All food crop varieties, regardless of species, must meet certain quality standards related to their role in food production. Humans have achieved these quality standards through millennia via the processes of domestication and breeding for improvement. Because use of plants for fuel is relatively recent, energy crops lack similar quality standards. There is a desire to create energy crops that will provide high biomass and high fuel yields while growing with few inputs on marginal land. To achieve these goals in a timely manner, it is necessary to identify the loci that underlie desirable traits in biofuel crops. Only through identification of these loci will we be able to use modern breeding technologies, such as marker-assisted selection, to rapidly improve biofuel feedstocks.