Amplified fragment length polymorphism (AFLP) has been proposed as a v
aluable tool for gene mapping in plant species. We compared the levels
of polymorphism for AFLP, RAPD, and microsatellite markers on 12 japo
nica and 2 indica rice cultivars. For AFLPs, seven EcoRI and seven Mse
I primers used in 18 primer combinations generated a total of 529 band
s, 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 th
e rice accessions into subspecies. Within japonica cultivars, the aver
age percent polymorphism between any two accessions was 22% for AFLP,
24% for RAPD, and 36% for microsatellite markers (monomorphic bands ex
cluded). The average percent polymorphism between indica and japonica
accessions was 65, 35, and 76%, for AFLP, RAPD, and microsatellite mar
kers, respectively. The total number of polymorphic bands was much hig
her for AFLPs, averaging over eight per gel. Seven AFLP primer combina
tions were assayed on 80 F-2 plants of an indica x japonica cross prev
iously mapped with RFLP markers. Of 54 AFLP bands scored, 50 could be
mapped to specific chromosomes, and these appeared to be distributed t
hroughout the rice genome. This indicates that AFLPs are a promising m
arker for mapping important genes in rice.