Genetically modified soybean lines exhibit less transcriptomic variation compared to natural varieties

References

• Raman R. The impact of Genetically Modified (GM) crops in modern agriculture: A review. GM Crops & Food. 2017;8(4):195–208. doi:10.1080/21645698.2017.1413522.
   PubMed Web of Science ®Google Scholar
• ISAA. Biotech crops continue to help meet the challenges of increased population and climate change. 2018.
   Google Scholar
• Klumper W, Qaim M, Albertini E. A meta-analysis of the impacts of genetically modified crops. Plos One. 2014;9(11):e111629. doi:10.1371/journal.pone.0111629.
   PubMed Web of Science ®Google Scholar
• Kok EJ, Pedersen J, Onori R, Sowa S, Schauzu M, De Schrijver A, Teeri TH. Plants with stacked genetically modified events: to assess or not to assess?. Trends Biotechnol. 2014;32(2):70–73. doi:10.1016/j.tibtech.2013.12.001.
   PubMed Web of Science ®Google Scholar
• Kovalic D, Garnaat C, Guo L, Yan YP, Groat J, Silvanovich A, Ralston L, Huang MY, Tian Q, Christian 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-Us. 2012;5(3):149–63. doi:10.3835/plantgenome2012.10.0026.
   Web of Science ®Google Scholar
• 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(1):2839. doi:10.1038/srep02839.
   PubMedGoogle Scholar
• Chu Y, Corey DR. RNA sequencing: platform selection, experimental design, and data interpretation. Nucleic acid therapeutics. Nucleic Acid Ther. 2012;22(4):271–74. doi:10.1089/nat.2012.0367.
   PubMed Web of Science ®Google Scholar
• Balsamo GM, Valentim-Neto PA, Mello CS, Arisi AC. Comparative Proteomic Analysis of Two Varieties of Genetically Modified (GM) Embrapa 5.1 Common Bean (Phaseolus vulgaris L.) and Their Non-GM Counterparts. J Agric Food Chem. 2015;63(48):10569–77. doi:10.1021/acs.jafc.5b04659.
   PubMed Web of Science ®Google Scholar
• Oms-Oliu G, Odriozola-Serrano I, Martin-Belloso O. Metabolomics for assessing safety and quality of plant-derived food. Food Res Int. 2013;54(1):1172–83. doi:10.1016/j.foodres.2013.04.005.
   Web of Science ®Google Scholar
• Vilperte V, Agapito-Tenfen SZ, Wikmark OG, Nodari RO. Levels of DNA methylation and transcript accumulation in leaves of transgenic maize varieties. Environ Sci Eur. 2016;28(1):28. doi:10.1186/s12302-016-0097-2.
   PubMedGoogle Scholar
• Haynes E, Jimenez E, Pardo MA, Helyar SJ. The future of NGS (Next Generation Sequencing) analysis in testing food authenticity. Food Control. 2019;101:134–43. doi:10.1016/j.foodcont.2019.02.010.
   Web of Science ®Google Scholar
• Wei W, Liang DW, Bian XH, Shen M, Xiao JH, Zhang WK, Ma B, Lin Q, Lv J, Chen X, et al. GmWRKY54 improves drought tolerance through activating genes in abscisic acid and Ca(2+) signaling pathways in transgenic soybean. Plant J. 2019;100(2):384–98. doi:10.1111/tpj.14449.
   PubMed Web of Science ®Google Scholar
• Wang D, Liu YX, Yu Q, Zhao SP, Zhao JY, Ru JN, Cao XY, Fang ZW, Chen J, Zhou Y-B. Functional Analysis of the Soybean GmCDPK3 Gene Responding to Drought and Salt Stresses. Int J Mol Sci. 2019;20(23):5909. doi:10.3390/ijms20235909.
   PubMed Web of Science ®Google Scholar
• Cheng H, Jin HX, Gai JY, Yu DY. Transgenic technology and soybean quality improvement. Yi chuan = Hereditas. 2011;33(5):431–36. doi:10.3724/SP.J.1005.2011.00431.
   PubMedGoogle Scholar
• Lin J, Mazarei M, Zhao N, Hatcher CN, Wuddineh WA, Rudis M, Tschaplinski TJ, Pantalone VR, Arelli PR, Hewezi T, et al. Transgenic soybean overexpressing GmSAMT1 exhibits resistance to multiple-HG types of soybean cyst nematode Heterodera glycines. Plant Biotechnol J. 2016;14(11):2100–09. doi:10.1111/pbi.12566.
   PubMed Web of Science ®Google Scholar
• Yang X, Niu L, Zhang W, He H, Yang J, Xing G, Guo D, Zhao Q, Zhong X, Li H, et al. Increased multiple virus resistance in transgenic soybean overexpressing the double-strand RNA-specific ribonuclease gene PAC1. Transgenic Res. 2019;28(1):129–40. doi:10.1007/s11248-018-0108-8.
   PubMed Web of Science ®Google Scholar
• Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinform. 2011;12(1):12. doi:10.1186/1471-2105-12-323.
   PubMedGoogle Scholar
• Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010;28(5):511–15. doi:10.1038/nbt.1621.
   PubMed Web of Science ®Google Scholar
• Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol. 2010;11(10):R106. doi:10.1186/gb-2010-11-10-r106.
   PubMed Web of Science ®Google Scholar
• Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics. 2005;21(18):3674–76. doi:10.1093/bioinformatics/bti610.
   PubMed Web of Science ®Google Scholar
• Ye J, Fang L, Zheng H, Zhang Y, Chen J, Zhang Z, Wang J, Li S, Li R, Bolund L, et al. WEGO: a web tool for plotting GO annotations. Nucleic Acids Res. 2006;34(Web Server issue):W293–W97. doi:10.1093/nar/gkl031.
   PubMed Web of Science ®Google Scholar
• Liu WX, Xu WT, Li L, Dong M, Wan YS, He XY, Huang KL, Jin WJ. iTRAQ-based quantitative tissue proteomic analysis of differentially expressed proteins (DEPs) in non-transgenic and transgenic soybean seeds. Sci Rep. 2018;8(1):8. doi:10.1038/s41598-018-35996-y.
   PubMedGoogle Scholar
• Liu Q, Yang X, Tzin V, Peng Y, Romeis J, Li Y. Plant breeding involving genetic engineering does not result in unacceptable unintended effects in rice relative to conventional cross-breeding. Plant J. 2020;103(6):2236–49. doi:10.1111/tpj.14895.
   PubMed Web of Science ®Google Scholar
• Fu W, Wang C, Xu W, Zhu P, Lu Y, Wei S, Wu X, Wu Y, Zhao Y, Zhu S. Unintended effects of transgenic rice revealed by transcriptome and metabolism. GM Crops & Food. 2019;10(1):20–34. doi:10.1080/21645698.2019.1598215.
   PubMed Web of Science ®Google Scholar
• Ioset JR, Urbaniak B, Ndjoko-Ioset K, Wirth J, Martin F, Gruissem W, Hostettmann K, Sautter C. Flavonoid profiling among wild type and related GM wheat varieties. Plant Mol Biol. 2007;65(5):645–54. doi:10.1007/s11103-007-9229-9.
   PubMed Web of Science ®Google Scholar
• Kogel KH, Voll LM, Schafer P, Jansen C, Wu YC, Langen G, Imani J, Hofmann J, Schmiedl A, Sonnewald S, et al. Transcriptome and metabolome profiling of field-grown transgenic barley lack induced differences but show cultivar-specific variances. Proc Natl Acad Sci USA. 2010;107(14):6198–203. doi:10.1073/pnas.1001945107.
   PubMed Web of Science ®Google Scholar
• Valentim-Neto PA, Rossi GB, Anacleto KB, de Mello CS, Balsamo GM, Arisi ACM. Leaf proteome comparison of two GM common bean varieties and their non-GM counterparts by principal component analysis. J Sci Food Agr. 2016;96(3):927–32. doi:10.1002/jsfa.7166.
   PubMed Web of Science ®Google Scholar