ABCD Figure S1: Arabidopsis plants during a progressive drought stress. (A-B): Plants collected at day 0 of drought treatment. (C-D): Plants collected at day 5 of drought treatment. Scale bar = 1cm

Figure S2: Summary of changes in gene expression in roots and shoots of Arabidopsis plants in response to a progressive drought stress. (A). Venn diagram indicating the number of genes up-regulated in roots and shoots in at least one stage of the progressive drought stress. (B). Heat map illustrating changes in gene expression in roots and shoots during different stages of the progressive drought stress. (C). Venn diagram indicating the number of genes significantly down-regulated in roots and shoots in at least one stage of the progressive drought stress. (D). Number of genes significantly down-regulated at different stages of the progressive drought stress. Shoot up Root up 2,857 1,633 1,906 1d3d5d7d9d Shoot Root Shoot down Root down A B C D Color key Row Z score ,936 2,218

Calcium-binding protein (PC00060) Cell adhesion molecule (PC00069) Cell junction protein (PC00070) Chaperone (PC00072) Cytoskeletal protein (PC00085) Defense/immunity protein (PC00090) Enzyme modulator (PC00095) Extracellular matrix protein (PC00102) Hydrolase (PC00121) Isomerase (PC00135) Kinase (PC00137) Ligase (PC00142) Lyase (PC00144) Membrane traffic protein (PC00150) Nucleic acid binding (PC00171) Oxidoreductase (PC00176) Phosphatase (PC00181) Protease (PC00190) Receptor (PC00197) Signaling molecule (PC00207) Storage protein (PC00210) Structural protein (PC00211) Transcription factor (PC00218) Transfer/carrier protein (PC00219) Transferase (PC00220) Transmembrane receptor regulatory/adaptor protein (PC00226) Transporter (PC00227) 3 day5 day7 day9 day Root Shoot 283/497474/824914/ / /122423/ / /4126 Figure S3: GO enrichment analysis (protein classification) of genes in roots and shoots of Arabidopsis plants in response to a progressive drought stress. Go functional analysis for protein classification was performed using the panther classification system maintained at GO hits/Total up

3 day 5 day 7 day 9 day RootShoot 5HT2 type receptor mediated signaling pathway (P04374) Acetate utilization (P02722) Adenine and hypoxanthine salvage pathway (P02723) Alzheimer disease-amyloid secretase pathway (P00003) Alzheimer disease-presenilin pathway (P00004) Angiogenesis (P00005) Apoptosis signaling pathway (P00006) Ascorbate degradation (P02729) Asparagine and aspartate biosynthesis (P02730) B cell activation (P00010) BMP_signaling_pathway-drosophila (P06211) Beta1 adrenergic receptor signaling pathway (P04377) Beta2 adrenergic receptor signaling pathway (P04378) CCKR signaling map (P06959) Cadherin signaling pathway (P00012) Cell cycle (P00013) Cholesterol biosynthesis (P00014) Chorismate biosynthesis (P02734) Coenzyme A biosynthesis (P02736) Cortocotropin releasing factor receptor signaling pathway (P04380) Cysteine biosynthesis (P02737) Cytoskeletal regulation by Rho GTPase (P00016) DNA replication (P00017) DPP-SCW_signaling_pathway (P06212) DPP_signaling_pathway (P06213) De novo purine biosynthesis (P02738) De novo pyrimidine deoxyribonucleotide biosynthesis (P02739) De novo pyrmidine ribonucleotides biosythesis (P02740) EGF receptor signaling pathway (P00018) Endothelin signaling pathway (P00019) FAS signaling pathway (P00020) FGF signaling pathway (P00021) Fructose galactose metabolism (P02744) GBB_signaling_pathway (P06214) General transcription by RNA polymerase I (P00022) General transcription regulation (P00023) Glutamine glutamate conversion (P02745) Glycolysis (P00024) Gonadotropin releasing hormone receptor pathway (P06664) Heme biosynthesis (P02746) Heterotrimeric G-protein signaling pathway (P00026) Heterotrimeric G-protein signaling pathway (P00027) Heterotrimeric G-protein signaling pathway(P00028) Histidine biosynthesis (P02747) Huntington disease (P00029) Hypoxia response via HIF activation (P00030) Inflammation mediated by chemokine and cytokine signaling pathway (P00031) Insulin/IGF pathway-mitogen activated protein kinase kinase/(P00032) Insulin/IGF pathway-protein kinase B signaling cascade (P00033) Integrin signalling pathway (P00034) Interleukin signaling pathway (P00036) Ionotropic glutamate receptor pathway (P00037) Isoleucine biosynthesis (P02748) JAK/STAT signaling pathway (P00038) Leucine biosynthesis (P02749) Lipoate_biosynthesis (P02750) Lysine biosynthesis (P02751) Mannose metabolism (P02752) Metabotropic glutamate receptor group II pathway (P00040) Methionine biosynthesis (P02753) Muscarinic acetylcholine receptor 1 and 3 signaling pathway (P00042) Muscarinic acetylcholine receptor 2 and 4 signaling pathway (P00043) N-acetylglucosamine metabolism (P02756) Nicotinic acetylcholine receptor signaling pathway (P00044) Notch signaling pathway (P00045) O-antigen biosynthesis (P02757) Oxytocin receptor mediated signaling pathway (P04391) P53 pathway feedback loops 1 (P04392) PDGF signaling pathway (P00047) PI3 kinase pathway (P00048) PLP biosynthesis (P02759) Parkinson disease (P00049) Pentose phosphate pathway (P02762) Phenylalanine biosynthesis (P02765) Phenylethylamine degradation (P02766) Proline biosynthesis (P02768) Purine metabolism (P02769) Pyridoxal phosphate salvage pathway (P02770) Pyruvate metabolism (P02772) Ras Pathway (P04393) SCW_signaling_pathway (P06216) Salvage pyrimidine ribonucleotides (P02775) Sulfate assimilation (P02778) Synaptic_vesicle_trafficking (P05734) T cell activation (P00053) TCA cycle (P00051) TGF-beta signaling pathway (P00052) Thiamine biosynthesis (P02779) Thyrotropin-releasing hormone receptor signaling pathway (P04394) Toll receptor signaling pathway (P00054) Toll_pathway_drosophila (P06217) Transcription regulation by bZIP transcription factor (P00055) Tryptophan biosynthesis (P02783) Ubiquitin proteasome pathway (P00060) Valine biosynthesis (P02785) Vitamin B6 biosynthesis (P02786) Vitamin B6 metabolism (P02787) Vitamin D metabolism and pathway (P04396) Wnt signaling pathway (P00057) mRNA splicing (P00058) p53 pathway by glucose deprivation (P04397) p53 pathway feedback loops 2 (P04398) p53 pathway (P00059) Figure S4: GO enrichment analysis (pathway) of genes in roots and shoots of Arabidopsis plants in response to a progressive drought stress. Go functional classification for pathway was performed using the panther classification system maintained at

Genes upregulated in roots and shootsGenes down regulated in roots and shoots Figure S5: Summary of GO enrichment analysis for genes up or down regulated both in roots and shoots of Arabidopsis plants in response to a progressive drought stress. The GO analysis were performed by AGRiGO maintained at

Root 5d Root 3d FigureS6: Differential expression of genes in roots and shoots of Arabidopsis at day 3 and day 5 of a progressive drought stress (MapMan 3.6.0RC1). Shoot 3d Shoot 5d Log2 His Phe Tyr Trp mis Ser Gly Cys mis Val Leu Iie Asn Thr Met Lys mis Gln Pro Arg Hyp mis His Phe Tyr Trp mis Ser Gly Cys mis Val Leu Iiel Asn Thr Met Lys mis Gln Pro Arg Hyp mis His Phe Tyr Trp mis Ser Gly Cys mis Val Leu Iie Asn Thr Met Lys mis Gln Pro Arg Hyp mis His Phe Tyr Trp mis Ser Gly Cys mis Val Leu Iiel Asn Thr Met Lys mis Gln Pro Arg Hyp mis His Phe Tyr Trp mis Ser Gly Cys mis Val Leu Iie Asn Thr Met Lys mis Gln Pro Arg Hyp mis His Phe Tyr Trp mis Ser Gly Cys mis Val Leu Iiel Asn Thr Met Lys mis Gln Pro Arg Hyp mis His Phe Tyr Trp mis Ser Gly Cys mis Val Leu Iie Asn Thr Met Lys mis Gln Pro Arg Hyp mis His Phe Tyr Trp mis Ser Gly Cys mis Val Leu Iiel Asn Thr Met Lys mis Gln Pro Arg Hyp mis

Shoot 9d Shoot 7d Root 9d Root 7d FigureS7: Differential expression of genes in roots and shoots of Arabidopsis at day 7 and day 9 of a progressive drought stress (MapMan 3.6.0RC1) Log2 His Phe Tyr Trp mis Ser Gly Cys mis Val Leu Iie Asn Thr Met Lys mis Gln Pro Arg Hyp mis His Phe Tyr Trp mis Ser Gly Cys mis Val Leu Iiel Asn Thr Met Lys mis Gln Pro Arg Hyp mis His Phe Tyr Trp mis Ser Gly Cys mis Val Leu Iie Asn Thr Met Lys mis Gln Pro Arg Hyp mis His Phe Tyr Trp mis Ser Gly Cys mis Val Leu Iiel Asn Thr Met Lys mis Gln Pro Arg Hyp mis His Phe Tyr Trp mis Ser Gly Cys mis Val Leu Iie Asn Thr Met Lys mis Gln Pro Arg Hyp mis His Phe Tyr Trp mis Ser Gly Cys mis Val Leu Iiel Asn Thr Met Lys mis Gln Pro Arg Hyp mis Phe Tyr Trp mis Ser Gly Cys mis Val Leu Iie Asn Thr Met Lys mis Gln Pro Arg Hyp mis His Phe Tyr Trp mis Ser Gly Cys mis Val Leu Iiel Asn Thr Met Lys mis Gln Pro Arg Hyp mis

Root Shoot 3d 5d 7d 9d Figure S8: Summary of PageMan analysis of up- and down-regulated bins in roots and shoots of Arabidopsis plants during a progressive drought stress. The bins shown in red are significantly up-regulated, while bins shown in blue are significantly down-regulated according to PageMan analysis (Wilcoxon test with BH correction, MapMan 3.6.0RC1). Major CHO metabolism Mitochondrial electron Transport/ATP synthesis Cell wall Secondary metabolism Amino acid metabolism Hormone metabolism Nucleotide metabolism RNA DNA synthesis/chromatin structure DNA DNA repair Protein Signaling Micro RNA Development Transport Up-regulated Down-regulated