Tian Yuezhen, An Jing, Zhang Xinning, Di Jiang, He Junmin, Yasen Ayinuer, Ma Yanpin, Sailikehan Gaohaer, Huang Xixia, Tian Kechuan
Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi 830011, China.
College of Animal Science and Technology, Northwest Agriculture and Forest University, Yangling, Xianyang 712100, China.
Animals (Basel). 2024 Oct 8;14(19):2897. doi: 10.3390/ani14192897.
Sheep are a vital species in the global agricultural economy, providing essential resources such as meat, milk, and wool. Merino sheep (Junken type) are a key breed of fine wool sheep in China. However, research on fine wool traits has largely overlooked the role of SNPs and their association with phenotypes. Copy number variations (CNVs) have emerged as one of the most important sources of genetic variation, influencing phenotypic traits by altering gene expression and dosage. To generate a comprehensive CNVR map of the ovine genome, we conducted genome-wide CNV detection using genotyping data from 285 fine wool sheep. This analysis revealed 656 CNVRs, including 628 on autosomes and 28 on the X chromosome, covering a total of 43.9 Mbs of the sheep genome. The proportion of CNVRs varied across chromosomes, from 0.45% on chromosome 26 to 3.72% on chromosome 10. Functional annotation through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses highlighted significantly enriched GO terms, including odorant binding, ATP binding, and sulfuric ester hydrolase activity. The KEGG analysis identified involvement in pathways such as neuroactive ligand-receptor interaction, axon guidance, ECM-receptor interaction, the one-carbon pool by folate, and focal adhesion ( < 0.05). To validate these CNVRs, we performed quantitative real-time PCR experiments to verify copy number predictions made by PennCNV software (v1.0.5). Out of 11 selected CNVRs with predicted gain, loss, or gain-loss statuses, 8 (IDs 68, 156, 201, 284, 307, 352, 411, 601) were successfully confirmed. This study marks a significant step forward in mapping CNVs in the ovine genome and offers a valuable resource for future research on genetic variation in sheep.
绵羊是全球农业经济中的重要物种，提供肉类、奶类和羊毛等重要资源。美利奴羊（军垦型）是中国细毛羊的一个关键品种。然而，关于细毛性状的研究在很大程度上忽略了单核苷酸多态性（SNP）的作用及其与表型的关联。拷贝数变异（CNV）已成为遗传变异的最重要来源之一，通过改变基因表达和剂量影响表型性状。为了生成绵羊基因组的全面CNVR图谱，我们利用285只细毛羊的基因分型数据进行了全基因组CNV检测。该分析揭示了656个CNVR，包括628个常染色体上的和28个X染色体上的，共覆盖绵羊基因组43.9兆碱基对。CNVR在各染色体上的比例不同，从26号染色体上的0.45%到10号染色体上的3.72%。通过基因本体论（GO）和京都基因与基因组百科全书（KEGG）通路分析进行的功能注释突出了显著富集的GO术语，包括气味结合、ATP结合和硫酸酯水解酶活性。KEGG分析确定其参与了神经活性配体 - 受体相互作用、轴突导向、细胞外基质 - 受体相互作用、叶酸一碳池和粘着斑等通路（<0.05）。为了验证这些CNVR，我们进行了定量实时PCR实验，以验证PennCNV软件（v1.0.5）做出的拷贝数预测。在11个预测有增加、减少或增减状态的选定CNVR中，8个（编号68、156、201、284、307、352、411、601）得到了成功确认。这项研究标志着在绘制绵羊基因组CNV图谱方面向前迈出了重要一步，并为未来绵羊遗传变异研究提供了宝贵资源。
