©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 7 (4): 1384-1391 (2008) Optimizing reproducibility evaluation for random amplifed polymorphic DNA markers J.R. Ramos 1 , M.P.C. Telles 1,2 , J.A.F. Diniz-Filho 3 , T.N. Soares 2,4 , D.B. Melo 2,4 and G. Oliveira 3 1 Mestrado em Genética, Universidade Católica de Goiás, Goiânia, GO, Brasil 2 Departamento de Biologia Geral, Laboratório de Genética and Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, Brasil 3 Departamento de Biologia Geral, Laboratório de Ecologia Teórica e Síntese, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, Brasil 4 Programa de Pós-graduação em Agronomia, Universidade Federal de Goiás, Goiânia, GO, Brasil Corresponding author: M.P.C. Telles E-mail: tellesmpc@gmail.com Genet. Mol. Res. 7 (4): 1384-1391 (2008) Received September 15, 2008 Accepted October 13, 2008 Published December 4, 2008 ABSTRACT. The random amplified polymorphic DNA (RAPD) technique is often criticized because it usually shows low levels of repeatability; thus it can generate spurious bands. These problems can be partially overcome by rigid laboratory protocols and by per- forming repeatability tests. However, because it is expensive and time-consuming to obtain genetic data twice for all individuals, a few randomly chosen individuals are usually selected for a priori repeatability analysis, introducing a potential bias in genetic param- eter estimates. We developed a procedure to optimize repeatability analysis based on RAPD data, which was applied to evaluate ge- netic variability in three local populations of Tibochina papyrus, an endemic Cerrado plant found in elevated rocky fields in Brazil. We used a simulated annealing procedure to select the smallest number of individuals that contain all bands and repeated the analyses only