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Organization of maize (Zea mays L.) germplasm into genetically divergent heterotic groups is the foundation of a successful hybrid maize breeding program.In this study,94 CIMMYT maize lines (CMLs) and 54 United States Germplasm Enhancement of Maize (GEM) lines were assembled and characterized using 1,266 SNPs with high quality.Based on principal component analysis (PCA),GEM lines and CMLs were clearly separated.In GEM lines,there were two groups classified by PCA corresponding to the heterotic group "stiffstalk" (SS) and "non-stiff stalk" (NSS).CMLs did not form obvious subgroups by PCA.Allelic frequency of each SNP differed in GEM lines and CMLs.In total,3.6% alleles (46/1,266) of CMLs are absent in GEM lines and 4.4% alleles (56/1,266) of GEM lines are absent in CMLs.The performance of F1 (n=654) produced by crossing between different groups based on pedigree information was evaluated at the breeding nurseries of two CIMMYT stations.Genomic estimated phenotypic values of plant height (PH) and days to anthesis (DA) for a testing set of 45 F1 crosses were predicted based on the training data of 600 F1 crosses using mixed effects models and best linear unbiased prediction (BLUP).Prediction accuracy benefitted from the adoption of the markers associated with QTLs for both traits.However,it does not necessarily increase with an increase of marker density.High correlations between actual and predicted F1 phenotypic values indicated the possibility of choosing parental combinations for desired phenotypic traits by using SNP markers.It is suggested that genomie selection combined with association analysis could improve prediction efficiency and reduce cost.For hybrid maize breeding in tropics,incorporating GEM lines which have unique alleles and clear heterotic patterns,into tropically adapted lines could be beneficial for enhancing heterosis in grain yields.