With the continual development of genetically modified (GM) crops, it has become necessary to develop detailed and effective molecular characterization methods to select candidate events from a large pool of transformation events. Relative to traditional molecular analysis methods such as the polymerase chain reaction (PCR) and Southern blot hybridization, next generation sequencing (NGS) technology for whole-genome sequencing of complex crop genomes had proven comparatively useful for in-depth molecular characterization. In this study, four transformation events, including one in Bacillus thuringiensis (Bt)-resistant rice, one in resveratrol-producing rice, and two in beta-carotene-enhanced soybeans, were selected for molecular characterization. To merge NGS analysis and Southern blot-hybridization results, we confirmed the transgene insertion sites, insertion construction, and insertion numbers of these four transformation events. In addition, the read-coverage depth assessed by NGS analysis for inserted genes might provide consistent results in terms of inserted T-DNA numbers in case of complex insertion structures and highly duplicated donor genomes; however, PCR-based methods can produce incorrect conclusions. Our combined method provides an effective and complete analytical approach for whole-genome visual inspection of transformation events that require biosafety assessment.

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• Molecular Characterization of CRISPR-Cas9-Edited Rice Across Generations and Associated Technical Challenges in Nucleotide Editing Tracing
  Yang Qin, Sang Dae Yun, Hye Lin Kim, Je Yeon Choi, Myung-Ho Lim, Sung Aeong Oh, Soon Ki Park
  Plant Breeding and Biotechnology.2025;[Epub]     CrossRef
• Combining Nanopore and Illumina Sequencing Permits Detailed Analysis of Insertion Mutations and Structural Variations Produced by PEG-Mediated Transformation in Ostreococcus tauri
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• Comparative transcriptome profiling of different tissues from beta-carotene-enhanced transgenic soybean and its non-transgenic counterpart
  Yang Qin, Hee-Jong Woo, Kong-Sik Shin, Myung-Ho Lim, Seong-Kon Lee
  Plant Cell, Tissue and Organ Culture (PCTOC).2020; 140(2): 341.     CrossRef

Beta-carotene, a defense chemical, is synthesized by the carotenoid biosynthesis pathway. In the present study, a transgenic soybean line, with a single copy insertion of phytoene synthase and carotene desaturase genes, having high beta-carotene content was studied for its response to systemically inoculated Soybean mosaic virus (SMV). Beta-carotene-enhanced transgenic soybean showed similar leaf and seed symptoms, viral RNA, and protein expression compared to the non-genetically modified (GM) ‘Kwangan’ control. Total antioxidant contents in the non-GM ‘Kwangan’ line were increased after SMV attack in both leaves and seeds; however, the antioxidant contents in the beta-carotene-enhanced soybean line have no significant changes. In addition, both GM and non-GM soybean were detected increased lipid hydroperoxide concentrations in leaves and seeds after SMV infection, even though they did not reach a statistical significant level. Abscisic acid (ABA) levels in beta-carotene-enhanced transgenic soybean seeds was determined 35-fold increase after SMV infections caused a lower seed germination rate and a higher SMV transmission rate to subsequent generations, compared to those of non-GM ‘Kwangan’. Thus, we concluded that the additional production of beta-carotene did not confer resistance of beta-carotene-enhanced transgenic soybean to SMV infections, but caused mass accumulations of ABA in seeds.

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• Comparison of the Nutritional Compositions of hybrid Soybean between β–carotene Enhanced Transgenic Soybean and wild Soybean
  Sung-Dug Oh, Ye-Jin Jang, Gyeong Min Lee, Kijong Lee, Sang Jae Suh, Tae-Hoon Ryu, Soo-Yun Park
  Journal of the Korean Society of International Agricultue.2020; 32(4): 339.     CrossRef
• Comparative transcriptome profiling of different tissues from beta-carotene-enhanced transgenic soybean and its non-transgenic counterpart
  Yang Qin, Hee-Jong Woo, Kong-Sik Shin, Myung-Ho Lim, Seong-Kon Lee
  Plant Cell, Tissue and Organ Culture (PCTOC).2020; 140(2): 341.     CrossRef
• Nutritional composition analysis for beta-carotene-enhanced transgenic soybeans (Glycine max L.)
  Yang Qin, Soo-Yun Park, Seon-Woo Oh, Myung-Ho Lim, Kong-Sik Shin, Hyun-Suk Cho, Seong-Kon Lee, Hee-Jong Woo
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