Single-base resolution methylomes of upland cotton (Gossypium hirsutum L.) reveal epigenome modifications in response to drought stress

文献类型： 外文期刊

第一作者： Xuke Lu

作者： Xuke Lu;Ye, Wuwei;Xiaoge Wang;Xiugui Chen;Na Shu;Junjuan Wang;Delong Wang;Shuai Wang;Weili Fan;Lixue Guo;Xiaoning Guo;Wuwei Ye

作者机构：

关键词： Methylomes;Upland cotton;Epigenome modifications;Long non-coding RNAs;Drought stress

期刊名称：BMC GENOMICS （ 影响因子：3.969； 五年影响因子：4.478 ）

ISSN： 1471-2164

年卷期： 2017 年 18 卷

页码：

收录情况： SCI

摘要： Background: DNA methylation, with a cryptic role in genome stability, gene transcription and expression, is involved in the drought response process in plants, but the complex regulatory mechanism is still largely unknown. Results: Here, we performed whole-genome bisulfite sequencing (WGBS) and identified long non-coding RNAs on cotton leaves under drought stress and re-watering treatments. We obtained 31,223 and 30,997 differentially methylated regions (representing 2.48% of the genome) after drought stress and re-watering treatments, respectively. Our data also showed that three sequence contexts, including (m)CpG, (m)CHG, (CHH)-C-m, all presented a hyper-methylation pattern under drought stress and were nearly restored to normal levels after the re-watering treatment. Among all the methylation variations, asymmetric CHH methylation was the most consistent with external environments, suggesting that methylation/demethylation in a CHH context may constitute a novel epigenetic modification in response to drought stress. Combined with the targets of long non-coding RNAs, we found that long non-coding RNAs may mediate variations in methylation patterns by splicing into microRNAs. Furthermore, the many hormone-related genes with methylation variations suggested that plant hormones might be a potential mechanism in the drought response. Conclusions: Future crop-improvement strategies may benefit by taking into account not only the DNA genetic variations in cotton varieties but also the epigenetic modifications of the genome.

分类号：

  • 相关文献

[1]Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression. Xie, Xianfa,Li, Xin,Zhang, Guojie,Wang, Wen,Li, Xin,Ye, Mingzhi,Xiang, Hui,Zhang, Guojie,Luo, Ruibang,Yu, Chang,Wang, Jun,Zhu, Jingde,Zhang, Hongyu,Yu, Jian,Sun, Jingfeng,Zou, Xiaoyu,Zhu, Jingde,Hu, Fengyi,Zhang, Shilai,Li, Qiong,Ge, Song,Zheng, Xiaoming,Luo, Ruibang,Cao, Xiaofeng,Wang, Jun. 2012

[2]Long Non-Coding RNAs: emerging and versatile Regulators in Host-virus interactions. Meng, Xing-Yu,Luo, Yuzi,Anwar, Muhammad Naveed,Sun, Yuan,Gao, Yao,Zhang, Huawei,Qiu, Hua-Ji,Munir, Muhammad. 2017

[3]Roles of LncRNAs in Viral Infections. Liu, Weiwei,Ding, Chan. 2017

[4]Enriching an intraspecific genetic map and identifying QTL for fiber quality and yield component traits across multiple environments in Upland cotton (Gossypium hirsutum L.). Xueying Liu,Zhonghua Teng,Liu, Fang,Zhang, Zhengsheng,Jinxia Wang,Tiantian Wu,Zhiqin Zhang,Xianping Deng,Xiaomei Fang,Zhaoyun Tan,Iftikhar Ali,Dexin Liu,Jian Zhang,Dajun Liu,Fang Liu,Zhengsheng Zhang.

[5]Study of Cotton Matured Fibre Quality and the Super-Molecular Structure in Upland Cotton RILs. Yongbo Wang,Caihong Li,Haihong Shang,Botao Li,Chengbo Li,Aiying Liu,Youlu Yuan. 2014

[6]Association mapping analysis of fiber yield and quality traits in Upland cotton (Gossypium hirsutum L.). Mulugeta Seyoum Ademe,Du, Xiongming,Jia, Yinhua,Shoupu He,Zhaoe Pan,Junling Sun,Qinglian Wang,Hongde Qin,Jinhai Liu,Hui Liu,Jun Yang,Dongyong Xu,Jinlong Yang,Zhiying Ma,Jinbiao Zhang,Zhikun Li,Zhongmin Cai,Xuelin Zhang,Xin Zhang,Aifen Huang,Xianda Yi,Guanyin Zhou,Lin Li,Haiyong Zhu,Baoyin Pang,Liru Wang,Yinhua Jia,Xiongming Du.

[7]Analysis of decision-making coefficients of three main fiber quality traits for upland cotton (Gossypium hirsutum L.). Yongjun Mei,Wenming Hu,Shuli Fan,Meizhen Song,Chaoyou Pang,Shuxun Yu.

[8]Genome-wide comparative transcriptome analysis of CMS-D2 and its maintainer and restorer lines in upland cotton. Jianyong Wu,Wu, Jianyong,Xing, Chaozhu,Meng Zhang,Bingbing Zhang,Xuexian Zhang,Liping Guo,Tingxiang Qi,Hailin Wang,Jinfa Zhang,Chaozhu Xing. 2017

[9]Primary analysis of QTG contribution to heterosis in upland cotton. ZHANG XianLiang,LIU Fang,WANG Wei,LI ShaoHui,WANG ChunYing,ZHANG XiangDi,WANG YuHong,WANG KunBo. 2010

[10]Quantitative Trait Locus Mapping for Verticillium wilt Resistance in an Upland Cotton Recombinant Inbred Line Using SNP-Based High Density Genetic Map. Palanga, Koffi Kibalou. 2017

[11]Genome-wide characterization and expression analysis of MYB transcription factors in Gossypium hirsutum. Haron Salih,Wenfang Gong,Shoupu He,Gaofei Sun,Junling Sun,Xiongming Du. 2016

[12]Identification of stable quantitative trait loci (QTLs) for fiber quality traits across multiple environments in Gossypium hirsutum recombinant inbred line population. Muhammad Jamshed,Fei Jia,Juwu Gong,;Koffi Kibalou Palanga,Yuzhen Shi,Junwen Li,Haihong Shang,Aiying Liu,Tingting Chen,Zhen Zhang,Juan Cai,Qun Ge,Zhi Liu,Quanwei Lu,Xiaoying Deng,Yunna Tan,Harun or Rashid,Zareen Sarfraz,Murtaza Hassan,Wankui Gong,Youlu Yuan. 2016

[13]Development of a core set of SNP markers for the identification of upland cotton cultivars in China. Kuang Meng,WEI Shou-jun,WANG Yan-qin,ZHOU Da-yun,MA Lei,FANG Dan,YANG Wei-hua,MA Zhi-ying. 2016

[14]High-Density Linkage Map Construction and Mapping of Salt-Tolerant QTLs at Seedling Stage in Upland Cotton Using Genotyping by Sequencing (GBS). Latyr Diouf,Du, Xiongming,Zhaoe Pan,Shou-Pu He,Wen-Fang Gong,Yin Hua Jia,Richard Odongo Magwanga,Kimbembe Romesh Eric Romy,Harun or Rashid,Joy Nyangasi Kirungu,Xiongming Du. 2017

[15]Genome-wide identification and characterization of SnRK2 gene family in cotton (Gossypium hirsutum L.). Zhao Liu,Xiaoyang Ge,Zuoren Yang,Li, Fuguang,Zhang, Xueyan,Chaojun Zhang,Ge Zhao,Eryong Chen,Ji Liu,Xueyan Zhang,Fuguang Li. 2017

[16]Dynamic QTL mapping for plant height in Upland cotton (Gossypium hirsutum). Shang, Lianguang,Abduweli, Abdugheni,Cai, Shihu,Liu, Fang,Wang, Kunbo,Wang, Yumei.

[17]Genome-wide SSR-based association mapping for fiber quality in nation-wide upland cotton inbreed cultivars in China. Nie, Xinhui,Huang, Cong,Zhao, Wenxia,Shen, Chao,Zhang, Beibei,Wang, Hantao,Yan, Zhenhua,Dai, Baoshen,Wang, Maojun,Zhang, Xianlong,Lin, Zhongxu,Nie, Xinhui,You, Chunyuan,Li, Wu. 2016

[18]Inheritance of resistance to Helicoverpa armigera of 3 kinds of transgenic Bt strains available in upland cotton in China. Tang, CM,Sun, J,Zhu, XF,Guo, WZ,Zhang, TZ,Shen, JL,Gao, CF,Zhou, WJ,Chen, ZX,Guo, SD.

[19]Genetic Analysis and QTL Detection on Fiber Traits Using Two Recombinant Inbred Lines and Their Backcross Populations in Upland Cotton. Lianguang Shang,Yumei Wang,Xiaocui Wang,Fang Liu,Abdugheni Abduweli,Shihu Cai,Yuhua Li,Lingling Ma,Kunbo Wang,Jinping Hua. 2016

[20]Main Effect QTL with Dominance Determines Heterosis for Dynamic Plant Height in Upland Cotton. Lianguang Shang,Lingling Ma,Yumei Wang,Ying Su,Xiaocui Wang,Yuhua Li,Abdugheni Abduweli,Shihu Cai,Fang Liu,Kunbo Wang,Jinping Hua. 2016

作者其他论文 更多>>

微信小程序