CTREP-finder:A web service for quick identification and visualization of clean transgenic and genome-edited plants  

作　　者：San-Ling Wu Yuan-Yuan Tan Yang Zhao Long-Jiang Fan Qi-Kang Gao Angharad M.R.Gatehouse Qing-Yao Shu 

机构地区：[1]State Key Laboratory of Rice Biology,Zhejiang Provincial Key Laboratory of Crop Genetic Resources,Institute of Crop Science,College of Agriculture and Biotechnology,Zhejiang University,Hangzhou,310058,China [2]Shandong(Linyi)Institute of Modern Agriculture,Zhejiang University,Linyi,276023,China [3]The Rural Development Academy,Zhejiang University,Hangzhou,310058,China [4]State Key Laboratory of Plant Physiology and Biochemistry,College of Life Sciences,Zhejiang University,Hangzhou,310058,China [5]Institute of Crop Science&Institute of Bioinformatics,College of Agriculture and Biotechnology,Zhejiang University,Hangzhou,310058,China [6]Analysis Center of Agrobiology and Environmental Sciences,Faculty of Agriculture,Life and Environment Sciences,Zhejiang University,Hangzhou,310058,China [7]School of Natural and Environmental Sciences,Newcastle University,Newcastle Upon Tyne,NE17RU,UK A R

出　　处：《Crop Design》2022年第1期1-9,共9页作物设计（英文）

基　　金：supported by the Zhejiang Provincial S&T Project on Crop Breeding 3.0(No.2020C02002),China.

摘　　要：To feed 10 billion people in 30 years from now will heavily depend on new higher yield,yet safe,biotech crop varieties,which are developed using biotechnologies,particularly genetic transformation and genome editing.A clean transgenic plant(CTP)contains only the defined transgene,whilst a clean edited plant(CEP)is transgene-free.Currently,it is difficult and time-consuming to identify and locate transgenes within plant genomes due to the complex nature of transfer DNA(T-DNA)or plasmid backbone integration,which has led to a major obstacle in mass scale production of clean transgenic/edited plants(CTREPs).Here we have built a web-based portal,CTREP-finder,for fast detection,characterization and visualization of foreign DNA fragments in plants,based on next-generation whole genome sequencing data.We invented a novel bioinformatics strategy to handle three scenarios of transgene integration and successfully identified CTREPs by testing 132 samples.Furthermore,we compared the CTREP-finder with three public programs,FED,transgeneR and TDNAscan,and it showed that the CTREP-finder outperforms those programs particularly on the localization of transgene integration.The use of CTREP-finder needs little requirement for bioinformatics expertise.Therefore,it is a user-friendly web-based portal that could be used by plant breeders and regulatory agencies for the rapid selection/detection of CTREPs for crop breeding and production.

关 键 词：CTREP-finder Transgene integration BACKBONE Transgene localization BIOINFORMATICS 

分 类 号：F42[经济管理—产业经济]