Fingerprinting and variety identification of rice (Oryza sativa L.) based on simple sequence repeat markers

Fingerprinting with molecular markers allows precise, objective and rapid variety identification. In this study, simple sequence repeat (SSR) markers were used to fingerprint the forty-eight main commercial rice cultivars under cultivation at present in Zhejiang Province, China, and identify indica and japonica subspecies including eight groups of closely related cultivars. Eighteen of the thirty-two SSR primer pairs were polymorphic and generated a total of 42 distinct reproducible bands with an average of 2.33 bands per primer pair. 41 (97.6%) of the 42 bands amplified were polymorphic. The number of polymorphic bands detected with each primer pair ranged from 1 to 4 with an average of 2.28 per primer pair. The polymorphic information content (PIC) values of each primer pair ranged from 0.10 to 0.50 with an average of 0.31. The UPGMA cluster analysis separated the 48 cultivars into two major groups. The first major cluster consisted of the 34 indica cultivars, and the leaving 14 japonica cultivars formed the second major cluster. Primer pair RM249 or RM250 was able to differentiate between indica and japonica subspecies, respectively. Most of the closely related cultivars were identified with the fingerprinting based on the polymorphic SSR primer pairs, apart from cultivars ‘Xiushui 09’ and ‘Xiushui 114’. The results revealed a narrow genetic diversity among the forty-eight main commercial rice cultivars in Zhejiang Province of China, and combination of SSR with other marker systems might be a potential strategy for fingerprinting database development and authentification of rice cultivars in further study.