Page 7 - Molecular Plant Breeding

Molecular Plant Breeding 2013, Vol.4, No.38, 297-303
http://mpb.sophiapublisher.com
298
gene-based LD mapping could provide greater
resolution than conventional QTL mapping. Candidate
gene-based LD mapping was mostly advisable to be
used in plants with many megabase pairs per
centiMorgan but relatively rapid decay of
disequilibrium over short distance such as conifer and
onion (Oraguzie and Phillip, 2007). Thus, it is
important to know the pattern of LD in different
regions of the genome and in different populations in
one organism before making an informed choice of a
methodology for association genetics studies (Rafalski
et al., 2004).
In an attempt towards association mapping for drought
tolerance at vegetative stage in a diversity and stress
adaptation rice panel, we had already examined the
phenotypic performance of 184 rice germplasm
accession for vegetative drought tolerance under
natural drought conditions (Xiao et al., 2012a) and its
population structure and genetic relatedness using 141
polymorphic SSR markers that were nearly evenly
distributed at 3mb bin on the 12 rice chromosomes
(Xiao et al., 2012b), with the same genotypic data, we
were now trying to find out the LD model in this rice
panel and to check out if a whole-genome-scanning
association mapping could be used to identify loci for
drought tolerance at vegetative stage.
1 Results
Of the 156 SSR markers (Figure 1), thirteen produced
monomorphic bands and two produced blurred bands,
the rest 141 SSR markers produced either biallelic or
polymorphic bands and were used in population
structure, linkage disequilibrium and association
analysis. The number of alleles per locus varied from
2 to 7, with an average of 2.73.
Significant LD was detected across the genome of the
184 rice genotypes and extent of LD varied with
different chromosome (Figure 2). The pair-wise r2
among the 141 SSR markers varied from 0.0000 to
0.78197, the 95th percentile of the distribution of these
estimates was 0.3886, and it was used as a
population-specific threshold for this parameter as an
evidence of linkage, value of r 2>0.3886 were probably
due to genetic linkage.
Figure 1 Bands produced by SSR markers. A: RM192; B:
RM112; C: RM595
No genetic linkage was detected among the 141 SSR
markers across the 12 chromosome, however, two
pairs of SSR markers RM288 and RM464
(11.98758 Mb), RM215 and RM464 (14.61396 Mb)
showed significantly higher correlation at far distance
(Figure 3), all the three SSR makers were located on
chromosome 9.
2 Discussion
Significant LD was detected across the genome of the
184 rice genotypes (Figure 2), extent of LD varied
with different chromosome. A variety of mechanisms
could generate LD such as mutation, recombination
and selection and several of these can operate
simultaneously (Oraguzie et al., 2007). The
significance of LD detected here might be due to the
syntenic r 2 calculated from loci on the same
chromosome. Some SSR markers located on the same
chromosomes were relatively close to each other, such
as RM276 and RM19621, there was only 0.01mb
between the two markers, and RM547 and RM22554
on chromosome 8, which were lactated almost at the
same position on chromosome 8. Such a physically
close distance between nearby markers on the same
chromosome could produce a high LD. Secondly, LD
is commonly founded in natural populations between
loci for which recombination has not had sufficient
time to dissipate the initial disequilibrium, since the
materials used here were mostly parental lines and
released inbreeding lines, selfing in O. sativa leads to