Sequence diversity was accumulated through evolution and breeding process. A set of 595 PCR-based novel insertion/deletion (InDel) markers was designed in order to widen the genetic basis for national rice breeding programs. The markers were generated by analyzing of 40 Korean cultivars and published genome sequences of rice(Oryza sativa L. spp japonica). We selected 112 markers spread across all rice chromosomes among the 595 InDel markers, and they showed polymorphic between rice cultivars, which are 284 Korean japonica and Tongil varieties. Due to their simplicity in design and robustness in genotyping, these InDel markers have been routinely used in quantitative trait loci (QTL) mapping studies and marker assisted selection programs for rice. Moreover, the PCR amplification type of InDel markers was converged to digital code, 0 or 1 and then finally represented as one- and two dimensional bar-code system, which could easily differentiate genetically highly homologous japonica rice cultivars. The developed InDel markers uniquely discriminated among each of the Korean cultivars. Therefore, the systems we developed may be valuable tools in discrimination from cultivars

• Hyang Mi Park(National Institute of Crop Science, RDA) Corresponding Author
• Yul Ho Kim(National Institute of Crop Science, RDA)
• Jung Pil Suh(National Institute of Crop Science, RDA)
• Tae Young Hwang(National Institute of Animal Science, RDA)
• DongWoo Lee(Theragen Bio Institute, TheragenETex)
• Sunghoon Lee(Theragen Bio Institute, TheragenETex)