Gallus gallus duodenal transcriptome

In this study, we comprehensively characterized the complex interactions among host genomic variants, mucosal gene expression, and intestinal microbial composition encompassing various traits such as feed efficiency, egg production, egg quality, carcass traits, hepatic and serum biochemical indicators. We analyzed over 20,000 genes in liver and duodenum, along with hundreds of duodenal microbial taxa, and recognized their reciprocal influence on each other. Additionally, we developed and adapted innovative approaches, including heritability (h2), microbiability (m2), and regulability (r2, the proportion of the contribution of gene expression profile on host phenotypes) designed to address common challenges encountered in multi-omic integrations, such as high-dimensionality, sparsity, and multicollinearity. The methodologies facilitated the identification of robust and biologically meaningful associations between gut microbes and host genes.