Scientific opinion addressing the safety assessment of plants developed through cisgenesis and intragenesis

EFSA Journal

Volumn 10, Issue 2, 2012, Pages

[No Author Info available]

Author keywords

cisgenesis; Cisgenic; GM plant; intragenesis; intragenic; transgenic

Indexed keywords

EID: 84890407641     PISSN: None     EISSN: 18314732     Source Type: Journal    
DOI: 10.2903/j.efsa.2012.2561     Document Type: Article

References (173)

1. Abeel T, Van de Peer Y and Saeys Y, 2009. Toward a gold standard for promoter prediction evaluation. Bioinformatics, 25, I313–I320.
2. Alonso JM, Stepanova AN, Leisse TJ, Kim CJ, Chen HM, Shinn P, Stevenson DK, Zimmerman J, Barajas P, Cheuk R, Gadrinab C, Heller C, Jeske A, Koesema E, Meyers CC, Parker H, Prednis L, Ansari Y, Choy N, Deen H, Geralt M, Hazari N, Hom E, Karnes M, Mulholland C, Ndubaku R, Schmidt I, Guzman P, Aguilar-Henonin L, Schmid M, Weigel D, Carter DE, Marchand T, Risseeuw E, Brogden D, Zeko A, Crosby WL, Berry CC and Ecker JR, 2003. Genome-wide Insertional mutagenesis of Arabidopsis thaliana. Science, 301, 653–657.
3. An GH, 1987. A Ti plasmid determined function is responsible for chemotaxis of A. tumefaciens towards the plant wound compound acetosyringone. FEMS (Federation of European Microbiological Societies) Microbiology Letters, 41, 181–192.
4. Barta E, Sebestyen E, Palfy TB, Toth G, Ortutay CP and Patthy L, 2005. DoOP: Databases of orthologous promoters, collections of clusters of orthologous upstream sequences from chordates and plants. Nucleic Acids Research, 33, D86–D90.
5. Batista R, Saibo N, Lourenco T and Oliveira MM, 2008. Microarray analyses reveal that plant mutagenesis may induce more transcriptomic changes than transgene insertion. Proceedings of the National Academy of Sciences of the United States of America, 105, 3640–3645.
6. Bennetzen JL, 2002. Mechanisms and rates of genome expansion and contraction in flowering plants. Genetica, 115, 29–36.
7. Bhattramakki D, Dolan M, Hanafey M, Wineland R, Vaske D, Register JC, Tingey SV and Rafalski A, 2002. Insertion-deletion polymorphisms in 3 ' regions of maize genes occur frequently and can be used as highly informative genetic markers. Plant Molecular Biology, 48, 539–547.
8. Birchler JA, Yao H, Chudalayandi S, Vaiman D and Veitia RA, 2010. Heterosis. Plant Cell, 22, 2105–2112.
9. Bradshaw JE, 2009. Potato breeding at the Scottish Plant Breeding Station and the Scottish Crop Research Institute: 1920–2008. Potato Research, 52, 141–172.
10. Brettell RIS, Dennis ES, Scowcroft WR and Peacock WJ, 1986. Molecular analysis of a somaclonal mutant of maize alcohol-dehydrogenase. Molecular and General Genetics, 202, 235–239.
11. Brown PTH, Gobel E and Lorz H, 1991. RFLP analysis of Zea-mays callus-cultures and their regenerated plants. Theoretical and Applied Genetics, 81, 227–232.
12. Brown PTH, Kyozuka J, Sukekiyo Y, Kimura Y, Shimamoto K and Lorz H, 1990. Molecular-changes in protoplast-derived rice plants. Molecular and General Genetics, 223, 324–328.
13. Brunaud V, Balzergue S, Dubreucq B, Aubourg S, Samson F, Chauvin S, Bechtold N, Cruaud C, de Rose R, Pelletier G, Lepiniec L, Caboche M and Lecharny A, 2002. T-DNA integration into the Arabidopsis genome depends on sequences of pre-insertion sites. EMBO Reports, 3, 1152–1157.
14. Buckler ESI and Thornsberry JM, 2002. Plant molecular diversity and applications to genomics. Current Opinion in Plant Biology, 5, 107–111.
15. Casacuberta JM and Puigdomènech P, 2000. Genome fluidity. The case of plants. Contributions to Science, 1, 313–322.
16. Castle LA, Errampalli D, Atherton TL, Fransmann LH, Yoon ES and Meinke DW, 1993. Genetic and molecular characterization of embryonic mutants identified following seed transformation in Arabidopsis. Molecular and General Genetics, 241, 504–514.
17. Cellini F, Chesson A, Colquhoun I, Constable A, Davies HV, Engel KH, Gatehouse AM, Karenlampi S, Kok EJ, Leguay JJ, Lehesranta S, Noteborn HP, Pedersen J and Smith M, 2004. Unintended effects and their detection in genetically modified crops. Food and Chemical Toxicology, 42, 1089–1125.
18. Cheng M, Jarret RL, Li Z and Demski JW, 1997. Expression and inheritance of foreign genes in transgenic peanut plants generated by Agrobacterium-mediated transformation. Plant Cell Reports, 16, 541–544.
19. Ching A, Caldwell KS, Jung M, Dolan M, Smith OS, Tingey S, Morgante M and Rafalski AJ, 2002. SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genetics, 3.
20. Chu QR and Zhang LN, 1985. Cytogenetics of aneuploids derived by anther culture in rice. Acta Genetica Sinica, 12, 51–60.
21. Chyi YS, Jorgensen RA, Goldstein D, Tanksley SD and Loaiza-Figueroa F, 1986. Localisations and stability of Agrobacterium-mediated T-DNA insertions in Lycopersicon genome. Molecular and General Genetics, 204, 65–69.
22. Cisneros A and Tel-Zur N, 2010. Embryo rescue and plant regeneration following interspecific crosses in the genus Hylocereus (Cactaceae). Euphytica, 174, 73–82.
23. Conner A, Barrell P, Baldwin S, Lokerse A, Cooper P, Erasmuson A, Nap J-P and Jacobs J, 2007. Intragenic vectors for gene transfer without foreign DNA. Euphytica, 154, 341–353.
24. Conner AJ and Jacobs JM, 1999. Genetic engineering of crops as potential source of genetic hazard in the human diet. Mutation Research, 443, 223–234.
25. Constable A, Jonas D, Cockburn A, Davi A, Edwards G, Hepburn P, Herouet-Guicheney C, Knowles M, Moseley B, Oberdoerfer R and Samuels F, 2007. History of safe use as applied to the safety assessment of novel foods and foods derived from genetically modified organisms. Food and Chemical Toxicology, 45, 2513–2525.
26. Dai SH, Zheng P, Marmey P, Zhang SP, Tian WZ, Chen SY, Beachy RN and Fauquet C, 2001. Comparative analysis of transgenic rice plants obtained by Agrobacterium-mediated transformation and particle bombardment. Molecular Breeding, 7, 25–33.
27. Dale EC and Ow DW, 1991. Gene transfer with subsequent removal of the selection gene from the host genome. Proceeding of the National Academy of Science USA, 88, 10558–10562.
28. Daley M, Knauf VC, Summerfelt KR and Turner JC, 1998. Co-transformation with one Agrobacterium tumefaciens strain containing two binary plasmids as a method for producing marker-free transgenic plants. Plant Cell Reports, 17, 489–496.
29. Darbani B, Eimanifar A, Stewart CN, Jr. and Camargo WN, 2007. Methods to produce marker-free transgenic plants. Biotechnology Journal, 2, 83–90.
30. Daxinger L, Hunter B, Sheik M, Jauvion V, Gasciolli V, Vaucheret H, Matzke M and Furner I, 2008. Unexpected silencing effects from T-DNA tags in Arabidopsis. Trends in Plant Science, 13, 4–6.
31. De Buck S, Jacobs A, Van Monatgu M and Depicker A, 1998. Agrobacterium tumefaciens transformation and cotransformation frequencies of Arabidopsis thaliana root explants and tobacco protoplasts. Molecular Plant-Microbe Interactions, 16, 658–665.
32. de Framond AJ, Barton KA and Chilton MD, 1986. Mini-Ti: a new vector strategy for plant genetic engineering. Bio/Technology, 1, 262–269.
33. Dennis ES, Brettell RIS and Peacock WJ, 1987. A tissue-culture induced adh1 null mutant of maize results from a single base change. Molecular and General Genetics, 210, 181–183.
34. Deroles SC and Gardner RC, 1988. Analysis of the T-DNA structure in a large number of transgenic Petunias generated by Agrobacterium-mediated transformation. Plant Molecular Biology, 11, 365–377.
35. Dietz-Pfeilstetter A, 2010. Stability of transgene expression as a challenge for genetic engineering. Plant Science, 179, 164–167.
36. Ebinuma H, Sugita K, Endo S, Matsunaga E and Yamada K, 2005. Elimination of marker genes from transgenic plants using MAT vector systems. Methods in Molecular and Cellular Biology, 286, 237–254.
37. Ebinuma H, Sugita K, Matsunaga E and Yamakado M, 1997. Selection of marker-free transgenic plants using the isopentenyl transferase gene. Proceeding of the National Academy of Science USA, 94, 2117–2121.
38. Edlinger B and Schlogelhofer P, 2011. Have a break: determinants of meiotic DNA double strand break (DSB) formation and processing in plants. Journal of Experimental Botany, 62, 1545–1563.
39. EFSA, 2010. Guidance on the environmental risk assessment of genetically modified plants. EFSA Journal, 8, 1879.
40. EFSA, 2011. Guidance for risk assessment of food and feed from genetically modified plants. EFSA Journal, 9, 2150.
41. Engel KH, Vogel RF, Knorr D, Habermeyer M, Kochte-Clemens B and Eisenbrand G, 2011. The role of the concept of “history of safe use” in the safety assessment of novel foods and novel food ingredients. Opinion of the Senate Commission on Food Safety (SKLM) of the German Research Foundation (DFG). Molecular Nutrition & Food Research, 55, 957–963.
42. English JJ, Harrison K and Jones JDG, 1995. Aberrant transpositions of maize double ds-like elements usually involve ds ends on sister chromatids. Plant Cell, 7, 1235–1247.
43. Evans DA, 1983. Agricultural applications of plant protoplast fusion. Bio-Technology, 1, 253–261.
44. Evans DA, 1989. Somaclonal variation - genetic-basis and breeding applications. Trends in Genetics, 5, 46–50.
45. Evans DA, Bravo JE and Gleba YY, 1983. Somatic hybridization - fusion methods, recovery of hybrids, and genetic-analysis. International Review of Cytology-a Survey of Cell Biology, 143–159.
46. Fagard M and Vaucheret H, 2000. (TRANS)GENE SILENCING IN PLANTS: How Many Mechanisms? Annual Review of Plant Physiology and Plant Molecular Biology, 51, 167–194.
47. Fedak G, 1999. Molecular aids for integration of alien chromatin through wide crosses. Genome, 42, 584–591.
48. Filipecki M and Malepszy S, 2006. Unintended consequences of plant transformation: a molecular insight. Journal of Applied Genetics, 47, 277–286.
49. Filipenko EA, Deineko EV and Shumnyi VK, 2009. Specific features of T-DNA insertion regions in transgenic plants. Russian Journal of Genetics, 45, 1289–1301.
50. Forsbach A, Schubert D, Lechtenberg B, Gils M and Schmidt R, 2003. A comprehensive characterization of single-copy T-DNA insertions in the Arabidopsis thaliana genome. Plant Molecular Biology, 52, 161–176.
51. Fu HH and Dooner HK, 2002. Intraspecific violation of genetic colinearity and its implications in maize. Proceedings of the National Academy of Sciences of the United States of America, 99, 9573–9578.
52. Gheysen G, Angenon G and Van Montagu M, 1998. Agrobacterium-mediated plant transformation: a scientifically intriguing story with significant applications. Transgenic Plant Research, 1–33.
53. Gheysen G, Van Montagu M and Zambryski P, 1987. Integration of Agrobacterium tumefaciens DNA (T-DNA) involves rearrangements of target plant DNA sequences. Proceeding of the National Academy of Science USA, 84, 6169–6173.
54. Gilbertson L, 2003. Cre-lox recombination: Cre-ative tools for plant biotechnology. Trends in Biotechnology, 21, 550–555.
55. Gill KS, Gill BS, Endo TR and Taylor T, 1996. Identification and high-density mapping of gene-rich regions in chromosome group 1 of wheat. Genetics, 144, 1883–1891.
56. Glick BR and Pasternak JJ, 2003. Molecular biotechnology: principles and applications of recombinant DNA. BRPJJ Glick (Ed.). Molecular biotechnology: principles and applications of recombinant DNA.
57. Glimelius K, Fahlesson J, Landgren M, Sjodin C and Sundberg E, 1991. Gene-transfer via somatic hybridization in plants. Trends in Biotechnology, 9, 24–30.
58. Goettel W and Messing J, 2009. Change of Gene Structure and Function by Non-Homologous End-Joining, Homologous Recombination, and Transposition of DNA. PLoS Genetics, 5.
59. Goni JR, Perez A, Torrents D and Orozco M, 2007. Determining promoter location based on DNA structure first-principles calculations. Genome Biology, 8.
60. Gorbunova V and Levy AA, 1999. How plants make ends meet: DNA double-strand break repair. Trends in Plant Science, 4, 263–269.
61. Health Canada 2006. Guidelines for the Safety Assessment of Novel Foods. Available from: www.hc-sc.gc.ca/fn-an/legislation/guide-ld/nf-an/guidelines-lignesdirectrices-eng.php
62. Helgeson JP, Pohlman JD, Austin S, Haberlach GT, Wielgus SM, Ronis D, Zambolim L, Tooley P, McGrath JM, James RV and Stevenson WR, 1998. Somatic hybrids between Solanum bulbocastanum and potato: a new source of resistance to late blight. Theoretical and Applied Genetics, 96, 738–742.
63. Hermsen JGT and Ramanna MS, 1973. Double-bridge hybrids of Solanum bulbocastanum and cultivars of Solanum tuberosum. Euphytica, 22, 457–466.
64. HESI, 2010. HESI workshop on evaluating biological variation in non-transgenic crops. Regulatory Toxicology and Pharmacology, 58, s1–s70.
65. Hirochika H, Sugimoto K, Otsuki Y, Tsugawa H and Kanda M, 1996. Retrotransposons of rice involved in mutations induced by tissue culture. Proceedings of the National Academy of Sciences of the United States of America, 93, 7783–7788.
66. Hoa TT, Bong BB, Huq E and Hodges TK, 2002. Cre/ lox site-specific recombination controls the excision of a transgene from the rice genome. Theoretical and Applied Genetics, 104, 518–525.
67. Huang S, Gilbertson LA, Adams TH, Malloy KP, Reisenbigler EK, Birr DH, Snyder MW, Zhang Q and Luethy MH, 2004. Generation of marker free transgenic maize by regular two border Agrobacterium transformation vectors. Transgenic Research, 13, 451–461.
68. Intrieri MC and Buiatti M, 2001. The horizontal transfer of Agrobacterium rhizogenes genes and the evolution of the genus Nicotiana. Molecular Phylogenetics and Evolution, 20, 100–110.
69. Islam A, Shepherd KW and Sparrow DHB, 1981. Isolation and characterization of euplasmic wheat-barley chromosome addition lines. Heredity, 46, 161–&.
70. Jacobsen E and Schaart J, 2009. Risk assessment of T-DNA borders from Agrobacterium tumefaciens in cisgenic crops. Letter to minister Cramer (VROM) March 13. 2009, Department of Plant Breeding (WUR),
71. Jacobsen E and Schouten HJ, 2009. Cisgenesis: an important sub-invention for traditional plant breeding companies. Euphytica, 170, 235–247.
72. Jiang CF, Mithani A, Gan XC, Belfield EJ, Klingler JP, Zhu JK, Ragoussis J, Mott R and Harberd NP, 2011. Regenerant Arabidopsis Lineages Display a Distinct Genome-Wide Spectrum of Mutations Conferring Variant Phenotypes. Current Biology, 21, 1385–1390.
73. Kaeppler SM and Phillips RL, 1993. Tissue culture-induced DNA methylation variation in maize. Proceedings of the National Academy of Sciences of the United States of America, 90, 8773–8776.
74. Kaeppler SM, Phillips RL and Olhoft P, 1998. Molecular basis of heritable tissue culture-induced variation in plants. In: Somaclonal Variation and Induced Mutations in Crop Improvement. Current Plant Science and Biotechnology in Agriculture Vol. 32. Kluwer Academic Publishers, Dordrecht, Netherlands, pp. 465–484.
75. Kang S, Kang K, Lee K and Back K, 2007. Characterization of rice tryptophan decarboxylases and their direct involvement in serotonin biosynthesis in transgenic rice. Planta, 227, 263–272.
76. Khrustaleva LI and Kik C, 2000. Introgression of Allium fistulosum into A-cepa mediated by A-roylei. Theoretical and Applied Genetics, 100, 17–26.
77. Kim JH and Lee S, 2007. Analysis of junctions between T-DNA and plant genome in transgenic Arabidopsis thaliana. Journal of Plant Biology, 50, 455–460.
78. Kim SH and Grierson D, 2005. Subcellular localisation and silencing of ripening-associated membrane protein (TRAMP) in tomato Lycopersicon esculentum Mill. Plant Science, 169, 1022–1029.
79. Kim SR, Lee J, Jun SH, Park S, Kang HG, Kwon S and An G, 2003. Transgene structures in T-DNA –inserted rice plants. Plant Molecular Biology, 52, 761–773.
80. Kloeckenergruissem B and Freeling M, 1995. Transposon-induced promoter scrambling - a mechanism for the evolution of new alleles. Proceedings of the National Academy of Sciences of the United States of America, 92, 1836–1840.
81. Ko JM, Seo BB, Suh DY, Do GS, Park DS and Kwack YH, 2002. Production of a new wheat line possessing the 1BL.1RS wheat-rye translocation derived from Korean rye cultivar Paldanghomil. Theoretical and Applied Genetics, 104, 171–176.
82. Kobayashi S, Goto-Yamamoto N and Hirochika H, 2004. Retrotransposon-induced mutations in grape skin color. Science, 304, 982.
83. Kogel KH, Voll LM, Schafer P, Jansen C, Wu YC, Langen G, Imani J, Hofmann J, Schmiedl A, Sonnewald S, von Wettstein D, Cook RJ and Sonnewald U, 2010. Transcriptome and metabolome profiling of field-grown transgenic barley lack induced differences but show cultivar-specific variances. Proceedings of the National Academy of Sciences of the United States of America, 107, 6198–6203.
84. Kohli A, Twyman RM, Abranches R, Wegel E, Stoger E and Christou P, 2003. Transgene integration, organization and interaction in plants. Plant Molecular Biology, 52, 247–258.
85. Komari T, Hiei Y, Saito Y, Murai N and Kumashiro T, 1996. Vectors carrying two separate T-DNAs for co-transformation of higher plants mediated by Agrobacterium tumefaciens and segregation of transformants free from selection markers. Plant Journal, 10, 165–174.
86. Kononov ME, Bassuner B and Gelvin SB, 1997. Integration of T-DNA binary vector ‘backbone’ sequences into the tobacco genome: evidence for multiple complex patterns of integration. Plant Journal, 11, 945–957.
87. Krysan P, Young J, Jester P, Monson S, Copenhaver G, Preuss D and Sussman M, 2002. Characterization of T-DNA insertion sites in Arabidopsis thaliana and the implications for saturation mutagenesis. OMICS: A Journal of Integrative Biology, 6, 163–174.
88. Labra M, Vannini C, Grassi F, Bracale M, Balsemin M, Basso B and Sala F, 2004. Genomic stability in Arabidopsis thaliana transgenic plants obtained by floral dip. Theoretical and Applied Genetics, 109, 1512–1518.
89. Larkin PJ and Scowcroft WR, 1981. SOMACLONAL VARIATION - A NOVEL SOURCE OF VARIABILITY FROM CELL-CULTURES FOR PLANT IMPROVEMENT. Theoretical and Applied Genetics, 60, 197–214.
90. Laufs P, Autran D and Traas J, 1999. A chromosomal paracentric inversion associated with T-DNA integration in Arabidopsis. Plant Journal, 18, 131–139.
91. Lawrence E, 1995. Henderson's Dictionary of Biological Terms. 11th Edition, Wiley-Liss,
92. Lehesranta SJ, Davies HV, Shepherd LVT, Nunan N, McNicol JW, Auriola S, Koistinen KM, Suomalainen S, Kokko HI and Karenlampi SO, 2005. Comparison of tuber proteomes of potato varieties, landraces, and genetically modified lines. Plant Physiology, 138, 1690–1699.
93. Lewis RS, Milla SR and Levin JS, 2005. Molecular and genetic characterization of Nicotiana glutinosa L. chromosome segments in Tobacco mosaic virus-resistant tobacco accessions. CropScience, 45, 2355–2362.
94. Liu JH, Xu XY and Deng XX, 2005. Intergeneric somatic hybridization and its application to crop genetic improvement. Plant Cell Tissue and Organ Culture, 82, 19–44.
95. Lu HJ, Zhou XR, Gong ZX and Upadhyaya NM, 2001. Generation of selectable marker free transgenic rice using double right border (DRB) binary vectors. Australian Journal of Plant Physiology, 28, 241–248.
96. Lusser M, Parisi C, Plan D and E Rodríguez-Cerezo (IPTS (EC-JRC) report), 2011. New plant breeding techniques: State-of-the-art and prospects for commercial development. [pp 220].
97. Lynch PT, Davey MR and Power JB, 1993. Plant protoplast fusion and somatic hybridization. Methods in Enzymology, 221, 379–393.
98. Malcolmson JF, 1969. Factors involved in resistance to blight (Phytophthora infestans (Mont.) de Bary) in Potatoes and assessment of resistance using detached leaves. Annals of Applied Biology, 64, 461–468.
99. Malcolmson JF and Black W, 1966. New R genes in Solanum demissum Lindl. and their complementary races of Phytophthora infestans (Mont.) De Bary. Euphytica, 15, 199–203.
100. Manning K, Tor M, Poole M, Hong Y, Thompson AJ, King GJ, Giovannoni JJ and Seymour GB, 2006. A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening. Nature Genetics, 38, 948–952.
101. Martin A, Troadec C, Boualem A, Rajab M, Fernandez R, Morin H, Pitrat M, Dogimont C and Bendahmane A, 2009. A transposon-induced epigenetic change leads to sex determination in melon. Nature, 461, 1135–U1237.
102. Mathias R, Espinosa S and Robbelen G, 1990. A new embryo rescue procedure for interspecific hybridization. Plant Breeding, 104, 258–261.
103. Matzke AJM and Matzke MA, 1998. Position effects and epigenetic silencing of plant transgenes. Current Opinion in Plant Biology, 1, 142–148.
104. Matzke MA, Neuhuber F and Matzke AJM, 1993. A variety of epistatic interactions can occur between partially homologous transgene loci brought together by sexual crossing. Molecular and General Genetics, 236, 379–386.
105. Mauseth J, 1991. Botany, An introduction to Plant Biology. SC Publishing (Ed.). 2nd.
106. Messing J and Bennetzen JL, 2008. Grass genome structure and evolution. Genome Dynamics, 41–56.
107. Meyer P, 2000. Transcriptional transgene silencing and chromatin components. Plant Molecular Biology, 43, 221–234.
108. Meza TJ, Stangeland B, Mercy IS, Skarn M, Nymoen DA, Berg A, Butenko MA, Hakelien AM, Haslekas C, Meza-Zepeda L and Aalen RB, 2002. Analyses of single-copy Arabidopsis T-DNA transformed lines show that the presence of vector backbone sequences, short inverted repeats and DNA methylation is not sufficient or necessary for the induction of transgene silencing. Nucleic Acids Research, 30, 4556–4566.
109. Miyajima D, 2006. Ovules that failed to form seeds in zinnia (Zinnia violacea Cav.). Scientia Horticulturae, 107, 176–182.
110. Morgante M, De Paoli E and Radovic S, 2007. Transposable elements and the plant pan-genomes. Current Opinion in Plant Biology, 10, 149–155.
111. Muller KO and Black W, 1952. Potato breeding for resistance to blight and virus diseases during the last hundred years. Zeitschrift fur Pflanzenzuchtung, 31, 305–318.
112. Nacry P, Camilleri C, Courtial B, Caboche M and Bouchez D, 1998. Major chromosomal rearrangements induced by T-DNA transformation in Arabidopsis. Genetics, 149, 641–650.
113. Napoli C, Lemieux C and Jorgensen R, 1990. Introduction of a chimeric chalcone synthase gene into Petunia results in reversible co-suppression of homologous genes in trans. Plant Cell, 2, 279–289.
114. Nielsen KM, 2003. Transgenic organisms - time for conceptual diversification? Nature Biotechnology, 21, 227–228.
115. Ohba T, Yoshioka Y, Machida C and Machida Y, 1995. DNA rearrangement associated with the integration of T DNA in tobacco: an example of multiple duplications of DNA around the integration target. Plant Journal, 7, 157–164.
116. Permyakova NV, Shumnyi VK and Deineko EV, 2009. Agrobacterium-mediated transformation of plants: Transfer of vector DNA fragments in the plant genome. Russian Journal of Genetics, 45, 266–275.
117. Peschke VM and Phillips RL, 1991. Activation of the maize transposable element suppressor-mutator (spm) in tissue-culture. Theoretical and Applied Genetics, 81, 90–97.
118. Peschke VM, Phillips RL and Gengenbach BG, 1987. Discovery of transposable element activity among progeny of tissue-culture derived maize plants. Science, 238, 804–807.
119. Petti C, Wendt T, Meade C and Mullins E, 2009. Evidence of genotype dependency within Agrobacterium tumefaciens in relation to the integration of vector backbone sequence in transgenic Phytophthora infestans-tolerant potato. Journal of Bioscience and Bioengineering, 107, 301–306.
120. Podevin N, De Buck S, De Wilde C and Depicker A, 2006. Insights into recognition of the T-DNA border repeats as termination sites for T-strand synthesis by Agrobacterium tumefaciens. Transgenic Research, 15, 557–571.
121. Poysa V, 1990. The development of bridge lines for interspecific gene-transfer between Lycopersicon-esculentum and Lycopersicon-peruvianum. Theoretical and Applied Genetics, 79, 187–192.
122. Prins T and E Kok (RIKILT), 2010. COGEM report: Food and feed safety aspects of cisgenic crop plant varieties. Available from edepot.wur.nl/157733.
123. Puchta H, 2005. The repair of double-strand breaks in plants: mechanisms and consequences for genome evolution. Journal of Experimental Botany, 56, 1–14.
124. Ramanathan V and Veluthambi K, 1995. Transfer of non-T-DNA portions of the Agrobacterium tumefaciens Ti-plasmid pTiA6 from the left terminus of the TL DNA. Plant Molecular Biology, 28, 1149–1154.
125. Rayburn AL and Carver BF, 1988. Cytological identification of 1b/1r wheat-rye translocations in winter-wheat breeding lines. Euphytica, 38, 237–240.
126. Reed SM, 2005. Embryo rescue. Plant Development and Biotechnology, 235–239.
127. Rieger R, Michaelis A and Green MM, 1968. A glossary of genetics and cytogenetics. Classical and molecular. A glossary of genetics and cytogenetics. Classical and molecular.,
128. Robertson DS, 1978. Characterization of a mutator system in maize. Mutation Research, 51, 21–28.
129. Rommens CM, 2004. All-native DNA transformation: a new approach to plant genetic engineering. Trends in Plant Science, 9, 457–464.
130. Rommens CM, 2007. Intragenic crop improvement: Combining the benefits of traditional breeding and genetic engineering. Journal of Agricultural and Food Chemistry, 55, 4281–4288.
131. Rommens CM, Haring MA, Swords K, Davies HV and Belknap WR, 2007. The intragenic approach as a new extension to traditional plant breeding. Trends in Plant Science, 12, 397–403.
132. Rommens CM, Humara JM, Ye J, Yan H, Richael C, Zhang L, Perry R and Swords K, 2004. Crop Improvement through Modification of the Plant's Own Genome. Plant Physiology, 135, 421–431.
133. Rommens CM, Richael CM, Yan H, Navarre DA, Ye JS, Krucker M and Swords K, 2008. Engineered native pathways for high kaempferol and caffeoylquinate production in potato. Plant Biotechnology Journal, 6, 870–886.
134. Rosellini D, 2011. Selectable marker genes from plants: reliability and potential. In Vitro Cellular & Developmental Biology-Plant, 47, 222–233.
135. Rubin E and Levy AA, 1997. Abortive gap repair: Underlying mechanism for Ds element formation. Molecular and Cellular Biology, 17, 6294–6302.
136. Ruebelt MC, Lipp M, Reynolds TL, Schmuke JJ, Astwood JD, DellaPenna D, Engel KH and Jany KD, 2006. Application of two-dimensional gel electrophoresis to interrogate alterations in the proteome of genetically modified crops. 3. Assessing unintended effects. Journal of Agricultural and Food Chemistry, 54, 2169–2177.
137. Russell SH, Hoopes JL and Odell JT, 1992. Directed excision of a transgene from the plant genome. Molecular and General Genetics, 234, 49–59.
138. Sabot F, Picault N, El-Baidouri M, Llauro C, Chaparro C, Piegu B, Roulin A, Guiderdoni E, Delabastide M, McCombie R and Panaud O, 2011. Transpositional landscape of the rice genome revealed by paired-end mapping of high-throughput re-sequencing data. Plant Journal, 66, 241–246.
139. Salomon S and Puchta H, 1998. Capture of genomic and T-DNA sequences during double-strand break repair in somatic plant cells. EMBO Journal, 17, 6086–6095.
140. Sanseverino W, Roma G, De Simone M, Faino L, Melito S, Stupka E, Frusciante L and Ercolano MR, 2010. PRGdb: a bioinformatics platform for plant resistance gene analysis. Nucleic Acids Research, 38, D814–D821.
141. Schaart J and Visser R 2009. COGEM report - NOVEL PLANT BREEDING TECHNIQUES - Consequences of new genetic modification-based plant breeding techniques in comparison to conventional plant breeding. Available from www.cogem.net/showdownload.cfm.
142. Schouten HJ, Krens FA, Jacobsen K and Jacobsen E, 2006. Cisgenic plants are similar to traditionally bred plants - International regulations for genetically modified organisms should be altered to exempt cisgenesis. EMBO Reports, 7, 750–753.
143. Smith N, Kilpatrick JB and Whitelam GC, 2001. Superfluous transgene integration in plants. Critical Reviews in Plant Sciences, 20, 215–249.
144. Srivastava V and Ow DW, 2004. Marker-free site-specific gene integration in plants. Trends in Biotechnology, 22, 627–629.
145. Stewart JM, 1981. In vitro fertilization and embryo rescue. Environmental and Experimental Botany, 21, 301–315.
146. Sugati K, Kasahara T, Matsunaga E and Ebinuma H, 2000. A transformation vector for the production of marker-free transgenic plants containing a single copy transgene at high frequency. Plant Journal, 22, 461–469.
147. Sugati K, Matsunaga E and Ebinuma H, 1999. Effective selection system for generating marker-free transgenic plants independent of sexual crossing. Plant Cell Reports, 18, 941–947.
148. Sunderland N, 1973. Nuclear cytology. In: Plant Tissue and Cell Culture 2nd ed. HE Street (Ed.). Blackwell, Oxford,
149. Sunyaev SR, Lathe WC, 3rd Ramensky VE and Bork P, 2000. SNP frequencies in human genes an excess of rare alleles and differing modes of selection. Trends in Genetics, 16, 335–337.
150. Swanson-Wagner RA, Eichten SR, Kumari S, Tiffin P, Stein JC, Ware D and Springer NM, 2010. Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor. Genome Research, 20, 1689–1699.
151. Szankowski I, Waidmann S, Degenhardt J, Patocchi A, Paris R, Silfverberg-Dilworth E, Broggini G and Gessler C, 2009. Highly scab-resistant transgenic apple lines achieved by introgression of HcrVf2 controlled by different native promoter lengths. Tree Genetics & Genomes, 5, 349–358.
152. Tani M, Ito J, Nishioka M, Kohno T, Tachibana K, Shiraishi M, Takenoshita S and Yokota J, 2004. Correlation between histone acetylation and expression of the MYO18B gene in human lung cancer cells. Genes Chromosomes & Cancer, 40, 146–151.
153. Tax FE and Vernon DM, 2001. T-DNA associated duplication/translocations in Arabidopsis. Implications for mutant analysis and functional genomics. Plant Physiology, 126, 1527–1538.
154. Travella S, Ross SM, Harden J, Everett C, Snape JW and Harwood WA, 2005. A comparison of transgenic barley lines produced by particle bombardment and Agrobacterium-mediated techniques. Plant Cell Reports, 23, 780–789.
155. Tzfira T, Li JX, Lacroix B and Citovsky V, 2004. Agrobacterium T-DNA integration: molecules and models. Trends in Genetics, 20, 375–383.
156. Vain P, 2007. Thirty years of plant transformation technology development. Plant Biotechnology Journal, 5, 221–229.
157. van der Graaff E, den Dulk Ras A and Hooykaas PJJ, 1996. Deviating T DNA transfer from Agrobacterium tumefaciens to plants. Plant Molecular Biology, 31, 677–681.
158. van der Wiel C, Schaart J, Niks R and R Visser (Wageningen UR Plant Breeding), 2010. Traditional plant breeding methods. Report 338, Available frop edepot.wur.nl/141713.
159. Van Eijk JP, Raamsdonk LWD, Eikenboom W and R.J. B, 1991. Interspecific crosses between Tulipa gesneriana cultivars and wild Tulipa species: a survey. Sexual Plant Reproduction, 4, 1–5.
160. Vanblaere T, Szankowski I, Schaart J, Schouten H, Flachowsky H, Broggini GAL and Gessler C, 2011. The development of a cisgenic apple plant. Journal of Biotechnology, 154, 304–311.
161. Walker AR, Lee E, Bogs J, McDavid DA, Thomas MR and Robinson SP, 2007. White grapes arose through the mutation of two similar and adjacent regulatory genes. Plant Journal, 49, 772–785.
162. Walker EL, Robbins TP, Bureau TE, Kermicle J and Dellaporta SL, 1995. Transposon-mediated chromosomal rearrangements and gene duplications in the formation of the maize R-R complex. EMBO Journal, 14, 2350–2363.
163. Wallroth M, Gerats AGM, Rogers SG, Fraley RT and Horsch RB, 1986. Chromosomal location of foreign genes in Petunia hybrida. Molecular and General Genetics, 202, 6–15.
164. Wang Q and Dooner HK, 2006. Remarkable variation in maize genome structure inferred from haplotype diversity at the bz locus. Proceedings of the National Academy of Sciences of the United States of America, 103, 17644–17649.
165. Waterworth WM, Drury GE, Bray CM and West CE, 2011. Repairing breaks in the plant genome: the importance of keeping it together. New Phytologist, 192, 805–822.
166. Weil C and Martienssen R, 2008. Epigenetic interactions between transposons and genes: lessons from plants. Current Opinion in Genetics & Development, 18, 188–192.
167. Wenck A, Czako M, Kanevski I and Marton L, 1997. Frequent collinear long transfer of DNA inclusive of teh whole binary vector during Agrobacterium-mediated transformation. Plant Molecular Biology, 34, 913–922.
168. Wicker T, Buchmann JP and Keller B, 2010. Patching gaps in plant genomes results in gene movement and erosion of colinearity. Genome Research, 20, 1229–1237.
169. Windels P, De Buck S, Van Bockstaele E, De Loose M and Depicker A, 2003. T-DNA integration in Arabidopsis chromosomes. Presence and origin of filler DNA sequences. Plant Physiology, 133, 2061–2068.
170. Wolters AMA, Trindade LM, Jacobsen E and Visser RGF, 1998. Fluorescence in situ hybridization on extended DNA fibres as a tool to analyse complex T-DNA loci in potato. Plant Journal, 13, 837–847.
171. Woo H-J, Cho H-S, Lim S-H, Shin K-S, Lee S-M, Lee K-J, Kim D-H and Cho Y-G, 2009. Auto-excision of selectable marker genes from transgenic tobacco via a stress inducible FLP/FRT site-specific recombination system. Transgenic Research, 18, 455–465.
172. Xing AQ, Zhang ZY, Sato S, Staswick P and Clemente T, 2000. The use of the two T-DNA binary system to derive marker-free transgenic soybeans. In Vitro Cellular & Developmental Biology - Plant, 36, 456–463.
173. Zheng P, Allen WB, Roesler K, Williams ME, Zhang S, Li J, Glassman K, Ranch J, Nubel D, Solawetz W, Bhattramakki D, Llaca V, Deschamps S, Zhong GY, Tarczynski MC and Shen B, 2008. A phenylalanine in DGAT is a key determinant of oil content and composition in maize. Nature Genetics, 40, 367–372.