Reducing global carbon emission to limit climate change requires that we develop alternative source of renewable carbon to replace fossil carbon. Many tropical plants have the required growth rates and can be considered as options for use in generating the biomass required for this use. Efficient conversion of the biomass to end products requires that the biomass have a composition that facilitates processing. The engineering of plant biomass for this purpose may be accelerated by the development of high throughput systems for plant genome manipulation. This requires the availability of high-quality genomes sequences to allow targeting of genetic changes. Mutagenesis and gene editing are both options for use in creating the required genetic variation. Rice is being used as model to test the phenotype of altered plants. Sorghum and sugarcane are key potential species for agricultural use as fossil carbon replacements. Extensive analysis of the sugarcane transcriptome with both short and long read sequencing technology has been used to define targets for manipulation. Progress with these systems will be described.