A SEARCH FOR GENOMIC VARIANTS ASSOCIATED WITH BODY WEIGHT IN SHEEP BASED ON HIGH DENSITY SNP GENOTYPES ANALYSIS

Abstract

Body weight is one of the most important economically useful traits, which is characterized by complex inheritance. Therefore, a search for genetic mechanisms affecting its formation is of increased scientific interest. This work presents for the first time the results of the genome-wide association studies in the resource population of sheep (Ovis aries) from backcross (Romanov × Katah-din) × Romanov family, whose body weight was recorded in age dynamics, and SNP profiles were obtained using a high-density DNA chip. We identified 38 SNPs significantly associated with body weight (p < 0.00001) and functional candidate genes which affect skeletal muscle growth, bone scaffold formation, lipid, and carbohydrate metabolism. In addition, age-related changes in the set of significantly significant SNPs are shown. Our aim was to search for genomic variants that affect the body weight of (Romanov × Katahdin) × Romanov backcrosses from the resource population at different age periods. The study was performed on 95 sheep from backcross (Romanov × Katahdin) × Romanov family (Ernst Federal Research Center for Animal Husbandry, 2018-2021). Ear notch samples were taken from backcrosses for extraction of genomic DNA, which isolated using DNA-Extran-2 kits (Syntol LLC, Russia). Animals were genotyped using a high-density DNA chip Ovine Infinium® HD SNP BeadChip (Illumina, Inc., USA) containing ~600 thousand SNP markers. The body weight was recorded at the ages of 6(BW6), 42(BW42), 90(BW90), 180(BW180) and 270 days (BW270). To study genome-wide associations with body weight, we used regression analysis implemented in PLINK 1.90 (--assoc --adjust --qt-means). To confirm the significant effect of SNP and to identify significant regions in the genome of the studied sheep, a test was performed to check null hypotheses according to Bonferroni at a threshold value of p < 1.09×10-7, 0.05/459868. The search for candidate genes located in the region of identified SNPs was performed using the VEP (Ensembl Variant Effect Predictor) tool of Ensembl genome browser 103 (https://www.ensembl.org/index.html). After quality control, 459,868 SNPs were used to perform genome-wide association studies (GWAS). Average body weights in the studied sample were 3.28±0.07, 8.03±0.21, 13.74±0.39, 20.19±0.51, and 22.51±0.50 kg at the age of 6, 42, 90, 180, and 270 days, respectively. We found that in different age periods the set of SNPs associated with the integral indicator of the growth rate, the animal body weight, was different. Thus, out of 38 identified SNPs, 18 SNPs located on OAR2, OAR4, OAR9, and OAR15 were reliably associated with BW6 (p < 0.00001); 3 SNPs located on OAR6 and OAR11 with BW42 (p < 0.00001); 2 SNPs located on OAR10 and OAR19 with BW90 (p < 0.00001); 6 SNPs (p < 0.00001) located on OAR1 and OAR13 with BW180 (p < 0.00001) and 6 SNPs located on OAR1 with BW270 (p < 0.00001). Blocks of 3-5 SNPs were found on OAR1, OAR2, OAR4, and OAR5. Significance levels for six SNPs, including oar3_OAR4_87887519 (p < 7.13×10-8), oar3_OAR4_87889243(p < 1.51×10-7), oar3_OAR9_89145258 (p < 4.95×10-7), oar3_OAR1_192662599 (p < 4.79×10-7), OAR1_208070059.1 (p < 4.79×10-7) and oar3_OAR13_31446454 (p < 6.84×10-7) exceeded the threshold for GWAS (p < 1.09×10-7). Along with known candidate genes associated with body weight in sheep, we found new candidate genes whose effects on this trait have not been previously reported. The functional annotation of the identified candidates showed the presence of genes affecting skeletal muscle growth, bone frame formation, lipid, and carbohydrate metabolism. The obtained data will be useful for the development of marker and genomic selection programs in sheep breeding.