Comprehensive transcriptome and methylome analysis delineates the biological basis of hair follicle development and wool-related traits in Merino sheep
文献类型： 外文期刊
作者： Zhao, Bingru 1 ; Luo, Hanpeng 1 ; He, Junmin 2 ; Huang, Xixia 3 ; Chen, Siqian 1 ; Fu, Xuefeng 2 ; Zeng, Weidan 3 ; Tian, 1 ;
作者机构： 1.China Agr Univ, Coll Anim Sci & Technol, Minist Agr, Key Lab Anim Genet Breeding & Reprod,Natl Engn La, Beijing, Peoples R China
2.Xinjiang Acad Anim Sci, Inst Anim Sci, Key Lab Genet Breeding & Reprod Fine Wool Sheep &, Urumqi, Peoples R China
3.Xinjiang Agr Univ, Coll Anim Sci, Urumqi, Peoples R China
4.USDA, Agr Res Serv, Henry A Wallace Beltsville Agr Res Ctr, Anim Genom & Improvement Lab, Beltsville, MD 20705 USA
5.Univ Edinburgh, Inst Genet & Canc, MRC Human Genet Unit, Edinburgh, Midlothian, Scotland
6.Shandong Acad Agr Sci, Inst Anim Sci & Vet Med, Jinan, Peoples R China
关键词： Developmental stage; DNA methylation; Genome-wide association study; Hair follicle morphogenesis; Sheep; Transcriptome
期刊名称：BMC BIOLOGY （ 影响因子：7.431； 五年影响因子：8.182 ）
ISSN：
年卷期： 2021 年 19 卷 1 期
页码：
收录情况： SCI
摘要： Background Characterization of the molecular mechanisms underlying hair follicle development is of paramount importance in the genetic improvement of wool-related traits in sheep and skin-related traits in humans. The Merino is the most important breed of fine-wooled sheep in the world. In this study, we systematically investigated the complexity of sheep hair follicle development by integrating transcriptome and methylome datasets from Merino sheep skin. Results We analysed 72 sequence datasets, including DNA methylome and the whole transcriptome of four gene types, i.e. protein-coding genes (PCGs), lncRNAs, circRNAs, and miRNAs, across four embryonic days (E65, E85, E105, and E135) and two postnatal days (P7 and P30) from the skin tissue of 18 Merino sheep. We revealed distinct expression profiles of these four gene types across six hair follicle developmental stages, and demonstrated their complex interactions with DNA methylation. PCGs with stage-specific expression or regulated by stage-specific lncRNAs, circRNAs, and miRNAs were significantly enriched in epithelial differentiation and hair follicle morphogenesis. Regulatory network and gene co-expression analyses identified key transcripts controlling hair follicle development. We further predicted transcriptional factors (e.g. KLF4, LEF1, HOXC13, RBPJ, VDR, RARA, and STAT3) with stage-specific involvement in hair follicle morphogenesis. Through integrating these stage-specific genomic features with results from genome-wide association studies (GWAS) of five wool-related traits in 7135 Merino sheep, we detected developmental stages and genes that were relevant with wool-related traits in sheep. For instance, genes that were specifically upregulated at E105 were significantly associated with most of wool-related traits. A phenome-wide association study (PheWAS) demonstrated that candidate genes of wool-related traits (e.g. SPHK1, GHR, PPP1R27, CSRP2, EEF1A2, and PTPN1) in sheep were also significantly associated with dermatological, metabolic, and immune traits in humans. Conclusions Our study provides novel insights into the molecular basis of hair follicle morphogenesis and will serve as a foundation to improve breeding for wool traits in sheep. It also indicates the importance of studying gene expression in the normal development of organs in understanding the genetic architecture of economically important traits in livestock. The datasets generated here are useful resources for functionally annotating the sheep genome, and for elucidating early skin development in mammals, including humans.
- 相关文献
作者其他论文 更多>>
-
Proteomics Reveals the Role of PLIN2 in Regulating the Secondary Hair Follicle Cycle in Cashmere Goats
作者：Wu, Cuiling;Mamat, Nuramina;Aimaier, Gulinigaer;Lu, Qingwei;Ma, Shengchao;Tang, Sen;Liu, Wenna;Wang, Yaqian;Anwar, Asma;Lu, Yingjie;Ma, Qiangqiang;Fu, Xuefeng
关键词：Jiangnan cashmere goats; secondary hair follicle cycle; proteomics; PLIN2
-
Identification of lncRNAs involved in the hair follicle cycle transition of cashmere goats in response to photoperiod change
作者：Yang, Min;Li, Yingying;Liang, Qianqian;Dong, Huajiao;Han, Jilong;Ma, Yuehui;Andersson, Goeran;Bongcam-Rudloff, Erik;Ahmad, Hafiz Ishfaq;Fu, Xuefeng
关键词：Cashmere goat; LncRNA; Shortened photoperiod; Hair follicle cycle; WGCNA; Transcriptomic analysis
-
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
-
Genetic Evaluation of Early Growth Traits in Yunnan Semi-Fine Wool Sheep
作者：Wang, Yaqian;Lu, Qingwei;Wang, Yaqian;Lu, Qingwei;Tang, Sen;Fu, Xuefeng;Yang, Hongyuan;Zhao, Xiaoqi;Ni, Xiaojun;Quan, Guobo;Zhao, Yuanchong;You, Zhengrong
关键词：Yunnan semi-fine wool sheep; genetic parameters; early growth traits
-
The Farm Animal Genotype-Tissue Expression (FarmGTEx) Project
作者：Fang, Lingzhao;Lin, Qing;Bai, Zhonghao;Gong, Mian;Sorensen, Peter;Sahana, Goutam;Lund, Mogens Sando;Li, Jing;Liu, Xinfeng;Teng, Jinyan;Lin, Qing;Gao, Yahui;Pan, Xiangchun;Gong, Wentao;Yuan, Xiaolong;Li, Jiaqi;Zhang, Zhe;Liu, Shuli;Yang, Jian;Liu, Shuli;Yang, Jian;Guan, Dailu;Cheng, Hao;Zhou, Huaijun;Li, Bingjie;Hou, Yali;Gong, Mian;Pan, Zhangyuan;Zhao, Fuping;Jiang, Lin;Zhao, Guiping;Zhou, Zhengkui;Zhou, Rong;Yu, Ying;Chen, Siqian;Hou, Zhuocheng;Wang, Qin;Zhang, Yi;Ding, Xiangdong;Sun, Dongxiao;Zhang, Hao;Yang, Ning;Clark, Emily L.;Smith, Jacqueline;Clark, Emily L.;Smith, Jacqueline;Rawlik, Konrad;Xiang, Ruidong;Chamberlain, Amanda J.;Goddard, Michael E.;Xiang, Ruidong;Xiang, Ruidong;Goddard, Michael E.;Chamberlain, Amanda J.;Littlejohn, Mathew;Littlejohn, Mathew;Larson, Greger;MacHugh, David E.;O'Grady, John F.;MacHugh, David E.;MacHugh, David E.;Jiang, Zhihua;Jiang, Zhihua;Zhang, Haihan;He, Xi;Zhang, Yuebo;Gao, Ning;He, Jun;Yi, Guoqiang;Liu, Yuwen;Tang, Zhonglin;Li, Kui;Zhao, Pengju;Zhou, Yang;Fu, Liangliang;Zhao, Shuhong;Zhou, Yang;Liu, Lei;Zhao, Shuhong;Wang, Xiao;Hao, Dan;Young, Robert S.;Shen, Xia;Young, Robert S.;Shen, Xia;Shen, Xia;Shen, Xia;Xia, Charley;Xia, Charley;Ma, Li;Song, Jiuzhou;Cole, John B.;Cole, John B.;Cole, John B.;Cole, John B.;Baldwin, Ransom L.;Li, Cong-jun;Van Tassell, Curtis P.;Rosen, Benjamin D.;Bhowmik, Nayan;Liu, George E.;Lunney, Joan;Liu, Wansheng;Guan, Leluo;Guan, Leluo;Zhao, Xin;Ibeagha-Awemu, Eveline M.;Luo, Yonglun;Lin, Lin;Luo, Yonglun;Lin, Lin;Canela-Xandri, Oriol;Derks, Martijn F. L.;Crooijmans, Richard P. M. A.;Godia, Marta;Madsen, Ole;Groenen, Martien A. M.;Koltes, James E.;Tuggle, Christopher K.;McCarthy, Fiona M.;Rocha, Dominique;Giuffra, Elisabetta;Amills, Marcel;Clop, Alex;Amills, Marcel;Clop, Alex;Ballester, Maria;Tosser-Klopp, Gwenola;Li, Jing;Fang, Chao;Fang, Ming;Wang, Qishan;Liu, Hehe;Deng, Juan;Jin, Long;Li, Mingzhou;Mo, Delin;Liu, Xiaohong;Chen, Yaosheng;Sun, Hui-Zeng;Li, Cong;Wang, Yu;Jiang, Yu;Wu, Dongdong;Wang, Wenwen;Fan, Xinzhong;Zhang, Qin;Hu, Xiaoxiang;Huang, Wen;Wu, Yang;Wu, Weiwei;Kasper, Claudia;Liu, Xinfeng;Yu, Xiaofei;Cui, Leilei;Cui, Leilei;Zhou, Xiang;Kim, Seyoung;Li, Wei;Im, Hae Kyung;Buckler, Edward S.;Buckler, Edward S.;Buckler, Edward S.;Ren, Bing;Ren, Bing;Schatz, Michael C.;Li, Jingyi Jessica;Palmer, Abraham A.;Palmer, Abraham A.;Frantz, Laurent;Frantz, Laurent
关键词：
-
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
-
Metabolomics reveals metabolites associated with hair follicle cycle in cashmere goats
作者：Ma, Shengchao;Cao, Wenzhi;Ma, Xiaolin;Ye, Xiaofang;Wu, Cuiling;Ma, Shengchao;Cao, Wenzhi;Ma, Xiaolin;Ye, Xiaofang;Wu, Cuiling;Ma, Shengchao;Liu, Wenna;Lu, Qingwei;Fu, Xuefeng;Qin, Chongkai;Li, Bin
关键词：Cashmere goat; Hair follicle cycle; Metabolome of skin tissue; Relationships; Influencing factors
