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Computational Molecular Biology 2014, Vol. 4, No. 12, 1-8
http://cmb.biopublisher.ca
7
Table 2 The primers which used for checking amplification
SL NO.
PRIMER NAME
SEQUENCE ( 5-3)*
SPECIFIC
START-END
1
Dep1-1F
CGAGGGGTGGTTCTGAGTT
Overlapping
22
2
Dep1-1R
CGCTCTTCTTTTCTCCAACG
Overlapping
611
3
Dep1-2F
GCGTTGTTAATTGCGGTAGC
Exon1_2 (420-1080bp)
426
4
Dep1-2R
AGATTCCTGCTTTACTGTGTAAGTG
Exon1_2 (420-1080bp)
1029
5
Dep1-3F
AATCAAATGCGCTTTAGACATC
Exon1_3 (900-1560)
912
6
Dep1-3R
CAAAATATCTGTAATGCATGAAGGG
Exon1_3 (900-1560)
1502
17
APO-1F
CACTCCACTTCACCCTTGAAA
OVERLAPPING
6
18
APO-1R
GAAGGGGGACACGAGGTC
OVERLAPPING
644
27
GHD7-2F
TGATTGATTCATCGATCCTCC
Exon1_3 (900-1560bp)
818
28
GHD7-2R
TCAACAAACTGTAAGTAAATAGACCG
Exon1_3 (900-1560bp)
1549
Table 3 Amplification pattern of genomes of high and low grain rice varieties with designed primers
Gene Primer
Promoter/Exon
Annealing Temperature
(
0
C)
Size
of
product (bp)
Amplification*
Comment**
HGN1 Heera
HGN1
Heera
Dep1
Dep1-1
Promoter
53
600
+
-
F
-
54
600
+
-
F
-
55
600
+
-
F
-
56
600
+
-
M
-
57
600
+
-
M
-
58
600
+
-
D
-
Dep1-2
Exon 1
53
600
+
+
F
F
54
600
+
+
F
M
55
600
+
+
F
M
56
600
+
+
F
D
57
600
+
+
F
D
58
600
+
+
M
M
Dep1-3
Exon 2
53
600
+
+
F
VD
54
600
+
+
F
VD
55
600
+
+
F
VD
56
600
+
+
F
VD
57
600
+
+
M
VD
58
600
+
+
M
VD
Ghd7
Ghd7-2
Promoter
53
+
-
M
-
54
+
-
M
-
55
+
-
D
-
56
+
-
D
-
57
+
-
D
-
58
+
-
D
-
Apo1
Apo1-1
Promoter
53
-
-
-
-
-
54
-
-
-
-
-
55
-
-
-
-
-
56
-
-
-
-
-
57
-
-
-
-
-
58
-
-
-
-
-
Note: * + = Presence of band, - = Absence of band, ** Strength(concentration of amplified band; F= Faint band, M= Medium band,
D= Deep band, VD= Very deep band