Genomic Characterization of the Kazakh Fat-Tailed Coarse-Wool Sheep Breed Using ROH Analysis

Abstract

Simple Summary Sheep are an important source of food and income for people in Kazakhstan. Among the local breeds, the Kazakh fat-tailed coarse-wool sheep is especially valued because it grows well on natural pastures, produces a large amount of meat, and can survive in very hot summers and cold winters. To keep this breed healthy and productive, it is important to understand its genetic background. In our study, we used 500 sheep to learn how much variety exists within the breed and to find genomic regions to underline useful traits. We discovered multiple genes that are connected to growth, fat storage, reproduction and wool production. This knowledge will help farmers and breeders improve their flocks while protecting the genetic resources that are so valuable for the future of sheep farming in Kazakhstan. Abstract Sheep breeding is an important sector of livestock production in the Republic of Kazakhstan. The Kazakh fat-tailed coarse-wool sheep holds a prominent position among local breeds due to its high meat productivity, resilience to extreme climatic conditions, and efficient use of pasture resources. This study focuses on the analysis of runs of homozygosity (ROH) to evaluate the genetic diversity level, inbreeding and to detect selection signatures in the Kazakh fat-tailed coarse-wool sheep breed. A total of 500 animals were genotyped using the OvineSNP50 BeadChip (Illumina, San Diego, CA, USA). As a result, a total of 41,728 ROH segments were identified, with an average length of 1.59 Mb, distributed across the entire genome. The most prominent homozygous regions were detected on chromosomes OAR10, OAR13, and OAR22, which might be associated with selection signatures. Genomic inbreeding coefficients (FROH and FGRM) showed a strong positive correlation (r = 0.58, p < 0.001), supporting the effectiveness of ROH-based analysis. Several candidate genes were detected, including MYF5, PRDM16, TGM3, SLC26A4 and SMAD5 which are notably involved in muscle formation, wool traits, and fat metabolism. The findings have substantial practical value for breeding programs and for managing genetic diversity in sheep farming enterprises in the Republic of Kazakhstan.