New candidate genes of high productivity in North-Caucasian sheep using genome-wide association study (GWAS)

Abstract Genome-wide association study (GWAS) is a powerful tool for identifying loci and individual polymorphisms associated with economically important traits in various species of productive animals. The objective of this study was a genome-wide association search in sheep of the North-Caucasian meat and wool breed to identify single nucleotide polymorphisms (SNPs) associated with a class assessment determined by a set of productive parameters. Sixty rams of the North-Caucasian sheep breed were selected based on the criteria of phenotype and assigned to one of the groups - elite (control, 50 rams) and super-elite (case, 10 rams). They were genotyped using Ovine Infinium HD BeadChip 600 K DNA array and search of SNPs associations with productivity class were conducted. Candidate genes was annotated using ENSEMBLE database. Twelve SNPs were identified that have highly significant differences in the frequency of occurrence in animals with a super-elite score. From these twelve substitutions, five are in introns, seven are located at different distances from the genes. Most of the genes located next to the detected SNPs regulate development and functions of neurons. The greatest reliability in the associations was shown by the substitutions rs410503867 (p = 2 × 10−13) and rs428223899 (p = 1.2 × 10−10) located on chromosomes 4 and 21. Only in animals with a super-elite score three substitutions - rs404739757, rs402746571 and rs413668028 were found, they are presented together next to NALCN gene. The studies revealed a number of new candidate genes located near of SNPs associated with a general assessment of the complex of sheep traits (DGKB, PAK1, CHL1, CTTNBP2, NALCN and NFATC2) and proposed new molecular genetic markers in the form of single nucleotide polymorphisms. We are promising to use the identified genetic markers of super-elite animals in marker-associated breeding to improve the productive qualities of some sheep breed.