Genomics Inform.  2015 Sep;13(3):81-85. 10.5808/GI.2015.13.3.81.

Efficiency to Discovery Transgenic Loci in GM Rice Using Next Generation Sequencing Whole Genome Re-sequencing

• Park D
• Kim D
• Jang G
• Lim J
• Shin YJ
• Kim J
• Seo MS
• Park SH
• Kim JK
• Kwon TH
• Choi IY

• KMID: 2166519
• DOI: http://doi.org/10.5808/GI.2015.13.3.81

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 (~72x coverage) was sequenced with a 2 x 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.

Keyword

genetically modified organisms; next generation sequencing (NGS) T-DNA; rice; risk assessment

MeSH Terms

Biotechnology
Chromosomes, Human, Pair 4
Computational Biology
Epidermal Growth Factor
Genome*
Organisms, Genetically Modified
Polymerase Chain Reaction
Risk Assessment
Epidermal Growth Factor