Variety Identification among Major Japonica Rice Cultivars of Taiwan Based on Simple Sequence Repeat Markers

In order to identify the major Japonica type rice cultivars grown in Taiwan, this research used 46 pairs of simple sequence repeat (SSR) primers conducting analysis on 25 rice cultivars. After polymerase chain reaction (PCR) and automatic DNA fragment detection based on primer labeled with florescent dye, 20 pairs of primers showed polymorphism among cultivars. In total, there were 21 polymorphic loci, with average 2.9 alleles per locus, averaged Polymorphic Information Content is 0.383. All cultivars can be distinguished based on polymorphic SSR markers, except Taikeng No. 11 and Taikeng No. 15. The minimum set of primers that can be used to distinguish all 25 entries and 18 major cultivars are composed of 6 and 4 pairs or primers, respectively. For distinguishing major cultivars, a set of 4 pairs of primers, which are suitable for Multiplex PCR, is also found.