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Rice Genome Research Program, National Institute of Aerobiological Resources and Society for Techno-inovation of Agriculture, Kannondai 2-1-2, Tsukuba, 305 Japan
Two RFLP linkage maps, each made using a different F2 population, were combined to generate an integrate map as shown in Fig. 1. The map represented on the right/side of the 12 linkage groups was obtained tlirough the analysis of 190 F2 progenies from a cross of Nipponbare (japonica) and Kasalath (indica).
For linkage analysis we used the software MAPMAKER (Lander et al. 1987). For detailed mapping, we used four types of probes. The first-type probes on the right side are genomic clones, and correspond to the probes in the previous map of Saito et al. 1991 (XNpb-numbers on the left side). These markers are used as the references to link other DNA markers.
The second-type probes were cDNA probes, all of which were sequenced at least partially. These were used for placing tags of expressed gene sequences on the linkage map. Almost all of the cDNA mapped contained open reading frames with sequence similarity to proteins with known functions. The loci of these expressed genes were found to scatter almost evenly on all the linkage groups, except for the middle portion of the chromosome 8 and the lower half of chromosome 12, which had no cDNA markers. Such cDNA probes showed a high frequency of RFLP. When digested with 8 enzymes independently, total polymorphism was 75% between Nipponbare and Kasalath. Therefore, it appears that cDNA markers are useful and important for RFLP mapping.
The third-type probes were prepared from specific genomic clones which were produced as YAC-end clones and YAC-linking clones. These probes will be used for physical map construction after identification of their loci on the RFLP linkage map. In the same context, all other mapped RFLP markers are also being used to isolate corresponding genomic clones from YAC and cosmid genomic libraries. Application of RFLP probes to isolate multiple starting-point clones is an important first step for physical map construction and chromosome walking. Therefore we selected and used single-copy DNA sequences to detect their loci on the RFLP map.
The fourth-type DNA markers were derived from PCR products which showed polymorphism between Nipponbare and Kasalath. Polymorphic PCR markers detected by using 10 bp-long random primers are designated RA. To assign unique PCR, the products which showed clear polymorphism were cloned
1) Present address: Hokuriku National Agricultural Experiment Station, 1-2-1 Inada, Joetsu, Niigata-ken, 943-03 Japan.
Centimorgan was expressed by
the Kosanibi function)
Fig. 1.
and sequenced. Specific primers are then designed from the sequenced region
for amplifying only the restricted sequence in the genome. These markers are
shown with LP-number.
At present, our integrated map contains 605 loci including 68 markers given in the two maps. The DNA markers mapped in this new map (right side) contain about 120 genomic clones, about 170 cDNA clones, 36 PCR polymorphism markers and several YAC-end and YAC-linking clones. Distribution patterns of these DNA markers and other features of the unified map using these two F2 populations will be discussed elsewhere.
References
Lander, E.S., P. Green, J. Abrahamson, A. Barlow, M.J. Duly, S.E. Lincoln and L. Newburg, 1987. MAPMAKER: An interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1: 174-181.
Saito, A., M. Yano, N. Kishimoto, M. Nakagahara, A. Yoshimura, K. Saito, S. Kuhara, Y. Ukai, M. Kawase, T. Nagamine, S. Yoshimura, O. Ideta, R. Osawa, Y. Hayano, N. Iwata and M. Sugiura, 1991. Linkage map of restriction fragment length polymorphism loci in rice. Jpn. J. Breed. 41: 665-670.
Ukai, Y., R. Osawa and A. Saito, 1991. MAPL: A package of microcomputer program for RFLP linkage mapping. RGN 8: 155-158.
