A continuing supply of early emerging, high stalk population, disease and insect resistant varieties from breeding stations has been the major contributor to the management of yield-robbing pests. Major diseases of sugarcane include: (1) viruses: potyviruses that cause mosaic (Sugarcane mosaic virus and Sorghum mosaic virus) and sugarcane yellow leaf (Sugarcane yellow leaf virus); (2) bacteria: ratoon stunting disease (Leifsonia xyli subsp. xyli), leaf scald (Xanthomonas albilineans), and sugarcane brown rust (Puccinia melanocephala); and (3) fungi: sugarcane smut (Ustilago scitaminea). This complex of bacterial, fungal, and viral diseases are threats to energy cane as race changes are common. In most cane growing regions, sugarcane is grown as a monoculture. deVries et al. [1] concluded that of the various energy feedstocks being considered, the risk of yield loss associated with the buildup of soil-borne diseases in a continuous cropping system was the least with sugarcane, especially if a short fallow period or a legume is included between cane cycles.

The stem borers (Lepidoptera: Crambidae), including the sugarcane borer [(Diatraea saccharalis (Fabricius)] and the Mexican rice borer [Eoreuma loftini (Dyar)], represent the major insect threats to both sugarcane and energy cane. Economical control of both of these stalk borers in sugarcane is currently obtained by an integrated pest manage­ment program (IPM) that utilizes varietal resistance, manipulation of cultural practices, biological control through natural predators, and the judicious use of insecticides includ­ing Lepidoptera-specific insecticides. Insecticides are applied only when pressures exceed established economic thresholds, and these are determined by using frequent scouting during the grand growth period [38]. The impact of these borers is primarily on sugar pro­duction; hence, their impact on energy cane has not been thoroughly researched. However, it is likely that pest management in energy cane will mirror IPM as practiced in sugar­cane. Borer preference appears to be more towards the low-fiber, high-sugar varieties and less towards the high-fiber, low-sugar varieties of sugarcane, which may be an advantage for energy cane [39]. Energy cane is expected to be grown to a large extent on low-rent, marginal, or underutilized land and in many cases adjacent to traditional food, feed, and fiber crops, where other types of disease and insect pressures may be encountered. Energy cane may harbor diseases and insect pests that may be injurious to the food crops as well; however, these canes may also serve as important overwintering sites for beneficial insects, thereby enhancing the role of biological control.

Broad spectrum pre-emergence and post-emergence herbicides are labeled for use in sugarcane, and presumably this labeling will allow their use in the non-food use energy cane as well [40]. The non-food use designation may also allow the use of herbicides not currently labeled for use in sugarcane. Perennial weeds, such as johnsongrass (Sorghum halepense),

Bermuda grass (Cynodon dactylon), and nutsedge (Cyperus spp.) and a multitude of annual species, but most importantly itchgrass [Rottboellia cochinchinensis) and morning glory (Ipomoea spp.), are particularly problematic, as cultivation is limited to only in the early spring and to the inter-row space for a period of five or more years [41]. The most critical applications of herbicide are at planting and at the start of each growing season of the crop cycle when the crop is in its infancy period [42]. Energy cane appears to be more competitive with weeds than sugarcane because it emerges faster and produces more shoots. Because of the wide row spacing to accommodate mechanical culture and harvesting, an application of herbicide at the start of each growing season is recommended for sugarcane. As energy cane may be more aggressive, applications of herbicide may not be needed after the first ratoon production year.