Genomics & Informatics

Korea Genome Organization (한국유전체학회)
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Efficiency to Discovery Transgenic Loci in GM Rice Using Next Generation Sequencing Whole Genome Re-sequencing

  • Park, Doori (Institute of Green Bio Science and Technology, Seoul National University) ;
  • Kim, Dongin (National Instrumentation Center for Environmental Management, College of Agriculture and Life Sciences, Seoul National University) ;
  • Jang, Green (National Instrumentation Center for Environmental Management, College of Agriculture and Life Sciences, Seoul National University) ;
  • Lim, Jongsung (National Instrumentation Center for Environmental Management, College of Agriculture and Life Sciences, Seoul National University) ;
  • Shin, Yun-Ji (Natural Bio-Materials Inc.) ;
  • Kim, Jina (Natural Bio-Materials Inc.) ;
  • Seo, Mi-Seong (Natural Bio-Materials Inc.) ;
  • Park, Su-Hyun (Crop Biotech Institute, Green-Bio Science and Technology, Seoul National University) ;
  • Kim, Ju-Kon (Crop Biotech Institute, Green-Bio Science and Technology, Seoul National University) ;
  • Kwon, Tae-Ho (Natural Bio-Materials Inc.) ;
  • Choi, Ik-Young (Institute of Green Bio Science and Technology, Seoul National University)
  • Received : 2015.07.25
  • Accepted : 2015.08.24
  • Published : 2015.09.30
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Abstract

Molecular characterization technology in genetically modified organisms, in addition to how transgenic biotechnologies are developed now require full transparency to assess the risk to living modified and non-modified organisms. Next generation sequencing (NGS) methodology is suggested as an effective means in genome characterization and detection of transgenic insertion locations. In the present study, we applied NGS to insert transgenic loci, specifically the epidermal growth factor (EGF) in genetically modified rice cells. A total of 29.3 Gb (${\sim}72{\times}coverage$) was sequenced with a $2{\times}150bp$ paired end method by Illumina HiSeq2500, which was consecutively mapped to the rice genome and T-vector sequence. The compatible pairs of reads were successfully mapped to 10 loci on the rice chromosome and vector sequences were validated to the insertion location by polymerase chain reaction (PCR) amplification. The EGF transgenic site was confirmed only on chromosome 4 by PCR. Results of this study demonstrated the success of NGS data to characterize the rice genome. Bioinformatics analyses must be developed in association with NGS data to identify highly accurate transgenic sites.

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References

  1. Sabalza M, Christou P, Capell T. Recombinant plant-derived pharmaceutical proteins: current technical and economic bottlenecks. Biotechnol Lett 2014;36:2367-2379. https://doi.org/10.1007/s10529-014-1621-3
  2. Schurch C, Blum P, Zulli F. Potential of plant cells in culture for cosmetic application. Phytochem Rev 2008;7:599-605. https://doi.org/10.1007/s11101-007-9082-0
  3. Cohen SN, Chang AC, Boyer HW, Helling RB. Construction of biologically functional bacterial plasmids in vitro. Proc Natl Acad Sci U S A 1973;70:3240-3244. https://doi.org/10.1073/pnas.70.11.3240
  4. European Parliament. Commission Implementing Regulation (EC) No 1829/2003 of the European Parliament and of the Council of 22 September 2003 on genetically modified food and feed. European Union Legislation. OJ L 268, 1-23. 2003.
  5. European Parliament. REGULATION (EC) No 1830/2003 OF THE EUROPEAN PARLIAMENT AND OF THE COUNCIL of 22 September 2003 concerning the traceability and labelling of genetically modified organisms and the traceability of food and feed products produced from genetically modified organisms and amending Directive 2001/18/EC. European Union Legislation. OJ L 268, 24-28. 2003.
  6. European Parliament. Commission Implementing Regulation (EU) No 503/2013 of 3 April 2013 on applications for authorisation of genetically modified food and feed in accordance with Regulation (EC) No 1829/2003 of the European Parliament and of the Council and amending Commission Regulations (EC) No 641/2004 and (EC) No 1981/2006. European Union Legislation. OJ L 157, 1-48. 2013.
  7. Food and Agricultural Organization of the United Nations (FAO). Guideline for the conduct of food safety assessment of foods derived from recombinant-DNA plants. Rep. No. CAC/GL 45-2003. Rome: FAO, 2003.
  8. Food and Agricultural Organization of the United Nations (FAO). Guideline for the conduct of food safety assessment of foods derived from recombinant-DNA plants. Rep. No. CAC/GL. 68-2008. Rome: FAO, 2003.
  9. Yang L, Wang C, Holst-Jensen A, Morisset D, Lin Y, Zhang D. Characterization of GM events by insert knowledge adapted re-sequencing approaches. Sci Rep 2013;3:2839. https://doi.org/10.1038/srep02839
  10. Pauwels K, De Keersmaecker SC, De Schrijver A, du Jardin P, Roosens NH, Herman P. Next-generation sequencing as a tool for the molecular characterisation and risk assessment of genetically modified plants: added value or not? Trends Food Sci Technol 2015;45:319-326. https://doi.org/10.1016/j.tifs.2015.07.009
  11. Kovalic D, Garnaat C, Guo L, Yan Y, Groat J, Silvanovich A, et al. The use of next generation sequencing and junction sequence analysis bioinformatics to achieve molecular characterization of crops improved through modern biotechnology. Plant Genome 2012;5:149-163.
  12. Wahler D, Schauser L, Bendiek J, Grohmann L. Next-generation sequencing as a tool for detailed molecular characterisation of genomic insertions and flanking regions in genetically modified plants: a pilot study using a rice event unauthorised in the EU. Food Anal Methods 2013;6:1718-1727. https://doi.org/10.1007/s12161-013-9673-x
  13. Chan MT, Chang HH, Ho SL, Tong WF, Yu SM. Agrobacterium- mediated production of transgenic rice plants expressing a chimeric alpha-amylase promoter/beta-glucuronidase gene. Plant Mol Biol 1993;22:491-506. https://doi.org/10.1007/BF00015978
  14. Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, et al. Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res 2012;40:D1178-D1186. https://doi.org/10.1093/nar/gkr944