Welcome to Acta Agronomica Sinica,

Acta Agron Sin ›› 2016, Vol. 42 ›› Issue (04): 513-524.doi: 10.3724/SP.J.1006.2016.00513

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Analysis of DNA Methylation Patterns in Resynthesized Brassica napus and Diploid Parents

XIE Tao,RONG Hao,JIANG Jin-Jin*,KONG Yue-Qin,RAN Li-Ping,WU Jian,WANG You-Ping   

  1. College of Bioscience and Biotechnology, YangzhouUniversity, Yangzhou 225009, China
  • Received:2015-08-27 Revised:2016-01-11 Online:2016-04-12 Published:2016-01-25
  • Contact: 蒋金金, E-mail: jjjiang@yzu.edu.cn, Tel: 0514-87997303 E-mail:18505143324@163.com
  • Supported by:

    This study was supported by the National Key Basic Research Program of China (2015CB150201), Chinaand Jiangsu Postdoctoral Program (2014M561719, 2015T80591, 1401078B).

Abstract:

The genetic background of Brassica napus, one of the most important oil crops in China, is relatively narrow due to the short history of its polyploid origin. Resynthesized B. napus provides an optimal model for researches on plant polyploidization. In the present study, we compared the DNA methylation levels in synthesized B. napus (F1 generation) and diploid parents using high-performance liquid chromatography (HPLC) and DNA methylation-sensitive amplification polymorphism (MSAP) analysis. HPLC analysis indicated methylation rates of 8.33% and 15.88% in B. rapa and B. oleracea, respectively. While the methylation rate of two hybrids was 10.29% and 12.83%, which werein-between of the parents’values. MSAP analysis proved the different methylation levels in F1 generation and diploids, with the lowest and highest methylation levels identified in B. rapa and B. oleracea, respectively.Variance of the DNA methylation in F1was 23.71%, among which 6.60% and 10.16% were inherited from A and C genome, respectively. Sequence analysis of MSAP polymorphic fragments indicated genes involved in multiple molecular functions were changed during polyploidization. Expression analysis of these genes agreed to the corresponding methylation changes. This study provides preliminary basis for understanding epigenetic variations during B. napus polyploidization.  

Key words: Bassica napus, Resynthesized species, Polyploidization, DNA methylation

[1] Solti D E, Visger C J, Soltis P S. The polyploidyrevolution then…and now: Stebbins revised. Am J Bot, 2014, 101: 1057–1078

[2] Blanc G, Wolfe K H. Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell, 2004, 16: 1667–1678

[3] Nagahararu U. Genome analysis in Brassica with special reference to the experimental formation of B. napus and peculiar mode of fertilization. Jpn J Bot, 1935, 7: 389–452

[4] Li H T, Younas M, Wang X F, Li X M, Chen L, Zhao B, Chen X, Xu J S, Hou F, Hong B H, Liu G, Zhao H Y, Wu X L, Du H Z, Wu J S, Liu K D. Development of a core set of single-locus SSR markers for allotetraploid rapeseed (Brassica napus L.). Theor Appl Genet, 2013, 126: 937–947

[5] Rahman H. Breeding spring canola (Brassica napus L.) by the use of exotic germplasm. Can J Plant Sci, 2013, 93: 363–373

[6] Qian W, Meng J, Li M, Frauen M, Sass O, Noack J, Jung C. Introgression of genomic components from Chinese Brassica rapa contributes to widening the genetic diversity in rapeseed (B. napus L.), with emphasis on the evolution of Chinese rapeseed. Theor Appl Genet, 2006, 113: 49–54

[7] Mei J, Fu Y, Qian L, Xu X, Li J, Qian W. Effectively widening the gene pool of oilseed rape (Brassica napus L.) by using Chinese B. rapa in a ‘virtual allopolyploid’ approach. Plant Breed, 2011, 130: 333–337

[8] Gaeta R T, Pires J C, Iniguez-Luy F, Leon E, Osborn T C. Genomic changes in resynthesized Brassica napus and their effect on gene expression and phenotype. Plant Cell, 2007, 19: 3403–3417

[9] Jiang J, Shao Y, Du K, Ran L, Fang X, Wang Y. Use of digital gene expression to discriminate gene expression differences in early generations of resynthesized Brassica napus and its diploid progenitors. BMC Genom, 2013, 1: 72–82

[10] Karim M M, Siddika A, Tonu N N, Hossain D M, Meah M B, Kawanabe T, Fujimoto R, Okazaki K. Production of high yield short duration Brassica napus by interspecific hybridization between B. oleracea and B. rapa. Breed Sci, 2014, 63: 495–502

[11] Wen J, Tu J X, Li Z, Fu T D, Ma C Z, Shen J X. Improving ovary and embryo culture techniques for efficient resynthesis of Brassica napus from reciprocal crosses between yellow-seeded diploids B. rapa and B. oleracea. Euphytica, 2008, 162: 81–89

[12] Wendel JF. Genome evolution in polyploids. Plant Mol Biol, 2000, 42: 225–249

[13] Buggs R J, Chamala S, Wu W, Tate J A, Schnable P S, Soltis D E, Soltis P S, Barbazuk W B. Rapid, repeated, and clustered loss of duplicate genes in allopolyploid plant populations of independent origin.Curr Biol, 2012, 22: 248–252

[14] Feldman M, Liu B, Segal G, Abbo S, Levy A A, Vega J M. Rapid elimination of low-copy DNA sequences in polyploid wheat: a possible mechanism for differentiation of homoeologous chromosomes. Genetics, 1997, 147: 1381–1387

[15] Chen Z J. Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids. Annu Rev Plant Biol, 2007, 58: 377–406

[16] Udall J A, Quijada P A, Osborn T C. Detection of chromosomal rearrangements derived from homeologous recombination in four mapping populations of Brassica napus L. Genetics, 2005, 169: 967–979

[17] Doyle J J, Flagel L E, Paterson A H, Rapp R A, Soltis D E, Soltis P S, Wendel J F. Evolutionary genetics of genome merger and doubling in plants. Annu Rev Plant Biol, 2008, 42: 443–461

[18] Lukens L N, Pires J C, Leon E, Vogelzang R, Oslach L, Osborn T. Patterns of sequence loss and cytosine methylation within a population of newly resynthesized Brassica napus allopolyploids. Plant Physiol, 2006, 140: 336–348

[19] Comai L, Tyagi A P, Winter K, Holmes-Davis R, Reynolds S H, Stevens Y, Byers B. Phenotypic instability and rapid gene silencing in newly formed Arabidopsis allotetraploids. Plant Cell, 2000, 12: 1551–1568

[20] Lee H S, Chen Z J. Protein-coding genes are epigenetically regulated in Arabidopsis polyploids. Proc Natl Acad Sci USA, 2001, 98: 6753–6758

[21] Shaked H, Kashkush K, Ozkan H, Feldman M A, Levy A. Reproducible responses of the genome to wide hybridization and allopolyploidy in wheat. Plant Cell, 2001, 13: 1749–1759

[22] Xu Y H, Zhong L, Wu X M, Fang X P, Wang J B. Rapid alterations of gene expression and cytosine methylation in newly synthesized Brassica napus allopolyploids. Planta, 2009, 229: 471–483

[23] Doyle J J, Doyle J L. Isolation of plant DNA from fresh tissue. Focus, 1990, 12: 13–15

[24] Demeulemeester M A C, Stallen N Van, De Proft M P. Degree of DNA methylation in chicory (Cichorium intybus L.): in?uence of plant age and vernalization. Plant Sci, 1999, 142: 101–108

[25] Xu M L, Li X Q, Korban S S. DNA-methylation alterations and exchanges during in vitro cellular differentiation in rose (Rosa hybrida L.). Theor Appl Genet, 2004, 109: 899–910

[26] Kim J K, Samaranayake M, Pradhan S. Epigenetic mechanisms in mammals. Cell Mol Life Sci, 2009, 66: 596–612

[27] Meilinger D, Fellinger K, Bultlnann S, Rothbauer U, Bonapace I M, Klinkert W E F. Np95 interacts with de novo DNA methyltransferases, Dnmt3a and Dnmt3b, and mediates epigenetic silencing of the viral CMV promoter in embryonic stem cells. EMBO Rep, 2009, 10: 1259–1264

[28] Hwang I S, Choi D S, Kim N H, Kim D S, Hwang B K. The pepper cysteine/histidine-rich DC1 domain protein CaDC1 binds both RNA and DNA and is required for plant cell death and defense response. New Phytol, 2014, 201: 518–530

[29] Tan X, Yan S Z, Tan R, Zhang Z Y, Wang Z, Chen J. Characterization and expression of a GDSL-Like lipase gene from Brassica napus in Nicotiana benthamiana. Protein J, 2014, 33: 18–23

[30] Gao Y, Zhao Y, Li T T, Liu Y, Ren C X, Wang M L. Molecular cloning and expression analysis of an F-box protein gene responsive to plant hormones in Brassica napus. Mol Biol Rep, 2010, 37: 1037–1044

[31] Lou P, Wu J, Cheng F, Cressman L G, Wang X W, McClung C R. Preferential retention of circadian clock genes during diploidization following whole genome triplication in Brassica rapa. Plant Cell, 2012, 24: 2415–2426

[32] Ferry N, Jouanin L, Ceci L R, Mulligan E A, Emami K, Gatehouses J A, Gatehouse A M R. Impact of oilseed rape expressing the insecticidal serine protease inhibitor, mustard trypsin inhibitor-2 on the beneficial predator Pterostichus madidus. Mol Ecol, 2005, 14: 337–349

[33] Chao Y, Yang Q, Kang J, Zhang T, Sun Y. Expression of the alfalfa FRIGIDA-like gene, MsFRI-L delays flowering time in transgenic Arabidopsis thaliana. Mol Biol Rep, 2013, 40: 2083–2090

[34] Baumert A, Milkowski C, Schmidt J, Nimtz M, Wray V, Strack D. Formation of a complex pattern of sinapate esters in Brassica napus seeds, catalyzed by enzymes of a serine carboxypeptidase-like acyltransferase family? Phytochemistry, 2005, 66: 1334–1345

[35] Cervera M T, Ruiz-Garcia L, Martinez-Zapater J. Analysis of DNA methylation in Arabidopsis thaliana based on methylation-sensitive AFLP markers. Mol Genet Genom, 2002, 268: 543–552

[36] Madlung A, Masuelli R W, Watson B, Reynolds S H, Davison J, Comai L. Remodeling of DNA methylation and phenotypic and transcriptional changes in synthetic Arabidopsis allotetraploids. Plant Physiol, 2002, 129: 733–746

[37] Xiong L Z, Xu C G, Maroof M A S, Zhang Q F. 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

[38] Cai Y F, Xiang F N, Zhi D Y, Liu H, Xia G M. Genotyping of somatic hybrids between Festuca arundinacea Schred and Triticum aestivum L. Plant Cell Rep, 2007, 26: 1809–1819

[39] Salmon A, Ainouche M L, Wendel J F. Genetic and epigenetic consequences of recent hybridization and polyploidy in Spartina (Poaceae). Mol Ecol, 2005, 14: 1163–1175

[40] Gaeta R T, Pires J C, Iniguez-Luy F, Leon E, Osborn T C. Genomic changes in resynthesized Brassica napus and their effect on gene expression and phenotype. Plant Cell, 2007, 19: 3403–3417

[41] Birchler J A. Heterosis: The genetic basis of hybrid vigour. Nature Plants, 2015,15020, DOI: 10.1038/NPLANTS.2015.20

[1] LI Zeng-Qiang, DING Xin-Chao, LU Hai, HU Ya-Li, YUE Jiao, HUANG Zhen, MO Liang-Yu, CHEN Li, CHEN Tao, CHEN Peng. Physiological characteristics and DNA methylation analysis under lead stress in kenaf (Hibiscus cannabinus L.) [J]. Acta Agronomica Sinica, 2021, 47(6): 1031-1042.
[2] LI Peng-Cheng, BI Zhen-Zhen, SUN Chao, QIN Tian-Yuan, LIANG Wen-Jun, WANG Yi-Hao, XU De-Rong, LIU Yu-Hui, ZHANG Jun-Lian, BAI Jiang-Ping. Key genes mining of DNA methylation involved in regulating drought stress response in potato [J]. Acta Agronomica Sinica, 2021, 47(4): 599-612.
[3] LU Hai, LI Zeng-Qiang, TANG Mei-Qiong, LUO Deng-Jie, CAO Shan, YUE Jiao, HU Ya-Li, HUANG Zhen, CHEN Tao, CHEN Peng. DNA methylation in response to cadmium stress and expression of different methylated genes in kenaf [J]. Acta Agronomica Sinica, 2021, 47(12): 2324-2334.
[4] Yi YUAN,Shuang ZHU,Ting-Ting FANG,Jin-Jin JIANG,You-Ping WANG. Analysis of drought resistance and DNA methylation level of resynthesized Brassica napus [J]. Acta Agronomica Sinica, 2019, 45(5): 693-704.
[5] LI Peng-Cheng,BI Zhen-Zhen,LIANG Wen-Jun,SUN Chao,ZHANG Jun-Lian,BAI Jiang-Ping. DNA methylation involved in regulating drought stress response of potato [J]. Acta Agronomica Sinica, 2019, 45(10): 1595-1603.
[6] WANG Cui-Ping,HUA Xue-Jun,LIN Bin,LIU Ai-Hua. Evolutionary Fate and Expression Pattern of Genes Related to Proline Biosynthesis in Brassica napus [J]. Acta Agron Sin, 2017, 43(10): 1480-1488.
[7] ZHANG Yang,HU Zhong-Ying,ZHAO Yue-Ming,LI Na,XIE Li-Nan. DNA Methylation Dynamic Analysis of Self Compatible Line and Self-Incompatible Line of Brassica oleracea var. acephala at Seed Germination Stage [J]. Acta Agron Sin, 2016, 42(04): 532-539.
[8] ZHOU Yan-Hua,CAO Hong-Li,YUE Chuan,WANG Lu,HAO Xin-Yuan,WANG Xin-Chao*,YANG Ya-Jun*. Changes of DNA Methylation Levels and Patterns in Tea Plant (Camellia sinensis) during Cold Acclimation [J]. Acta Agron Sin, 2015, 41(07): 1047-1055.
[9] TAN He-Lin,XU Xin-Ying,FU Li-Man,XIANG Xiao-E,LI Jian-Qiao,GUO Hao-Lun,YE Wen-Xue. Cloningand Expression Pattern of DNA Methylase I (MET1) from Brassica napus L. and Its Progenitors [J]. Acta Agron Sin, 2015, 41(03): 405-413.
[10] HE Liang-Qiong,XIONG Fa-Qian,TANG Xiu-Mei,JIANG Jing,HAN Zhu-Qiang,ZHONG Rui-Chun,GAO Zhong-Kui,Li Zhong,HE Xin-Hua,TANG Rong-Hua. Analysis of Gene Expression Variation by cDNA-SCoT Technique at the Early Period of Arachis Artificial Allopolypoidy Evolution [J]. Acta Agron Sin, 2014, 40(10): 1767-1775.
[11] HUANG Zhi-Xiong,WANG Fei-Juan,JIANG Han,LI Zhi-Lan,DING Yan-Fei,JIANG Qiong,TAO Yue-Liang,ZHU Cheng. A Comparison of Cadmium-Accumulation-Associated Genes Expression and Molecular Regulation Mechanism between Two Rice Cultivars (Oryza sativa L. subspecies japonica) [J]. Acta Agron Sin, 2014, 40(04): 581-590.
[12] ZHAO Xu-Bo,LI Ai-Li,MAO Long*. Progress on Gene Regulatory Mechanisms by Small RNAs during Plant Polyploidization [J]. Acta Agron Sin, 2013, 39(08): 1331-1338.
[13] WU Shao-Hua,ZHANG Hong-Yu,XUE Jing-Jing,XU Pei-Zhou,WU Xian-Jun. DNA Methylation Site Analysis of Haploid, Diploid and Hybrids in Twin-Seedling Rice [J]. Acta Agron Sin, 2013, 39(01): 50-59.
[14] GAO Gui-Zhen, YING Fei, CHEN Bi-Yun, LI Hao, LV Xiao-Dan, YAN Gui-Xin, XU Kun, WU Xiao-Meng. Seed DNA Methylation in Response to Heat Stress in Brassica rapa L. [J]. Acta Agron Sin, 2011, 37(09): 1597-1604.
[15] WANG Bian-Yin, ZHAI Jun, HAO Yuan-Feng, LI An-Fei, KONG Lian-Rang. Microsatellite Variation in Synthetic Hexaploid Wheat [J]. Acta Agron Sin, 2011, 37(08): 1491-1496.
Viewed
Full text


Abstract

Cited

  Shared   
  Discussed   
No Suggested Reading articles found!