Corn germplasm with different mesocotyl elongation was characterized for High Valleys in Mexico by estimating the general combinatory aptitude (GCA), specific combinatory aptitude (SCA), heterosis (H), inbreeding depression (ID) and principal component aptitude (PCA), with the purpose of directing the improvement for deep sowing. The hypothesis was that the parents and crosses of mesocotyl present variability in seedling and adult plant traits based on deep sowing. The 36 F1 and F2 crosses—derived from nine parents, three with short mesocotyl (S), three medium (M) and three long (L), obtained through Griffing diallel II—plus the parents were planted in sand beds and polyethylene bags in a greenhouse during the spring–summer cycles of 2021 and 2022. The following traits were measured: length of mesocotyl (LM), length of coleoptile, total seedling dry matter and 10 cob traits in addition to total dry matter. In 11 of the 14 traits, there was a positive and significant correlation (p ≤ 0.05) between the GCA of the parents and their LM. The highest SCA, H and ID (p ≤ 0.05) were for crosses L × L for all the traits measured. When comparing the GCA/SCA proportions, this relation varied from 0.76 to 0.97, which points to practically equal additive effects with those of dominance; however, in parents and L × L crosses, this relation was on average 0.94, 1.07 in M × M, 0.22 in S × S and 0.36 in L × S. In both F1 and F2, the variation was explained by two principal components: 89.5% for GCA and 73.4% for SCA. In both generations, the parents with higher GCA were H-48, HS-2 and Promesa, the three with long mesocotyl, while those with the highest GCA were crosses between these three hybrids.