메뉴 건너뛰기




Volumn 9, Issue 5, 2014, Pages

Tissue culture-induced heritable genomic variation in rice, and their phenotypic implications

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE; TRANSPOSON;

EID: 84900526269     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0096879     Document Type: Article
Times cited : (72)

References (49)
  • 1
    • 0242554088 scopus 로고
    • Somaclonal variation - A novel source of variability from cell cultures for plant improvement
    • Larkin PJ, Scowcroft W (1981) Somaclonal variation - a novel source of variability from cell cultures for plant improvement. Theoretical and Applied Genetics 60: 197-214.
    • (1981) Theoretical and Applied Genetics , vol.60 , pp. 197-214
    • Larkin, P.J.1    Scowcroft, W.2
  • 2
    • 0000631967 scopus 로고
    • Morphologic, cytogenetic, and enzymatic variation in Saccharum species hybrid clones derived from callus tissue
    • Heinz D, Mee GW (1971) Morphologic, cytogenetic, and enzymatic variation in Saccharum species hybrid clones derived from callus tissue. American journal of botany: 257-262.
    • (1971) American Journal of Botany , pp. 257-262
    • Heinz, D.1    Mee, G.W.2
  • 3
    • 84858295560 scopus 로고    scopus 로고
    • Recent progress in the understanding of tissue culture-induced genome level changes in plants and potential applications
    • Neelakandan AK, Wang K (2012) Recent progress in the understanding of tissue culture-induced genome level changes in plants and potential applications. Plant cell reports 31: 597-620.
    • (2012) Plant Cell Reports , vol.31 , pp. 597-620
    • Neelakandan, A.K.1    Wang, K.2
  • 4
    • 80052022628 scopus 로고    scopus 로고
    • Regenerant arabidopsis lineages display a distinct genome-wide spectrum of mutations conferring variant phenotypes
    • Jiang C, Mithani A, Gan X, Belfield EJ, Klingler JP, et al. (2011) Regenerant arabidopsis lineages display a distinct genome-wide spectrum of mutations conferring variant phenotypes. Current Biology 21: 1385-1390.
    • (2011) Current Biology , vol.21 , pp. 1385-1390
    • Jiang, C.1    Mithani, A.2    Gan, X.3    Belfield, E.J.4    Klingler, J.P.5
  • 5
    • 79955028255 scopus 로고    scopus 로고
    • Transpositional landscape of the rice genome revealed by paired-end mapping of high-throughput re-sequencing data
    • Sabot F, Picault N, El-Baidouri M, Llauro C, Chaparro C, et al. (2011) Transpositional landscape of the rice genome revealed by paired-end mapping of high-throughput re-sequencing data. The Plant Journal 66: 241-246.
    • (2011) The Plant Journal , vol.66 , pp. 241-246
    • Sabot, F.1    Picault, N.2    El-Baidouri, M.3    Llauro, C.4    Chaparro, C.5
  • 6
    • 84855899144 scopus 로고    scopus 로고
    • Molecular spectrum of somaclonal variation in regenerated rice revealed by whole-genome sequencing
    • Miyao A, Nakagome M, Ohnuma T, Yamagata H, Kanamori H, et al. (2012) Molecular spectrum of somaclonal variation in regenerated rice revealed by whole-genome sequencing. Plant and Cell Physiology 53: 256-264.
    • (2012) Plant and Cell Physiology , vol.53 , pp. 256-264
    • Miyao, A.1    Nakagome, M.2    Ohnuma, T.3    Yamagata, H.4    Kanamori, H.5
  • 8
    • 84884237637 scopus 로고    scopus 로고
    • Genomewide Variation in an Introgression Line of Rice-Zizania Revealed by Whole-Genome re-Sequencing
    • Wang Z-H, Zhang D, Bai Y, Zhang Y-H, Liu Y, et al. (2013) Genomewide Variation in an Introgression Line of Rice-Zizania Revealed by Whole-Genome re-Sequencing. PloS one 8: e74479.
    • (2013) PloS One , vol.8
    • Wang, Z.-H.1    Zhang, D.2    Bai, Y.3    Zhang, Y.-H.4    Liu, Y.5
  • 9
    • 84885960825 scopus 로고    scopus 로고
    • Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data
    • Kawahara Y, de la Bastide M, Hamilton JP, Kanamori H, McCombie WR, et al. (2013) Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice 6: 1-10.
    • (2013) Rice , vol.6 , pp. 1-10
    • Kawahara, Y.1    De La Bastide, M.2    Hamilton, J.P.3    Kanamori, H.4    McCombie, W.R.5
  • 10
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 12
  • 13
    • 3142718393 scopus 로고    scopus 로고
    • Activation of a rice endogenous retrotransposon Tos17 in tissue culture is accompanied by cytosine demethylation and causes heritable alteration in methylation pattern of flanking genomic regions
    • DOI 10.1007/s00122-004-1618-8
    • Liu ZL, Han FP, Tan M, Shan XH, Dong YZ, et al. (2004) Activation of a rice endogenous retrotransposon Tos17 in tissue culture is accompanied by cytosine demethylation and causes heritable alteration in methylation pattern of flanking genomic regions. Theoretical and Applied Genetics 109: 200-209. (Pubitemid 38908567)
    • (2004) Theoretical and Applied Genetics , vol.109 , Issue.1 , pp. 200-209
    • Liu, Z.L.1    Han, F.P.2    Tan, M.3    Shan, X.H.4    Dong, Y.Z.5    Wang, X.Z.6    Fedak, G.7    Hao, S.8    Liu, B.9
  • 14
    • 68349154098 scopus 로고    scopus 로고
    • Tissue culture-induced transpositional activity of mPing is correlated with cytosine methylation in rice
    • Ngezahayo F, Xu C, Wang H, Jiang L, Pang J, et al. (2009) Tissue culture-induced transpositional activity of mPing is correlated with cytosine methylation in rice. BMC plant biology 9: 91.
    • (2009) BMC Plant Biology , vol.9 , pp. 91
    • Ngezahayo, F.1    Xu, C.2    Wang, H.3    Jiang, L.4    Pang, J.5
  • 15
    • 84867875610 scopus 로고    scopus 로고
    • A map of rice genome variation reveals the origin of cultivated rice
    • Huang X, Kurata N, Wei X, Wang Z-X, Wang A, et al. (2012) A map of rice genome variation reveals the origin of cultivated rice. Nature 490: 497-501.
    • (2012) Nature , vol.490 , pp. 497-501
    • Huang, X.1    Kurata, N.2    Wei, X.3    Wang, Z.-X.4    Wang, A.5
  • 16
    • 51149203927 scopus 로고
    • Canalization of development and the inheritance of acquired characters
    • Waddington CH (1942) Canalization of development and the inheritance of acquired characters. Nature 150: 563-565.
    • (1942) Nature , vol.150 , pp. 563-565
    • Waddington, C.H.1
  • 19
    • 0034029892 scopus 로고    scopus 로고
    • Robustness against mutations in genetic networks of yeast
    • Wagner A (2000) Robustness against mutations in genetic networks of yeast. Nature genetics 24: 355-361.
    • (2000) Nature Genetics , vol.24 , pp. 355-361
    • Wagner, A.1
  • 21
    • 11244329008 scopus 로고    scopus 로고
    • The population genetic theory of hidden variation and genetic robustness
    • DOI 10.1534/genetics.104.029173
    • Hermisson J, Wagner GP (2004) The population genetic theory of hidden variation and genetic robustness. Genetics 168: 2271-2284. (Pubitemid 40066360)
    • (2004) Genetics , vol.168 , Issue.4 , pp. 2271-2284
    • Hermisson, J.1    Wagner, G.P.2
  • 22
    • 84871329875 scopus 로고    scopus 로고
    • How important are transposons for plant evolution?
    • Lisch D (2013) How important are transposons for plant evolution? Nature Reviews Genetics 14: 49-61.
    • (2013) Nature Reviews Genetics , vol.14 , pp. 49-61
    • Lisch, D.1
  • 23
    • 37249012285 scopus 로고    scopus 로고
    • Large-scale survey of cytosine methylation of retrotransposons and the impact of readout transcription from long terminal repeats on expression of adjacent rice genes
    • DOI 10.1534/genetics.107.080234
    • Kashkush K, Khasdan V (2007) Large-scale survey of cytosine methylation of retrotransposons and the impact of readout transcription from long terminal repeats on expression of adjacent rice genes. Genetics 177: 1975-1985. (Pubitemid 350276981)
    • (2007) Genetics , vol.177 , Issue.4 , pp. 1975-1985
    • Kashkush, K.1    Khasdan, V.2
  • 24
    • 0037226595 scopus 로고    scopus 로고
    • Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat
    • DOI 10.1038/ng1063
    • Kashkush K, Feldman M, Levy AA (2003) Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat. Nature genetics 33: 102-106. (Pubitemid 36068691)
    • (2003) Nature Genetics , vol.33 , Issue.1 , pp. 102-106
    • Kashkush, K.1    Feldman, M.2    Levy, A.A.3
  • 25
    • 37049183894 scopus 로고
    • Discovery of transposable element activity among progeny of tissue culture-derived maize plants
    • Peschke VM, Phillips RL, Gengenbach BG (1987) Discovery of transposable element activity among progeny of tissue culture-derived maize plants. Science 238: 804-807.
    • (1987) Science , vol.238 , pp. 804-807
    • Peschke, V.M.1    Phillips, R.L.2    Gengenbach, B.G.3
  • 26
    • 0024759440 scopus 로고
    • Molecular and genetic characterization of Mu transposable elements in Zea mays: Behavior in callus culture and regenerated plants
    • Planckaert F, Walbot V (1989) Molecular and genetic characterization of Mu transposable elements in Zea mays: behavior in callus culture and regenerated plants. Genetics 123: 567.
    • (1989) Genetics , vol.123 , pp. 567
    • Planckaert, F.1    Walbot, V.2
  • 27
    • 0026092071 scopus 로고
    • Reactivation of a silent Ac following tissue culture is associated with heritable alterations in its methylation pattern
    • Brettell RI, Dennis ES (1991) Reactivation of a silent Ac following tissue culture is associated with heritable alterations in its methylation pattern. Molecular and General Genetics MGG 229: 365-372.
    • (1991) Molecular and General Genetics MGG , vol.229 , pp. 365-372
    • Brettell, R.I.1    Dennis, E.S.2
  • 28
    • 0002260129 scopus 로고
    • Activation of the maize transposable element Suppressor-mutator (Spm) in tissue culture
    • Peschke V, Phillips R (1991) Activation of the maize transposable element Suppressor-mutator (Spm) in tissue culture. Theoretical and applied genetics 81: 90-97.
    • (1991) Theoretical and Applied Genetics , vol.81 , pp. 90-97
    • Peschke, V.1    Phillips, R.2
  • 29
    • 0025847497 scopus 로고
    • Specific expression of the tobacco Tnt1 retrotransposon in protoplasts
    • Pouteau S, Huttner E, Grandbastien M, Caboche M (1991) Specific expression of the tobacco Tnt1 retrotransposon in protoplasts. The EMBO journal 10: 1911.
    • (1991) The EMBO Journal , vol.10 , pp. 1911
    • Pouteau, S.1    Huttner, E.2    Grandbastien, M.3    Caboche, M.4
  • 30
    • 0027168422 scopus 로고
    • Activation of tobacco retrotransposons during tissue culture
    • Hirochika H (1993) Activation of tobacco retrotransposons during tissue culture. The EMBO journal 12: 2521.
    • (1993) The EMBO Journal , vol.12 , pp. 2521
    • Hirochika, H.1
  • 32
    • 0346003772 scopus 로고    scopus 로고
    • The plant MITE mPing is mobilized in anther culture
    • DOI 10.1038/nature01218
    • Kikuchi K, Terauchi K, Wada M, Hirano H-Y (2003) The plant MITE mPing is mobilized in anther culture. Nature 421: 167-170. (Pubitemid 36090983)
    • (2003) Nature , vol.421 , Issue.6919 , pp. 167-170
    • Kikuchi, K.1    Terauchit, K.2    Wada, M.3    Hirano, H.-Y.4
  • 33
    • 0043030233 scopus 로고    scopus 로고
    • Two-step regulation and continuous retrotransposition of the rice LINE-type retrotransposon Karma
    • DOI 10.1105/tpc.011809
    • Komatsu M, Shimamoto K, Kyozuka J (2003) Two-step regulation and continuous retrotransposition of the rice LINE-type retrotransposon Karma. The Plant Cell Online 15: 1934-1944. (Pubitemid 37078345)
    • (2003) Plant Cell , vol.15 , Issue.8 , pp. 1934-1944
    • Komatsu, M.1    Shimamoto, K.2    Kyozuka, J.3
  • 34
    • 23944452612 scopus 로고    scopus 로고
    • RYS1, a foldback transposon, is activated by tissue culture and shows preferential insertion points into the rye genome
    • DOI 10.1007/s00122-005-2013-9
    • Alves E, Ballesteros I, Linacero R, Vazquez A (2005) RYS1, a foldback transposon, is activated by tissue culture and shows preferential insertion points into the rye genome. Theoretical and Applied Genetics 111: 431-436. (Pubitemid 41204226)
    • (2005) Theoretical and Applied Genetics , vol.111 , Issue.3 , pp. 431-436
    • Alves, E.1    Ballesteros, I.2    Linacero, R.3    Vazquez, A.M.4
  • 35
    • 34247340840 scopus 로고    scopus 로고
    • A sequence related to rice Pong transposable element displays transcriptional activation by in vitro culture and reveals somaclonal variations in maize
    • DOI 10.1139/G06-109
    • Bureau T, Barret P, Brinkman M, Beckert M (2006) A sequence related to rice Pong transposable element displays transcriptional activation by in vitro culture and reveals somaclonal variations in maize. Genome 49: 1399-1407. (Pubitemid 46640328)
    • (2006) Genome , vol.49 , Issue.11 , pp. 1399-1407
    • Barret, P.1    Brinkman, M.2    Beckert, M.3
  • 36
    • 59749106750 scopus 로고    scopus 로고
    • Identification of a high frequency transposon induced by tissue culture, nDaiZ, a member of the hAT family in rice
    • Huang J, Zhang K, Shen Y, Huang Z, Li M, et al. (2009) Identification of a high frequency transposon induced by tissue culture, nDaiZ, a member of the hAT family in rice. Genomics 93: 274-281.
    • (2009) Genomics , vol.93 , pp. 274-281
    • Huang, J.1    Zhang, K.2    Shen, Y.3    Huang, Z.4    Li, M.5
  • 38
    • 77951902248 scopus 로고    scopus 로고
    • A c2 allele of maize identified in regenerant-derived progeny from tissue culture results from insertion of a novel transposon
    • Rhee Y, Lin H, Buell R, Childs K, Kaeppler S (2009) A c2 allele of maize identified in regenerant-derived progeny from tissue culture results from insertion of a novel transposon. Maydica 54: 429.
    • (2009) Maydica , vol.54 , pp. 429
    • Rhee, Y.1    Lin, H.2    Buell, R.3    Childs, K.4    Kaeppler, S.5
  • 39
    • 84879056945 scopus 로고    scopus 로고
    • Plants regenerated from tissue culture contain stable epigenome changes in rice
    • Stroud H, Ding B, Simon SA, Feng S, Bellizzi M, et al. (2013) Plants regenerated from tissue culture contain stable epigenome changes in rice. eLife 2013.
    • (2013) eLife , vol.2013
    • Stroud, H.1    Ding, B.2    Simon, S.A.3    Feng, S.4    Bellizzi, M.5
  • 40
    • 14844295120 scopus 로고    scopus 로고
    • RNA polymerase IV directs silencing of endogenous DNA
    • DOI 10.1126/science.1106910
    • Herr A, Jensen M, Dalmay T, Baulcombe D (2005) RNA polymerase IV directs silencing of endogenous DNA. Science 308: 118-120. (Pubitemid 40471011)
    • (2005) Science , vol.308 , Issue.5718 , pp. 118-120
    • Herr, A.J.1    Jensen, M.B.2    Dalmay, T.3    Baulcombe, D.C.4
  • 41
    • 33748323138 scopus 로고    scopus 로고
    • Epigenetic regulation of the rice retrotransposon Tos17
    • DOI 10.1007/s00438-006-0141-9
    • Cheng C, Daigen M, Hirochika H (2006) Epigenetic regulation of the rice retrotransposon Tos17. Molecular Genetics and Genomics 276: 378-390. (Pubitemid 44328126)
    • (2006) Molecular Genetics and Genomics , vol.276 , Issue.4 , pp. 378-390
    • Cheng, C.1    Daigen, M.2    Hirochika, H.3
  • 42
    • 33745561418 scopus 로고    scopus 로고
    • Endogenous targets of RNA-directed DNA methylation and Pol IV in Arabidopsis
    • DOI 10.1038/sj.emboj.7601150, PII 7601150
    • Huettel B, Kanno T, Daxinger L, Aufsatz W, Matzke AJ, et al. (2006) Endogenous targets of RNA-directed DNA methylation and Pol IV in Arabidopsis. The EMBO journal 25: 2828-2836. (Pubitemid 43980389)
    • (2006) EMBO Journal , vol.25 , Issue.12 , pp. 2828-2836
    • Huettel, B.1    Kanno, T.2    Daxinger, L.3    Aufsatz, W.4    Matzke, A.J.M.5    Matzke, M.6
  • 43
    • 77249170184 scopus 로고    scopus 로고
    • Establishing, maintaining and modifying DNA methylation patterns in plants and animals
    • Law JA, Jacobsen SE (2010) Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nature Reviews Genetics 11: 204-220.
    • (2010) Nature Reviews Genetics , vol.11 , pp. 204-220
    • Law, J.A.1    Jacobsen, S.E.2
  • 44
    • 84877040915 scopus 로고    scopus 로고
    • The initiation of epigenetic silencing of active transposable elements is triggered by RDR6 and 21-22 nucleotide small interfering RNAs
    • Nuthikattu S, McCue AD, Panda K, Fultz D, DeFraia C, et al. (2013) The initiation of epigenetic silencing of active transposable elements is triggered by RDR6 and 21-22 nucleotide small interfering RNAs. Plant Physiology 162: 116-131.
    • (2013) Plant Physiology , vol.162 , pp. 116-131
    • Nuthikattu, S.1    McCue, A.D.2    Panda, K.3    Fultz, D.4    DeFraia, C.5
  • 45
    • 0037986743 scopus 로고    scopus 로고
    • Mining for single nucleotide polymorphisms and insertions/deletions in maize expressed sequence tag data
    • DOI 10.1104/pp.102.019422
    • Batley J, Barker G, O'Sullivan H, Edwards KJ, Edwards D (2003) Mining for single nucleotide polymorphisms and insertions/deletions in maize expressed sequence tag data. Plant physiology 132: 84-91. (Pubitemid 36590403)
    • (2003) Plant Physiology , vol.132 , Issue.1 , pp. 84-91
    • Batley, J.1    Barker, G.2    O'Sullivan, H.3    Edwards, K.J.4    Edwards, D.5
  • 46
    • 38549148784 scopus 로고    scopus 로고
    • High throughput SNP discovery and genotyping in grapevine (Vitis vinifera L.) by combining a re-sequencing approach and SNPlex technology
    • Lijavetzky D, Cabezas JA, Ibáñez A, Rodríguez V, Martínez-Zapater JM (2007) High throughput SNP discovery and genotyping in grapevine (Vitis vinifera L.) by combining a re-sequencing approach and SNPlex technology. BMC genomics 8: 424.
    • (2007) BMC Genomics , vol.8 , pp. 424
    • Lijavetzky, D.1    Cabezas, J.A.2    Ibáñez, A.3    Rodríguez, V.4    Martínez-Zapater, J.M.5
  • 47
    • 74849090833 scopus 로고    scopus 로고
    • The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana
    • Ossowski S, Schneeberger K, Lucas-Lledó JI, Warthmann N, Clark RM, et al. (2010) The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science 327: 92-94.
    • (2010) Science , vol.327 , pp. 92-94
    • Ossowski, S.1    Schneeberger, K.2    Lucas-Lledó, J.I.3    Warthmann, N.4    Clark, R.M.5
  • 48
    • 84876968886 scopus 로고    scopus 로고
    • Tissue culture-induced genetic and epigenetic alterations in rice pure-lines, F1 hybrids and polyploids
    • Wang X, Wu R, Lin X, Bai Y, Song C, et al. (2013) Tissue culture-induced genetic and epigenetic alterations in rice pure-lines, F1 hybrids and polyploids. BMC plant biology 13: 77.
    • (2013) BMC Plant Biology , vol.13 , pp. 77
    • Wang, X.1    Wu, R.2    Lin, X.3    Bai, Y.4    Song, C.5
  • 49
    • 80054718602 scopus 로고    scopus 로고
    • Spontaneous epigenetic variation in the Arabidopsis thaliana methylome
    • Becker C, Hagmann J, Müller J, Koenig D, Stegle O, et al. (2011) Spontaneous epigenetic variation in the Arabidopsis thaliana methylome. Nature 480: 245-249.
    • (2011) Nature , vol.480 , pp. 245-249
    • Becker, C.1    Hagmann, J.2    Müller, J.3    Koenig, D.4    Stegle, O.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.