Supplemental Tables
Table 1. Genes upregulated with cold acclimation in ‘Bluecrop’ field plants and their fold expression changes from microarray data.
______
Gene product 67 hours 399 hours 779 hours 1234 hours
______
Dehydrin
AF030180 1.9148 3.2926 3.6103 1.7409
AF222738 2.2288 3.6350 2.9366 –––––a
AF222739 1.9747 3.7647 2.9717 –––––
AF222740 2.0437 3.9337 2.8080 –––––
AF222741 1.5561 1.8730 2.2948 –––––
CF811663 3.8376 4.4093 7.4670 2.1619
CF811265 3.6166 4.6066 6.0778 2.0252
CF811272 3.7125 5.3539 6.5642 2.0946
CV091437 ––––– 2.0020 ––––– –––––
CV091466 1.9342 2.4538 2.3559 –––––
CF811614 2.4528 3.7280 3.8324 1.5195
CV091131 ––––– 1.8179 ––––– –––––
CF811137 ––––– ––––– 1.6189 1.5338
CV091312 2.0686 3.6721 3.3215 1.5049
AY660959 2.5793 4.0185 4.1139 2.0430
CV826719 3.0312 3.6626 4.2970 2.4753
CF810618 2.0656 2.9789 3.2610 1.6134
CV090829 3.3343 4.5902 5.3958 2.0232
CV090332 1.7925 2.4603 2.5978 –––––
CV090537 3.0308 1.9517 4.3097 1.7946
CV090724 1.6084 2.3088 1.9206 –––––
Early light-inducible protein
CV090897 ––––– 1.6809 ––––– –––––
CV091016 ––––– 2.2962 1.8295 –––––
CV091100 ––––– 2.9029 2.9238 –––––
CF810877 ––––– 4.5264 3.2423 –––––
CF810917 ––––– 6.5314 3.3452 –––––
CF810668 ––––– 4.7877 2.5630 –––––
CV090885 ––––– 2.7821 2.1106 –––––
CV090446 ––––– 8.7660 4.1574 –––––
CV090499 ––––– 3.8198 3.3928 –––––
Probable beta-amylase
CV091360 ––––– 3.1292 2.8433 –––––
CV091081 ––––– 2.9358 2.7637 –––––
CF810476 ––––– 4.2098 2.4738 –––––
CF810753 ––––– 4.0072 2.7492 –––––
CV090504 ––––– 3.6837 3.3996 –––––
CV090771 ––––– 3.0143 2.6734 –––––
Wheat endosperm cDNA library Triticum aestivum cDNA clone WHE0073_B10_D19
CF811328 2.3841 4.2909 4.0826 2.0409
CF811493 1.8258 2.5581 2.3697 1.5420
CV091278 2.2167 3.7477 3.4879 1.8763
CF810763 2.5539 3.5079 4.2853 1.8273
LEA
CF810442 ––––– 2.9204 1.6290 –––––
CV090832 ––––– 2.4828 2.1197 1.5687
CV090880 ––––– 2.0222 ––––– –––––
CV090393 ––––– ––––– 1.6438 1.6610
Putative methyl transferase
CV826720 2.3991 3.9828 3.6597 –––––
CV090242 ––––– 2.0232 1.9814 –––––
DnaJ protein
CF810686 ––––– 1.7222 ––––– –––––
CF810527 ––––– 1.5026 ––––– –––––
Auxin repressed protein
CF811432 ––––– 1.6676 2.0020 –––––
CF810519 ––––– 1.7566 ––––– –––––
Sgs1 gene product-Rec Q family of ATP-dependent DNA helicases
CV090482 ––––– ––––– 1.8329 –––––
CV090492 ––––– ––––– 1.8056 –––––
Granule-bound glycogen (starch) synthase
CF810992 ––––– ––––– 1.5885 –––––
CV090603 ––––– ––––– 1.5396 –––––
Low temperature and salt responsive protein
CF811428 ––––– ––––– 1.6022 –––––
CF810754 ––––– ––––– 1.6613 –––––
Photosystem II D1 protein
CF810742 ––––– ––––– 2.0869 1.5719
Photosytem II CP 47 protein
CF810690 ––––– ––––– 1.6638 –––––
Protein kinase PINOID
CV090257 2.3492 4.4330 5.4536 2.2883
Pectate lyase-like protein
CF811560 1.7248 1.9853 2.2811 –––––
DNA-binding domain protein
CV091089 1.7181 3.8386 3.6317 –––––
Glycine-rich protein
CV090428 1.5465 4.1710 4.5989 1.6417
60Sribosomal protein L11
CV826721 1.6424 ––––– ––––– –––––
Proteinase inhibitor
CF811673 1.6027 ––––– ––––– –––––
Putative transketolase
CV090837 1.5141 ––––– 1.6310 –––––
Receptor-like protein kinase 1
CV091384 ––––– ––––– ––––– 1.5634
Leucine-rich repeat disease resistance protein
CV091093 ––––– 3.0390 2.9060 –––––
Blind, potato abiotic stress protein
CV090776 ––––– 2.9773 1.7238 –––––
Galactinol synthase
CF810581 ––––– 2.7522 1.5670 –––––
F-box family protein
CV090254 ––––– 2.6327 1.9610 –––––
S-adenosylmethionine decarboxylase proenzyme
CV090423 ––––– 2.2502 2.1825 –––––
MutF
CV090600 ––––– 2.0258 ––––– –––––
Formin homology 2 domain-containing protein
CV091120 ––––– 1.9405 1.8859 –––––
Maturation protein
CF810607 ––––– 1.8590 ––––– –––––
20S proteasome alpha subunit B (PAB1)
CV090407 ––––– 1.7255 ––––– –––––
Probable protein kinase PK1-potato
CV090713 ––––– 1.7246 1.9158 –––––
Bile acid: sodium symporter family protein
CV090298 ––––– 1.6908 2.1998 –––––
Embryonic protein ecp31
CV090586 ––––– 1.6902 1.6508 –––––
L-ascorbate peroxidase
CF810947 ––––– 1.6673 ––––– –––––
Low-temperature-induced 65 kD protein
CF810644 ––––– 1.6252 ––––– –––––
Serine-arginine-rich splicing regulatory protein
CV090882 ––––– 1.5815 1.6623 –––––
Stretch regulated skeletal muscle protein
CV090597 ––––– 1.5592 ––––– –––––
Putative deoxyguanosine kinase
CF810718 ––––– 1.5568 ––––– –––––
Putative aldo/keto reductase
CV091316 ––––– 1.5491 ––––– –––––
DNA directed RNA polymerase I 190K
CF810490 ––––– 1.5367 ––––– –––––
Potential calcium-transporting ATPase 9
CV091314 ––––– 1.5309 ––––– –––––
Lysine decarboxylase-like protein
CF810885 ––––– 1.5280 ––––– –––––
ABC transporter family protein
CF811558 ––––– 1.5178 1.6124 –––––
RNA polymerase I, II, and III 24.3 kDa subunit
CF811571 ––––– 1.5136 ––––– –––––
ADP-ribosylation factor-like protein
CV091470 ––––– 1.5089 ––––– –––––
Putative transposase
CF810529 ––––– 1.5026 ––––– –––––
Water stress-induced ER5 protein
CV091388 ––––– 1.5002 1.7444 –––––
Der1-like family protein-component of ER-associated protein degradation system
CV090276 ––––– ––––– 1.7654 –––––
Probable membrane protein YLR162w
CV090514 ––––– ––––– 1.7619 –––––
Metallothionein 1 homolog
CF811363 ––––– ––––– 1.7012 –––––
Membrane bound O-acyl transferase (MBOAT) family protein
CV090287 ––––– ––––– 1.6540 –––––
ATP-dependent Clp protease ATP-binding subunit precursor
CV090611 ––––– ––––– 1.6087 –––––
Myb-related transcription factor
CV090223 ––––– ––––– 1.5403 –––––
Hypothetical protein
CV091113 –––––– ––––– 1.5186 –––––
CV091266 –––––– 1.5245 1.5434 –––––
CV091267 ––––– 1.7807 1.5634 –––––
CV091301 ––––– 1.5750 ––––– –––––
CV091324 ––––– ––––– 1.6202 –––––
CF810483 ––––– 1.5685 ––––– –––––
CF810521 ––––– 1.6675 ––––– –––––
CF810524 ––––– 1.7953 ––––– ––––– CF810733 ––––– 1.6747 1.5909 –––––
CF810744 ––––– 1.5070 ––––– –––––
CF810805 ––––– 1.9736 ––––– –––––
CV090894 ––––– 1.5436 1.6008 –––––
CV090267 –––– ––––– 1.5639 –––––
CV090386 1.6193 5.0391 2.6378 1.8162
CV090388 ––––– 2.3430 2.5612 1.5446
CV090392 ––––– ––––– 1.7395 –––––
CV090398 ––––– 2.7288 2.1495 –––––
CV090409 ––––– 2.3453 2.4446 –––––
CV090436 ––––– 1.9190 1.5357 –––––
CV090438 ––––– 1.5261 ––––– –––––
CV090442 ––––– ––––– 1.7201 –––––
CV090445 ––––– 1.5197 1.8696 –––––
CV090447 ––––– 1.5998 ––––– –––––
CV090450 ––––– ––––– 1.7965 –––––
CV090627 1.7161 2.4586 2.5799 1.5108
CV090718 ––––– ––––– 2.3418 –––––
CV090745 ––––– ––––– 2.1888 –––––
No significant similarity
CF811188 ––––– ––––– ––––– 1.7582
CV091005 1.6074 2.1647 2.1783 –––––
CF810595 ––––– 2.8042 1.5373 –––––
CV090231 ––––– 2.2278 3.0244 –––––
CV090247 2.2773 2.6337 3.6470 1.6588
CV090268 1.6854 1.8897 ––––– –––––
CV090434 ––––– 2.3994 2.5385 –––––
CV090437 ––––– 2.5829 1.9896 –––––
CV090730 ––––– ––––– 5.6916 –––––
______
aDashes indicate no significant difference between test and reference levels.
Table 2. Genes downregulated with cold acclimation in ‘Bluecrop’ field plants and their fold expression changes from microarray data.
______
Gene product 67 hours 399 hours 779 hours 1234 hours
______
Dehydration-induced RD22-like protein/BURP domain-containing protein
CF811598 ––––––a -3.7684 -3.2331 ––––––
CF811246 –––––– -3.5659 -2.0074 -1.7340
CV091382 –––––– -2.8128 –––––– ––––––
CV091401 –––––– -1.8353 –––––– ––––––
CF811485 –––––– -3.5782 -2.0023 ––––––
CF811494 –––––– -3.8090 -1.9736 -1.7954
CF811563 –––––– -3.4026 -1.6417 -1.6668
CV091031 –––––– -1.8831 –––––– ––––––
CV091057 –––––– -1.9538 –––––– ––––––
CV091273 –––––– -3.5849 ––––––– ––––––
CF810541 –––––– -2.7798 -2.1693 ––––––
Lipid transfer protein precursor
CF811685 –––––– -1.9275 –––––– ––––––
CF810602 –––––– -1.5318 -1.5362 ––––––
CV090838 –––––– -2.3055 –––––– ––––––
CV090572 –––––– -2.3332 –––––– ––––––
CV090581 –––––– -1.9745 –––––– ––––––
Lipid transferase protein precursor
CF810421 –––––– -2.9814 -1.8423 ––––––
Nonspecific lipid-transfer protein 2 (LTP 2)
CV091492 –––––– -1.5920 –––––– ––––––
Metallothionein-like protein
CF811206 –––––– -1.9167 –––––– ––––––
CF811381 –––––– -1.8748 –––––– ––––––
CF811648 –––––– -1.6614 –––––– ––––––
CF811168 –––––– -1.5766 –––––– ––––––
CF810547 –––––– -1.6772 –––––– ––––––
Major latex-like protein
CF811472 –––––– -4.8232 -3.4879 ––––––
CF811356 –––––– -4.2820 -2.1360 ––––––
CV091434 –––––– -1.6514 –––––– ––––––
CV090991 –––––– -3.6139 -2.0430 ––––––
Ubiquitin-homolog
CV091371 –––––– -1.9762 –––––– ––––––
CV091386 –––––– -1.5126 –––––– ––––––
CF810800 –––––– -1.6314 –––––– ––––––
CF810959 –––––– -1.7066 –––––– ––––––
Ubiquitin-conjugating enzyme UBC2
CV091255 –––––– -2.6206 -1.6552 ––––––
Putative heat shock protein
CF811441 –––––– -2.2642 –––––– -1.6993
CF810579 –––––– -2.0833 –––––– ––––––
CV090571 –––––– -2.8292 –––––– ––––––
Heat shock protein 82
CF811551 –––––– -1.5052 –––––– ––––––
CV091285 –––––– -1.6035 –––––– ––––––
CF810427 –––––– -2.0661 –––––– ––––––
Heat shock protein hslJ
CV090544 –––––– -2.2270 –––––– ––––––
Putative aquaporin PIP2-1
CV090435 –––––– -3.3135 –––––– ––––––
CV090723 –––––– -1.7103 –––––– ––––––
CV090727 –––––– -1.9991 –––––– ––––––
Probable cytochrome P450 monooxygenase
CF810460 -1.7801 –––––– –––––– ––––––
CF810605 -1.9275 -2.1556 –––––– ––––––
CF810841 -1.6214 –––––– –––––– ––––––
CV090239 -1.5107 –––––– –––––– ––––––
CV090314 –––––– –––––– –––––– -1.5233
CV090340 -1.9507 –––––– –––––– ––––––
CV090374 -1.5461 –––––– –––––– ––––––
CV090521 -1.8349 -1.7739 –––––– ––––––
CV090636 –––––– -1.5126 –––––– ––––––
Actin-depolymerizing factor 2
CV090467 –––––– -1.8598 –––––– ––––––
CV090477 –––––– -1.7071 –––––– ––––––
CV090487 –––––– -1.7981 –––––– ––––––
F1 ATPase subunit alpha
CF811146 –––––– -1.8592 –––––– ––––––
CF810729 –––––– –––––– -1.5490 ––––––
CV090738 –––––– -1.6955 –––––– ––––––
CV090755 –––––– -1.5940 –––––– ––––––
Phospholipid hydroperoxide glutathione peroxidase
CF811238 -2.1090 -2.2684 –––––– -2.2313
CF811306 -1.5131 -1.7401 –––––– -1.5920
CF810441 -1.5402 –––––– –––––– -1.8620
Ascorbate peroxidase
CF811271 –––––– -1.6742 –––––– ––––––
CV090907 –––––– -2.1192 –––––– ––––––
CBL-interacting protein kinase 11 (CIPK11)
CF810544 –––––– –––––– –––––– -1.6318
CV090827 –––––– -1.6510 –––––– -1.6806
CV090765 –––––– -1.7823 –––––– ––––––
Zinc finger (CCCH-type) family protein
CV090253 –––––– -3.1026 –––––– ––––––
Nam-like protein 1
CF811419 –––––– -2.9753 -1.9052 -1.7941
60S acidic ribosomal protein P2
CF811387 –––––– -2.5606 –––––– ––––––
Ribosomal protein L33
CV090915 –––––– -1.7565 –––––– ––––––
14-3-3-like protein
CF811371 –––––– -2.1080 -1.6967 ––––––
UDP-glucose dehydrogenase-like protein
CV090601 –––––– -2.0651 –––––– ––––––
26S proteasome regulatory subunit S2
CV090400 –––––– -2.0380 –––––– ––––––
DEMETER protein
CV090532 –––––– -1.9702 –––––– ––––––
3-deoxy-D-arabino-heptulosonate 7-phosphate synthase
CF811248 –––––– -1.9568 –––––– ––––––
Phosphatase 2C-like protein
CV090426 –––––– -1.9274 –––––– ––––––
S-adenosylmethionine synthetase 3
CF811124 –––––– -1.8989 –––––– ––––––
Reticulon family protein
CV090297 -1.7124 -1.8926 –––––– ––––––
HMG1/2-like protein
CV090671 –––––– -1.8918 –––––– ––––––
Non-functional folate binding protein
CV090816 –––––– -1.8723 –––––– ––––––
Inorganic pyrophosphatase
CV090558 –––––– -1.8668 –––––– ––––––
Beta-glucosidase precursor isoform AH 1
CV091310 –––––– -1.8470 –––––– ––––––
Putative senescence-associated protein
CF810823 –––––– -1.8423 –––––– ––––––
3-hydroxy-3-methylglutaryl coenzyme a reductase
CV090291 –––––– -1.8399 –––––– ––––––
Protein kinase
CF811368 –––––– -1.8395 –––––– ––––––
BEL1-related homeotic protein 29
CV091094 –––––– -1.7857 –––––– ––––––
Alpha-expansin precursor
CV091353 –––––– -1.7754 –––––– ––––––
Extensin
CV091000 –––––– -1.7499 –––––– ––––––
DNA-directed RNA polymerase I 190K chain homolog
CV090250 –––––– -1.6993 –––––– ––––––
Dihydroorotase precursor
CV090833 –––––– -1.6722 –––––– ––––––
GDP-mannose pyrophosphorylase
CV091485 –––––– -1.6573 –––––– ––––––
ADP, ATP carrier protein precursor
CV090567 -1.6806 -1.6475 –––––– -1.5568
Myo-inositol-1-phosphate synthase
CV091489 –––––– -1.6348 –––––– ––––––
Homeobox leucine zipper protein ATHB-12
CF810532 –––––– -1.6202 –––––– ––––––
RNA-binding protein RBP37
CV090906 –––––– -1.6171 –––––– ––––––
Cysteine protease component of protease-inhibitor complex
CV090543 –––––– -1.6116 –––––– ––––––
Cysteine proteinase
CF810657 –––––– -1.5872 –––––– ––––––
Acetoacetyl-CoA thiolase
CF811681 –––––– -1.6091 –––––– ––––––
B2 protein
CV091013 –––––– -1.5806 –––––– ––––––
3-hydroxy-3-methylglutaryl coenzyme a reductase
CV090391 –––––– -1.5782 –––––– ––––––
ADP-ribosylation factor 1
CF811336 –––––– -1.5724 –––––– ––––––
SCAR1
CV090245 –––––– -1.5722 –––––– ––––––
Putative SCARECROW gene regulator
CV091258 –––––– -1.5456 –––––– ––––––
Dehydrin
CV090290 –––––– -1.5295 –––––– ––––––
P48h-10 protein precursor
CF811127 –––––– -1.5274 –––––– ––––––
Cinnamyl alcohol dehydrogenase
CF810867 –––––– -1.5250 –––––– ––––––
Farnesylated protein ATFP6
CV090480 –––––– -1.5211 –––––– ––––––
Malate dehydrogenase cytoplasmic 1
CV090585 –––––– -1.5119 –––––– ––––––
Phosphatidylinositol transfer-like protein
CF810470 –––––– -1.5102 –––––– ––––––
Phenylcoumaran benzylic ether reductase homolog TH7
CF811483 –––––– -1.5037 –––––– ––––––
Low-temperature-induced 65 kD protein
CF810644 -1.5567 –––––– –––––– ––––––
Low-temperature induced 78 kD protein
CF810862 -2.1819 –––––– –––––– ––––––
Hypothetical protein
CF811182 –––––– -2.3371 –––––– ––––––
CF811332 –––––– -1.9110 –––––– ––––––
CF811538 –––––– -1.5213 –––––– ––––––
CF811155 –––––– –––––– -1.5472 ––––––
CF811258 –––––– -1.8784 –––––– ––––––
CV091339 –––––– -1.5964 –––––– ––––––
CF811402 –––––– -1.8854 –––––– ––––––
CF811446 –––––– -1.8170 –––––– ––––––
CF811468 –––––– -1.9030 -1.5274 ––––––
CF811535 –––––– -2.8807 –––––– ––––––
CV091488 –––––– -1.5691 –––––– ––––––
CF811517 –––––– -2.5384 –––––– ––––––
CF811540 –––––– -1.9183 –––––– ––––––
CF811635 –––––– -1.5725 –––––– ––––––
CF811172 –––––– -1.5537 –––––– ––––––
CV090980 –––––– -1.8798 –––––– ––––––
CV091287 –––––– -1.5311 –––––– ––––––
CF810961 –––––– -1.5575 –––––– ––––––
CV090305 -1.5428 –––––– –––––– ––––––
CV090328 –––––– -1.7955 –––––– ––––––
CV090380 –––––– -1.5869 –––––– ––––––
CV090444 –––––– -1.5633 –––––– ––––––
CV090522 –––––– -1.6825 –––––– ––––––
CV090580 –––––– -2.0628 –––––– ––––––
CV090718 -1.5497 –––––– –––––– ––––––
No significant similarity
CF811333 –––––– -1.8624 –––––– ––––––
CF811188 –––––– -1.6592 –––––– ––––––
CF811240 –––––– -1.5854 –––––– ––––––
CF811241 –––––– -1.5281 –––––– ––––––
CF811249 –––––– -1.6782 –––––– ––––––
CV091383 –––––– -2.0682 –––––– ––––––
CF811396 –––––– -1.6180 –––––– ––––––
CF811414 –––––– -2.1801 –––––– ––––––
CV090916 –––––– -1.5917 –––––– ––––––
CV091014 –––––– -1.8103 –––––– ––––––
CV091037 –––––– -1.9316 –––––– ––––––
CV091052 –––––– -1.5315 –––––– ––––––
CV091118 –––––– -1.8493 –––––– ––––––
CV091275 –––––– -3.3715 -2.0626 ––––––
CF810759 –––––– -1.5827 –––––– ––––––
CF811109 -1.5789 –––––– –––––– ––––––
CV090816 -1.5837 –––––– –––––– ––––––
CV090849 –––––– -3.2236 –––––– ––––––
CV090286 –––––– -1.6834 –––––– ––––––
CV090328 -1.5479 –––––– –––––– ––––––
CV090349 -1.5164 -1.6704 –––––– ––––––
CV090576 -1.8008 -1.9412 –––––– ––––––
CV090607 –––––– -1.9195 –––––– -1.7411
CV090711 -1.7801 –––––– –––––– -1.6786
CV090726 -1.7226 –––––– –––––– -1.6768
______
aDashes indicate no significant difference between test and reference levels.
Table 3. Genes upregulated in ‘Bluecrop’ cold room-treated plants and their fold expression changes from microarray data.
______
Gene product 500 hours 1000 hours
______
Dehydrin
AF030180 5.3633 4.7806
AF222738 2.9622 3.6948
AF222739 3.7372 4.0856
AF222740 5.5129 3.6862
AF222741 1.8650 2.2219
CF811663 9.9553 6.5690
CF811265 9.0806 9.1412
CF811272 13.7564 9.9041
CF811339 4.0006 3.0644
CV091437 1.5124 1.6989
CV091466 2.4538 1.7744
CV091484 2.6361 2.8473
CF811614 11.1327 5.1985
CF811137 2.0604 2.2756
CV091131 1.9061 1.8271
CV091312 6.1977 4.6326
AY660959 8.6337 5.9861
CV826719 7.5517 4.1257
CF810618 4.2030 4.5676
CV090815 2.2537 2.7479
CV090829 9.4918 5.4255
CF810954 1.5288 ––––––a
CV090332 2.3378 2.5064
CV090537 6.2764 4.9362
CV090724 3.1112 3.0229
Early light-inducible protein
CV090897 1.5341 ––––––
CV091016 1.7033 1.5097
CV091100 4.2261 3.1450
CF810877 2.7197 ––––––
CF810917 2.6133 1.7280
CF810668 1.7150 1.6466
CV090885 1.6869 ––––––
CV090499 2.1054 1.6277
Probable beta-amylase
CV091360 1.5674 1.9126
CF810476 2.6163 2.2620
CF810753 1.5376 2.0718
CV090504 2.1161 2.0994
Wheat endosperm cDNA library Triticum aestivum cDNA clone WHE0073_B10_D19
CF811328 6.6069 6.0902
CF811493 3.0005 3.3353
CV091278 3.9476 5.8520
CF810763 4.5494 4.3967
CV090758 1.6798 1.7955
LEA
CF810442 2.5439 2.2846
CF810588 3.2067 2.4475
CV090832 7.8755 2.1690
CV090880 5.0311 2.7955
CV090393 –––––– 2.2473
Putative methyl transferase
CV826720 6.9670 6.3644
Auxin repressed protein
CF811432 –––––– 2.2994
CF810519 –––––– 1.5116
CV090422 –––––– 1.5660
Proteinase inhibitor
CF811673 3.6136 3.2394
CV091481 1.8245 1.8168
CF810438 2.6213 2.1373
60S ribosomal protein L6
CF810786 1.7846 1.5883
CV090493 1.7509 1.5777
60Sribosomal protein L11
CV826721 2.5834 2.8375
60S ribosomal protein L19
CV091298 1.8084 ––––––
Putative 60S ribosomal protein L22