欢迎访问作物学报，今天是
作物学报

作物学报 ›› 2013, Vol. 39 ›› Issue (01): 50-59.doi: 10.3724/SP.J.1006.2013.00050

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

双胚苗水稻来源的单倍体、二倍体及其杂交F1的DNA甲基化位点分析

吴绍华1,2,张红宇1,薛晶晶1,徐培洲1,吴先军1,*   

  1. 1 四川农业大学水稻研究所 / 西南作物基因资源与遗传改良教育部重点实验室, 四川成都 611130; 2 中国热带农业科学院橡胶研究所, 海南儋州 571737
  • 收稿日期:2012-03-07 修回日期:2012-09-05 出版日期:2013-01-12 网络出版日期:2012-11-14
  • 通讯作者: 吴先军, E-mail: wuxj@sicau.edu.cn, Tel: 028-86290906
  • 基金资助:

    本研究由国家自然科学基金项目(30971618, 30771157)资助。

DNA Methylation Site Analysis of Haploid, Diploid and Hybrids in Twin-Seedling Rice

WU Shao-Hua1,2,ZHANG Hong-Yu1,XUE Jing-Jing1,XU Pei-Zhou1,WU Xian-Jun1,*   

  1. 1 Rice Research Institute, Key Laboratory of Southwest Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural University, Chengdu 611130, China; 2 Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China
  • Received:2012-03-07 Revised:2012-09-05 Published:2013-01-12 Published online:2012-11-14
  • Contact: 吴先军, E-mail: wuxj@sicau.edu.cn, Tel: 028-86290906

RichHTML

PDF

1193

被引次数

1

摘要：

全基因组倍增或多倍化, 伴随着基因丢失和二倍化进程, 被认为是植物进化的重要推动力量。DNA甲基化与miRNA的表观遗传调控机制在植物生长发育及进化过程中起着重要的作用。本文采用MSAP (甲基化敏感扩增多态性)技术分析同一双胚苗水稻来源的单倍体、二倍体及其杂交F1的基因组DNA 5'-CCGG位点胞嘧啶的甲基化及遗传特点。对部分甲基化位点进行切胶、回收、测序及功能注释, 并结合miRNA靶基因预测探讨特定甲基化位点的遗传特点及其与miRNA的相关性。16对选择性扩增引物在双亲及杂交F1中共检测了462个DNA甲基化位点, 杂交F1甲基化水平平均为43.20%, 与双亲相差不大(单倍体为46.75%, 二倍体为41.99%)。以TargetFinder软件分析发现其中的7个甲基化位点基因序列上存在1~4个miRNA的结合位点, 这些基因的功能注释包括逆转录转座子蛋白、ras相关蛋白、H2A/H2B/H3/H4核心组蛋白等。同时, 探讨了逆转录转座子在植物进化中的作用。研究结果为进一步阐明水稻基因组倍增过程中DNA甲基化与miRNA的关系提供了参考。

关键词: 双胚苗水稻, 单倍体, DNA甲基化, MSAP, miRNA

Abstract:

Whole-genome duplication or polyploidy, followed by gene loss and diploidization has long been recognized as an important evolutionary force in plants. Epigenetic mechanism, such as DNA methylation and miRNA, plays an important role in plant growth and development, and may also change its regulation pattern to adapt genomic duplication in new species. In this study, the DNA cytosine methylation at the 5'-CpCpGpG sites was analyzed by MSAP (methylation-sensitive amplification polymorphism) method in haploid, diploid and their hybrids derived from twin-seedling rice. And also, the relationships between DNA methylation and miRNA were investigated by sequencing the methylated DNA fragments and predicting the targets of miRNA. A total of 462 DNA methylated sites were detected. The hybrid’s methylation level was 43.20% and a little different from that of its parents (haploid, 46.75%; diploid, 41.99%). TargetFinder was used to find that seven methylated genes matched in sequence of rice database had 1-4 binding sites of miRNAs. The annotation indicated that the genes might include retrotransposon protein, ras-related protein and core histone H2A/H2B/H3/H4 domain containing protein. Most of the genes were annotated as retrotransposons and their functions in evolution were discussed. The results might help us to understand the relationships between DNA methylation and miRNA in rice genome duplication.

Key words: Twin-seedling rice, Haploid, DNA methylation, MSAP, miRNA

[1]Zhang H-Y(张红宇), Peng H(彭海), Li Y(李云), Xu P-Z(徐培洲), Wang X-D(汪旭东), Wu X-J(吴先军). Patterns of DNA cytosine methylation between haploids and corresponding diploids in rice. Chin Sci Bull (科学通报), 2006, 51(13): 1529–1535 (in Chinese)



[2]Peng H(彭海), Zhang H-Y(张红宇), Li Y(李云), Xu P-Z(徐培洲), Wang X-D(汪旭东), Wu X-J(吴先军). Natural homologous triploidization and DNA methylation of twin-seedling rice SARII-628. Chin J Rice Sci (中国水稻科学), 2006, 20(5): 469–474 (in Chinese with English abstract)



[3]Wu S-H(吴绍华), Xue J-J(薛晶晶), Zhang H-Y(张红宇), Xu P-Z(徐培洲), Wu X-J(吴先军). Analysis of special DNA methylated sites between haploid of twin-seedling and its hybrids in rice. Chin J Rice Sci (中国水稻科学), 2011, 25(3): 249–253 (in Chinese with English abstract)



[4]Jiao Y N, Wickett N J, Ayyampalayam S, Chanderbali A S, Landherr L, Ralph P E, Tomsho L P, Hu Y, Liang H Y, Soltis P S, Soltis D E, Clifton S W, Schlarbaum S E, Schuster S C, Ma H, Leebens-Mack J, dePamphilis C W. Ancestral polyploidy in seed plants and angiosperms. Nature, 2011, 473: 97–100



[5]Feng S, Cokus S J, Zhang X, Chen P Y, Bostick M, Goll M G, Hetzel J, Jain J, Strauss S H, Halpern M E, Ukomadu C, Sadler K C, Pradhan S, Pellegrini M, Jacobsen S E. Conservation and divergence of methylation patterning in plants and animals. Proc Natl Acad Sci USA, 2010, 107: 8689–8694



[6]Zemach A, McDaniel I E, Silva P, Zilberman D. Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science, 2010, 328: 916–919



[7]Cuperus J T., Fahlgren N, Carrington J C. Evolution and functional diversification of MIRNA genes. Plant Cell, 2011, 23: 431–442



[8]Fahlgren N, Jogdeo S, Kasschau K D, Sullivan C M, Chapman E J, Laubinger S, Smith L M, Dasenko M, Givan S A, Weigel D, Carrington J C. MicroRNA gene evolution in Arabidopsis lyrata and Arabidopsis thaliana. Plant Cell, 2010, 22: 1074–1089



[9]Wang S, Zhu Q H, Guo X, Gui Y, Bao J, Helliwell C, Fan L. Molecular evolution and selection of a gene encoding two tandem microRNAs in rice. FEBS Lett, 2007, 581: 4789–4793



[10]Xu Y-M(徐艳敏), Guo Y-H(郭艳合), Liu L(刘立), Cai R(蔡荣), Qian C(钱程). The reciprocal modulation between epigenetic and microRNA and the application for treatment of malignant tumors. Prog Biochem Biophys (生物化学与生物物理进展), 2008, 35(12): 1343–1350 (in Chinese with English abstract)



[11]Weber B, Stresemann C, Brueckner B, Lyko F. Methylation of human microRNA genes in normal and neoplastic cells. Cell Cycle, 2007, 6: 1001–1005



[12]Onodera Y, Haag J R, Ream T, Nunes P C, Pontes O, Pikaard C S. Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation. Cell, 2005, 120: 613–622



[13]Zilberman D, Cao X, Jacobsen S E. ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. Science, 2003, 299: 716–719



[14]Wu L, Zhou H, Zhang Q, Zhang J, Ni F, Liu C, Qi Y. DNA methylation mediated by a microRNA pathway. Mol Cell, 2010, 38: 465–475



[15]Panaud O, Chen X, McCouch S R. Development of microsatellite markers and characterization of simple length polymorphism (SSLP) in rice (Oryza sativa L.). Mol Gen Genet, 1996, 252: 597–607



[16]Xiong L Z, Xu C G, Saghai Maroof M A, Zhang Q. Patterns of cytosine methylation in an elite rice hybrid and its parental lines detected by a methylation-sensitive amplification polymorphism technique. Mol Gen Genet, 1999, 261: 439–446



[17]Allen E, Xie Z, Gustafson A M, Carrington J C. microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell, 2005, 121: 207–221



[18]Fahlgren N, Howell M D, Kasschau K D, Chapman E J, Sullivan C M, Cumbie J S, Givan S A, Law T F, Grant S R, Dangl J L, Carrington J C. High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. PLoS One, 2007, 2: e219



[19]Chen X. A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science, 2004, 303: 2022–2025



[20]Li J, Yang Z, Yu B, Liu J, Chen X. Methylation protects miRNAs and siRNAs from a 3'-end uridylation activity in Arabidopsis. Curr Biol, 2005, 15: 1501–1507



[21]Jia X Y, Yan J, Tang G L. MicroRNA-mediated DNA methylation in plants. Front Biol, 2011, 6: 133–139



[22]Bao N, Lye K W, Barton M K. MicroRNA binding sites in Arabidopsis class III HD-ZIP mRNAs are required for methylation of the template chromosome. Dev Cell, 2004, 7: 653–662



[23]Khraiwesh B, Arif M A, Seumel G I, Ossowski S, Weigel D, Reski R, Frank W. Transcriptional control of gene expression by microRNAs. Cell, 2010, 140: 111–122
[1] 李增强, 丁鑫超, 卢海, 胡亚丽, 岳娇, 黄震, 莫良玉, 陈立, 陈涛, 陈鹏. 铅胁迫下红麻生理特性及DNA甲基化分析[J]. 作物学报, 2021, 47(6): 1031-1042.
[2] 文钦, 贾思思, 王加峰, 黄翠红, 王慧, 陈志强, 郭涛. 水稻单倍体诱导基因OsMATL突变体的创制与分析[J]. 作物学报, 2021, 47(5): 827-836.
[3] 李鹏程, 毕真真, 孙超, 秦天元, 梁文君, 王一好, 许德蓉, 刘玉汇, 张俊莲, 白江平. DNA甲基化参与调控马铃薯响应干旱胁迫的关键基因挖掘[J]. 作物学报, 2021, 47(4): 599-612.
[4] 卢海, 李增强, 唐美琼, 罗登杰, 曹珊, 岳娇, 胡亚丽, 黄震, 陈涛, 陈鹏. 红麻DNA甲基化响应镉胁迫及甲基化差异基因的表达分析[J]. 作物学报, 2021, 47(12): 2324-2334.
[5] 殷家明,钟荣棋,林呐,唐章林,李加纳. 诸葛菜小孢子培养及其单倍体减数分裂染色体配对观察[J]. 作物学报, 2020, 46(02): 194-203.
[6] 袁溢,朱双,方婷婷,蒋金金,王幼平. 人工合成甘蓝型油菜抗旱性及DNA甲基化水平分析[J]. 作物学报, 2019, 45(5): 693-704.
[7] 李鹏程,毕真真,梁文君,孙超,张俊莲,白江平. DNA甲基化参与调控马铃薯干旱胁迫响应[J]. 作物学报, 2019, 45(10): 1595-1603.
[8] 王琪月, 孟淑君, 张柯, 张战辉, 汤继华, 丁冬. 玉米雌穗发育杂种优势相关miRNA的研究[J]. 作物学报, 2018, 44(6): 796-813.
[9] 张旸,胡中影,赵月明,李娜,解莉楠. 羽衣甘蓝自交不亲和与自交亲和系种子萌发期DNA甲基化的动态变化[J]. 作物学报, 2016, 42(04): 532-539.
[10] 周艳华,曹红利,岳川,王璐,郝心愿,王新超*,杨亚军*. 冷驯化不同阶段茶树DNA甲基化模式的变化[J]. 作物学报, 2015, 41(07): 1047-1055.
[11] 谭河林,许欣颖，付立曼，向小娥，李剑桥，郭昊伦，叶文雪. 甘蓝型油菜及其亲本物种甲基化酶I基因的克隆及表达模式[J]. 作物学报, 2015, 41(03): 405-413.
[12] 黄志熊,王飞娟,蒋晗,李志兰,丁艳菲,江琼,陶月良,朱诚. 两个水稻品种镉积累相关基因表达及其分子调控机制[J]. 作物学报, 2014, 40(04): 581-590.
[13] 陈新民,王凤菊,李思敏,张文祥. 小麦与玉米杂交产生小麦单倍体与双单倍体的稳定性[J]. 作物学报, 2013, 39(12): 2247-2252.
[14] 赵旭博,李爱丽,毛龙. 植物多倍化过程中小分子RNA调控基因表达机制研究进展[J]. 作物学报, 2013, 39(08): 1331-1338.
[15] 赵志刚,富贵,邓昌蓉,杜德志. 人工合成甘蓝型油菜早期世代基因组变异的AFLP和MSAP标记研究[J]. 作物学报, 2013, 39(07): 1231-1239.
Viewed
Full text


Abstract

Cited
  Shared   
  Discussed   
No Suggested Reading articles found!
京ICP备15008789号-2