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Molecular Plant Breeding 2010, Vol.1 No.5
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Table 1 Polymorphic information of markers
Item
Genomic-SSR
EST-SSR
All markers
No. of marker loci
76
40
116
No. of alleles
562
152
714
Variation of allele no.
2~16
2~10
2~16
Average allele no.
7.4
3.7
6.1
Variation of PIC
0.38~0.87
0.10~0.84
0.10~0.87
Average PIC
0.72
0.45
0.57
1.3 Linkage disequilibrium
The background LD (unlinked LD) in the genome
created by population structure was used to determine
specific critical value of LD on 4A chromosome
markers. The unlinked r
2
were obtained by analysis of
a total of 89 unlinked markers. The unlinked r
2
values
ranged from 0.000 to 0.299 for all unlinked loci pairs
with an average of 0.021. The 95th percentile of the
distribution of unlinked r
2
estimates was used as a
population-specific threshold for this parameter as an
evidence of linkage (
Breseghello
and Sorrels, 2006),
and the critical value is 0.054. The syntenic r
2
were
obtained by analysis of 31 SSR markers on
chromosome 4A, which covered the whole
chromosome. The syntenic r
2
values ranged from
0.000 to 0.388 with an average of 0.031, significantly
higher than the average of unlinked r
2
. Decay
scatterplots of the LD values based on the syntenic r
2
value for 103 accessions are shown in Figure 1. The
extent of LD on chromosome 4A was ~3 cM with the
critical value r
2
=0.054, and about 89% of LD pairs
were detected with r
2
<0.054.
Figure 1
Scatterplot of the LD (r
2
) against genetic distance (cM)
between all loci pairs on chromosome 4A. Horizontal straight
lines indicate the 95
th
percentile of the distribution of unlinked r
2
LD block was referred to a chromosomal region where
all pairs of adjacent loci were in LD (Stich et al. 2005).
Three LD blocks were detected on 4A. The first one
was observed in the centromeric region, including
barc206, barc138 and wmc420 within 3.5 cM (positions
3.6~7.1 cM, Figure
2). The second one was in the long
arm, including gwm637, wmc468, wmc707 and
wmc161 within 9.5 cM (positions 36.5~46 cM,
Figure
2). The last one was in the bottom of 4A long arm,
including wmc313, wmc497 and wmc219 within 4.7
cM (positions 82.9~87.6 cM, Figure 2).
Figure 2
Consensus map of loci tested on chromosome 4A
(Somers et al., 2004)
Note: Significant markers (
right
) are shown for six agronomic
traits and LD blocks indicated with
black
. The results of
previous studies on chromosome 4A (
left
) (long arm: Li et al.,
2002; Jantasuriyarat et al., 2004; Kumar et al., 2007; short arm:
Kirigwi et al., 2007);
PH:
Plant height;
SL: Spike length; SPS:
Spikelets per spike; SD: Spikelets density; GPS: Grains per
spike; TKW: Thousand kernel weight; GY: Grain yield