Genome-Wide Scan for Copy Number Variations in Chinese Merino Sheep Based on Ovine High-Density 600K SNP Arrays
文献类型： 外文期刊
作者： Tian, Yuezhen 1 ; An, Jing 1 ; Zhang, Xinning 3 ; Di, Jiang 1 ; He, Junmin 4 ; Yasen, Ayinuer 1 ; Ma, Yanpin 1 ; Sailikehan, Gaohaer 3 ; Huang, Xixia 3 ; Tian, Kechuan 4 ;
作者机构： 1.Xinjiang Acad Anim Sci, Inst Anim Sci, Key Lab Genet Breeding & Reprod Xinjiang Cashmere, Urumqi 830011, Peoples R China
2.Northwest Agr & Forest Univ, Coll Anim Sci & Technol, Yangling 712100, Xianyang, Peoples R China
3.Xinjiang Agr Univ, Coll Anim Sci, Urumqi 830052, Peoples R China
4.Shandong Acad Agr Sci, Inst Anim Sci & Vet Med, Jinan 250100, Peoples R China
关键词： copy number variations; fine wool sheep; Ovine HD BeadChip
期刊名称：ANIMALS （ 影响因子：2.7； 五年影响因子：3.2 ）
ISSN： 2076-2615
年卷期： 2024 年 14 卷 19 期
页码：
收录情况： SCI
摘要： 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 (p < 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.
- 相关文献
作者其他论文 更多>>
-
A Developmental Gene Expression Atlas Reveals Novel Biological Basis of Complex Phenotypes in Sheep
作者：Zhao, Bingru;Zhang, Guoming;Wang, Feng;Zhang, Yanli;Luo, Hanpeng;Fu, Xuefeng;Zhang, Guoming;Clark, Emily L.;Dalrymple, Brian Paul;Xiang, Ruidong;Dalrymple, Brian Paul;Vercoe, Philip E.;Dalrymple, Brian Paul;Vercoe, Philip E.;Oddy, V. Hutton;Wu, Cuiling;Liu, George E.;Li, Cong-jun;Xiang, Ruidong;Xiang, Ruidong;Xiang, Ruidong;Tian, Kechuan;Fang, Lingzhao
关键词：Sheep; Developmental biology; Gene Expression Atlas; Genome-wide association study; Complex trait
-
Machine learning driven multi-omics analysis of the genetic mechanisms behind the double-coat fleece formation in Hetian sheep
作者：Zhang, Yanwei;Xie, Mengwan;Tang, Liping;Zheng, Peiyu;Song, Nannan;Yu, Lijuan;Di, Jiang;Li, Wenrong;Xu, Xinming
关键词：Hetian sheep; Chinese merino sheep; coat fleece type; multi-omics; machine learning
-
Two mutations at KRT74 and EDAR synergistically drive the fine-wool production in Chinese sheep
作者：Liang, Benmeng;Bai, Tianyou;Zhao, Yuhetian;Han, Jiangang;He, Xiaohong;Pu, Yabin;Ma, Yuehui;Jiang, Lin;Liang, Benmeng;Liu, Jianfeng;Liang, Benmeng;Liu, Jianfeng;Liang, Benmeng;Bai, Tianyou;Zhao, Yuhetian;Han, Jiangang;He, Xiaohong;Pu, Yabin;Ma, Yuehui;Jiang, Lin;Han, Jiangang;Wang, Chunxin;Liu, Wujun;Ma, Qing;Tian, Kechuan;Tian, Kechuan;Zheng, Wenxin;Liu, Nan
关键词：Chinese fine wool sheep; Whole genome sequencing; Genomic selection signature; Follicle density; Missense; Regulatory
-
Whole-genome resequencing provides insights into the diversity and adaptation to desert environment in Xinjiang Mongolian cattle
作者：Xu, Lei;Zhou, Kaiqing;Huang, Xixia;Chen, Hong;Chen, Qiuming;Dong, Hong
关键词：
-
Transcriptomic and Metabolomics Joint Analyses Reveal the Influence of Gene and Metabolite Expression in Blood on the Lactation Performance of Dual-Purpose Cattle (Bos taurus)
作者：Ma, Shengchao;Wang, Dan;Zhang, Menghua;Xu, Lei;Zhang, Tao;Yan, Mengjie;Huang, Xixia;Ma, Shengchao;Fu, Xuefeng
关键词：dual-purpose cattle; blood; lactation performance; metabolomics; transcriptomics; joint analysis
-
Drivers of plateau adaptability in cashmere goats revealed by genomic and transcriptomic analyses
作者：Wu, Cuiling;Ma, Shengchao;Di, Jiang;Fu, Xuefeng;Ma, Shengchao;Zhao, Bingru;Qin, Chongkai;Wu, Yujiang;Suo, Langda
关键词：Plateau adaptability; Tibetan and jiangnan cashmere goats; Genetic; Gene expression and PSGs
-
Transcriptome analysis reveals genes associated with wool fineness in merinos
作者：Ma, Shengchao;Long, Li;Huang, Xixia;Wu, Cuiling;Zhao, Zhiwen;Tian, Kechuan;Wu, Cuiling;Tian, Yuezhen;Wu, Cuiling
关键词：Merinos; Wool fineness; RNA-Seq; DEGs
