Table 1

Genes up-regulated in the tomato pedicel abscission zone (AZ) compared with the proximal (Prox) and distal (Dis) regions of the pedicel
AZ > Prox AZ > Dis
Tomato Gene ID Probe ID Gene name / EST accession number Arabidopsis homologue Annotation Fold change (log2) p-value Fold change (log2) p-value
Transcription factor
Solyc02g083950 A_96_P013906 LeWUS AJ538329 AT2G17950 WUS (WUSCHEL) 8.5 0.002 8.3 0.002
Solyc03g117130a A_96_P240288 SlERF52 AK327476 AT5G25190 ethylene-responsive element-binding protein, putative 7.3 < 0.001 6.7 0.002
Solyc07g066250 A_96_P000266 Ls AF098674 AT1G55580 LAS (Lateral Suppressor) 6.0 0.008 5.9 0.008
Solyc11g069030 A_96_P012746 Bl AF426174 AT5G57620 MYB36 (myb domain protein 36) 5.5 0.008 4.5 0.007
Solyc07g062840 A_96_P226779 GOB FJ435163 AT5G53950 ANAC098 | CUC2 (CUP-SHAPED COTYLEDON 2) 5.2 0.002 3.8 0.003
Solyc09g066360 A_96_P115892 SlERF56 TA54084_4081 AT3G23240 ERF1 (ETHYLENE RESPONSE FACTOR 1) 4.9 0.014 2.3 0.019
Solyc01g080960a A_96_P017531 AK330067 AT4G17800 DNA-binding protein-related | Predicted AT-hook DNA-binding family protein 4.7 0.014 4.1 0.009
Solyc08g076010 A_96_P172039 BE431711 AT5G45580 transcription factor | Homeodomain-like superfamily protein 3.6 0.017 3.1 0.011
Solyc02g085500a A_96_P013166 OVATE AK247861 AT2G18500 ATOFP7 (ARABIDOPSIS THALIANA OVATE FAMILY PROTEIN 7) 2.8 0.002 1.8 < 0.001
Solyc01g102980 A_96_P226304 CK715116 AT1G75240 AtHB33 (ARABIDOPSIS THALIANA HOMEOBOX PROTEIN 33) 2.3 0.022 1.7 0.022
Solyc08g065420 A_96_P014181 BL4 AF375967 AT4G32980 ATH1 (ARABIDOPSIS THALIANA HOMEOBOX GENE 1) 2.1 0.019 4.0 0.018
Solyc08g078180 A_96_P030681 SlERF68 AW034080 AT5G47220 ERF2 (ETHYLENE RESPONSIVE ELEMENT BINDING FACTOR 2) 2.0 0.010 3.2 0.044
Solyc05g005090 A_96_P012291 TKn3 U76408 AT1G23380 KNAT6 (KNOTTED1-LIKE HOMEOBOX GENE 6) 1.9 0.018 4.1 < 0.001
Phytohormone metabolism/signaling/response
Solyc07g063850 A_96_P127252 AK319847 AT5G54510 GH3.6, DFL1 | DFL1 (DWARF IN LIGHT 1); indole-3-acetic acid amido synthetase 3.7 0.003 1.6 0.028
Solyc01g109150 A_96_P011856 AF461042 AT5G42650 AOS (ALLENE OXIDE SYNTHASE) 3.1 0.039 3.6 0.004
Solyc03g070380a A_96_P257477 AK328818 AT2G23620 MES1 (METHYL ESTERASE 1); hydrolase, acting on ester bonds / methyl indole-3-acetate esterase/ methyl jasmonate esterase/ methyl salicylate esterase 2.5 < 0.001 1.6 0.004
Solyc03g120060 A_96_P054606 AB223041 AT2G26710 BAS1 (PHYB ACTIVATION TAGGED SUPPRESSOR 1) 3.1 0.011 3.2 0.015
Solyc02g089160 A_96_P173339 Dwarf BE433666 AT3G30180 BR6OX2 (BRASSINOSTEROID-6-OXIDASE 2) 3.3 0.024 2.8 0.048
Solyc12g042500 A_96_P137617 AI779761 AT5G59845 gibberellin-regulated family protein 2.0 0.020 1.7 0.002
Cell wall hydrolysis/modification
Solyc12g096750 A_96_P012556 TAPG4 U70481 AT3G59850 polygalacturonase, putative / pectinase, putative 8.7 0.016 8.6 0.022
Solyc12g019180 A_96_P128437 NP000616 AT3G59850 polygalacturonase, putative / pectinase, putative 3.0 0.005 2.1 0.017
Solyc01g094970 A_96_P232064 AK323960 AT3G61490 glycoside hydrolase family 28 protein / polygalacturonase (pectinase) family protein 4.5 0.012 4.4 0.015
Solyc03g093390 A_96_P085969 EXPB2 DQ205653 AT1G65680 ATEXPB2 (ARABIDOPSIS THALIANA EXPANSIN B2) 3.7 0.040 2.9 0.047
Solyc03g006700 A_96_P077754 TA38392_4081 AT5G05340 peroxidase, putative 2.6 < 0.001 4.3 0.004
Defense function
Solyc10g017980 A_96_P216559 TA36496_4081 AT3G12500 ATHCHIB (ARABIDOPSIS THALIANA BASIC CHITINASE) 4.2 0.004 6.7 < 0.001
Solyc07g009530 A_96_P035581 BW687719 AT3G12500 ATHCHIB (ARABIDOPSIS THALIANA BASIC CHITINASE) 3.5 0.014 3.3 0.034
Solyc10g055800 A_96_P198339 BI209334 AT3G12500 ATHCHIB (ARABIDOPSIS THALIANA BASIC CHITINASE) 1.8 0.004 2.5 0.017
Solyc08g080640 A_96_P089294 TA36568_4081 AT4G11650 ATOSM34 (osmotin 34) 5.2 0.037 2.2 < 0.001
Solyc08g080650 A_96_P156561 pr p23 AK322366 AT4G11650 ATOSM34 (osmotin 34) 3.6 0.048 3.3 0.011
Solyc01g106620 A_96_P076884 AK324158 AT2G14580 ATPRB1 (ARABIDOPSIS THALIANA BASIC PATHOGENESIS-RELATED PROTEIN 1) 5.4 0.036 6.0 0.011
Solyc09g090970 A_96_P077909 AK326776 AT1G24020 MLP423 (MLP-LIKE PROTEIN 423) 3.4 0.046 2.2 0.033
Solyc01g097270 A_96_P148266 AW037799 AT3G04720 PR4 (PATHOGENESIS-RELATED 4) 2.6 0.020 1.7 0.028
Lipid metabolism
Solyc01g090350 A_96_P084944 BW688588 AT4G33355 lipid binding 2.3 0.002 1.8 0.004
Solyc10g085740a A_96_P204184 BI928574 AT5G03820 GDSL-motif lipase/hydrolase family protein 4.2 0.041 5.3 0.035
Solyc12g044950 A_96_P191076 cevi19 AK323674 AT3G12120 FAD2 (FATTY ACID DESATURASE 2) 3.5 0.046 3.3 0.042
Solyc02g086490 A_96_P038006 GO374663 AT3G01570 glycine-rich protein / oleosin 3.4 0.018 3.6 0.016
Solyc03g083990 A_96_P077599 AI777049 AT2G45180 protease inhibitor/seed storage/lipid transfer protein (LTP) family protein 3.2 0.010 3.7 0.029
Solyc09g065240 A_96_P144011 AW030712 AT3G63200 PLP9 (PATATIN-LIKE PROTEIN 9) 1.6 0.031 2.7 0.005
Transporter/Channel
Solyc02g085170 A_96_P127407 TA56865_4081 AT1G19450 integral membrane protein, putative / sugar transporter family protein 3.8 0.014 4.1 0.016
Solyc01g103030 A_96_P114407 AK325211 AT1G59740 proton-dependent oligopeptide transport (POT) family protein 1.9 0.023 2.0 0.034
Solyc10g084950a A_96_P231269 DB697130 AT2G37900 proton-dependent oligopeptide transport (POT) family protein 2.6 0.005 2.5 0.026
Solyc07g063930 A_96_P137262 AI778966 AT3G20660 AtOCT4 (Arabidopsis thaliana ORGANIC CATION/CARNITINE TRANSPORTER4) 3.0 0.002 1.7 0.003
Solyc03g005980 A_96_P190219 BG134199 AT4G18910 NIP1;2 (NOD26-LIKE INTRINSIC PROTEIN 1;2); arsenite transmembrane transporter/ water channel 1.8 0.006 2.4 0.016
Solyc01g010080 A_96_P054371 AW218955 AT4G32650 ATKC1 (ARABIDOPSIS THALIANA K+ RECTIFYING CHANNEL 1) 3.5 0.018 2.8 0.027
Others
Solyc12g013820a A_96_P147601 AK325708 AT1G53020 UBC26 (UBIQUITIN-CONJUGATING ENZYME 26) 2.2 < 0.001 2.9 0.017
Solyc03g034020 A_96_P202249 BI925250 AT4G36550 binding / ubiquitin-protein ligase 2.1 0.014 1.6 0.009
Solyc01g010250 A_96_P215689 BP892102 AT1G13700 glucosamine/galactosamine-6-phosphate isomerase family protein 2.1 0.006 1.7 0.002
Solyc12g042470 A_96_P109252 TA51045_4081 AT1G59950 aldo/keto reductase, putative 4.2 0.018 3.8 0.045
Solyc00g071180 A_96_P016051 AF083253 AT3G12490 ATCYSB | cysteine protease inhibitor, putative / cystatin, putative 1.7 < 0.001 1.6 0.002
Solyc09g089500 A_96_P141479 AJ319916 AT2G38870 protease inhibitor, putative 1.8 0.044 2.7 0.035
Solyc01g087820 A_96_P139602 AK324419 AT5G67090 subtilase family protein 2.0 0.005 2.2 0.027
Solyc03g112420 A_96_P203679 BI927360 AT1G64310 pentatricopeptide (PPR) repeat-containing protein 2.2 0.023 1.8 0.017
Solyc02g086270 A_96_P238007 DB715353 AT1G67025 unknown 1.8 0.010 1.7 0.007
Solyc01g109720 A_96_P043946 AK323257 AT2G18360 hydrolase, alpha/beta fold family protein 2.8 0.006 2.5 0.003
Solyc09g008740 A_96_P160421 AW625490 AT2G22880 VQ motif-containing protein 2.8 0.012 2.1 0.022
Solyc12g005700 A_96_P016566 BT012940 AT2G32280 unknown protein 2.4 0.011 5.4 0.004
Solyc10g007310 A_96_P084909 BW687670 AT2G42610 LSH10 (LIGHT SENSITIVE HYPOCOTYLS 10) 2.3 0.017 3.6 0.002
Solyc03g114130 A_96_P219824 AK329003 AT3G01430 unknown 1.8 0.002 1.9 0.003
Solyc01g081270 A_96_P152326 AK320517 AT3G09270 ATGSTU8 (GLUTATHIONE S-TRANSFERASE TAU 8) 1.6 0.011 1.6 0.041
Solyc08g059710 A_96_P039956 AK246959 AT3G11760 unknown protein 2.8 0.011 2.4 0.014
Solyc06g062800 A_96_P214714 BP889760 AT3G13920 EIF4A1 (EUKARYOTIC TRANSLATION INITIATION FACTOR 4A1) 2.2 0.015 2.8 0.023
Solyc12g097060 A_96_P065581 BI210672 AT3G23930 unknown protein 2.4 0.013 4.0 0.018
Solyc04g074300 A_96_P191679 BG626643 AT3G57490 40S ribosomal protein S2 (RPS2D) 3.3 0.018 3.3 < 0.001
Solyc08g023270 A_96_P259047 TC213163 AT4G03620 myosin heavy chain-related 1.8 0.016 2.9 0.047
Solyc10g054440a A_96_P089580 ADC1 AK319876 AT4G34710 ADC2 (ARGININE DECARBOXYLASE 2) 1.9 < 0.001 2.0 0.010
Solyc12g010960 A_96_P127072 TA56779_4081 AT5G16990 NADP-dependent oxidoreductase, putative 2.7 0.007 1.7 0.039
Solyc06g082030 A_96_P226684 CK720539 AT5G58660 oxidoreductase, 2OG-Fe(II) oxygenase family protein 4.7 0.006 2.7 0.004
Solyc03g114820 A_96_P112182 TA53188_4081 AT5G17390 universal stress protein (USP) family protein 2.1 0.015 1.8 < 0.001
Solyc04g050790 A_96_P170549 BE344440 AT5G18310 unknown protein 1.9 0.005 2.9 0.003
Solyc01g095960 A_96_P129692 AI483484 AT5G53390 unknown protein 3.9 0.022 1.8 0.022
Solyc06g075690 A_96_P235420 AK326143 AT5G59790 unknown protein 2.4 0.049 1.6 0.036
Solyc09g055950 A_96_P108797 BI211136 ATCG00270 PSBD | PSII D2 (PHOTOSYSTEM II REACTION CENTER PROTEIN D2) 4.1 0.019 3.9 0.038
Solyc09g091400a A_96_P196349 BI204004 AT3G24240 leucine-rich repeat transmembrane protein kinase, putative 4.0 0.020 3.5 0.039
Solyc02g084670 A_96_P112502 TA53264_4081 no hits found 5.7 0.018 4.8 < 0.001
Solyc01g091400a A_96_P197999 BI208492 no hits found 5.4 0.003 5.2 0.011
Solyc02g031990 A_96_P224639 CD002083 no hits found 4.0 0.013 3.0 0.038
Solyc03g070430 A_96_P106729 AK247727 no hits found 3.7 0.020 3.8 0.005
ND A_96_P181929 BF097523 no hits found 3.3 0.007 3.3 0.001
Solyc03g034360 A_96_P110867 TA52360_4081 no hits found 3.0 0.043 3.1 0.031
Solyc08g074680 A_96_P207909 BM410550 no hits found 2.8 0.005 2.9 0.012
Solyc04g055050 A_96_P062011 AW222670 no hits found 2.8 0.001 1.9 0.001
ND A_96_P261677 TC215751 no hits found 2.3 0.022 2.2 0.033
ND A_96_P246260 AK325898 no hits found 2.1 0.028 1.6 0.012
ND A_96_P104119 AK325900 no hits found 2.0 0.016 1.9 0.021
ND A_96_P204674 BI929508 no hits found 2.0 0.047 3.5 0.030
Solyc07g056280 A_96_P131347 AI487047 no hits found 1.8 0.008 2.1 0.015
ND A_96_P069949 DB717716 no hits found 1.6 0.026 3.6 0.025
Solyc03g113910 A_96_P201699 BI924325 no hits found 1.6 0.049 3.6 0.026
ND A_96_P160681 AW626075 no hits found 1.6 0.013 2.0 0.011

If more than two probes derived from the same gene were selected, only the result of the probe indicating the highest fold change value was shown in this table. Each assay result is shown in Additional file 1 and 2. Genes examined by RT-PCR are marked with lower case “a”.

Nakano et al.

Nakano et al. BMC Plant Biology 2013 13:40   doi:10.1186/1471-2229-13-40

Open Data