Table 1 Analysis of the three (GATA)n-containing subclones with respect to repeat number, allele length and number of alleles
From: Potential of (GATA)n microsatellites from rice for inter- and intra-specific variability studies
No. | 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 | |||
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 | |||
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 | - |