Molecular Plant Breeding 2016, Vol.7, No.12, 1
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Table 3 Molecular marker polymorphism and their linkage
analysis
Chromosome
Total marker tested
percentage
(%)
Polymorphic markers
Chromosome length
a
1
90
14.4%
13
276.13
2
72
13.9%
10
224.16
3
82
12.2%
10
246.68
4
102
9.8%
10
129.22
5
60
15%
9
232.15
6
90
11.1%
10
194.44
7
45
15.5%
7
201.52
8
58
17.2%
9
183.15
9
50
14%
7
138.45
10
55
14.5%
8
104.24
11
62
11.3%
7
136.28
12
54
14.8%
8
118.85
Total
820
13.4%
110
2185.27
Note:
a
Unit: cM
1.4 QTL mapping for grain size related traits
Fifteen QTLs for 5 grain size related traits with phenotypic variation ranged from 4.81 to 27.60% were identified,
respectively (Figure 3, 4; Table 4). LOD scores of identified QTLs varied from 2.50 to 9.40.
Four QTLs were detected for GL on chromosome 1, 3, 4 and 9, respectively.
qGL-3
, a major QTL for GL, which
was mapped in the interval flanking by markers 03M36.3 and 03M33.1, accounted for 27.60% of phenotypic
variation. All the QTLs have positive additive effect on phenotypic variation (Table 4), indicating the alleles
derived from NYZ at those QTL loci have increasing effect on long grain phenotype.
Four QTLs for GW were mapped on chromosome 2, 3, and 5, with phenotypic contributions varying from 8.16%
to 21.33%. Among them,
qGW-5a
and
qGW-5b
were located at the intervals on the chromosome 5, flanked by two
pairs of markers, M06502-M040 and M13153-05m26.62, respectively (Figure 3, 4; Table 4). The major QTL
qGW-5a
, with the largest LOD score (9.40), explained 21.33% of phenotypic variation. All the QTLs have
positive additive effect on phenotypic variation except
qGW-3
(Table 4). The results suggest that wider grain
phenotype was mainly controlled by the alleles derived from NYZ.
Although no statistically significant difference of LWR between two parents (Supplement Figure 1), five QTLs
underlying LWR were detected on chromosome 2, 3, 5, and 12, with the range of phenotypic contributions from
8.60% to 16.86% (Figure 3, 4; Table 4). Of which, both
qLWR-3a
and
qLWR-3b
were mapped on chromosome 3,
and flanked by 03M24.29-RM5488 and RM14391-M023, respectively. All QTLs have negative additive effect to
LWR except
qLWR-3b
, indicating the QTL alleles from Ce253 mainly contributed to the higher values of LWR.
Two identified TGW QTLs
qTGW-5
and
qTGW-6
, were mapped on chromosome 5 and 6, respectively. Both of
them have positive additive effect on TGW. This indicated that QTL alleles from NYZ increase TGW (Table 4).
We identified any QTL for GT in this study (Supplement Figure 2).
It is worth noting that there were three chromosome regions clustered with QTLs for grain size related traits in our
study. The first region, which was delimited by markers M018 and RM1211 on chromosome 2, was clustered with
qGW-2
and
qLWR-2
. The second region was mapped in the interval flanking by markers RM14391 and M023 on
chromosome 3, with which
qGW-3
and
qLWR-3b
clustered. The third region, flanked by M06502 and M09668 on
chromosome 5, was clustered with
qTGW-5
,
qGW-5a
, and
qLWR-5
. These results suggest that these regions might
exist a single QTL with pleiotropic effect for grain size related traits (Figure 4; Supplement Figure 3).
