Table 3.
135 genes with predicted root-enrichment expression profiles by Audic-Claverie statistic
| Gene ID | Gene Description | Gene Function (via VitisNet) | Root EST count (frequency) | Non-root EST count (frequency) | AC statistic |
|---|---|---|---|---|---|
| GSVIVP00030165001 | Lectin | 7.0 Stress-related | 68 (40.1) | 32 (1.2) | < 1E-06 |
| GSVIVP00027836001 | Curculin (mannose-binding) lectin | 6.0 Binding | 59 (34.8) | 5 (0.2) | < 1E-06 |
| GSVIVP00024394001 | Aquaporin TIP1;4 | 5.3 Transport System | 57 (33.6) | 2 (0.1) | < 1E-06 |
| GSVIVP00029248001 | Aquaporin TMP-C | 5.3 Transport System | 57 (33.6) | 15 (0.6) | < 1E-06 |
| GSVIVP00015118001 | Aspartic proteinase nepenthesin-1 | 2.3 Folding, Sorting & Degradation | 47 (27.7) | 38 (1.4) | < 1E-06 |
| GSVIVP00036222001 | Endochitinase 1, basic | 1.0 Primary Metabolism | 33 (19.5) | 1 (0.1) | < 1E-06 |
| GSVIVP00032953001 | Glutamine synthetase (cytosolic) 2 | 1.2 Energy Metabolism | 32 (18.9) | 26 (1) | < 1E-06 |
| GSVIVP00018661001 | Resveratrol O-methyltransferase | 1.9 Secondary Metabolism | 30 (17.7) | 0 (0) | < 1E-06 |
| GSVIVP00013365001 | Mannitol dehydrogenase | 1.0 Primary Metabolism | 26 (15.3) | 26 (1) | < 1E-06 |
| GSVIVP00006171001 | Phosphate-induced protein 1 | Unclear | 26 (15.3) | 37 (1.4) | < 1E-06 |
| GSVIVP00015200001 | Phosphate-induced protein 1 | Unclear | 24 (14.2) | 5 (0.2) | < 1E-06 |
| GSVIVP00027842001 | (E,E)-alpha-Farnesene synthase | 1.9 Secondary Metabolism | 23 (13.6) | 0 (0) | < 1E-06 |
| GSVIVP00004164001 | IAA beta-glucosyltransferase | 3.2 Hormone Signaling | 20 (11.8) | 1 (0.1) | < 1E-06 |
| GSVIVP00037746001 | C2 domain-containing | 3.1 Signal Transduction | 20 (11.8) | 7 (0.3) | < 1E-06 |
| GSVIVP00036564001 | Carboxylesterase | 1.0 Primary Metabolism | 19 (11.2) | 0 (0) | < 1E-06 |
| GSVIVP00011776001 | Polyphenol oxidase II, chloroplast | 5.3 Transport System | 19 (11.2) | 17 (0.7) | < 1E-06 |
| GSVIVP00020241001 | Unknown | Unknown | 19 (11.2) | 30 (1.1) | < 1E-06 |
| GSVIVP00013172001 | Octicosapeptide/Phox/Bem1p (PB1) | Unknown | 18 (10.6) | 12 (0.5) | < 1E-06 |
| GSVIVP00030638001 | Xyloglucan endotransglycosylase | 4.3 Cell Wall | 18 (10.6) | 28 (1) | < 1E-06 |
| GSVIVP00036411001 | RD22 | 7.0 Stress-related | 17 (10) | 5 (0.2) | < 1E-06 |
| GSVIVP00021415001 | Glutathione S-transferase 8 | 1.0 Primary Metabolism | 16 (9.4) | 14 (0.5) | < 1E-06 |
| GSVIVP00009226001 | Stilbene synthase | 1.9 Secondary Metabolism | 15 (8.8) | 7 (0.3) | < 1E-06 |
| GSVIVP00017772001 | ATP synthase beta chain 2 | 5.3 Transport System | 15 (8.8) | 18 (0.7) | < 1E-06 |
| GSVIVP00025990001 | Caffeic acid O-methyltransferase | 1.9 Secondary Metabolism | 14 (8.3) | 22 (0.8) | < 1E-06 |
| GSVIVP00011267001 | Flavonol sulfotransferase | 1.9 Secondary Metabolism | 13 (7.7) | 0 (0) | < 1E-06 |
| GSVIVP00002185001 | DNA-binding protein | 2.4 Replication & Repair | 13 (7.7) | 1 (0.1) | < 1E-06 |
| GSVIVP00036600001 | Nitrite reductase | 1.2 Energy Metabolism | 13 (7.7) | 5 (0.2) | < 1E-06 |
| GSVIVP00034550001 | Unknown protein | Unknown | 13 (7.7) | 7 (0.3) | < 1E-06 |
| GSVIVP00018662001 | Orcinol O-methyltransferase 2 | 1.9 Secondary Metabolism | 12 (7.1) | 0 (0) | < 1E-06 |
| GSVIVP00022812001 | Germin | 8.0 Storage | 12 (7.1) | 0 (0) | < 1E-06 |
| GSVIVP00019908001 | 7S globulin precursor, basic | 2.3 Folding, Sorting & Degradation | 12 (7.1) | 4 (0.2) | < 1E-06 |
| GSVIVP00021582001 | E8 protein | 3.2 Hormone Signaling | 12 (7.1) | 4 (0.2) | < 1E-06 |
| GSVIVP00013571001 | Strictosidine synthase | 1.9 Secondary Metabolism | 12 (7.1) | 5 (0.2) | < 1E-06 |
| GSVIVP00020905001 | Aldose 1-epimerase | 1.0 Primary Metabolism | 12 (7.1) | 10 (0.4) | < 1E-06 |
| GSVIVP00002589001 | Unknown protein | Unknown | 12 (7.1) | 11 (0.4) | < 1E-06 |
| GSVIVP00004581001 | Carboxyesterase 20 | 1.0 Primary Metabolism | 11 (6.5) | 1 (0.1) | < 1E-06 |
| GSVIVP00027736001 | 4-Amino-4-deoxychorismate lyase | 1.0 Primary Metabolism | 11 (6.5) | 1 (0.1) | < 1E-06 |
| GSVIVP00036840001 | Ferulate-5-hydroxylase | 1.9 Secondary Metabolism | 11 (6.5) | 3 (0.1) | < 1E-06 |
| GSVIVP00001860001 | UDP-glucose:anthocyanidin 5,3-O-glucosyltransferase | 1.9 Secondary Metabolism | 11 (6.5) | 4 (0.2) | < 1E-06 |
| GSVIVP00032824001 | Aspartic proteinase nepenthesin-2 | 2.3 Folding, Sorting & Degradation | 11 (6.5) | 4 (0.2) | < 1E-06 |
| GSVIVP00023389001 | WRKY DNA-binding protein 11 | 2.11 Transcription Factors | 11 (6.5) | 6 (0.3) | < 1E-06 |
| GSVIVP00031491001 | UDP-glucose glucosyltransferase | 1.0 Primary Metabolism | 10 (5.9) | 1 (0.1) | < 1E-06 |
| GSVIVP00037558001 | Flavonol O-glucosyltransferase | 1.9 Secondary Metabolism | 10 (5.9) | 1 (0.1) | < 1E-06 |
| GSVIVP00036143001 | Monooxygenase | Unclear | 10 (5.9) | 1 (0.1) | < 1E-06 |
| GSVIVP00017017001 | Trans-cinnamate 4-monooxygenase | 1.9 Secondary Metabolism | 10 (5.9) | 2 (0.1) | < 1E-06 |
| GSVIVP00033062001 | Senescence-associated gene (SAG101) | 4.2 Cell Growth & Death | 10 (5.9) | 3 (0.1) | < 1E-06 |
| GSVIVP00018298001 | Phosphate translocator protein2, plastid | 5.3 Transport System | 10 (5.9) | 7 (0.3) | < 1E-06 |
| GSVIVP00005745001 | Octicosapeptide/Phox/Bem1p (PB1) domain | Unknown | 10 (5.9) | 13 (0.5) | < 1E-06 |
| GSVIVP00005849001 | Anthocyanidin 3-O-glucosyltransferase | 1.9 Secondary Metabolism | 10 (5.9) | 16 (0.6) | < 1E-06 |
| GSVIVP00036485001 | CYP82C4 | 1.0 Primary Metabolism | 9 (5.3) | 1 (0.1) | < 1E-06 |
| GSVIVP00002954001 | Cinnamyl-alcohol dehydrogenase | 1.9 Secondary Metabolism | 9 (5.3) | 1 (0.1) | < 1E-06 |
| GSVIVP00031199001 | Cytokinin-O-glucosyltransferase 2 | 1.9 Secondary Metabolism | 9 (5.3) | 3 (0.1) | < 1E-06 |
| GSVIVP00015320001 | Nitrate reductase 2 (NR2) | 3.1 Signal Transduction | 9 (5.3) | 3 (0.1) | < 1E-06 |
| GSVIVP00025346001 | beta-1,3-Glucanase | 1.0 Primary Metabolism | 9 (5.3) | 4 (0.2) | < 1E-06 |
| GSVIVP00013928001 | Phenylalanine ammonia-lyase | 1.9 Secondary Metabolism | 9 (5.3) | 8 (0.3) | < 1E-06 |
| GSVIVP00005194001 | Stilbene synthase | 1.9 Secondary Metabolism | 9 (5.3) | 8 (0.3) | < 1E-06 |
| GSVIVP00001453001 | Salt tolerance zinc finger | 2.11 Transcription Factors | 9 (5.3) | 11 (0.4) | < 1E-06 |
| GSVIVP00037055001 | Metal-nicotianamine transporter YSL7 | 5.3 Transport System | 9 (5.3) | 11 (0.4) | < 1E-06 |
| GSVIVP00020070001 | Sulfate adenylyltransferase 3 | 1.2 Energy Metabolism | 9 (5.3) | 13 (0.5) | < 1E-06 |
| GSVIVP00000463001 | Cinnamyl alcohol dehydrogenase | 1.9 Secondary Metabolism | 9 (5.3) | 14 (0.5) | < 1E-06 |
| GSVIVP00024717001 | Peroxidase | 1.0 Primary Metabolism | 8 (4.7) | 0 (0) | < 1E-06 |
| GSVIVP00031214001 | Cytokinin-O-glucosyltransferase 2 | 1.9 Secondary Metabolism | 8 (4.7) | 0 (0) | < 1E-06 |
| GSVIVP00034489001 | 2-Oxoglutarate-dependent dioxygenase | Unclear | 8 (4.7) | 0 (0) | < 1E-06 |
| GSVIVP00036965001 | Glutathione S-transferase 10 GSTU10 | 1.0 Primary Metabolism | 8 (4.7) | 1 (0.1) | < 1E-06 |
| GSVIVP00018322001 | Glucosyltransferase-2 | 1.0 Primary Metabolism | 8 (4.7) | 2 (0.1) | < 1E-06 |
| GSVIVP00019233001 | Isoflavone reductase | 1.9 Secondary Metabolism | 8 (4.7) | 2 (0.1) | < 1E-06 |
| GSVIVP00029527001 | Unknown protein | Unknown | 8 (4.7) | 2 (0.1) | < 1E-06 |
| GSVIVP00003722001 | Zinc finger (C3HC4-type RING finger) | 2.11 Transcription Factors | 8 (4.7) | 3 (0.1) | < 1E-06 |
| GSVIVP00010417001 | Zinc finger (C3HC4-type RING finger) | 6.0 Binding | 8 (4.7) | 5 (0.2) | < 1E-06 |
| GSVIVP00034781001 | Kelch repeat-containing F-box | Unknown | 8 (4.7) | 5 (0.2) | < 1E-06 |
| GSVIVP00020913001 | Aldose 1-epimerase | 1.0 Primary Metabolism | 8 (4.7) | 6 (0.3) | < 1E-06 |
| GSVIVP00022605001 | Nicotianamine synthase | 1.0 Primary Metabolism | 8 (4.7) | 7 (0.3) | < 1E-06 |
| GSVIVP00023306001 | p-Coumaroyl shikimate 3'-hydroxylase 1 | 1.9 Secondary Metabolism | 8 (4.7) | 7 (0.3) | < 1E-06 |
| GSVIVP00002706001 | Unknown protein | Unknown | 8 (4.7) | 7 (0.3) | < 1E-06 |
| GSVIVP00031130001 | DNA-damage-repair/toleration (DRT102) | 2.4 Replication & Repair | 8 (4.7) | 8 (0.3) | < 1E-06 |
| GSVIVP00024773001 | Acyl-CoA synthetase (Acyl-activating 18) | 5.3 Transport System | 8 (4.7) | 9 (0.4) | < 1E-06 |
| GSVIVP00000809001 | Phosphoesterase | Unclear | 8 (4.7) | 11 (0.4) | < 1E-06 |
| GSVIVP00010326001 | Esterase/lipase/thioesterase family | Unclear | 8 (4.7) | 12 (0.5) | 2E-06 |
| GSVIVP00015215001 | UDP-glycosyltransferase 85A1 | 1.0 Primary Metabolism | 7 (4.1) | 0 (0) | < 1E-06 |
| GSVIVP00026343001 | NADPH HC toxin reductase | 1.0 Primary Metabolism | 7 (4.1) | 0 (0) | < 1E-06 |
| GSVIVP00036190001 | Catechol O-methyltransferase | 1.0 Primary Metabolism | 7 (4.1) | 0 (0) | < 1E-06 |
| GSVIVP00010293001 | F-box domain containing | 2.3 Folding, Sorting & Degradation | 7 (4.1) | 0 (0) | < 1E-06 |
| GSVIVP00025242001 | Aspartyl protease | 2.3 Folding, Sorting & Degradation | 7 (4.1) | 0 (0) | < 1E-06 |
| GSVIVP00026388001 | Pectinesterase family | 4.3 Cell Wall | 7 (4.1) | 0 (0) | < 1E-06 |
| GSVIVP00015805001 | AT-hook DNA-binding protein | Unknown | 7 (4.1) | 0 (0) | < 1E-06 |
| GSVIVP00008086001 | Myb family TF-like b | 2.11 Transcription Factors | 7 (4.1) | 1 (0.1) | < 1E-06 |
| GSVIVP00017803001 | Laccase | 5.3 Transport System | 7 (4.1) | 1 (0.1) | < 1E-06 |
| GSVIVP00036529001 | Open stomata 1 (OST1) | 3.1 Signal Transduction | 7 (4.1) | 2 (0.1) | < 1E-06 |
| GSVIVP00024338001 | Fasciclin arabinogalactan-protein (FLA4) | 4.3 Cell Wall | 7 (4.1) | 2 (0.1) | < 1E-06 |
| GSVIVP00024285001 | Zinc transporter (ZIP2) | 5.3 Transport System | 7 (4.1) | 2 (0.1) | < 1E-06 |
| GSVIVP00017555001 | UDP-glycosyltransferase 89B2 | 1.0 Primary Metabolism | 7 (4.1) | 3 (0.1) | < 1E-06 |
| GSVIVP00018198001 | Patatin | 8.0 Storage | 7 (4.1) | 3 (0.1) | < 1E-06 |
| GSVIVP00029089001 | Kelch repeat-containing | Unknown | 7 (4.1) | 3 (0.1) | < 1E-06 |
| GSVIVP00012218001 | Myb divaricata | 2.11 Transcription Factors | 7 (4.1) | 4 (0.2) | < 1E-06 |
| GSVIVP00031610001 | Unknown protein | Unknown | 7 (4.1) | 4 (0.2) | < 1E-06 |
| GSVIVP00023356001 | alpha-L-Arabinofuranosidase | 1.0 Primary Metabolism | 7 (4.1) | 5 (0.2) | < 1E-06 |
| GSVIVP00028303001 | beta-1,3-Glucanase precursor | 1.0 Primary Metabolism | 7 (4.1) | 5 (0.2) | < 1E-06 |
| GSVIVP00030576001 | Receptor-like protein kinase | 3.1 Signal Transduction | 7 (4.1) | 5 (0.2) | < 1E-06 |
| GSVIVP00019610001 | IAA-amido synthetase GH3.2 | 3.2 Hormone Signaling | 7 (4.1) | 5 (0.2) | < 1E-06 |
| GSVIVP00024987001 | Allergen Alt a 7 | 7.0 Stress-related | 7 (4.1) | 5 (0.2) | < 1E-06 |
| GSVIVP00002843001 | Kelch repeat-containing F-box | Unknown | 7 (4.1) | 5 (0.2) | < 1E-06 |
| GSVIVP00001138001 | Flavonoid 3-monooxygenase | 1.9 Secondary Metabolism | 7 (4.1) | 6 (0.3) | < 1E-06 |
| GSVIVP00021523001 | Aspartyl protease | 2.3 Folding, Sorting & Degradation | 7 (4.1) | 6 (0.3) | < 1E-06 |
| GSVIVP00023266001 | Serine carboxypeptidase K10B2.2 | 2.3 Folding, Sorting & Degradation | 7 (4.1) | 8 (0.3) | < 1E-06 |
| GSVIVP00003796001 | Glycosyl hydrolase family 1 | 1.0 Primary Metabolism | 6 (3.5) | 0 (0) | < 1E-06 |
| GSVIVP00005841001 | UDP-glucose glucosyltransferase | 1.0 Primary Metabolism | 6 (3.5) | 0 (0) | < 1E-06 |
| GSVIVP00006924001 | Peroxidase | 1.0 Primary Metabolism | 6 (3.5) | 0 (0) | < 1E-06 |
| GSVIVP00023878001 | CYP94A1 | 1.0 Primary Metabolism | 6 (3.5) | 0 (0) | < 1E-06 |
| GSVIVP00023969001 | Class III peroxidase 40 | 1.0 Primary Metabolism | 6 (3.5) | 0 (0) | < 1E-06 |
| GSVIVP00037866001 | Peroxidase | 1.0 Primary Metabolism | 6 (3.5) | 0 (0) | < 1E-06 |
| GSVIVP00006201001 | AP2/ERF114 | 2.11 Transcription Factors | 6 (3.5) | 0 (0) | < 1E-06 |
| GSVIVP00033054001 | Protein phosphatase 2C | 3.1 Signal Transduction | 6 (3.5) | 0 (0) | < 1E-06 |
| GSVIVP00000122001 | Chromosome maintenance MAG2 | 2.4 Replication & Repair | 6 (3.5) | 1 (0.1) | < 1E-06 |
| GSVIVP00018988001 | Transposon protein | 9.0 Transposons | 6 (3.5) | 1 (0.1) | < 1E-06 |
| GSVIVP00014792001 | Carboxylesterase | 1.0 Primary Metabolism | 6 (3.5) | 3 (0.1) | < 1E-06 |
| GSVIVP00033506001 | beta-1,3-Glucanase | 1.0 Primary Metabolism | 6 (3.5) | 3 (0.1) | < 1E-06 |
| GSVIVP00014758001 | Calmodulin-binding protein AR781 | 3.1 Signal Transduction | 6 (3.5) | 3 (0.1) | < 1E-06 |
| GSVIVP00019639001 | Peroxidase 73 | 1.0 Primary Metabolism | 6 (3.5) | 4 (0.2) | < 1E-06 |
| GSVIVP00009234001 | Stilbene synthase | 1.9 Secondary Metabolism | 6 (3.5) | 4 (0.2) | < 1E-06 |
| GSVIVP00020035001 | MLK/Raf-related protein kinase 1 | 3.1 Signal Transduction | 6 (3.5) | 4 (0.2) | < 1E-06 |
| GSVIVP00025363001 | Myb family TF-like a | 2.11 Transcription Factors | 5 (2.9) | 0 (0) | < 1E-06 |
| GSVIVP00026190001 | NGA1 TF (NGATHA1) | 2.11 Transcription Factors | 5 (2.9) | 0 (0) | < 1E-06 |
| GSVIVP00037318001 | Myb divaricata | 2.11 Transcription Factors | 5 (2.9) | 0 (0) | < 1E-06 |
| GSVIVP00007503001 | ACC oxidase homolog 1 | 3.2 Hormone Signaling | 5 (2.9) | 0 (0) | < 1E-06 |
| GSVIVP00006975001 | Kinesin family member 2/24 | 4.1 Cell Motility | 5 (2.9) | 0 (0) | < 1E-06 |
| GSVIVP00021432001 | Laccase | 5.3 Transport System | 5 (2.9) | 0 (0) | < 1E-06 |
| GSVIVP00012703001 | Aquaporin TIP2;2 | 5.3 Transport System | 5 (2.9) | 0 (0) | < 1E-06 |
| GSVIVP00008708001 | Monooxygenase (MO3) | 1.0 Primary Metabolism | 5 (2.9) | 0 (0) | < 1E-06 |
| GSVIVP00020827001 | AAA-type ATPase | Unclear | 5 (2.9) | 0 (0) | < 1E-06 |
| GSVIVP00017947001 | Unknown protein | Unknown | 5 (2.9) | 0 (0) | < 1E-06 |
| GSVIVP00021666001 | Unknown protein | Unknown | 5 (2.9) | 0 (0) | < 1E-06 |
| GSVIVP00001266001 | Unknown | Unknown | 5 (2.9) | 0 (0) | < 1E-06 |
| GSVIVP00017730001 | CYP77A5P | 1.0 Primary Metabolism | 5 (2.9) | 1 (0.1) | < 1E-06 |
| GSVIVP00006293001 | Jasmonate O-methyltransferase | 3.2 Hormone Signaling | 5 (2.9) | 1 (0.1) | < 1E-06 |
| GSVIVP00020849001 | ABC transporter B member 11 | 5.3 Transport System | 5 (2.9) | 1 (0.1) | < 1E-06 |
Root-enriched genes were identified by EST frequency comparison of Vitis vinifera roots compared with all other tissues, using the Audic-Claverie (AC) statistic [60]. Gene identifier (ID) from GSVIV, gene description, gene function (from VitisNet annotation), frequency in root and non-root cDNA libraries, and AC confidence statistic are presented. Genes tested for root-enriched expression by real-time qRT-PCR are indicated in bold (Figure 7).