Supplemental Data. Gutjahr et al. (2008). Arbuscular mycorrhiza-specific signaling in rice transcends the common symbiosis signaling pathway.

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1 Supplemental Data. Gutjahr et al. (2008). Arbuscular mycorrhiza-specific signaling in rice transcends the common symbiosis signaling pathway. A H S S H B P. i. M H 2 O Pi Tef CP2 Supplemental Figure 1. Colonization of rice roots by Piriformpora indica (A) Roots inoculated with P. indica at 5 wpi stained with trypan blue. H = hyphae, S = zoospores, size bar = 50 µm. (B) Amplification of Pi Tef from cdna of colonized roots. Rice CYCLOPHILIN2 (CP2) was used as an internal control.

2 A Root Gi Root M (Gi) Shoot Gi Shoot M (Gi) Embryo Stem Leaf Panicle Root Pi Root M (Pi) Callus gdna -RT PT11 AM1 AM2 AM3 AM10 AM11 AM14 AM15 AM24 AM25 AM26 AM31 AM34 AM39 CP2 B relative expression 1,E+00 1,E-01 1,E-02 1,E-03 AM18 AM20 AM29 AM42 1,E-04 Root Gi Root M (Gi) Shoot Gi Shoot M (Gi) Embryo Stem Leaf Panicle Root Pi Root M (Pi) Callus Supplemental Figure 2: Expression analysis of marker genes (A) RT-PCR-based expression analysis of 14 genes in different rice organs and callus, in roots and shoots of plants colonized by G. intraradices (Gi) and in roots colonized by P. indica (Pi). Genomic DNA (gdna) was used as technical control for RT-PCR and rice CYCLOPHILIN2 (CP2) served as a constitutively expressed control gene. (B) Real-time RT-PCR-based expression analysis of low-abundant transcripts. Error bars represent S.D. for three technical replicates. The experiment was repeated twice with similar results.

3 PT11 LPC control gdna -RT CP2 Supplemental Figure 3. Absence of PT11 induction upon LPC treatment of rice roots RT-PCR-based expression analysis of PT11 in roots treated with lysophphatidylcholine (LPC). Solvent treated roots were used as a control. Genomic DNA (gdna) was used as a technical control for PCR and rice CYCLOPHILIN2 (CP2) served as a constitutively expressed control gene. -RT, control PCR reaction on RNA not reverse transcribed. The experiment was repeated twice with similar results.

4 Root Gi Root M Embryo Stem Leaf Panicle Callus gdna -RT SYMRK CASTOR NUP85 NUP133 CP2 Supplemental Figure 4: Expression of rice common SYM genes Expression of rice SYMRK, CASTOR,, NUP85, NUP133, and in mycorrhizal (Gi) and mock-inoculated (M) roots and other organs or callus of rice. Genomic DNA (gdna) was used as a technical control for PCR. Rice CYCLOPHILIN2 (CP2) served as a constitutively expressed control gene. The experiment was repeated twice with similar results.

5 A B root length colonization [%] total ext hyphae hyphopodia int hyphae arbuscules vesicles wpi relative Gi ITS DNA level 1,E+00 1,E-01 1,E-02 1,E-03 1,E wpi Supplemental Figure 5. Quantification of AM colonization by microscopy and real-time RT-PCR. (A) Percent (%) root colonization of different structures of G. intraradices. The mean ± S.E. are displayed (n = 5). (B) Quantity of G. intraradices ITS-DNA relative to rice CYCLOPHILIN 2 (CP2) at each indicated time-point. The mean ± S.D. for three technical replicates is shown.

6 Supplemental Table 1. Putative function of proteins encoded by genes exclusively expressed in mycorrhizal roots TIGR ID Gene-ID Putative Function LOC_01g46860 PT11 PT11 ph phate transporter LOC_04g04750 AM1 putative class III peroxidase (Prx53) LOC_08g34249 AM2 hypothetical protein (O. s.), proteinase inhibitor I13 in potato 1 LOC_01g57400 AM3 contains peptidoglycan binding LysM domain 1 LOC_05g22300 AM10 similarity to putative hypersensitivity-related (Hsr) protein LOC_06g20120 AM11 hypothetical protein, similarity to nucleoid DNA-binding protein cnd41 LOC_11g26140 AM14 serine-threonine kinase like LOC_01g57390 AM15 contains peptidoglycan binding LysM domain 2 LOC_03g40080 AM18 putative scarecrow-like gene regulator LOC_04g21160 AM20 similar to AB-hydrolase associated lipase region LOC_02g03190 AM24 putative cdna LOC_06g35930 AM25 putative MIP aquaporin, nodulin 26-like LOC_12g30300 AM26 serine-threonine kinase, calcium dependent (EF hand) LOC_06g34470 AM29 similar to Ring-H2 zinc finger protein-like LOC_02g03150 AM31 hypothetical protein (O. s.), proteinase inhibitor I13 in potato 2 LOC_10g18510 AM34 putative UDP-glucuronyl/UDP-glucyltransferase LOC_04g13090 AM39 cysteine peptidase, protease family C1 LOC_03g38600 AM42 putative secretory carrier membrane protein

7 Supplemental Table 2. Insertion lines of rice common SYM signaling genes and their mycorrhizal phenotypes Mycorrhizal Structure SYM gene TIGR ID RAP ID Insertion line Hyphopodia Rhizodermal Coils/Branches/ Swellings Cortex Hyphae Vesicles Arbuscules wild-type Dongjin (DJ) wild-type Hwayoung (HY) wild-type Nipponbare (N) SYMRK LOC_07g g no insertion line CASTOR LOC_03g g B (DJ) LOC_01g g C (HY) NC6423 (N) ND5050 (N) NUP85 LOC_01g g no insertion line NUP133 LOC_03g g no insertion line LOC_05g g NE1115 (N) NF8513 (N) a LOC_06g g NG0782 (N) NC2415 (N) NC2713 (N) b a Previously described by Chen et al., b Previously described by Chen et al., 2008.

8 Supplemental Table 3: Primers used for SYM transcript analysis in sym mutants. Gene Primer Sequences CASTOR Forward: GAGCAGCAGAAGCAGCAGCAG 5 Reverse: CGGATACCATCCCTGACCATCG castor-1 Forward: CGATGGTCAGGGATGGTATCCG insertion flanking Reverse: GTTACAAGCCCAAGCATCATGG CASTOR Forward: GGGAACGAGATGCAAATACG 3 Reverse: TCCGCCTTGAAACTTTGTCT Forward: GACAGATGGGGCACCAGCAAC 5 Reverse: GAAGAGCCTCGCTTCCGTGG pollux-1 Forward: GGAGGAGAAGAGCCTCGCTTCC insertion flanking Reverse: GGAAGCTAAATTCCAGTCCGCG pollux-2 Forward: GGAGGAGAAGAGCCTCGCTTCC insertion flanking Reverse: CACAAGCCCAAGCATTGTGGC pollux-3 Forward: GCCACAATGCTTGGGCTTGTG insertion flanking Reverse: CTCCACATGGAACAGCGTCAGG Forward: GCGGCACTTAGAAAGTTTGC 3 Reverse: ATGCCATGCTGACAAGTTCA Forward: AAGGAGGGGAGTGAGCAAGT 5 Reverse: CGTCGGAGATCGATACCTGT ccamk-1 Forward: GATCTCATGGATGCAGAGGTCGTC Insertion flanking Reverse: TGATGCAGCCTGACCGATCAG Forward: TTTGAGCAGGTGCTGAGAGC 3 Reverse: TGATGCAGCCTGACCGATCAG Forward: GCGATGATGGAGAACTCGATGG 5 Reverse: CTGCATTCCTGTCATGGGAGAC cyclops-1,2,3 Forward: CTGATTCCGCAGAATTTGGC insertion flanking Reverse: ATGCTGTACCAAGCCAAACC 3 Forward: Reverse: GGCAGAAGCAAAGGAAAGAA CGCTCTTTTTCTTCCACCAG

9 Supplemental Table 4: Primers used for genotyping of rice insertion lines. Gene Primer Sequences CASTOR 1B Castor.genot.F CGATGGTCAGGGATGGTATCCG WT Castor.genot.R GCCAACCGCTTGTTTATGGG CASTOR 1B Castor.genot.F CGATGGTCAGGGATGGTATCCG mutant p2717_2364.r CGCGTCGGCAGTTTGCTGC 1C Pollux.genot.F1 GGAGGAGAAGAGCCTCGCTTCC WT Pollux.genot.R1 GGAAGCTAAATTCCAGTCCGCG 1C GUS1 RB GCCGTAATGAGTGACCGCATCG mutant Pollux.genot.R1 GGAAGCTAAATTCCAGTCCGCG NC6423 Pollux.genot.F2 GCAGCTAGCTATAGCAAACAAGAG WT Pollux.genot.R2 TTTCATCGGATGCTAAAACAATAA NC6423 Pollux.genot.F2 GCAGCTAGCTATAGCAAACAAGAG mutant T17_left ATTGTTAGGTTGCAAGTTAGTTAAGA ND5050 Pollux.genot.F3 AGCTGCTGTGCTATATATGTTTGG WT Pollux.genot.R2 TTTCATCGGATGCTAAAACAATAA ND5050 Pollux.genot.F3 AGCTGCTGTGCTATATATGTTTGG mutant T17_left ATTGTTAGGTTGCAAGTTAGTTAAGA NE1115 CcamK.genot.F1 TGTTCTCTTCCACAAAAGACACAT WT CcamK.genot.R1 GAGGTTTTAGGCTGATCAAGTCAT NE1115 CcamK.genot.F1 TGTTCTCTTCCACAAAAGACACAT mutant T17_right CAGCAACGATGTAGATGGTCAAGC NF8513 CcamK.genot.F2 GCTCTCAGCACCTGCTCAAAC WT CcamK.genot.R2 CTGAAGAATTATGGGTTCCATTATC NF8513 CcamK.genot.F2 GCTCTCAGCACCTGCTCAAAC mutant T17_left ATTGTTAGGTTGCAAGTTAGTTAAGA NG0782 Cyclops.genot.F1 CACCCAGTCAGACTCCAACA WT Cyclops.genot.R1 ATGCTGTACCAAGCCAAACC NG0782 Cyclops.genot.F2 AGGCATTTTCATCACCCATC mutant T17_left ATTGTTAGGTTGCAAGTTAGTTAAGA NC2415 Cyclops.genot.F1 CACCCAGTCAGACTCCAACA WT Cyclops.genot.R1 ATGCTGTACCAAGCCAAACC NC2415 Cyclops.genot.F2 AGGCATTTTCATCACCCATC mutant T17_left ATTGTTAGGTTGCAAGTTAGTTAAGA NC1713 Cyclops.genot.F1 CACCCAGTCAGACTCCAACA WT Cyclops.genot.R1 ATGCTGTACCAAGCCAAACC NC2713 mutant T17_left Cyclops.genot.R1 ATTGTTAGGTTGCAAGTTAGTTAAGA ATGCTGTACCAAGCCAAACC

10 Supplemental Table 5 : Primers used for quantification of fungal DNA and gene expression by real-time RT - PCR. Gene Primer Sequences Forward: GAGACCATGATCAGAGGTCAGGT Gi ITS1 Reverse: GGTCATTTAGAGGAAGTAAAAGTCGTAAC Forward: GATGTTACGGATCTGGGTATATCGA Gr ITS2 Reverse: CGGCTATAATTAGTACGCTTCACATT Forward: GAGAAGTTCCCTGCTTCAAGCA PT11 Reverse: CATATCCCAGATGAGCGTATCATG Forward: ACCTCGCCAAAATATATGTATGCTATT AM1 Reverse: TTTGCTTGCCACACGTTTTAA Forward: ATGCCGTTGTCGTCCATGA AM2 Reverse: CCCTCACGCCGGATTTC Forward: CTGTTGTTACATCTACGAATAAGGAGAAG AM3 Reverse: CAACTCTGGCCGGCAAGT Forward: AGAACACTTGTGGCCGTACTATAAGA AM10 Reverse: CCTCTCGACGAAAGTACGGACTA Forward: TGAACGAAGACAGCAATACATCAA AM11 Reverse: CGATCGATGGATTCATACTTCAGT Forward: CCAACACCGTTGCAAGTACAATAC AM14 Reverse: GCACTTTGAAATTGGACTGTAAGAAA Forward: TCCGGCGCCACATAGTG AM15 Reverse: TCCGTCGCACACGAGAAG Forward: TGCCATGTGGATGATGCATAG AM18 Reverse: CGACGAGGAAGATCAATGGTTAGT Forward: TTTGGAAGGAACACTACTGGAGAAT AM20 Reverse: CCGAAATCTAGTTTCGACAATGATT Forward: TCTTCATCACCGCCGACAT AM24 Reverse: CGGCGAGATAGTGAGCATAAAGA Forward: CTTGCTGCCTTCCTCTATGGA AM25 Reverse: CGAGAAGTCGACGACTCCTACAC Forward: GGTTGTTGCGGCATGTGTAC AM26 Reverse: AGCCATGTCCCTAGCGAGGTA Forward: TGCGACGTGATCAGCCAC Os AM29 Reverse: TGCACGCACCTGTTCCAC Forward: CGATGAAGTTGTTGTCCACGAA AM31 Reverse: CGTCTCGCCGGAGTTCAA Forward: TTGCCAAAAATAGAAGCATCACA AM34 Reverse: CATAGTACTTAAAGTGAAAGGGCAAGGT Forward: CCGAATCTCAAGCAGGATGTG AM39 Reverse: AAATTGTCGTTTGTGTACCCTGACT Forward: ATTTGTTGAACGAGCACAATCG AM42 Reverse: ACATCAACACTCTTACACTCACACACA Forward: TCTAATTCTTCGGACCCAAGAATG ACTIN1 Reverse: AGCAGGAGGACGGCGATAA Forward: GTGGTGTTAGTCTTTTTATGAGTTCGT CYCLOPHILIN2 Reverse: ACCAAACCATGGGCGATCT

11 Forward: CTGATGATATGGACCTGAGTCTACTTTT Os GAPDH Reverse: CAACTGCACTGGACGGCTTA Forward: CATGGAGCTGCTGCTGTTCTAG Os UBIQUITIN Reverse: CAGACAACCATAGCTCCATTGG

12 Supplemental Table 6: Primers for detection of rice gene expression by RT-PCR. For AM1, AM3 and PT11 the same primers were used to generate probes for in situ hybridization. Gene Primer Sequences Forward: AGCTCTCCTAGATCTGTGCTG CYCLOPHILIN 2 Reverse: GCGATATCATAGAACGAGCGAC Forward: CCTGGCATAAAAGGGCAATA SYM RK Reverse: GTGCTTTCGATGGACCTCAT Forward: GGGAACGAGATGCAAATACG CASTOR Reverse: TCCGCCTTGAAACTTTGTCT Forward: GCGGCACTTAGAAAGTTTGC Reverse: ATGCCATGCTGACAAGTTCA Forward: GCACAAGAAGGAAGGACTGG NUP 85 Reverse: GCATGGCTTGGTAGGTGAAT Forward: CTGATCGAGATGTGCCTGAA NUP 133 Reverse: AGGACAGTGCCCTGAAGAGA Forward: GATCTCATGGATGCAGAGGTCGTC CCAM K Reverse: GCTCTCAGCAC CTGCTCAAAC Forward: GGCAGAAGCAAAGGAAAGAA Reverse: CGCTCTTTTTCTTCCACCAG Forward: CATCACCAACATGCTCGGCTTC PT11 Reverse: GTATGCATATCCCAGATGAGC Forward: CACCAAGAGCTGCAGGG CTACCAAC AM1 Reverse: TTTGCTTGCCACACGTTTTAA Forward: ATGAGCCAGAAGTCGT CGTG AM2 Reverse: TATTTCGCGATGACGGGAAT Forward: GTTACGTGGTGGTGGAGGAT AM3 Reverse: GTCGAGGCAGACCCACTG Forward: GAGGAGGGGTATGTGCAGTC AM10 Reverse: CCCCTTGTTCACCTCCTGTA Forward: ACTTCAGTTTCGTCGCGATT AM11 Reverse: GGCAAAATCTGCTTCAATCC Forward: GAT TCAAAGGTTGGCAGAGC AM14 Reverse: CCAACACCGTTGCAAGTACA Forward: CGAGAAGTTCCACGGAGACG AM15 Reverse: AGTTGATGTTCGGGTTGAGG Forward: CGGCGAGATAGTGAGCATAA AM24 Reverse: GTCGTTGAGGAAGACGAGGA Forward: TCGTCATCGAGTTCGTCATC AM25 Reverse: TCCCAAGATGTACACCCACA Forward: CAACCAAATCATGCGAAACA AM26 Reverse: TGAATGCCATTTAGCCCATT Forward: TGGAGAAGAAGAAGGTGAGGTG AM31 Reverse: TAACTGATGACGGGGACCTT Forward: AAAGTGAAAGGGCAAGGTGA AM34 Reverse: CTCAAGAGGGGAGGTTGGAT Forward: TAGCATTGACACGCTTCCAGC AM39 Reverse: TGCCGCTGTGTATGGGTACTTAG