Genome-wide association studies (GWAS) is one of the most popular methods of studying the genetic control of traits. This methodology has been intensely performed on inbred genotypes to identify causal variants. Nonetheless, the lack of covariance between the phenotype of inbred lines and their offspring in cross-pollinated species (such as maize) raises questions on the applicability of these findings in a hybrid breeding context. To address this topic, we incorporated previously reported parental lines GWAS information into the prediction of a low heritability trait in hybrids. This was done by marker-assisted selection based on significant markers identified in the lines and by genomic prediction having these markers as fixed effects. Additive-dominance GWAS of hybrids, a non-conventional procedure, was also performed for comparison purposes. Our results suggest that incorporating information from parental inbred lines GWAS led to decreases in the predictive ability of hybrids. Correspondingly, inbred lines and hybrids-based GWAS yielded different results. These findings do not invalidate GWAS on inbred lines for selection purposes, but mean that it may not be directly useful for hybrid breeding.