title: Genome-wide profiling of genetic variation in Agrobacterium-transformed rice plants.
abstract: Agrobacterium-mediated transformation has been widely used in producing transgenic plants, and was recently used to generate "transgene-clean" targeted genomic modifications coupled with the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas9) system. Although tremendous variation in morphological and agronomic traits, such as plant height, seed fertility, and grain size, was observed in transgenic plants, the underlying mechanisms are not yet well understood, and the types and frequency of genetic variation in transformed plants have not been fully disclosed. To reveal the genome-wide variation in transformed plants, we sequenced the genomes of five independent T0rice plants using next-generation sequencing (NGS) techniques. Bioinformatics analyses followed by experimental validation revealed the following: (1) in addition to transfer-DNA (T-DNA) insertions, three transformed plants carried heritable plasmid backbone DNA of variable sizes (855-5216 bp) and in different configurations with the T-DNA insertions (linked or apart); (2) each transgenic plant contained an estimated 338-1774 independent genetic variations (single nucleotide variations (SNVs) or small insertion/deletions); and (3) 2-6 new Tos17 insertions were detected in each transformed plant, but no other transposable elements or bacterial genomic DNA.
authors.affiliation: State Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou 310058, China.|Institute for Wheat Research, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China.
authors.forename: Wen-Xu
authors.initials: WX
authors.lastname: Li
authors.affiliation: Analysis Center of Agrobiology and Environmental Sciences, Faculty of Agriculture, Life and Environment Sciences, Zhejiang University, Hangzhou 310058, China.
authors.forename: San-Ling
authors.initials: SL
authors.lastname: Wu
authors.affiliation: State Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou 310058, China.
authors.forename: Yan-Hua
authors.initials: YH
authors.lastname: Liu
authors.affiliation: Hangzhou Guhe Information and Technology Co., Ltd., Hangzhou 310058, China.
authors.forename: Gu-Lei
authors.initials: GL
authors.lastname: Jin
authors.affiliation: State Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou 310058, China.
authors.forename: Hai-Jun
authors.initials: HJ
authors.lastname: Zhao
authors.affiliation: IBM Biocomputational Laboratory, Institute of Crop Sciences, Zhejiang University, Hangzhou 310058, China.
authors.forename: Long-Jiang
authors.initials: LJ
authors.lastname: Fan
authors.affiliation: State Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou 310058, China.
authors.forename: Qing-Yao
authors.initials: QY
authors.lastname: Shu
mesh_terms: D060054:Agrobacterium / Q000235:genetics*; D019295:Computational Biology; D004251:DNA Transposable Elements; D014644:Genetic Variation; D059014:High-Throughput Nucleotide Sequencing; D012275:Oryza / Q000235:genetics*; D030821:Plants, Genetically Modified; D014169:Transformation, Bacterial
chemical_list: D004251:DNA Transposable Elements
keywords: Genetic variation; Genome-wide; Rice; Transfer-DNA; Transposon