332 PCR-based genetic markers on rice chromosomes
We have developed 332 PCR-based genetic markers including 161 sequence tagged site (STS) markers and 171 cleaved amplified polymorphic sequence (CAPS) markers. The table (chr 1 to chr 12) summarizes all information for these markers, such as chromosomal location, primer sequences, size of amplified fragment (Nipponbare), restriction enzyme, etc. These markers have been developed to detect polymorphism between Nipponbare (japonica) and Kasalath (indica). Although detection of polymorphism of these markers will depend on the combination of varieties or lines, they may be used for the analysis of other combinations.
The 161 STS markers have been developed using clone-specific sequences (3'end)
designed from the EST sequence derived from several cDNA libraries (Yamamoto et al.
1997). The chromosomal location of each marker has been identified by EST mapping
(Wu et al. Plant Cell 2002) using a YAC-based physical map of rice. For all
polymorphic markers, we have confirmed the chromosomal location by linkage analysis
using 46 randomly selected BILs (Lin et al. 1998).
We have developed 171 CAPS markers including 6 derived CAPS (dCAPS)
markers (Konieczny and Ausbel 1993, Neff et al. 1998) using the information derived
from a high-density RFLP linkage map (A HIGH-DENSITY RICE GENETIC MAP Harushima et al. 1998, The Latest High-Density Rice Genetic Map, Including 3267 Markers Rice Genome Research
Program 2000). Using 5' and 3' sequence data for the clones used for RFLP linkage
analysis, we designed unique primer pairs for the specific amplification of genome.
Then, restriction digestion was carried out to detect polymorphism. In order to confirm
the chromosomal location of CAPS markers, linkage analysis was performed using 14
randomly selected F2 plants (Harushima et al. 1998).
Harushima Y, Yano M, Shomura A, Sato M, Shimano T, Kuboki Y, Yamamoto T, Lin SY, Antonio BA, Parco A, Kajiya H, Huang N, Yamamoto K, Nagamura Y, Kurata N, Khush GS and Sasaki T (1998) A high-density rice genetic linkage map with 2275 markers using a single F2 population. Genetices 148: 479-494.
Konieczny A and Ausbel FM (1993) A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers. Plant J. 4: 403-410.
Lin SY, Sasaki T and Yano M (1998) Mapping quantitative trait loci controlling seed dormancy and heading date in rice, Oryza sativa L., using backcross inbred lines. Theor Appl Genet 96: 997-1003.
Neff MM, Neff JD, Chory J and Pepper AE (1998) dCAPS, a simple technique for the genetic analysis of single nucleotide polymorphisms: experimental applications in Arabidopsis taliana genetics. Plant J. 14: 387-392.
Wu J, Maehara T, Shimokawa T, Yamamoto S, Harada C, Takazaki Y, Ono N, Mukai Y, Koike K, Yazaki J, Fujii F, Shomura A, Ando T, Kono I, Waki K, Yamamoto K, Yano M, Matsumoto T and Sasaki T (2002) A comprehensive rice transcript map containing 6591 EST site. Plant Cell
Yamamoto K and Sasaki T (1997) Large-scale EST sequencing in rice. Plant Mol Biol 35: 135-144.