Conserved DNA-Derived Polymorphism (CDDP): A Simple and Novel Method for Generating DNA Markers in Plants

A novel method for generating plant DNA markers was developed based on data mining for short conserved amino acid sequences in proteins and designing polymerase chain reaction (PCR) primers based on the corresponding DNA sequence. This method uses single 15- to 19-mer primers for PCR and an annealing temperature of 50A degrees C. PCR amplicons are resolved using standard agarose gel electrophoresis. Using a reference set of rice genotypes, reproducible polymorphisms were generated. Since primers were designed using highly conserved regions of genes, markers should be generated in other plant species. We propose that this method could be used in conjunction with or as a substitute to other technically simple dominant marker methods for applications such as targeted quantitative trait loci mapping, especially in laboratories with a preference for agarose gel electrophoresis.