Genotype data of Karacabey Merino, Middle Anatolian Merino (Oamer), Akkaraman, HASMER, and HASAK sheep breeds.

This study aimed to comparatively detect genomic signatures of selection in indigenous and crossbred Turkish sheep breeds using high-density SNP genotyping. A total of 1,612 individuals were analyzed, comprising the indigenous Akkaraman breed and four crossbreds: Karacabey Merino, Oamer, Hasak, and Hasmer. PCA revealed clear genetic separation of Akkaraman, partial overlap between Karacabey Merino and Oamer, and distinct variation in the small Hasak and Hasmer populations. Genetic diversity metrics indicated moderate and relatively homogeneous diversity across breeds, with slightly negative FIS, reflecting heterozygote excess. Selection signatures were identified using ROH, iHS, and Tajima’s D statistics. ROH analysis highlighted breed-specific candidate genes associated with growth (e.g., BGLAP, MYF6, GHR), milk production (PRL, LTF, casein cluster), immune response (TLR2, TLR5, IL15), and reproduction (FSHB, BMPR1B). iHS detected additional loci under positive selection, including MSTN, POU1F1, LEPR, and LALBA, while Tajima’s D identified selective sweeps in genes related to muscle development (CAPN2, CAST), reproduction (PAG4), and immune function (IRF2, ITGB2). Fifty candidate genes were shared among all breeds, whereas others were breed-specific, suggesting both common and unique adaptive pathways. These findings provide valuable insights into the genomic architecture and adaptive evolution of indigenous and crossbred Turkish sheep, with implications for conservation and breeding strategies.

本研究旨在利用高密度单核苷酸多态性（Single Nucleotide Polymorphism, SNP）基因分型技术，对土耳其本土绵羊品种与杂交绵羊品种的基因组选择特征进行比较检测。本研究共分析1612个个体，涵盖本土阿克卡拉曼（Akkaraman）绵羊品种，以及4个杂交绵羊品种：卡拉卡贝美利奴（Karacabey Merino）、奥梅尔（Oamer）、哈萨克（Hasak）和哈斯梅尔（Hasmer）。主成分分析（Principal Component Analysis, PCA）结果显示，阿克卡拉曼绵羊与其余品种呈现清晰的遗传分化；卡拉卡贝美利奴与奥梅尔存在部分遗传重叠；而规模较小的哈萨克与哈斯梅尔种群则表现出显著的遗传差异。遗传多样性指标显示，各绵羊品种的多样性水平处于中等且相对均一，FIS值略呈负值，反映出杂合子过剩现象。本研究采用纯合子连续片段（Runs of Homozygosity, ROH）、整合单倍型得分（iHS）与塔伊马D（Tajima’s D）统计量，鉴定基因组选择特征。其中，纯合子连续片段分析筛选出品种特异性候选基因，涉及生长性状（如BGLAP、MYF6、GHR）、泌乳性状（PRL、LTF、酪蛋白基因簇）、免疫应答（TLR2、TLR5、IL15）及繁殖性状（FSHB、BMPR1B）。整合单倍型得分分析检测到额外的受正选择作用的基因座，包括MSTN、POU1F1、LEPR与LALBA；而塔伊马D统计量则在与肌肉发育（CAPN2、CAST）、繁殖（PAG4）及免疫功能（IRF2、ITGB2）相关的基因中鉴定出选择性清除区域。共有50个候选基因在所有绵羊品种中共享，其余候选基因则为品种特有，这表明土耳其绵羊既存在共同的适应性演化通路，也存在品种特异性的适应性演化路径。本研究结果为解析土耳其本土与杂交绵羊的基因组结构及其适应性演化提供了宝贵见解，同时可为绵羊种质资源保护与育种策略制定提供理论参考。