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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

-