Advantages of Using Energy Crops to Produce Biofuels
Recent technology advancements have made it possible to make biofuels from plants, called cellulosic biofuels, from inedible biomass—all of the stems, stalks, and leaves of plants. By applying advanced plant breeding and biotechnology methods to dedicated energy crops, Ceres can deliver sustainable energy solutions that displace vast amounts of fossil fuels, provide greater energy security, and create new economic opportunities for farmers and rural communities. According to Timothy Swaller, energy crops in the U.S. could meet 75% of the current gasoline demand. Energy crops are an ideal raw material as they are productive in areas marginal for food crop production. One of the energy crops that is used by Ceres is switchgrass (Panicum virgatum), which is a perennial crop and a native prairie grass in the United States.

Using Genomics to Study Energy Crops
Genetic improvement of energy crops like switchgrass as a dedicated bioenergy feedstock crop is necessary to reduce delivered feedstock cost. Ceres has set up a joint collaboration with the Noble Foundation in Oklahoma to produce a genetic map for switchgrass, as no reference map or significant molecular work had been done in this species. Mr. Swaller commented, “One of our main goals is to improve the composition and conversion process efficiencies of harvested biomass. Ceres’s energy crop breeding improvement program is based on knowledge of the genetics of the species and the use of molecular markers to follow the genes determining useful traits.”

Simplified Workflow Using the SNPlex Genotyping System
Mr. Swaller and his team made full length cDNA libraries from switchgrass, designed oligonucleotide sets for these cDNAs, performed PCR on a diverse set of switchgrass genotypes, and then looked for SNPs (single nucleotide polymorphisms). His research group used the SNPlex Genotyping System and TaqMan® assays to look at genetic diversity and trait associations. Mr. Swaller noted, “The SNPlex Genotyping System is cost-effective and easy-to-use. I don’t want to spend more money than necessary. We have Applied Biosystems 3730xl DNA Analyzers, liquid handling robots, and the GeneAmp® 9700 PCR System; and the SNPlex Genotyping System easily integrated into our existing infrastructure.” Mr. Swaller also added that moving from sequencing to genotyping was easy, and his laboratory utilized the 3730xl DNA Analyzers to their full capacity. They use TaqMan assays for low-throughput genotyping projects. But for large-scale genotyping, like running core SNP sets on thousands of samples, they use 4−5 SNPlex genotyping pools, and easily screen large populations quickly. Also, the SNPlex Genotyping System’s pool format is a very nice way of keeping inventory of their species-specific or trait-associated SNP marker sets. Mr. Swaller commented, “If we need to look at the germplasm for a certain trait, we just need to find the respective SNPlex pool. This really simplifies inventory.”