Table 1 |
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|
Selection of SAS showing differential expression when high and low Brix plants were compared or when mature and immature internodes were compared. |
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|
SAS |
category |
sub category 1 |
sub category 2 |
HB vs LB |
MI vs II |
Drought |
ABA |
Suc |
Gluc |
|
|
|||||||||
|
SCCCLR1022D05.g |
adapter |
14-3-3 protein |
GF14 |
↓ |
|||||
|
SCCCRZ1001D02.g |
adapter |
14-3-3 protein |
GF14 |
↓↓↓↓ |
|||||
|
SCEQRT1031D02.g |
adapter |
14-3-3 protein |
GF14 |
↓↓ |
|||||
|
SCEQRT1025D06.g |
adapter |
14-3-3 protein |
GF14 |
↓ |
↓↓ |
||||
|
SCVPLR1049C09.g |
calcium metabolism |
calmodulin-binding protein |
AAA family ATPase (cell division cycle protein 48 sub-family) |
↓ |
|||||
|
SCCCRZ1C01H06.g |
calcium metabolism |
calmodulin-binding protein |
Apyrase (Nucleoside diphosphatase) |
↓↓↓↓ |
↓↓ |
||||
|
SCJLLR1108H07.g |
calcium metabolism |
calmodulin-binding protein |
Ca(2+)-ATPase |
↓ |
|||||
|
SCEZLB1012F10.g |
calcium metabolism |
calmodulin-binding protein |
Cyclic nucleotide-gated calmodulin-binding ion channel |
↑ |
|||||
|
SCCCAM1001A03.g |
calcium metabolism |
calmodulin-binding protein |
Multidrug resistant (MDR) ABC transporter |
↑ |
↑↑ |
||||
|
SCRFLR2037F09.g |
calcium metabolism |
calreticulin |
CRT2 Calreticulin 2 |
↓ |
↓↓ |
↑↑ |
↑↑↑ |
↑↑↑ |
|
|
SCCCLR2C02A05.g |
cell wall metabolism |
expansin |
EXPA11 |
↓ |
↓↓ |
||||
|
SCQGRT1040G03.g |
cell wall metabolism |
expansin |
OsEXPA23 |
↑ |
↓↓ |
||||
|
SCACSB1037A07.g |
cell wall metabolism |
cytochrome P450 |
P-coumaroyl shikimate 3'-hydroxylase |
↓↓ |
|||||
|
SCEZHR1087F06.g |
cell wall metabolism |
cytochrome P450 |
Ferulate-5-hydroxylase |
↓ |
↑↑ |
||||
|
SCSGFL4193B05.g |
cell wall metabolism |
cytochrome P450 |
Cinnamic acid 4-hydroxylase |
↓ |
|||||
|
SCRFLR1012F12.g |
cell wall metabolism |
. |
Caffeic acid 3-O-methyltransferase |
↑↑ |
↑↑ |
||||
|
SCBFLR1039B05.g |
cell wall metabolism |
polysaccharide metabolism |
Xyloglucan endotransglycosylase |
↓↓↓↓ |
|||||
|
SCCCLR1048D07.g |
cell wall metabolism |
lignin |
Phenylalanine ammonia-lyase |
↑ |
↓↓ |
||||
|
SCEQRT1024E12.g |
cell wall metabolism |
lignin |
Phenylalanine ammonia-lyase |
↑ |
↓ |
↓↓ |
↑↑ |
↑↑↑ |
↑↑↑ |
|
SCSGAM1094D05.g |
cell wall metabolism |
lignin |
Phenylalanine ammonia-lyase |
↓ |
↓ |
||||
|
SCCCCL6002B05.g |
hormone biosynthesis |
auxin |
Nitrilase |
↑ |
↑↑ |
||||
|
SCEQRT1028H06.g |
hormone biosynthesis |
auxin |
Nitrilase |
↓↓ |
↑↑ |
||||
|
SCRFLR1012D12.g |
hormone biosynthesis |
auxin |
Nitrilase |
↑ |
↓ |
↑↑ |
|||
|
SCVPLR2012A10.g |
hormone biosynthesis |
ethylene |
ACC oxidase |
↑ |
↓↓ |
||||
|
SCCCRT1001E01.g |
hormone biosynthesis |
jasmonic acid |
Lipoxygenase |
↓ |
↓↓↓↓ |
↓↓ |
↓↓↓ |
↓↓↓ |
|
|
SCJFRT1007H07.g |
hormone biosynthesis |
jasmonic acid |
Lipoxygenase |
↓ |
↓ |
||||
|
SCCCLR1C03G01.g |
hormone biosynthesis |
jasmonic acid |
Omega-6 fatty acid desaturase |
↓ |
↓ |
↑↑ |
↑↑ |
||
|
SCCCAM2004G02.g |
hormone-related |
auxin |
Auxin transport/auxin eflux carrier (OsPIN1c) |
↓ |
|||||
|
SCCCLR2002F08.g |
hormone-related |
auxin |
dormancy/auxin associated family (auxin-repressed) |
↓ |
↑↑ |
||||
|
SCBGLR1023D05.g |
pathogenicity |
R-gene transduction |
Zinc finger protein (LSD1) |
↑ |
↓↓↓ |
↓↓ |
↑↑↑ |
||
|
SCAGLR1043F02.g |
protein metabolism |
calmodulin-binding protein |
HSP70 (heat shock) |
↑↑ |
↓ |
↑↑ |
|||
|
SCCCCL3120G07.g |
protein metabolism |
calmodulin-binding protein |
HSP70 (heat shock) |
↑ |
↑↑ |
||||
|
SCCCRZ1003A03.g |
protein metabolism |
calmodulin-binding protein |
HSP70 (heat shock) |
↑ |
|||||
|
SCEQRT2099H01.g |
protein kinase |
calcium-dependent |
ScCDPK-27 |
↓ |
|||||
|
SCVPAM1055A12.g |
protein kinase |
casein kinase |
ScCKI-11 |
↑ |
↓ |
↑↑ |
|||
|
SCCCLR1C04G08.g |
protein kinase |
casein kinase |
ScCKI-3 |
↑ |
|||||
|
SCCCLR1022H07.g |
protein kinase |
cell cycle-related |
ScCDK-11 |
↓ |
|||||
|
SCBGLR1096C08.g |
protein kinase |
cell cycle-related |
ScCDK-18 |
↓ |
|||||
|
SCVPRT2081G05.g |
protein kinase |
cell cycle-related |
ScCDK-3 |
↓ |
|||||
|
SCRLFL1012B10.g |
protein kinase |
cell cycle-related |
ScCDK-6 |
↓ |
|||||
|
SCSBAM1084E01.g |
protein kinase |
MAPK/MAPKK/MAPKKK |
ScMAPK-4 |
↑ |
↑↑ |
↓↓ |
|||
|
SCEPAM1020A03.g |
protein kinase |
other |
ScATN1-2 |
↓ |
|||||
|
SCVPCL6042B07.g |
protein kinase |
other |
ScCyclin G-associated kinase-like protein-1 |
↓ |
|||||
|
SCJFRZ2032C08.g |
protein kinase |
SNF-like kinase |
ScCIPK-14 |
↑ |
↑↑ |
||||
|
SCBFSB1046D04.g |
protein kinase |
SNF-like kinase |
ScCIPK-16 |
↑ |
↓↓↓ |
||||
|
SCMCRT2103B04.g |
protein kinase |
SNF-like kinase |
ScCIPK-21 |
↑↑ |
↑ |
↓↓ |
↓↓ |
||
|
SCCCLR1C05B07.g |
protein kinase |
SNF-like kinase |
ScCIPK-3 |
↑ |
↑↑ |
↓↓↓ |
↓↓↓ |
||
|
SCJLRZ1023H04.g |
protein kinase |
SNF-like kinase |
ScCIPK-9 |
↓↓ |
↓↓ |
||||
|
SCEPRZ1009C10.g |
protein kinase |
SNF-like kinase |
ScOSA PK-1 |
↓↓ |
↓↓ |
↓↓ |
|||
|
SCCCST1004A07.g |
protein kinase |
SNF-like kinase |
ScOSA PK-7 |
↓ |
|||||
|
SCACLR2007G02.g |
protein kinase |
SNF-like kinase |
ScPKABA1-1 |
↑↑ |
↓↓ |
↓↓↓ |
|||
|
SCRFLR1034G06.g |
protein kinase |
SNF-like kinase |
ScPKABA1-3 |
↑ |
↓↓ |
↓↓↓ |
↓↓↓ |
||
|
SCJFRZ2032G01.g |
protein kinase |
SNF-like kinase |
ScSnRK1-2 |
↓↓ |
↓↓ |
↑ |
|||
|
SCCCCL5002B10.g |
protein kinase |
undefined |
ScPK-BI2 |
↓↓↓ |
|||||
|
SCJLLR1054C03.g |
protein kinase |
undefined |
ScPK-BIII7 |
↑ |
|||||
|
SCMCSD2061D05.g |
protein kinase |
undefined unclassified |
ScUPK-46 (CIPK) |
↓ |
|||||
|
SCCCLB1001D03.g |
protein phosphatase |
serine/threonine PPM family |
PP2A/Catalytic Subunit |
↓ |
|||||
|
SCEZLR1052F07.g |
protein phosphatase |
serine/threonine PPM family |
PP2A/Subunit A |
↓ |
|||||
|
SCEPRZ1010E06.g |
protein phosphatase |
serine/threonine PPM family |
PP2C-like |
↓↓ |
↓ |
↑↑ |
↑↑ |
↓↓↓ |
↓↓↓ |
|
SCEZHR1088E02.g |
protein phosphatase |
tyrosine phosphatase |
Dual Specificity Protein Phosphatases (DSPP) |
↑↑↑ |
↓ |
↑↑ |
↓↓↓ |
↓↓↓ |
|
|
SCMCST1051F08.g |
protein phosphatase |
tyrosine phosphatase |
Tyrosine Specific Protein Phosphatases (PTP) |
↓↓ |
|||||
|
SCSBHR1056H08.g |
receptor |
ethylene |
EIN2 |
↑ |
|||||
|
SCUTLR2023D06.g |
transcription factor |
CCAAT |
ScCA2P5 |
↑ |
|||||
|
SCCCLR1066G08.g |
transcription factor |
HGM (high mobility group protein) |
↑ |
↓↓ |
|||||
|
SCBFAD1046D01.g |
transcription factor |
HLH (helix-loop-helix) |
ScbHLH1 |
↓↓ |
|||||
|
SCCCRZ1001H05.g |
transcription factor |
HLH (helix-loop-helix) |
ScbHLH7 |
↑↑ |
↓↓ |
↓↓↓ |
↓↓↓ |
||
|
SCAGLR1021G10.g |
transcription factor |
homeobox |
ScHB2 |
↓↓ |
↓↓↓ |
↓↓↓ |
|||
|
SCRLAM1010D08.g |
transcription factor |
homeobox |
ScHB41 |
↓↓ |
|||||
|
SCEZLB1010E10.g |
transcription factor |
hormone-related/auxin |
ScABI40 |
↓ |
|||||
|
SCCCLR1024F10.g |
transcription factor |
hormone-related/auxin |
ScARF46 |
↓ |
|||||
|
SCCCRZ1001G10.g |
transcription factor |
hormone-related/Aux/IAA |
ScAUXI134 |
↓↓↓↓ |
↓↓ |
↓↓↓ |
↓↓↓ |
||
|
SCVPLR2005H03.g |
transcription factor |
hormone-related/Aux/IAA |
↓↓ |
||||||
|
SCJFRZ2009F04.g |
factor transcription |
hormone-related/Aux/IAA |
↓ |
||||||
|
SCJLLR1054C09.g |
transcription factor |
hormone-related/Aux/IAA |
↓↓ |
||||||
|
SCUTST3086B02.g |
transcription factor |
hormone-related/ethylene/AP2/ERE BP |
ScEREB59 |
↓ |
|||||
|
SCCCLR1001D10.g |
transcription factor |
hormone-related/ethylene/AP2/ERE BP |
DRE binding factor 2 |
↑ |
↑↑ |
||||
|
SCBGFL4052C11.g |
transcription factor |
hormone-related/ethylene |
ScEIL1 |
↓ |
|||||
|
SCCCRZ1004H12.g |
transcription factor |
hormone-related/ethylene |
ScEIL2 |
↓ |
↓ |
||||
|
SCCCRZ2C03D11.g |
transcription factor |
hormone-related/gibberellin |
ScGRAS71 |
↓↓ |
|||||
|
SCEPRZ1008F02.g |
transcription factor |
LIM (protein-protein interaction) |
↓ |
↓↓ |
|||||
|
SCQGLR1085G10.g |
transcription factor |
MADS |
ScMADS17 |
↑ |
↓↓ |
||||
|
SCSFAD1124E07.g |
transcription factor |
MYB |
ScMYB70 |
↑ |
|||||
|
SCRURT2010A10.g |
transcription factor |
MYB |
ScMYB120 |
↓ |
|||||
|
SCCCLR2003E10.g |
transcription factor |
NAM (no apical meristem) |
ScNAC27 |
↓↓ |
↓↓↓ |
↓↓↓ |
|||
|
SCRUAD1132D09.g |
transcription factor |
NAM (no apical meristem) |
ScNAC51 |
||||||
|
SCACLR1130H08.g |
transcription factor |
zinc finger protein |
ScYAB16 |
↓ |
|||||
|
SCEZST3147A10.g |
transcription factor |
zinc finger protein |
ScC3H84 |
↓ |
↓ |
||||
|
SCCCCL4003D08.g |
transcription factor |
zinc finger protein |
ScC3H95 |
↓ |
|||||
|
SCQGRZ3011D06.g |
transcription factor |
zinc finger protein/alfin-like |
ScALF9 |
↓ |
|||||
|
SCCCRZ1002E08.g |
stress |
drought and cold response |
Aquaporin (plasma membrane) |
↓ |
↓↓ |
||||
|
SCCCST3001H12.g |
stress |
drought and cold response |
Aquaporin (plasma membrane) |
↑ |
↓↓ |
||||
|
SCEQRT2100B02.g |
stress |
drought and cold response |
Aquaporin (plasma membrane) |
↑ |
↓↓ |
||||
|
SCCCLR1024C03.g |
stress |
drought and cold response |
Aquaporin (tonoplast intrinsic protein) |
↓ |
↓ |
||||
|
SCCCRZ1001F02.g |
stress |
drought and cold response |
Aquaporin (tonoplast intrinsic protein) |
↓ |
↓ |
||||
|
SCQGLR1085F11.g |
stress |
drought-induced |
Dehydrin |
↓ |
↓↓↓ |
↑↑ |
↓↓↓ |
↓↓↓ |
|
|
SCCCLR2C01F06.g |
stress |
wound-induced |
wound-responsive family protein |
↑↑↑ |
↑ |
↑↑↑ |
↑↑↑ |
||
|
|
|||||||||
|
The table also shows differential expression of the same SAS as seen in [31] for plants submitted to drought and ABA treatment. Differential expression refers to cDNA microarray analysis except for the last two columns, which refer to qRT-PCR data obtained in samples of plantlets treated with sucrose or glucose. The table lists a selection of SAS whose expression was enriched or decreased in two technical replicates for each biological sample. For a complete list see additional file 2. The up arrow indicates that the SAS is more expressed, the down arrow indicates that the SAS is less expressed. The number of arrows indicates the number of hybridizations. |
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|
Papini-Terzi et al. BMC Genomics 2009 10:120 doi:10.1186/1471-2164-10-120 |
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