Table 2 Genes used in “NeoVigen96” chip that were analyzed in the Biomark HD system, classified according to functions and pathways
Gene Functions | Gene Names | N° accession | Primer Sens - 5′ > 3′ (F) | Primer AntiSens - 5′ > 3′ (R) | PCR efficacies | |
|---|---|---|---|---|---|---|
Reference genes | Elongation factor1 chain γ | EF1γ a | AF176496 | GAAGGTTGACCTCTCGGATG | AGAGCCTCTCCCTCAAAAGG | 1.09 |
Serine/threonine-protein phosphatase 2A | PP2A | XM_002276144 | TCCGGCGGCTCTCGACGATT | TTCGCGTGCTCAACACCTCCG | 0.97 | |
SAND family protein (endocytosis) | SAND | XM_002285134 | GCCCCACAGCCAAACCCCTC | ACGATCCGTTTGCGACCCCG | 1.05 | |
Pentatricopeptide repeat-containing protein | Unknown | XM_002274855 | TGGTGAACTTGAGGCTGCAAGGG | ACCATTTGGGGAGTAGCCCTTCCTC | 1.01 | |
Ubiquitin Conjugating Enzyme 9 | UBC9 | XM_002274238 | TCCTCCTGACAGTCCATATGCTGGT | GGGCTGGGCTCCACTGCTCC | 1.00 | |
TIP41-like protein | TIP41 | XM_002270674 | CAGCGGGCAGCGATCGAAGA | CATTTCCGCTCCGGCAGCCTT | 1.05 | |
Catalytic thioredoxin-like protein 4A | THIORYLS8 | XM_002283586 | TCACTCTGGATGGGCCGTCG | TCCCAATCGTGGCCGAACCG | 1.14 | |
Tubulin alpha | TuA | XM_002285685.1 | GTCGGCGCTGAAGGTGTGGA | GAGGTGGCGGGCAAACCCTC | 0.97 | |
Tubulin beta | βTub | XM_002275270.1 | TGAACCACTTGATCTCTGCGACTA | CAGCTTGCGGAGGTCTGAGT | 0.99 | |
TuB | XM_02275270.1 | CGCCACCCGAGTCTCACTGC | CACACCGTGCTCGTCGCAGA | 1.04 | ||
Glyceraldehyde 3-phosphate dehydrogenase | GADPH | XM_002263109.1 | GAAATCAACGGCCCAGCGCG | CCGGTGGATACTGGGGCGGA | 0.83 | |
PR protein | PR1 Unknown function | PR1 a | AJ536326 | CCCAGAACTCTCCACAGGAC | GCAGCTACAGTGTCGTTCCA | 1.00 |
PR1 bis | XM_002273752.1 | GGGGTTGTGTAGGAGTCCATTAGCA | TGGGCACAGCAGATGTGAGCT | 1.13 | ||
Beta-1,3-glucanase | GLU a | AF239617 | GGGGAGATGTGAGGGGTTAT | TGCAGTGAACAAAGCGTAGG | 1.18 | |
PR2 | XM_002277475 | CAACTTGCCACCGCCAGGGC | AGGGCTTGGAGAGCAGCTTGG | 0.96 | ||
Endochitinase (Chitinase type I, II, IV,, VI and VII) | PR3 | U97522.1 | ACTACGGCGCTGCTGGAAACA | TGGCACCGAAACCTTGGCTTAG | 1.16 | |
CHIT4a a | U97521.1 | TATCCATGTGTCTCCGGTCA | TGAATCCAATGCTGTTTCCA | 1.14 | ||
Chitin binding Chitinases type I, II | PR4 | XM_002264684.1 | CCCAGAGCGCCAGCAATGTGA | TTGCTGCGCCATGCCAAGGG | 0.95 | |
PR4bis | XM_002264611.1 | TGGCTACTGCGGAACAACGGC | CAAGTGGCGCAGTAGGCGCT | 1.02 | ||
Thaumatin-like/Osmotin | PR5 | XM_002282928.1 | GGAGGCAATGGTTTCCACCTTGGG | ACTTGGACGGGACCATAGAGGTTAG | 0.99 | |
PR5bis | XM_002282874.1 | CCCCGGCACCACCAATGCTC | TGGGGGAGAACCGTAGCCCTG | 1.18 | ||
Proteinase inhibitor | PIN a | XM_002284418 | ACGAAAACGGCATCGTAATC | TCTTACTGGGGCACCATTTC | 1.23 | |
PR6 | XM_002277772 | TGGGAAGCAGGCTTGGCCTGA | ACCTGGCTCTCACCGAAGGG | 0.99 | ||
PR6bis | XM_002280597.1 | GCCAGAGCTGGTGGGCGTAC | AGGCGCCATACTCACGATGCC | 1.10 | ||
Subtilisin-like endoprotease | PR7 | XM_002275435.2 | TGCTCCCAATCATGGTGGCTGT | TGAAGACTCTGCGGTGTGTCCT | 1.01 | |
PR7 bis | XM_002275435.1 | CGTTAAGCAGCTGGAAAGGAGCA | TCCTCCGTCAGTCTGGCTGCAA | 1.04 | ||
Chitinase type III | CHIT3 a | Z68123 | AATGATGCCCAAAACGTAGC | ATAAGGCTCGAGCAAGGTCA | 0.98 | |
PR8 | XM_002276329 | GCAACAAAGCTCAATGGCACACCAC | CAGCCAAGCTGCCCTCGTTCC | 0.96 | ||
Lignin-forming peroxidase | POX a | XM_002285687.1 | ACTGCACCAAGAAAGAGCACCAG | AGCTGTGCATGTGCCATCCCC | 1.14 | |
PR9-b | XM_002285613.1 | AGCGAGCGAGAAAGACGCGA | GAGACGACGCCTGGGCAGAC | 0.91 | ||
Ribonuclease-like | PR10 a | AJ291705 | GCTCAAAGTGGTGGCTTCTC | CTCTACATCGCCCTTGGTGT | 0.99 | |
Chitinase type I | PR11 | XM_002270543.1 | CTCCACTGCGCAAACCGTGGT | TTTGCGTTTTCGGAGGAAATCGTGA | 1.10 | |
Defensin | PR12 | XM_002281153 | GTGCAAGAACTGGGAGGGTGCC | GCAGAAGCATGCAACTCCCGGG | 0.88 | |
Lipid Transfer Protein | PR14 | XM_002271080 | ACAGTTGATCGCCAGGCCGC | GCCCGGAAGCCCACTTGCAA | 1.18 | |
PR 14bis | XM_002270934 | CGCCACCACACAAGACCGCA | AGGGAGGCCAGCAGCCAGAC | 1.01 | ||
Germin-like Protein- Oxalate oxidase | PR15 | GTTTCCTGGCCCTCATGGAATTGGC | GTGTCCTGCAGTGGGCTTGGA | 1.19 | ||
PR15bis | XM_002284176.1 | GCCATGGCAGATGATTTCTT | TGCAATTTGGGCAACATTTA | 0.87 | ||
Polygalacturonase Inhibiting Protein | PGIP a | XM_002263487.1 | GAGCGATGCCACCCCAGTGA | CCGTTGAGTCGGACGCTCGAC | 0.96 | |
Secondary metabolites biosynthesis | Phenylalanine ammonialyase | PAL a | X75967 | ACAACAATGGACTGCCATCA | CACTTTCGACATGGTTGGTG | 1.10 |
Stilbene synthase (resveratrol synthase) | STS a | X76892.1 | ATCGAAGATCACCCACCTTG | CTTAGCGGTTCGAAGGACAG | 0.95 | |
Resveratrol O-methyl-transferases | ROMT | FM178870 | TGCCTCTAGGCTCCTTCTAA | TTTGAAACCAAGCACTCAGA | 0.96 | |
ROMT2 | XM_002281445.1 | TCCACACTGCTTACGAGCGGT | CAACCCCGCAAATACGCCCTGG | 0.99 | ||
Chalcone Synthase | CHS a | X75969.1 | CCAACAATGGTGTCAGTTGC | CTCGGTCATGTGCTCACTGT | 1.01 | |
CHS2 | XM_002276885.1 | GCATTTTCCGACGAAGTTCACACTG | GTGCCGATGGCCAGAACCGT | 1.04 | ||
Chalcone Isomerase | CHI a | X75963 | AGAAGCCAAAGCCATTGAGA | CCAAGGGGAGAATGAGTGAA | 1.04 | |
CHI2 | XM_002280122 | TGTGGGCCATCTGCAACCATGG | GCACTCTCTAGCTGCACCCCG | 1.12 | ||
Dihydro Flavonol Reductase | DFR | XM_002281822.1 | GGCCACCGTTCGCGATCCAA | GAAGACGCCGGTGCAGCCTT | 1.05 | |
Anthocyanidine synthase | LDOX a | X75966 | TGGTGGGATGGAAGAGCTAC | CCCACTTGCCCTCATAGAAA | 0.84 | |
Polyphenol Oxidase | PPO | XM_002275806.1 | GGTCCCTCGTTATGGGGCCGA | CCTGGATGGAAATCAGGGCGCC | 0.98 | |
3-hydroxy-3-methylglutaryl Coenzyme A reductase | HMGR | XM_002275791.1 | AACGCACACTCCGCTCCACG | GCGGCGGCGATCTTCATCGA | 0.93 | |
Farnesyl Pyrophosphate Synthase | FPPS | XM_002272605.1 | TCGCCAATGGGTCGAGCGTA | TGCCTGCCTTGCAGCAACTTGT | 1.03 | |
(E,E)-alpha-farnesene synthase | FAR | XM_002281343.1 | GCCATGGCACTCCACCTCTCCTAA | AGGCGGGCTGGTAATGCGCT | 0.99 | |
FAR2 | XM_002264969.1 | TTGCGAGGCAGAAGCTGGCC | TTTGGCCCACGAAAGGCGGG | 1.08 | ||
Flavanone-3-hydroxylase | F3H a | X75965.1 | TGACTCGCTCTCTTCAAGCA | CACCTTGGGACGTTCATCTT | 0.87 | |
F3H bis | XM_002275553.1 | TCCAGCCCGTGGAAGGAGCA | TGCTCAGATACTGCCCACCCAA | 0.96 | ||
Carboxylesterase | HSR-203 J | XM_002285050.1 | TGGAGGAAACATCGTTCACA | CCTGGACAATTCTGCCATCT | 1.02 | |
Indole biosynthesis | Antranilate Synthase | ANTS a | XM 002281597 | AAAAATCCAAGAGGGGTGCT | AAGCTTCTCCGATGCACTGT | 0.84 |
Chorismate mutase | CHORM a | FJ604854 | TCATTGAGAGGGCCAAATTC | AGGAGGCAGAAAAAGCATCA | 1.05 | |
CHORM2 | XM_002284083.1 | GGCAAGTTCGTGGCAGAGGCA | GCCGCTGGCTGTCTTGTGCT | 1.11 | ||
Chorismate Synthase | CHORS a | FJ604855 | GCCTTCACATGCAGATGCTA | CTGCAACTCTCCCAATGGTT | 1.00 | |
CHORS2 | XM_002282263 | TGTTATGGCGCGCGGTGACT | GCAGCTCTGGCCAGTTGAGCT | 1.11 | ||
Redox status | Glutathione S-transferase | GST1 a | AY156048.1 | GGGATCTCAAAGGCAAAACA | AAAAGGGCTTGCGGAGTAAT | 0.99 |
GST2 | AY156049 | CATGAAGGCCGGCCAGCACA | CGCGAAGAATTCGCTCTGGCCA | 0.84 | ||
GST3 | XM_002283178 | TGTTTGGCCGCAAACGGGGT | TCCCCAGCCAGGTACTTGCTCT | 1.06 | ||
GST4 | XM_002271673 | AGCTGGAATGGCGCACTTGGT | TGGAAAGGTGCATACATGGCCACG | 1.00 | ||
GST5 | XM_002283173 | CCTTGAGCTCTACCCTGCCCCA | AGCAGCCAGCCCTAGACATGGA | 0.86 | ||
Oxylipines | Lipoxygenase 13 | LOX2 | XM_002285538 | AAACCGTGCATTCCCGGCCC | GGCAGGGACGTAGCCAACCC | 1.02 |
LOX3 | XM_002284499.2 | GGACCGGGTTCATGAGCTGTTGG | TGAATGCAGACTCGCCAGCGGT | 1.09 | ||
LOX4 | XM_002280615.1 | CCACAAGCGAAGGCGGGCTT | AGCAATGTGCATTTCAGCCATCGA | 1.10 | ||
Lipoxygenase 9 | LOX9 a | AY159556 | GACAAGAAGGACGAGCCTTG | CATAAGGGTACTGCCCGAAA | 0.92 | |
Cell wall reinforcement | Alliinase | Alli | XM_002265837.1 | CGGCTCAGCCTCATCAAGACCC | GGCATGCATGTCATCTTCCTCAGCC | 1.04 |
Alli2 | XM_002266017.1 | AGCCCTTCTGGATGCAGCATGC | TGTAGCTTGCGGATGAGCTTCACT | 1.00 | ||
Ascorbate peroxidase | APOX | XM_002284731.1 | AGCTCAGAGGCCTCATCGCTGA | TACCGGCAGAGTGCCATGCG | 1.07 | |
APOX2 | XM_002278245.1 | TCGAAGCTCAGCAGACGCCG | ACGTCCCCGCATCATGCCAC | 1.14 | ||
Glycosyl transferase (Coniferyl alcohol glucosyl transferase) | CAGT a | XM02273320.2 | TCGGAAGGGAATGCAATAAG | TGTAGGAGGAACCACCCTTG | 0.81 | |
CAGT2 | XM_002276999.1 | TGTTCATGAGGGCTGCGCCG | CACCAGGCAGCTCACTGGCC | 1.00 | ||
Callose Synthase | CALS a | AJ430780.1 | TGGAAATGCAATTCAAACGA | CGAATGCCATGTCTGTATGG | 0.86 | |
CALS2 | XM_002283262 (CS-like 12) | ATGGCGTCCAGAAGCGGCTC | GCCGTCTGTGTCCGCGTGAT | 0.86 | ||
CALS3 | XM_002285608.1 (CS-like-10) | GCAGCAGATTGCCACTGCCCA | AGGCAGAATGAGGTGCTCGCC | 1.14 | ||
Lignin-forming peroxidase | PER a | XM_002274762.1 | TAAGCGCCACAAGAACACTG | GGACCTCCTTGTTGAGTCCA | 0.93 | |
Pectin methyl esterase | PECT1 | XM_002275783.2 | TGTTGGCCTCGAGGAGAGGGG | GGGAGGCCTACAGACCAAAAGTCA | 1.18 | |
PECT2 | XM_002283905.1 | GGGTTGCGCCCTGAGGACAC | CAATCACCCGAGCCGCCTGG | 1.08 | ||
CAD Cinnamyl alcohol dehydrogenase | CAD | XM_002285332.1 | AGTCCGATTGGAAGACGGCAGT | TGCCCCTGTCACACACACCA | 1.05 | |
CAD2 | XM_002268086.1 | TCCGGGTATCCCAGGAGAAAGCA | TCCACGGTATCCTTCATGCTCACC | 1.07 | ||
Signaling | SA Methyl Transferase | SAMT1 | XM_002262982.1 | AATCCTTGCCCAAGTTCCAG | GAGACAACCATTGGAGACTG | 1.16 |
Allene Oxide Synthase | AOS1 | XM_002281190.1 | TTATGGCTTGCCCTTCTTTGG | ATGGAGTCGAGGAGGACGAT | 0.94 | |
Lipase 3/enhanced disease susceptibility 1 | EDS1a | XM_002281059.1 | CAGGTCACAGCCTGGGTGCG | TCGGGCGGGACGATCTCGTT | 1.01 | |
EDS1b | XM_002281871.1 | GGAGACGGGGCTGAACGTGC | CCATCGCCGGCACTTGCTCA | 0.89 | ||
EDS1c | XM_002275822.1 | CCAGCACTGCTTGCAGGCGT | TGCTGTGTTCCTGAGTGCCCC | 1.04 | ||
Transcription Factors | WRKY1 | AY585679.1 | GGAAATATGGGCAGAAAGCA | ATCTTTTGAGAGGCGTTGGA | 1.00 | |
WRKY2 | AY596466 | AGAGGCAAGGCGATGTAGAA | CTGGGGAACAAGCCTTCATA | 1.01 | ||
JAR = Jasmonate-resistant 1 | JAR | XM_002283193.1 | GCAACGGGGCACGACTACTGT | GCCGTGGCGGTGCAAGTACT | 0.89 | |
JAR2 | XM_002280702.1 | CCGAAGTGCTGGCCCCAGAG | AACGCTCACTTCGCCGCTGA | 1.00 | ||
JAR3 | XM_002268242.1 | GGAGCAATGCTGCTCCACAGTGG | GGCGTCGAATGTGCCAGGCT | 1.01 | ||
ACCO 1 | ACO1 | XM_002273394.1 | GCCGGTTTGAAGTTCCAGGCCA | ACTCAAACTGTGGCAATGGGACCC | 1.06 | |
ACO1b | XM_002275305.1/XM_002275284.1 | CGAGCCCACACTGATGCCGG | TTGAGGAGCTGGAGGCCGCT | 1.00 | ||
ACC a | AF424611 | GAAGGCCTTTTACGGGTCTC | CCAGCATCAGTGTGTGCTCT | 0.86 | ||
EIN3-Binding F Box Protein 1 | EIN3 | XM_002285090.1 | TTGGCTCTGAACGCGTCCGA | CCCCGGGGCAGAAGGCATCA | 0.88 | |
EIN3bis | XM_02285213.1 | CCTCGCAAGCGGTCTCGCAT | TGGAGACCCGAGCGCAGGAG | 0.98 | ||