Investigation of Critical Genes and Quantitative Trait Loci Related to Economic Traits in Broiler Chicken Genome Using Protein-Protein Interaction Network

The availability of genomic data, such as quantitative trait loci (QTL), has played a pivotal role in understanding the genetic components of various traits. This study aims to investigate critical and hub genes related to economic traits such as growth rate, body fat deposition, and feed consumption by investigating known QTLs by using protein-protein interaction networks (PPI) in chicken species. QTL coordinates for these traits were acquired through the Animal QTL database. Then, genes related to each QTL were obtained from the chicken reference genome (Gallus gallus bGalGal1.mat.broiler. GRCg7b) provided in the NCBI database. Critical genes related to known QTLs based on PPI were identified using Network Analyzer, CytoHubba, and MCODE applications in Cytoscape_v3.8.0 software. The results of this study showed 452, 83, and 75 genes involved in growth rate, body fat deposition, and feed consumption traits, respectively. Several new hub genes related to each trait were found and confirmed by PPI in Cytoscape. Some novel genes for studied traits were EEF1D, UBE2D1, TRIP13, PSMB3, and FZR1 for growth rate, ARPC2, NCAN, and SUGP1 for body fat deposition and LAP3, and SGPP2 for feed consumption. Some hub genes reported in previous studies were also identified in this research for growth rate (NCAPG, MED1, KPNA3, and EP300), body fat deposition (TULP), and feed consumption (MED9, LCORL, COPS3, LAP3, and TAPT1). The common important genes identified between the three traits that were reported in previous studies related to the traits were MNR2, CRYBA2, and MIR375 genes. It can be concluded that novel genes have molecular functions related to economically important traits. Therefore, newly discovered hub genes can be suggested to be used for selecting birds in future broiler breeding programs and basic research on functional genomics.