Abstract:Sugarcane breeding is very difficult and it takes 12 to 14 years to develop a new cultivar for commercial production. This is because sugarcane varieties are highly polyploid, inter-specific hybrids with 100 to 130 chromosomes that may vary across geographical areas. Other obstacles/constraints include the small size of flowers that may not synchronize but may self-pollinate, difficulty in distinguishing hybrids from self progenies, extreme (GˆE) interactive effect, and potential variety mis-identification during vegetative propagation and varietal exchange. To help cane breeders circumvent these constraints, a simple sequence repeats (SSR)-based molecular identity database has been developed at the United States Department of Agriculture-Agricultural Research Service, Sugarcane Research Unit in Houma, LA. Since 2005, approximately 2000 molecular identities have been constructed for clones of sugarcane and related Saccharum species that cover geographical areas including Argentina, Australia, Bangladesh, China, Colombia, India, Mexico, Pakistan, South Africa, Thailand, USA (Louisiana, Florida, Texas, and Hawaii), and Venezuela. The molecular identity database is updated annually and has been utilized to: (1) provide molecular descriptors to newly registered cultivars; (2) identify in a timely fashion any mislabeled or unidentifiable clones from cross parents and field evaluation plots; (3) develop de novo clones of energy cane with S. spontaneum cytoplasm; (4) provide clone-specific fingerprint information for assessing cross quality and paternity of polycross; (5) determine genetic relatedness of parental clones; (6) select F 1 hybrids from (eliteˆwild) or (wildˆelite) crosses; and (7) investigate the inheritance of SSR markers in sugarcane. The integration of the molecular identity database into the sugarcane breeding program may improve the overall efficacy of cultivar development and commercialization.Keywords: sugarcane breeding; SSR; molecular identity database Generally speaking, there are probably nine key issues that affect both the productivity and the sustainability of sugarcane agriculture and integrated industry. These issues are land, fertility, water, variety, planting density, crop protection, cultural practices, harvesting and processing, and recently, computer information technology [1]. To all sugarcane farmers, it remains of top-most concern to grow the right cultivars. While it is the duty of conventional breeders to develop desirable sugarcane cultivars, biotechnologists can contribute greatly to the variety development process (crossing, selection, and evaluation) through the development and application of molecular breeding tools. Conventional sugarcane breeding is probably the most difficult job of any crop, due to the fact that sugarcane cultivars (Saccharum spp. hybrids) are highly polyploidy inter-specific hybrids containing 100 to 130 chromosomes [2,3]. The number of chromosomes may vary across geographical areas. Other obstacles/constraints include small flower size, the de...