The present invention includes methods for using favorable functional allele variants to optimize transgene effects and achieve the maximum potential of transgene efficacy. The present invention provides heterozygous allelic combinations of the transgene by stacking alleles from different heterotic pools, methods to increase crop yield by driving genes (maize or other species) by using heterozygous promoter allele combinations that consist of differentially regulatory allelic elements from heterotic pools, methods to increase crop yield utilizing transgenic complementary paired alleles controlling plant growth and yield. Plants, plant progeny, seeds and tissues created by these methods are also described. Polynucleotides encoding the alleles are provided for expression in a plant of interest. Expression cassettes, plants, plant cells, plant parts and seeds comprising the sequences of the invention are further provided. In specific embodiments, the polynucleotide is operably linked to a native promoter and a transcriptional enhancer.