Development of a Compact SNP Panel for Hereditary Disease Screening in Kazakh Horse Breeds through Integration of OMIA and Genome-Wide Genotyping Data

Genetic monitoring of hereditary disease-associated variants is becoming an increasingly important component of modern horse breeding. However, information on the distribution of disease-associated loci in Kazakh horse breeds remains limited. Integrating genome-wide SNP data with curated disease databases may provide a practical approach to population-level genetic screening. To develop a compact SNP panel for monitoring hereditary disease-associated variation in Adai and Kostanai horses using genome-wide SNP genotypes and disease loci obtained from the Online Mendelian Inheritance in Animals (OMIA) database. A total of 341 horses (291 Adai and 50 Kostanai) genotyped with a high-density equine SNP array were included in the study. After quality-control filtering, we retained 74,210 SNPs for analysis. Disease-associated loci were extracted from OMIA and mapped to SNP-array markers. When direct representation was unavailable, we identified and incorporated linkage disequilibrium proxies into the analysis. Differences in risk-allele frequencies between breeds were evaluated using Fisher’s exact test with false discovery rate correction. Individual burden scores were calculated to assess cumulative disease-associated variation. Thirty-five hereditary disease loci were identified, including 26 loci represented directly on the SNP array and eight represented by LD proxies. The final dataset contained 33 polymorphic disease-associated SNP markers. Significant differences between breeds were detected for loci linked to congenital stationary night blindness (GRM6), glycogen storage disease type IV (GBE1), and polysaccharide storage myopathy type 1 (GYS1). Despite these differences, we observed no significant difference in the cumulative burden of disease-associated alleles between populations. Based on biological relevance, marker coverage, and population frequencies, we developed a candidate screening panel of eight markers (GRM6, GBE1, GYS1, EDNRB, RAPGEF5, SEL1L, PLOD1, and ACAN). Integration of OMIA-derived disease loci with genome-wide SNP genotypes enabled the development of a compact SNP panel suitable for monitoring hereditary disease-associated variation in Kazakh horse breeds. The proposed panel may support genetic monitoring, breeding management, and future validation studies of disease-associated variants in local horse populations.