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We have studied the agronomic, yield and quality traits of 151 soybean accessions for 2 years.SCoT, CDDP and ISSR molecular markers were utilized in analyzing the relation between molecular markers and traits in order to identify the highly associated loci to these traits, and to sequence the elite loci.The results were as follows:1.There were different LD among 27028 locus combinations induced from the 233 marker loci;correlation analysis between 233 polymorphic marker loci and mean phenotype (two years) of 151 accessions of soybean, using General linear model (GLM) and Mixed linear model (MLM) programs of TASSEL 4.0 software, indicated that there was significant association between 41 loci and 14 phenotype traits for 141 times (P<0.005).