Table I.

Genes induced in roots of P-deficient plants identified by macroarray analysis

Functional categories are in bold. TC No., Tentative consensus sequence assignment (TIGR/DFCI Common Bean Gene Index, version 1.0); blank cells correspond to singletons with no TC number assigned.

EST IdentificationTC No.GenBank Accession No. of ESTAnnotationBLASTX E-ValueExpression Ratio −P to +PP-Value
Pi cycling
    RTS_113_H08EH791066(Q84MA2) Type I inositol-1,4,5-trisphosphate 5-phosphatase4.00E-102.599.8E-04
    RTS_145_F08TC1447CV544205(Q6J5M7) Purple acid phosphatase 11.00E-1002.102.2E-02
    RTS_105_G04CV541472(Q9LDA7) Protein phosphatase type 2C1.00E-652.124.8E-02
C/N metabolism
    RTS_101_F08TC1804CV541174(Q96558) UDP-Glc-6-dehydrogenase1.00E-653.631.7E-07
    RTS_122_G12TC733CV542619(Q8S532) Cytosolic aldehyde dehydrogenase RF2C3.00E-483.487.1E-04
    RTS_104_C06TC1280CV541371(P39866) Nitrate reductase1.00E-1222.652.5E-04
    RTS_117_F10CV542239(Q75GR9) Inosine-uridine preferring nucleoside hydrolase3.00E-782.283.8E-03
Amino acid/protein metabolism
    RTS_104_E06CV541391(Q8LSY7) Phosphoribosyltransferase3.00E-196.183.60E-05
    RTS_117_A02(TC1704)aEH791074(Q8LJW0) 40S Ribosomal S4 protein1.00E-1262.437.30E-04
    RTS_108_F01TC492CV541666(Q7DLS1) Proteasome subunit-β type1.00E-1352.413.20E-03
    RTS_120_H04TC486CV542476(P29144) Tripeptidyl-peptidase 22.00E-142.395.00E-02
    RTS_101_D04TC250CV541149(Q8LKU3) 60S Ribosomal protein1.00E-1032.346.80E-04
    RTS_117_A07(TC1704)aEH792674(Q8LJW0) 40S Ribosomal S4 protein1.00E-1262.303.30E-04
    RTS_135_E01TC112CV543464(Q41119) Cyclophilin1.00E-882.251.70E-03
    RTS_123_H06CV542691(Q9ZNS5) Ribosomal protein S284.00E-192.205.20E-03
    RTS_121_C06TC1703CV542506(Q5YJR8) 60S Acidic ribosomal protein1.00E-232.083.80E-03
    RTS_101_B01TC85CV541126(Q8W3Y4) S-adenosyl-methionine synthetase0.02.005.70E-03
Lipid metabolism
    RTS_110_A04TC1739CV541751(Q69JE2) Putative CLB1 protein0.02.514.2E-02
    RTS_127_F12CV542902(Q8LG07) GlcNAc-1-P-transferase2.00E-792.211.2E-03
Cell structure/cell cycle/development
    RTS_109_B06EH792671(Q9LVI9) Senescence-related dihydroorotate dehydrogenase1.00E-505.113.30E-08
    RTS_125_D07TC63CV542788(Q944T2) Translationally controlled tumor protein3.00E-773.727.60E-04
    RTS_127_C08(TC1617)aEH792676(Q41125) Pro-rich, 14-kD protein1.00E-502.437.10E-05
    RTS_137_A05TC114CV543578(Q41707) Extensin class 1 protein precursor1.00E-1342.409.10E-05
    RTS_119_E03TC254CV542369(Q9XHD5) B12D/Leaf senescence protein4.00E-352.217.60E-04
    RTS_136_B08TC415CV543516(Q09085) Hydroxy-Pro-rich glycoprotein2.00E-802.108.80E-04
Stress/defense/secondary metabolism
    RTS_138_E12TC1903CV543709(Q6K1Q5) Glycolipid transfer protein-like2.00E-824.622.10E-05
    RTS_101_C10TC280CV541144(Q2KTE6) ACC oxidase1.00E-1603.591.10E-03
    RTS_107_E03TC64CV541595(P25985) Pathogenesis-related protein (PvPR1)b2.00E-823.005.40E-05
    RTS_135_E10TC459CV543472(Q9C939) Putative oxidoreductaseb1.00E-592.634.40E-04
    RTS_117_E09TC2562CV542227(Q700B1) Noncyanogenic β-glucosidaseb9.00E-412.542.30E-05
    RTS_113_H03TC1260CV541991(Q2LAL0) Cyt P450 monooxygenaseb1.00E-722.521.80E-03
    RTS_111_F07TC2443CV541849(Q2LAL4) Cyt P450 monooxygenaseb1.00E-562.491.50E-03
    RTS_103_E06TC1890CV541320(Q9SWS4) Ripening-related protein/(O65884) MLP protein1.00E-712.392.10E-03
    RTS_136_E10TC397CV543546(O22443) Seed coat peroxidase precursorb1.00E-1032.313.30E-03
    RTS_113_H10CV541995(P32292) Indole-3-acetic acid-induced protein ARG25.00E-392.282.60E-03
    RTS_119_F09TC146CV542386(O48561) Catalase-40.02.271.30E-04
    RTS_102_H03TC2059CV541272(O23961) Peroxidase precursorb1.00E-1192.263.10E-02
    RTS_135_B05CV543440(Q1SGR7) TIR; Disease resistance protein1.00E-492.184.50E-03
    RTS_138_A10TC257CV543662(P07218) Phe ammonia-lyase0.02.182.80E-03
    RTS_108_H02CV541683(Q4QTI9) Pathogenesis-related 10 protein1.00E-152.152.10E-02
    RTS_125_H01CV542814(Q1SGA8) 2OG-Fe(II) oxygenase2.00E-382.122.90E-02
    RTS_118_D09CV542294(Q8LJ95) NBS-LRR resistance protein RGH1-like1.00E-062.041.40E-02
    RTS_105_D07TC1309CV541452(O65152) Cinnamyl alcohol dehydrogenaseb1.00E-1152.043.80E-03
Transport/membrane proteins
    RTS_113_A06CV541934(Q1SI67) Dynamin central region1.00E-433.965.00E-04
    RTS_108_A08TC220CV541629(Q506K0) Putative aquaporinb1.00E-1642.912.70E-05
    RTS_133_A05TC2513CV543276(O65744) GDP dissociation inhibitor4.00E-222.482.80E-02
    RTS_109_H05TC2647CV541745(Q6YZC3) Glc-6-P/phosphate translocator1.00E-1092.332.30E-02
    RTS_108_H06TC587CV541687(Q9MAX8) Epsilon1-COP1.00E-1572.238.10E-03
    RTS_108_F03TC2564CV541668(Q8H4Q9) GTP-binding protein Rab65.00E-342.214.70E-02
    RTS_124_F11CV542748(Q65CB1) ATP-binding cassette transporterb9.00E-782.091.10E-03
    RTS_119_F08TC1933CV542385(Q9FVE8) Plasma membrane Ca2+-ATPase1.00E-1502.053.80E-02
    RTS_136_H04CV543570(Q6K5Y4) Putative UDP-GlcNAc transporter8.00E-632.054.10E-02
    RTS_103_G05TC2845CV541336(Q1T029) Sugar transporter superfamily2.00E-752.001.30E-02
Regulation/signal transduction
    RTS_121_B11TC189CV542500(Q9LEB4) RNA Binding Protein 451.00E-1223.218.40E-04
    RTS_104_H09CV541419(Q41109) Regulator of MAT21.00E-233.111.50E-04
    RTS_119_D05TC1707CV542360(Q39892) Nucleosome assembly protein 11.00E-1223.092.10E-07
    RTS_104_D03TC1670CV541379(Q1SGW5) ZIMc1.00E-242.764.70E-05
    RTS_101_E04CV541158(Q1RVC8) HMG-I and HMG-Y, DNA-binding1.00E-222.442.20E-03
    RTS_138_A05CV543658(O65573) PRL1-associated protein6.00E-342.391.70E-02
    RTS_128_D02CV542946(Q8GXM5) RING-H2 finger protein RHB1a4.00E-252.371.00E-02
    RTS_142_A06TC778CV543967(Q9SK39) Putative steroid-binding protein 32.00E-402.346.20E-03
    RTS_102_F11CV541259(Q8LCS8) NTGP54.00E-142.302.50E-03
    RTS_108_H08CV541689(Q1T5G4) Zinc finger, CCCH-type1.00E-292.202.70E-02
    RTS_103_H07TC2434CV541346(Q5Z6C2) Putative mlo2 protein4.00E-632.172.50E-02
    RTS_101_B04TC2165CV541128(Q8H1A5) DEAD box RNA helicase0.02.162.20E-02
    RTS_101_F12TC1622CV541178(Q3HLY8) U-box protein1.00E-1092.091.70E-02
    RTS_104_B03TC348CV541358(Q5MJ53) AT-rich element binding factor 33.00E-912.082.90E-03
    RTS_110_H08TC221CV541801(Q93XA5) Homeodomain Leu zipper protein1.00E-1192.082.80E-03
    RTS_119_B12TC100CV542349(Q7F8L1) Histone H32.00E-652.051.40E-03
    RTS_137_H03TC165CV543649(Q93VL8) Calmodulin1.00E-752.003.20E-02
    RTS_123_D08TC1622CV542656(Q3HLY8) U-box protein1.00E-1092.003.70E-02
Unknown
    RTS_117_G02TC1992CV542243(Q1SEK2) Hypothetical protein1.00E-367.155.20E-05
    RTS_113_E03CV541966No BLAST hit <10–44.892.90E-05
    RTS_121_D02CV542512No BLAST hit <10–42.634.70E-04
    RTS_123_C04EH792675No BLAST hit <10–42.467.50E-04
    RTS_119_F10EH791078(Q8W4E6) Hypothetical protein1.00E-902.221.40E-03
    RTS_104_C07CV541372No BLAST hit <10–42.063.30E-02
    RTS_123_D12CV542660No BLAST hit <10–42.005.80E-03
  • a BLAST analysis of this new gene sequence revealed an overlap with the indicated TC from the TIGR/DFCI Common Bean Gene Index.

  • b Genes reported as bean candidate P stress-induced genes through clustering analysis across five or four plant species by Graham et al. (2006).

  • c Annotation according to TF genes identified in this work (Table III; supplemental data).