Kichamu Nelly, Wanjala George, Dossybayev Kairat, Bagi Zoltán, Bekmanov Bakhytzhan, Kusza Szilvia
Centre for Agricultural Genomics and Biotechnology, University of Debrecen, Debrecen, 4032, Hungary.
Doctoral School of Animal Science, University of Debrecen, Debrecen, 4032, Hungary.
Sci Rep. 2025 Jun 2;15(1):19327. doi: 10.1038/s41598-025-02427-8.
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.
为了解哈萨克斯坦当地山羊种群的遗传结构，我们首次使用70K SNP芯片进行了全面的基因组分析，检测了来自六个地区的120个样本。这些种群（昆迪兹迪、达尔巴扎、绍克帕尔、乌什捷雷克、凯涅斯和科塞伊特）根据其繁育地区命名，被称为生态型。我们的结果显示出高遗传多样性，观察到的杂合度（Ho）范围为0.389至0.444。绍克帕尔和昆迪兹迪表现出过量杂合性，而科塞伊特和达尔巴扎则有较高的近交水平。除了更为独特的乌什捷雷克山羊外，大多数种群的遗传分化较弱。在适应性方面，纯合性片段（ROH）和综合单倍型分数（iHS）确定了71个受选择的基因，基因本体富集表明定位是对细胞反应最重要的最具代表性的生物学途径。此外，这些基因中有超过60%是共表达的，表明它们在这些山羊在当地环境中的生存中发挥着重要作用。一些鉴定出的基因，如NLRC4、HCLS1、IL17D、IL17RE和IL17RC，与免疫反应有关，在气候变化背景下这是一个重要的适应性状。这项研究不仅强调了哈萨克斯坦当地山羊的高遗传变异性，还为制定哈萨克斯坦及其他类似农业生态区域当地山羊的保护和繁育计划奠定了基础，以使其在不断变化的环境条件下具有适应性和恢复力。
