Multiplex PCR analysis of Indica-japonica differentiation of the chloroplast DNA in weedy rice

The whole chloroplast genomes of the Indica cultivar 93-11 and Japonica cultivar Peiai64S were analyzed and compared. A multiplex PCR marker of the chloroplast DNA ORF100 and ORF29-TrnCGCA region was optimized and constructed. More than 200 weedy rice,Asian cultivated rice and common wild rice accessions were then tested using the multiplex PCR. The results showed that there were obvious chloroplast DNA indica-japonica differentiations amongst the weedy,Asian cultivated and common wild rice accessions. Furthermore,the differentiations in weedy rice were correlated to the collected regions that were in accordance with the south indica type and north japonica type of cultivated rice in China. It was suggested that the japonica line of weedy rice should evolve from degraded cultivated rice or the japonica varieties(as the female parent) natural hybridization with other oryza materials for there was no wild form in north China.