Genetic Markers of Karachaevsky Sheep Identified by Genome-Wide Association Study

A genome-wide association study (GWAS) was carried out in Karachaevsky sheep using Illumina Ovine Infinium HD BeadChip 600K DNA biochips to identify single nucleotide polymorphisms (SNPs) associated with the breed. On the basis of the analysis, more than 100 SNPs were identified that have highly significant differences in the frequency of occurrence in animals of the Karachaevsky breed; for subsequent assessment, five single polymorphisms were selected with the highest indicators on chromosomes 12, 13, and 14. Three substitutions are located in the exons of genes, one is located in the intron, and the rest are located at different distances from the genes. The substitutions rs408511664, rs429132161, and rs409651063 (p = 4.637 x 10(-84)), located on chromosome 14 and found only in sheep of the Karachaevsky breed, showed the highest reliability in associations with breed affiliation. Most of the detected SNPs are localized near genes that play an important role in the development of phenotypic traits (TUBB3, MC1R, BMP2, LYPLAL1-201, PAPPA2). The studies make it possible to use the set of identified SNPs as informative molecular markers in identifying the breed of Karachaevsky sheep.