Genome-Wide Indel Markers for Rice Cultivar Identification

In order to widen the genetic basis for national rice breeding programs, a set of 595 PCR-based novel insertion/deletion (InDel) markers were designed. The markers were generated by published genome sequences of rice (Oryza sativa L. spp japonica). Among the 595 InDel markers, we selected 112 markers spread across all rice chromosomes and they showed polymorphic between rice cultivars, which are 284 Korean japonica and Tongil varieties. The PIC value of Indel markers were in the range of 0.20–0.45 with an average of 0.37. As a result, the PCR product can be efficiently separated and easily scored by running 80 min of electrophoresis on 3 % agarose gels. 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. We suggest that InDel markers with moderate size differences could be a valuable alternative in addition to the widely used SSR and SNP markers for rice breeding, and particularly suitable for field laboratories at breeding stations. 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.