Additional file 1 of Genome-Wide Association Study (GWAS) to Identify Salt-Tolerance QTLs Carrying Novel Candidate Genes in Rice During Early Vegetative Stage

Additional file 1: Table S1. Rice varieties used in this study. Table S2. Analysis of variance for the studied traits in germplasm set of rice under normal and salinity stress conditions. Table S3. Pearson correlation coefficients between different traits under normal condition. Table S4. Pearson correlation coefficients between different traits under salinity condition. Table S5. Co-ancestory coefficients (Q) in 4 sub-populations for germplasm set used in the study. Table S6. Results of association mapping using MLM-Q-K model for detection of SNPs with significant association to the studied traits under normal condition. Table S7. Results of association mapping using MLM-Q-K model for detection of SNPs with significant association to the studied traits under salinity condition. Table S8. Approximate expression levels of candidate genes (in view of transcript per million, TPM) inferred from EST sources in Unigene database. Table S9. Haplotype analysis of candidate genes on rice chromosomes. Table S10. Co-expression analysis of candidate genes using riceFREND database. Table S11. Comparison of the locations of the detected genomic regions in this study (QTLs) and the known reported QTLs.

附加文件1：表S1。本研究所用的水稻品种。
表S2。正常及盐胁迫条件下水稻种质群体相关性状的方差分析。
表S3。正常条件下各性状间的皮尔逊相关系数。
表S4。盐胁迫条件下各性状间的皮尔逊相关系数。
表S5。本研究所用水稻种质群体的4个亚群的共祖系数（Q）。
表S6。采用MLM-Q-K模型开展关联定位的结果，用于检测正常条件下与所研究性状显著关联的单核苷酸多态性（Single Nucleotide Polymorphisms，SNPs）。
表S7。采用MLM-Q-K模型开展关联定位的结果，用于检测盐胁迫条件下与所研究性状显著关联的单核苷酸多态性（SNPs）。
表S8。从Unigene数据库的表达序列标签（Expressed Sequence Tag，EST）来源推断的候选基因近似表达水平（以每百万转录本数，Transcripts Per Million，TPM）计。
表S9。水稻染色体上候选基因的单倍型分析。
表S10。采用riceFREND数据库对候选基因进行共表达分析。
表S11。本研究中检测到的基因组区域（数量性状基因座，Quantitative Trait Locus，QTLs）与已报道的已知数量性状基因座的位置比较。