Sequence Imputation in One Genomic Window Reveals Putative Candidate Genes for Abdominal Fat in Chickens

Abdominal fat content is an economically important trait in commercial chickens. The aims of this study were to identify the genomic window that explains the highest percentage of genetic variance, perform imputation in this window and identify putative candidate genes for abdominal fat weight in chickens. A total of 497 42 days-old chickens from the EMBRAPA F2 Chicken Resource Population developed for QTL studies were genotyped with the 600K SNP genotyping array (Affymetrix®) and abdominal fat weights (AbF) were measured in these birds. After genotyping quality control, DishQC≥0.82, sample call rate≥90%, SNP call rate ≥98%, MAF≥2% and SNPs located in autosomal chromosomes, there were 480 samples and 371,557 SNPs remaining for further analyses. GWAS analyses were performed with GenSel software using BayesB method (π=0.9988) to identify genomic windows associated with AbFg. Imputation to sequence was performed with FImpute software (default parameters) using the parental whole-resequencing data as the reference population. The genomic window that explained the highest percentage of genetic variance (3.12%) was on GGA1 at 52-54 Mb and SNPs near to TIMP3, FBXO7, TOM1 and LARGE genes exibithed the highest effects within the window. A total of 18,292 SNPs with a MAF≥2% were imputed which represents an increase in SNP density from 0.30 SNPs/Kb to 9.45 SNPs/Kb in this window. TIMP3 and LARGE play an important role in lipid metabolism and after imputation, 207 and 3,290 SNPs were annotated in these genes respectively. This study identified candidate genes and genetic variants that potentially regulate AbF in chickens.