Identification of Functional SNPs in CTGF Regulating Fat Deposition in Broilers

Broilers are one of the most important sources of animal protein worldwide due to their rapid growth rate and high feed efficiency. However, excessive abdominal fat deposition in broilers reduces feed efficiency and carcass quality, resulting in substantial economic losses to the poultry industry. In previous studies, we have demonstrated that connective tissue growth factor (CTGF) is a key gene affecting chicken fat deposition, but its specific molecular mechanism is still unclear. This study aimed to identify functional single-nucleotide polymorphisms (SNPs) within the CTGF gene associated with abdominal fat deposition and to elucidate their potential regulatory mechanisms in broilers. Whole-genome resequencing data from the 19th generation of broiler lines divergently selected for abdominal fat content were used to identify SNPs within CTGF and its flanking regions (±3 kb). Association analyses between SNPs and abdominal fat traits, including abdominal fat weight (AFW) and abdominal fat percentage (AFP), were subsequently performed. Seven SNPs were significantly associated with AFW and AFP, among which four were further validated as functional SNPs by Reverse Transcription Quantitative Polymerase Chain Reaction (RT-qPCR) and luciferase reporter assay, including g + 516T > C, g + 954T > C, g − 982A > G, and g *2702A > T. The results of RT-qPCR indicated that the exonic SNPs g + 516T > C and g + 954T > C may regulate CTGF expression by altering mRNA secondary structure stability. The SNP g − 982A > G, located in the 5′ flanking region, may affect CTGF transcriptional activity through allele-dependent responses to transcription factors CCAAT/enhancer-binding protein alpha (C/EBPα), upstream stimulatory factor 1 (USF1), and MYC-associated factor X (MAX). In addition, the SNP g *2702A > T, located in the 3′ flanking region, may influence CTGF regulation by affecting a potential gga-miR-1812-5p-responsive element. These findings improve our understanding of the genetic mechanisms underlying abdominal fat deposition and provide potential molecular markers for marker-assisted selection for abdominal fat content in broiler breeding programs.