Driving superior hybrids by breeding programs needs assessment of various genetic resources for detecting promising parents. The present study aimed to assess the polymorphism impact of five parental Glycine max genotypes on the genetic structure of the F1 hybrid to detect compatible crosses with distinguishable superiority compared to parents regarding some yield traits. Protein, RAPD, and ISSR patterns revealed the de novo presence/absence of alleles and genetic similarities (GS) among parents and hybrids. Results mentioned polymorphism among parental genotypes with an average of 24.2%, 100%, and 73.8% for protein profile and RAPD and ISSR markers, respectively. Giza111 had moderate polymorphism, segregation, and GS, while Line30 and D89-8940 were highly polymorphic segregated genotypes. Giza111 were compatible parents for crossing with Line30 and D89-8940, giving rise to the superiority of hybrids regarding most tested yield traits. Line30 X Giza111 recorded the highest percentage of polymorphism with one marker band specific to the cross. Giza111 and Giza83 had the lowest polymorphism and were incompatible parents due to the too-narrow genetic distance that led to inbreeding depression for the tested yield traits. Toano was an incompatible parent, causing inbreeding depression, and needing molecular markers set for efficient characterization.
For hybrid superiority, the study suggested Giza111 as a good parent when crossed with Line30 or D89-8940, followed by Giza83 crossing with either Line30 regarding branch number, pod number, 100-seed/plant, and seeds/plant, or D89-8940 regarding the number of branches and 100-seed/plant.