Further, e-polymerase chain reaction (PCR ) was carried out by BLASTN alignment between the genome sequences of Oryza sativa ssp. japonica ‘Nipponbare’ and ssp. indica ‘9311’. After, the specific fragments were mapped that were associated with percentage of chalky grain, and twelve SSR markers in this region were selected for fine mapping. The genomic sequence was obtained from the International Rice Genome Sequencing Project (IRGSP; http:// www.rgp.dna.affrc.go.jp/E/IRGSP/index.html)