Table 1 |
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CAPS markers converted from RFLP markers and microsyntenic ESTs* |
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|
Arabidopsis gene† |
C/P/H‡ |
Molecular markers mapped in the dgt region§ |
Type |
Expect value¶ |
Primer sequences# |
Restriction enzyme |
|
|
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|
AT4g38580 |
- |
CT190¥ |
RFLP |
- |
5'-TTCTCGTCGCTAAAGGCAGT-3' 5'-TCACACAAAACAATGGGTGTTCTT-3' |
HinfI |
|
AT4g38620 |
2 / 2 / 40 |
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|
AT4g38630 |
1 / 1 / 1 |
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|
AT4g38660 |
1 / 2 / 16 |
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|
AT4g38670 |
1 / 2 / 15 |
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|
AT4g38680 |
1 / 1 / 1 |
TC98260 (GRP) |
EST |
1.7e-40 |
5'-GTGCCTCACAATCAAAGGGTTTTA-3' 5'-CTCCATAACCACGATTTCCTCCTC-3' |
RsaI |
|
AT4g38690 |
4 / 4 / 5 |
TC92082 (PPLC) |
EST |
1.4e-84 |
5'-TGGTTGAGCTGATTTTCTTGGTTT-3' 5'-CCTGGTTCTGATTATCGCTCAGAT-3' |
HinfI |
|
AT4g38700 |
1 / 2 / 5 |
AW624844 (DRRP) |
EST |
1.2e-28 |
5'-AAACGTCATGGGCTAAGAGAGTTG-3' 5'-TCTAGATGCAATGGCTTGTTTTCC-3' |
ApoI |
|
AT4g38730 |
- |
TG389 |
RFLP |
- |
5'-TCACTAGCTCAAGGGAGTCATCTG-3' 5'-ACCACTTTGACCATCATCGCAAGC-3' |
HinfI |
|
AT4g38740 |
1 / 3 / 10 |
TC89380 (PPI) |
EST |
5.2e-76 |
5'-CAAATCCAAAGGTTTTCTTTGACC-3' 5'-CTGGTAGAAGCAACACAACAACCA-3' |
HaeIII |
|
AT4g38790 |
1 / 2 / 4 |
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|
AT4g38810 |
1 / 2 / 2 |
TC85079 (EFP) |
EST |
4.0e-129 |
5'-CGAAACTGGCTTCCCTTCTA-3' 5'-AGTCAGGTGATGGACGGTTC-3' |
BanI |
|
AT4g38830 |
10 / 12 /146 |
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|
AT4g38840 |
1 / 1 / 6 |
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|
AT4g38850 |
- |
TG269 |
RFLP |
- |
5'-CAAATTCTTCCTCAGCTTGACT-3' 5'-TGATCTCACATCTTGCTTGCG-3' |
DdeI |
|
AT4g38880 |
1 / 1 / 1 |
TC87150 (APRT) |
EST |
3.8e-90 |
5'-CAGAAAAATGACTTGGAGGGAGAG-3' 5'-CCAAGATTGTGAGGCTGTTAAAGG-3' |
RsaI |
|
AT4g38900 |
1 / 1 / 3 |
TC47447 (bZIP) |
EST |
1.3e-98 |
5'-AACTTGGAAGCGTCTGCACT-3' 5'-GGACGACCTGTTTTCTGCAT-3' |
RsaI |
|
AT4g34830 |
1 / 1 / 1 |
BG643476 |
EST |
5.3e-86 |
5'-GGTTGATGGACTGCATAAAAATCC-3' 5'-TGCAAATTCCCAATTTACCATTTT-3' |
HhaI |
|
AT4g35050 |
2 / 3 / 4 |
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|
|
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*The conversion rate of the amplicons, generated from ESTs in the target region, to CAPS was 75% (30/40) and 20% of CAPS markers (6/30) were successfully mapped in the dgt region. †Genes in MSR1 with exceptions of AT4g34830 and AT4g35050 in MSR2. ‡C/P/H, the number of CAPS markers developed/the number of PCR products investigated/the number of TBLASTN matches of interest (< e-20). §Abbreviations in parentheses: GRP, glycine-rich protein; PPLC, phosphatidylinositol-specific phospholipase C precursor; DRRP, disease-resistance response protein; PPI, cyclophilin-type peptidyl-prolyl isomerase; EFP, EF-hand containing protein-like protein; APRT, amidophosphoribosyl transferase; bZIP; basic leucine zipper transcription factor. ¶Each value represents the E-value of a TBLASTN search using the Arabidopsis microsyntenic gene against the Tomato Gene Index using the Blosum 62 scoring matrix and default parameters. The E-value of a BLASTN search using tomato RFLP markers is not described in this table (see text). #Oligonucleotide sequences are only indicated for each MEST marker. ¥ Amplified by modified PCR conditions: 3 min 30 sec for elongation and 2.5 mM MgCl2. |
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Oh et al. Genome Biology 2002 3:research0049.1 doi:10.1186/gb-2002-3-9-research0049 |
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