From: Potential of (GATA)n microsatellites from rice for inter- and intra-specific variability studies
No. | Â | OS1A6 | OS1H10 | OS2E7 |
---|---|---|---|---|
1 | Original phage clone | GATA 7.1 | GATA 3.1 | GATA 8.1 |
 | number from which |  |  |  |
 | derived |  |  |  |
2 | Restriction endonuclease | Msp I | Taq I | Taq I |
 | used to digest phage DNA |  |  |  |
3 | Subcloning vector | pUC-18 | pUC-18 | pUC-18 |
4 | Cloning site | Acc I | Acc I | Acc I |
5 | GenBank accession | AF294726 | AF285877 | AF284424 |
 | number |  |  |  |
6 | Number of GATA motifs | 7 imperfect | 7 perfect | 13 imperfect |
 |  | GATATA (GATA)6 | (GATA)7 | AATA (GATA)3 GAA (GATA)4 |
 |  |  |  | AGTA GAAA GATG AGTA |
7 | Primer sequences used for | F | F | F |
 |  | 5'GCTGCGCAGTGTATGCGTCT3' | 5'GAGTGGTCTCAGTTTGGTGC3' | 5'AAGTGGCGACGTGAGAGCG3' |
 | PCR amplification |  |  |  |
 |  | R | R | R |
 |  | 5'ACCATTTAACAGCTAATCGA3' | 5'TGGCGGCTGGAGAGCGTTTG3' | 5'GTTAAGACAGTCCCCAGTG3' |
8 | Annealing temperature | 55°C | 67°C with 2% formamide | 57°C with 2% formamide |
9 | Size of expected PCR | 184 bp | 263 bp | 141 bp |
 | product (from genomic |  |  |  |
 | subclone sequence) |  |  |  |
10 | Number and size range of | Â | Â | Â |
 | alleles detected in |  |  |  |
 | (A) Wild and cultivated rice | 7 (184 bp–208 bp) | 22 (116–521 bp) | Unscorable ladder-like |
 | genotypes |  |  | pattern obtained |
 | (B) Indian elite rice | 3 (174–197 bp) | 10 (218–292 bp) | 4 (157–179 bp) |
 | varieties |  |  |  |
 | (C)Bacterial blight | 5 (171–198 bp) | 19 (140–535 bp) | 6 (117–143 bp) |
 | resistant and |  |  |  |
 | (D) Cereal genotypes | 1 (184 bp) | 6 (168–270 bp) | - |
11 | Maximum number of | Â | Â | Â |
 | bands per lane in |  |  |  |
 | (A) Wild and cultivated rice | 2 | 7 | - |
 | genotypes |  |  |  |
 | (B) Indian elite rice | 3 | 3 | 3 |
 | varieties |  |  |  |
 | C) Bacterial blight resistant | 2 | 9 | 4 |
 | and susceptible lines |  |  |  |
 | (D) Cereal genotypes | 1 | 3 | - |