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    D. J. Mackill, Z. Zhang and E. D. Redona
    USDA-ARS and Department of Agronomy & Range Science, University of California, Davis, CA
    95616. USA

    RFLP maps developed at Cornell (Causse et al. 1994), and in Japan (Kurata et al. 1994) continue to
form the basis of gene mapping research in rice. Polymprphism is highest between members of the indica and japonica subspecies, and most mapping studies utilize indica x japonica crosses. Unfortunately, inter-subspecific crosses suffer from sterility and distorted segregation (Wang et al. 1994). RAPD markers (Welsh and McClelland 1990; Williams et al. 1990) have been proposed as an alternative to RFLPs. Within the japonica subspecies, RAPDs have been shown to be polymorphic between the tropical and temperate types (Mackill 1995), and have recently been used to construct a genetic map in a tropical x temperate japonica cross (Redona and Mackill, this issue). As with RFLPs, however, the level of polymorphism is relatively low within japonica rices, and many primers are needed for mapping quantitative trait loci. Microsatellite (or simple sequence repeats-SSR)(Akkaya et al. 1992) and amplified fragement length polymorphism (AFLP)(Zabeau and Vos 1993) markers have been proposed for gene mapping in species where RFLPs are limited. Studies in rice indicate that microsatellite markers are highly polymorphic (Wu and Tanksley 1993; Zhao and Kochert 1993; Yang et al. 1994). Information on polymorphism of AFLP markers in rice is currently not available. In the present study, we compared the levels of polymorphism of AFLP, RAPD and microsatellite markers on 12 japonica cultivars and 2 indica cultivars. For RAPD markers, 21 primers gave 43 polymorphic bands; and for AFLP markers, 17 primer combinations gave 140 polymorphic bands. The 10 microsatellite markers were based on sequences of Dr. Susan McCouch, Cornell University.
    All marker types gave the same classification of the rice accessions into subspecies. Both RAPDs and AFLPs agreed on classification of japonica rices into tropical and temperate types. Within japonica cultivars, the average percent polymorphism was 22% for AFLP, 24% for RAPD, and 36% for microsatellite markers, respectively (mo-nomorphic bands excluded). While the percent polymorphism was highest for microsatellite markers, the abundance and ease of using RAPDs indicate that this marker can be used for mapping within japonica rice. For example, Redona and Mackill (submitted and in this issue) used RAPDs to map QTLs in a temperate x tropical japonica cross. The average percent polymorphism between indica and japonica accessions was 31, 35 and 76%, for AFLP, RAPD and microsatellite markers, respectively. While the percent polymorphism was lowest for AFLPs, the number of polymorphic bands was much higher, averaging over eight per gel (Fig. 1 ).
    We mapped AFLP markers produced by seven primer combinations on 80 F₂plants of the japonica/indica cross Labelle/Black Gora used by Redona and Mackill (1994). Of 54 bands scored, 50 could be mapped, and these appeared to be distributed throughout the rice genome (3 on chromosomel, 1 on chr.2, 6 on chr.3, 4 on chr.4, 4 on chr.5, 8 on chf.6, 3 on chr.7, 5 on chr.8, 3 on chr.9, 5 on chr.l0 and 8 on chr.l1). This indicates that AFLPs are a promising marker for mapping important genes in indica x. japonica crosses.