Table S9 Genes associated with the metabolism of amino acids, carbohydrates, organic acids, co-factors and energy production down-regulated during mealiness/woolliness
Function / ID / Unigene annotation / AIG code / Arab gene symbol / Pattern cold+SLR / Normal SLR pattern / CSR1
T vs R-T / CSR1
S vs R-S / CSR2
T vs R-T / CSR2
S vs R-S / CSR3
T vs R-T / CSR3
S vs R-S
Amino acid metabolism
Alanine and aspartate metabolism / PPN067D04 / Bifunctional aspartate kinase/homoserine dehydrogenase / AT4G19710 / AK-HSDH / eRG1 / eRG-U / DOWN / DOWN
Cyanoamino acid metabolism / PPN075E10 / Beta-cyanoalanine synthase 1 / AT3G61440 / CYSC1 / NeRG6 / DOWN
Cyanoaminoacid metabolism / PPN066C01 / Putative mandelonitrile lyase / NeRG6 / DOWN
Cysteine metabolism / PP1005A09 / Cysteine synthase / O-acetylserine (thiol)-lyase / O-acetylserine sulfhydrylase / AT4G14880 / OASA1 / NeRG6 / DOWN / DOWN
PPN052H05 / Putative 1-aminocyclopropane-1-carboxylate deaminase / AT1G48420 / ACD1 / eRG1 / eRG-U / DOWN / DOWN
PPN074E01 / Putative plastidic cysteine synthase 1 / AT3G59760 / OASC / NeRG6 / DOWN
Glutamate metabolism / PP1003C04 / Putative aminotransferase / AT1G77670 / eRG1 / eRG-U
PPN048G12 / Glutamine synthetase, cytosolic isozyme / AT3G17820 / GLN1.3 / NeRG6 / DOWN / DOWN
PPN078D06 / Glutathione synthetase, chloroplast precursor / AT5G27380 / GSH2 / NeRG6 / DOWN / DOWN
Glycine, serine and threonine metabolism / PPN001D12 / Threonine synthase, chloroplast precursor / AT4G29840 / MTO2 / NeRG6 / DOWN / DOWN
PPN055F09 / D-3-phosphoglycerate dehydrogenase / AT4G34200 / EDA9 / eRG1 / eRG-U
Lysine metabolism / PP1005H01 / Lysine ketoglutarate reductase / NeRG7
Methionine metabolism / PPN034C12 / 1,2-Dihydroxy-3-keto-5-methylthiopentene dioxygenase 3 / AT4G14710 / ARD2 / NeRG2
PPN065A08 / Cystathionine beta-lyase, chloroplast / beta-cystathionase / cysteine lyase / AT3G57050 / CBL / NeRG6
Phenylalanine, tyrosine and tryptophan
metabolism / PPN017C03 / Fumarylacetoacetase / AT1G12050 / NeRG6
PPN031A01 / C2 domain-containing protein / AT5G12970 / eRG1 / eRG-U / DOWN / DOWN / DOWN
PPN058D11 / Anthranilate synthase beta subunit / AT1G25220 / ASB1 / eRG1 / eRG-U
Unknown amino acid binding protein / PPN019G11 / ACT domain-containing protein / AT2G39570 / ACR9 / eRG3 / eRG-D / DOWN
PPN078C06 / ACT domain-containing protein / AT5G04740 / ACR12 / NeRG6 / DOWN / DOWN
Unknown aminotransferase protein / PP1009E12 / Pyridoxal phosphate dependent transferases superfamily protein / AT5G26600 / NeRG2 / DOWN
Valine, leucine and isoleucine metabolism / PPN008G08 / Ketol-acid reductoisomerase, chloroplast precursor / AT3G58610 / NeRG6 / UP
PPN019F08 / Acetolactate synthase small subunit / AT2G31810 / NeRG6
PPN045B05 / Branched-chain amino acid aminotransferase 3, chloroplast precursor / AT3G49680 / BCAT3 / eRG1 / eRG-U / DOWN / DOWN
PPN069B12 / Branched-chain amino acid aminotransferase 5 / AT5G65780 / BCAT5 / eRG1 / eRG-U / DOWN / DOWN
Carbohydratemetabolism
Calvin cycle / PP1004D12 / Transaldolase / AT5G13420 / NeRG6 / DOWN / DOWN
PPN030G05 / Rubisco subunit binding-protein beta subunit-like / AT1G79270 / ECT8 / NeRG6
PPN036E07 / Putative 6-phosphogluconolactonase / AT5G24400 / PGL3 / eRG1 / eRG-U
PPN060F08 / Ribulose-phosphate 3-epimerase, chloroplast precursor / AT5G61410 / RPE / NeRG6 / DOWN
PPN061A11 / Transaldolase / AT1G12230 / NeRG6 / DOWN / DOWN / DOWN
D-ribose catabolism / PPN079H08 / Fructokinase 3 / AT1G66430 / NeRG6 / DOWN
D-ribose metabolism / PPN051C01 / Carbohydrate kinase, PfkB / AT1G49350 / NeRG7
Galactose metabolism / PPN029F03 / Aldose 1-epimerase family protein / AT5G57330 / NeRG6 / DOWN
PPN065G06 / Aldose 1-epimerase family protein / AT5G66530 / NeRG2 / DOWN
PPN064E04 / Galactokinase / AT3G06580 / GALK / NeRG6 / DOWN
Glycolysis/ pentose phosphate pathway bypass / PPN008E10 / Ribulose bisphosphate carboxylase/oxygenase activase, chloroplast precursor / AT2G39730 / RCA / NeRG6
Hexose phosphate pool interconversion / PPN039B08 / Phosphoglucomutase, cytoplasmic / AT1G23190 / PGM3 / eRG1 / eRG-U
Non-nucleotide phosphate glycolysis bypass / PPN022G07 / Pyrophosphate--fructose 6-phosphate 1-phosphotransferase subunit beta / AT1G12000 / NeRG6
Nucleotide sugar metabolism / PPN043C08 / UTP--glucose-1-phosphate uridylyltransferase / AT5G17310 / UGP2 / NeRG6 / DOWN / DOWN
PAY-OFF GLYCOLITIC PHASE / PPN009E12 / Putative enolase / AT1G74030 / ENO1 / NeRG6
PPN017H09 / Pyruvate kinase isozyme A, chloroplast precursor / AT3G22960 / PKP1 / NeRG2 / DOWN
PPN031F11 / NADP-dependent glyceraldehyde-3-phosphate dehydrogenase / AT2G24270 / ALDH11A3 / NeRG6
PPN075F04 / Pyruvate kinase, cytosolic isozyme / AT5G08570 / eRG1 / eRG-U / DOWN
PPN078D05 / Glyceraldehyde-3-phosphate dehydrogenase, cytosolic / AT1G79530 / GAPCP-1 / NeRG6 / DOWN / DOWN / DOWN
PREPARATORY STAGE OF GLYCOLISIS / PPN005F10 / Triosephosphate isomerase, chloroplast precursor / AT2G21170 / TIM / NeRG6 / DOWN
PPN038B03 / Fructose-bisphosphate aldolase / AT5G03690 / FBA4 / eRG1 / eRG-U / UP
Raffinose family sugar biosynthesis / PP1004A10 / Putative galactinol synthase / AT1G56600 / GolS2 / NeRG2 / DOWN / DOWN / DOWN / DOWN / DOWN
Sucrose and starch metabolism / PP1001D10 / Beta-amylase / AT5G18670 / BAM9 / NeRG2 / DOWN
PPN042B09 / Beta-amylase / AT5G18670 / BAM9 / NeRG2 / DOWN / DOWN
PPN035A04 / beta-amylase / AT4G00490 / BAM2 / eRG3 / eRG-D / DOWN
PP1003A01 / Soluble starch synthase / AT4G18240 / SS4 / eRG1 / eRG-U
PPN017F12 / Granule-bound starch synthase 1, chloroplast precursor / AT1G32900 / GBSS1 / NeRG6 / DOWN / DOWN / DOWN / DOWN / DOWN
PPN070D09 / Protein tyrosine phosphatase / AT3G52180 / SEX4 / NeRG2 / DOWN
PPN063A04 / Inorganic pyrophosphatase / AT1G01050 / PPa1 / NeRG7
PPN014B06 / Soluble inorganic pyrophosphatase / AT1G01050 / PPa1 / NeRG6
PPN002E08 / ADP-glucose pyrophosphorylase small subunit / AT5G48300 / ADG1 / eRG1 / eRG-U
PPN031H05 / Cytosolic alpha-glucan phosphorylase / AT3G46970 / PHS2 / NeRG6 / DOWN / DOWN
PPN019G12 / Beta-fructofuranosidase / AT5G22510 / INV-E / NeRG6 / DOWN
PPN034B06 / Beta-fructofuranosidase / AT5G22510 / INV-E / eRG1 / eRG-U / DOWN
PPN021E05 / Sucrose synthase 1 / AT4G02280 / SUS3 / NeRG2 / DOWN / DOWN / DOWN / DOWN / DOWN
PPN040F09 / Sucrose phosphate synthase / AT5G20280 / SPS1F / eRG1 / eRG-U
Threalose biosyntehsis / PP1001D07 / Trehalose 6-phosphate synthase / AT1G23870 / TPS9 / eRG1 / eRG-U / DOWN
PPN022E03 / Putative trehalose synthase / AT1G06410 / TPS7 / NeRG6 / DOWN
PPN037G04 / Putative trehalose-6-phosphate synthase / AT1G68020 / TPS6 / NeRG6 / DOWN / DOWN
PPN063H04 / Putative trehalose-6-phosphate synthase / AT1G68020 / TPS6 / NeRG6 / DOWN / DOWN / DOWN / DOWN
PPN067C09 / Trehalose-6-phosphate synthase like protein / AT4G17770 / TPS5 / eRG1 / eRG-U / DOWN
Unknown carbohydrate oxydation / PPN019D09 / Putative aldose reductase-related protein / AT2G36360 / NeRG6 / DOWN
Unknown epimerase / PPN024B04 / NAD-dependent epimerase/dehydratase family protein-like / eRG1 / eRG-U
Unknown glycosyl transferase / PPN025F04 / Glycosyl transferase family 1 / AT1G75420 / eRG1 / eRG-U / DOWN
Cofactor and vitamin metabolism
Ascorbate biosynthesis / PPN058H10 / L-galactose-1-phosphate phosphatase / AT3G02870 / VTC4 / NeRG6
Biotin metabolism / PP1002F07 / Holocarboxylase synthetase 1 / AT2G25710 / HCS1 / eRG1 / eRG-U / DOWN
PPN079B12 / Biotin synthesis protein bioC / AT1G22800 / NeRG2 / DOWN
Chlorophyl degradation / PP1006D04 / Rieske (2Fe-2S) domain-containing protein / AT3G44880 / ACD1/PAO / NeRG6 / DOWN
PPN049D07 / Rieske (2Fe-2S) domain-containing protein / AT3G44880 / ACD1/PAO / NeRG6 / DOWN / DOWN
Folate metabolism / PPN014H12 / Dihydrofolate synthetase /folylpolyglutamate synthetase / AT5G05980 / FPGS1 / NeRG6
PPN032C10 / Methylenetetrahydrofolate reductase 2 / AT2G44160 / MTHFR2 / NeRG6 / DOWN
PPN078D10 / Bifunctional dihydrofolate reductase-thymidylate synthase / AT2G16370 / THY-1 / eRG1 / eRG-U / DOWN
Folate receycling and breakdown / PPN017F11 / Gamma-glutamyl hydrolase precursor / AT1G78680 / GGH2 / eRG1 / eRG-U / DOWN / DOWN / DOWN
Iron sulfur cluster biosynthesis / PPN037D06 / Cysteine desulfurase 1, mitochondrial precursor / AT5G65720 / NIFS1 / NeRG7
PPN052A02 / ABC transporter-like protein / AT5G58270 / ATM3 / NeRG7
PPN068E11 / SufE-like protein, chloroplast precursor / AT4G26500 / SUFE1 / NeRG6 / DOWN
Lipoate metabolism / PP1003G11 / Lipoate protein ligase-like protein / AT3G29010 / eRG1 / eRG-U
Molybdenum cofactor biosynthesis / PPN058B01 / Co-factor for nitrate reductase and xantine dehydrogenase / AT5G55130 / CNX5 / eRG1 / eRG-U / DOWN
PPN073D08 / Molybdenum cofactor sulfurase family protein / AT1G30910 / NeRG6 / DOWN
Nicotinamide metabolism / PPN022E05 / L-aspartate oxidase family protein / AT5G14760 / AO / eRG3 / eRG-D / DOWN
Pantothenate and CoA biosynthesis / PPN073C07 / Pantothenate kinase 2 / AT4G32180 / PANK2 / NeRG6 / DOWN / DOWN
Phytol savage pathway / PPN025G12 / Probable phytol kinase 3, chloroplast precursor / AT5G58560 / FOLK / NeRG6
Stable accumulation of Fe-S clusters / PPN009H03 / APO protein 1, chloroplast precursor / AT1G64810 / APO1 / NeRG6
Ubiquinone biosynthesis / PPN075G02 / Para-hydroxybenzoate-polyprenyltransferase / AT4G23660 / PPT1 / NeRG7 / UP
Energy production
Mitochondrial electron chain / PPN004H09 / NADH-ubiquinone oxidoreductase B16.6 subunit / AT2G31670 / CI-15kDa-2 / NeRG7 / UP
PPN008E02 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6 / AT3G18410 / CI-PDSW1 / NeRG7 / UP
PPN070E05 / NADH-ubiquinone oxidoreductase 24 kDa subunit, mitochondrial precursor / AT4G02580 / CI-24kDa / NeRG6
PPN044F06 / NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial precursor / AT5G37510 / CI76 / NeRG6
PPN048H09 / Alternative oxidase / AT4G22260 / PTOX / NeRG2 / DOWN / DOWN
PPN054E11 / Alternative oxidase / AT4G22260 / PTOX / NeRG2 / DOWN / DOWN / DOWN
PPN066A02 / Alternative oxidase, mitochondrial precursor / AT5G64210 / AOX2 / NeRG6
PPN060G01 / Cytochrome oxidase I / AT1G28140 / NeRG6 / DOWN
Photosyntethic machinery / PP1001H04 / Alkenal/one oxidoreductase / AT1G23740 / AOR / NeRG6
Photosystem assembly / PPN019F12 / TPR protein with homology to Ycf37 / AT1G22700 / NeRG6
Unknown ATPase / PPN058G09 / AAA-type ATPase family protein / AT4G02480 / NeRG6 / DOWN
Vacuolar and plasma membrane ATP production/ cytoplasmic PH regulation / PPN028B06 / Vacuolar H+-pyrophosphatase / AT1G15690 / AVP1 / NeRG6 / DOWN / DOWN
PPN059F12 / Pyrophosphate-energized vacuolar membrane H+ pump / AT1G15690 / AVP1 / eRG1 / eRG-U / DOWN / DOWN
PPN049C11 / Vacuolar ATP synthase 16 kDa proteolipid subunit 4 / AT1G19910 / AVA-P2 / NeRG7
PPN060A06 / Vacuolar-type H+-translocating inorganic pyrophosphatase / AT1G78920 / AVP2 / NeRG6 / DOWN
PPN061H08 / AAA-type ATPase family protein / AT1G64110 / DAA1 / eRG1 / eRG-U / DOWN
PPN078C04 / Plasma membrane ATPase 1 / AT3G47950 / AHA4 / eRG1 / eRG-U / DOWN / DOWN
Organic acid metabolism
Acetate conversion to acetyl-CoA / PPN028G08 / Acetyl-CoA synthetase / AT5G36880 / ACS / NeRG6
PPN029B03 / Acetyl-CoA synthetase / AT1G55320 / AAE18 / NeRG2
PPN038F10 / Acetyl-CoA synthetase / AT1G55320 / AAE18 / NeRG2
Acetyl-CoA biosynthesis / PPN023A09 / Dihydrolipoamide S-acetyltransferase / AT1G34430 / EMB3003 / NeRG7
Conversion of PEP to oxalacetate / PP1001A05 / Pyruvate decarboxylase 1 / AT4G33070 / PDC1 / eRG1 / eRG-U
Glyoxal pathway / PPN073B09 / Hydroxyacylglutathione hydrolase cytoplasmic-like / AT3G10850 / GLX2-2 / NeRG2
PPN075A11 / Lactoylglutathione lyase, putative / glyoxalase I / AT1G67280 / NeRG6 / DOWN
Photorespiratory pathway / PPN035B04 / 2-oxo acid dehydrogenase, lipoyl-binding site / AT2G35120 / eRG1 / eRG-D / UP
PPDK regulation by reversible phophorylation / PPN055A10 / Pyruvate orthophosphate dikinase regulatory protein / AT4G21210 / RP1 / NeRG2 / DOWN
Pyruvate fermentation to ethanol / PPN063G07 / Alcohol dehydrogenase / AT1G77120 / ADH1 / eRG3 / eRG-D / DOWN / DOWN / DOWN / DOWN / DOWN
Pyruvate-lactate interconversions / PPN008B03 / Aldehyde dehydrogenase family 7 member A1 / AT1G54100 / ALDH7B4 / NeRG2 / DOWN
PPN077G06 / Aldehyde dehydrogenase family 7 member A1 / AT1G54100 / ALDH7B4 / NeRG2 / DOWN
Tricarboxylic acid cycle / PPN005D04 / Succinate dehydrogenase / AT1G08480 / SDH6 / NeRG7
PPN066F10 / Phosphoenolpyruvate carboxylase family protein / AT2G43180 / NeRG7
PPN073E08 / Phosphoenolpyruvate carboxylase family protein / AT2G43180 / NeRG6
eRG: early ripening gene; NeRG: non-early ripening gene; D: down; U: up