Additional file 1 of Integration of Dual Stress Transcriptomes and Major QTLs from a Pair of Genotypes Contrasting for Drought and Chronic Nitrogen Starvation Identifies Key Stress Responsive Genes in Rice

Additional file 1: Supplementary Table 1: All differentially expressed genes identified under N-W+, N + W- and N_W- treatments compared to optimal input supply (N + W+) in root and shoot tissues of IR64 and N22. Supplementary Table 2: Comparison of the expression of N transporters, sensors and regulators under various stress treatments in IR64 and N22. Supplementary Table 3: Comparison of the expression of known transcription factors (TFs) under various stress treatments in IR64 and N22. Supplementary Table 4: Comparison of the expression of novel (not annotated) genes under various stress treatments in IR64 and N22. Supplementary Table 5: Comparison of plant hormone metabolism genes and their receptors under various stress treatments in IR64 and N22. Supplementary Table 6: Comparison of the expression profile of the genes and QTLs known for Nitrogen use efficiency. Supplementary Table 7: Details of primers designed for validation of the DEGs identified from transcriptome analysis by qPCR assay. Supplementary Table 8: SNPs in the two major QTL hotspot regions identified on chromosomes 1 and 6. Supplementary Table 9: Relative water content (%) under optimal and all the three stress conditions measured in an independent experiment. Supplementary Table 10: DEGS identified in genes encoding for major enzymes involved in C and N skeleton. Supplementary Table 11: Details of variations in cis elements between IR64 and N22 genotypes for 20 N transporter, N regulator, TOND1, Dof genes and candidate genes identified from the major QTLs mapped in the present study. Supplementary Table 12: miRNAs in the candidate genes present in interval of the QTL hotspot region identified on chromosome 6. Supplementary Table 13: Comparison of expression of DE ABA related genes under different stress treatments in two rice genotypes N22 and IR64.附加文件1：补充表1：相较于最优养分供应（N + W+）处理，在IR64与N22的根系和地上组织中，经N-W+、N+W-及N_W-处理后鉴定得到的全部差异表达基因（differentially expressed genes, DEGs）。补充表2：对比IR64与N22在各类胁迫处理下的氮转运蛋白、感应因子及调控因子的表达水平。补充表3：对比IR64与N22在各类胁迫处理下的已知转录因子（transcription factors, TFs）的表达水平。补充表4：对比IR64与N22在各类胁迫处理下的未注释新型基因的表达水平。补充表5：对比IR64与N22在各类胁迫处理下的植物激素代谢基因及其受体的表达水平。补充表6：对比已知氮素利用效率相关基因与数量性状位点（quantitative trait loci, QTLs）的表达谱。补充表7：用于通过实时荧光定量聚合酶链式反应（quantitative polymerase chain reaction, qPCR）验证转录组分析鉴定得到的差异表达基因的引物设计详情。补充表8：1号与6号染色体上鉴定得到的两个主要数量性状位点热点区域内的单核苷酸多态性（single nucleotide polymorphisms, SNPs）。补充表9：在独立实验中测得的最优养分供应及全部三种胁迫条件下的相对含水量（%）。补充表10：在编码参与碳氮骨架代谢的主要酶的基因中鉴定得到的差异表达基因。补充表11：20个氮转运蛋白、氮调控因子、TOND1、Dof基因以及本研究通过主要数量性状位点定位得到的候选基因，在IR64与N22基因型间的顺式作用元件变异详情。补充表12：6号染色体上鉴定得到的数量性状位点热点区域区间内候选基因中的微小RNA（microRNAs, miRNAs）。补充表13：在两种水稻基因型N22与IR64中，不同胁迫处理下的脱落酸（abscisic acid, ABA）相关差异表达基因的表达对比。