A Potassium-Dependent Oxygen Sensing Pathway Regulates ...€¦ · Zaigham Shahzad, Matthieu Canut, Colette Tournaire-Roux, Alexandre Martinière, Yann Boursiac, Olivier Loudet, and

Cell, Volume 167

Supplemental Information

A Potassium-Dependent Oxygen Sensing

Pathway Regulates Plant Root Hydraulics

Zaigham Shahzad, Matthieu Canut, Colette Tournaire-Roux, Alexandre Martinière, YannBoursiac, Olivier Loudet, and Christophe Maurel

1

SUPPLEMENTAL TABLES

Table S1. Means, Ranges, and Broad-Sense Heritabilities (h²) of Hydraulic and Growth Phenotypic Traits

in Two Parental Lines (Bur-0, Col-0) and in RILs Derived from their Cross, Related to Figure 1

Trait Means (±SEM) RIL Range h²

Bur-0 Col-0 RILs Root hydraulic conductivity (ml g-1 hr-1 MPa-1) :

Lpr 99.3 ±6.4 134.3±6.2 128.9 ±2.8 75.1-221.3 0.45

Root hydraulic conductance (ml hr-1 MPa-1) :

L0 0.50±0.02 0.65±0.02 0.40±0.01 0.07-0.72 0.59

Root dry weight (g) : DWr 0.0052±0.0002

0.0049±0.0002

0.0032±0.0001

0.0007-0.0069 0.59

Shoot dry weight (g): DWs 0.030±0.001

0.026±0.001

0.020±0.001

0.007-0.036 0.51

Shoot dry weight to Root dry weight ratio:

DWs/DWr 5.75±0.30 5.29±0.31 6.84±0.19 4.07-16.54 0.61

2

Table S2. Quantitative Trait Loci (QTLs) Identified Using a Multiple QTL Mapping Method

Implemented in R/qtl, Related to Figure 1

Trait and QTL(a) Chromosome Map

position (cM)

Marker(b) LOD score

% of variance

(R2)

Additive effect (c)

Root hydraulic conductivity [Lpr (ml g-1 hr-1 MPa-1)] Lprm120 1 42.1 c1_15634 4.10 15.1 11.64 Lprt320 3 3.7 c3_01901 2.81 10.9 -9.88

Lprm320 3 19.3 c3_08042 4.47 15.4 -11.74 Root dry weight [DWr (g)]

DWrm120 1 50.8 c1_16875 3.40 14.4 -0.00040 Shoot dry weight to root dry weight ratio (DWs/DWr)

DWs/DWrb120 1 84.6 c1_25698 2.69 13.5 0.643 DWs/DWrb420 4 46.4 c4_15765 2.53 12.5 -0.620

(a) The name given to the QTL starts with the trait code (refer to table S1), followed by the relative chromosomal position (top: t; middle: m; bottom: b), the chromosome number and the RIL population (i.e. 20 for 20RV). (b) Closest left marker flanking the LOD score peak. (c) Mean effect (in trait unit) of the replacement of the Col-0 allele by the Bur-0 allele

3

Table S3. Origin and Haplogroups of Arabidopsis Accessions Used in the Study, Related

to Figure 1

Accession name NASC entry name Country of origin Haplogroup (a)

Ag-0 76087 FRA H1 Bla-1 76097 ESP H1 Bor-4 76100 CZE H1 Col-0 76113 GER H1 Hey-1 28344 NED H1 Hod 76141 CZE H1

Lp2-2 76176 CZE H1 Lp2-6 76177 CZE H1 N13 76194 RUS H1

Pu2-23 76215 CZE H1 Sei-0 28729 ITA H1

Sparta-1 76229 SWE H1 Tottarp-2 76251 SWE H1

Gr-1 76137 AUT H1 Nd-1 76197 SUI H1

Amel-1 28014 NED H2 Bur-0 76105 IRL H2 Ct-1 76114 ITA H2

Hov4-1 76142 SWE H2 Tomegap-2 76250 SWE H2

Ge-0 76135 SUI H2 T1110 76236 SWE H2 Alst-1 28013 UK H3 An-1 76091 BEL H3

Boot-1 28091 UK H3 Fei-0 76129 POR H3 Got-7 76136 GER H3 Ha-0 28336 GER H3

Kelsterbach-4 76152 GER H3 NFA-10 76198 UK H3

Tsu-0 28780 JPN H3 Uk-1 28787 GER H3

Ang-0 28018 BEL H4 Gel-1 28279 NED H4 Ler-1 76164 POL H4 Ste-3 76232 USA H4 Wei-0 76301 SUI H4

4

Zu-1 28847 SUI H4 App1-16 76092 SWE H5

Hn-0 28350 GER H5 Kl-5 28394 GER H5

Lom1-1 76174 SWE H5 Mt-0 76192 LIB H5 Est-1 76127 RUS H5 In-0 76147 AUT H5 Jl-3 28369 CZE H5

Rev-2 76219 SWE H5 Se-0 76226 ESP H5

Ting-1 28759 SWE H5 Yo-0 76305 USA H5 Aa-0 28007 GER H6

Bsch-0 28099 GER H6 Hh-0 28345 GER H6 Koln 76155 GER H6 Kro-0 28420 GER H6 Oy-0 76203 NOR H6

Utrecht 28795 NED H6 Ba-1 28053 UK H7 Edi-0 76126 UK H7 Gy-0 76139 FRA H7

Hovdala-2 76143 SWE H7 Hs-0 76145 GER H7 Mz-0 76193 GER H7 No-0 28564 GER H7 Nw-0 28573 GER H7 Ren-1 76218 FRA H7 Sg-1 28732 GER H7 Sp-0 28743 GER H7 Ty-0 28786 UK H7 Bu-0 76103 GER H7

Rsch-4 76222 RUS H7 Sanna-2 76223 SWE H7

(a) To determine haplogroups, predicted HCR1 protein sequences were retrieved from Arabidopsis 1001 Genomes database, http://signal.salk.edu/atg1001/3.0/gebrowser.php.

5

Table S4. Elemental Composition of Different Media Used in this Study, Related to Figure 2

Salt/ hormone

Standa-rd

(mM)

Low NO3

(mM)

Minus PO4

(mM)

Low SO4

(mM)

Minus K

(mM)

Minus Fe

(mM)

NaCl (mM)

Cytok-inin

(mM)

Ethep-hon

(mM)

Jasm-onic acid

(mM) KNO3 1.25 _ 1.25 1.25 _ 1.25 1.25 1.25 1.25 1.25 KCl _ 1.25 0.50 _ _ _ _ _ _ _ KH2PO4 0.50 0.50 _ 0.50 _ 0.50 0.50 0.50 0.50 0.50 Ca(NO3)2 1.50 0.10 1.50 1.50 1.50 1.50 1.50 1.50 1.50 1.50 CaCl2 _ 1.40 _ _ _ _ _ _ _ _ MgSO4 0.75 0.75 0.75 _ _ 0.75 0.75 0.75 0.75 0.75 MgCl2 _ _ _ 0.75 0.29 _ _ _ _ _ Fe-EDTA 0.05 0.05 0.05 0.05 0.05 _ 0.05 0.05 0.05 0.05 Na2SiO3 0.10 0.10 0.10 0.10 0.10 0.10 0.10 0.10 0.10 0.10 Na2MoO4 0.00024 0.00024 0.00024 0.00024 0.00024 0.00024 0.00024 0.00024 0.00024 0.00024 H3BO3 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 MnSO4 0.012 0.012 0.012 0.012 0.012 0.012 0.012 0.012 0.012 0.012 ZnSO4 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 CuSO4 0.0007 0.0007 0.0007 0.0007 0.0007 0.0007 0.0007 0.0007 0.0007 0.0007 NaNO3 _ _ _ _ 1.25 _ _ _ _ _ NaCl _ _ _ _ _ _ 50.00 _ _ _ NaH2P04 _ _ _ _ 0.50 _ _ _ _ _ EDTA _ _ _ _ _ 0.05 _ _ _ Cytokinin _ _ _ _ _ _ _ 0.001 Ethephon _ _ _ _ _ _ _ _ 1 Jasmonic acid

_ _ _ _ _ _ _ _ 0.1

6

Table S5. List of Genes that are Differentially Regulated Between Col-0 and hcr1 Mutants, Related to

Figure 3

Transcript Cluster ID

Gene AGI number

log2 Col-0

log2 hcr1-1

log2 hcr1-2

FC (L) hcr1-1 vs. Col-0

FC (L) hcr1-2 vs. Col-0

ANOVA P-value (hcr1-1 vs Col-0)

ANOVA P-value (hcr1-2 vs Col-0)

Gene description

13499814 AT5G10040 9.31 8.87 5.99 -1.36 -9.99 0.4220 0.0483 hypothetical protein

13416753 AT2G34390 8.97 8.65 6.28 -1.24 -6.43 0.3690 0.0453 aquaporin NIP2-1

13499817 AT5G10050 8.14 7.87 6.06 -1.21 -4.25 0.4689 0.0432 Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain-containing protein

13492757 AT4G33070 10.33 9.94 8.34 -1.31 -3.99 0.3482 0.0417 pyruvate decarboxylase

13455664 AT3G43190 10.44 10.13 8.58 -1.24 -3.63 0.4024 0.0418 sucrose synthase 4

13405943 AT2G46790 4.49 3.83 2.65 -1.58 -3.6 0.2605 0.0130 two-component response regulator-like APRR9

13491826 AT4G31020; AT4G31010

6.11 6.03 4.28 -1.06 -3.56 0.4896 0.0474 alpha/beta-Hydrolases superfamily protein; CRS2-associated factor 1-like protein

13335374 AT1G03610 7.22 6.55 5.53 -1.6 -3.24 0.2994 0.0257 hypothetical protein

13443997 AT3G03270 7.57 7.23 5.93 -1.26 -3.11 0.4393 0.0421 adenine nucleotide alpha hydrolases-like protein

13514081 AT5G52640 4.83 4.3 3.22 -1.44 -3.05 0.5332 0.0227 heat shock protein 90.1

13409116 AT2G15880 7.93 7.88 6.44 -1.03 -2.8 0.4077 0.0136 pollen-specific leucine-rich repeat extensin-like protein 3

13477244 AT4G33950 5 4.78 3.61 -1.16 -2.63 0.4015 0.0233 calcium-independent ABA-activated protein kinase

13427024 AT3G11930 8.42 8.01 7.02 -1.32 -2.63 0.2923 0.0337 universal stress protein-like protein

13540794 AT5G58070 8.06 7.9 6.67 -1.11 -2.61 0.4281 0.0390 temperature-induced lipocalin TIL1; VAMP-like protein YKT61

13528865 AT5G20830 9.33 8.97 8 -1.28 -2.5 0.4126 0.0394 sucrose synthase 1

13448447 AT3G12580 6.91 6.56 5.73 -1.27 -2.27 0.3635 0.0363 heat shock protein 70-4

13360077 AT1G77120 11.13 10.98 10.01 -1.11 -2.17 0.3628 0.0448 alcohol dehydrogenase 1

13490383 AT4G27450 9.94 9.7 8.84 -1.18 -2.14 0.4047 0.0214 aluminum induced protein with YGL and LRDR motifs

13507422 AT5G35940 4.71 3.75 3.62 -1.95 -2.13 0.0544 0.0014 jacalin-like lectin family protein

13383179 AT1G64720 8.32 8.24 7.28 -1.06 -2.06 0.4182 0.0438 membrane related protein CP5

13375066 AT1G33050; AT1G33055

7.33 7.01 6.31 -1.25 -2.02 0.3082 0.0315 hypothetical protein

13356037 AT1G67105 5.3 4.89 4.31 -1.33 -1.98 0.3651 0.0396 other rna

13354090 AT1G61450 3.56 2.96 2.6 -1.51 -1.95 0.0300 0.1053 hypothetical protein

13453440 AT3G24730 4.56 4.28 3.62 -1.22 -1.92 0.0541 0.0084 mRNA splicing factor, thioredoxin-like U5 snRNP

13509474 AT5G42200 4.84 4.48 3.9 -1.28 -1.92 0.4017 0.0399 E3 ubiquitin-protein ligase ATL23

13350046 AT1G49560 4.44 4.28 3.5 -1.11 -1.91 0.7515 0.0376 myb family transcription factor

13456681 AT3G46230 2.65 2.22 1.71 -1.35 -1.91 0.4218 0.0448 heat shock protein 17.4

13345677 AT1G28760 5.23 4.75 4.36 -1.39 -1.83 0.2612 0.0299 hypothetical protein

13538481 AT5G51900 1.93 1.12 1.11 -1.75 -1.77 0.0464 0.0487 Cytochrome P450 family protein

13431526 AT3G21560 4.13 3.81 3.37 -1.26 -1.7 0.3603 0.0208 sinapic acid:UDP-glucose glucosyltransferase

13429761 AT3G17860 7.07 6.84 6.32 -1.17 -1.68 0.2824 0.0295 jasmonate-zim-domain protein 3

13384742 AT1G67910 3.41 2.91 2.7 -1.41 -1.63 0.0413 0.0109 hypothetical protein

13345673 AT1G28820 2.15 1.47 1.45 -1.61 -1.63 0.0056 0.0182 pre-tRNA; tRNA-Pro (anticodon: AGG)

7

13345675 AT1G28870 2.15 1.47 1.45 -1.61 -1.63 0.0056 0.0182 pre-tRNA; tRNA-Pro (anticodon: AGG)

13400438 AT2G33920 2.15 1.47 1.45 -1.61 -1.63 0.0056 0.0182 pre-tRNA; tRNA-Pro (anticodon: AGG)

13400442 AT2G33960 2.15 1.47 1.45 -1.61 -1.63 0.0056 0.0182 pre-tRNA; tRNA-Pro (anticodon: AGG)

13434526 AT3G29095 2.15 1.47 1.45 -1.61 -1.63 0.0056 0.0182 pre-tRNA; tRNA-Pro (anticodon: AGG)

13459065 AT3G52285 2.15 1.47 1.45 -1.61 -1.63 0.0056 0.0182 pre-tRNA; tRNA-Pro (anticodon: AGG)

13465228 AT4G03135 2.15 1.47 1.45 -1.61 -1.63 0.0056 0.0182 pre-tRNA; tRNA-Pro (anticodon: AGG)

13533574 AT5G39535 2.15 1.47 1.45 -1.61 -1.63 0.0056 0.0182 pre-tRNA; tRNA-Pro (anticodon: AGG)

13351485 AT1G53110 4.96 4.61 4.26 -1.27 -1.62 0.0829 0.0122 putative proton pump interactor protein

13493428 AT4G34340 3.43 2.72 2.74 -1.64 -1.62 0.3825 0.0271 TBP-associated factor 8

13386584 AT1G72850 5.63 5.6 4.95 -1.02 -1.61 0.3864 0.0278 TIR-NBS class of disease resistance protein

13523895 AT5G09620 4.88 4.58 4.19 -1.23 -1.61 0.2045 0.0467 octicosapeptide/Phox/Bem1p family protein

13506278 AT5G27090 1.76 0.94 1.07 -1.76 -1.61 0.0361 0.2131 protein agamous-like 54

13509906 AT5G43080 3.56 3.23 2.9 -1.26 -1.59 0.1830 0.0027 cyclin A3-1

13453585 AT3G25410 5.42 4.91 4.75 -1.42 -1.59 0.1361 0.0351 probable sodium/metabolite cotransporter BASS3

13510415 AT5G44286 2.45 1.82 1.78 -1.55 -1.59 0.0864 0.0026 SnoRNA

13503312 AT5G19140 7.54 7.44 6.87 -1.07 -1.58 0.3986 0.0219 aluminum induced protein with YGL and LRDR motifs

13422444 AT2G47560 6.74 6.35 6.08 -1.31 -1.57 0.1698 0.0206 RING-H2 finger protein ATL64

13540961 AT5G58570; AT5G58560

2.76 2.76 2.13 -1.01 -1.55 0.5443 0.0380 hypothetical protein; farnesol kinase

13406472 AT2G47890 6.9 6.87 6.27 -1.02 -1.55 0.4913 0.0472 zinc finger protein CONSTANS-LIKE 13

13517645 AT5G60750 5.21 5.16 4.6 -1.03 -1.53 0.5540 0.0156 CAAX amino terminal protease family protein

13390195 AT1G80670 6.69 6.58 6.07 -1.08 -1.53 0.7580 0.0486 Rae1-like protein

13443795 AT3G02800 5.79 5.58 5.18 -1.16 -1.53 0.4265 0.0125 atypical dual-specificity phosphatase

13435789 AT3G45450 2.7 2.49 2.09 -1.16 -1.53 0.3180 0.0299 Double Clp-N motif-containing P-loop nucleoside triphosphate hydrolases superfamily protein

13449344 AT3G14200 6.92 6.73 6.31 -1.14 -1.52 0.2724 0.0209 chaperone DnaJ-domain containing protein

13414031 AT2G28010 3.46 3.07 2.86 -1.3 -1.51 0.1294 0.0137 aspartyl protease-like protein

13366036 AT1G10140 5.69 5.08 5.11 -1.53 -1.5 0.0488 0.0167 hypothetical protein

13432844 AT3G24715 4.87 3.31 4.3 -2.94 -1.48 0.0072 0.0085 octicosapeptide/Phox/Bem1p domain-containing protein kinase

13466702 AT4G09360 2.5 1.72 1.97 -1.71 -1.44 0.0323 0.1693 NB-ARC domain-containing disease resistance protein

13408437 AT2G09970 1.58 0.93 1.1 -1.57 -1.39 0.0083 0.0381 hypothetical protein

13531075 AT5G26000 4.5 3.79 4.04 -1.63 -1.37 0.0492 0.1069 myrosinase 1

13405201 AT2G45080 3.74 3.05 3.46 -1.62 -1.21 0.0393 0.1163 cyclin p3;1

13509140 AT5G41360 5.22 4.64 4.99 -1.5 -1.17 0.0150 0.1800 DNA repair helicase XPB2

13403582 AT2G41110 3.21 2.6 3.03 -1.52 -1.13 0.0120 0.5218 calmodulin 2; calmodulin 3; calmodulin 5

13478283 AT4G36100 3.14 3.81 3.14 1.59 1 0.0370 0.6349 sec1/munc18-like (SM) family protein

13435953 AT3G45970 4.04 4.77 4.06 1.66 1.01 0.0090 0.3223 expansin-like A1

13392313 AT2G07722 8.33 9.14 8.34 1.76 1.01 0.0023 0.9524 hypothetical protein

13545327 ATMG00870; ATMG00880

6.29 6.99 6.38 1.63 1.07 0.0264 0.3296 hypothetical protein

13499623 AT5G09570 2.04 2.72 2.2 1.61 1.12 0.0171 0.5286 Cox19-like CHCH family protein

13392216 AT2G07674 3.41 4.02 3.63 1.53 1.16 0.0199 0.0411 hypothetical protein

8

13395771 AT2G22121 1.1 1.91 1.33 1.76 1.18 0.0399 0.0240 low-molecular-weight cysteine-rich 35

13545319 ATMG00810 4.68 5.36 4.94 1.6 1.2 0.0445 0.6212 hypothetical protein

13387433 AT1G74890 1.48 2.11 1.75 1.55 1.21 0.0158 0.0286 two-component response regulator ARR15

13383470 AT1G65346 3.76 4.49 4.1 1.66 1.27 0.0441 0.8933 hypothetical protein

13510116 AT5G43620 3.17 4.06 3.52 1.85 1.27 0.0056 0.0476 Pre-mRNA cleavage complex II

13355450 AT1G65295 3.58 4.2 4.04 1.54 1.38 0.0356 0.2020 hypothetical protein

13539938 AT5G56080 3.81 4.85 4.38 2.05 1.48 0.0230 0.0197 nicotianamine synthase 2

13399221 AT2G31085 4.18 4.35 4.77 1.13 1.5 0.6518 0.0272 protein CLAVATA3/ESR-related 6

13355853 AT1G66590 1.64 1.83 2.22 1.15 1.5 0.3643 0.0373 cytochrome c oxidase 19-1; cytochrome c oxidase 19-2

13477693 AT4G34800 3.32 3.53 3.91 1.15 1.5 0.5933 0.0470 SAUR-like auxin-responsive protein

13346750 AT1G31490 3.02 3.3 3.6 1.22 1.5 0.4046 0.0124 HXXXD-type acyl-transferase-like protein

13517652 AT5G60760 7.65 7.96 8.23 1.24 1.5 0.6850 0.0202 phytic acid metabolising protein

13467349 AT4G11190 5.4 6.28 5.99 1.83 1.5 0.2525 0.0078 disease resistance-responsive, dirigent domain-containing protein

13405811 AT2G46440 1.38 1.41 1.97 1.02 1.51 0.8472 0.0467 cyclic nucleotide-gated ion channel protein

13539206 AT5G54030 3.56 3.63 4.16 1.04 1.51 0.2639 0.0044 cysteine/histidine-rich C1 domain-containing protein

13530284 AT5G24290 4.73 4.8 5.34 1.05 1.52 0.7783 0.0153 membrane protein of ER body 2

13468583 AT4G14630 7.49 7.73 8.11 1.17 1.53 0.8738 0.0473 germin-like protein subfamily 1 member 8

13389964 AT1G80180 3.68 3.97 4.29 1.23 1.53 0.3047 0.0154 MAPK kinase substrate

13379279 AT1G53860 2.06 2.47 2.67 1.34 1.53 0.0069 0.0381 remorin-like protein

13513745 AT5G51780 4.09 4.28 4.71 1.14 1.54 0.5241 0.0430 transcription factor bHLH36

13381792 AT1G61130 4.58 4.79 5.2 1.15 1.54 0.2174 0.0054 serine carboxypeptidase-like 32

13437715 AT3G50460 4.95 4.96 5.58 1.01 1.55 0.6952 0.0233 RPW8-like protein 2

13355403 AT1G65250 2.43 3.13 3.08 1.62 1.56 0.0294 0.0484 probable inactive receptor-like protein kinase

13542764 AT5G63100 1.94 2.13 2.6 1.14 1.57 0.1335 0.0186 S-adenosyl-L-methionine-dependent methyltransferase domain-containing protein

13507391 AT5G35732 3.42 3.67 4.07 1.19 1.57 0.0619 0.0071 hypothetical protein

13439783 AT3G55485 4.6 4.84 5.27 1.18 1.59 0.3981 0.0301 other rna

13433258 AT3G25790 5.63 5.94 6.3 1.24 1.59 0.5730 0.0061 myb-like transcription factor family protein

13367697 AT1G14048 2.07 2.45 2.76 1.3 1.61 0.0146 0.0231 GCK domain-containing protein

13390498 AT2G01530 7.41 7.62 8.11 1.16 1.62 0.8770 0.0196 MLP-like protein 329

13412893 AT2G25685 1.37 1.48 2.08 1.08 1.64 0.3166 0.0260 SCR-like protein 17

13544240 AT5G66320 3.17 3.7 3.9 1.44 1.65 0.1190 0.0251 GATA transcription factor 5

13493194 AT4G33790 3.22 3.53 3.95 1.24 1.66 0.3241 0.0265 fatty acyl-CoA reductase CER4

13448753 AT3G13170 1.92 2.15 2.68 1.17 1.7 0.2550 0.0069 meiotic recombination protein SPO11-1

13361537 AT1G80440 4.61 4.98 5.38 1.29 1.7 0.0797 0.0111 F-box/kelch-repeat protein

13417491 AT2G36180 2.28 2.52 3.12 1.18 1.78 0.7172 0.0459 putative calcium-binding protein CML31

13467535 AT4G11655 2.72 2.95 3.57 1.18 1.8 0.6116 0.0474 hypothetical protein

13481985 AT4G05508 1.06 1.27 1.99 1.16 1.91 0.4473 0.0179 MIR405D

13334405 AT1G01580 6.06 6.67 7.02 1.52 1.94 0.2446 0.0227 ferric reduction oxidase 2

13394463 AT2G19050 2.95 3.34 3.92 1.31 1.96 0.2599 0.0235 GDSL esterase/lipase

13427382 AT3G12900 4.96 5.66 6.24 1.62 2.42 0.2779 0.0279 oxidoreductase, 2OG-Fe(II) oxygenase family protein

9

Table S6. Gene Ontology (GO) Biological Process Analysis of Genes Deregulated in hcr1, Related to

Figure 3

Biological processes displaying only results at P<0.05 are represented. Analysis Type: PANTHER Overrepresentation Test (release 20150430) Annotation Version and Release Date: GO Ontology database Released 2015-08-06 Analyzed List: hcr1 (Arabidopsis thaliana) Reference List: Arabidopsis thaliana (all genes in database) Bonferroni correction: true

Reference list hcr1 Mapped IDs: 26684 95 Unmapped IDs: 0 17

GO biological process complete

Arabidopsis thaliana - REFLIST (26684)

hcr1 list (95)

hcr1 (expected)

hcr1 (over/under)

hcr1 (fold enrichment)

hcr1 (P-value)

Response to hypoxia 83 6(a) .30 + > 5 1.16E-03 Response to decreased oxygen levels

88 6(a) .31 + > 5 1.62E-03

Response to oxygen levels

88 6(a) .31 + > 5 1.62E-03

Regulation of hydrogen peroxide metabolic process

130 6(a) .46 + > 5 1.50E-02

Regulation of reactive oxygen species metabolic process

145 6(a) .52 + > 5 2.76E-02

Unclassified 7452 30 26.53 + 1.13 0.00E00 (a) AT1G77120 (ADH1), AT4G33070 (PDC1), AT5G20830 (SUS1), AT3G43190 (SUS4), AT4G27450, AT5G10040

10

Table S7. List of Primer Sequences Used in the Study, Related to Methods and Resources Section

Primer name Primer sequence Primer use(a) LBb1.3 ATTTTGCCGATTTCGGAAC T-DNA SailLB GCCTTTTCAGAAATGGATAAATAGCCTTGCTT

CC T-DNA

At3g24710.1RP TGCAAAGAGATTCAATCAGGG SALK_020102C At3g24710.1LP TTAGGCTGATCAGACTGTGGC SALK_020102C hcr1-1RP CAGATGAAGTTCCAGCTCCAG SALK_205151C hcr1-1LP TCAGACTTTGGCTGGTGATTC SALK_205151C hcr1-2RP ACAGACCAGCATTGTTCCATC SALK_203216C hcr1-2LP TTGCAGGGAGATCATCTGAAC SALK_203216C msf-1RP(b) CATTCACCGAAATAACATGCC SALK_142720C msf-1LP(b) AAAAACATTTGCACTTGCGTC SALK_142720C msf-2RP(b) CCTAAACCGGCTTTAATCAGC SALK_018763 (AE) msf-1LP(b) TCCCCAAAGTTCAAAAACAAC SALK_018763 (AE) dcp-1RP(b) ATCACAAGAAGCAACGGATTG SAIL_407_C05 dcp-1LP(b) AAAGAGACGCAAGTGCAAATG SAIL_407_C05 dcp-2RP(b) CAGCAGAACCAAAGCAAGAAC SALK_205796C dcp-2LP(b) CATCGATTCTCCTTTGTTTCG SALK_205796C At3g24750-1RP CTTCGGTTTTTCAACTCCATC SALK_113933 (BS) At3g24750-1LP TTGATACAATCCCACGTTGTG SALK_113933 (BS) At3g24750-2RP TTGACCAGATCTTTCAATGGC SAIL_158_H07 At3g24750-2LP GCATTTCCTGGATCTACATCG SAIL_158_H07 MSAT3.06375F GGGGAACGAAACTGAAAGAA Genetic mapping MSAT3.06375R TCTTGGATGTCCCTTTCTGG Genetic mapping MSAT3.06774F TGTCTCCTTTGTAATCTCATAACAC Genetic mapping MSAT3.06774R TCGAGTCTCTTTATTTGATTCTGA Genetic mapping MSAT3.07213F CTTTCCACCAGCTTCCTGAG Genetic mapping MSAT3.07213R CGAAAACCCTACCAGGAAAA Genetic mapping IND3.07395F TGCGCTTTTATTGGCTTATG Genetic mapping IND3.07395R CTGCATCATTTTCGCGTTTA Genetic mapping IND3.07586F AGGCGCGAGAATCAAGTAAA Genetic mapping IND3.07586R CGTGGAAATGTCAAATGTGG Genetic mapping IND3.07731F GGAGTGGACTGGCTTTACACA Genetic mapping IND3.07731R TCTCGATCGTCTCGTCGAAT Genetic mapping MSAT3.08063F GTGATGGCGGTGGAGGATAC Genetic mapping MSAT3.08063R TTGGCTGCTCTCCACCTAGT Genetic mapping MSAT3.08519F GTGCCACGTGGGATAAAAAT Genetic mapping MSAT3.08519R GTTTCGGGCAAAGTAACGAA Genetic mapping MSAT3.08624F TTGATTCGGTCAAACACCAA Genetic mapping MSAT3.08624R TTCGCGAAAGTACAGAGAGG Genetic mapping MSAT3.08709F GTCCCGAATTGAGCAAATGT Genetic mapping MSAT3.08709R CCCGATCTTCTCATATCACG Genetic mapping MSAT3.08899F TGTTCATCAAATATATGTTTTTCACAT Genetic mapping MSAT3.08899R ACCGGATTTGTTCCAACATT Genetic mapping IND3.08927F TGGAGGCATATAACCAATTCA Genetic mapping IND3.08927R GATTTGCCCAATTTAAGCTGT Genetic mapping IND3.08950F GGCTAATGTTTGGGATAGGG Genetic mapping IND3.08950R TCGCTGATGAAGATTCATGTTT Genetic mapping IND3.08959F AAATCGGCCTCCTCAAAATC Genetic mapping IND3.08959R CATGCCGGAGATATTTTGGT Genetic mapping IND3.08984F TTGGGTTTGATCCATCTGGT Genetic mapping IND3.08984R GGTGAAATGGTCTGTCGAGTT Genetic mapping IND3.08985bF GGAGTGGTAAATTTAGAGATGCAGA Genetic mapping IND3.08985bR GCTTTATGGAGATGGATTTCAAG Genetic mapping IND3.08994F TTTCTTTTTATCGATTTAGTTACACCA Genetic mapping IND3.08994R TTTTTGTCAGCATCACTATATGTTTT Genetic mapping IND3.09011F GCGTCACTCGTCAATCAAAA Genetic mapping IND3.09011R TTGTTTGCCCGACTATTCCT Genetic mapping

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SNP3.09014F TCGGAAAATAACCAAGGAGAAA Genetic mapping SNP3.09014R CTGAAGCATTGTCGTTCAGC Genetic mapping SNP3.09017F GGAAAACCAGAACGAAACCA Genetic mapping SNP3.09017R ATTTGATCGAACCGATGGAG Genetic mapping SNP3.09020F GGTCGCATGGGTATAAACCTT Genetic mapping SNP3.09020R CTTGCGGAGAGTACGGAGAC Genetic mapping SNP3.09023bF TTCAGAAGCGAGAGATTTGGA Genetic mapping SNP3.09023bR AGTTTGATGGGAGACCGAAA Genetic mapping SNP3.09025bF CCGACCTTCCTCAGTTCAAA Genetic mapping SNP3.09025bR TGCAACGATAGGAGATTGGA Genetic mapping SNP3.09031F TGATGCGCATTGAAGAAGAA Genetic mapping SNP3.09031R ACGACAATCAGCGGCAAATA Genetic mapping SNP3.09038F GGTCGTATGGTTTGGGACAT Genetic mapping SNP3.09038R TGCAATACGATTACGCTCCA Genetic mapping IND3.09040F ACAATGGCGTTCACTCATCA Genetic mapping IND3.09040R GAGCCAGGTGTTGGAGAGAG Genetic mapping IND3.09043F GCGGATTCCAAACAACAAGT Genetic mapping IND3.09043R TGTTTTGACCAAAAATGCAAA Genetic mapping IND3.09044F GGGCACGAATTTGATTGTCT Genetic mapping IND3.09044R GCAAATAAAGCTTCGGTCTTG Genetic mapping IND3.09050F ACAATAGCCGCAGCATCTCT Genetic mapping IND3.09050R GCTACCCTTAGCTCCCTCGT Genetic mapping IND3.09053F TGGTTTTTATAGGACTGTTGGGTA Genetic mapping IND3.09053R CGAAGAACCTTCATTGTCCAG Genetic mapping msat3.2F AAGGTACGGCGGTGGATATTG Genetic mapping msat3.2R CGGGGATTTCTTCTTCCTGTG Genetic mapping MSAT3.09517F TCTCTATGCCAACGAAGCAA Genetic mapping MSAT3.0951R CAAAACCATGACCCAGAAGG Genetic mapping MSAT3.09878F CCACAATCGCTTGATTTTCA Genetic mapping MSAT3.09878R ACATCAGGCAGTCTCCTTGG Genetic mapping MSAT3.20F ATGAGTGGAAGAGATGGCTC Genetic mapping MSAT3.20R GGTACGCCGAAAGGG Genetic mapping msat3.23F CATGAACACATATTTGTAA Genetic mapping msat3.23R ATCTCCAATTTTCCC Genetic mapping AT3g24715promoterFor1 GGGCTCGAGCTCGCGGAGCTTGTGTTGCACG Genomic HCR1 Col-0,

Bur-0, Fei-0, Zu-1 /promHCR1::GUS

AT3g24715msforfRSpe1 GGGACTAGTGATCATACTAAATGGGTTGGTG Genomic HCR1 Col-0, Bur-0, Fei-0, Zu-1

AT3g24715prNcoI GGGCCATGGAATTAACCTCTCTCAAACAG promHCR1::GUS AT3g24715ATGXhoI GGGCTCGAGATGTCAGATAGATGGGCTCGA d35S::HCR1 AT3g24715UGASacI GGGGAGCTCTCAGGGTTTATTTTCTCTTCTT d35S::HCR1 NCstkGFPprF GGGCTCGAGCTCGCGGAGCTTGTGTTG promHCR1::GFP::HCR1/

promHCR1::HCR1::GFP NGFPprR CTCCTCGCCCTTGCTCACCATAATTAACCTCT

CTCAAACAGCTG promHCR1::GFP::HCR1

NGFPGFPF CAGCTGTTTGAGAGAGGTTAATTATGGTGAGCAAGGGCGAGGAG

promHCR1::GFP::HCR1

NGFPGFPR CGAGCCCATCTATCTGACATTCTAGATCGAACCACTTTGTACAAGAAAGCTGGGTCCTTGTACAGCTCGTCCATG

promHCR1::GFP::HCR1

NGFPCDSF CATGGACGAGCTGTACAAGGACCCAGCTTTCTTGTACAAAGTGGTTCGATCTAGAATGTCAGATAGATGGGCTCG

promHCR1::GFP::HCR1

NGFPCDSR CTTGATTTCTGAAGTTTTGAAGTCAGGGTTTATTTTCTCTTCTTTTGC

promHCR1::GFP::HCR1

NGFPterF GCAAAAGAAGAGAAAATAAACCCTGACTTCAAAACTTCAGAAATCAAG

promHCR1::GFP::HCR1

NCGFPstkterR CCCACTAGTGATCATACTAAATGGGTTGGTGC promHCR1::GFP::HCR1/promHCR1::HCR1::GFP

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CGFPprR CGAGCCCATCTATCTGACATAATTAACCTCTCTCAAACAG

promHCR1::HCR1::GFP

CGFPCDSF CTGTTTGAGAGAGGTTAATTATGTCAGATAGATGGGCTCG

promHCR1::HCR1::GFP

CGFPCDSR CTCCTCGCCCTTGCTCACCATTCTAGATCGAACCACTTTGTACAAGAAAGCTGGGTCGGGTTTATTTTCTCTTCTTTTGC

promHCR1::HCR1::GFP

CGFPGFPF GCAAAAGAAGAGAAAATAAACCCGACCCAGCTTTCTTGTACAAAGTGGTTCGATCTAGAATGGTGAGCAAGGGCGAGGAG

promHCR1::HCR1::GFP

CGFPGFPR CTTGATTTCTGAAGTTTTGAAGTTACTTGTACAGCTCGTCCAT

promHCR1::HCR1::GFP

CGFPterF ATGGACGAGCTGTACAAGTAACTTCAAAACTTCAGAAATCAAG

promHCR1::HCR1::GFP

ADH1F TGCTTGAAGCCATTCTCTCG At1g77120 qRT-PCR ADH1R GAAAACCAAAAGCGATGGAG At1g77120 qRT-PCR ARR15F GGTGGTGAAGCTGAAGAAGG At1g74890 qRT-PCR ARR15R CTCTTGGAAGATGGAGTGTCG At1g74890 qRT-PCR At1g10140F GGCGAGGATAGAGGAAGAGG At1g10140 qRT-PCR At1g10140R ACAGTGCACGAAAAATCGAG At1g10140 qRT-PCR At5g15710F TTTCGGCTGAGAGGTTCGAGT At5g15710 qRT-PCR At5g15710R GATTCCAAGACGTAAAGCAGATCAA At5g15710 qRT-PCR FRO2F CGTTGCACGAGCGATTCTTG At1g01580 qRT-PCR FRO2R GCGACTTGTAGTGCGGCTATG At1g01580 qRT-PCR HRE1F GGCCTCTGCCTTATCCCTCTGT At1g72360 qRT-PCR HRE1R GCGTAAACCCGTCTCAGTGAGTG At1g72360 qRT-PCR HRE2F GAAGCGTAAACCCGTCTCAGT At2g47520 qRT-PCR HRE2R TTTGCTCGGGCACGAATCT At2g47520 qRT-PCR NAS2F AAGCTTGGTGGTTCAAATGG At5g56080 qRT-PCR NAS2R TCTCCATACCACGATTGTTCA At5g56080 qRT-PCR PDC1F AGCAACACAGAATCTTCAATGC At4g33070 qRT-PCR PDC1R TGAAACTGCAAAAGGAGCTT At4g33070 qRT-PCR Rap2.12F AAGCCAATCCAGCTAAGAAGC At1g53910 qRT-PCR Rap2.12R GTTTGCACCATTGTCCTGAGT At1g53910 qRT-PCR Rap2.2F CACTAGAAGTGGAAGCCATGC At3g14230 qRT-PCR Rap2.2R GGAACCATCGATCACTTCAAA At3g14230 qRT-PCR Rap2.3F GCCGGATTATGATCTGAAACA At3g16770 qRT-PCR Rap2.3R CAAGCATCCACATATCCACCT At3g16770 qRT-PCR HCR1F AACAAGCAGGAGGCAGAGAA At3g24715 qRT-PCR HCR1R GGATTCCCAAGCAAGAATCA At3g24715 qRT-PCR SUS1F AGTGGTTCCGGTGTTTGAAG At5g20830 qRT-PCR SUS1R GAATTCAAAGCAATGCCACA At5g20830 qRT-PCR SUS4F CACTGAAGTACCGCCCACTG At3g43190 qRT-PCR SUS4R AAAACAATGGTGAAGCATATCA At3g43190 qRT-PCR F-boxF TTTCGGCTGAGAGGTTCGAGT At5g15710 qRT-PCR F-boxR GATTCCAAGACGTAAAGCAGATCAA At5g15710 qRT-PCR UBQ10F CTGCGACTCAGGGAATCTTCTAA At4g05320 qRT-PCR UBQ10R TTGTGCCATTGAATTGAACCC At4g05320 qRT-PCR HCR1-KD-EcoRI ACACTCTTTGTTGAATTCATGGAAGC GST:HCR1821-1117 HCR1-KDext-EcoRI AGCCGAATTCGAAGCTGAAGCCAATAC CGG GST:HCR1801-1117 HCR1XhoI CGCGGCTCGAGTCAGGGTTTATTTTCTCTT GST:HCR1821-1117 &

GST:HCR1801-1117 R2.12pVIXNcoMA GGGCCATGGCGTGTGGAGGAGCTATAATA RAP2.12 in vitro

translation R2.12pVIXSmaI CCCCCCGGGGAAGACTCCTCCAATCATGGAA

TGA RAP2.12 in vitro translation

(a) Primers were used for confirmation of T-DNA insertion in SALK or SAIL mutant lines, making constructs for transformation/in vitro kinase assays, genetic mapping, and qRT-PCR. (b) Abbreviations msf and dcp are described in Figure S1A.