Table 1 Selection of genes putatively involved in the regulation of berry ripening.
AffyID | TIGR TC | Clustera | UniprotIDb | Descriptionb | E-value(b) |
|---|---|---|---|---|---|
HORMONE METABOLISM AND SIGNALING | |||||
AUXIN | |||||
Auxin synthesis | |||||
1610647_at | TC40710 | 8 | Q9FR37 | Amidase (At1g08980 AtAMI1) | 3,89E-152 |
Auxin transport | |||||
1612060_at | TC48033 | 6 | Q76DT1 | AUX1-like auxin influx carrier protein | 2,97E-143 |
1621946_at | TC50194 | 7 | Q8H0E0 | PIN1-like auxin transport protein | 1,05E-51 |
Aux/IAA | |||||
1618875_s_at | TC46557 | 1 | Q8LAL2 | IAA26 (Phytochrome-associated protein 1) | 2,95E-63 |
1617513_at | 8 | Q8LAL2 | IAA26 (Phytochrome-associated protein 1) | 6,04E-62 | |
1615985_at | TC42737 | 1 | O24542 | AUX22D | 2,40E-69 |
1614660_at | TC45938 | 4 | P13088 | AUX22 | 6,35E-60 |
1621754_at | TC41728 | 8 | Q84V38 | Aux/IAA protein | 9,19E-89 |
1615728_at | TC45614 | 8 | Q84V38 | Aux/IAA protein | 0,00E+00 |
1611390_a_at | TC39148 | 8 | Q8RW16 | Aux/IAA protein | 2,92E-98 |
1620512_at | TC46080 | 8 | Q9ZSY8 | IAA27 (Phytochrome-associated protein 2) | 9,42E-86 |
1613468_at | TC38800 | 8 | Q8LSK7 | Auxin-regulated protein (IAA1) | 3,38E-99 |
SAUR | |||||
1621201_at | TC41864 | 1 | Q6ZKQ7 | Auxin-induced protein (SAUR) | 5,99E-15 |
GH3 | |||||
1610880_s_at | CF371851 | 8 | O22190 | Indole-3-acetic acid-amido synthetase GH3.3 | 1,78E-33 |
1612001_s_at | TC43261 | 8 | Q6QUQ3 | Auxin and ethylene responsive GH3-like protein | 6,67E-111 |
1607503_s_at | TC38370 | 8 | Q52QX4 | Auxin-repressed protein-like protein ARP1 | 2,50E-48 |
Other auxin responsive proteins | |||||
1619856_at | TC45354 | 1 | O48629 | Putative auxin-repressed protein (dormancy) | 6,41E-44 |
1621185_s_at | TC45354 | 1 | O48629 | Putative auxin-repressed protein (dormancy) | 6,41E-44 |
1613204_at | TC38341 | 2 | O49235 | 2.4-D inducible glutathione S-transferase | 1,74E-98 |
1619913_at | TC46727 | 4 | Q9SV71 | auxin-responsive protein | 5,97E-116 |
ARF (transcription factor) | |||||
1612180_at | TC51304 | 8 | Q6L8T9 | Auxin response factor 5 | 1,24E-64 |
1616225_at | TC44210 | 8 | Q9C5W9 | Auxin response factor 18 | 3,69E-88 |
Auxin receptor | |||||
1612090_s_at | TC45186 | 8 | Q9ZRA4 | Auxin-binding protein ABP19a precursor | 1,75E-88 |
ETHYLENE | |||||
Ethylene synthesis | |||||
1615952_s_at | TC38453 | 1 | Q84X67 | 1-aminocyclopropane-1-carboxylic acid oxidase 1. ACO | 1,20E-167 |
1622308_at | TC40451 | 8 | Q8S933 | 1-aminocyclopropane-1-carboxylate synthase. ACC synthase | 3,92E-68 |
1612699_at | BQ798614 | 8 | Q9XIA5 | Similar to ethylene-forming-enzyme-like dioxygenase | 5,03E-29 |
Ethylene responsive transcription factors | |||||
1617012_at | TC45046 | 3 | Q8S9H4 | Tomato Ethylene response factor 1 | 5,10E-61 |
1611910_s_at | - | 8 | Q6TKQ3 | Putative ethylene response factor ERF3b | 7,26E-124 |
1609990_at | TC39828 | 8 | Q6TKQ3 | Putative ethylene response factor ERF3b | 1,45E-123 |
1620278_at | TC46710 | 3 | Q6J9Q4 | Putative AP2/EREBP transcription factor | 2,74E-64 |
1621270_at | TC47575 | 8 | Q9LYD3 | Putative AP2/EREBP transcription factor (DREB3) | 3,34E-63 |
Ethylene induced genes | |||||
1618213_at | - | 1 | Q9SWV2 | ER6 protein (Fragment) | 3,89E-18 |
1619086_at | TC39832 | 8 | Q93W91 | Putative ER6 protein | 2,55E-51 |
1609780_at | TC47621 | 8 | Q94E74 | Putative ER6 protein. Ethylene-responsive protein | 5,74E-33 |
1613123_at | CF215236 | 1 | Q8S3D1 | bHLH transcription factor (tomato ER33 homolog) | 1,04E-61 |
1613177_at | TC47351 | 8 | Q9LSP8 | Ethylene-induced calmodulin-binding transcription activator | 3,76E-94 |
1622850_at | TC49495 | 3 | O48631 | Ethylene-forming-enzyme-like dioxygenase (tomato E8 homolog) | 7,27E-78 |
Pathogenesis related genes putatively induced by ethylene | |||||
1611058_at | TC47119 | 4 | Q7XAJ6 | Putative pathogenesis related protein 1 precursor | 1,55E-73 |
1618835_s_at | TC38693 | 4 | O81228 | PR-4 type protein | 1,62E-80 |
1622360_at | TC40938 | 4 | Q42966 | NtNitrilase 4B (EC 3.5.5.1) | 1,05E-135 |
ABSCISIC ACID | |||||
Abscisic acid synthesis | |||||
1607029_at | TC42536 | 4 | Q8LP14 | Nine-cis-epoxycarotenoid dioxygenase4 | 1,32E-51 |
Abscisic acid responsive proteins | |||||
1618211_at | TC47430 | 4 | P93615 | ABA induced plasma membrane protein PM 19 | 1,37E-60 |
1614372_at | TC47836 | 4 | Q6H5X2 | ABA-responsive protein-like | 3,03E-61 |
1614788_at | TC45479 | 4 | Q4VT48 | Dehydrin | 2,92E-69 |
1621592_s_at | TC45479 | 4 | Q4VT48 | Dehydrin | 2,92E-69 |
1606669_s_at | - | 4 | Q5PXH0 | Aquaporin (PIP2_1) | 9,87E-74 |
1615808_s_at | TC38121 | 4 | Q5PXH0 | Aquaporin (PIP2_1) | 2,63E-162 |
1610982_at | TC38138 | 8 | O24049 | Major intrinsic protein C, aquaporin | 6,31E-141 |
1614916_at | TC38138 | 8 | O24049 | Major intrinsic protein C, aquaporin | 6,31E-141 |
1612244_s_at | TC38281 | 8 | Q9M7B0 | Putative aquaporin PIP2-2 | 2,40E-158 |
BRASSINOSTEROIDS | |||||
Brassinosteroid synthesis | |||||
1608099_at | TC40368 | 8 | Q43147 | Cyt. P450 85A1, C6-oxidase, Dwarf protein | 2,89E-74 |
Brassinosteroid receptor | |||||
1612516_at | TC47080 | 1 | Q76FZ8 | Brassinosteroid receptor | 0,00E+00 |
GIBBERELLINS | |||||
1610607_at | TC40495 | 5 | Q6NMQ7 | Gibberellin-responsive protein (At1g74670) | 1,04E-28 |
1609893_at | TC38517 | 8 | O24040 | LtCOR11 (Gibberellin regulated protein) | 1,62E-36 |
1618503_at | TC47765 | 8 | Q75V70 | Gibberellin 2-oxidase 1 | 1,50E-69 |
CYTOKININS | |||||
1612955_at | TC47637 | 4 | Q71BZ3 | Type-A response regulator | 3,73E-11 |
1619945_at | CB345883 | 8 | Q39636 | CR9 protein. cytokinin-repressed gene | 3,12E-30 |
1620306_at | TC47826 | 8 | Q67YU0 | Cytokinin oxidase 5 (cytokinin degradation) | 6,29E-113 |
LIGHT STIMULUS | |||||
Circadian rhythm | |||||
1608397_at | TC43962 | 8 | Q6LA43 | Two-component response regulator-like APRR2 (TOC2 protein) | 2,77E-34 |
1617059_at | TC42407 | 4 | Q9CAV6 | WNK1 kinase | 8,07E-26 |
1609874_at | TC43754 | 8 | Q6R3R2 | CONSTANS-like protein CO1 | 1,80E-76 |
1614417_at | TC47511 | 3 | O81834 | Transcription factor Constans-like family (At4g27310) | 1,32E-32 |
1613978_at | TC49120 | 3 | Q5GA60 | Putative EARLY flowering 4 protein | 1,22E-30 |
Flowering control | |||||
1614189_at | TC47473 | 8 | Q76CC3 | Flowering locus T | 1,68E-66 |
Transcription factors | |||||
1620877_at | TC40824 | 8 | Q948G4 | Putative GATA-1 zinc finger protein | 1,14E-31 |
Hormone and light signals | |||||
1612955_at | TC47637 | 4 | Q71BZ3 | Type-A response regulator | 3,73E-11 |
1616694_at | TC46350 | 7 | Q94KS0 | Histidine-containing phosphotransfer protein | 1,96E-57 |
1614802_at | TC41815 | 7 | Q94KS0 | Histidine-containing phosphotransfer protein | 6,27E-59 |
1617513_at | 8 | Q8LAL2 | IAA26 (Phytochrome-associated protein 1) | 6,04E-62 | |
1618875_s_at | TC46557 | 1 | Q8LAL2 | IAA26 (Phytochrome-associated protein 1) | 2,95E-63 |
1620512_at | TC46080 | 8 | Q9ZSY8 | IAA27 (Phytochrome-associated protein 2) | 9,42E-86 |
Other light regulated genes | |||||
1614237_a_at | TC38178 | 1 | Q7XAB8 | Light-regulated chloroplast-localized protein | 5,16E-23 |
1618107_at | TC46244 | 1 | Q93WJ7 | Leaf Lethal Spot 1-like protein | 0,00E+00 |
1614720_at | TC46244 | 1 | Q93WJ7 | Leaf Lethal Spot 1-like protein | 0,00E+00 |
1616605_at | TC45785 | 1 | Q8W5A3 | Lethal leaf spot 1-like protein | 0,00E+00 |
1617173_s_at | 4 | Q6T6I9 | ELIP Early light-induced protein | 3,88E-54 | |
1610360_at | TC38699 | 8 | Q6Q9W1 | Ultraviolet-B-repressible protein | 2,47E-36 |
1620292_at | TC38866 | 8 | Q6Q9W1 | Ultraviolet-B-repressible protein | 2,00E-33 |
TRANSCRIPTION FACTORS | |||||
MADS-BOX TF | |||||
1621827_at | TC39767 | 1 | Q6UGQ6 | MADS-box protein 15 | 1,95E-47 |
1621836_at | TC45777 | 7 | Q8LLQ9 | MADS-box protein 5 | 6,25E-119 |
1607973_at | TC38620 | 8 | Q9ZTV9 | MADS1-like | 4,87E-107 |
1613748_at | TC40277 | 8 | Q8LLR2 | Vitis. MADS-box protein 2, Ap1-like, MADS-RIN-like | 1,73E-77 |
MYB TF | |||||
1611920_at | TC40303 | 1 | Q9M9A3 | F27J15.20 (Hypothetical protein) (MYB transcription factor) | 3,83E-84 |
1618260_s_at | TC42111 | 3 | Q8L5N7 | Myb-related transcription factor VlMYBB1-2, similar to | 4,47E-43 |
1620959_s_at | TC48485 | 4 | Q6L973 | Myb-related transcription factor VvMYBA1 | 2,04E-119 |
1609612_at | TC47332 | 7 | Q688D6 | Putative myb transcription factor (MYB16 protein) | 3,17E-21 |
1612686_at | TC48806 | 8 | Q5NDD2 | Putative MYB transcription factor | 6,03E-84 |
1613486_at | TC45686 | 8 | O04544 | F20P5.26 protein (At1g70000) (MYB transcription factor) | 1,60E-74 |
1614932_at | TC48806 | 8 | Q5NDD2 | Putative MYB transcription factor | 6,03E-84 |
1618514_at | TC51437 | 8 | O22059 | CPC (Putative MYB family transcription factor) | 4,70E-11 |
1619201_at | TC49224 | 8 | Q8GV05 | TRIPTYCHON (MYB transcription factor) | 2,93E-29 |
NAC TF | |||||
1621448_at | TC47141 | 2 | Q52QR1 | NAC domain protein NAC5 | 1,39E-27 |
1609172_at | TC39120 | 3 | Q52QR2 | NAC domain protein NAC4 | 1,10E-126 |
1606678_at | TC42489 | 4 | Q8LKN7 | Nam-like protein 17 (Fragment) | 6,53E-19 |
1607120_at | TC46243 | 4 | Q84K00 | NAC-domain containing protein 78 (ANAC078) | 1,43E-34 |
1621255_at | TC41700 | 4 | Q8LRL4 | Nam-like protein 11 | 1,85E-46 |
WRKY TF | |||||
1609130_at | TC46341 | 3 | Q9FGZ4 | WRKY DNA-binding protein 48 | 1,62E-56 |
1622333_at | TC40428 | 3 | O22900 | WRKY DNA-binding protein 23 | 5,68E-46 |
1611285_s_at | CA809190 | 7 | Q6IEL3 | WRKY transcription factor 68 | 1,84E-39 |
Homeotic TF | |||||
1616863_at | TC41982 | 1 | Q8LLD9 | BEL1-related homeotic protein 29 (Fragment) | 1,20E-78 |
1618774_at | TC40997 | 1 | Q4VPE9 | Lateral organ boundaries-like 1 (Fragment). | 6,51E-52 |
1611583_at | TC40246 | 3 | Q9FJ90 | Similarity to AP2 domain transcription factor | 2,85E-55 |
1609295_at | TC47034 | 3 | P46897 | Homeobox-leucine zipper protein ATHB-7 | 2,41E-53 |
1620170_at | TC42225 | 7 | Q9XHC9 | APETALA2 protein homolog HAP2 | 4,04E-46 |
1607122_at | TC51295 | 8 | Q546G6 | Homeodomain-leucine zipper protein HAT22 | 4,82E-15 |
1607284_at | TC40589 | 8 | Q7Y0Z9 | Bell-like homeodomain protein 3 (Fragment) | 3,12E-114 |
1617931_at | TC40185 | 8 | Q9M276 | Homeobox-leucine zipper protein ATHB-12 | 4,41E-34 |
1615625_at | TC39581 | 8 | O04136 | Homeobox protein knotted-1 like 3 (KNAP3) | 6,59E-86 |
1613036_at | TC39310 | 4 | Q56R05 | Putative pollen specific LIM domain-containing protein | 2,68E-90 |
1606561_at | TC41613 | 7 | O81384 | Putative basic helix-loop-helix DNA binding protein TCP2 | 1,25E-20 |
1611070_at | TC49539 | 7 | Q8L8A5 | GRF1-interacting factor 1 (Hypothetical protein At5g28640) | 7,97E-43 |
1606591_at | TC41789 | 8 | Q8RU28 | Putative SHORT-ROOT (SHR) protein (Fragment) | 1,28E-38 |
1610187_a_at | TC47632 | 8 | Q9FL03 | SCARECROW gene regulator | 1,11E-110 |
1619334_at | TC47632 | 8 | Q9FL03 | SCARECROW gene regulator | 1,11E-110 |
1612362_at | TC41970 | 8 | Q6SS00 | YABBY-like transcription factor GRAMINIFOLIA | 3,06E-69 |
1613445_at | TC40338 | 8 | Q6XX20 | Mutant cincinnata | 3,64E-16 |
1614851_s_at | TC40029 | 8 | Q9SIV3 | Expressed protein (GPRI1) (Golden2-like protein 1) | 2,10E-39 |
1617877_at | TC41303 | 8 | Q8SBC9 | Transcription factor LIM | 1,71E-92 |