Molecular-marker screening
Amplified fragment length polymorphism (AFLP) analysis was conducted according to
Jia et al. (2001). The AFLP fragments, which were cloned in the pUCm-T easy vector system,
were then sequenced. 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).