The objective of this study was to select soybean genotypes derived from crosses between conventional and transgenic lines Roundup Ready (RR), using jointly Restricted Maximum Likelihood/Best Linear Unbiased Prediction (REML/BLUP) approaches, factors analysis and principal components analysis, processed with favorable agronomic traits, during the 2013/2014 growing season. Three agronomic selection processes were identified to select genotypes that discriminate genotypes containing more specific properties. Process 1 (insertion height of first pod, HFP; number of branches, NB; number of pods, NP; number of nodes, NN; and grain yield, GY) was efficient to select earlier, smaller genotypes with good yield/production components and lodging resistance. The junction between mixed model via REML/BLUP and the applied multivariate statistic using factor analysis helped to select suitable genotypes with high performance to carry on the soybean plant-breeding program.