Several kinds of molecular markers such as RFLP, RAPD, STS, AFLP and microsatellite markers, have been developed and applied in plant genetics and breeding. Of these, microsatellite markers are valuable because they are co-dominant, can detect high levels of allelic diversity and are economically assayed by PCR. In rice, molecular linkage map consisting of more than 500 microsatellite markers are now available to the public (Temnykh et al. 2001). These markers are expected to be efficiently used for QTL analysis and markerassisted selection. In this study, molecular linkage maps between Oryza sativa and O. rufipogon were constructed using microsatellite markers, to confirm the utility of microsatellite markers in studies using wild species of rice.

A single wild Myanmar accession (O. rufipogon W630) was crossed with two O. sativa

rice cultivars Japonica Nipponbare and Indica IR36). Two BC1 mapping populations (W630/Nipponbare//Nipponbare and W630/IR36//IR36) consisting of 79 and 91 plants, respectively, were produced. Total DNA was extracted from these plants. PCR amplification and band detection were carried out using the method of Panaud et al. (1996). In total, 112 and 119 microsatellite markers were examined for Nipponbare and IR36 background populations. The markers were selected from 12 rice linkage groups (Temnykh et al. 2000) with an average marker distance of ca. 20 cM. Of these, 106 (94.6%) and 106 (89.1%) markers showed obvious polymorphisms between mapping parents; these were used to check the segregation in BC1 populations. For most of the markers, segregation followed the expected ratio of 1:1 (P < 0.05). However, 14 (13.2%) and 10 (9.4%) markers showed significantly deviated segregation in Nipponbare and IR36 background populations, respectively. Linkage analysis was carried out with these polymorphic markers using MapMaker ver. 2.0 (Lander et al. 1987).

Two interspecific linkage maps were constructed between Nipponbare and O. rufipogon W630, and between IR36 and O. rufipogon W630 (Fig. 1). Total map size were 1505 cM and 1662 cM, respectively. The marker order of the microsatellites was consistent with that reported by Temnykh et al. (2000), using double-haploid population between IR64 (O. sativa Indica) and Azucena (O. sativa Javanica). To examine the size of 12 linkage groups between interspecific and intraspecific maps, the maximum common interval size between two markers shared by both maps was used. Table 1 summarizes the respective length of 12 chromosomes compared between two maps. Majority of the linkage groups showed similar interval size. However, some showed either a relatively short or long map size. This was probably due to a small number of markers used to compare maps.

The present results suggest that most microsatellite markers can be used with O. rufipogon and applied for map-based studies, such as gene tagging and interspecific QTL analysis.

References

Lander, E. S., P. Green, J. Abrahamson, M. J. Barlow, M. J. Daly, 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.

Panaud, O., X. Chen and S. R. McCouch, 1996. Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.) Mol. Gen. Genet. 252: 597-607.

Temnykh, S., W. D. Park, N. Ayres, S. Cartinhour, N. Hauck, L. Lipovich, Y. G. Cho, T. Ishii and S. R. McCouch, 2000. Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theor. Appl. Genet. 100: 697-712.

Temnykh, S., G. DeClerck, A. Lukashova, L. Lipovich, S. Cartinhour and S. R. McCouch, 2001. Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): Frequency, length variation, transposon associations, and genetic marker potential. Genome Res. 11: 1441-1452.