Technical Abstract: Marker-trait association mapping techniques were first developed by computational biologists to analyze the genotypes of individual people in human populations and subsequently identify DNA markers associated with important traits, especially diseases. If populations of agronomically important crops like rice have the appropriate molecular diversity, it should be possible to apply these marker-trait association mapping techniques to plant germplasm collections and subsequently identify genes controlling agronomically important traits like pest resistance. In the reported study, the molecular diversity of rice germplasm accessions was evaluated for three different groups of accessions using 176 DNA markers spread out over all twelve rice chromosomes. The three groups were rice varieties from international sources, U.S. rice varieties released over the past 25 years, and rice wild relatives. Each accession was genotyped with DNA markers. Evaluation of the diversity in these DNA markers using statistical methods divided the accessions into three different clusters which represented the three original groups of rice accessions. Analysis of the relationships between all 176 DNA markers revealed the molecular variation within and between the three groups of accessions was more than adequate for marker-trait association mapping techniques to be used to ascertain possible novel genes for agronomically important traits like pest resistance. This study demonstrates that marker-trait association mapping techniques also can be used to detect novel traits in rice germplasm collections. As these novel genes are identified, DNA markers will be developed so that rice breeders can incorporate these desired genes into U.S. rice varieties.