Comparison of the Efficiency of SSR and RAPD Markers in Marker-Assisted Selection (MAS) Program in Rice

Several reports were published in regard to the comparison of the efficiency of different molecular markers in genetic diversity studies for estimating genetic parameters. Most researches have been conducted out in different plant genomes and in different breeding programs, but there isn`t any report on comparing the efficiency of SSR and RAPD markers in marker-assisted selection (MAS) programs in rice genome. In this line, a research was conducted out to compare the two marker systems for estimating some genetic parameters in advanced backcross lines in rice. One hundred SSR primer pairs and 20 RAPD primers were used for fingerprinting of the studied genotypes. Polymorphism of RAPD markers was higher than SSR markers, while polymorphism information content (PIC) of SSR markers was more than 2 fold relative to RAPD markers. A weak correlation was observed between the two systems for estimating genetic similarity of progenies to recurrent parent. Also, results showed that increasing the number of RAPD markers didn`t cause any increase in estimation precision. The results of this research suggested the use of SSR markers in selection programs.