Assessing the Impact of Gene Replacement and Genetic Modification Methods in a Crop Species at the Whole Genome Level

Genome editing using sequence specific nucleases (SSNs) is rapidly becoming a mainstream approach to genetic engineering in both plants and animals. The development of transcription activator-like nucleases (TALENs) and clustered regularly interspaced short palindromic repeats (CRISPR) associated systems (Cas) has accelerated the progress of SSN technology and has provided the means to target virtually any genomic sequence.  However, the specificity and degree of off-targeting of these SSN platforms is not well understood and quantifiable data is needed. This project will provide foundational information on alterations in the whole genome, whole transcriptome, and agronomic phenotypes for a major crop species following tissue culture regeneration, Agrobacterium-mediated transformation, CRISPR/Cas-mediated gene modification, and TALEN-mediated gene modification. We will be able to make estimates of random vs. non-random effects on the genome, transcriptome, and phenotype attributable to these methods providing a robust dataset for regulatory assessments. With respect to biology, these data will be informative as to how manipulation of plant transformation and manipulation of genomes, either targeted or non-targeted, impact the genome, transcriptome and plant growth and development in comparison to induced mutation techniques.