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

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 (F_ROH and F_GRM) showed a strong positive correlation (<i>r</i> = 0.58, <i>p</i> < 0.001), supporting the effectiveness of ROH-based analysis. Several candidate genes were detected, including <i>MYF5</i>, <i>PRDM16</i>, <i>TGM3</i>, <i>SLC26A4</i> and <i>SMAD5</i> 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.