Additional file 1 of Genome- and Transcriptome-wide Association Studies to Discover Candidate Genes for Diverse Root Phenotypes in Cultivated Rice

Supplementary Material 1: Table S1. BIC values and the selected models for GWAS and TWAS. Table S2. Candidate genes for the GWAS peak identified at 6,199,732 bp on chromosome 8. Table S3. Candidate genes for the GWAS peak identified at 20,665,890 bp on chromosome 8. Table S4. Candidate genes for the GWAS peak identified at 17,902,506 bp on chromosome 11. Table S5. Summary of the top ten gene-phenotype associations for the 12 root phenotypes in TWAS. Table S6. Candidate gene selection from the 70 unique genes in the top-ten gene-phenotype associations in TWAS. Table S7. Summary of the six genes with a significant cis-eGWAS peak. Table S8. Summary of the filtering, GWAS, and eGWAS results for the 43 polymorphic variants from 2 kb upsteam to the end of the OsENT1 gene region. Table S9. Summary of the filtering, GWAS, and eGWAS results for the 24 polymorphic variants from 2 kb upsteam to the end of the OsDjA6 gene region. Table S10. SNP genotype of the 57 WRC acccessions at the putative TATA box-like motif, at the GWAS peak SNP, and at the eGWAS peak SNP补充材料1：附表S1。全基因组关联分析（Genome-Wide Association Study, GWAS）与转录组全关联分析（Transcriptome-Wide Association Study, TWAS）的贝叶斯信息准则（Bayesian Information Criterion, BIC）取值及最优模型筛选结果。附表S2：8号染色体6199732 bp位点处鉴定到的GWAS信号峰对应的候选基因。附表S3：8号染色体20665890 bp位点处鉴定到的GWAS信号峰对应的候选基因。附表S4：11号染色体17902506 bp位点处鉴定到的GWAS信号峰对应的候选基因。附表S5：12种根系表型的TWAS分析中排名前十的基因-表型关联汇总结果。附表S6：TWAS排名前十的基因-表型关联所涉及的70个独特基因的候选基因筛选情况。附表S7：携带显著顺式表达全基因组关联分析（expression Genome-Wide Association Study, eGWAS）信号峰的6个基因汇总结果。附表S8：OsENT1基因区域（上游2 kb至基因末端）内43个多态性变异的筛选、GWAS及eGWAS分析结果汇总。附表S9：OsDjA6基因区域（上游2 kb至基因末端）内24个多态性变异的筛选、GWAS及eGWAS分析结果汇总。附表S10：57份WRC种质材料在推定TATA盒样基序、GWAS峰值单核苷酸多态性（Single Nucleotide Polymorphism, SNP）及eGWAS峰值SNP处的SNP基因型数据。