Abstract
To understand the genetic structure of local goat populations in Kazakhstan, we present the first comprehensive genomic analysis using a 70 K SNP array, examining 120 samples from six regions. The populations (Kundyzdy, Darbaza, Shokpar, Ushterek, Kenes and Kosseit) are named based on their breeding regions and are referred to ecotypes. Our results present a high genetic diversity, with observed heterozygosity (Ho) ranging from 0.389 to 0.444. Shokpar and Kundyzdy showed excess heterozygosity, while Kosseit and Darbaza had high inbreeding levels. Most populations recorded weak genetic differentiation, except for Ushterek goats, which were more distinct. For adaptability, Runs of Homozygosity (ROH) and Integrated Haplotype Score (iHS) identified 71 genes under selection, with gene ontology enrichment indicating localization as the most represented biological pathway important for cell response. Additionally, over 60% of these genes are co-expressed, suggesting their significant role in survival of these goats in their local environments. Some identified genes, such as NLRC4, HCLS1, IL17D, IL17RE, and IL17RC, were linked to immune response, an important adaptation trait in the context of climate change. This study not only emphasizes on high genetic variability of local goats in Kazakhstan but also lays the groundwork for developing conservation and breeding programs for local goats in Kazakhstan and other similar agroecological regions for adaptability and resilience under changing environmental conditions.