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Molecular Plant Breeding 2013, Vol.5, No.9, 47
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63
http://mpb.biopublisher.ca
52
Table 4 Distribution and number of polymorphic SNP s used for mapping in the F
5
–derived recombinant inbred lines from
IR29×Hasawi
Chromosome number
Number of polymorphic SNPs
Total interval size (cM)
Mean interval size (cM)
1
28
172.38
6.38
2
13
144.55
11.12
3
19
137.93
7.26
4
16
127.09
7.94
5
18
116.32
6.46
6
20
126.75
6.34
7
17
115.64
6.80
8
12
107.37
8.95
9
17
93.44
5.50
10
8
93.95
11.74
11
15
112.57
7.50
12
11
93.97
8.54
Total
194
1441.96
7.88
Table 5 Allele’s distribution across chromosomes in the F
5
–derived recombinant inbred lines from IR29×Hasawi
Chromosome number
Allele percentage
Missing
Homozygous
Heterozygous
*
G
A
T
C
A/G
C/G
A/T
A/C
1
0.4
28.2
42.9
6.2
13.1
6.8
0.5
0.9
0.8
2
0.4
44.6
38.1
3.5
6.7
5.1
0
0.7
1.0
3
0.4
33.8
35.3
4.6
19.2
3.7
1.5
0.2
1.3
4
2.4
32.3
43.2
7.4
7.3
4.7
1.3
1.1
0.2
5
0.7
23.3
50.9
6.8
12.8
4.3
0.3
0.4
0.6
6
0.3
34
46.7
5.0
9.3
3.0
0.2
1.1
0.4
7
0.6
30.4
49.1
4.2
7.0
5.1
0.0
1.6
2.0
8
0.7
25.2
28.2
12
25.3
3.1
1.1
2.4
1.9
9
0.5
51.6
37.7
0.1
5.5
3.0
0.7
0.4
0.5
10
0.4
46.4
24.7
4.4
16.1
4.1
0.3
1.7
1.8
11
0.8
18.1
57.5
11.9
5.3
4.6
0.0
1.0
0.8
12
0.8
41.8
31.4
4.9
14.1
5.4
0.3
1.0
0.4
Total
0.7
33.1
41.9
5.8
11.5
4.5
0.5
1.0
0.9
0.7
92.3
6.9
Note: A/G, C/G, A/T, and A/C are the heterozygous of the four different DNA nucleosides
1.6 QTL
identification
There
were
four
QTL
for
shoot
dry
weight,
2
each
on
chromosomes
1
and
2
(Table
6;
Figure
6),
two
QTL
for
plant
height,
and
one
QTL
for
shoot
fresh
weight.
All
QTL
were
in
chromosomes
1,
2
and
6,
and
their
contribution
to
the
phenotypic
variation
observed
for
each
characteristic
associated
with
salt
tolerance
ranged
from
10.6
to
42.3%
(Figure
6),
The
LOD
score
for
these
seven
QTL
varied
from
3.49
to
17.17.
No
peak marker
at
a
particular
position
could
be
noted
and
the
nearest markers were
therefore
used
as
peak.
Figure 6 Quantitative trait loci for shoot dry weight on chromosome
2 with the SNPmarker ID on the x-axis and LOD score on the Y-axis