Identification of rice hybrids using microsatellite and RAPD markers

Having produced a series of hybrid rice varieties especially the first Iranian hybrid rice (IRH1), fingerprinting and genetic purity determination of hybrid seeds were conducted using microsatellite (SSR) and random amplified polymorphic DNA (RAPD) markers. Sixteen rice genotypes including 3 cytoplasmic male sterile (CMS) lines, 5 restorer lines and their 8 hybrid combinations were used in this study. Ten out of fourteen SSR markers produced polymorphic bands in the 16 rice genotypes. The first Iranian hybrid rice, IRH1, could be differentiated from other hybrids possessing a unique SSR fingerprint. Although the SSR markers amplified the unique fingerprints for the restorer lines, they could not differentiate between 2 CMS lines (Neda-A and Nemat-A) and their resultant hybrids. The rice CMS lines and restorer lines could be uniquely identified by RAPD multilocus amplified profile at 7 informative loci. Cluster analysis based on shared alleles and Jaccard’s similarity coefficient using UPGMA algorithm, grouped the rice genotypes into 3 and 4 major clusters according to their microsatellite and RAPD fragment similarities respectively. Non-parental bands were also observed in addition to parental bands which probably correspond to heteroduplex molecules formed by two allelic sequences of different amplified fragments. This demonstrates that heteroduplex bands can be an indicative feature for identifying hybrid individuals.