Level of polymorphism and genetic mapping of AFLP markers in rice

Amplified fragment length polymorphism (AFLP) has been proposed as a valuable tool for gene mapping in plant species. We compared the levels of polymorphism for AFLP, RAPD, and microsatellite markers on 12 japonica and 2 indica rice cultivars. For AFLPs, seven EcoRI and seven MseI primers used in 18 primer combinations generated a total of 529 bands, of which 147 were clearly polymorphic among the accessions. The 21 RAPD primers produced 103 bands of which 43 were polymorphic. For the microsatellite markers the number of alleles per locus ranged from one (1 locus) to six. All marker types gave the same classification of the rice accessions into subspecies. Within japonica cultivars, the average percent polymorphism between any two accessions was 22% for AFLP, 24% for RAPD, and 36% for microsatellite markers (monomorphic bands excluded). The average percent polymorphism between indica and japonica accessions was 65, 35, and 76%, for AFLP, RAPD, and microsatellite markers, respectively. The total number of polymorphic bands was much higher for AFLPs, averaging over eight per gel. Seven AFLP primer combinations were assayed on 80 F2 plants of an indica x japonica cross previously mapped with RFLP markers. Of 54 AFLP bands scored, 50 could be mapped to specific chromosomes, and these appeared to be distributed throughout the rice genome. This indicates that AFLPs are a promising marker for mapping important genes in rice.