title: Efficiency to Discovery Transgenic Loci in GM Rice Using Next Generation Sequencing Whole Genome Re-sequencing.
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 (~72× coverage) was sequenced with a 2 × 150 bp 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.
authors.affiliation: Institute of Green Bio Science and Technology, Seoul National University, Pyeongchang 25354, Korea.
authors.forename: Doori
authors.initials: D
authors.lastname: Park
authors.affiliation: National Instrumentation Center for Environmental Management, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.
authors.forename: Dongin
authors.initials: D
authors.lastname: Kim
authors.affiliation: National Instrumentation Center for Environmental Management, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.
authors.forename: Green
authors.initials: G
authors.lastname: Jang
authors.affiliation: National Instrumentation Center for Environmental Management, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.
authors.forename: Jongsung
authors.initials: J
authors.lastname: Lim
authors.affiliation: Natural Bio-Materials Inc., Wanju 55322, Korea.
authors.forename: Yun-Ji
authors.initials: YJ
authors.lastname: Shin
authors.affiliation: Natural Bio-Materials Inc., Wanju 55322, Korea.
authors.forename: Jina
authors.initials: J
authors.lastname: Kim
authors.affiliation: Natural Bio-Materials Inc., Wanju 55322, Korea.
authors.forename: Mi-Seong
authors.initials: MS
authors.lastname: Seo
authors.affiliation: Crop Biotech Institute, Green-Bio Science and Technology, Seoul National University, Pyeongchang 25354, Korea.
authors.forename: Su-Hyun
authors.initials: SH
authors.lastname: Park
authors.affiliation: Crop Biotech Institute, Green-Bio Science and Technology, Seoul National University, Pyeongchang 25354, Korea.
authors.forename: Ju-Kon
authors.initials: JK
authors.lastname: Kim
authors.affiliation: Natural Bio-Materials Inc., Wanju 55322, Korea.
authors.forename: Tae-Ho
authors.initials: TH
authors.lastname: Kwon
authors.affiliation: Natural Bio-Materials Inc., Wanju 55322, Korea.
authors.forename: Ik-Young
authors.initials: IY
authors.lastname: Choi
keywords: genetically modified organisms; next generation sequencing (NGS) T-DNA; rice; risk assessment