Glyma10g15850 aagggatccattctggaaccatatcttgctgtg ttgggtacccttggatgcaggatgacacg AtMKK6, AT5g56580

Supplemental table 1. Soybean MAPK, MAPKK, and MAPKKK genes and primers for VIGS cloning Gene_ID Forward Primer Reverse Primer Arabidopsis Ortholog Glyma04g03210 aagggatcctgcagcaagaaccagttcat ttgggtaccctaatggatgcgcattaggataaag AtMPK1,At1g10210 Glyma12g07770 aagggatccttcttgtaccagattcttcgtgg ttgggtacccctctgtcaat AGGCGCATCT G AtMPK3, At3g45640 Glyma16g03670 aagggatccctgtatcaattgttacgagggctc ttgggtacccctctgtgataagtctcagctgatga AtMPK4a, At4g01370 Glyma02g15690 aagggatccccagagcttctgttgaactcttc ttgggtacccatgttgttcaaagtcaaagttgaagg AtMPK6, At2g43790 Glyma08g05700 aagggatccatgggtggtggaggaacact ttgggtacccctttttgtgatgatccatggaag AtMPK9, AT3G18040 Glyma09g39190 aagggatccctgtatcagttgttacgaggactcaa ttgggtaccccagcctgagc TGATGAACAT AAT AtMPK4c Glyma11g15590 aagggatccctcttgcgaggattgaagtacatc ttgggtacccctcagttataagggccaactgttg AtMPK13, At1g07880 Glyma12g07850 aagggatcccaactcttgcgagggttgaa ttgggtacccctcagttataagggccaactgct AtMPK13, At1g07880 Glyma13g28120 aagggatcccagattcttcgtgggcttaagt ttgggtacccctctgtcaataggcgcatctg MPK16/17, At5g19010 Glyma17g02220 aagggatccggaagctatggtgttgtttgctc ttgggtaccctcggtgtatatacttcaagcctcg MPK16, At5g19010 Glyma13g05700 aagggatccggcgaagttgcttctccagt ttgggtacccgagaacacgtagctgtgaaagga SNF1 kinase homolog 10, At3G01090 Glyma13g33860 aagggatccacgcttatgaccaaagggtc ttgggtaccctgacaatccatactgaaaggcc MPK19, At3g14720 Glyma08g42240 aagggatcctcatatgatcctaggtcattcatcag ttgggtacccaggaccaacttttctatgagcagt MPK20, At2G42880 Glyma15g18860 aagggatccgaaatccaaatgcctattgagga ttgggtacccgttaggcatgcagcgaaaag AtMKK1, AT4G29810 or At4g26070 Glyma17g06020 aagggatccgtgctgaagggtctagtttatctcc ttgggtaccctgcagagataaatgagcaaaattct AtMKK2, AT4G29810, Glyma13g16650 aagggatccgtgctgaagggtttagtttatctcc ttgggtacccatgctgagataaatgagcaaaattct AtMKK2, AT4G29810, Glyma19g00220 aagggatcc TCTGGGAAACAACATCGTGG ttgggtaccc GCTAGTTGGT TCGCATCCAA TA AtMKK3, At5g40440 Glyma07g00520 aagggatcc AATCAGACGATGGATCCGTG ttgggtacccgagtagctga TGGAGGTTGG GA AtMKK4/5, At1G51660, AT3G21220 Glyma08g23900 aagggatcc AATCAGACGATGGATCCGTG ttgggtaccc GAGTAGCTGA TGGAGGTTTG GA AtMKK5, AT3G21220 Glyma10g15850 aagggatccattctggaaccatatcttgctgtg ttgggtacccttggatgcaggatgacacg AtMKK6, AT5g56580 Glyma02g41340 aagggatcctatgctttgggagttgttctattg ttgggtacccacactctgga ACTCCTAGCA TAGCT Protein kinase superfamily protein, AT5G37790.1 Glyma14g39690 aagggatccgctaaacctttgctgagaaaagg ttgggtacccatgaccatagagaaaatcatcatcc Protein kinase superfamily protein, AT5G37790.1 Glyma15g05390 aagggatccatgggtaataaaattggtagggc ttgggtacccggtgaagccttcatagacggt AtMEKK1a, AT4G08500 Glyma15g05400 aagggatccatggaagctgagcggaag ttgggtacccgtggtcatcagcaaaaccag AtMEKK1b, AT4G08500 Glyma08g08300 aagggatccaccactcctcctcctcacac ttgggtacccattgaagccttcatagacagttcc AtMEKK1c, AT4G08500 Glyma05g25290 aagggatccatggactggaggcgcag ttgggtacccggaggaagaagaaaccgca AtMEKK1d, AT4G08500 Glyma19g42340 aagggatccaacgatgatgatatgtgtgtgattg ttgggtaccctggtgacctgcttttaggagg AtNPK1, AT1g09000 Glyma06g15870 aagggatccagcaagagcaaggaccaacaa ttgggtacccgtgacaggtagggtgatcatcgta AtMKKK3, AT1G53570 Glyma06g03970 aagggatcctcgtgtaaagatcacagagaactctct ttgggtaccctgcatgataaacagatccaaatgat AtMKKK5, Glyma11g02520 aagggatccgaagcccatacaccaaggaac ttgggtacccgaagcccatacaccaaggaac MEKK related, AT1G63700 Glyma17g19800 aagggatccgatatatgggctttgggatgtg ttgggtacccatcaaaaccccacttttcttgaaat MPKKK21, AT4G36950 Glyma13g28570 aagggatccctagagttgagtgcctctgcagaa ttgggtaccctgaatttttg AGTTCAGAAA CTATGACT MAPKK RELATED KINASE with ARM domain, AT5G18700

Supplemental table 2. False discovery rate (q value) and log2 fold change (FC) of ribosomal RNA probe sets Affymetrix Soybean Probe ID p value q value log2 FC soybean_rrna_114_at 0.25 0.38 1.92 soybean_rrna_666_at 0.46 0.58 1.26 soybean_rrna_692_at 0.4 0.53 1.2 soybean_rrna_637_at 0.36 0.5 1.14 soybean_rrna_918_at 0.42 0.55 1.09 soybean_rrna_1352_at 0.36 0.49 0.99 soybean_rrna_274_at 0.46 0.59 0.93 soybean_rrna_218_at 0.42 0.56 0.91 soybean_rrna_57_at 0.51 0.63 0.9 soybean_rrna_176_at 0.38 0.51 0.84 soybean_rrna_349_at 0.41 0.54 0.83 soybean_rrna_176_rc_at 0.01 0.03 0.77 soybean_rrna_114_rc_at 0.03 0.08 0.73 soybean_rrna_1479_at 0.56 0.68 0.7 soybean_rrna_718_at 0.47 0.6 0.67 soybean_rrna_808_at 0.47 0.6 0.67 soybean_rrna_1665_at 0.53 0.65 0.67 soybean_rrna_485_at 0.38 0.51 0.66 soybean_rrna_666_rc_at 0.5 0.63 0.61 soybean_rrna_838_at 0.38 0.52 0.61 soybean_rrna_57_rc_at 0.23 0.35 0.6 soybean_rrna_1021_at 0.55 0.67 0.54 soybean_rrna_918_rc_at 0.05 0.1 0.51 soybean_rrna_776_at 0.51 0.63 0.47 soybean_rrna_1531_at 0.68 0.78 0.34 soybean_rrna_1057_at 0.72 0.81 0.32 soybean_rrna_637_rc_at 0.27 0.39 0.32 soybean_rrna_1391_at 0.81 0.88 0.24 soybean_rrna_218_rc_at 0.72 0.81 0.23 soybean_rrna_274_rc_at 0.48 0.61 0.21 soybean_rrna_349_rc_at 0.8 0.87 0.07 soybean_rrna_838_rc_at 0.8 0.86 0.066 soybean_rrna_718_rc_at 0.98 0.99 7.30E 03 soybean_rrna_1721_at 0.95 0.97 0.05 soybean_rrna_1057_rc_at 0.76 0.84 0.09 soybean_rrna_1692_at 0.87 0.92 0.11 soybean_rrna_776_rc_at 0.64 0.74 0.11 soybean_rrna_808_rc_at 0.31 0.45 0.18 soybean_rrna_485_rc_at 0.29 0.42 0.21 soybean_rrna_692_rc_at 0.7 0.79 0.23 soybean_rrna_1721_rc_at 0.44 0.57 0.29 soybean_rrna_1391_rc_at 0.09 0.17 0.36 soybean_rrna_1021_rc_at 0.12 0.21 0.38 soybean_rrna_1479_rc_at 0.008 0.02 0.54 soybean_rrna_1531_rc_at 0.005 0.02 0.6 soybean_rrna_1665_rc_at 0.02 0.05 0.63 soybean_rrna_1352_rc_at 0.09 0.18 0.72 soybean_rrna_1692_rc_at 8.50E 03 3.40E 03 1.11

Supplemental table 3. False discovery rate (q value) and log2 fold change (FC) of defense related probe sets Affymetrix Soybean Probe ID Soybean gene locus p value q value log 2 FC Annotation GmaAffx.82055.1.S1_at Glyma13g35320.1 3.90E 10 1.62E 07 8.3 Defensin, PDF2.4 Gma.2821.1.S1_at Glyma01g42660.1 2.34E 09 4.09E 07 6.4 PR 5 protein GmaAffx.92699.1.S1_s_at Glyma01g42660.1 1.31E 08 1.05E 06 6.4 PR 5 protein Gma.2821.2.S1_a_at Glyma11g02770.1 6.09E 09 6.76E 07 5.9 PR 5 protein Gma.2821.2.S1_at Glyma11g02770.1 1.85E 08 1.29E 06 5.6 PR 5 protein Gma.2033.1.S1_s_at Glyma05g38110.1 1.61E 10 1.09E 07 5.5 PR5 Thaumatin family, response_to_abiotic_or_biotic_stimulus GmaAffx.1338.1.S1_at Glyma02g35210.1 2.30E 07 6.11E 06 5.5 Syntaxin 121 GmaAffx.77256.1.S1_at Glyma14g00730.1 4.94E 07 1.02E 05 5.2 NUDIX HYDROLASE RELATED GmaAffx.42847.2.S1_at Glyma15g06800.1 1.74E 07 5.12E 06 5.1 CYSTEINE RICH SECRETORY PROTEIN (CRISP/SCP/TPX1) RELATED GmaAffx.88182.1.S1_at Glyma03g35930.1 5.47E 09 6.35E 07 5 Syringolide induced protein, Hairpin inducing protein GmaAffx.8704.1.A1_at Glyma02g15280.1 9.38E 09 8.66E 07 5 Peroxidase Gma.169.1.S1_at Glyma09g23140.1 4.29E 08 2.08E 06 4.8 Acidic chitinase GmaAffx.42847.1.S1_s_at Glyma15g06790.1 2.35E 09 4.09E 07 4.8 CYSTEINE RICH SECRETORY PROTEIN (CRISP/SCP/TPX1) RELATED Gma.2833.1.S1_s_at Glyma02g04820.1 2.18E 08 1.42E 06 4.7 Chitinase class I Gma.12028.1.S1_at Gma.12028.1.S1_at 1.98E 08 1.34E 06 4.6 GLYCOLIPID TRANSFER PROTEIN RELATED GmaAffx.88845.1.S1_at Glyma15g06790.1 5.30E 09 6.20E 07 4.6 CYSTEINE RICH SECRETORY PROTEIN (CRISP/SCP/TPX1) RELATED Gma.5622.1.S1_at Glyma10g01300.1 2.98E 11 6.89E 08 4.3 negative_regulation_of_transcription regulation_of_systemic_acquired_resistance defense_response_to_bacterium GmaAffx.91964.1.S1_at No Soybean Match 5.33E 08 2.40E 06 4.2 Glutamine synthetase PR 2 GmaAffx.9145.1.S1_s_at Glyma17g03330.1 2.60E 07 6.65E 06 4 Pathogenesis related protein Bet v I family GmaAffx.93031.1.S1_x_at Glyma16g28590.1 1.10E 07 3.81E 06 3.8 Extensin GmaAffx.89999.1.S1_x_at Glyma07g37280.1 8.62E 07 1.50E 05 3.8 Pathogenesis related protein Bet v I family Gma.10216.2.S1_at Glyma07g05480.1 1.64E 08 1.19E 06 3.8 O METHYLTRANSFERASE GmaAffx.36484.1.S1_s_at Glyma15g06780.1 2.09E 08 1.38E 06 3.7 Defense related protein containing SCP domain GmaAffx.4968.1.S1_at Glyma16g08420.1 9.27E 10 2.54E 07 3.7 Avr9/Cf 9 rapidly elicited protein Gma.9501.1.A1_at Glyma19g39990.1 5.58E 08 2.46E 06 3.7 pectin methylesterase GmaAffx.17961.3.S1_at Glyma13g29580.1 6.06E 09 6.76E 07 3.4 GRP78/BiP/KAR2, HSP70 superfamily Gma.3452.1.S1_at Glyma01g01510.1 6.20E 06 6.29E 05 3.4 CGI 141 RELATED/LIPASE CONTAINING PROTEIN; Lipase (class 3) GmaAffx.91442.1.S1_at Glyma17g03350.4 3.73E 07 8.49E 06 3.4 Pathogenesis related protein 2 Gma.10216.1.S1_a_at Glyma07g05480.1 2.44E 06 3.14E 05 3.3 O METHYLTRANSFERASE GmaAffx.80842.1.S1_at Glyma06g19900.1 5.66E 09 6.47E 07 3.3 EDS1 like GmaAffx.93487.1.S1_x_at No Soybean Match Iden3.11E 05 2.20E 04 3.2 Stress and pathogenesis related protein Gma.16778.1.S1_at Glyma15g40000.1 7.49E 06 7.28E 05 3.2 Avr9/Cf 9 rapidly elicited protein GmaAffx.89772.4.S1_at Glyma17g03360.1 6.72E 06 6.68E 05 3 Pathogenesis related protein Bet v I family Gma.8480.1.S1_at Glyma16g25120.1 1.99E 08 1.35E 06 2.9 Resistance protein LM12 GmaAffx.90663.1.S1_at Glyma13g36950.1 3.80E 08 1.96E 06 2.9 GLUTAREDOXIN GmaAffx.40841.1.S1_at Glyma13g43870.5 3.11E 07 7.48E 06 2.9 lead_ion_transport multidrug_transport response_to_biotic_stimulus Gma.5947.1.S1_s_at Glyma09g04530.1 5.22E 08 2.36E 06 2.8 Pathogenesis related class 10 protein SPE 16 Gma.8478.1.S1_at Glyma16g34100.1 1.10E 06 1.78E 05 2.7 Resistance protein MG13 GmaAffx.76391.1.S1_s_at Glyma01g01510.1 1.29E 05 1.11E 04 2.7 lipase class 3 family protein GmaAffx.86629.1.S1_at Glyma11g10080.1 4.19E 07 9.17E 06 2.7 Endo 1,3 beta glucanase GmaAffx.18040.1.S1_s_at Glyma09g04520.1 9.03E 07 1.55E 05 2.7 Class 10 pathogenesis related protein GmaAffx.89772.10.S1_s_at No Soybean Match Iden1.65E 05 0.000134 2.7 Stress induced protein SAM22 Gma.1756.1.S1_at Glyma14g10620.1 9.68E 07 1.63E 05 2.5 Vacuolar processing enzyme GmaAffx.86629.2.S1_at Glyma11g10080.1 7.76E 07 1.39E 05 2.44 Glucan endo 1,3 beta d glucosidase Gma.2715.2.S1_at Glyma09g38410.1 4.88E 07 1.01E 05 2.4116 Calreticulin 3 Gma.9010.1.S1_at Glyma15g31520.1 4.28E 08 2.08E 06 2.39 Pathogenesis related protein Bet v I family Gma.17223.1.S1_at Glyma20g34260.1 3.29E 06 3.94E 05 2.35 DELLA protein Gma.10199.1.A1_at Glyma03g32520.2 1.18E 05 1.03E 04 2.31 PDR like ABC transporter Gma.11119.2.S1_s_at Glyma07g37270.1 6.14E 06 6.25E 05 2.29 Pathogenesis related protein Bet v I family Gma.6999.1.S1_s_at Glyma07g37250.1 1.75E 05 1.40E 04 2.29 PR 10 like

Gma.2470.1.S1_s_at Glyma03g38630.1 5.36E 07 1.08E 05 2.1732 Oxalate oxidase GmaAffx.92230.1.A1_at No Soybean Match Iden 2.02E 05 0.000157 2.13 Thaumatin like protein Gma.5489.1.S1_at Glyma20g36810.1 1.99E 04 1.00E 03 2.11 CHITINASE RELATED PR4 GmaAffx.92230.1.A1_s_at Glyma01g42670.1 2.51E 07 6.48E 06 2.08 Thaumatin like protein Gma.2382.1.S1_s_at Glyma02g26160.1 2.34E 05 1.77E 04 2.06 lipoxygenase_activity GmaAffx.91208.1.S1_s_at Glyma15g19580.1 6.07E 09 6.76E 07 2.01 CYSTEINE PROTEASE FAMILY C1 RELATED Gma.6838.1.S1_at Glyma15g13320.2 7.77E 08 3.03E 06 1.98 NPR1 like protein Gma.16812.1.S1_x_at Glyma15g13500.1 2.19E 06 2.91E 05 1.98 Peroxidase GmaAffx.76062.1.S1_at AT2G40000.1 4.17E 05 2.78E 04 1.97 Nematode resistance HS1pro1 protein Gma.6999.1.S1_x_at Glyma07g37240.3 7.73E 06 7.46E 05 1.91 Intracellular Pathogenesis related protein or Stress induced protein SAM22 Gma.4543.1.S1_at Glyma14g38610.1 1.55E 06 2.28E 05 1.81 Pathogenesis related genes transcriptional activator PTI6 Gma.2346.1.S1_at No Soybean Match Iden1.35E 05 1.15E 04 1.69 Class 10 pathogenesis related protein 1 GmaAffx.93635.1.S1_s_at Glyma13g32540.1 7.58E 03 2.22E 02 1.68 Pathogenesis related protein PR 1 Gma.5867.1.A1_s_at 8.30E 06 7.87E 05 1.68 Salicylic acid binding protein 2 GmaAffx.20155.1.S1_at Glyma02g35230.1 1.51E 07 4.67E 06 1.66 Syntaxin related protein 121 GmaAffx.132.1.S1_at Glyma13g30720.1 1.01E 07 3.59E 06 1.63 Pathogenesis related genes transcriptional activator PTI5 Gma.3149.1.S1_a_at Glyma02g02780.1 4.17E 06 4.68E 05 1.47 TIR domain Gma.12911.1.A1_s_at Glyma02g06070.1 1.88E 04 9.56E 04 1.45 Salicylic acid methyl transferase like protein Gma.233.1.S1_at Glyma08g13630.2 1.09E 05 9.75E 05 1.34 LSD1 GmaAffx.86728.3.S1_s_at Glyma05g30490.3 5.13E 06 5.46E 05 1.27 LSD1 GmaAffx.79817.2.S1_x_at Glyma09g23980.1 1.61E 06 2.33E 05 1 SGT1 2 GmaAffx.32324.1.A1_at Glyma02g40320.1 1.72E 05 1.39E 04 1 Pathogenesis related genes transcriptional activator PTI6 GmaAffx.47649.1.S1_at Glyma02g13340.1 2.42E 06 3.13E 05 1.51 Salicylic acid methyl transferase like protein Gma.13535.1.S1_at Glyma18g10080.1 1.71E 06 2.44E 05 2.13 salicylic acid carboxyl methyltransferase like protein

Supplemental table 4. WRKY probe sets differentially expressed in MPK4 silenced plants Affymetrix Soybean Probe ID Soybean gene locus p value q value log2 FC Annotation No. W box GmaAffx.6438.2.S1_at AT2G38470.1 1.17E 07 3.94E 06 4.7 WRKY33 Gma.3364.1.S1_at Glyma15g20990.1 3.61E 07 8.29E 06 4.6 WRKY42 1 gmaaffx.6438.7.s1_at Glyma11g29720.1 1.13E 07 3.87E 06 4.5 WRKY33 2 GmaAffx.12883.1.S1_at Glyma17g33890.1 3.33E 10 1.48E 07 4.5 WRKY60 0 GmaAffx.73009.1.S1_at AT5G64810.1 2.17E 08 1.42E 06 4.5 WRKY51 Gma.16733.2.S1_at Glyma14g11920.1 3.80E 08 1.96E 06 4.3 WRKY40 0 GmaAffx.6438.3.S1_s_at Glyma11g29720.1 5.17E 08 2.35E 06 4.2 WRKY33 2 gmaaffx.41719.1.s1_at Glyma17g33890.1 2.16E 08 1.41E 06 4.0 WRKY40 0 GmaAffx.74525.2.S1_at Glyma08g15050.1 2.98E 09 4.50E 07 3.8 WRKY51 0 GmaAffx.73009.1.S1_s_at Glyma06g15220.1 1.00E 08 8.91E 07 3.7 WRKY51 0 Gma.4400.1.S1_at Glyma19g26400.1 3.11E 09 4.56E 07 3.7 WRKY75 1 GmaAffx.91506.1.S1_at Glyma15g11680.2 6.17E 07 1.19E 05 3.6 WRKY31 0 gmaaffx.73009.2.s1_at Glyma06g15220.1 9.64E 09 8.79E 07 3.6 WRKY51 0 GmaAffx.69709.1.S1_at Glyma09g00820.1 6.07E 06 6.19E 05 3.5 WRKY31 1 Gma.4281.1.S1_at Glyma18g44560.1 1.00E 09 2.65E 07 3.5 WRKY70 1 GmaAffx.32330.1.A1_at Glyma17g33920.1 3.07E 08 1.74E 06 3.4 WRKY40 0 GmaAffx.14300.1.S1_at Glyma13g38630.1 1.50E 07 4.66E 06 3.3 WRKY31 0 gmaaffx.14300.1.s1_at Glyma13g38630.1 1.50E 07 4.66E 06 3.3 WRKY6 0 Gma.12112.1.S1_at Glyma06g13090.1 4.04E 06 4.57E 05 3.3 WRKY53 4 Gma.744.1.S1_at Glyma01g43420.1 6.00E 07 1.16E 05 3.1 WRKY53 4 GmaAffx.83326.2.S1_at AT1G62300.1 4.36E 07 9.42E 06 3.1 WRKY6 GmaAffx.68985.1.S1_at Glyma06g06530.1 5.01E 08 2.31E 06 3.1 WRKY40 0 Gma.15889.1.S1_s_at Glyma05g29310.1 1.78E 07 5.20E 06 3.0 WRKY65 0 gmaaffx.92842.1.s1_x_at Glyma09g00820.1 2.55E 07 6.55E 06 3.0 WRKY31 1 GmaAffx.90598.1.S1_at Glyma07g39250.1 2.65E 06 3.34E 05 3.0 WRKY6 1 gmaaffx.83326.1.s1_at Glyma07g39250.1 1.79E 07 5.23E 06 3.0 WRKY6 1 Gma.9913.2.S1_a_at Glyma04g40130.1 3.16E 10 1.47E 07 3.0 WRKY70 2 GmaAffx.92945.1.S1_x_at Glyma02g39870.1 9.47E 08 3.45E 06 2.8 WRKY26 4 gma.2526.1.s1_x_at Glyma09g00820.1 9.90E 08 3.54E 06 2.7 WRKY31 1 gma.2526.1.s1_at Glyma09g00820.1 9.90E 08 3.54E 06 2.7 WRKY31 1 gma.2526.3.s1_s_at Glyma09g00820.1 9.90E 08 3.54E 06 2.7 WRKY31 1 gmaaffx.92945.1.s1_at Glyma02g39870.1 2.24E 07 6.00E 06 2.7 WRKY26 4 gma.8336.1.s1_at Glyma19g40560.1 3.62E 06 4.21E 05 2.6 WRKY23 0 GmaAffx.36938.1.S1_at Glyma01g31920.1 2.29E 07 6.08E 06 2.6 WRKY33 4 Gma.9111.1.S1_at Glyma16g03570.1 1.09E 04 6.09E 04 2.6 WRKY22/29 2 gmaaffx.83326.2.s1_s_at Glyma07g39250.1 1.10E 06 1.78E 05 2.5 WRKY6 1 gma.4342.1.s1_at Glyma13g38630.1 1.18E 06 1.88E 05 2.5 WRKY6 0 gmaaffx.91389.1.s1_s_at Glyma02g39870.1 9.14E 06 8.48E 05 2.3 WRKY33 4 GmaAffx.73842.2.S1_at Glyma05g36970.1 1.25E 05 1.08E 04 2.3 WRKY53/55 1 gma.11203.1.s1_a_at AT2G38470.1 1.45E 07 4.54E 06 2.3 WRKY33 GmaAffx.25598.1.S1_at Glyma02g12830.1 1.56E 08 1.15E 06 2.3 WRKY57 0 GmaAffx.93343.1.S1_at Glyma09g41050.1 2.58E 07 6.59E 06 2.3 WRKY70 0 gmaaffx.78486.3.s1_at Glyma02g12830.1 6.39E 08 2.68E 06 2.2 WRKY57 0 gmaaffx.91389.1.s1_x_at Glyma02g39870.1 3.73E 07 8.49E 06 2.1 WRKY33 4 gmaaffx.7166.1.s1_at Glyma19g44380.1 2.52E 07 6.51E 06 2.1 WRKY41 3 Gma.16547.1.S1_s_at Glyma03g37940.1 1.96E 06 2.69E 05 2.1 WRKY23 1 gmaaffx.51816.1.s1_at AT4G23810.1 7.56E 06 7.33E 05 2.1 WRKY53 Gma.7467.1.A1_at Glyma01g06550.1 7.80E 08 3.04E 06 2.0 WRKY4 0 GmaAffx.91449.1.S1_at Glyma08g26230.1 1.19E 07 3.98E 06 1.9 WRKY4 0 Gma.3504.2.S1_a_at Glyma13g00380.1 6.41E 07 1.22E 05 1.9 WRKY11 2 gma.3504.2.s1_at Glyma13g00380.1 1.31E 06 2.01E 05 1.8 WRKY11 2 GmaAffx.93596.1.S1_at Glyma17g03950.2 2.60E 05 1.92E 04 1.8 WRKY48 1 GmaAffx.91895.1.S1_at Glyma13g17800.1 2.78E 05 2.02E 04 1.7 WRKY47 2 gma.16547.1.s1_at Glyma03g37940.1 1.05E 05 9.44E 05 1.7 WRKY23 1 Gma.3504.1.S1_at Glyma17g06450.1 1.61E 07 4.83E 06 1.7 WRKY11 1 GmaAffx.73842.1.S1 Glyma08g02580.1 1.75E 05 1.40E 04 1.7 WRKY53 3 GmaAffx.91538.1.S1_s_at Glyma13g36540.1 2.76E 05 2.01E 04 1.6 WRKY69 0 Gma.3762.2.S1_at Glyma17g18480.1 2.20E 03 7.72E 03 1.6 WRKY15 4 GmaAffx.28998.1.S1_at Glyma17g04710.1 4.85E 06 5.24E 05 1.6 WRKY31 0 GmaAffx.48074.1.S1_x_at AT1G13960.2 2.03E 06 2.75E 05 1.6 WRKY4 gmaaffx.86377.1.s1_at Glyma07g06320.1 3.72E 06 4.29E 05 1.5 WRKY53 2 gmaaffx.81988.1.s1_at No Soybean Match 1.40E 05 1.18E 04 1.5 WRKY11 GmaAffx.87142.1.S1_at Glyma06g08120.1 4.77E 05 3.10E 04 1.4 WRKY11 0 GmaAffx.33784.1.S1_at Glyma08g01430.1 1.49E 05 1.24E 04 1.4 WRKY75 3 Gma.3996.2.S1_s_at Glyma12g33990.1 1.09E 05 9.70E 05 1.4 WRKY69 0 GmaAffx.47893.1.S1_at Glyma01g39600.2 2.83E 03 9.60E 03 1.3 WRKY15 4 gmaaffx.87142.3.s1_s_at Glyma06g08120.1 4.54E 05 2.01E 03 1.3 WRKY17 0 gmaaffx.21523.2.s1_at Glyma19g40950.2 2.93E 06 3.62E 05 1.3 WRKY42 1 gmaaffx.82051.1.s1_at No Soybean Match 6.51E 05 2.72E 03 1.2 WRKY33 GmaAffx.66949.1.S1_at Glyma02g47650.1 8.42E 06 7.96E 05 1.2 WRKY1 1 GmaAffx.61116.1.S1_at Glyma16g02960.1 2.80E 03 9.50E 03 1.1 WRKY46 2 Gma.13481.1.A1_at Glyma03g37870.1 3.04E 04 1.43E 03 1.0 WRKY35 0 Gma.12782.1.A1_at Glyma03g31630.1 8.32E 06 7.89E 05 1.1 WRKY21 2 GmaAffx.69401.1.S1_at Glyma09g37930.1 1.69E 05 1.37E 04 1.2 WRKY13 1 GmaAffx.52704.3.S1_at Glyma03g33380.1 8.93E 07 1.54E 05 1.2 WRKY2/TTG2 2

Supplemental table 5. Differentially expressed probe sets corresponding to auxin regulated genes in MPK4 silenced plants Affymetrix Soybean Probe ID Soybean gene locus p value q value log2 FC Annotation Gma.2590.1.A1_s_at Glyma10g35870.1 2.86E 08 1.68E 06 6 Auxin down regulated protein Gma.2115.1.S1_at Glyma08g22190.1 7.31E 06 7.15E 05 4.6 Auxin induced protein AUX22 GmaAffx.74676.2.S1_at Glyma11g11310.1 3.98E 06 4.52E 05 4.5 Auxin transporter like protein 5 GmaAffx.79139.1.S1_at Glyma09g30700.1 7.28E 09 7.48E 07 4.2 Auxin efflux carrier GmaAffx.52963.1.S1_at Glyma13g17400.1 2.23E 07 5.97E 06 3.7 Response_to_auxin_stimulus Gma.7655.2.A1_at Glyma08g37070.1 7.00E 07 1.29E 05 3.4 GH1 protein GmaAffx.310.1.S1_at Glyma07g06060.1 3.32E 08 1.81E 06 3.3 Auxin response factor 18 GmaAffx.15800.1.S1_at Glyma06g43380.1 3.93E 05 2.65E 04 3.2 Auxin induced protein 15 Gma.13034.1.S1_at Glyma12g03990.1 1.10E 05 9.83E 05 3.1 Auxin responsive protein; SAUR protein Gma.4259.1.S1_at Glyma10g30440.3 3.49E 07 8.10E 06 3.1 Auxin regulated protein GmaAffx.49300.1.S1_at Glyma02g00260.1 5.97E 05 3.73E 04 3 Auxin induced protein IAA4 GmaAffx.75503.1.S1_at Glyma06g00950.1 1.27E 05 1.10E 04 3 Auxin responsive protein GmaAffx.76295.1.S1_at Glyma08g16510.1 6.07E 06 6.19E 05 3 Indole 3 acetic acid induced protein ARG7 Gma.4576.1.S1_at AT4G38840.1 1.60E 05 0.000131 2.9 Auxin induced protein GmaAffx.3727.1.S1_at Glyma11g15910.1 6.97E 09 7.22E 07 2.9 Auxin response factor; Aux/IAA_ARF Gma.10333.1.S1_at Glyma17g05760.1 2.30E 05 1.74E 04 2.9 Auxin binding protein ABP19 GmaAffx.11297.1.S1_at Glyma08g15480.1 1.35E 08 1.07E 06 2.8 response_to_auxin_stimulus root_development Gma.2414.1.S1_at Glyma14g05250.1 3.45E 06 4.07E 05 2.8 Proteolysis response_to_auxin_stimulus lateral_root_morphogenesis Gma.5105.1.S1_at Glyma10g03720.1 1.72E 05 1.39E 04 2.7 Auxin induced protein AUX28 GmaAffx.26943.1.S1_at Glyma12g07560.1 5.44E 08 2.42E 06 2.7 Auxin response factor; Aux/IAA_ARF_ GmaAffx.11052.1.S1_at Glyma08g21050.1 3.30E 09 4.68E 07 2.7 Auxin conjugate hydrolase Gma.3571.1.S1_at Glyma10g02440.1 2.31E 06 3.02E 05 2.6 Putative indole 3 acetic acid amido synthetase GH3.9 Gma.17944.1.S1_at Glyma13g43780.1 7.02E 09 7.25E 07 2.6 Auxin induced protein 22 (AUX22) GmaAffx.38425.1.S1_at Glyma09g35620.1 2.08E 06 2.80E 05 2.6 Auxin responsive protein Gma.1411.1.S1_at Glyma08g04070.1 1.54E 07 4.74E 06 2.5 AUX/IAA family GmaAffx.46821.1.S1_at Glyma16g02650.1 6.49E 08 2.71E 06 2.5 Auxin response factor 18 GmaAffx.20811.1.S1_at Glyma08g16520.1 7.21E 07 1.32E 05 2.4 Auxin responsive protein Gma.10738.2.S1_s_at Glyma08g15480.1 4.33E 09 5.59E 07 2.4 Response_to_auxin_stimulus root_development GO:0005200 Gma.4162.1.S1_at Glyma07g04850.1 2.52E 03 8.69E 03 2.4 Response_to_auxin_stimulus Gma.15110.1.S1_at Glyma18g42640.1 6.87E 08 2.79E 06 2.4 AUX1 like auxin influx carrier protein Gma.5427.2.S1_a_at Glyma08g22880.1 1.81E 08 1.27E 06 2.4 Auxin_polar_transport establishment_or_maintenance_of_transmembrane_electrochemical_grad GmaAffx.2721.1.S1_s_at AT5G37020.1 3.81E 09 5.12E 07 2.4 Auxin response factor 8 GmaAffx.91675.1.S1_s_at Glyma02g38260.4 6.43E 05 3.96E 04 2.3 Response_to_auxin_stimulus auxin_mediated_signaling_pathway GO:0003700 GmaAffx.49777.1.S1_at Glyma17g34300.1 6.20E 07 1.19E 05 2.3 unidimensional_cell_growth auxin_polar_transport phloem_or_xylem_histogenesis GO:0010487 GmaAffx.60895.1.S1_s_at Glyma10g28250.1 3.04E 06 3.72E 05 2.2 Regulation_of_transcription,_DNA dependent response_to_auxin_stimulus regulation_of_stomata Gma.3208.2.S1_a_at Glyma16g00980.1 2.60E 04 1.26E 04 2.2 Auxin binding protein ABP19 GmaAffx.77780.1.S1_at Glyma13g40310.1 9.13E 06 8.48E 05 2.2 Auxin response factor; Aux/IAA_ARF_ GmaAffx.63970.1.S1_at Glyma20g28340.1 6.07E 07 1.17E 05 2.2 Unidimensional cell growth auxin polar_transport phloem or xylem histogenesis GO:0010487 Gma.13491.1.S1_at Glyma13g30750.1 1.36E 06 2.08E 05 2.2 _DNA dependent auxin_metabolic_process response_to_auxin_stimulus Gma.5427.1.S1_at Glyma07g03220.2 2.27E 08 1.46E 06 2.1 auxin polar transport establishment Gma.1411.2.S1_at Glyma05g35640.1 8.07E 07 1.43E 05 2.1 Auxin responsive protein IAA27 GmaAffx.38591.1.A1_at Glyma16g21930.1 3.62E 07 8.31E 06 2.1 auxin polar transport GmaAffx.17944.1.S1_at Glyma18g51090.1 2.80E 06 3.49E 05 2.1 Putative auxin independent growth promoter protein (At3g30300) GmaAffx.44808.1.A1_at Glyma16g21870.1 1.84E 05 0.000146 2 auxin polar transport

Gma.493.1.S1_at Glyma12g08110.1 2.09E 05 0.000162 2 Putative auxin response factor ARF16 Gma.8412.1.S1_at Glyma15g02350.2 8.98E 07 1.54E 05 2 Auxin responsive protein IAA26 Gma.4259.3.S1_at Glyma20g36790.1 7.52E 06 7.30E 05 2 AUX/IAA family, Auxin regulated protein GmaAffx.40399.1.S1_at AT2G01420.2 1.77E 07 5.18E 06 2 PIN1 like auxin transport protein GmaAffx.50615.1.A1_at Glyma15g08540.1 2.10E 07 5.75E 06 2 DNA dependent auxin_metabolic_process response_to_auxin_stimulus Gma.14647.1.S1_at Glyma10g32330.1 2.54E 04 1.23E 03 2 Auxin induced protein IAA4; IAA31? GmaAffx.91229.1.S1_s_at AT3G04730.1 7.84E 05 4.65E 04 1.9 Putative uncharacterized protein; response_to_auxin_stimulus; transcription_factor_activity Gma.15747.1.A1_at Glyma04g00830.1 3.71E 05 2.53E 04 1.9 Auxin responsive protein GmaAffx.7250.1.A1_at Glyma12g29280.1 8.28E 08 3.15E 06 1.9 Auxin response factor 4; Aux/IAA_ARF_ GmaAffx.75691.1.S1_at Glyma07g05770.1 9.79E 05 5.57E 04 1.9 Putative uncharacterized protein GmaAffx.56884.1.A1_at Glyma09g35360.1 3.03E 04 1.43E 03 1.9 Auxin induced protein X10A GmaAffx.36330.1.S1_at NO BLASTX HIT (E<10 66.41E 06 6.45E 05 1.9 Auxin response factor GmaAffx.91229.1.S1_x_at Glyma20g35270.1 2.58E 04 1.25E 03 1.8 Aux/IAA protein, AXR3 Gma.14155.3.S1_at Glyma06g07130.1 1.68E 04 8.70E 04 1.8 Auxin responsive protein IAA29 Gma.7493.1.A1_at Glyma07g16170.1 8.23E 07 1.45E 05 1.8 Auxin response factor 9 GmaAffx.22799.1.S1_at Glyma13g24240.1 1.12E 06 1.80E 05 1.8 Auxin response factor GmaAffx.53937.1.A1_at Glyma17g37580.1 1.26E 05 1.10E 04 1.7 Auxin response factor 5 GmaAffx.91046.1.S1_at Glyma09g20580.1 3.94E 05 2.66E 04 1.7 Auxin efflux carrier protein; PIN1 like auxin transport protein; PIN7 GmaAffx.79246.2.S1_at Glyma14g38940.1 1.54E 05 1.27E 04 1.6 Auxin response factor 8 Gma.13060.1.S1_at Glyma19g34370.3 1.55E 04 5.73E 04 1.6 Auxin induced protein 22 GmaAffx.21473.1.S1_at AT2G33860.1 4.13E 05 0.000276 1.6 Auxin response factor Gma.6544.1.A1_at Glyma10g38900.1 3.91E 06 4.46E 05 1.6 Auxin induced protein PCNT115 Gma.7407.1.S1_at AT4G14550.1 8.31E 05 4.87E 04 1.5 Auxin induced protein AUX28 Gma.7655.1.S1_at AT5G65670.2 4.37E 05 2.89E 04 1.5 GH1 protein GmaAffx.92679.1.S1_s_at Glyma02g16090.2 1.40E 04 7.51E 04 1.5 Auxin induced protein 22 GmaAffx.69813.1.A1_at Glyma19g42210.1 4.21E 07 9.20E 06 1.5 Putative auxin response factor 75 GmaAffx.43149.1.A1_at Glyma09g35520.1 6.16E 05 3.83E 04 1.5 Auxin induced protein 10 GmaAffx.51803.1.S1_at Glyma08g05900.1 2.29E 05 1.74E 04 1.5 Auxin efflux carrier GmaAffx.19384.1.S1_at Glyma19g36820.1 3.45E 05 2.39E 04 1.5 Multidrug resistance protein 1 Gma.13027.1.A1_at Glyma11g35080.1 3.13E 06 3.80E 05 1.5 Auxin transporter like protein 1 Gma.13027.1.A1_at Glyma11g35080.1 3.13E 06 3.80E 05 1.5 Auxin transporter like protein LAX1 Gma.3241.1.S1_a_at Glyma15g19510.1 9.84E 05 5.60E 04 1.4 Auxin binding protein ABP20 GmaAffx.34031.1 Glyma13g20610.1 1.43E 04 7.65E 04 1.4 Auxin responsive family protein GmaAffx.44729.1.S1_at Glyma10g02440.2 3.76E 04 1.71E 03 1.4 Putative indole 3 acetic acid amido synthetase GH3.9 GmaAffx.8250.2.S1_at Glyma02g16090.2 3.61E 05 2.48E 04 1.3 Auxin induced protein Gma.9961.1.S1_at Glyma09g35330.1 5.93E 03 1.80E 02 1.3 Auxin induced protein Gma.7341.1.A1_s_at AT2G22670.3 3.76E 06 4.32E 05 1.3 Aux/IAA protein GmaAffx.93321.1.S1_x_at Glyma10g32340.1 4.51E 04 2.00E 03 1.3 Auxin responsive protein IAA7 GmaAffx.86578.1.S1_at Glyma01g24100.1 3.99E 04 1.86E 03 1.2 Auxin regulated protein; AUX/IAA family GmaAffx.24386.1.A1_at Glyma12g17510.1 2.99E 04 1.41E 03 1.2 Indole 3 acetic acid amido synthetase GH3.6 GmaAffx.50350.1.S1_at Glyma13g09030.1 3.13E 06 3.79E 05 1.2 Putative auxin efflux carrier protein GmaAffx.91653.1.S1_s_at Glyma15g02040.4 1.33E 04 7.20E 04 1.2 regulation_of_translation response_to_auxin_stimulus GmaAffx.2721.2.S1_at Glyma18g05330.1 3.00E 04 1.43E 03 1.1 Auxin response factor 8 Gma.1557.1.S1_a_at Glyma19g39420.1 6.45E 05 3.97E 04 1 ubiquitin dependent_protein_catabolic_process response_to_auxin_stimulus pollen_maturation s GmaAffx.80265.1.S1_at Glyma07g04830.1 2.09E 06 2.81E 05 1 Auxin induced related / indole 3 acetic acid induced related like Gma.3158.1.S1_at Glyma09g33630.1 1.03E 03 4.02E 03 1 GH1 protein; Aux/IAA protein