The delivery of improved rice varieties with C4-like yield advantages will require a precise modeling of the genome. Interestingly, the novelty of C4 photosynthesis appears to have evolved from a key reservoir of genes present also in C3 plants through gene duplication and neofunctionalization. Both specific patterns of gene expression and kinetic properties of the enzymes together with anatomical changes are observed in C4 plants. Improved photosynthesis in rice can probably be achieved by engineering alleles involved in biochemical pathways and plant development. Key limiting steps in C3 photosynthesis have also been envisaged as a possible strategy to lead to yield increases. From these results, I believe that a dual approach based on directed evolution and allele engineering could boost the yield potential of rice. Here, we discuss briefly some possible options from allele engineering to phenotype.