Linkage Disequilibrium in a Diversity and Stress Adaptation Rice Panel for Association Mapping 
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Chuanyuan Yu1 ,
Jonalyn M. Yabes2 ,
Jianguo Lei1 ,
Xiaoling Wang1 ,
Zhiquan Wang1 ,
Hongping Chen1 ,
Dindo A. Tabanao2 
2. Plant Breeding and Biotechnology Division, Philrice, Science City of Munoz, Nueva Ecija, 3119, Philippines
Author Correspondence author
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
Estimated of linkage disequilibrium (LD) are important as an indication of how useful LD-base association genetics approaches can be when compared with other available mapping methods. The success of association mapping efforts depends on the possibilities of separating LD due to linkage from LD due to other causes. 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 3 mb 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.