Genome-Wide Characterization of Heterozygosity-Rich Regions in Kazakh Native Sheep Breeds.

Abstract

Heterozygosity-rich regions (HRR) are genomic segments characterized by high heterozygosity that may arise from admixture, introgression, or balancing selection and may harbor loci associated with adaptation and fitness-related traits. This study aimed to characterize HRR patterns in five Kazakh sheep breeds using a publicly available OvineSNP50 genotyping dataset. After quality control, ~25 000 SNPs were retained for 1634 Akzhaiyk, 1089 Edilbay, 532 Kazakh Fine-Wool, 932 Kazakh Semi-Coarse, and 282 Saryarka sheep. HRR were detected separately in each breed using the sliding-window approach in detectRUNS R package, with a minimum segment length of 250 kb, at least 10 SNPs per window and segment, and a maximum of two opposing homozygous and one missing SNP per window. The average number of HRR per individual ranged from 40.75 ± 6.38 in Saryarka to 54.75 ± 7.34 in Kazakh Fine-Wool sheep. HRR lengths ranged from 259.07 kb to 3.26 Mb, with an average of 0.7 Mb across breeds. Seventeen HRR islands, defined as regions shared by HRR in at least 25% of individuals within a breed, were identified, including regions on chromosomes 8 and 17 shared across all breeds. Genes overlapping these islands were associated with cellular homeostasis, immunity, metabolism, growth, and stress response, while the HRR islands overlapped with QTL associated with health, wool characteristics, and reproduction. These findings highlight the potential of HRR analysis to identify candidate genomic regions relevant to adaptation and economically important traits, providing insights for the conservation and genetic improvement of Kazakh sheep populations.