Abstract：Molecular marker is DNA sequence which can directly reflect the nucleotide sequence variation among individuals and the genetic polymorphism. The identification of hybrid rice by molecular marker will provide strong evidence for the registration and protection of new cultivars, test of seed quality and evaluation of genetic resources. In this study, in order to develop new molecular markers and establish the corresponding molecular marker system, PCR was carried out with molecular markers ISSR (inter-simple sequence repeat) and SCAR (sequence-characterized amplified region) in some new blast resistant varieties such as rice (Oryza sativa) Junyou 522 (JY522) and other common rice accessions. Results demonstrated that the amplification of 17 out of 40 ISSR primers were good polymorphic with all 41 accessions. There were 65 out of 119 polymorphic bands ranged from 250~2 000 bp. The frequency of polymorphism was 54.6%. The combination of 4 SCAR markers (822-CGA-1, 40N23R, NBS2PI9 and Pibdom) deriving from the specific PCR products in ISSR primers could identify the authenticity and purity of JY522 effectively. The genetic similarity coefficient ranged from 0.53 to 1.00 among all accessions. The identification of hybrid rice by the combination of molecular markers will provide strong evidence for the registration and protection of new cultivars, JY522, test of seed quality and evaluation of genetic resources.
