Patel et al.
Table 4: List of SSR primers predicted for specific bacterial leaf blight resistance genes, Position of genes on chromosomes,
total number of amplified bands, range of molecular weight amplified by primers, number of amplified alleles,
Polymorphism Information Content (PIC) values obtained by analyzing 30 genotypes of rice
Range of
No. of
Sr.
Primer
Chromosome
Total No.
PIC
Predicted gene
molecular
amplified
No.
name
No.
of bands
weight (bp)
alleles
value
1
RM 167
Xa4
11
30
128-133
3
0.39
2
RM 144
Xa4
11
38
120-325
3
0.55
3
RM 13
xa5
5
36
124-400
4
0.67
4
RM 31
xa5
5
31
137-172
4
0.59
5
RM 122
xa5
5
30
230-250
3
0.46
6
RM 164
xa5
5
30
246-256
2
0.39
7
RM 390
xa5
5
37
166-185
3
0.39
8
RM 611
xa5
5
67
130-250
4
0.66
9
RM 39
xa5
5
30
113-122
2
0.39
10
SR 6
xa13
8
28
234-259
2
0.07
11
SR 11
xa13
8
40
202-785
8
0.46
12
RM 21
Xa21
11
43
110-400
6
0.73
13
RM 349
Xa2
4
75
108-435
7
0.81
14
RM 317
Xa2
4
33
78-170
3
0.73
15
M3
Xa7
6
16
513-560
3
0.54
16
RM 500
xa8
7
30
153-200
3
0.49
17
RM 533
xa8
7
33
270-279
2
0.50
18
RM 206
Xa10
11
34
127-175
3
0.64
19
RM 139
Not gene specific
11
107
65-1289
12
0.86
20
RM 331
Not gene specific
8
30
173-184
2
0.39
TOTAL
798
75
10.71
AVERAGE
39.9
4
0.53
SSR amplification
(3U/ µ l) and 19 µl of sterile distilled water. The
SSR amplification reactions were carried out in 25µl
amplification reaction consisted of an initial denaturation
volume containing 1.5 µl of DNA (50 ng/ µ l), 2.5 µl
step at 94°C for 5min, followed by 30 cycles of 1 min
of PCR buffer (10 x) Bangalore Genei, India, 0.5 µl
at 94°C (denaturation), 1min at a specific annealing
of Forward Primer and 0.5 µl of Reverse Primer (10 p
temperature, and 1min at 72°C (extension) followed by
moles/ µ l) (MWG) (Table-3), 0.5 µl of dNTPs (2.5 mM)
a final extension step at 72°C for 5min. Amplification
Bangalore Genei, India, 0.5 µl of Taq DNA polymerase
products were electrophoresed in 2.6% agarose in 1 x TBE
buffer. The gels were stained with ethidium bromide
432