Genome-wide association study of reproductive traits in a gene pool breed of the Russian White chickens

Studies of candidate genes and SNP associations with reproductive traits provide a valuable source of information for managing small populations of gene pool breeds and their genomic selection. Genome Wide Association Studies (GWAS) were done using SNP chip genotyping technology in the Russian White chicken breed maintained in a genetic research collection of rare and endangered poultry breeds. This breed was developed in the early 1930s by crossing local Russian chicken breeds and White Leghorns, with selection of the breed being started in 1954. An increased sustainability of growing chicks to low temperatures and the white color of embryo down are main breed’s distinctive features. Understanding of the genetic background of these unique traits has become a vital part of the ongoing breeding program. For that purpose, the breed was genotyped using the Illumina 60K SNP Chicken BeadChip. Phenotypic data on age at first egg and pedigree were collected from 163 birds. Genomic data were obtained using the Plink 1.9 software. SNP quality control criteria were applied, with minor allele frequencies being less than 0.001, and Hardy Weinberg equilibrium, more than 0.0001. The GWAS analysis was performed using a mixed model approach employing EMMAX software. A significant effect (p = 9.985225 × 10 −6) of a SNP, rs317931060, was detected. Two genes, FGF9 and TNFRSF19, were close to this SNP, with the distance being 280 and 314 Kb, respectively. Both genes are responsible for sex determination and cell proliferation and differentiation (Studies were supported by a Russian Scientific Foundation grant (No. 1616- 04060) and by a FASO program for developing a bio resource collection.).