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Design and Application of Microsatellite Marker Panels for Semiautomated Genotyping of Rice (Oryza sativa L.)

^a Dep. of Plant Breeding, 252 Emerson Hall, Cornell Univ., Ithaca, NY 14853-1901
^b GeneFlow Inc., 503 Mt. Vernon Ave., Alexandria, VA 22301
^c Dep. of Plant Breeding, 240 Emerson Hall, Cornell Univ., Ithaca, NY 14853-1901

View larger version (41K): [in a new window]   Fig. 1. Electropherogram of a typical multiplex panel, with shaded regions indicating the range of allele size variation among 13 diverse rice cultivars for a given locus. A 20-bp buffer zone is required between markers labeled with the same fluorophore to separate the zones corresponding to different loci.

View larger version (110K): [in a new window]   Fig. 2. Pair-wise comparison of average P.I.C. values of SSR markers evaluated on 13 cultivars of Oryza sativa vs. 256 diverse O. sativa cultivars (Y. Xu, personal communication) (Comparison 1), and 5 vs. 51 O. sativa spp. Japonica cultivars (Ji et al., 1998) (Comparison 2). Differences between P.I.C. values for individual markers for each comparison are shown graphically.

View larger version (68K): [in a new window]   Fig. 3. Comparison of Genotypes output of GeneFlow Genotype Module indicating distribution of fluorescently labeled microsatellite markers on the 12 chromosomes of rice. The marker positions are based on the map published by Temnykh et al. (2001). Accessions are numbered as: 1. IR36, 2. IR64, 3. Kasalath, 4. N22, 5. Teqing, 6. Zhai-Ye-Qing-8, 7. BS125, 8. Acucena, 9. Gihobyeo, 10. Jing-Xi 17, 11. Lemont, 12. Nipponbarre. Numbers to the right of the chromosomes indicate the Rice Microsatellite (RM) locus-ID. Different alleles are represented by different colors for any given marker. Marker names in black font indicate markers that were omitted during the GeneFlow analysis, but are part of the panels. Marker names written in underscored black font were mapped on different populations. Black rectangles located on the chromosome bars represent approximate centromere locations. Circles indicate markers with japonica- or indica-specific alleles for the accessions tested; diamonds and triangles denote markers that were hypervariable for the japonica or indica accessions tested, respectively.

View larger version (17K): [in a new window]   Fig. 4. NTSYS principle component analysis (P.C.A.) diagram illustrating the genetic relationships among the 13 Oryza sativa accessions evaluated with the set of 159 fluorescently labeled microsatellites.