Runs of Homozygosity in a Broiler Chicken Reference Population

Understanding the genetic architecture of carcass traits is important for breeders and poultry production. The aim of this study was to identify genomic regions under selection in a Brazilian broiler chicken line. A total of 1,462 chickens from the broiler TT Reference Population were genotyped with the 600K genotyping array (Affymetrix®). This population was under selection over several generations for different traits such as growth, development and body weight. After genotype quality control, DishQC≥0.82, sample call rate≥90%, SNP call rate≥98%, MAF≥2%, HWE p-value (P<0,000001) and SNPs located in autosomal chromosomes, there were 1,408 samples and 355,680 SNPs for further analysis. Runs of homozygosity (ROH) were identified using PLINK with ≥250 SNPs, density of 50 kb/SNP, allowed gap of 5,000 kb, 3 heterozygous calls allowed within a run and 0.99 of allele matching for overlapping ROH. All the genes that resided within ROH were analyzed using DAVID to identify over-enriched biological terms. The total of 6,250 ROH were identified across the 28 autosomal chromosomes with an average size of 36.11 Kb (SD 56.13 Kb) and a maximum size of 833.07 Kb. A total of 11,955 genes were analyzed and the top five significant biological terms were: intracellular signaling cascade, regulation of cell death, regulation of cell proliferation, regulation of apoptosis and regulation of programmed cell death. Thus, there appear to be regions of the genome under positive selection related to growth and development, which will help provide a better understanding of the genetic architecture of these traits in chickens.