Food intake-related genes in chicken determined through combinatorial genome-wide association study and transcriptome analysis

The chicken gizzard is the primary digestive and absorptive organ regulating food intake and metabolism. Body weight is a typical complex trait regulated by an interactive polygene network which is under the control of an interacting network of polygenes. To simplify these genotype–phenotype associations, the gizzard is a suitable target organ to preliminarily explore the mechanism underlying the regulation of chicken growth through controlled food intake. This study aimed to identify key food intake-related genes through combinatorial GWAS and transcriptome analysis. We performed GWAS of body weight in an F₂ intercrossed population and transcriptional profiling analysis of gizzards from chickens with different body weight. We identified a major 10 Mb quantitative trait locus (QTL) on chromosome 1 and numerous minor QTL distributed among 24 chromosomes. Combining data regarding QTL and gizzard gene expression, two hub genes, MLNR and HTR2A, and a list of core genes with small effect were found to be associated with food intake. Furthermore, the neuroactive ligand–receptor interaction pathway was found to play a key role in regulating the appetite of chickens. The present results show the major–minor gene interactions in metabolic pathways and provide insights into the genetic architecture and gene regulation during food intake in chickens.