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Table 3 Genes discussed in the text correlated with tolerance

From: Pre-symptomatic transcriptome changes during cold storage of chilling sensitive and resistant peach cultivars to elucidate chilling injury mechanisms

Function Specific process Chillpeach ID Unigene annotation Arab AGI Arab gene symbol Hormone signaling Sugar signaling/ partioning Hormone and secondary metabolite biosynthesis regulation Cell wall and cytoesqueleton related Cell polarity
k-means 5. Correlated with tolerance at harvest and during cold storage
Aminoacid metabolism
  Cyanide detoxification PPN075E10 Beta-cyanoalanine synthase 1 AT3G61440 CYSC1      
  Methionine metabolism PPN034A06 1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase 4 AT5G43850 ARD4    Yang Cycle associated to VN tissue  
   PPN034C12 1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase 3 AT4G14710 ARD2    Yang Cycle associated to VN tissue  
   PPN072E05 Cystathionine gamma synthase AT3G01120 MTO1/CGS1      
Antioxidant system
  GLUTHATHIONE-GLUTAREDOXIN AND THIOREDOXIN REDOX HOMEOSTASIS PPN039H11 Glutathione S-transferase AT5G17220 TT19/GSTF12    PA monomer transporter   
Cytoskeleton organization and biogenesis
  Actin microfilament-actin depolimerization PPN047E05 Actin depolymerizing factor 2 AT5G59880 ADF3      
  Microtubule-Microtubule binding and stabilization PPN073D05 Microtubule-associated proteins AT5G55230 MAP65-1      
  Microtubule-microtubule organization and formation PPN075E12 Tubulin folding cofactor B AT3G10220 EMB2804/ TFC      
RNA transcription regulation
  AP2/ EREBP family PPN054F05 AP2-related transcription factor AT5G47220 ERF2 ET signaling    VN cell division  
  AUX/IAA family PPN014H03 Auxin-induced protein AUX28 AT1G04250 AXR3/IAA17 AUX and ABA nuclear signaling; negative regulator     
   PPN057F01 AUX/IAA protein AT4G29080 PAP2/IAA27 AUX nuclear signaling; negative regulator     
  LIM-family PPN009B01 Pollen-specific protein SF3, putative AT1G10200 WLIM1      
   PPN069C01 Transcription factor lim1 AT1G10200 WLIM1     Actin stabilizing protein  
  MADS-box family PP1006G03 MADS-box transcription factor AT5G60910 FUL/ AGL8    Positive regulatior of caroterne and anthocyanin biosynthesis, Negative regulation of lignin  
   PPN042H02 MADS4 AT4G18960 AG ET up-regulation   Postisitive carotene biosynthesis regulation; Negative regulation of lignin biosynthesis  
RNA translation and protein assembly
  Regulation of protein biosynthesis PPN006H04 Translationally-controlled tumor protein homolog AT3G16640 TCTP AUX cytoplasmic signaling Sugar signaling   CW biosynthesis regulation  
Secondary metabolism
  Anthocyanin metabolism PpLDOX (PpLDOX) Leucoanthocyanidin dioxygenase   PpLDOX    Flavonoid/PA biosynthesis   
   PPN055C03 Anthocyanidin reductase AT1G61720 BAN    PA biosynthess   
  Aspartate biosyntheis PPN046D06 1-aminocyclopropane-1-carboxylate synthase AT1G62960 ACS10      
  Carotenoid metabolism PPN006A10 Phytoene synthase AT5G17230 PSY      
   PPN067A01 Capsanthin/ capsorubin synthase AT3G10230 LYC      
  Cyanide detoxification PP1000E01 Cyanate hydratase AT3G23490 CYN      
   PPN066B01 Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase family protein AT5G12040       
  Flavonoid metabolism PPN050G05 Dihydroflavonol 4-reductase-like AT5G58490     Flavonoid/PA biosynthesis   
   PPN052H09 Chalcone synthase 2 AT5G13930 CHS/TT4 Negative regulation of AUX transport     
Signal transduction pathway
  Cytoplasmic TOR signaling PPN076G10 Protein lethal with sec thirteen 8-2 AT3G18140 LST8-1 AUX cytoplasmic signaling Sugar signaling   CW biosynthesis regulation  
  ET signaling/ ET signal transduction PPN011G11 GTP-binding protein AT3G46060 ARA3/RAB8A ET signaling     
Trafficking machinery and membrane dynamics
  CME;EE;internalization and intracellular trafficking of PM proteins PPN011F03 Clathrin_L-chain AT2G40060 CLC2 Regulates cellular AUX levels by controlling the abundance and distribution of PIN proteins at the PM     Cell polarity regulation
  CME;internalization and intracellular trafficking of PM proteins PPN017G03 Calcium-binding EF-hand AT3G01780 TPLATE Regulates cellular AUX levels by controlling the abundance and distribution of PIN proteins at the PM    Regulation of cellulose synthesis by controlling the abundance of active CESA complexes at the PM Cell polarity regulation
  Endosomal sorting complex PPN060A04 Putative endosomal Vps protein complex subunit AT5G22950 VPS24.1 Required for internalize PIN1, PIN2, and AUX1 to the MVB/ LE for vacuolar degradation     
  Golgy to ER/ COPI vesicles PPN044E10 ARF-like small GTPase 1 AT2G47170 ARF1A1C/BEX1 Essential for recycling of PIN transporters to the PM and for vacuolar targeting     Cell polarity
  Retromer complex;LE to vacuole PPN007G03 Sorting nexin-like protein AT5G06140 SNX1 Regulates both the recycling VSR from the TGN/ EE to the ER and the balance between vacuolar degradation and recycling of PIN proteins     
   PPN023B01 Ras-related protein Rab7 AT3G18820 RABG3F/RAB7B      
k-means 8. Associated with high tolerance to chilling injury
Aminoacid metabolism
  AUX biosynthesis PPN058D11 Anthranilate synthase beta subunit AT1G25220 ASB1 AUX biosynthesis     
RNA transcription regulation
  AUX/ IAA family PP1009D02 IAA16 protein AT1G04250 AXR3/IAA17 AUX and ABA nuclear signaling; negative regulator     
   PPN060G07 AUX/IAA protein AT1G04240 IAA3/SHY2 AUX nuclear signaling; negative regulator     
  HD-ZIP family PPN074H05 HB2 homeodomain protein AT4G35550 HB-4/WOX13 AUX regulated    SCW biosynthesis; negative regulator lignin biosynthesis  
  MYB-family PPN067A04 MYB-like DNA-binding domain protein AT4G38620 MYB4     SCW biosynthesis; negative regulator lignin biosynthesis  
Signal transduction pathway
  ET signaling/ ET receptor PPN054G06 Ethylene receptor AT3G04580 EIN4 ET signaling     
  Cooper transport PPN035H02 Copper-transporting ATPase RAN1 AT5G44790 RAN1 ET signaling; delivers cooper ion into the ET receptors; is required for both ET binding and the receptor functionality     
  1. Abbreviations: AUX:auxin; ET; ethylene; ABA: Abcisic acid; PM:plasma membrane; CW: cell wall; SCW: secondary cell wall; ER: endoplasmic reticulum; MVB/LE: microvesicular body/late endosome; TGN/EE:trans-golgy network/early endosome; VSR: vacuolar sorting receptors VN:vascular networks; PA: proanthocyanines; PIN; PIN formed auxin efflux carrier; RG: rhamnogalacturonan; XyG: xyloglucan.
  2. References supporting information in Table 3 are provided in Additional file 8: Table S7.