Department of Animal Science, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran.
Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran.
PLoS One. 2024 Aug 16;19(8):e0309023. doi: 10.1371/journal.pone.0309023. eCollection 2024.
The present study aimed to identify the selection signature associated with temperature adaptation in Iranian sheep breeds raised in cold and hot environments. The Illumina HD ovine SNP600K BeadChip genomic arrays were utilized to analyze 114 animals from eight Iranian sheep breeds, namely Ghezel, Afshari, Shall, Sanjabi, Lori-Bakhtiari, Karakul, Kermani, and Balochi. All animals were classified into two groups: cold-weather breeds and hot-weather breeds, based on the environments to which they are adapted and the regions where they have been raised for many years. The unbiased FST (Theta) and hapFLK tests were used to identify the selection signatures. The results revealed five genomic regions on chromosomes 2, 10, 11, 13, and 14 using the FST test, and three genomic regions on chromosomes 10, 14, and 15 using the hapFLK test to be under selection in cold and hot groups. Further exploration of these genomic regions revealed that most of these regions overlapped with genes previously identified to affect cold and heat stress, nervous system function, cell division and gene expression, skin growth and development, embryo and skeletal development, adaptation to hypoxia conditions, and the immune system. These regions overlapped with QTLs that had previously been identified as being associated with various important economic traits, such as body weight, skin color, and horn characteristics. The gene ontology and gene network analyses revealed significant pathways and networks that distinguished Iranian cold and hot climates sheep breeds from each other. We identified positively selected genomic regions in Iranian sheep associated with pathways related to cell division, biological processes, cellular responses to calcium ions, metal ions and inorganic substances. This study represents the initial effort to identify selective sweeps linked to temperature adaptation in Iranian indigenous sheep breeds. It may provide valuable insights into the genomic regions involved in climate adaptation in sheep.
本研究旨在鉴定与伊朗在寒冷和炎热环境中饲养的绵羊品种的温度适应相关的选择信号。使用 Illumina HD 绵羊 SNP600K BeadChip 基因组芯片分析了来自 8 个伊朗绵羊品种（Ghezel、Afshari、Shall、Sanjabi、Lori-Bakhtiari、Karakul、Kermani 和 Balochi）的 114 只动物。所有动物根据其适应的环境和多年来的饲养地区分为两组：寒冷气候品种和炎热气候品种。使用无偏 FST（Theta）和 hapFLK 检验来鉴定选择信号。结果表明，使用 FST 检验在染色体 2、10、11、13 和 14 上鉴定了 5 个基因组区域，在 hapFLK 检验中在染色体 10、14 和 15 上鉴定了 3 个基因组区域在冷、热群中受到选择。进一步探索这些基因组区域发现，这些区域中的大多数与先前鉴定出影响冷、热应激、神经系统功能、细胞分裂和基因表达、皮肤生长和发育、胚胎和骨骼发育、适应缺氧条件以及免疫系统的基因重叠。这些区域与先前鉴定与体重、肤色和角特征等各种重要经济性状相关的 QTL 重叠。基因本体和基因网络分析揭示了区分伊朗冷、热气候绵羊品种的显著途径和网络。我们鉴定了与伊朗绵羊细胞分裂、生物学过程、细胞对钙离子、金属离子和无机物质的反应相关的正选择基因组区域。本研究代表了鉴定与伊朗本土绵羊品种温度适应相关的选择信号的初步努力。它可能为涉及绵羊气候适应的基因组区域提供有价值的见解。
