Use of molecular markers for diversity analysis in rice

The genetic relationship between seven japonica, two indica and one tropical japonica rice varieties was analysed by using PCR with Random Amplified Polymorphic DNA (RAPD) and Amplified Fragment Length Polymorphism (AFLP) methods. In RAPD analysis PCR with 10 arbitrary primers applied to ten rice varieties produced 84 useful markers, of which 77.4% were polymorphic. Fifteen AFLP primer combinations produced 285 markers, of which 70.8% were polymorphic. Thus, sufficient polymorphism could be detected to allow identification of individual varieties. Visual examination of electrophoresis gels and analysis of banding patterns confirmed that all the seven japonica types were closely related, with similarity indices of 50–85%. Two indica varieties were classified into separate group. However, the tropical japonica type was easily distinguished, producing variety specific amplification profiles and expressing a lower similarity index to all other varieties tested. Thus, both RAPD and AFLP methods of fer a potentially simple, rapid and reliable method for rice genotype identification and recognition of lines that could contribute genetic diversity to new commercial varieties. AFLP was more useful than RAPD because the potential number of loci that could be assayed with AFLP far exceeds that with RAPD.