Genome-Wide Association Study Revealed the Effect of rs312715211 in ZNF652 Gene on Abdominal Fat Percentage of Chickens

SIMPLE SUMMARY: With intensive selection in broilers, excessive abdominal fat accumulation is also present and causes economic concerns. Abdominal fat percentage (AFP) is one of the main indices of abdominal fat traits. We identified key SNP and candidate gene affecting AFP by a genome-wide association study (GWAS). Additionally, the main findings show that rs312715211 on the ZNF652 gene can increase body weight (BW), reduce eviscerated carcass weight (ECW), and increase abdominal fat percentage (AFP). ABSTRACT: Abdominal fat percentage (AFP) is an important economic trait in chickens. Intensive growth selection has led to the over-deposition of abdominal fat in chickens, but the genetic basis of AFP is not yet clear. Using 520 female individuals from selection and control lines of Jingxing yellow chicken, we investigated the genetic basis of AFP using a genome-wide association study (GWAS) and fixation indices (F(ST)). A 0.15 MB region associated with AFP was located on chromosome 27 and included nine significant single nucleotide polymorphisms (SNPs), which could account for 3.34–5.58% of the phenotypic variation. In addition, the π value, genotype frequency, and dual-luciferase results identified SNP rs312715211 in the intron region of ZNF652 as the key variant. The wild genotype was associated with lower AFP and abdominal fat weight (AFW), but higher body weight (BW). Finally, annotated genes based on the top 1% SNPs were used to investigate the physiological function of ZNF652. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis suggested that ZNF652 may reduce AFW and BW in broilers through the TGF-β1/SMad2/3 and MAPK/FoxO pathways via EGFR and TGFB1. Our findings elucidated the genetic basis of chicken AFP, rs312715211 on the ZNF652 gene, which can affect BW and AFW and was the key variant associated with AFP. These data provide new insight into the genetic mechanism underlying AF deposition in chickens and could be beneficial in breeding chickens for AF.