Plant Genetic Engineering and GM Crops: Merits and Demerits

  • Javid Ahmad Parray
  • Mohammad Yaseen Mir
  • Nowsheen Shameem


Genetic transformation in plants agreements a great potential to modify crops for improved agronomic traits including resistance to diseases, pests and good nutritional quality along with enhanced productivity. The transgene could be derived from unrelated plant species and even from non-plant sources leading to a revolution in molecular agriculture. In this chapter, the main approach lies on concept of genetic engineering techniques to improve the plant architect. The concept of GM crops and environmental implications besides their safety assessment is documented in detail and also in the end future perspective for adopting the next generation quantitative genetics is also elaborated.


GM crops Genetic Engineering Bt crop Safety assessment Transformation 


  1. Abuodeh, R. O., Orbach, M. J., Mandel, M. A., Das, A., & Galgiani, J. N. (2000). Genetic transformation of Coccidioides immitis facilitated by Agrobacterium tumefaciens. The Journal of Infectious Diseases, 181, 2106–2110.CrossRefPubMedPubMedCentralGoogle Scholar
  2. Addo-Quaye, C., Eshoo, T. W., Bartel, D. P., & Axtell, M. J. (2008). Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome. Current Biology, 18, 758–762.CrossRefPubMedPubMedCentralGoogle Scholar
  3. Adhikari, U., Nejadhashemi, A. P., & Woznicki, S. A. (2015). Climate change and eastern Africa: A review of impact on major crops. Food and Energy Security, 4, 110–132.CrossRefGoogle Scholar
  4. Agapito-Tenfen, S. Z., Vilperte, V., Benevenuto, R. F., Rover, C. M., Traavik, T. I., & Nodari, R. O. (2014). Effect of stacking insecticidal cry and herbicide tolerance epsps transgenes on transgenic maize proteome. BMC Plant Biology, 4, 346.Google Scholar
  5. Agrawal, A. A. (2000). Mechanisms, ecological consequences and agricultural implications of tri-trophic interactions. Current Opinion in Plant Biology, 3, 329–335.CrossRefPubMedPubMedCentralGoogle Scholar
  6. Ahmed, F. E. (2002). Detection of genetically modified organisms in food. Trends in Biotechnology, 20(5), 215–223.CrossRefPubMedPubMedCentralGoogle Scholar
  7. Aird, D., Ross, M. G., Chen, W. S., Danielsson, M., Fennell, T., Russ, C., Jaffe, D. B., Nusbaum, C., & Gnirke, A. (2011). Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biology, 12, R18.CrossRefPubMedPubMedCentralGoogle Scholar
  8. Alexander, T. W., Sharma, R., Deng, M. Y., Whetsell, A. J., Jennings, J. C., Wang, Y., Okine, E., Damgaard, D., & McAllister, T. A. (2004). Use of quantitative real-time and conventional PCR to assess the stability of the cp4 epsps transgene from roundup ready canola in the intestinal, ruminal, and fecal contents of sheep. Journal of Biotechnology, 112, 255–266.CrossRefPubMedPubMedCentralGoogle Scholar
  9. Alicai, T., Omongo, C. A., Maruthi, M. N., Hillocks, R. J., Baguma, Y., Kawuki, R., Bua, A., Otim-Nape, G. W., & Colvin, J. (2007). Re-emergence of cassava brown streak disease in Uganda. Plant Disease, 91, 24–29.CrossRefPubMedPubMedCentralGoogle Scholar
  10. Ammann, K., Jacot, Y., Rufener, P., & Al-Mazyad. (2000). Weediness in the light of new transgenic crops and their potential hybrids. Journal of Plant Diseases and Protection, 17, 19–29.Google Scholar
  11. Anand, A., Krichevsky, A., Schornack, S., Lahaye, T., Tzfira, T., Tang, Y., Citovsky, V., & Kirankumar, S. M. (2007). Arabidopsis VIRE2 INTERACTING PROTEIN2 is required for Agrobacterium T-DNA integration, in plants. Plant Cell, 19, 1695–1708.CrossRefPubMedPubMedCentralGoogle Scholar
  12. Anandalakshmi, R., Pruss, G. J., Ge, X., Marathe, R., Mallory, A. C., Smith, T. H., & Vance, V. B. (1998). A viral suppressor of gene silencing in plants. Proceedings of the National Academy of Sciences of the United States of America, 95, 13079–13084.CrossRefPubMedPubMedCentralGoogle Scholar
  13. Anders, S., & Huber, W. (2010). Differential expression analysis for sequence count data. Genome Biology, 11, R106.CrossRefPubMedPubMedCentralGoogle Scholar
  14. Anderson, A., & Moore, L. (1979). Host specificity in the genus Agrobacterium. Phytopathology, 69, 320–323.CrossRefGoogle Scholar
  15. Anderson, J. M., Palukaitis, P., & Zaitlin, M. (1992). A defective replicase gene induces resistance to cucumber mosaic virus in transgenic tobacco plants. Proceedings of the National Academy of Sciences of the United States of America, 89, 8759–8763.CrossRefPubMedPubMedCentralGoogle Scholar
  16. Andow, D. A. (2003). UK farm-scale evaluations of transgenic herbicide-tolerant crops. Nature Biotechnology, 21, 1453–1454. Scholar
  17. Appel, J. D., Fasy, T. M., Kohtz, D. S., Kohtz, J. D., & Johnson, E. M. (1988). Asbestos fibers mediate transformation of monkey cells by exogenous plasmid DNA. Proceedings of the National Academy of Sciences of the United States of America, 85, 7670–7674.CrossRefPubMedPubMedCentralGoogle Scholar
  18. Aragão, F. J. L., & Faria, J. C. (2009). First transgenic geminivirus-resistant plant in the field. Nature Biotechnology, 27, 1086–1088.CrossRefPubMedPubMedCentralGoogle Scholar
  19. Aris, A., & Leblanc, S. (2011). Maternal and fetal exposure to pesticides associated to genetically modified foods in eastern townships of Quebec, Canada. Reproductive Toxicology, 31, 528–533. Scholar
  20. Astwood, J. D., Leach, J. N., & Fuchs, R. L. (1996). Stability of food allergens to digestion in vitro. Nature Biotechnology, 14, 1269–1273.CrossRefPubMedPubMedCentralGoogle Scholar
  21. Atkinson, H. A. C., Johnson, I. T., Gee, J. M., Grigoriadou, F., & Miller, K. (1996). Brown Norway rat model of food allergy: Effect of plant components on the development of oral sensitisation. Food and Chemical Toxicology, 34, 27/32.CrossRefGoogle Scholar
  22. Auer, P. L., & Doerge, R. W. (2010). Statistical design and analysis of RNA sequencing data. Genetics, 185, 405–416.CrossRefPubMedPubMedCentralGoogle Scholar
  23. Avery Oswald, T., Colin, M., & MacLeod, M. M. C. (1944). Studies on the chemical nature of the substance inducing transformation of pneumococcal types: Induction of transformation by a deoxyribonucleic acid fraction isolated from pneumococcus type III. The Journal of Experimental Medicine, 79, 137–158.CrossRefGoogle Scholar
  24. Baktavachalam, G. B., Delaney, B., Fisher, T. L., Ladics, G. S., Layton, R. J., Locke, M. E. H., Schmidt, J., Anderson, J. A., Weber, N. N., Herman, R. A., & Evans, S. L. (2015). Transgenic maize event TC1507: Global status of food, feed, and environmental safety. GM Crops Food, 6, 80–102. Scholar
  25. Barnes, M. A., & Turner, C. R. (2016). The ecology of environmental DNA and implications for conservation genetics. Conservation Genetics, 17, 1–17. Scholar
  26. Barski, A., Cuddapah, S., Cui, K., Roh, T. Y., Schones, D. E., Wang, Z., Wei, G., Chepelev, I., & Zhao, K. (2007). High-resolution profiling of histone methylations in the human genome. Cell, 129, 823–837.CrossRefGoogle Scholar
  27. Bart, R. S., & Taylor, N. J. (2017). New opportunities and challenges to engineer disease resistance in cassava, a staple food of African small-holder farmers. PLoS Pathogens, 13, e1006287.CrossRefPubMedPubMedCentralGoogle Scholar
  28. Barton, K. A., et al. (1983). Regeneration of intact tobacco plants containing full length copies of genetically engineered T-DNA and transmission of T-DNA to R1-progeny. Cell, 32, 1033–1043.CrossRefPubMedPubMedCentralGoogle Scholar
  29. Baylis, A. D. (2000). Why glyphosate is a global herbicide: Strengths, weaknesses, and prospects. Pest Management Science, 56, 299–308.CrossRefGoogle Scholar
  30. Benbrook, C. M. (2012). Impacts of genetically engineered crops on pesticide use in the U.S. – The first sixteen years. Environmental Sciences Europe, 24.
  31. Benbrook, C. M. (2016). Trends in glyphosate herbicide use in the United States and globally. Environmental Sciences Europe, 28.
  32. Bennett, R., Buthelezi, T., Ismael, Y., & Morse, S. (2003). Bt cotton, pesticides, labour and health: A case study of smallholder farmers in the Makhathini flats Republic of South Africa. Outlook on Agriculture, 32, 123–128.CrossRefGoogle Scholar
  33. Bertsch, C., Beuve, M., Dolja, V. V., Wirth, M., Pelsy, F., Herrbach, E., & Lemaire, O. (2009). Retention of the virus-derived sequences in the nuclear genome of grapevine as a potential pathway to virus resistance. Biology Direct, 4.Google Scholar
  34. Beusmann, V., & Stirn, S. (2001). In N. Transgene, G. Hrsg Schutte, S. Stirn, & V. S. Beusmann (Eds.), Hintergrund, Begriffsklarungen und Aufbau (pp. 1–7). Basel: Birkhäuser.Google Scholar
  35. Beyene, G., Chauhan, R. D., Wagaba, H., Moll, T., Alicai, T., Miano, D., Carrington, J. C., & Taylor, N. J. (2016). Loss of CMD2-mediated resistance to cassava mosaic disease in plants regenerated through somatic embryogenesis: Uniform loss of CMD resistance in cassava. Molecular Plant Pathology, 17, 1095–1110.CrossRefPubMedPubMedCentralGoogle Scholar
  36. Blomme, G., Ploetz, R., Jones, D., De Langhe, E., Price, N., Gold, C., Geering, A., Viljoen, A., Karamura, D., Pillay, M., et al. (2013). A historical overview of the appearance and spread of Musa pests and pathogens on the African continent: Highlighting the importance of clean Musa planting materials and quarantine measures: A historical overview of the appearance and spread of Musa pests and pathogens in Africa. The Annals of Applied Biology, 162, 4–26.CrossRefGoogle Scholar
  37. Bock, R. (2007). Plastid biotechnology: Prospects for herbicide and insect resistance, metabolic engineering and molecular farming. Current Opinion in Biotechnology, 18, 100–106.CrossRefPubMedPubMedCentralGoogle Scholar
  38. Bohan, D. A., Boffey, C. W. H., Brooks, D. R., Clark, S. J., Dewar, A. M., Firbank, L. G., Haughton, A. J., Hawes, C., Heard, M. S., May, M. J., et al. (2005). Effects on weed and invertebrate abundance and diversity of herbicide management in genetically modified herbicide- tolerant winter-sown oilseed rape. Proceedings of the Royal Society B, 272, 463–474.CrossRefPubMedPubMedCentralGoogle Scholar
  39. Bohn, T., Cuhra, M., Traavik, M., Sanden, M., Fagan, J., & Primicerio, R. (2014). Compositional differences in soybeans on the market: Glyphosate accumulates in roundup ready GM soybeans. Food Chemistry, 153, 207–215.CrossRefPubMedPubMedCentralGoogle Scholar
  40. Bonny, S. (2016). Genetically modified herbicide-tolerant crops, weeds, and herbicides: Overview and impact. Environmental Management, 57, 31–48. Scholar
  41. Boyle, A. P., Davis, S., Shulha, H. P., Meltzer, P., Margulies, E. H., Weng, Z., Furey, T. S., & Crawford, G. E. (2008). High-resolution mapping and characterization of open chromatin across the genome. Cell, 132, 311–322.CrossRefPubMedPubMedCentralGoogle Scholar
  42. Breitler, J. C., Labeyrie, A., Meynard, D., Legavre, T., & Guiderdoni, E. (2002). Efficient micro projectile bombardment mediated transformation of rice using gene cassettes. Theoretical and Applied Genetics, 104, 709–719.CrossRefPubMedPubMedCentralGoogle Scholar
  43. Brower, L. P., Taylor, O. R., Williams, E. H., Slayback, D. A., Zubieta, R. R., & Ramirez, M. I. (2012). Decline of monarch butterflies overwintering in Mexico: Is the migratory phenomenon at risk? Insect Conservation and Diversity, 5, 95–100.CrossRefGoogle Scholar
  44. Bullard, J. H., Purdom, E., Hansen, K. D., & Dudoit, S. (2010). Evaluation of statistical methods for normalization and differential expression in mRNA-seq experiments. BMC Bioinformatics, 11, 94. Scholar
  45. Bundock, P., & Hooykaas, P. J. J. (1996). Integration of Agrobacterium tumefaciens T-DNA in the Saccharomyces cerevisiae genome by illegitimate recombination. Proceedings of the National Academy of Sciences of the United States of America, 93, 15272–15275.CrossRefPubMedPubMedCentralGoogle Scholar
  46. Burgio, G., Lanzoni, A., Accinelli, G., Dinelli, G., Bonetti, A., Marotti, I., & Ramilli, F. (2007). Evaluation of Bt-toxin uptake by the non-target herbivore, Myzus persicae (Hemiptera: Aphididae), feeding on transgenic oilseed rape. Bulletin of Entomological Research, 97, 211–215.CrossRefPubMedPubMedCentralGoogle Scholar
  47. Busi, R., Neve, P., & Powles, P. (2013). Evolved polygenic herbicide resistance in Lolium rigidum by low-dose herbicide selection within standing genetic variation. Evolutionary Applications, 6, 231–242.CrossRefPubMedPubMedCentralGoogle Scholar
  48. Caprio, M. E. (2001). Source-sink dynamics between transgenic and non-transgenic habitats and their role in the evolution of resistance. Journal of Economic Entomology, 94, 698–705.CrossRefPubMedPubMedCentralGoogle Scholar
  49. Chabannes, M., & Iskra-Caruana, M.-L. (2013). Endogenous pararetroviruses – A reservoir of virus infection in plants. Current Opinion in Virology, 3, 615–620.CrossRefPubMedPubMedCentralGoogle Scholar
  50. Chakrabarty, R., Banerjee, R., Chung, S. M., Farman, M., Citovsky, V., Hogenhout, S. A., Tzfira, T., & Goodin, M. (2007). pSITE vectors for stable integration or transient expression of auto fluorescent protein fusions in plants: Probing Nicotiana benthamiana -virus interactions. Molecular Plant-Microbe Interactions, 20, 740–750.CrossRefPubMedPubMedCentralGoogle Scholar
  51. Chapotin, S. M., & Wolt, J. D. (2007). Genetically modified crops for the bioeconomy: Meeting public and regulatory expectations. Transgenic Research, 16, 675–688.CrossRefPubMedPubMedCentralGoogle Scholar
  52. Chee, P. P., Fober, K. A., & Slightom, J. L. (1989). Transformation of soybean (Glycine max) by infecting germinating seeds with Agrobacterium tumefaciens. Plant Physiology, 91, 1212–1218.CrossRefPubMedPubMedCentralGoogle Scholar
  53. Chen, W. S., Chiu, C. C., Liu, H. Y., Lee, T. L., & Cheng, J. T. (1998). Gene transfer via pollen-tube pathway for anti-fusarium wilt in watermelon. IUBMB Life, 46, 1201–1209.CrossRefGoogle Scholar
  54. Chen, X., Xu, H., Yuan, P., Fang, F., Huss, M., Vega, V. B., Wong, E., Orlov, Y. L., Zhang, W., Jiang, J., Loh, Y. H., Yeo, H. C., Yeo, Z. X., Narang, V., Govindarajan, K. R., Leong, B., Shahab, A., Ruan, Y., Bourque, G., Sung, W. K., Clarke, N. D., Wei, C. L., & Ng, H. H. (2008). Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell, 133, 1106–1117. Scholar
  55. Chiba, S., Kondo, H., Tani, A., Saisho, D., Sakamoto, W., Kanematsu, S., & Suzuki, N. (2011). Widespread endogenization of genome sequences of non-retroviral RNA viruses into plant genomes. PLoS Pathogens, 7, e1002146.CrossRefPubMedPubMedCentralGoogle Scholar
  56. Chilton, M. D., Drummond, M. H., Merlo, D. J., Sciaky, D., Montoya, A. L., Gordon, M. P., & Nester, E. W. (1977). Stable incorporation of plasmid DNA into higher plant cells: The molecular basis of crown gall tumorigenesis. Cell, 11, 263–271.CrossRefPubMedPubMedCentralGoogle Scholar
  57. Christodoulou, D. C., Gorham, J. M., Herman, D. S., & Seidman, J. (2011). Construction of normalized RNA-seq libraries for next-generation sequencing using the crab duplex-specific nuclease. Current Protocols in Molecular Biology, 94, 4.12.1–4.12.11.Google Scholar
  58. Christou, P., et al. (1991). Genotype-independent stable transformation of rice (Oryza sativa) plants. Biotechnology, 9, 957–962.CrossRefGoogle Scholar
  59. Chung, B. N., Yoon, J.-Y., & Palukaitis, P. (2013). Engineered resistance in potato against potato leafroll virus, potato virus A and potato virus Y. Virus Genes, 47, 86–92.CrossRefPubMedPubMedCentralGoogle Scholar
  60. Churchman, L. S., & Weissman, J. S. (2011). Nascent transcript sequencing visualizes transcription at nucleotide resolution. Nature, 469, 368–373.CrossRefPubMedPubMedCentralGoogle Scholar
  61. Clark, B. W., Phillips, T. A., & Coats, J. R. (2005). Environmental fate and effects of Bacillus thuringiensis (Bt) proteins from transgenic crops: A review. Journal of Agricultural and Food Chemistry, 53, 4643–4653.CrossRefPubMedPubMedCentralGoogle Scholar
  62. Cokus, S. J., Feng, S., Zhang, X., Chen, Z., Merriman, B., Haudenschild, C. D., Pradhan, S., Nelson, S. F., Pellegrini, M., & Jacobsen, S. E. (2008). Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature, 452, 215–219.CrossRefPubMedPubMedCentralGoogle Scholar
  63. Conner, A. J., Glare, T. R., & Nap, J. (2003). The release of genetically modified crops into the environment. Part II. Overview of ecological risk assessment. The Plant Journal, 33, 19–46.CrossRefPubMedPubMedCentralGoogle Scholar
  64. Costa, V., Angelini, C., De Feis, I., & Ciccodicola, A. (2010). Uncovering the complexity of transcriptomes with RNA-seq. Journal of Biomedicine & Biotechnology, 2010, 853916.CrossRefGoogle Scholar
  65. Crooks, H. L., Burton, M. G., York, A. C., & Brownie, C. (2005). Vegetative growth and competitiveness of common Cocklebur resistant and susceptible to acetolactate synthase-inhibiting herbicides. Journal of Cotton Science, 9, 229–237.Google Scholar
  66. Crossway, A., Oakes, J. W., Irvine, J. M., Ward, B., Knauf, V. C., & Shewmaker, C. K. (1986). Integration of foreign DNA following microinjection of tobacco mesophyll protoplasts. Molecular & General Genetics, 202, 179–185.CrossRefGoogle Scholar
  67. Cruz-Reyes, R., Vila-Sakar, G. A., Sanchez-Montoya, G., & Quesada, M. (2015). Experimental assessment of gene flow between transgenic squash and a wild relative in the center of origin of cucurbits. Ecosphere, 6, 248–260.CrossRefGoogle Scholar
  68. Cuellar, W. J., Kreuze, J. F., Rajamaki, M.-L., Cruzado, K. R., Untiveros, M., & Valkonen, J. P. T. (2009). Elimination of antiviral defense by viral RNase III. Proceedings of the National Academy of Sciences of the United States of America, 106, 10354–10358.CrossRefPubMedPubMedCentralGoogle Scholar
  69. Cuellar, W. J., Galvez, M., Fuentes, S., Tugume, J., & Kreuze, J. (2015). Synergistic interactions of begomo viruses with Sweet potato chlorotic stunt virus (genus Crinivirus) in sweet potato (Ipomoea batatas L.). Molecular Plant Pathology, 16, 459–471.CrossRefPubMedPubMedCentralGoogle Scholar
  70. da Fonseca, G. C., de Oliveira, L. F. V., de Morais, G. L., Abdelnor, R. V., Nepomuceno, A. L., Waterhouse, P. M., Farinelli, L., & Margis, R. (2016). Unusual RNA plant virus integration in the soybean genome leads to the production of small RNAs. Plant Science, 246, 62–69.CrossRefPubMedPubMedCentralGoogle Scholar
  71. Dale, P. J., Clarke, B., & Fontes, E. M. G. (2002). Potential for the environmental impact of transgenic crops. Nature Biotechnology, 20, 567–574.CrossRefPubMedPubMedCentralGoogle Scholar
  72. Dale, J., Paul, J.-Y., Dugdale, B., & Harding, R. (2017). Modifying bananas: From transgenics to organics? Sustainability, 9, 333.CrossRefGoogle Scholar
  73. Daniell, H., Muthukumar, B., & Lee, S. B. (2001). Marker free transgenic plants: Engineering the chloroplast genome without the use of antibiotic selection. Current Genetics, 39, 109–116.CrossRefPubMedPubMedCentralGoogle Scholar
  74. Datta, K., Baisakh, N., Thet, K. M., Tu, J., & Datta, S. K. (2002). Pyramiding transgenes for multiple resistance in rice against bacterial blight, yellow stem borer and sheath blight. Theoretical and Applied Genetics, 106, 1–8.CrossRefPubMedPubMedCentralGoogle Scholar
  75. Daveya, M. R., Anthonya, P., Powera, J. B., & Loweb, K. C. (2005). Plant protoplasts: Status and biotechnological perspectives. Biotechnology Advances, 23, 131–171.CrossRefGoogle Scholar
  76. de Framond, A. J., Barton, K. A., & Chilton, M. D. (1983). Mini-Ti: A new vector strategy for plant genetic engineering. Biotechnology (N Y), 5, 262–269.Google Scholar
  77. de la Peña, A., Lörz, H., & Schell, J. (1987). Transgenic rye plants obtained by injecting young floral tillers. Nature, 235, 274–276.CrossRefGoogle Scholar
  78. De Schrijver, A., De Clercq, P., de Maagd, R. A., & van Frankenhuyzen, K. (2015). Relevance of Bt toxin interaction studies for environmental risk assessment of genetically modified crops. J. Plant Biotechnol., 13, 1221–1223. Scholar
  79. Degner, J. F., Marioni, J. C., Pai, A. A., Pickrell, J. K., Nkadori, E., Gilad, Y., & Pritchard, J. K. (2009). Effect of read-mapping biases on detecting allele-specific expression from RNA- sequencing data. Bioinformatics, 25, 3207–3212.CrossRefPubMedPubMedCentralGoogle Scholar
  80. Depristo, M. A., Banks, E., Poplin, R., Garimella, K. V., Maguire, J. R., Hartl, C., Philippakis, A. A., Del Angel, G., Rivas, M. A., Hanna, M., Mckenna, A., Fennell, T. J., Kernytsky, A. M., Sivachenko, A. Y., Cibulskis, K., Gabriel, S. B., Altshuler, D., & Daly, M. J. (2011). A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genetics, 43, 491–498. Scholar
  81. Dietz-Pfeilstetter, J., & Zwerger, P. (2009). In-field frequencies and characteristics of oilseed rape with double herbicide resistance. Environmental Biosafety Research, 8, 101–111. Scholar
  82. Dohm, J. C., Lottaz, C., Borodina, T., & Himmelbauer, H. (2008). Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Research, 36, e105.CrossRefPubMedPubMedCentralGoogle Scholar
  83. Domingo, J. L. (2000). Health risks of GM foods: Many opinions but few data. Science, 288, 1748–1749.CrossRefPubMedPubMedCentralGoogle Scholar
  84. Domingo, J. L. (2007). Toxicity studies of genetically modified plants: A review of the published literature. Critical Reviews in Food Science and Nutrition, 47, 721–733.CrossRefPubMedPubMedCentralGoogle Scholar
  85. Domingo, J. L. (2011). Human health effects of genetically modified (GM) plants: Risk and perception. Human and Ecological Risk Assessment, 17, 535–537.CrossRefGoogle Scholar
  86. Domingo, J. L. (2016). Safety assessment of GM plants: An updated review of the scientific literature. Food and Chemical Toxicology, 95, 12–18.CrossRefPubMedPubMedCentralGoogle Scholar
  87. Domingo, J. L., & Giné Bordonaba, J. (2011). A literature review on the safety assessment of genetically modified plants. Environment International, 37, 734–742.CrossRefPubMedPubMedCentralGoogle Scholar
  88. Dong, S., Liu, Y., Yu, C., Zhang, Z., Chen, M., & Wang, C. (2016). Investigating pollen and gene flow of WYMV-resistant transgenic wheat N12-1 using a dwarf male-sterile line as the pollen receptor. PLoS One, 11, e0151373. Scholar
  89. Doty, S. L., Yu, M. C., Lundin, J. I., Heath, J. D., & Nester, E. W. (1996). Mutational analysis of the input domain of the VirA protein of Agrobacterium tumefaciens. Journal of Bacteriology, 178, 961–970.CrossRefPubMedPubMedCentralGoogle Scholar
  90. Drost, D. R., Benedict, C. I., Berg, A., Novaes, E., Novaes, C. R., Yu, Q., Dervinis, C., Maia, J. M., Yap, J., Miles, B., & Kirst, M. (2010). Diversification in the genetic architecture of gene expression and transcriptional networks in organ differentiation of Populus. Proceedings of the National Academy of Sciences of the United States of America, 107, 8492–8497.CrossRefPubMedPubMedCentralGoogle Scholar
  91. Duke, S. O., Lydon, J., Koskinen, W. C., Moorman, T. B., Chaney, R. L., & Hammerschmidt, R. (2012). Glyphosate effects on plant mineral nutrition, crop rhizosphere microbiota, and plant disease in glyphosate-resistant. Crops. Journal of Agricultural and Food Chemistry, 60, 10375–10397. Scholar
  92. EFSA. (2013). International frameworks dealing with human risk assessment of combined exposure to multiple chemicals. EFSA Journal, 11, 3313. Scholar
  93. Egan, J. F., Maxwell, B. D., Mortensen, D. A., Ryan, M. R., & Smith, R. G. (2011). 2,4- Dichlorophenoxyacetic acid (2,4-D)-resistant crops and the potential for evolution of 2,4-D-resistant weeds. PNAS, 108, E37. Scholar
  94. Einspanier, R., Lutz, B., Rief, S., Berezina, O., Zverlov, V., Schwarz, W., & Meyer, J. (2004). Tracing residual recombinant feed molecules during digestion and rumen bacterial diversity in cattle fed transgene maize. European Food Research and Technology, 218, 269–273.CrossRefGoogle Scholar
  95. Ellstrand, N. C. (2002). Gene flow from transgenic crops to wild relatives: what have we learned, what do we know, what do we need to know? In: Scientific methods workshop: Ecological and agronomic consequences of gene flow from transgenic crops to wild relatives. Meeting proceedings, pp. 39–46.Google Scholar
  96. Ellstrand, N. C. (2003). Current knowledge of gene flow in plants: Implications for transgene flow. Philosophical Transactions of the Royal Society B: Biological Sciences, 358, 1163–1170.CrossRefGoogle Scholar
  97. Ellstrand, N. C. (2012). Over a decade of crop transgenes out-of-place. In C. A. Wozniak & A. McHughen (Eds.), Regulation of agricultural biotechnology: The United States and Canada. London: Springer.Google Scholar
  98. Etter, P. D., Preston, J. L., Bassham, S., Cresko, W. A., & Johnson, E. A. (2011). Local de novo assembly of RAD paired-end contigs using short sequencing reads. PLoS One, 6, e18561. Scholar
  99. European Food Safety Authority. (2016). Assessment of new scientific elements supporting the prolongation of prohibition of the placing on the market of genetically modified oilseed rape GT73 for food and feed purposes in Austria. Technical report.Google Scholar
  100. FAO (Food and Agriculture Organization). (2015). FAO statistical pocketbook 2015: World Food and Agriculture. Rome: FAO.CrossRefGoogle Scholar
  101. FAO/WHO. (2000). Safety aspects of genetically modified foods of plant origin. In Report of a joint FAO/WHO expert consultation on foods derived from biotechnology. Geneva: World Health Organisation.Google Scholar
  102. FAO/WHO. (2001). Evaluation of Allergenicity of genetically modified foods. Report of a joint FAO/WHO expert consultation on allergenicity of foods derived from biotechnology. Geneva: World Health Organisation.Google Scholar
  103. Fargette, D., Konate´, G., Fauquet, C., Muller, E., Peterschmitt, M., & Thresh, J. M. (2006). Molecular ecology and emergence of tropical plant viruses. Annual Review of Phytopathology, 44, 235–260.CrossRefPubMedPubMedCentralGoogle Scholar
  104. Faria, J., Aragao, F. J. L., Souza, T. L. P. O., Quintela, E., Kitajima, E. W., & Ribeiro, S. (2016). Golden mosaic of common beans in Brazil: Management with a transgenic approach. APSnet Feature Artic.
  105. Farre, G., et al. (2011). Nutritionally enhanced crops and food security: Scientific achievements versus political expediency. Current Opinion in Biotechnology, 22, 245–251.CrossRefPubMedPubMedCentralGoogle Scholar
  106. Ferreira, S. A., Pitz, K. Y., Manshardt, R., Zee, F., Fitch, M., & Gonsalves, D. (2002). Virus coat protein transgenic papaya provides practical control of papaya ringspot virus in Hawaii. Plant Disease, 86, 101–105.CrossRefPubMedPubMedCentralGoogle Scholar
  107. Fischer, R., Stoger, E., Schillberg, S., Christou, P., & Twyman, R. M. (2004). Plant based production of biopharmaceuticals. Current Opinion in Plant Biology, 7, 152–158.CrossRefPubMedPubMedCentralGoogle Scholar
  108. Fischhoff, D. A., BowdishKS, P. F. J., Marrone, P. G., McCormick, S. M., Niedermayer, E. J., Rochester, E. J., Rogers, S. G., & Fray, R. T. (1987). Insect tolerant transgenic tomato plants. Bio/Technology, 5, 807–813.Google Scholar
  109. Fisher, R. A. (1918). The correlation between relatives on the supposition of Mendelian inheritance. Proceedings of the Royal Society of Edinburgh, 52, 399–433.CrossRefGoogle Scholar
  110. Flachowsky, G., Chesson, A., & Aulrich, K. (2005). Animal nutrition with feeds from genetically modified plants. Archives of Animal Nutrition, 59, 1–40.CrossRefPubMedPubMedCentralGoogle Scholar
  111. Fondong, V. N. (2017). The search for resistance to cassava mosaic geminiviruses: How much we have accomplished, and what lies ahead. Frontiers in Plant Science, 8.Google Scholar
  112. Fontanillas, P., Landry, C. R., Wittkopp, P. J., Russ, C., Gruber, J. D., Nusbaum, C., & Hartl, D. L. (2010). Key considerations for measuring allelic expression on a genomic scale using high-throughput sequencing. Molecular Ecology, 19(Suppl 1), 212–227.CrossRefPubMedPubMedCentralGoogle Scholar
  113. Fontes, E. M. G., Pires, C. S. S., Sujii, A. R., & Panizzi, A. R. (2002). The environmental effects of genetically modified crops resistant to insects. Neotropical Entomology, 31, 497–513.CrossRefGoogle Scholar
  114. Francis, K. E., & Spiker, S. (2004). Identification of Arabidopsis thaliana transformants without selection reveals a high occurrence of silenced T-DNA integrations. The Plant Journal, 41(3), 464–477.CrossRefGoogle Scholar
  115. Friesen, L. F., Nelson, A. G., & Van Acker, R. C. (2003). Evidence of contamination of pedigreed canola (Brassica napus) seedlots in western Canada with genetically engineered herbicide resistance traits. Agronomy Journal, 95, 1342–1347.CrossRefGoogle Scholar
  116. Frizzel, L. A. (1988). Biological effects of acoustic cavitation. In K. Suslick (Ed.), Ultrasound, its chemical, physical and biological effects (pp. 287–303). Weinheim: VCH Publication.Google Scholar
  117. Fuentes, A., Ramos, P. L., Fiallo, E., Callard, D., Sánchez, Y., Peral, R., Rodríguez, R., & Pujol, M. (2006). Intron–hairpin RNA derived from replication associated protein C1 gene confers immunity to tomato yellow leaf curl virus infection in transgenic tomato plants. Transgenic Research, 15, 291–304.CrossRefPubMedPubMedCentralGoogle Scholar
  118. Gad, A. E., Rosenberg, N., & Altman, A. (1990). Liposome-mediated gene delivery into plant cells. Physiologia Plantarum, 79, 177–183.CrossRefGoogle Scholar
  119. Gan, X., Stegle, O., Behr, J., Steffen, J. G., Drewe, P., Hildebrand, K. L., Lyngsoe, R., Schultheiss, S. J., Osborne, E. J., Sreedharan, V. T., Kahles, A., Bohnert, R., Jean, G., Derwent, P., Kersey, P., Belfield, E. J., Harberd, N. P., Kemen, E., Toomajian, C., Kover, P. X., Clark, R. M., Rätsch, G., & Mott, R. (2011). Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature, 477, 419–423.CrossRefPubMedPubMedCentralGoogle Scholar
  120. Garber, M., Grabherr, M. G., Guttman, M., & Trapnell, C. (2011). Computational methods for transcriptome annotation and quantification using RNA-seq. Nature Methods, 8, 469–477.CrossRefPubMedPubMedCentralGoogle Scholar
  121. Gassmann, A. J., Jennifer, L., Petzold-Maxwell, Eric, H. C., Mike, W. D., Amanda, M. H., David, A. I., & Ryan, S. K. (2014). Field-evolved resistance by western corn rootworm to multiple Bacillus thuringiensis toxins in transgenic maize. PNAS, 111, 5141–5146.CrossRefPubMedPubMedCentralGoogle Scholar
  122. Gendel, S. M. (1998). Sequence databases for assessing the potential allergenicity of proteins used in transgenic foods. Advances in Food and Nutrition Research, 42, 63/92.Google Scholar
  123. Gepts, P., & Papa, R. (2003). Possible effects of (trans) gene flow from crops on the genetic diversity from landraces and wild relatives. Environmental Biosafety Research, 2, 89–103.CrossRefPubMedPubMedCentralGoogle Scholar
  124. Geraldes, A., Pang, J., Thiessen, N., Cezard, T., Moore, R., Zhao, Y., Tam, A., Wang, S., Friedmann, M., Birol, I., Jones, S. J., Cronk, Q. C., & Douglas, C. J. (2011). SNP discovery in black cottonwood (Populus trichocarpa) by population transcriptome resequencing. Molecular Ecology Resources, 11(Suppl 1), 81–92. Scholar
  125. Gilbert, N. (2013). Case studies: A hard look at GM crops. Superweeds? Suicides? Stealthy Genes? The true, the false and the still unknown about transgenic crops. Nature, News Feature.Google Scholar
  126. Goecks, J., Nekrutenko, A., & Taylor, J. (2010). Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biology, 11, R86.CrossRefPubMedPubMedCentralGoogle Scholar
  127. Golemboski, D. B., Lomonossoff, G. P., & Zaitlin, M. (1990). Plants transformed with a tobacco mosaic virus nonstructural gene sequence are resistant to the virus. Proceedings of the National Academy of Sciences of the United States of America, 87, 6311–6315.CrossRefPubMedPubMedCentralGoogle Scholar
  128. Goodin, M. M., Dietzgen, R. G., Schichnes, D., Ruzin, S., & Jackson, A. O. (2002). pGD vectors: Versatile tools for the expression of green and red fluorescent protein fusions in agro infiltrated plant leaves. The Plant Journal, 31, 375–383.CrossRefPubMedPubMedCentralGoogle Scholar
  129. Gressel, J. (2000). Molecular biology of weed control. Transgenic Research, 9, 355–382.CrossRefPubMedPubMedCentralGoogle Scholar
  130. Griesbach, R. J. (1987). Chromosome-mediated transformation via microinjection. Plant Science, 50, 69–77.CrossRefGoogle Scholar
  131. Griffitts, J. S., Whitacre, J. L., Stevens, D. E., & Aroian, R. V. (2001). Bt toxin resistance from loss of a putative carbohydrate-modifying enzyme. Science, 293, 860–864.CrossRefPubMedPubMedCentralGoogle Scholar
  132. Guan, Z. J., Zhang, P., Wei, W., Mi, X., Kang, D., & Liu, B. (2015). Performance of hybrid progeny formed between genetically modified herbicide-tolerant soybean and its wild ancestor. Annals of Botany, 7, 121–128.Google Scholar
  133. Gulden, R. H., Lerat, S., Hart, M. M., Powell, J. R., Trevors, J. T., Pauls, K. P., Klironomos, J. N., & Swanton, C. J. (2005). Quantitation of transgenic plant DNA in leachate water: Real-time polymerase chain reaction analysis. Journal of Agricultural and Food Chemistry, 53, 5858–5865.CrossRefPubMedPubMedCentralGoogle Scholar
  134. Halpin, C. (2005). Gene stacking in transgenic plants-the challenge for 21st century plant biotechnology. Plant Biotechnology Journal, 3, 141–155.CrossRefPubMedPubMedCentralGoogle Scholar
  135. Hamilton, C. M. (1997). A binary-BAC system for plant transformation with high-molecular weight DNA. Gene, 200, 107–116.CrossRefPubMedPubMedCentralGoogle Scholar
  136. Hammond, B. G., Vicini, J. L., Hartnell, G. F., Naylor, M. W., Knight, C. D., Robinson, E. H., Fuchs, R. L., & Padgette, S. R. (1996). The feeding value of soybeans fed to rats, chickens, catfish and dairy cattle is not altered by genetic incorporation of glyphosate tolerance. The Journal of Nutrition, 126, 717–727.CrossRefPubMedPubMedCentralGoogle Scholar
  137. Han, S. M., Lee, B., Won, O. J., Hwang, K. S., Suh, S. J., Kim, C., & Park, K. W. (2015). Gene flow from herbicide resistant genetically modified rice to conventional rice (Oryza sativa L.) cultivars. Journal of Ecology and Environment, 38, 397–403.CrossRefGoogle Scholar
  138. Hancock, J. F. (2003). A framework for assessing the risk of transgenic crops. BioScience, 53, 512–519.CrossRefGoogle Scholar
  139. Hansen, G., Tempe, J., & Brevet, J. (1992). A T-DNA transfer stimulator sequence in the vicinity of the right border of pRi8196. Plant Molecular Biology, 20, 113–122.CrossRefPubMedPubMedCentralGoogle Scholar
  140. Hansen, K. D., Brenner, S. E., & Dudoit, S. (2010). Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Research, 38, e131.CrossRefPubMedPubMedCentralGoogle Scholar
  141. Harper, G., Osuji, J. O., Heslop-Harrison, J. S., & Hull, R. (1999). Integration of banana streak badnavirus into the Musa genome: Molecular and cytogenetic evidence. Virology, 255, 207–213.CrossRefPubMedPubMedCentralGoogle Scholar
  142. Hawkins, R. D., Hon, G. C., & Ren, B. (2010). Next-generationgenomics: An integrativeapproach. Nature Reviews Genetics, 11, 476–486.CrossRefPubMedPubMedCentralGoogle Scholar
  143. Haygood, R., Ives, R. A., & Andow, D. A. (2003). Consequences of recurrent gene flow from crops to wild relatives. Proceedings of the Biological Sciences, 270, 1879–1886.CrossRefGoogle Scholar
  144. Heinemann, J. A., Agapito-Tenfen, S. Z., & Carman, J. A. (2013). A comparative evaluation of the regulation of GM crops or products containing dsRNA and suggested improvements to risk assessments. Environment International, 55, 43–55.CrossRefPubMedPubMedCentralGoogle Scholar
  145. Hellens, R. P., Edwards, E. A., Leyland, N. R., Bean, S., & Mullineaux, P. M. (2000). pGreen: A versatile and flexible binary Ti vector for Agrobacterium mediated plant transformation. Plant Molecular Biology, 42, 819–832.CrossRefPubMedPubMedCentralGoogle Scholar
  146. Hepburn, A. G., White, J., Pearson, L., Maunders, M. J., Clarke, L. E., Prescott, A. G., & Blundy, K. S. (1985). The use of pNJ5000 as an intermediate vector for the genetic manipulation of Agrobacterium Ti-plasmids. Journal of General Microbiology, 131, 2961–2969.PubMedPubMedCentralGoogle Scholar
  147. Hernandez, A. F., Parron, T., Tsatsakis, A. M., et al. (2013). Toxic effects of pesticide mixtures at a molecular level: Their relevance to human health. Toxicology, 307, 136–145.CrossRefPubMedPubMedCentralGoogle Scholar
  148. Heuberger, S., Ellers-Kirk, C., Tabashnik, B. E., & Carriere, Y. (2010). Pollen- and seed mediated transgene flow in commercial cotton seed production fields. PLoS One, 5, e14128. Scholar
  149. Ho, M. W., Ryan, A., & Cummins, J. (2000). Cauliflower mosaic viral promoter – A recipe for disaster? Microbial Ecology in Health and Disease, 11, 194–197.CrossRefGoogle Scholar
  150. Höfte, H., & Whiteley, H. R. (1989). Insecticidal crystal proteins of Bacillus thurengiensis. Microbiological Reviews, 53, 242–255.PubMedPubMedCentralGoogle Scholar
  151. Hohenlohe, P. A., Bassham, S., Etter, P. D., Stiffler, N., Johnson, E. A., & Cresko, W. A. (2010). Population genomics of parallel adaptation in three spine stickleback using sequenced RAD tags. PLoS Genetics, 6, e1000862. Scholar
  152. Hong, L. Z., Li, J., Schmidt-Kuntzel, A., Warren, W. C., & Barsh, G. S. (2011). Digital gene expression for non-model organisms. Genome Research. (Epub ahead of print).
  153. Hood, E. E., Gelvin, S. B., Melchers, L. S., & Hoekema, A. (1993). New Agrobacterium helper plasmids for gene transfer to plants. Transgenic Research, 2(4), 208–218.CrossRefGoogle Scholar
  154. Hu, C. Y., & Wang, L. (1999). In planta soyabean transformation technologies developed in China: Procedure, confirmation and field performance. In Vitro Cellular & Developmental Biology. Plant, 35, 417–420.CrossRefGoogle Scholar
  155. Huang, X., Feng, Q., Qian, Q., Zhao, Q., Wang, L., Wang, A., Guan, J., Fan, D., Weng, Q., Huang, T., Dong, G., Sang, T., & Han, B. (2009). High throughput genotyping by whole- genome resequencing. Genome Research, 19, 1068–1076.CrossRefPubMedPubMedCentralGoogle Scholar
  156. Huffman, G. Α., White, F. F., Gordon, M. P., & Nester, E. W. (1984). Hairy root inducing plasmid: Physical map and homology to tumor inducing plasmids. Journal of Bacteriology, 157, 269–276.PubMedPubMedCentralGoogle Scholar
  157. Husken, A., Prescher, S., & Schiemann, J. (2010). Evaluating biological containment strategies for pollen-mediated gene flow. Environmental Biosafety Research, 9, 67–73. Scholar
  158. Hyten, D. L., Song, Q., Fickus, E. W., Quigley, C. V., Lim, J. S., Choi, I. Y., Hwang, E. Y., Pastor-Corrales, M., & Cregan, P. B. (2010). High-throughput SNP discovery and assay development in common bean. BMC Genomics, 11, 475. Scholar
  159. Ingelbrecht, I. L., Irvine, J. E., & Mirkov, T. E. (1999). Posttranscriptional gene silencing in transgenic sugarcane. Dissection of homologydependent virus resistance in a monocot that has a complex polyploid genome. Plant Physiology, 119, 1187–1198.CrossRefPubMedPubMedCentralGoogle Scholar
  160. Ingolia, N. T. (2010). Genome-wide translational profiling by ribosome foot printing. Methods in Enzymology, 470, 119–142.CrossRefPubMedPubMedCentralGoogle Scholar
  161. James, C. (2006). Global status of commercialized biotech/GM crops: 2006. Ithaca: International Service for the Acquisition of Agri-Biotech Applications.Google Scholar
  162. James, C. (2015). Global status of commercialized biotech/ GM crops: 2015. Ithaca: International Service for the Acquisition of Agri-biotech Applications.Google Scholar
  163. Ji, Y., Xu, Y., Zhang, Q., Tsui, K.-W., Yuan, Y., Norris, C., Jr., Liang, S., & Liang, H. (2011). BM-map: Bayesian mapping of multi reads for next-generation sequencing data. Biometrics.
  164. Jimenez-Gomez, J. M., Wallace, A. D., & Maloof, J. N. (2010). Network analysis identifies ELF3 as a QTL for the shade avoidance response in Arabidopsis. PLoSGenetics, 6, e1001100. Scholar
  165. Jin, S., Prusti, R. K., Roitsch, T., Ankenbauer, R. G., & Nester, E. W. (1990a). Phosphorylation of the VirG protein of Agrobacterium tumefaciens by the auto-phosphorylated VirA protein: Essential role in biological activity of VirG. Journal of Bacteriology, 172, 4945–4950.CrossRefPubMedPubMedCentralGoogle Scholar
  166. Jin, S., Roitsch, T., Ankenbauer, R. G., Gordon, M. P., & Nester, E. W. (1990b). The VirA protein of Agrobacterium tumefaciens is auto phosphorylated and is essential for vir gene regulation. Journal of Bacteriology, 172, 525–530.CrossRefPubMedPubMedCentralGoogle Scholar
  167. Jogdand, S. N. (2006). Gene biotechnology (2nd ed., pp. 237–249). Mumbai: Himalaya Publishing House.Google Scholar
  168. Johal, G. S., & Huber, D. M. (2009). Glyphosate effects on diseases of plants. European Journal of Agronomy, 31, 144–152.CrossRefGoogle Scholar
  169. Johnston, S. A., Anziano, P. Q., Shark, K., Sanford, J. C., & Butow, R. A. (1988). Mitochondrial transformation in yeast by bombardment with microprojectiles. Science, 240, 1538–1541.CrossRefPubMedPubMedCentralGoogle Scholar
  170. Jones, D. K., Hammond, J. I., & Relyea, R. A. (2010). Roundup and amphibians: The importance of concentration, application time, and stratification. Environmental Toxicology and Chemistry, 29, 2016–2025.PubMedPubMedCentralGoogle Scholar
  171. Joos, H., Timmerman, B., Montagu, M. V., & Schell, J. (1983). Genetic analysis of transfer and stabilization of Agrobacterium DNA in plant cells. The EMBO Journal, 2(12), 2151–2160.CrossRefPubMedPubMedCentralGoogle Scholar
  172. Jooste, A., Wessels, N., & van der Merwe, M. (2016). First report of banana bunchy top virus in banana (Musa spp.) from South Africa. Plant Disease, 100, 1251.CrossRefGoogle Scholar
  173. Kaeppler, H. E., Gu, W., Somers, D. A., Rines, H. W., & Cockburn, A. E. (1990). Silicon carbide fiber-mediated DNA delivery into plant cells. Plant Cell Reports, 9, 415–418.CrossRefPubMedPubMedCentralGoogle Scholar
  174. Kaeppler H, Somers DA, Rines HW, Cockburn AF (1992) Silicon carbide fiber-mediated stable.Google Scholar
  175. Kaniewski, W., Lawson, C., Sammons, B., Haley, L., Hart, J., Delannay, X., & Tumer, N. E. (1990). Field resistance of transgenic russet Burbank potato to effects of infection by potato virus X and potato virus Y. Nature Biotechnology, 8, 750–754.CrossRefGoogle Scholar
  176. Karyeija, R. F., Kreuze, J. F., Gibson, R. W., & Valkonen, J. P. T. (2000). Synergistic interactions of a potyvirus and a phloem-limited crinivirus in sweet potato plants. Virology, 269, 26–36.CrossRefPubMedPubMedCentralGoogle Scholar
  177. Kaur, S., Cogan, N. O., Pembleton, L. W., Shinozuka, M., Savin, K. W., Materne, M., & Forster, J. W. (2011). Transcriptome sequencing of lentil based on second-generation technology permits large-scale unigene assembly and SSR marker discovery. BMC Genomics, 12, 265. Scholar
  178. Keese, P. (2008). Risks from GMOs due to horizontal gene transfer. Environmental Biosafety Research, 7, 123–149.CrossRefPubMedPubMedCentralGoogle Scholar
  179. Kenny, E. M., Cormican, P., Gilks, W. P., Gates, A. S., O’dushlaine, C. T., Pinto, C., Corvin, A. P., Gill, M., & Morris, D. W. (2011). Multiplex target enrichment using DNA indexing for ultra-high throughput SNP detection. DNA Research, 18, 31–38.CrossRefPubMedPubMedCentralGoogle Scholar
  180. Kimber, I., Atherton, K. T., Kenna, G. J., & Dearman, R. J. (2000). Predictive methods for food allergenicity: Perspective and current status. Toxicology, 147, 147–150.CrossRefPubMedPubMedCentralGoogle Scholar
  181. King, J. J., & Wagner, R. S. (2010). Toxic effects of the herbicide roundup® regular on Pacific northwestern amphibians. Northwestern Naturalist, 91, 318–324. Scholar
  182. King, C. A., Purcell, L. C., & Vories, E. D. (2001). Plant growth and nitrogenase activity of glyphosate-tolerant soybeans in response to foliar application. Agronomy Journal, 93, 179–186.CrossRefGoogle Scholar
  183. Kliebenstein, D. J., West, M. A., Van Leeuwen, H., Loudet, O., Doerge, R. W., & St Clair, D. A. (2006). Identification of QTLs controlling gene expression networks defined a priori. BMC Bioinformatics, 7, 308. Scholar
  184. Kok, E., Pedersen, J., Onori, R., Sowa, S., Schauzu, M., De Schrijver, A., & Teeri, T. H. (2014). Plants with stacked genetically modified events: To assess or not to assess. Trends in Biotechnology, 1128, 1–4.Google Scholar
  185. Kremer, R., Means, N., & Kim, S. (2005). Glyphosate affects soybean root exudation and rhizosphere micro-organisms. International Journal of Environmental Analytical Chemistry, 85, 1165–1174.CrossRefGoogle Scholar
  186. Kreuze, J. F., Klein, I. S., Lazaro, M. U., Chuquiyuri, W. J. C., Morgan, G. L., PGC, M.’. A., Ghislain, M., & Valkonen, J. P. T. (2008). RNA silencing-mediated resistance to a crinivirus (Closteroviridae) in cultivated sweet potato (Ipomoea batatas L.) and development of sweet potato virus disease following co-infection with a potyvirus. Molecular Plant Pathology, 9, 589–598.CrossRefPubMedPubMedCentralGoogle Scholar
  187. Kruger, M., Shehata, A. A., Schrodl, W., & Rodloff, A. (2013). Glyphosate suppresses the antagonistic effect of enterococcus spp. on Clostridium botulinum. Anaerobe, 20, 74–78. Epub 2013 Feb 6.CrossRefPubMedPubMedCentralGoogle Scholar
  188. Ku, M. S. B., Agarie, S., Nomura, M., Fukayama, H., Tsuchida, H., Ono, K., Hirose, S., Toki, S., Miyao, M., & Matsuoka, M. (1999). High level expression of maize phosphoenol pyruvate carboxylase in transgenic rice plants. Nature Biotechnology, 17, 76–80.CrossRefPubMedPubMedCentralGoogle Scholar
  189. Kumar, P. L., Hanna, R., Alabi, O., Soko, M., Oben, T., Vangu, G., & Naidu, R. (2011). Banana bunchy top virus in sub-Saharan Africa: Investigations on virus distribution and diversity. Virus Research, 159, 171–182.CrossRefPubMedPubMedCentralGoogle Scholar
  190. Kunik, T., Tzfira, T., Kapulnik, Y., Gafni, Y., Dingwall, C., & Citovsky, V. (2001). Genetic transformation of HeLa cells by Agrobacterium. Proceedings of the National Academy of Sciences of the United States of America, 98, 1871–1876.CrossRefPubMedPubMedCentralGoogle Scholar
  191. Kyndt, T., Quispe, D., Zhai, H., Jarret, R., Ghislain, M., Liu, Q., Gheysen, G., & Kreuze, J. F. (2015). The genome of cultivated sweet potato contains Agrobacterium T-DNAs with expressed genes: An example of a naturally transgenic food crop. Proceedings of the National Academy of Sciences of the United States of America, 112, 5844–5849.CrossRefPubMedPubMedCentralGoogle Scholar
  192. Lalonde, E., Ha, K. C., Wang, Z., Bemmo, A., Kleinman, C. L., Kwan, T., Pastinen, T., & Majewski, J. (2011). RNAsequencing reveals the role of splicing polymorphisms in regulating human gene expression. Genome Research, 21, 545–554.CrossRefPubMedPubMedCentralGoogle Scholar
  193. Laney, A. G., Hassan, M., & Tzanetakis, I. E. (2012). An integrated badnavirus is prevalent in fig germplasm. Phytopathology, 102, 1182–1189.CrossRefPubMedPubMedCentralGoogle Scholar
  194. Lawrence, J. G., & Retchless, A. C. (2009). The interplay of homologous recombination and horizontal gene transfer in bacterial speciation. Methods in Molecular Biology, 532, 29–53. Scholar
  195. Lawson, E., Weiss, J., Thomas, P., & Kaniewski, W. (2001). NewLeaf Plus® Russet Burbank potatoes: Replicase-mediated resistance to potato leafroll virus. Molecular Breeding, 7, 1–12.CrossRefGoogle Scholar
  196. Layton, R., Smith, J., Macdonald, P., Letchumanan, R., Keese, P., & Lema, M. (2015). Building better environmental risk assessments. Frontiers in Bioengineering and Biotechnology, 3(110).
  197. Lazo, G. R., Stein, P. A., & Ludwig, R. A. (1991). A DNA transformation-competent Arabidopsis genomic library in Agrobacterium. Biotechnology (N Y), 9, 963–967.CrossRefGoogle Scholar
  198. Lee, L. Y., Kononov, M. E., Bassuner, B., Frame, B. R., Wang, K., & Gelvin, S. B. (2007). Novel plant transformation vectors containing the superpromoter. Plant Physiology, 145, 1294–1300.CrossRefPubMedPubMedCentralGoogle Scholar
  199. Lee, Y. H., Jung, M., Shin, S. H., Lee, J. H., Choi, S. H., Her, N. H., Lee, J. H., Ryu, K. H., Paek, K. Y., & Harn, C. H. (2009). Transgenic peppers that are highly tolerant to a new CMV pathotype. Plant Cell Reports, 28, 223–232.CrossRefPubMedPubMedCentralGoogle Scholar
  200. Leke, W. N., Mignouna, D. B., Brown, J. K., & Kvarnheden, A. (2015). Begomovirus disease complex: Emerging threat to vegetable production systems of West and Central Africa. Agriculture & Food Security, 4(1).Google Scholar
  201. Levin, J. Z., Yassour, M., Adiconis, X., Nusbaum, C., Thompson, D. A., Friedman, N., Gnirke, A., & Regev, A. (2010). Comprehensive comparative analysis of strand- specific RNA sequencing methods. Nature Methods, 7, 709–715.CrossRefPubMedPubMedCentralGoogle Scholar
  202. Liu, N., Zhu, P., Peng, C., Kang, L., Gao, H., Clarke, N. J., & Clarke, J. L. (2010a). Effect on soil chemistry of genetically modified (GM) vs. non-GM maize. GM Crops, 1, 1–5.CrossRefGoogle Scholar
  203. Liu, S., Lin, L., Jiang, P., Wang, D., & Xing, Y. (2010b). A comparison of RNA-seq and high-density exon array for detecting differential gene expression between closely related species. Nucleic Acids Research, 39, 578–588.CrossRefPubMedPubMedCentralGoogle Scholar
  204. Losey, J. E., Rayor, L. S., & Carter, M. E. (1999). Transgenic pollen harms monarch larvae. Nature, 399, 214.CrossRefPubMedPubMedCentralGoogle Scholar
  205. Lou, S. K., Ni, B., Lo, L. Y., Tsui, S. K., Chan, T. F., & Leung, K. S. (2011). ABMapper: A suffix array- based tool for multi-location searching and splice-junction mapping. Bioinformatics, 27, 421–422.CrossRefPubMedPubMedCentralGoogle Scholar
  206. Lu, B. R. (2008). Transgene escape from GM crops and potential biosafety consequences: An environmental perspective. Collection of Biosafety Reviews, 4, 66–141.Google Scholar
  207. Lu, B. R., & Snow, A. A. (2005). Gene flow from genetically modified rice and its environmental consequences. BioScience, 55, 669–678.CrossRefGoogle Scholar
  208. Lu, B. R., & Yang, C. (2009). Gene flow from genetically modified rice to its wild relatives: Assessing potential ecological consequences. Biotechnology Advances, 27, 1083–1091.CrossRefPubMedPubMedCentralGoogle Scholar
  209. Lu, C., Tej, S. S., Luo, S., Haudenschild, C. D., Meyers, B. C., & Green, P. J. (2005). Elucidation of the small RNA component of the transcriptome. Science, 309, 1567–1569.CrossRefPubMedPubMedCentralGoogle Scholar
  210. Luby, J. J., & McNichol, R. F. (1995). Gene flow from cultivated to wild raspberries in Scotland: Developing a basis for risk assessment for testing and deployment of transgenic cultivars. Theoretical and Applied Genetics, 90, 1133–1137.CrossRefPubMedPubMedCentralGoogle Scholar
  211. Madsen, K. H., Valverde, B. E., & Jensen, J. E. (2002). Risk assessment of herbicide resistant crops: A Latin American perspective using rice (Oryza sativa) as a model. Weed Tech, 16, 215–223.CrossRefGoogle Scholar
  212. Magbanua, Z. V., Wilde, H. D., Roberts, J. K., Chowdhury, K., Abad, J., Moyer, J. W., Wetzstein, H. Y., & Parrott, W. A. (2000). Field resistance to tomato spotted wilt virus in transgenic peanut (Arachis hypogaea L.) expressing an antisense nucleocapsid gene sequence. Molecular Breeding, 6, 227–236.CrossRefGoogle Scholar
  213. Mahuku, G., Lockhart, B. E., Wanjala, B., Jones, M. W., Kimunye, J. N., Stewart, L. R., Cassone, B. J., Sevgan, S., Nyasani, J. O., Kusia, E., Kumar, P. L., Niblett, C. L., Kiggundu, A., Asea, G., Pappu, H. R., Wangai, A., Prasanna, B. M., & Redinbaugh, M. G. (2015). Maize lethal necrosis (MLN), an emerging threat to maize-based food security in sub-Saharan Africa. Phytopathology, 105, 956–965.CrossRefPubMedPubMedCentralGoogle Scholar
  214. Marchetti, M. F. (2014). The effects of a Glyphosate-based herbicide (roundups) and temperature on the foraging of the wolf spider Pardosa milvina (Araneae: Lycosidae) master thesis. Department of Zoology. Faculty of Miami University.
  215. Marri, P. R., Hao, W., & Golding, G. B. (2007). The role of laterally transferred genes in adaptive evolution. BMC Evolutionary Biology, 7, 21.CrossRefGoogle Scholar
  216. Martin, J. A., & Wang, Z. (2011). Next-generation transcriptome assembly. Nature Reviews. Genetics, 12, 671–682. Scholar
  217. Matthews, S., Rao, V. S., & Durvasula, R. V. (2011). Modeling horizontal gene transfer (HGT) in the gut of the Chagas disease vector Rhodnius Prolixus. Parasites Vectors, 4, 77.CrossRefPubMedPubMedCentralGoogle Scholar
  218. Matveeva, T. V., Bogomaz, D. I., Pavlova, O. A., Nester, E. W., & Lutova, L. A. (2012). Horizontal gene transfer from genus Agrobacterium to the plant Linaria in nature. Molecular Plant-Microbe Interactions, 25, 1542–1551.CrossRefPubMedPubMedCentralGoogle Scholar
  219. McAfee, B. J., White, E. E., Pelcher, L. E., & Lapp, M. S. (1993). Root induction in pine (Pinus) and larch (Larix) spp. using Agrobacterium rhizogenes. Plant Cell, Tissue and Organ Culture, 34, 53–62.CrossRefGoogle Scholar
  220. McCabe, D. E., et al. (1988). Stable transformation of soybean (Glycine max) by particle acceleration. Biotechnology, 6, 923–926.Google Scholar
  221. Mcintyre, L. M., Lopiano, K. K., Morse, A. M., Amin, V., Oberg, A. L., Young, L. J., & Nuzhdin, S. V. (2011). RNA-seq: Technical variability and sampling. BMC Genomics, 12, 293. Scholar
  222. Mercer, K. L., Emry, D. J., Snow, A. A., Kost, M. A., Pace, B. A., & Alexander, H. M. (2014). Fitness of crop-wild hybrid sunflower under competitive conditions: Implications for crop-to-wild introgression. PLoS One, 9, e109001.CrossRefPubMedPubMedCentralGoogle Scholar
  223. Mertens, M. (2008). Assessment of environmental impacts of genetically modified plants BfN – Skripten 217. New York: Federal Agency for Nature Conservation.Google Scholar
  224. Mesnage, R., Clair, E., Gress, S., Then, C., & Szekacs, S. (2012). Cytotoxicity on human cells of Cry1Ab and Cry1Ac Bt insecticidal toxins alone or with a glyphosate based herbicide. Journal of Applied Toxicology, 33, 695–699.CrossRefPubMedPubMedCentralGoogle Scholar
  225. Mesnage, R., Defarge, N., Spiroux de Vendomois, J., & Seralini, G. E. (2015). Potential toxic effects of glyphosate and its commercial formulations below regulatory limits. Food and Chemical Toxicology, 84, 133–153.CrossRefPubMedPubMedCentralGoogle Scholar
  226. Metcalfe, D. D., Astwood, J. D., Townsend, R., Sampson, H. A., Taylor, S. L., & Fuchs, R. L. (1996). Assessment of allergenic K.T. Atherton/toxicology 181/182 (2002) 421/426 425 potential of foods derived from genetically engineered crop plants. Critical Reviews in Food Science and Nutrition, 36(S), S165–S186.CrossRefPubMedPubMedCentralGoogle Scholar
  227. Miller, D. L., Pislaru, S. V., & Greenleaf, J. F. (2002). Sonoporation: Mechanical DNA delivery by ultrasonic cavitation. Somatic Cell and Molecular Genetics, 27, 115–134.CrossRefPubMedPubMedCentralGoogle Scholar
  228. Missiou, A., Kalantidis, K., Boutla, A., Tzortzakaki, S., Tabler, M., & Tsagris, M. (2004). Generation of transgenic potato plants highly resistant to potato virus Y (PVY) through RNA silencing. Molecular Breeding, 14, 185–197.CrossRefGoogle Scholar
  229. Mizuno, K., Takahashi, W., Ohyama, T., Shimada, T., & Tanaka, O. (2004). Improvement of the aluminum borate whisker-mediated method of DNA delivery into rice callus. Plant Protection Science, 7, 45–49.Google Scholar
  230. Montes, J. M., Melchinger, A. E., & Reif, J. C. (2007). Novel through put phenotyping platforms in plant genetic studies. Trends in Plant Science, 12, 433–436.CrossRefPubMedPubMedCentralGoogle Scholar
  231. Morales, F. J., & Jones, P. G. (2004). The ecology and epidemiology of whitefly-transmitted viruses in Latin America. Virus Research, 100, 57–65.CrossRefPubMedPubMedCentralGoogle Scholar
  232. Morgan, M., & Pagès, H. (2010). Rsamtools: Import Aligned BAM File Format Sequences into R/Bioconductor. Available at:
  233. Morjan, W. E., Pedigo, L. P., & Lewis, L. C. (2002). Fungicidal effects of glyphosate and glyphosate formulations on four species of entomopathogenic fungi. Environmental Entomology, 31, 1206–1212.CrossRefGoogle Scholar
  234. Mortazavi, A., Williams, B. A., Mccue, K., Schaeffer, L., & Wold, B. (2008). Mapping and quantifying mammalian transcriptomes byRNA-seq. Nature Methods, 5, 621–628.CrossRefPubMedPubMedCentralGoogle Scholar
  235. Mortensen, D. A., Egan, J. F., Maxwell, B. D., Ryan, M. R., & Smith, R. G. (2012). Navigating a critical juncture for sustainable weed management. BioScience, 62.Google Scholar
  236. Mullany, P. (2000). Gene transfer in the GI tract and oral cavity. Microbial Ecology in Health and Disease, 29(Suppl 2), 73–80.CrossRefGoogle Scholar
  237. Murry, L. E., Elliott, L. G., Capitant, S. A., West, J. A., Hanson, K. K., Scarafia, L., Johnston, S., DeLuca-Flaherty, C., Nichols, S., Cunanan, D., Dietrich, P. S., Mettler, I. J., Dewald, S., Warnick, D. A., Rhodes, C., & Sinibaldi, R. M. (1993). Transgenic corn plants expressing MDMV strain B coat protein are resistant to mixed infections of maize dwarf mosaic virus and maize chlorotic mottle virus. Biotechnology, 11, 1559–1564.PubMedPubMedCentralGoogle Scholar
  238. Nagatani, N., Honda, H., Shimada, T., & Kobayashi, T. (1997). DNA delivery into rice cells and transformation using silicon carbide whiskers. Biotechnology Techniques, 11, 781–786.CrossRefGoogle Scholar
  239. Nandiyanto, A. B. D., Kim, S. G., Iskandar, F., & Okuyama, K. (2009). Synthesis of silica nanoparticles with nanometer-size controllable mesopores and outer diameters. Microporous and Mesoporous Materials, 120, 447–453.CrossRefGoogle Scholar
  240. Naqvi, S., et al. (2009). Transgenic multivitamin corn through biofortification of endosperm with three vitamins representing three distinct metabolic pathways. Proceedings of the National Academy of Sciences of the United States of America, 106, 7762–7767.CrossRefPubMedPubMedCentralGoogle Scholar
  241. NAS (National Academy of Sciences). (2016). Genetically engineered crops: Experiences and prospects. NAS Press. Retrieved from
  242. Neuhaus, G., Spangenberg, G., MittelstenScheid, O., & Schweiger, H. G. (1987). Transgenic rapeseed plants obtained by the microinjection of DNA into microspore-derived embryoids. TAG Theoretical and Applied Genetics, 75, 30–36.CrossRefGoogle Scholar
  243. Nicolae, M., Mangul, S., Mandoiu, I. I., & Zelikovsky, A. (2011). Estimation of alternative splicing isoform frequencies from RNA-seq data. Algorithms for Molecular Biology, 6, 9.CrossRefPubMedPubMedCentralGoogle Scholar
  244. Nielsen, R., Paul, J. S., Albrechtsen, A., & Song, Y. S. (2011). Genotype and SNP calling from next-generation sequencing data. Nature Reviews. Genetics, 12, 443–451. Scholar
  245. Njiti, V. N., Myers, O., Jr., Schroeder, D., & Lightfoot, D. A. (2003). Roundup ready soybean: Glyphosate effects on Fusarium solani root colonization and sudden death syndrome. Agronomy Journal, 95, 1140–1145.CrossRefGoogle Scholar
  246. Nordlee, J. A., Taylor, S. L., Townsend, J. A., Thomas, L. A., & Bush, R. K. (1996). Identification of a Brazil nut allergen in transgenic soybeans. The New England Journal of Medicine, 334, 688–692.CrossRefPubMedPubMedCentralGoogle Scholar
  247. Obrycki, J. J., Losey, J. E., Taylor, O. R., & Jesse, L. C. H. (2001). Transgenic insecticidal corn: Beyond insecticidal toxicity to ecological complexity. Bioscience, 51, 353–361.CrossRefGoogle Scholar
  248. Ondreickova, K., Mihalik, D., Ficek, A., Hudcovicova, M., Kraic, J., & Drahovska, H. (2014). Impact of genetically modified maize on the genetic diversity of rhizosphere bacteria: A two-year study in Slovakia. Polish Journal of Ecology, 62, 67–76. Scholar
  249. Oraby, H., Kandil, M., Shaffie, N., & Ghaly, I. (2015). Biological impact of feeding rats with a genetically modified-based diet. Turkish Journal of Biology, 39, 265–275.CrossRefGoogle Scholar
  250. Orbegozo, J., Solorzano, D., Cuellar, W. J., Bartolini, I., Roman, M. L., Ghislain, M., & Kreuze, J. (2016). Marker-free PLRV resistant potato mediated by Cre-loxP excision and RNAi. Transgenic Research, 25, 813–828.CrossRefPubMedPubMedCentralGoogle Scholar
  251. Orson, J. (2002). Gene stacking in herbicide tolerant oilseedrape: Lessons from the North American experience. English Nature Research Reports No. 443.
  252. Otten, L., DeGreve, H., Leemans, J., Hain, R., Hooykaas, P., & Schell, J. (1984). Restoration of virulence of vir region mutants of Agrobacterium tumefaciens strain B6S3 by coinfection with normal and mutant Agrobacterium strains. Molecular & General Genetics, 195, 159–163.CrossRefGoogle Scholar
  253. Ow, D. W. (1996). Recombinase-directed chromosome engineering in plants. Current Opinion in Biotechnology, 7, 181–186.CrossRefGoogle Scholar
  254. Owen, M. D., & Zelaya, I. A. (2005). Herbicide-resistant crops and weed resistance to herbicides. Pest Management Science, 61, 301–311.CrossRefPubMedPubMedCentralGoogle Scholar
  255. Palanichelvam, K., Oger, P., Clough, S. J., Cha, C., Bent, A. F., & Farrand, S. K. (2000). A second T-region of the soybean-super virulent chrysopine-type Ti plasmid pTiChry5, and construction of a fully disarmed vir helper plasmid. Molecular Plant-Microbe Interactions, 13, 1081–1091.CrossRefPubMedPubMedCentralGoogle Scholar
  256. Papa, R., & Gepts, P. (2004). Gene flow between crops and their wild progenitors. Encyclopedia of Plant and Crop Science, 488–491.
  257. Parkhomchuk, D., Borodina, T., Amstislavskiy, V., Banaru, M., Hallen, L., Krobitsch, S., Lehrach, H., & Soldatov, A. (2009). Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Research, 37, e123.CrossRefPubMedPubMedCentralGoogle Scholar
  258. Phipps, R. H., Beever, D. E., & Humphries, D. J. (2002). Detection of transgenic DNA in milk from cows receiving herbicide tolerant (CP4EPSPS) soyabean meal. Livestock Production Science, 74, 269–273.CrossRefGoogle Scholar
  259. Pinel-Galzi, A., Rakotomalala, M., Sangu, E., Sorho, F., Kanyeka, Z., Oumar, T., Drissa, S., Nils, P., Yvonne, R., Yacouba, S., et al. (2007). Theme and variations in the evolutionary pathways to virulence of an RNA plant virus species. PLoS Pathogens, 3, e180.CrossRefPubMedPubMedCentralGoogle Scholar
  260. Pinel-Galzi, A., Traoré, O., Séré, Y., Hébrard, E., & Fargette, D. (2015). The biogeography of viral emergence: Rice yellow mottle virus as a case study. Current Opinion in Virology, 10, 7–13.CrossRefPubMedPubMedCentralGoogle Scholar
  261. Pineyro-Nelson, A., Heerwaarden, J. V., Perales, H. R., Serratoshernandez, J. A., Rangel, A., Hufford, M. B., Gepts, P., Aray-Arroyo, A., Riverabustamante, R., & Alvarez-Buylla, E. R. (2009). Transgenes in Mexican maize: Molecular evidence and methodological considerations for GMO detection in landrace populations. Molecular Ecology, 18, 750–761. Scholar
  262. Pinto, Y. M., Kok, R. A., & Baulcombe, D. C. (1999). Resistance to rice yellow mottle virus (RYMV) in cultivated African rice varieties containing RYMV transgenes. Nature Biotechnology, 17, 702–707.CrossRefPubMedPubMedCentralGoogle Scholar
  263. Plessy, C., Bertin, N., Takahashi, H., Simone, R., Salimullah, M., Lassmann, T., Vitezic, M., Severin, J., Olivarius, S., Lazarevic, D., Hornig, N., Orlando, V., Bell, I., Gao, H., Dumais, J., Kapranov, P., Wang, H., Davis, C. A., Gingeras, T. R., Kawai, J., Daub, C. O., Hayashizaki, Y., Gustincich, S., & Carninci, P. (2010). Linking promoters to functional transcripts in small samples with nanoCAGE and CAGE scan. Nature Methods, 7, 528–534.CrossRefPubMedPubMedCentralGoogle Scholar
  264. Pline, W. A., Viator, R., Wilcut, J. W., Edmisten, K. L., Thomas, J., & Wells, R. (2002). Reproductive abnormalities in glyphosate-resistant cotton caused by lower CP4- EPSPS levels in the male reproductive tissue. Weed Science, 50, 438–447.CrossRefGoogle Scholar
  265. Popping, B. (2010). Genetically modified organisms. In B. Popping, C. Diaz-Amigo, & Hoenicke (Eds.), Molecular biological and immunological -techniques and applications for food chemists (pp. 157–174). New York: Wiley.CrossRefGoogle Scholar
  266. Potrykus, I. (1991). Gene transfer to plants: Assessment of published approaches and results. Annual Review of Plant Physiology and Plant Molecular Biology, 42, 205–225.CrossRefGoogle Scholar
  267. Powell Abel, P., Nelson, R., De, B., Hoffmann, N., Rogers, S., Fraley, R., & Beachy, R. (1986). Delay of disease development in transgenic plants that express the tobacco mosaic virus coat protein gene. Science, 232, 738–743.CrossRefGoogle Scholar
  268. Powell, J. R., Levy-Booth, D. J., Gulden, R. H., Asbil, W. L., Campbell, R. J., Dunfield, K. E., Hamill, A. S., Hart, M. M., Lerat, S., Nurse, R. E., Pauls, K. P., Sikkema, P. H., Swanton, C. J., Trevors, J. T., & Klironomos, J. N. (2009). Effects of genetically modified, herbicide tolerant crops and their management on soil food web properties and crop litter decomposition. Journal of Applied Ecology, 388–396.
  269. Presotto, A., Ureta, M. S., Cantamutto, M., & Poverene, M. (2012). Effects of gene flow from IMI resistant sunflower crop to wild Helianthus annuus populations. Agriculture, Ecosystems and Environment, 146, 153–161. Scholar
  270. Prieto, H. (2006). Proyecto Desarrollo de un sistema de trazabilidad molecular y de evaluaci_on del impacto sobre la biodiversidad local de plantas gen_eticamente modificadas a trav_es de transgenia. In yel Mercado Europeo & Servicio Agrıcola y Ganadero (Eds.), Seminario Internacional sobre Organismos Geneticamente Modificados (GMOS) (pp. 111–126). Santiago: Servicio Agrıcola y Ganadero.Google Scholar
  271. Puchta, H. (1998). Towards targeted transformation in plants. Trends in Plant Science, 3, 77–78.Google Scholar
  272. Ramessar, K., et al. (2010). Going to ridiculous lengths – European coexistence regulations for GM crops. Nature Biotechnology, 28, 133–136.CrossRefPubMedPubMedCentralGoogle Scholar
  273. Rappuoli, R., & Montecucco, C. (Eds.). (1997). Protein toxins and their use in cell biology. Oxford: Oxford University Press. ISBN 0-19-859954-4.Google Scholar
  274. Ratan, A., Zhang, Y., Hayes, V., Schuster, S., & Miller, W. (2010). Calling SNPs without a reference sequence. BMC Bioinformatics, 11, 130. Scholar
  275. Rauschen, S., Nguyen, H. T., Schuphan, I., Jehle, J. A., & Eber, S. (2008). Rapid degradation of the Cry3Bb1 protein from Diabrotica resistant Bt-corn Mon88017 during ensilation and fermentation in biogas production facilities. Journal of the Science of Food and Agriculture, 88, 1709–1715.CrossRefGoogle Scholar
  276. Raybould, A., Higgins, L. S., Horak, M. J., Layton, R. J., Storer, N. P., De La Fuente, J. M., & Herman, R. M. (2012). Assessing the ecological risks from the persistence and spread of feral populations of insect-resistant transgenic maize. Transgenic Research, 21(3), 655–664. Scholar
  277. Raz, T., Kapranov, P., Lipson, D., Letovsky, S., Milos, P. M., & Thompson, J. F. (2011). Protocol dependence of sequencing- based gene expression measurements. PLoSONE, 6, e19287. Scholar
  278. Reddy, M. S. S., Ghabrial, S. A., Redmond, C. T., Dinkins, R. D., & Collins, G. B. (2001). Resistance to Bean pod mottle virus in transgenic soybean lines expressing the capsid polyprotein. Phytopathology, 91, 831–838.CrossRefPubMedPubMedCentralGoogle Scholar
  279. Regulation 1272/2008/EC. (2015).
  280. Relyea, R. (2005). The impact of insecticides and herbicides on the biodiversity and productivity of aquatic communities. Ecological Applications, 15, 618–627.CrossRefGoogle Scholar
  281. Salmenkallio-Marttila, M., Aspegren, K., Kerman, S., Kurt, U., Mannonen, L., Ritala, A., Teeriz, T. H., & Kauppinen, V. (1995). Transgenic barley (Hordeum vulgare L.) by electroporation of protoplasts. Plant Cell Reports, 15, 301–304.CrossRefPubMedPubMedCentralGoogle Scholar
  282. Samsel, A., & Seneff, S. (2013). Glyphosate’s suppression of Cytochrome P450 enzymes and amino acid biosynthesis by the gut microbiome: Pathways to modern diseases. Entropy, 3, 1416–1463. Scholar
  283. Sanahuja, G., et al. (2011). Bacillus thuringiensis – A century of research, development and commercial applications. Plant Biotechnology Journal, 9, 283–300.CrossRefPubMedPubMedCentralGoogle Scholar
  284. Sanchez, M. A., Cid, P., Navarrete, H., Aguirre, C., Chacon, G., Salazar, E., & Prieto, H. (2016). Outcrossing potential between 11 important genetically modified crops and the Chilean vascular flora. Journal of Plant Biotechnology, 14, 625–637.CrossRefGoogle Scholar
  285. Sanford, J. C. (1990). Biolistic plant transformation. Physiologia Plantarum, 79, 206–209.CrossRefGoogle Scholar
  286. Santarem, E. R., Trick, H. N., Essig, J. S., & Finer, J. J. (1998). Sonication-assisted Agrobacterium -mediated transformation of soybean immature cotyledons: Optimization of transient expression. Plant Cell Reports, 17, 752–759.CrossRefPubMedPubMedCentralGoogle Scholar
  287. Savenkov, E. I., & Valkonen, J. P. T. (2001). Coat protein gene-mediated resistance to potato virus A in transgenic plants is suppressed following infection with another potyvirus. The Journal of General Virology, 82, 2275–2278.CrossRefPubMedPubMedCentralGoogle Scholar
  288. Sawahel, W., & Saker, M. (1997). Stable genetic transformation of mature wheat embryos using silicon carbide fibers and DNA imbibitions. Cellular & Molecular Biology Letters, 2, 421–429.Google Scholar
  289. Schell, J., & Van Montagu, M. (1977). The Ti-plasmid of agrobacterium tumefaciens, a natural vector for the introduction of NIF genes in plants? In A. Hollaender, R. H. Burris, P. R. Day, R. W. F. Hardy, D. R. Helinski, M. R. Lamborg, L. Owens, & R. C. Valentine (Eds.), Genetic engineering for nitrogen fixation, basic life sciences (Vol. 9, pp. 159–179). Boston: Springer. Scholar
  290. Schmidt-Dannert, C., Umeno, D., & Arnold, F. H. (2000). Molecular breeding of carotenoid biosynthesis pathways. Nature Biotechnology, 18, 750–753.CrossRefPubMedPubMedCentralGoogle Scholar
  291. Schmieder, R., & Edwards, R. (2011). Quality control and preprocessing of metagenomic datasets. Bioinformatics, 27, 863–864.CrossRefPubMedPubMedCentralGoogle Scholar
  292. Schneeberger, K., & Weigel, D. (2011). Fast-forward genetics enabled by new sequencing technologies. Trends in Plant Science, 16, 282–288.CrossRefPubMedPubMedCentralGoogle Scholar
  293. Schnell, J., Steele, M., Bean, J., Neuspiel, M., Girard, C., Dormann, N., et al. (2015). A comparative analysis of insertional effects in genetically engineered plants: Considerations for pre-market assessments. Transgenic Research, 24, 1–17. Scholar
  294. Schulze, J., Frauenknecht, T., Brodmann, P., & Bagutti, C. (2014). Unexpected diversity of feral genetically modified oilseed rape (Brassica napus L.) despite a cultivation and import ban in Switzerland. PLoS One, e114477.
  295. Schuppener, M., Muhlhause, J., Muller, A. K., & Rauschen, S. (2012). Environmental risk assessment for the small tortoiseshell Aglais urticae and a stacked Bt-maize with combined resistances against Lepidoptera and Chrysomelidae in central European agrarian landscapes. Molecular Ecology, 21, 4646–4662. Scholar
  296. Schutte, G., & Schmitz, G. (2001). In: Transgene, Nutzpflanzen, Hrsg. Schütte, G., Stirn, S., Beusmann, V., S. (Eds.), Herbizidresistenz. Basel, Birkhäuser, pp. 102–122.Google Scholar
  297. Seema, G., Pande, H. P., Lal, J., & Madan, V. K. (2001). Plantlet regeneration of sugarcane varieties and transient GUS expression in calli by electroporation. Sugar Tech: An International Journal of Sugar Crops and Related Industries, 3, 27–33.CrossRefGoogle Scholar
  298. Sen, P., Pazour, G. J., Anderson, D., & Das, A. (1989). Cooperative binding of Agrobacterium tumefaciens- VirE2 protein to single-stranded DNA. Journal of Bacteriology, 171, 2573–2580.CrossRefPubMedPubMedCentralGoogle Scholar
  299. Seralini, G. E., Clair, E., Mesnage, R., Gress, S., Defarge, N., Malatesta, M., Hennequin, D., & de Vendomois, J. S. (2014). Republished study: Long-term toxicity of a roundup herbicide and a roundup-tolerant genetically modified maize. Environmental Sciences Europe, 26, 14.CrossRefPubMedPubMedCentralGoogle Scholar
  300. Sessitsch, A., Gyamfi, S., Tscherko, D., Gerzabek, M. H., & Kandeler, E. (2005). Activity of microorganisms in the rhizosphere of herbicide treated and untreated transgenic glufosinate-tolerant and wildtype oilseed rape grown in containment. Plant and Soil, 266, 105–116.CrossRefGoogle Scholar
  301. Shah, D. M., Rommens, C. M. T., & Beachy, R. N. (1995). Resistance to diseases and insects in transgenic plants: Progress and applications to agriculture. Trends in Biotechnology, 13, 362–368.CrossRefGoogle Scholar
  302. Shekhawat, U. K. S., Ganapathi, T. R., & Hadapad, A. B. (2012). Transgenic banana plants expressing small interfering RNAs targeted against viral replication initiation gene display high-level resistance to banana bunchy top virus infection. The Journal of General Virology, 93, 1804–1813.CrossRefPubMedPubMedCentralGoogle Scholar
  303. Shepherd, D. N., Mangwende, T., Martin, D. P., Bezuidenhout, M., Kloppers, F. J., Carolissen, C. H., Monjane, A. L., Rybicki, E. P., & Thomson, J. A. (2007). Maize streak virus-resistant transgenic maize: A first for Africa. Plant Biotechnology Journal, 5, 759–767.CrossRefPubMedPubMedCentralGoogle Scholar
  304. Shepherd, D. N., Martin, D. P., Van der Walt, E., Dent, K., Varsani, A., & Rybicki, E. P. (2010). Maize streak virus: An old and complex “emerging” pathogen. Molecular Plant Pathology, 11, 1–12.CrossRefPubMedPubMedCentralGoogle Scholar
  305. Shepherd, D. N., Dugdale, B., Martin, D. P., Varsani, A., Lakay, F. M., Bezuidenhout, M. E., Monjane, A. L., Thomson, J. A., Dale, J., & Rybicki, E. P. (2014). Inducible resistance to maize streak virus. PLoS One, 9, e105932.CrossRefPubMedPubMedCentralGoogle Scholar
  306. Shimamoto, K., Teralda, R., Izawa, T., & Fujimoto, H. (1989). Fertile transgenic rice plants regenerated from transformed protoplasts. Nature, 338, 274–276.CrossRefGoogle Scholar
  307. Shimizu, T., Yoshii, M., Wei, T., Hirochika, H., & Omura, T. (2009). Silencing by RNAi of the gene for Pns12, a viroplasm matrix protein of Rice dwarf virus, results in strong resistance of transgenic rice plants to the virus. Plant Biotechnology Journal, 7, 24–32.CrossRefPubMedPubMedCentralGoogle Scholar
  308. Singh, N., & Chawla, H. S. (1999). Use of silicon carbide fibers for Agrobacterium mediated transformation in wheat. Current Science, 76, 1483–1485.Google Scholar
  309. Slater, A., Scott, N., & Fowler, M. (2008). Plant biotechnology: The genetic manipulation of plants (2nd ed.). Oxford: Oxford University Press.Google Scholar
  310. Smith, D. R., Quinlan, A. R., Peckham, H. E., Makowsky, K., Tao, W., Woolf, B., Shen, L., Donahue, W. F., Tusneem, N., Stromberg, M. P., Stewart, D. A., Zhang, L., Ranade, S. S., Warner, J. B., Lee, C. C., Coleman, B. E., Zhang, Z., Mclaughlin, S. F., Malek, J. A., Sorenson, J. M., Blanchard, A. P., Chapman, J., Hillman, D., Chen, F., Rokhsar, D. S., Mckernan, K. J., Jeffries, T. W., Marth, G. T., & Richardson, P. M. (2008). Rapid whole-genome mutational profiling using next-generation sequencing technologies. Genome Research, 18, 1638–1642.CrossRefPubMedPubMedCentralGoogle Scholar
  311. Souaiaia, T., Frazier, Z., & Chen, T. (2011). ComB: SNP calling and mapping analysis for color and nucleotide space platforms. Journal of Computational Biology, 18, 795–807. Scholar
  312. Stein, L. D. (2010). The case for cloud computing in genome informatics. Genome Biology, 11, 207.CrossRefPubMedPubMedCentralGoogle Scholar
  313. Stern, D. L., & Orgogozo, V. (2008). The loci of evolution: How predictable is genetic evolution? Evolution, 62, 2155–2177.CrossRefPubMedPubMedCentralGoogle Scholar
  314. Stotzky, G. (2004). Persistence and biological activity in soil of the insecticidal proteins from Bacillus thuringiensis, especially from transgenic plants. Plant and Soil, 266, 77–89.CrossRefGoogle Scholar
  315. Subramanyam, K., Subramanyam, K., Sailaja, K. V., Srinivasulu, M., & Lakshmidevi, K. (2011). Highly efficient Agrobacterium -mediated transformation of banana cv. Rasthali (AAB) via sonication and vacuum infiltration. Plant Cell Reports, 30, 425–436.CrossRefPubMedPubMedCentralGoogle Scholar
  316. Suzuki, K., Hattori, Y., Uraji, M., Ohta, N., Iwata, K., Murata, K., Kato, A., & Yoshida, K. (2000). Complete nucleotide sequence of a plant tumor inducing Ti plasmid. Gene, 242, 331–336.CrossRefPubMedPubMedCentralGoogle Scholar
  317. Svensson, I., Artursson, E., Leanderson, P., Berglind, R., & Lindgren, F. (1997). Toxicity in vitro of some silicon carbides and silicon nitrides: Whiskers and powders. American Journal of Industrial Medicine, 31, 335–343.CrossRefPubMedPubMedCentralGoogle Scholar
  318. Szenasi, A., Palinkas, Z., Zalai, M., Schmitz, O. J., & Balog, A. (2014). Short-term effects of different genetically modified maize varieties on arthropod food web properties: An experimental field assessment. Scientific Reports, 4(5315).
  319. Tabashnik, B. E., Biggs, R. W., Higginson, D. M., Henderson, S., Unnithan, D. C., Unnithan, G. C., Ellersk-Kirk, C., Sisterson, M. S., Dennehy, T. J., Carriere, Y., & Morin, S. (2005). Association between resistance to Bt cotton and cadherin genotype in pink bollworm. Journal of Economic Entomology, 98, 635–644.CrossRefPubMedPubMedCentralGoogle Scholar
  320. Tabashnik, B. E., Brevault, T., & Carriere, Y. (2013). Insect resistance to Bt crops: Lessons from the first billion acres. Nature Biotechnology, 31, 510–521. Scholar
  321. Tachibana, K., Uchida, T., Ogawa, K., Yamashita, N., & Tamura, K. (1999). Induction of cell-membrane porosity by ultrasound. Lancet, 353, 1409.CrossRefPubMedPubMedCentralGoogle Scholar
  322. Takahashi, W., Shimada, T., Matsushita, J., & Tanaka, O. (2000). Aluminium borate whisker-mediated DNA delivery into callus of rice and production of transgenic rice plant. Plant Protection Science, 3, 219–224.Google Scholar
  323. Tarazona, S., Garcia-Alcalde, F., Dopazo, J., Ferrer, A., & Conesa, A. (2011). Differential expression in RNA-seq: A matter of depth. Genome Research. Epub ahead of print.
  324. Taylor, S. L., & Lehrer, S. B. (1996). Principles and characteristics of food allergens. Critical Reviews in Food Science and Nutrition, 36(S), S91–S118.CrossRefPubMedPubMedCentralGoogle Scholar
  325. Tepfer, D., Garcia-Gonzales, R., Mansouri, H., Seruga, M., Message, B., Leach, F., & Perica, M. C. (2003). Homology, dependent DNA transfer from plants to a soil bacterium under laboratory conditions: Implications in evolution and horizontal gene transfer. Transgenic Research, 12, 425–437.CrossRefPubMedPubMedCentralGoogle Scholar
  326. Thornton, M. (2003). The rise and fall of New Leaf potatoes. NABC Report, 15, 235–243.Google Scholar
  327. Thottappilly, G., NA, B.-P.’r., & Rossel, H. W. (1993). Viruses and virus diseases of maize in tropical Africa. Plant Pathology, 42, 494–509.CrossRefGoogle Scholar
  328. Tindall, K. V., Stout, M. J., & Williams, B. J. (2004). Evaluation of the potential role of glufosinate-tolerant rice in integrated pest management programs for rice water weevil (Coleoptera: Curculionidae). Journal of Economic Entomology, 97, 1935–1942.CrossRefPubMedPubMedCentralGoogle Scholar
  329. Topping, J. F., Wei, W., & Lindsey, K. (1991). Functional tagging of regulatory elements in the plant genome. Development, 112, 1009–1019.PubMedPubMedCentralGoogle Scholar
  330. Torney, F., Trewyn, B. G., Lin, V. S. Y., & Wang, K. (2007). Mesoporous silica nanoparticles deliver DNA and chemicals into plants. Nature Nanotechnology, 2, 295–300.CrossRefPubMedPubMedCentralGoogle Scholar
  331. Toro, N., Datta, A., Carmi, O. A., Young, C., Prusti, R. K., & Nester, E. W. (1989). The Agrobacterium tumefaciens virC1 gene product binds to overdrive, a T-DNA transfer enhancer. Journal of Bacteriology, 171, 6845–6849.CrossRefPubMedPubMedCentralGoogle Scholar
  332. Trapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., VanBaren, M. J., Salzberg, S. L., Wold, B. J., & Pachter, L. (2010). Transcript assembly and quantification by RNA- seq reveals unannotated transcripts and isoforms witching during cell differentiation. Nature Biotechnology, 28, 511–515.CrossRefPubMedPubMedCentralGoogle Scholar
  333. Trevisan, F., Mendes, B. M. J., Maciel, S. C., Vieira, M. L. C., Meletti, L. M. M., & Rezende, J. A. M. (2006). Resistance to passion fruit woodiness virus in transgenic passionflower expressing the virus coat protein gene. Plant Disease, 90, 1026–1030.CrossRefPubMedPubMedCentralGoogle Scholar
  334. Tu, J., Datta, K., Khush, G. S., Zhang, Q., & Datta, S. K. (2000a). Field performance of Xa21 transgenic indica rice (Oryza sativa L.) IR72. Theoretical and Applied Genetics, 101, 15–20.CrossRefGoogle Scholar
  335. Tu, J., Zhang, G., Datta, K., Xu, C., He, Y., Zhang, Q., Khush, G. S., & Datta, S. K. (2000b). Field performance of transgenic elite commercial hybrid rice expressing Bacillus thuringiensis d-endotoxin. Nature Biotechnology, 18, 1101–1104.CrossRefPubMedPubMedCentralGoogle Scholar
  336. Tutelyan, V. A., Gapparov, M. M. G., Avrenjeva, L. I., Guseva, G. V., Zhminchenko, V. M., Kravchenko, L. V., Pashorina, V. A., Saprikin, V. P., Seliaskin, K. E., & Tyshko, N. V. (2010). Medical and biological safety assessment of genetically modified soybean event MON 89788. Report 1. Toxicologo-hygienic examinations. Vopr. Pitan. (Problem of Nutrition), 79, 4–12.Google Scholar
  337. Tzfira, T., Vaidya, M., & Citovsky, V. (2002). Increasing plant susceptibility to Agrobacterium infection by overexpression of the Arabidopsis nuclear protein VIP1. Proceedings of the National Academy of Sciences of the United States of America, 99, 10435–10440.CrossRefPubMedPubMedCentralGoogle Scholar
  338. Underwood, J. G., Uzilov, A. V., Katzman, S., Onodera, C. S., Mainzer, J. E., Mathews, D. H., Lowe, T. M., Salama, S. R., & Haussler, D. (2010). FragSeq: Transcriptome- wide RNA structure probing using high-throughput sequencing. Nature Methods, 7, 995–1001.CrossRefPubMedPubMedCentralGoogle Scholar
  339. Unger, E. C., Hersh, E., Vannan, M., Matsunaga, T. O., & McCreery, T. (2001). Local drug and gene delivery through microbubbles. Progress in Cardiovascular Diseases, 44, 45–54.CrossRefPubMedPubMedCentralGoogle Scholar
  340. Vaeck, N., Reynaerts, A., Hofte, H., Jansens, S., Beukeleer, M. D., Dean, C., Zabeau, M., Montagu, M. C., & Leemans, J. (1987). Transgenic plants protected from insect attacks. Nature, 328, 33–37.CrossRefGoogle Scholar
  341. Vain, P. (2007). Thirty years of plant transformation technology development. Plant Biotechnology Journal, 5, 221–229.CrossRefPubMedPubMedCentralGoogle Scholar
  342. Valkonen, J., Kreuze, J., & Ndunguru, J. (2015). Disease management, especially viruses in potato and sweet potato. In Potato and sweetpotato in Africa: Transforming the value chains for food and nutrition security. Wallingford: CABI.Google Scholar
  343. Van de Water, P. K., Watrud, L. S., Lee, E. H., et al. (2007). Long-distance GM pollen movement of creeping bentgrass using modeled wind trajectory analysis. Ecological Applications, 17, 1244–1256.CrossRefPubMedPubMedCentralGoogle Scholar
  344. van Engelen, F. A., Molthoff, J. W., Conner, A. J., Nap, J. P., Pereira, A., & Stiekema, W. J. (1995). pBINPLUS: An improved plant transformation vector based on pBIN19. Transgenic Research, 4, 288–290.CrossRefPubMedPubMedCentralGoogle Scholar
  345. Van Hoek, A. H. A. M., Mevius, D., Guerra, B., Mullany, P., Roberts, A. P., & Aarts, H. J. M. (2011). Acquired antibiotic resistance genes: An overview. Frontiers in Microbiology, 2, 1–27. Scholar
  346. Vaucheret, H., Béclin, C., Elmayan, T., Feuerbach, F., Godon, C., Morel, J. B., Mourrain, P., Palauqui, J. C., & Vernhettes, S. (1998). Transgene-induced gene silencing in plants. The Plant Journal, 16, 651–659.CrossRefPubMedPubMedCentralGoogle Scholar
  347. Veena. (2008). Engineering plants for future: Tools and options. Physiology and Molecular Biology of Plants, 14, 131–135.CrossRefPubMedPubMedCentralGoogle Scholar
  348. Veluthambi, K., Ream, W., & Gelvin, S. B. (1988). Virulence genes, borders, and overdrive generate single- stranded T-DNA molecules from the A6 Ti plasmid of Agrobacterium tumefaciens. Journal of Bacteriology, 170, 1523–1532.CrossRefPubMedPubMedCentralGoogle Scholar
  349. Vergunst, A. C., Schrammeijer, B., den Dulk-Ras, A., de Vlaam, C. M. T., Regensburg-Tuink, T. J. G., & Hooykaas, P. J. J. (2000). VirB/D4-dependentprotein translocation from Agrobacterium into plant cells. Science, 290, 979–982.CrossRefPubMedPubMedCentralGoogle Scholar
  350. Wakelin, A. M., Lorraine-Colwill, D. F., & Preston, C. (2004). Glyphosate resistance in four different populations of Lolium rigidum is associated with reduced translocation of glyphosate to meristematic zones. Weed Research, 44, 453–459.CrossRefGoogle Scholar
  351. Wang, K., Drayton, P., Frame, B., Dunwell, J., & Thompson, J. A. (1995). Whisker mediated plant transformation: An alternative technology. In Vitro Cellular & Developmental Biology. Plant, 31, 101–104.CrossRefGoogle Scholar
  352. Wang, Z., Zemetra, R. S., Hansen, J., & Mallory-Smith, C. A. (2001). The fertility of wheat x jointed goat grass hybrid and its backcross progenies. Weed Science, 49, 340–345.CrossRefGoogle Scholar
  353. Wang, X., Wu, Z., & Zhang, X. (2010). Isoform abundance inference provides a more accurate estimation of gene expression levels in RNA-seq. Journal of Bioinformatics and Computational Biology, 8(Suppl 1), 177–192.CrossRefPubMedPubMedCentralGoogle Scholar
  354. Warwick, S. I., Legere, A., Simard, M. J., & James, T. (2008). Do escaped transgenes persist in nature? The case of an herbicide resistance transgene in a weedy Brassica rapa population. Molecular Ecology, 17, 1387–1395. Scholar
  355. Warwick, S. I., Beckie, H. J., & Hall, L. M. (2009). Gene flow, invasiveness, and ecological impact of genetically modified crops. Annals of the New York Academy of Sciences, 1168, 72–99. New York Academy of Sciences.CrossRefPubMedPubMedCentralGoogle Scholar
  356. Waterhouse, P. M., Graham, M. W., & Wang, M.-B. (1998). Virus resistance and gene silencing in plants can be induced by simultaneous expression of sense and antisense RNA. Proceedings of the National Academy of Sciences of the United States of America, 95, 13959–13964.CrossRefPubMedPubMedCentralGoogle Scholar
  357. Weber, S., Friedt, W., Landes, N., Molinier, J., Himber, C., Rousselin, P., et al. (2003). Improved Agrobacterium -mediated transformation of sunflower (Helianthus annuus L.): Assessment of macerating enzymes and sonication. Plant Cell Reports, 21, 475–482.CrossRefPubMedPubMedCentralGoogle Scholar
  358. Wei, W., Qi, X., Wang, L., Zhang, Y., Hua, W., Li, D., Lv, H., & Zhang, X. (2011). Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers. BMC Genomics, 12, 451. Scholar
  359. White, F. F., Ghidossi, G., Gordon, M. P., & Nester, E. W. (1982). Tumor induction by Agrobacterium rhizogenes involves the transfer of plasmid DNA to the plant genome. Proceedings of the National Academy of Sciences of the United States of America, 79, 3193–3197.CrossRefPubMedPubMedCentralGoogle Scholar
  360. White, F. F., Taylor, B. H., Huffman, G. Α., Gordon, M. P., & Nester, E. W. (1985). Molecular and genetic analysis of the transferred DNA regions of the root inducing plasmid of Agrobacterium rhizogenes. Journal of Bacteriology, 164, 33–44.PubMedPubMedCentralGoogle Scholar
  361. Williamson, M., Perrings, J., & Fitter, A. (1990). Releasing genetically engineered plants: Present proposals and possible hazards. Trends in Ecology & Evolution, 5, 417–419.CrossRefGoogle Scholar
  362. Willing, E. M., Hoffmann, M., Klein, J. D., Weigel, D., & Dreyer, C. (2011). Paired-end RAD-seq for de novo assembly and marker design without available reference. Bioinformatics, 27, 2187–2193. Scholar
  363. Willmitzer, L., Sanchez-Serrano, J., Busfeld, E., & Schell, J. (1982). DNA from Agrobacterium rhizogenes is transferred to and expressed in axenic hairy root plant tissue. Molecular & General Genetics, 186, 16–22.CrossRefGoogle Scholar
  364. Willmitzer, L., Dhaese, P., Schreier, P. H., Schmalenbach, W., Van Montagu, Μ., & Schell, J. (1983). Size, location and polarity of T-DNA-encoded transcripts in nopaline crown gall tumours; common transcripts of octopine and nopaline tumours. Cell, 32, 1045–1056.CrossRefPubMedPubMedCentralGoogle Scholar
  365. Wood, D. W., Setubal, J. C., Kaul, R., Monks, D. E., Kitajima, J. P., Okura, V. K., et al. (2001). The genome of the natural genetic engineer Agrobacterium tumefaciens C58. Science, 294, 2317–2323.CrossRefPubMedPubMedCentralGoogle Scholar
  366. Wordragen, M. V., Roshani, S., Ruud, V., Regis, P., Abvan, K., & Pim, Z. (1997). Liposome-mediated transfer of YAC DNA to tobacco cells. Plant Molecular Biology Reporter, 15, 170–178.CrossRefGoogle Scholar
  367. Wrinn, K. M., Evans, S. C., & Rypstra, A. L. (2012). Predator cuas and an herbicide affect activity and emigration in an agrobiont wolf spider. Chemosphere, 87, 390–396. Epub 2012 Jan 4.CrossRefPubMedPubMedCentralGoogle Scholar
  368. Wu, X., Ren, C., Joshi, T., Vuong, T., Xu, D., & Nguyen, H. T. (2010). SNP discovery by high-throughput sequencing in soybean. BMC Genomics, 11, 469. Scholar
  369. Wyber, J. A., Andrew, J., & D’Emanuele, A. (1997). The use of sonication for the efficient delivery of plasmid DNA into cells. Pharmaceutical Research, 14, 750–756.CrossRefPubMedPubMedCentralGoogle Scholar
  370. Xie, D. X., Fan, Y. L., & Ni, P. C. (1990). Transgenic rice plant obtained by transferring the Bacillus thuringiensis toxin gene into a Chinese rice cultivar Zhonghua 11. Rice Genetics Newsletter, 7, 147–148.Google Scholar
  371. Xie, W., Feng, Q., Yu, H., Huang, X., Zhao, Q., Xing, Y., Yu, S., Han, B., & Zhang, Q. (2010). Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing. Proceedings of the National Academy of Sciences of the United States of America, 107, 10578–10583.CrossRefPubMedPubMedCentralGoogle Scholar
  372. Yamagishi, N., Teraichi, H., Kanematsu, S., & Hidaka, S. (2007). Biolistic inoculation of soybean plants. Journal of Virological Methods, 137, 164–167.CrossRefGoogle Scholar
  373. Yang, X., Wang, F., Su, J., & Lu, B. R. (2012). Limited fitness advantages of crop-weed hybrid progeny containing insect-resistant transgenes (Bt/CpTI) in transgenic rice field. PLoS One, 7, e41220. Scholar
  374. Ye, X. D., et al. (2000). Engineering the provitamin A (beta-carotene) biosynthetic pathway into (carotenoid-free) rice endosperm. Science, 287, 303–305.CrossRefPubMedPubMedCentralGoogle Scholar
  375. You, F. M., Huo, N., Deal, K. R., Gu, Y. Q., Luo, M. C., Mcguire, P. E., Dvorak, J., & Anderson, O. D. (2011). Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence. BMC Genomics, 12, 59. Scholar
  376. Young, M. D., Wakefield, M. J., Smyth, G. K., & Oshlack, A. (2010). Gene ontology analysis for RNA- seq: Accounting for selection bias. Genome Biology, 11, R14.CrossRefPubMedPubMedCentralGoogle Scholar
  377. Young, F., Ho, D., Glynn, D., & Edwards, V. (2015). Endocrine disruption and cytotoxicity of glyphosate and roundup in human JAr cells in vitro. Integrative Pharmacology, Toxicology and Genotoxicology, 1, 12–19. Scholar
  378. Yu, H. L., Li, Y. H., & Wu, K. M. (2011). Risk assessment and ecological effects of transgenic Bacillus thuringiensis crops on non-target organisms. Journal of Integrative Plant Biology, 53, 520–538.CrossRefPubMedPubMedCentralGoogle Scholar
  379. Zabaloy, M. C., Carné, I., Viassolo, R., Gómez, M. A., & Gomez, E. (2016). Soil ecotoxicity assessment of glyphosate use under field conditions: Microbial activity and community structure of Eubacteria and ammonia-oxidising bacteria. Pest Management Science, 72, 684–691.CrossRefPubMedPubMedCentralGoogle Scholar
  380. Zambryski, P., Holsters, M., Kruger, K., DepickerA, S. J., Van Montagu, M., & Goodman, H. M. (1980). Tumor DNA structure in plant cells transformed by A. tumefaciens. Science, 209, 1385–1391.CrossRefPubMedPubMedCentralGoogle Scholar
  381. Zambryski, P., Joos, P. H., Genetello, C., Leemans, J., Van Montagu, M., & Schell, J. (1983). Ti plasmid vector for the introduction of DNA into plant cells without alteration of their normal regeneration capacity. The EMBO Journal, 2, 2143–2150.CrossRefPubMedPubMedCentralGoogle Scholar
  382. Zhang, L.-J., Chen, L.-M., Xu, N., Zhao, N.-M., Li, C.-G., Jing, Y., et al. (1991). Efficient transformation of tobacco by ultrasonication. Biotechnology, 9, 996–997.CrossRefGoogle Scholar
  383. Zhang, G., Guo, G., Hu, X., Zhang, Y., Li, Q., Li, R., Zhuang, R., Lu, Z., He, Z., Fang, X., Chen, L., Tian, W., Tao, Y., Kristiansen, K., Zhang, X., Li, S., Yang, H., & Wang, J. (2010). Deep RNAsequencing at single base-pair resolution reveals high complexity of the rice transcriptome. Genome Research, 20, 646–654.CrossRefPubMedPubMedCentralGoogle Scholar
  384. Zheng, W., Chung, L. M., & andZhao, H. (2011). Bias detection and correction in RNA-sequencing data. BMC Bioinformatics, 12, 290. Scholar
  385. Zhou, G. Y., Weng, J., Zeng, Y., Huang, J., Qian, S., & Liu, G. (1983). Introduction of exogenous DNA into cotton embryos. Methods in Enzymology, 101, 433–481.CrossRefPubMedPubMedCentralGoogle Scholar
  386. Zhou, X., Liu, Y., Calvert, L., Munoz, C., Otim-Nape, G. W., Robinson, D. J., & Harrison, B. D. (1997). Evidence that DNA-A of a geminivirus associated with severe cassava mosaic disease in Uganda has arisen by interspecific recombinations. The Journal of General Virology, 78, 2101–2111.CrossRefPubMedPubMedCentralGoogle Scholar
  387. Zhu, B. (2006). Degradation of plasmid and plant DNA in water microcosms monitored by natural transformation and real-time polymerase chain reaction (PCR). Water Research, 40, 3231–3238.CrossRefPubMedPubMedCentralGoogle Scholar
  388. Zimmermann, U., Pilwat, G., & Riemann, F. (1974). Dielectric breakdown of cell membranes. Biophysical Journal, 14, 881–889.CrossRefPubMedPubMedCentralGoogle Scholar
  389. Zupan, J., Muth, T. R., Draper, O., & Zambryski, P. (2000). The transfer of DNA from Agrobacterium tumefaciens into plants: A feast of fundamental insights. The Plant Journal, 23, 11–28.CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2019

Authors and Affiliations

  • Javid Ahmad Parray
    • 1
  • Mohammad Yaseen Mir
    • 2
  • Nowsheen Shameem
    • 3
  1. 1.Department of Environmental ScienceGovernment SAM Degree CollegeBudgamIndia
  2. 2.Centre of Research for DevelopmentUniversity of KashmirSrinagarIndia
  3. 3.Department of Environmental ScienceCluster UniversitySrinagarIndia

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