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.