Cis‐eQTL‐Driven Allele‐Specific Expression Contributes to Feed Efficiency Heterosis in Broilers

Hybrid breeding is central to global broiler production, yet the genetic basis of feed efficiency heterosis remains largely unclear. Here, we used Cornish and White Plymouth Rock chickens to generate purebred (CC and RR) and crossbred (CR) populations, and observed significant heterosis for average daily gain (5.78%), average daily feed intake (3.81%), and feed conversion ratio (−2.01%), indicating improved feed efficiency in hybrids relative to the mid‐parent expectation. Genome‐wide gene expression profiling of the cecal mucosa revealed that nonadditive gene expression predominated in hybrids, accounting for 88.5% of differentially expressed genes, with overdominance identified as the most prevalent inheritance pattern. To elucidate the genetic architecture of this nonadditivity, we performed allele‐specific expression (ASE) and cis‐eQTL mapping. ASE analysis identified 3122 genes with stable allelic bias, of which 1000 overlapped with both nonadditive genes and cis‐eQTL‐associated eGenes. Moreover, paternal‐ and maternal‐biased ASE genes showed complementary functional enrichment and converged on metabolic and protein homeostasis pathways, suggesting coordinated allelic regulation in hybrids. Additionally, cis‐eQTL mapping identified 5695 high‐confidence SNP–gene associations. Integrative analyses of cis‐eQTL architecture, linkage disequilibrium, protein interaction networks, and co‐expression modules prioritized six key candidate genes: CWC15 , MRPL15 , DENND11 , PRPF40A , EWSR1 , and PIKFYVE . Collectively, these findings indicate that cis‐eQTL–driven ASE contributes to nonadditive gene expression and feed efficiency heterosis in broilers.