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Molecular Plant Breeding 2013, Vol.4, No.38, 297
-
303
http://mpb.sophiapublisher.com
297
Research Report Open Access
Linkage Disequilibrium in a Diversity and Stress Adaptation Rice Panel for
Association Mapping
Yulong Xiao
1
, Chuanyuan yu
1
, Jonalyn M. Yabes
2
, Jianguo Lei
1
, Xiaoling Wang
1
, Zhiquan Wang
1
,
Hongping Chen
1
, Dindo A. Tabanao
2
1. Rice Research Institute, JiangXi Academy of Agricultural Science, 330200, China.
2. Plant Breeding and Biotechnology Division, Philrice, Science City of Munoz, Nueva Ecija, 3119, Philippines
Corresponding authors email:
databanao@yahoo.com
Authors
Molecular Plant Breeding, 2013, Vol.4, No.38 doi: 10.5376/mpb.2013.04.0038
Received: 03 Sep., 2013
Accepted: 22 Nov., 2013
Published: 30 Dec., 2013
Copyright
©2013 Xiao et al. This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted
use, distribution, and reproduction in any medium, provided the original work is properly cited.
Preferred citation for this article:
Xiao et al., Linkage Disequilibrium in a Diversity and Stress Adaptation Rice Panel for Association Mapping, Molecular Plant Breeding, Vol.4, No. 38:
297
-
303 (doi: 10.5376/mpb.2013.04.0038)
Abstract
Linkage disequilibrium (LD), arises due to several factors
，
is the genetic basis for association studies
。
The possibility of
separating LD due to linkage from LD due to other causes determines whether or not an association mapping can be conducted
successfully
。
In an attempt to associate markers with drought tolerance at vegetative stage, we examined the pattern of LD in a
diversity and stress adaptation rice panel containing 184 rice germplasm accessions with 141 polymorphic SSR markers that were
nearly evenly distributed at 3mb bin on the 12 rice chromosomes. Significant LD was detected across the genome of the 184 rice
genotypes and the extent of LD varied with different chromosomes, selfing in
O. sativa
species and existing of population structure
in the rice panel might be the major factors of creating high LD. No genetic linkage was detected except for two pairs of SSR
markers RM288 and RM464 (11.98758 Mb), RM215 and RM464 (14.61396 Mb), which were located on chromosome 9 at a
relatively far distance but showed significantly higher correlation. The high degree of LD and fast decay of LD detected in this
experiment indicating the 141 SSR markers used in the experiment could be feasible to carry out the whole-genome scan association
studies with a relatively high resolution.
Keywords
Linkage disequilibrium (LD); LD Decay; Rice; Association mapping
Introduction
In the last decades or so, the conventional genetic
based strategies have been used successfully in QTL
(quantitative trait loci) mapping for agronomically and
economically important genes in different crops
species such as tomato
、
Arabidopsis and rice
，
however,
QTLs identified throught this method is limited to loci
with large effects on the target quantitative trait
variation, other techniques that enable the rapidly
identification of genes playing modest roles associate
with the variation of quantitative traits are also needed.
Association mapping via linkage disequilibrium or LD
(non-random association of alleles at different loci)
offers promise in this area. The traditional approach of
linkage/QTL mapping reliant on developing large
mapping populations continues to suffer from lack of
mapping resolution inherent in samples with limited
meiotic cross-over events, while in association
mapping, there may not be any need to make crosses
initially to generate segregating populations, the
natural variation that exists in the available germplasm
can be utilized for mapping straightaway (Oraguzie et
al., 2007).
LD plays a central role in association analysis,
estimated of LD are important as an indication of how
useful LD-base association genetics approaches can be
when compared with other available mapping methods
(Rafalski et al., 2004), the distance over which LD
persists will determine the number and density of
markers and experimental design needed to perform
an association analysis. Garris et al. (2003) found out
rapid decay of LD around the
Xa5
locus in rice (
Oryza
sativa L.
) happed at each 100 kb as a result of more
recombination events, under this condition an average
of one marker per centiMorgan (where 1 cM =
200-300 kb) were requested for a whole-genome
association mapping, suggesting that candidate