Previous association analyses showed that variation at major regulatory genes contributes to standing variation for complex traits in Balsas teosinte, the progenitor of maize. This study expands our previous association mapping effort in teosinte by testing 123 markers in 52 candidate genes for association with 31 traits in a population of 817 individuals. Thirty-three significant associations for markers from 15 candidate genes and 10 traits survive correction for multiple testing. Our analyses suggest several new putative causative relationships between specific genes and trait variation in teosinte. For example, two ramosa genes (ra1 and ra2) associate with ear structure, and the MADS-box gene, zagl1, associates with ear shattering. Since zagl1 was previously shown to be a target of selection during maize domestication, we suggest that this gene was under selection for its effect on the loss of ear shattering, a key domestication trait. All observed effects were relatively small in terms of the percentage of phenotypic variation explained (,10%). We also detected several epistatic interactions between markers in the same gene that associate with the same trait. Candidategene-based association mapping appears to be a promising method for investigating the inheritance of complex traits in teosinte.T HROUGH the characterization of major loss-offunction mutants, geneticists have determined the function of a vast number of genes. Despite a general knowledge of how these genes control developmental and physiological processes, very little is known about how (or if) they contribute to natural variation for complex traits. Association mapping with its high mapping resolution, its potential to sample multiple alleles, and its use of preexisting populations provides a powerful tool to investigate the role of these genes in the genetic architecture of complex traits ( Previously, we detected significant associations between polymorphisms in nine candidate genes and phenotypic variation in the maize ancestor, Balsas teosinte (Zea mays ssp. parviglumis) (Weber et al. 2007). Our study builds upon our prior analyses in several ways, including an increase in the numbers of individuals, candidate genes, and traits. We also selected our association mapping panel to decrease the amount of population structure as compared to our prior study. With this strategy, we detected 33 associations between complex traits in teosinte and our candidate genes that survive a correction for multiple testing. These include associations between indeterminate spikelet1 and inflorescence branching, ramosa1 and ramosa2 and ear structure, sugary1 and seed oil content, and terminal ear1 and ear length. We also observed an association between zea agamous-like1 (zagl1) and ear shattering. Since zagl1 was a target of selection during domestication, we propose that it was selected for its role in ear disarticulation. Several epistatic 1