Genome-wide association study (GWAS) of high productivity classes in the Karachaevsky sheep breed

Abstract

Using the Illumina Ovine Infinium HD BeadChip 600K DNA array, we performed a genome-wide association study (GWAS) in Karachaevsky breed sheep with different class evaluations (elite and super-elite). The classification was carried out according to complex criteria, including live weight, the presence of horns, colour and length of the coat, and body size. Fifteen single nucleotide polymorphisms (SNPs) were detected, the frequency of occurrence of which reliably depends on the individual belonging to the assessed class groups. The search for candidate genes near to these SNPs allowed us to divide them into several groups. Five SNPs are in the introns of genes, four are in the exons, two are associated with genes encoding long non-coding RNAs, and the rest are intergenic variants. Most of the detected candidate genes are associated with the processes of growth and development of the body. The most significant differences in the frequency of occurrence were shown by the SNPs rs427394436, rs429383103, rs398161871 and rs421966191 (p = 1.022×10-14) located on chromosomes 1, 2 and 21. As new candidate genes, we proposed: MAEL, EPHA4, CPT1, FCER1A, CWC27, SHISAL2B, SCIN, MYO16 and ITPKB. In addition, SNPs with a significant difference in the frequency of occurrence can be used as molecular genetic markers when conducting breeding work in sheep of the Karachaevsky breed.