The goal of breeding by design can be reached by following a three-step approach (Peleman and Van der Voort, 2003): “ 1) mapping loci involved in all agronomic relevant traits, 2) assessment of the allelic variation at those loci, and 3) breeding by design.” Recent advances in sequenced rice genome information have made it possible to utilize phenotypic mutants to characterize relevant genes at the molecular level and reveal their functions. To date, 1698 genes have been reported for mutant or variant phenotypes were listed (Nori Kurata et al., 2005; Chen H et al., 2013). All of these achievements made it increasingly possible to practice breeding by design.