数字农科院2.0

Whole-genome sequencing of copy number variation analysis in Ethiopian cattle reveals adaptations to diverse environments

文献类型： 外文期刊

作者： Wondossen Ayalew;Wu Xiaoyun;Getinet Mekuriaw Tarekegn;Tesfaye Sisay Tessema;Min Chu;Chunnian Liang;Rakan Naboulsi;Renaud Van Damme;Erik Bongcam-Rudloff;Yan Ping

作者机构：

关键词： Adaptation;Copy number variation;Ethiopian cattle;Whole-genome sequencing

期刊名称： BMC Genomics

ISSN： 1471-2164

年卷期： 2024 年 25 卷 1 期

页码：

收录情况： SCIE（2024版）

摘要： Background: Genomic structural variations (GSVs), notably copy number variations (CNVs), significantly shape genetic diversity and facilitate adaptation in cattle populations. Despite their importance, the genome-wide characterization of CNVs in indigenous Ethiopian cattle breeds—Abigar, Fellata, and Gojjam-Highland remains largely unexplored. In this study, we applied a read-depth approach to whole genome sequencing (WGS) data to conduct the first comprehensive analysis of CNVs in these populations. Results: We identified 3,893 CNV regions (CNVRs) covering 19.15 Mb (0.71% of the cattle genome). These CNVRs ranged from 1.60 kb to 488.0 kb, with an average size of 4.92 kb. These CNVRs included deletions (1713), duplications (1929), and mixed events (251) showing notable differences in distribution among the breeds. Four out of five randomly selected CNVRs were successfully validated using real time polymerase chain reaction (qPCR). Further analyses identified candidate genes associated with high-altitude adaptation (GBE1 and SOD1), heat stress adaptation (HSPA13, DNAJC18, and DNAJC8) and resistance to tick infestations (BoLA and KRT33A). In addition, variance stabilizing transformation (VST) statistics highlighted population-specific CNVRs, emphasizing the unique genetic signatures of high-altitude adaptation in the Gojjam-Highland cattle breed. Among the detected CNVRs, 4.93% (192 out of 3,893) overlapped with 520 quantitative traits loci (QTLs) associated with six economically important trait categories suggesting that these CNVRs may significantly contribute to the genetic variation underlying these traits. Conclusions: Our comprehensive analysis reveals significant CNVRs associated with key adaptive traits in Ethiopian cattle breeds highlighting their genetic diversity and resilience. These findings offer valuable insights into the genetic basis of adaptability and can inform sustainable breeding practices and conservation efforts. Future research should prioritize the functional validation of these CNVRs and their integration into breeding programs to enhance traits such as disease resistance and environmental adaptability.

分类号：

  • 相关文献

[1]Genomic adaptation of Ethiopian indigenous cattle to high altitude. Terefe E.,Belay G.,Han J.,Hanotte O.,Tijjani A.. 2022

[2]DNA methylation pattern of Photoperiod-B1 is associated with photoperiod insensitivity in wheat (Triticum aestivum). Sun, Han,Guo, Zhiai,Gao, Lifeng,Zhao, Guangyao,Zhang, Wenping,Zhou, Ronghua,Wu, Yongzhen,Jia, Jizeng,Sun, Han,An, Hailong,Wang, Haiyang.

[3]Evolution of the cyclin gene family in plants. Jia, Rui-Dong,Guo, Chun-Ce,Xu, Gui-Xia,Shan, Hong-Yan,Kong, Hong-Zhi,Jia, Rui-Dong,Jia, Rui-Dong. 2014

[4]Analysis of agouti signaling protein (ASIP) gene polymorphisms and association with coat color in Tibetan sheep (Ovis aries). Han, J. L.,Yue, Y. J.,Guo, T. T.,Liu, J. B.,Niu, C. E.,Yang, B. H.,Yang, M.. 2015

[5]Porcine MAP3K5 analysis: molecular cloning, characterization, tissue expression pattern, and copy number variations associated with residual feed intake. Pu, L.,Zhang, L. C.,Zhang, J. S.,Wang, L. G.,Liang, J.,Zhang, Y. B.,Liu, X.,Yan, H.,Zhang, T.,Yue, J. W.,Wang, L. X.,Song, X.,Li, N.,Wu, Q. Q.. 2016

[6]A tandem segmental duplication (TSD) in green revolution gene Rht-D1b region underlies plant height variation. Li, Yiyuan,Xiao, Jianhui,Wu, Jiajie,Duan, Jialei,Liu, Yue,Ye, Xingguo,Zhang, Xin,Guo, Xiuping,Zhang, Lichao,Jia, Jizeng,Kong, Xiuying,Li, Yiyuan,Duan, Jialei,Gu, Yongqiang.

[7]Molecular cloning, tissue expression pattern, and copy number variation of porcine SCUBE3. Liu, X.,Wang, L. G.,Zhang, L. C.,Yan, H.,Zhao, K. B.,Liang, J.,Li, N.,Pu, L.,Zhang, T.,Wang, L. X.. 2016

[8]High-resolution genetic mapping of maize pan-genome sequence anchors. Lu, Fei,Romay, Maria C.,Glaubitz, Jeffrey C.,Elshire, Robert J.,Buckler, Edward S.,Bradbury, Peter J.,Buckler, Edward S.,Wang, Tianyu,Li, Yu,Li, Yongxiang,Semagn, Kassa,Zhang, Xuecai,Hernandez, Alvaro G.,Mikel, Mark A.,Mikel, Mark A.,Soifer, Ilya,Barad, Omer.

[9]Diversity Of Copy Number Variation I.n A Worldwide Population O f Sheep. Yang, L, Xu, LY, Zhou, Y, Liu, M, Wang, L, Kijas, JW, Zhang, HP, Li, L, Liu, GE. 2018

[10]Characterization Of Copy Number Variation'S P.otential Role In Marek'S D isease. Xu, LY, He, YH, Ding, Y, Sun, GR, Carrillo, JA, Li, YK, Ghaly, MM, Ma, L, Zhang, HM, Liu, GE, Song, JZ. 2017

[11]Ntn1 Affects Porcine Intramuscular Fat C.ontent By Affecting The E xpression Of Myogenic Regulatory Factors. Wang, LG, Zhao, LL, Zhang, LC, Liu, X, Hou, XH, Gao, HM, Yan, H, Zhao, FP, Wang, LX. 2019

[12]Genome-wide association analysis reveals 6 copy number variations associated with the number of cervical vertebrae in Pekin ducks. Yaxi Xu,Jian Hu,Wenlei Fan,Hehe Liu,Yunsheng Zhang,Zhanbao Guo,Wei Huang,Xiaolin Liu,Shuisheng Hou. 2022

[13]Towards the detection of copy number variation from single sperm sequencing in cattle. Liu Yang,Yahui Gao,Adam Oswalt,Lingzhao Fang,Clarissa Boschiero,Mahesh Neupane,Charles G. Sattler,Cong jun Li,Eyal Seroussi,Lingyang Xu,Lv Yang,Li Li,Hongping Zhang,Benjamin D. Rosen,Curtis P. Van Tassell,Yang Zhou,Li Ma,George E. Liu. 2022

[14]The Copy Number Variation of OsMTD1 Regulates Rice Plant Architecture. Qing Liu,Jinke Xu,Yunhua Zhu,Yuxing Mo,Xue-Feng Yao,Ruozhong Wang,Wenzhen Ku,Zhigang Huang,Shitou Xia,Jianhua Tong,Chao Huang,Yi Su,Wanhuang Lin,Keqin Peng,Chun-Ming Liu,Langtao Xiao. 2021

[15]The Tempo and Mode of Angiosperm Mitochondrial Genome Divergence Inferred from Intraspecific Variation in Arabidopsis thaliana. Wu, Zhiqiang,Waneka, Gus,Wu, Zhiqiang,Sloan, Daniel B.. 2020

[16]Genome-Wide Characterization Of Copy Number Variations In The Host Genome In Genetic Resistance To Marek'S Disease Using Next Generation Sequencing. Bai, H, He, YH, Ding, Y, Chu, Q, Lian, L, Heifetz, EM, Yang, N, Cheng, HH, Zhang, HM, Chen, JL, Song, JZ. 2020

[17]A genome-wide survey of copy number variations reveals an asymmetric evolution of duplicated genes in rice . Li, Sanfeng,Zeng, Longjun,Qian, Qian,Hu, Jiang,Qian, Qian,Ruan, Jue,Kang, Shujing,Wu, Shigang,Wang, Quan,Shang, Lianguang,Zeng, Longjun,Li, Alun,Ai, Cheng,Wen, Yanling,Deng, Xiaojuan,Hong, Kai,Zheng, Jianshu,Wang, Yuexing,Zhao, Fengli,Wu, Zhichao,Zeng, Dali,Xiong, Guosheng,Xiong, Guosheng,Qin, Xing,Wang, Xiaobo,Qu, Minghao. 2020

[18]Probe-Based Association Analysis Identifies Several D.eletions Associated With Average D aily Gain In Beef Cattle. Xu, LY, Yang, L, Wang, L, Zhu, B, Chen, Y, Gao, HJ, Gao, X, Zhang, LP, Liu, GE, Li, JY. 2019

[19]Genomic Sequencing Analysis Reveals Copy Number Variations And Their Associations With Economically Important Traits In Beef Cattle. Yang, L, Niu, QH, Zhang, TL, Zhao, GY, Zhu, B, Chen, Y, Zhang, LP, Gao, X, Gao, HJ, Liu, GE, Li, JY, Xu, LY. 2021

[20]Genetic Association Analysis of Copy Number Variations for Meat Quality in Beef Cattle. Jiayuan Wu,Tianyi Wu,Xueyuan Xie,Qunhao Niu,Zhida Zhao,Bo Zhu,Yan Chen,Lupei Zhang,Xue Gao,Xiaoyan Niu,Huijiang Gao,Junya Li,Lingyang Xu. 2023

作者其他论文 更多>>