Setaria viridis isolate:ME034 Raw sequence reads. Setaria viridis isolate:ME034

Genetic modification of model organisms has become routine practice in many academic and commercial laboratories. In plant species, introduction of new genes using A. tumefaciens harboring transfer DNA vectors represents a highly efficient approach for generating many new transgenic lines in parallel, with standard practice generating ten or more independent transgenic plants for downstream phenotypic characterization. Here, we describe a method for locating transgene insertion sites in the model plant Setaria viridis. This approach can be completed in as few as three days, with minimal hands-on time. We describe a software package for routine identification of transgene insertion sites called Transgene Insertion Finder (TgIF; https://github.com/jhuapl-bio/TgIF). Using this approach, we validate identified transgene insertion locations using a simple PCR assay that is suitable for screening purposes, including plants that contain only a single copy of a plant transgene. This approach increases traceability of genetically modified plant lines, and has potential to accelerate plant breeding timelines through definitive characterization of wild type, heterozygous, and homozygous transgenic plant offspring.