Rice (Oryza sativa L.) feeds more than half the worlds population, and accounts for 20％ of the worlds total calorie intake.Rice grain shape related traits (grain length, width,thickness,andlength to-width ratio) have a direct bearing on grain weight and quality, and hence commercial success, of modern rice (Oryza sativa L.) cultivars.Grain yield in rice is determined by three major components: number of panicles per plant, number of grains per panicle, and grain weight.Among these, the most reliable trait is grain weight, which is measured as the 1,000-grain weight (TGW).Grain shape is characterized by a combination of grain length, grain width, and grain thickness.Grain size, as specified by grain length (GL), grain width (GW), and grain length to-width ratio (GL/GW), is a major determinant of grain appearance quality and grain weight in rice.Therefore, the identification of these important quality traits loci become a significant practice for improvement of rice as a stable crop.In this study, 262 pairs of simple sequence repeat (SSR) markers and 628 rice accession from different ecological regions were assessed on genetic diversity, population structure and linkage disequilibrium.628 rice varieties were planted on Jiangpu Experimental Farm, Nanjing Agricultural University, to investigate 5 seed components traits in 2013 and 2014.The linear mixed model method in software TASSEL was used to analyze the association between SSR markers and 5 seed components traits.The main results are summarized as follows:　　1.In the population which is made up of 628 rice varieties, phenotypic variation of five seed grain traits was high, coefficient of variation ranged from 8.37％ (grain thickness) to 30.0％ (grain length to width ratio), heritability in broad sense traits ranged from 88.24％ (grain thickness) to 98.79％ (grain length), and manifested stably in both of the years of study.　　2.A total of 2953 alleles were detected by 262 pairs of SSR markers in the population studied.These alleles ranged from 3 among the 628 varieties to 25 alleles with an average of 11.3 per marker locus.The average gene diversity of population was 0.7620 ranging from 0.2543 to 0.9406.An average of PIC was 0.7365 which range from 0.2465 to 0.9373.　　3.Seven subpopulations were found in the population constituted of 628 rice varieties by using two methods, i.e., STRUCTURE 2.2 analysis method and the Neighbor-Joining cluster method.The number of varieties contained from subpopulation 1 to subpopulation 7 were 31, 96, 86, 143, 96, 96 and 80 respectively.Linkage disequilibrium at certain extent was found between SSR marker loci either intra-chromosome or inter-chromosome within each subpopulations.The average D value and the standard disequilibrium coefficient from subpopulation 1 to subpopulation 7 were 0.64, 0.54, 0.59, 0.55, 0.59, 0.57 and 0.52 respectively.The minimum distance (D＜0.5) of decay from subpopulation 1 to subpopulation 7 were 79.39, 42.82, 83.67, 78.26, 73.70, 67.48 and 34.35 cM, respectively.　　4.A total of 62 SSR marker loci were detected significantly (P＜0.05) associated with five seed grain components traits in both years.Among them, 32 loci distributed on chromosome 1 to chromosome 12 were significantly related with grain length.RM297 had the highest contribution rate (22.0％); 1 locus was distributed on chromosome 1 with a contribution rate (7.2％) and was significantly related to grain width.RM84 had the highest contribution rate (16.3％); 23 loci were all distributed on chromosome 1 and was significantly related with grain thickness.RM297 had the highest contributing rate (13.9％); 5 loci were distributed on chromosome 1, 2 and was significantly related to grain length to width ratio.RM259 also had the highest contributing rate (5.64％); only 1 locus was distributed on chromosome 1 and was significantly related with 1,000-grain weight.　　5.Among the significantly associated loci detected in grain length (GL), 10 loci with the PVE were above 5％.And 62 positive elite were identified.The mean range of two years for the positive allele increasing GL phenotypic effect was 0.05mm (RM153-170bp) 4.3mm (RM6976-240bp and RM297-155bp).The carrier materials carried larger effect value (more than 3mm) for GL included Yuzhenxiang, Yuedao 41.　　In grain width (GW), 10 positive elite alleles were identified.The mean range of two years for the positive allele increasing GW phenotypic effect was 0.07mm (RM1-80bp) ～0.62mm (RM1-360bp).The carrier materials carried larger effect value for GW (more than 0.25mm) included Cuganhuangdao, Haonuopie, Luhuabai.　　Among the significantly associated loci detected in GLT, 7 loci with the PVE were above 5％.And 36 positive elite alleles were identified.The mean range of two years for the positive allele increasing GT phenotypic effect was 0.01 mm (RM259-215bp)～0.31 mm (RM3453-135bp).The carrier materials carried larger effect value for GL included Zhendao9424, Zhengdao18, Ningjing1R-122, Ningjing1R-61, Ningjing1R-37 and Zhendao99.And the effect values were more than 0.15mm.　　Among the significantly associated loci detected in GL/GW, 29 positive elite alleles were identified.The mean range of two years for the positive allele increasing GT phenotypic effect was 0.05 (RM300-170bp and RM300-115bp) ～3.35 (RM297-155bp).The carrier materials carried larger effect value for GL included Yuzhenxiang, Yuedao41 and Yuedao51.And the effect values were more than 1.5.　　In TGW, 11 positive elite alleles were identified.The mean range of two years for the positive allele increasing TGW phenotypic effect was 0.07g (RM259-80bp) ～2.74g (RM259-130bp).The carrier materials carried larger effect (more than 1.5g) value for TGW included Zhendao 10, Ningjing1 R-62 and Xiaobaiyedao.　　6.Parental combination for hybridization were predicted for improving grain sizes and weight by using carrier materials screened in this study.For instance, parental combinations which could improve GL were Yuzhenxiang×Yuedao41, Yuedao61× Yuedao41; parental combinations which could improve GT were Ningjing1R-122 × Zhendao99, Ningiing1R-122 × Ningjing1R-61; and parental combination which could improve grain length to width ratio wasYuzhenxiang× Yuedao62.