A widely used and accepted method of functional genomics is to disrupt the genes through mutations and study the effects in the following generations. There are several methods employed for this, e. g., the insertional mutagenesis such as T-DNA insertions in model plants such as Arabidopsis [38] and rice [39]. Also, transposon tagging is another method of choice for functional genomics in the model plants. The transposons or jumping genes were identified and isolated by Barbara McClintock from maize and it was cloned by [40]. The Ac/Ds system based on the transposons is being used as a tool for functional genomics in several plant systems [41,42]. Using these methods one can generate and study a pool of insertion mutants in the biofuel crops and look for desirable phenotypes and genes associated with them. Such experiments will increase our understating of the genetics of biofuel crops and will open the doors for genetic modifications of such crops to enhance biomass and biofuel production. However, generating large number of mutants is not feasible in all cases, and to address that there are several alternate tools. For example, if the crop has synteny with model crops such as rice that can be tested in the biofuel species. Thus, an aluminum tolerance (Alt3) locus was mapped in rye using rice/rye synteny [43]. Another valuable reverse genetics technique called ‘Targeting Induced Local Lesions IN Genomes’ (TILLING), involves high throughput PCR screens of genomic DNA from M2 mutant populations induced by chemical mutagens [44, 45].

Genomic and functional genomics projects are being applied to one of the model grass species, Brachypodium, and its whole genome sequence has been released [46] similar to what has been achieved with the rice genome project. Also, functional genomics tools are being employed to the biomass crops such as switchgrass, Miscanthus and sorghum. These studies include genome-wide analysis of miRNA targets, developing low input switchgrass biomass using its bacterial endophytes and studying root physiology using root hair response to abiotic stresses. To study the gene functions there are other functional genomics approaches such as microarray studies which are useful to understand the global changes in gene expression. All these approaches will yield valuable information on the genetic nature of the biofuel crops, which have been ignored for a long time primarily due to the lack of investment in this area of research. Using these powerful genetic tools, one can generate and study a pool of insertion mutants in the biofuel crops and look for desirable phenotypes and genes associated with it. A better understating of genetic nature of biofuel crops will open the doors for genetic modifications to enhance biomass and biofuel production.