Table II.

Genes repressed 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/−PaP-Value
C/N metabolism
    RTS_112_G12TC1864CV541923(Q40345) Isocitrate dehydrogenase (NADP)1.00E-58−3.362.97E-02
    RTS_114_F03CV542030(Q9C9W6) Trehalose-6-P synthase2.00E-86−2.572.79E-02
    RTS_140_E03TC2520CV543865(Q9SEK4) Succinic semialdehyde dehydrogenase1.00E-138−2.251,45E-02
    RTS_141_C04TC851CV543912(Q8LBR3) Alcohol dehydrogenase4.00E-56−2.072.92E-02
    RTS_114_C03EH791068(Q9C9W6) Trehalose-6-P synthase4.00E-87−2.022.56E-02
Amino acid/protein metabolism
    RTS_140_C05TC83CV543847(Q8W3Y2) S-adenosyl-methionine decarboxylase0.0−2.823.56E-04
    RTS_139_D07CV543777(Q9SKA3) Phosphoribosylanthranilate transferase4.00E-55−2.661.22E-02
    RTS_141_B12TC1262CV543909(Q6XJF4) 26S Proteasome subunit RPN121.00E-114−2.438.06E-03
    RTS_131_C09TC1689CV543154(Q9FKC0) 60S Ribosomal protein L13a-41.00E-104−2.393.25E-03
    RTS_132_D01TC1613CV543229(O81361) 40S Ribosomal protein S81.00E-83−2.343.98E-02
    RTS_129_D12TC267CV543033(Q9AV87) 60S Ribosomal protein L213.00E-84−2.155.54E-03
    RTS_141_C11(TC836)bEH792677(Q8W538) Ribosomal S15 protein6.00E-73−2.154.23E-02
    RTS_140_D04TC163CV543856(O24322) Cys proteinase precursor0.0−2.113.68E-02
    RTS_140_H12EH791103(Q9FY64) Ribosomal protein S15-46.00E-77−2.042.33E-02
    RTS_112_A10TC110CV541878(Q71EW8) Met synthase0.0−2.009.52E-03
    RTS_123_G08TC209CV542684(P17093) 40S Ribosomal protein S113.00E-76−2.001.96E-02
Cell structure/cell cycle/development
    RTS_102_C02TC184CV541220(Q2PK12) Actin depolymerizing factor6.00E-68−2.814.49E-04
    RTS_143_D10CV544078(Q6ZH89) Caffeine-induced death protein 15.00E-43−2.761.55E-03
    RTS_139_D02TC1176CV543772(O80452) AMP deaminase3.00E-29−2.707.85E-03
    RTS_112_C11EH791061(Q41125) Pro-rich 14-kD protein1.00E-10−2.599.88E-03
    RTS_114_F01(TC1723)bEH792673(O04300) α-1,4-Glucan-protein synthase0.0−2.341.21E-02
    RTS_129_G01TC697CV543049(P93273) Fruit development protein (PAFD103)2.00E-16−2.332.94E-02
    RTS_115_A08(TC1617)bEH792678(Q41125) Pro-rich 14-kD protein1.00E-50−2.041.47E-02
Stress/defense/secondary metabolism
    RTS_105_B12(TC2799)bEH791098(Q9LJX0) Multidrug resistance protein 111.00E-116−2.761.78E-02
    RTS_142_B04TC692CV543977(Q9SZB9) Peroxidase 47 precursor4.00E-83−2.191.50E-02
    RTS_139_B06CV543755(Q9SPJ5) Dihydroflavonol-4-reductase DFR11.00E-86−2.142.73E-02
Transport/membrane proteins
    RTS_120_F09EH791079(Q1SG4) TFG-β receptor, type I/II extracellular region1.00E-62−5.885.25E-03
    RTS_132_D07CV543235(Q1SEG6) Heavy metal transport/detoxification protein5.00E-38−2.482.73E-02
    RTS_140_E05TC558CV543867(P31167) ADP, ATP carrier protein 13.00E-51−2.432.73E-02
    RTS_129_C07TC2875CV543019(Q9LX35) Transporter-like protein1.00E-56−2.291.01E-03
    RTS_129_H01TC1373CV543060(Q8H9B7) Putative lipid transfer protein3.00E-28−2.254.69E-02
    RTS_143_E05CV544083(Q8RYH0) GPI-anchored protein-like4.00E-22−2.251.25E-02
    RTS_143_E09TC1952CV544086(Q9LF59) Gly/Pro-rich protein5.00E-38−2.209.54E-05
    RTS_114_C05TC1657CV542010(Q9SMK5) Plasma membrane intrinsic polypeptide2.00E-51−2.086.63E-03
    RTS_141_F10TC2300CV543942(Q9FQ21) Putative Hs1pro-1-like receptor2.00E-56−2.029.57E-03
Regulation/signal transduction
    RTS_140_A08TC2273CV543830(Q1SDP0) Pathogenesis-related transcriptional factor6.00E-61−2.764.91E-02
    RTS_139_D11CV543780(Q6ZFY4) BHLH protein-like1.00E-06−2.611.88E-02
    RTS_129_G09TC829CV543056(Q9M9V8) Calcium-dependent protein kinase 11.00-38−2.361.60E-02
    RTS_142_D10(TC1606)bEH791104(Q9FNV7) Auxin-repressed protein4.00E-35−2.239.36E-03
Unknown
    RTS_114_E05CV542025No BLAST Hit <10–4−2.913.43E-02
    RTS_112_A12EH791058No BLAST Hit <10–4−2.883.59E-02
    RTS_131_E06EH791092Hypothetical protein2.00E-21−2.482.11E-03
    RTS_129_B07EH795233No BLAST Hit <10–4−2.431.13E-02
    RTS_132_A02EH791093Hypothetical protein3.00E-75−2.294.89E-02
    RTS_112_C10EH792672(Q60EX8) Hypothetical protein4.00E-51−2.133.64E-02
    RTS_122_G01CV542612No BLAST Hit <10–4−2.121.23E-02
    RTS_129_H03TC1470CV543062(Q1S1H6) Hypothetical protein4.00E-19−2.033.95E-02
    RTS_142_E11TC2851CV544015(Q93VT6) Hypothetical protein1.00E-65−2.031.58E-02
  • a For ratios lower than 1 (genes repressed in P deficiency), the inverse of the ratio was estimated and the sign was changed.

  • b BLAST analysis of this new gene sequence revealed an overlap with the indicated TC from the TIGR/DFCI Common Bean Gene Index.