seq (Illumina, TPM-normalized) across the brain, liver, and muscle tissues. Both cis (≤1 Mb) and trans ( >1 Mb) eQTLs were considered (FDR < 0.05). Quality control included minor allele frequency (MAF > 0.05), genotyping call rate lower than 95% (geno > 0.05), missingness per individual (mind > 0.20), and Hardy-Weinberg equilibrium exact test (HWE p > 1 à— 10⁻⁶), followed by linkage disequilibrium pruning (r² > 0.7). RNA-seq data were filtered for lowly expressed genes before normalization, and microbiome data were evaluated for read quality and taxonomic accuracy. Functional annotation was performed using the Ensembl (v. 112) database (Sus scrofa 11.1), providing gene names, symbols, and biological descriptions for interpretation. Significant host-microbiome associations were detected for both genera, involving predominantly brain-associated eQTLs and distinct intestinal niches (feces for Leyella and cecum for Xylanibacter), with all associated variants showing negative allelic effects; these results are summarized in Table 1. These findings indicate specific host genomic regulation of carbohydrate-fermenting bacteria and highlight Leyella and Xylanibacter as potential targets for microbiome-informed breeding. Given the modest sample size, the results should be interpreted as exploratory and hypothesis-generating, supporting future validation and functional studies. These findings expand the understanding of host-microbiome genomic regulation and reveal Leyella and Xylanibacter as promising microbial targets for microbiome-informed breeding strategies with potential to improve digestive efficiency and metabolic resilience in pigs.

Keywords: 2026

How to Cite:

Sabino de Oliveira, C., Felício Ament, A., Silva-Vignato, B., Durval, M., Nery Ciconello, F., Oliveira Freitas, F., Fanalli, S., Carvalho Gervásio, I., Sugizaki dos Santos, T., Echevarria Nascimento, L., Brito, L. & Cesar, A., (2026) “eQTL-based genomic regulation of Leyella and Xylanibacter in pigs identifies candidate targets for breeding”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2285902. doi: https://doi.org/10.31274/wcgalp.23818

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