Genetic basis and detection of unintended effects in genetically modified crop plants

Transgenic Research

Volumn 24, Issue 4, 2015, Pages 587-603

  Ladics, Gregory S ^a   Bartholomaeus, Andrew ^b,c   Bregitzer, Phil ^d   Doerrer, Nancy G ^e   Gray, Alan ^f   Holzhauser, Thomas ^g   Jordan, Mark ^h   Keese, Paul ⁱ   Kok, Esther ^j   Macdonald, Phil ^k   Parrott, Wayne ^l   Privalle, Laura ^m   Raybould, Alan ^n,s   Rhee, Seung Yon ^o   Rice, Elena ^p   Romeis, Jörg ^q   Vaughn, Justin ^l   Wal, Jean Michel ^r   Glenn, Kevin ^p  

^a DUPONT COMPANY   (United States)

^b UNIVERSITY OF QUEENSLAND   (Australia)

^c UNIVERSITY OF CANBERRA   (Australia)

^d AGRICULTURAL RESEARCH SERVICE   (United States)

^e ILSI HEALTH AND ENVIRONMENTAL SCIENCES INSTITUTE   (United States)

^f CENTRE FOR ECOLOGY AND HYDROLOGY   (United Kingdom)

^g PAUL EHRLICH INSTITUT   (Germany)

^h AGRICULTURE AND AGRI FOOD CANADA   (Canada)

ⁱ NATIONAL HEALTH AND MEDICAL RESEARCH COUNCIL   (Australia)

^j WAGENINGEN UNIVERSITY   (Netherlands)

^k CANADIAN FOOD INSPECTION AGENCY   (Canada)

^l UNIVERSITY OF GEORGIA   (United States)

^m BAYER CROPSCIENCE   (United States)

ⁿ JEALOTT S HILL INTERNATIONAL RESEARCH CENTRE   (United Kingdom)

^o GEOPHYSICAL LABORATORY   (United States)

^p MONSANTO COMPANY   (United States)

^q AGROSCOPE   (Switzerland)

^r AGROPARISTECH   (France)

^s SYNGENTA CROP PROTECTION AG   (Switzerland)

more..

Author keywords

Allergenicity; Environmental risk assessment; GM crop plants; Toxicity; Unintended effects

Indexed keywords

CROP; GENETICALLY MODIFIED FOOD; GENETICS; HUMAN; PRODUCT SAFETY; RISK ASSESSMENT; TRANSGENIC PLANT;

CONSUMER PRODUCT SAFETY; CROPS, AGRICULTURAL; FOOD, GENETICALLY MODIFIED; HUMANS; PLANTS, GENETICALLY MODIFIED; RISK ASSESSMENT;

EID: 84938963819     PISSN: 09628819     EISSN: 15739368     Source Type: Journal    
DOI: 10.1007/s11248-015-9867-7     Document Type: Review

References (105)

1. Allen DK, Libourel IG, Shachar-Hill Y (2009) Metabolic flux analysis in plants: coping with complexity. Plant Cell Environ 32:1241–1257
2. Auld B (2012) An overview of pre-border weed risk assessment and post-border weed risk management protocols. Plant Prot Q 7:105–111
3. Bassel GW, Gaudinier A, Brady SM, Hennig L, Rhee SY, Smet ID (2012) Systems analysis of plant functional, transcriptional, physical interaction, and metabolic networks. Plant Cell 24:3859–3875
4. Bolhaar ST, van de Weg WE, van Ree R, Gonzalez-Mancebo E, Zuidmeer L, Bruijnzeel-Koomen CA, Fernandez-Rivas M, Jansen J, Hoffmann-Sommergruber K, Knulst AC, Gilissen LJ (2005) In vivo assessment with prick-to-prick testing and double-blind, placebo-controlled food challenge of allergenicity of apple cultivars. J Allergy Clin Immunol 116:1080–1086
5. Bombarely A, Menda N, Tecle IY, Buels RM, Strickler S, Fischer-York T, Pujar A, Leto J, Gosselin J, Mueller LA (2011) The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl. Nucleic Acids Res 39(Database issue):D1149–D1155
6. Bovy A, de Vos R, Kemper M, Schijlen E, Pertejo MA, Muir S, Collins G, Robinson S, Verhoeyen M, Hughes S, Santos-Buelga C, van Tunen A (2002) High-flavonol tomatoes resulting from the heterologous expression of the maize transcription factor genes LC and C1. Plant Cell 14:2509–2526
7. Bregitzer P, Dahleen LS (2008) A single backcross effectively eliminates agronomic and quality alterations caused by somaclonal variation in barley. Crop Sci 48:471–479
8. Bregitzer P, Halbert SE, Lemaux PG (1998) Somaclonal variation in the progeny of transgenic barley. Theor Appl Genet 96:421–425
9. Burgard AP, Maranas CD (2003) Optimization-based framework for inferring and testing hypothesized metabolic objective functions. Biotechnol Bioeng 82:670–677
10. Caspi R, Altman T, Dreher K, Fulcher CA, Subhraveti P, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Pujar A, Shearer AG, Travers M, Weerasinghe D, Zhang P, Karp PD (2012) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res 40(Database issue):D742–D753
11. Castiglioni P, Warner D, Bensen RJ, Anstrom DC, Harrison J, Stoecker M, Abad M, Kumar G, Salvador S, D’Ordine R, Navarro S, Back S, Fernandes M, Targolli J, Dasgupta S, Bonin C, Luethy MH, Heard JE (2008) Bacterial RNA chaperones confer abiotic stress tolerance in plants and improved grain yield in maize under water-limited conditions. Plant Physiol 147:446–455
12. Cellini F, Chesson A, Colquhoun I, Constable A, Davies HV, Engel KH, Gatehouse AM, Kärenlampi S, Kok EJ, Leguay JJ, Lehesranta S, Noteborn HP, Pedersen J, Smith M (2004) Unintended effects and their detection in genetically modified crops. Food Chem Toxicol 42:1089–1125
13. Chaikam V, Karlson D (2008) Functional characterization of two cold shock domain proteins from Oryza sativa. Plant Cell Environ 31:995–1006
14. Chang RL, Ghamsari L, Manichaikul A, Hom EF, Balaji S, Fu W, Shen Y, Hao T, Palsson BØ, Salehi-Ashtiani K, Papin JA (2011) Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism. Mol Syst Biol 7:518
15. Codex Alimentarius (2003) Guideline for the conduct of food safety assessment of foods derived from recombinant-DNA plants. CAC/GL 45-2003
16. Craig W, Tepfer M, Degrassi G, Ripandelli D (2008) An overview of general features of risk assessments of genetically modified crops. Euphytica 164:853–860
17. Cristofari G, Darlix JL (2002) The ubiquitous nature of RNA chaperone proteins. Prog Nucleic Acid Res Mol Biol 72:223–268
18. de Ligt J, Willemsen MH, van Bon BW, Kleefstra T, Yntema HG, Kroes T, Vulto-van Silfhout AT, Koolen DA, de Vries P, Gilissen C, del Rosario M, Hoischen A, Scheffer H, de Vries BB, Brunner HG, Veltman JA, Vissers LE (2012) Diagnostic exome sequencing in persons with severe intellectual disability. N Engl J Med 367:1921–1929
19. de Oliveira Dal’Molin CG, Quek LE, Palfreyman RW, Brumbley SM, Nielsen LK (2010) AraGEM, a genome-scale reconstruction of the primary metabolic network in Arabidopsis. Plant Physiol 152:579–589
20. EC (2013) Commission Implementing Regulation (EU) No 503/2013 of 3 April 2013 on applications for authorisation of genetically modified food and feed in accordance with Regulation (EC) No 1829/2003 of the European Parliament and of the Council and amending Commission Regulations (EC) No 641/2004 and (EC) No 1981/2006. Off J Eur Union L157:1–48
21. EFSA (2010) Guidance on the environmental risk assessment of genetically modified plants. EFSA J 8:1879
22. EFSA (2011) EFSA Panel on Genetically Modified Organisms (GMO). Guidance for risk assessment of food and feed from genetically modified plants. EFSA J 9:2150
23. Evans J, Wood G, Miller M (2006) The risk assessment–policy gap: an example from the UK contaminated land regime. Environ Int 32:1066–1071
24. Fagan J, Antoniou M, Robinson C (2014) GMO Myths and Truths, 2nd ed. Earth Open Source, London. http://www.earthopensource.org/index.php/reports/gmo-myths-and-truths
25. Feist AM, Palsson BØ (2008) The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. Nat Biotechnol 26:659–667
26. Fernandez A, Mills ENC, Lovik M, Spoek A, Germini A, Mikalsen A, Wal JM (2013) Endogenous allergens and compositional analysis in the allergenicity assessment of genetically modified plants. Food Chem Toxicol 62:1–6
27. Fernie AR, Schauer N (2009) Metabolomics-assisted breeding: a viable option for crop improvement? Trends Genet 25:39–48
28. Flint-Garcia SA (2013) Genetics and consequences of crop domestication. J Agric Food Chem 61:8267–8276
29. Foetisch K, Dahl L, Jansen B, Becker WM, Lidholm J, van Ree R, Broll H, Kaul S, Vieths S, Holzhauser T (2011) Development and in-house validation of allergen-specific ELISA tests for the quantification of Dau c 1.01, Dau c 1.02 and Dau c 4 in carrot extracts (Daucus carota). Anal Bioanal Chem 399:935–943
30. Forsbach A, Schubert D, Lechtenberg B, Gils M, Schmidt R (2003) A comprehensive characterization of single-copy T-DNA insertions in the Arabidopsis thaliana genome. Plant Mol Biol 52:161–176
31. Garcia-Alonso M, Raybould A (2014) Protection goals in environmental risk assessment: a practical approach. Transgenic Res 23:945–956
32. Goodman RE, Panda R, Ariyarathna H (2013) Evaluation of endogenous allergens for the safety evaluation of genetically engineered food crops: review of potential risks, test methods, examples and relevance. J Agric Food Chem 61:8317–8332
33. Gray A (2012) Problem formulation in environmental risk assessment for genetically modified crops: a practitioner’s approach. Colln Biosaf Rev 6:10–65
34. Hammond B, Kough J, Herouet-Guicheney C, Jez JM (2013) Toxicological evaluation of proteins introduced into food crops. Crit Rev Toxicol 43(Suppl 2):25–42
35. Herrgård MJ, Fong SS, Palsson BØ (2006) Identification of genome-scale metabolic network models using experimentally measured flux profiles. PLoS Comput Biol 2(7):e72
36. Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M (2012) KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res 40(Database issue):D109–D114
37. Keese PK, Robold AV, Myers RC, Weisman S, Smith J (2014) Applying a weed risk assessment approach to GM crops. Transgenic Res 23:957–969
38. Kessler DA, Taylor MR, Maryanski JH, Flamm EL, Kahl LS (1992) The safety of foods developed by biotechnology. Science 256:1747–1749
39. Kok EJ, Keijer J, Kleter GA, Kuiper HA (2008) Comparative safety assessment of plant-derived foods. Regul Toxicol Pharmacol 50:98–113
40. Krattinger SG, Lagudah ES, Spielmeyer W, Singh RP, Huerta-Espino J, McFadden H, Bossolini E, Selter LL, Keller B (2009) A putative ABC transporter confers durable resistance to multiple fungal pathogens in wheat. Science 323:1360–1363
41. Lai J, Li R, Xu X, Jin W, Xu M, Zhao H, Xiang Z, Song W, Ying K, Zhang M, Jiao Y, Ni P, Zhang J, Li D, Guo X, Ye K, Jian M, Wang B, Zheng H, Liang H, Zhang X, Wang S, Chen S, Li J, Fu Y, Springer NM, Yang H, Wang J, Dai J, Schnable PS, Wang J (2010) Genome-wide patterns of genetic variation among elite maize inbred lines. Nat Genet 42:1027–1030
42. Lam HM, Xu X, Liu X, Chen W, Yang G, Wong FL, Li MW, He W, Qin N, Wang B, Li J, Jian M, Wang J, Shao G, Wang J, Sun SS, Zhang G (2010) Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat Genet 42:1053–1059
43. Larkin PJ, Scowcroft WR (1981) Somaclonal variation: a novel source of variability from cell cultures for plant improvement. Theor Appl Genet 60:197–214
44. Liu R, Koyanagi KO, Chen S, Kishima Y (2012) Evolutionary force of AT-rich repeats to trap genomic and episomal DNAs into the rice genome: lessons from endogenous pararetrovirus. Plant J 72:817–828
45. Lloyd AH, Wang D, Timmis JN (2012) Single molecule PCR reveals similar patterns of non-homologous DSB repair in tobacco and Arabidopsis. PLoS One 7:e32255
46. Lusser M, Parisi C, Plan D, Rodríguez-Cerezo E (2011) New plant breeding techniques: state-of-the-art and prospects for commercial development. IPTS report, JRC 63971, EUR 24760 EN. doi:10.2791/54761. Accessed 20 Oct 2014
47. May P, Christian JO, Kempa S, Walther D (2009) ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii. BMC Genomics 10:209
48. McClintock B (1984) The significance of responses of the genome to challenge. Science 226:792–801
49. McHale LK, Haun WJ, Xu WW, Bhaskar PB, Anderson JE, Hyten DL, Gerhardt DJ, Jeddeloh JA, Stupar RM (2012) Structural variants in the soybean genome localize to clusters of biotic stress-response genes. Plant Physiol 159:1295–1308
50. Meissle M, Zünd J, Waldburger M, Romeis J (2014) Development of Chrysoperla carnea (Stephens) (Neuroptera: Chrysopidae) on pollen from Bt-transgenic and conventional maize. Sci Rep 4:5900
51. Metcalfe DD, Astwood JD, Townsend R, Sampson HA, Taylor SL, Fuchs RL (1996) Assessment of the allergenic potential of foods derived from genetically engineered crop plants. Crit Rev Food Sci Nutr 36:S165–S186
52. Mueller LA, Zhang P, Rhee SY (2003) AraCyc: a biochemical pathway database for Arabidopsis. Plant Physiol 132:453–460
53. Naito K, Cho E, Yang G, Campbell MA, Yano K, Okumoto Y, Tanisaka T, Wessler SR (2006) Dramatic amplification of a rice transposable element during recent domestication. Proc Natl Acad Sci USA 47:17620–17625
54. Nemali KS, Bonin C, Dohleman FG, Stephens M, Reeves WR, Nelson DE, Whitsel JE, Sammons B, Silady RA, Anstrom D, Sharp RE, Patharkar OR, Clay D, Coffin M, Nemeth MA, Leibman ME, Luethy M, Lawson M (2014) Physiological responses related to increased grain yield under drought in the first biotechnology-derived drought tolerant maize. Plant Cell Environ. doi:10.1111/pce.12446
55. NRC (2004) Safety of genetically engineered foods: approaches to assessing unintended health effects. Chapter 3. Unintended effects from breeding, pp 39–71. Committee on Identifying and Assessing Unintended Effects of Genetically Engineered Foods on Human Health, National Research Council. National Academies Press, Washington
56. Oms-Oliu G, Odriozola-Serrano I, Martín-Belloso O (2013) Metabolomics for assessing safety and quality of plant-derived food. Food Res Int 54:1172–1183
57. Ossowski S, Schneeberger K, Lucas-Lledó JI, Warthmann N, Clark RM, Shaw RG, Weigel D, Lynch M (2010) The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science 327:92–94
58. Paes de Andrade P, Parrott W, Mercedes Roca M (2014) Genetically modified organisms—environmental risk assessment guide, 2nd edn. ILSI Brasil. http://www.ilsi.org/Brasil/Pages/ViewItemDetails.aspx?WebId=C34AB3F5-C89B-49B3-9740-31F407A2A6FD&ListId=91D4243D-A11D-4CB9-B694-551373D9E8C5&ItemID=73. Accessed 14 Aug 2014
59. Phillips McDougall (2011) The cost and time involved in the discovery, development and authorisation of a new plant biotechnology derived trait. http://croplife.org/plant-biotechnology/regulatory-2/cost-of-bringing-a-biotech-crop-to-market/. Accessed 14 Aug 2014
60. Poolman MG, Miguet L, Sweetlove LJ, Fell DA (2009) A genome-scale metabolic model of Arabidopsis and some of its properties. Plant Physiol 151:1570–1581
61. Potato Genome Sequencing Consortium (2011) Genome sequence and analysis of the tuber crop potato. Nature 475:189–195
62. Privalle LS, Chen J, Clapper G, Hunst P, Spiegelhalter F, Zhong CX (2012) Development of an agricultural biotechnology crop product: testing from discovery to commercialization. J Agric Food Chem 60:10179–10187
63. Quanbeck SM, Brachova L, Campbell AA, Guan X, Perera A, He K, Rhee SY, Preeti Bais P, Dickerson JA, Dixon P, Wohlgemuth G, Fiehn O, Barkan L, Lange I, Lange BM, Lee I, Cortes D, Salazar C, Shuman J, Shulaev V, Huhman DV, Sumner LW, Roth MR, Welti R, Ilarslan H, Wurtele ES, Nikolau BJ (2012) Metabolomics as a hypothesis-generating functional genomics tool for the annotation of Arabidopsis thaliana genes of “unknown function”. Front Plant Sci 3:1–12
64. Randall RP (2012) A global compendium of weeds, 2nd edn. Department of Agriculture and Food, Western Australia, Perth
65. Rauch A, Wieczorek D, Graf E, Wieland T, Endele S, Schwarzmayr T, Albrecht B, Bartholdi D, Beygo J, Di Donato N, Dufke A, Cremer K, Hempel M, Horn D, Hoyer J, Joset P, Röpke A, Moog U, Riess A, Thiel CT, Tzschach A, Wiesener A, Wohlleber E, Zweier C, Ekici AB, Zink AM, Rump A, Meisinger C, Grallert H, Sticht H, Schenck A, Engels H, Rappold G, Schröck E, Wieacker P, Riess O, Meitinger T, Reis A, Strom TM (2012) Range of genetic mutations associated with severe non-syndromic sporadic intellectual disability: an exome sequencing study. Lancet 380:1674–1682
66. Raybould A (2011) The bucket and the searchlight: formulating and testing risk hypotheses about the weediness and invasiveness potential of transgenic crops. Environ Biosaf Res 9:123–133
67. Raybould A, Stacey D, Vlachos D, Graser G, Li X, Joseph R (2007) Non-target organism risk assessment of MIR604 maize expressing mCry3A for control of corn rootworm. J Appl Entomol 131:391–399
68. Risk JM, Selter LL, Chauhan H, Krattinger SG, Kumlehn J, Hensel G, Viccars LA, Richardson TM, Buesing G, Troller A, Lagudah ES, Keller B (2013) The wheat Lr34 gene provides resistance against multiple fungal pathogens in barley. Plant Biotechnol J 11:847–854
69. Romeis J, Bartsch D, Bigler F, Candolfi MP, Gielkens MMC, Hartley SE, Hellmich RL, Huesing JE, Jepson PC, Layton R, Quemada H, Raybould A, Rose RI, Schiemann J, Sears MK, Shelton AM, Sweet J, Vaituzis Z, Wolt JD (2008) Assessment of risk of insect-resistant transgenic crops to nontarget arthropods. Nat Biotechnol 26:203–208
70. Romeis J, Hellmich RL, Candolfi MP, Carstens K, De Schrijver A, Gatehouse AMR, Herman RA, Huesing JE, McLean MA, Raybould A, Shelton AM, Waggoner A (2011) Recommendations for the design of laboratory studies on non-target arthropods for risk assessment of genetically engineered plants. Transgenic Res 20:1–22
71. Romeis J, McLean MA, Shelton AM (2013) When bad science makes good headlines: Bt maize and regulatory bans. Nat Biotechnol 31:386–387
72. Saha R, Suthers PF, Maranas CD (2011) Zea maysiRS1563: a comprehensive genome-scale metabolic reconstruction of maize metabolism. PLoS One 6(7):e21784
73. Sammons B, Whitsel J, Stork LAG, Reeves W, Horak M (2014) Characterization of drought-tolerant maize MON 87460 for use in environmental risk assessment. Crop Sci 54:719–729
74. Sancho AI, Foxall R, Browne T, Dey R, Zuidmeer L, Marzban G, Waldron KW, van Ree R, Hoffmann-Sommergruber K, Laimer M, Mills EN (2006a) Effect of postharvest storage on the expression of the apple allergen Mal d 1. J Agric Food Chem 54:5917–5923
75. Sancho AI, Foxall R, Rigby NM, Browne T, Zuidmeer L, van Ree R, Waldron KW, Mills EN (2006b) Maturity and storage influence on the apple (Malus domestica) allergen Mal d 3, a nonspecific lipid transfer protein. J Agric Food Chem 54:5098–5104
76. Sanvido O, Romeis J, Gathmann A, Gielkens M, Raybould A, Bigler F (2012) Evaluating environmental risks of genetically modified crops—ecological harm criteria for regulatory decision-making. Environ Sci Policy 15:82–91
77. Sarevitz D (2004) How science makes environmental controversies worse. Environ Sci Policy 7:385–403
78. SCBD (2000) Cartagena Protocol on Biosafety to the Convention on Biological Diversity: annex III, risk assessment. Montreal, Canada. http://bch.cbd.int/protocol/text/. Accessed 14 Jan 2015
79. Schiessl S, Samans B, Hüttel B, Reinhardt R, Snowdon RJ (2014) Capturing sequence variation among flowering-time regulatory gene homologs in the allopolyploid crop species Brassica napus. Front Plant Sci. doi:10.3389/fpls.2014.00404
80. Schnell J, Steele M, Bean J, Neuspiel M, Girard C, Dormann N, Pearson C, Savoie A, Bourbonnière L, Macdonald P (2015) A comparative analysis of insertional effects in genetically engineered plants: considerations for pre-market assessments. Transgenic Res 24:1–17. doi:10.1007/s11248-014-9843-7
81. Schwender J (2008) Metabolic flux analysis as a tool in metabolic engineering of plants. Curr Opin Biotechnol 19:131–137
82. Segrè D, Vitkup D, Church GM (2002) Analysis of optimality in natural and perturbed metabolic networks. Proc Natl Acad Sci USA 99:15112–15117
83. Shlomi T, Berkman O, Ruppin E (2005) Regulatory on/off minimization of metabolic flux changes after genetic perturbations. Proc Natl Acad Sci USA 102:7695–7700
84. Staginnus C, Gregor W, Mette MF, Teo CH, Borroto-Fernández EG, Laimer da Câmara Machado M, Matzke M, Schwarzacher T (2007) Endogenous pararetroviral sequences in tomato (Solanum lycopersicum) and related species. BMC Plant Biol 7:24
85. Steiner HY, Halpin C, Jez JM, Kough J, Parrott W, Underhill L, Weber N, Hannah LC (2013) Evaluating the potential for adverse interactions within genetically engineered breeding stacks. Plant Physiol 161:1587–1594
86. Stone LM, Byrne M (2011) Comparing the outputs of five weed risk assessment models implemented in Australia: are there consistencies across models? Plant Prot Q 26:29–35
87. Sweetlove LJ, Fell D, Fernie AR (2008) Getting to grips with the plant metabolic network. Biochem J 409:27–41
88. Tanaka H (2010) Omics-based medicine and systems pathology: a new perspective for personalized and predictive medicine. Methods Inf Med 49:173–185
89. Tenaillon MI, Sawkins MC, Long AD, Gaut RL, Doebley JF, Gaut BS (2001) Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.). Proc Natl Acad Sci USA 98:9161–9166
90. Tepfer M, Racovita M, Craig W (2013) Putting problem formulation at the forefront of GMO risk analysis. GM Crops Food 4:10–15
91. Thiele I, Palsson BØ (2010) A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat Protoc 5:93–121
92. Tian Z, Zhao M, She M, Du J, Cannon SB, Liu X, Xu X, Qi X, Li MW, Lam HM, Ma J (2012) Genome-wide characterization of nonreference transposons reveals evolutionary propensities of transposons in soybean. Plant Cell 24:4422–4436
93. Tollenaar M, Lee EA (2010) Strategies for enhancing grain yield in maize. In: Janick J (ed) Plant breeding reviews, vol 34. Wiley, Hoboken
94. Urbanczyk-Wochniak E, Sumner LW (2007) MedicCyc: a biochemical pathway database for Medicago truncatula. Bioinformatics 23:1418–1423
95. van Dijk JP, Leifert C, Barros E, Kok EJ (2010) Gene expression profiling for food safety assessment: examples in potato and maize. Regul Toxicol Pharmacol 58:S21–S25
96. van Dijk JP, Cankar K, Hendriksen PJM, Beenen HG, Zhu M, Scheffer S, Shepherd LVT, Stewart D, Davies HV, Leifert C, Wilkockson SJ, Gruden K, Kok EJ (2012) The identification and interpretation of differences in the transcriptomes of organically and conventionally grown potato tubers. J Agric Food Chem 60:2090–2101
97. van Dijk JP, de Mello CS, Voorhuijzen MM, Hutten RCB, Arisi ACM, Jansen JJ, Buydens LMC, van der Voet H, Kok EJ (2014) Safety assessment of plant varieties using transcriptomics profiling and a one-class classifier. Regul Toxicol Pharmacol 70:297–303
98. Vaughn JN, Bennetzen JL (2014) Natural insertions in rice commonly form tandem duplications indicative of patch-mediated double-strand break induction and repair. Proc Natl Acad Sci USA 111:6684–6689. doi:10.1073/pnas.1321854111
99. Virtue JG, Spencer JE, Weiss JE, Reichard SE (2008) Australia’s Botanic Gardens weed risk assessment procedure. Plant Prot Q 23:166–178
100. Vu GT, Cao HX, Watanabe K, Hensel G, Blattner FR, Kumlehn J, Schubert I (2014) Repair of site-specific DNA double-strand breaks in barley occurs via diverse pathways primarily involving the sister chromatid. Plant Cell 26:2156–2167
101. Weber N, Halpin C, Hannah LC, Jez J, Kough J, Parrott W (2012) Crop genome plasticity and its relevance to food and feed safety of genetically engineered breeding stacks. Plant Physiol 160:1842–1853
102. Wolt JD, Keese P, Raybould A, Fitzpatrick JW, Burachik M, Gray A, Olin SS, Schiemann J, Sears M, Wu F (2010) Problem formulation in the environmental risk assessment for genetically modified plants. Transgenic Res 19:425–436
103. Youens-Clark K, Buckler E, Casstevens T, Chen C, Declerck G, Derwent P, Dharmawardhana P, Jaiswal P, Kersey P, Karthikeyan AS, Lu J, McCouch SR, Ren L, Spooner W, Stein JC, Thomason J, Wei S, Ware D (2011) Gramene database in 2010: updates and extensions. Nucleic Acids Res 39(Database issue):D1085–D1094
104. Zhang P, Dreher K, Karthikeyan A, Chi A, Pujar A, Caspi R, Karp P, Kirkup V, Latendresse M, Lee C, Mueller LA, Muller R, Rhee SY (2010) Creation of a genome-wide metabolic pathway database for Populus trichocarpa using a new approach for reconstruction and curation of metabolic pathways for plants. Plant Physiol 153:1479–1491
105. Zuidmeer L, Goldhahn K, Rona RJ, Gislason D, Madsen C, Summers C, Sodergren E, Dahlstrom J, Lindner T, Sigurdardottir ST, McBride D, Keil T (2008) The prevalence of plant food allergies: a systematic review. J Allergy Clin Immunol 121:1210–1218