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Molecular Plant Breeding 2013, Vol.4, No.38, 297
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303
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4 Materials and Methods
A diversity and drought adaptation panel including
184 rice germplasm accessions which including all
kinds of rice genotypes:
indica
parental lines such as
Zhenshan 97B, Minghui 63 and IR72 etc; released
indica
conventional varieties such as NSIC RC9, PSB
Rc18, PSB RC 82 etc; local varieties such as Azucena,
Li-Jiang-Xin-Tuan-Hei-Gu etc; Aus type rice
genotypes such as Dular, FR13A, Nagina 22 etc,
tropical and temperate japonica type such as JAVA,
Moroberekan, Cypress, deep water rice genotypes
such as Aswina and Rayada; aromatic rice genotypes
such as KDML 105, and interspecific rice genotypes
such as WA878-6-20-1-4-P1-HB, WA880-1-32-1-1-
P2-HB and WAB 891SG33, as had been reported
previously
(Xiao et al., 2012a) were used for DNA
extraction, total genomic DNA was extracted from the
leaf tissue of six seedlings per variety following the
methods described by Murray and Thompson (Murray
and Thompson, 1980). 156 SSR markers that were
nearly evenly distributed at 3 Mb bin on the 12 rice
chromosomes were selected in this study, the map
position of the SSR loci was inferred on line
(http://www.Gramene.org/, 2006) (Table 1). The SSR
markers were first screened for their polymorphism,
allele diversity of the SSR markers in 184 varieties
was calculated using the PowerMarker V3.25 program
(Liu and Muse, 2005), markers that produced
monomorphic bands were abandoned and only those
produced biallelic or polymorphic bands were used for
LD analysis.
LD was analyzed followed the way used by
Flavio
and Mark (Flavio and Mark, 2006), in detail: the
program TASSEL (http://www.maizegenetics.net) was
used to estimate the LD parameter
r
2
among loci and
the comparison-wise significance was computed by
1000 permutations. The unlinked
r
2
and the syntenic
r
2
were estimated separately based on the LD for
unlinked loci and for loci on the same chromosome. A
critical value of
r
2
derived from the distribution of the
unlinked
r
2
by square root transformed the unlinked
estimates was used as an evidence of linkage. The
parametric 95
th
percentile of the distribution was taken
as the population-specific critical value of
r
2
, beyond
which LD was considered to be caused by genetic
linkage and the interception of the syntenic
r
2
with
this baseline was considered as the estimate of the
extent of LD in the chromosome.
Acknowledgments
This research was supported by the National Key Technologies
R&D Program of China during the 12th Five-Year Plan Period
(2012BAD20B03), the Innovation Fund Project of Jiangxi
Academy of Agricultural Science (2012CBS013), and the
Philippine Rice Research Institute (Phil Rice).
References
Agrama H.A., Eizenga G.C., and Yan W., 2007, Association Mapping of
Yield and its Components in Rice Cultivars. Molecular Breeding, 19:
341-356
Flavio B., and Mark E.S., 2006, Association Mapping of Kernel Size and
Milling Quality in Wheat (
Triticum aestivum
L.) Cultivars, Genetics,
172: 1165-1177.
Garris A.J., McCouch S.R., and Kresovich S., 2003, Population Structure
and its Effects on Haplotype Diversity and Linkage Disequilibrium
Surrounding the Xa5 locus of Rice (
Oryza sativa
L.), Genetics, 165:
759-769.
Gaut B.S., and Long A.D., 2003, The lowdown on linkage disequilibrium,
Plant Cell, 15: 1502-1506.
Liu K.J., and Muse S.V., 2005, Power Marker: An Integrated Analysis
Environment for Genetic Marker Analysis, Bioinformatics, 21:
2128-2129
Mather K.A., Caicedo A.L, Polato N.R., Olsen K.M., McCouch S., and
Purugganan M.D., 2007, The extent of linkage disequilibrium in rice
(
Oryza sativa
L.), Genetics, 177(4): 2223-2232.
Murray M.G., and Thompson W.F., Rapid isolation of high molecular weight
plant DNA, Nucleic Acid Res., 1980, 8: 4321-4325
Oraguzie N.C., Rikkerink E.H.A., and Gardiner S.E., 2007, Nihal De Silva
H. Association Mapping in Plants, Springer Science + Business Media,
LLC
Oraguzie N.C., Phillip L.W., Rikkerink E.H.A., and Silva H.N.D., 2007,
Linkage Disequilibrium: in Association Mapping in Plants. Springer
Science + Business Media, LLC
Oraguzie N.C., and Phillip L.W., 2007, An Overview of Association
Mapping: in Association Mapping in Plants. Springer Science +
Business Media, LLC
Palaisk K., Morgante M., Williams M., and Rafalski A., 2003, Contrasting
Effects of Selection on Sequence Diversity and Linkage Disequilibrium
at two Phtoene Synthease Loci, Plant Cell, 15:1795-1806
Rafalski A., and Morgante M., 2004, Corn and humans: recombination and
linkage disequilibrium in two genomes of similar size, Trends Genet.,
20(2): 103-111
Rakshit S., Rakshit A., Matsumura H., Takahashi Y., and Hasegawa Y., ,
2007, Large-Scale DNA Polymorphism Study of
Oryza sativa
and
O.
rufipogon
Reveals the Origin and Divergence of Asian Rice, Theor
Appl Genet., 114:731-743
Skot L., Humphreys Mo, Armstead I., Heywood S., Skot K.P., Sanderson R.,
Thomas I.D., Sanderson R., CHorlton K.H., and Hamilton N.R.S.,
2005, An association mapping approach to identify lowering time
genes in natural populations of
Lolium perenne
(L.), Mol. Breed.,
15:233-245
Xiao Y.L., Lei J.G., Yu C.Y., Quirino D.D.C., Jonalyn M.C., and Dindo A.T.,
2012, Genetic Similarity and Population Structure in a Rice Drought
Stress Adaptation Panel, Acta Agricultural Universitatis Jiangxiensis,
34(5): 886-892
Xiao Y.L., Yu C.Y., Lei J.G., Quirino D.D.C., Jonalyn M.C., and Dindo A.T.,
2012, Screening of Rice Germplasm Accessions for Vegetative
Drought Tolerance. Acta Agricultural Universitatis Jiangxiensis, 34(3):
0428-0433