Table of Contents:

Targetting Pathways: Manipulating Regulatory Genes

Role of Transcription Factors in the Activation of Stress Responsive Genes

A striking strategy for manipulation and gene regulation is the small group of transcription factors that have been identified to bind to promoter regulatory elements in genes that are regulated by abiotic stresses (Shinozaki and Yamaguchi-Shinozaki 1997; Winicov and Bastola 1997). The transcription factors activate cascades of genes that act together in enhancing tolerance towards multiple stresses.

Dozens of transcription factors are involved in the plant response to drought stress (Vincour and Altman 2005; Bartels and Sunkar 2005). Most of these falls into several large transcription factor families, such as AP2/ERF, bZIP, NAC, MYB, MYC, Cys2His2 zinc-finger and WRKY. Individual members of the same family often respond differently to various stress stimuli. On the other hand, some stress responsive genes may share the same transcription factors, as indicated by the significant overlap of the gene expression profiles that are induced in response to different stresses (Seki et al, 2001; Chen and Murata 2002). Transcriptional activation of stress-induced genes has been possible in transgenic plants over expressing one or more transcription factors that recognize promoter regulatory elements of these genes. Two families, bZIP and MYB, are involved in ABA signaling and its gene activation. Many ABA inducible genes share the (C/T) ACGTGGC consensus, cis-acting ABA-responsive element (ABRE) in their promoter regions (Guiltinan et al., 1990; Mundy et al., 1990). Introduction of transcription factors in the ABA signaling pathway can also be a mechanism of genetic improvement of plant stress tolerance. Constitutive expression of ABF3 or ABF4 demonstrated enhanced drought tolerance in Arabidopsis, with altered expression of ABA/stress-responsive genes, e.g. rd29B, rabl8, ABI1 and ABI2 (Kagaya et al., 2002). Several ABA-associated phenotypes, such as ABA hypersensitivity and sugar hypersensitivity, were obseived in such plants. Moreover, salt hypersensitivity was observed in ABF3- and ABF4-over expressing plants at the germination and young seedling stages indicating the possible participation of ABF3 and ABF4 in response tosalinityat these particular developmental stages. Improved osmotic stress tolerance in35S:At-MYC2/AtMYB2 transgenic plants as judged by an electrolyte-leakage test was reported by (Abebe et al., 2003). Transgenic Arabidopsis plants constitutively over-expressing a cold inducible transcription factor (CBF1; CRT/DRE binding protein) showed tolerance to freezing without any negative effect on the development and growth characteristics (Jaglo- Ottosen et al, 1998). Over expression of Arabidopsis CBF1 (CRT/DRE binding protein) has been shown to activate or homologous genes at non-acclimating temperatures (Jaglo et al., 2001). The CBF1 cDNA when introduced into tomato (Lycopersicon esculentum) under the control of a CaMV35S promoter improved tolerance to chilling, drought and salt str ess but exhibited dwarf phenotype and reduction in fruit set and seed number (Hsieh et al., 2002).

Another transcriptional regulator, Alfinl, when over expressed in transgenic alfalfa (Medicago sativa L.) plants regulated endogenous MsPRP2 (NaCl-inducible gene) mRNA levels, resulting in salinity tolerance, comparable, to a few available salt tolerant plants (Winicov and Bastola 1999). Lee et al. (1995) produced thermo- tolerant Arabidopsis plants by de-repressing the activity of ATHSF1, a heat shock transcription factor leading to the constitutive expression of heat shock proteins at normal temperature. Several stress induced cor genes such as rd29A, corl5A, kinl and согб.б are triggered in response to cold treatment, ABA and water deficit stress (ThomashoT998).

The promoters of stress responsive genes have typical cri-regulatory elements like DRE/CRT, ABRE, MYCRS/MYBRS and are regulated by various upstream transcriptional factors (Figure 4). These transcription factors fall in the category of early genes and are induced within minutes of stress. The transcriptional activation of some of the genes including RD29A has been well worked out. The promoter of this gene family contains both ABRE as well as DRE/ CRT elements (Stockinger and Gilmour, 1997). Transcription factors, which can bind to these elements were isolated and were found to belong to AP2/EREBP family and were designated as CBF1/ DREB1B, CBF2/DREB1C, and CBF3/DREB1A (Medina et al, 1999). These transcription factors (CBF1, 2 and 3) are cold responsive and in turn bind CRT/DRE elements and activate the transcription of various stress responsive genes. A novel transcription factor responsive to cold as well as ABA was isolated from soybean and termed as SCOF-1 (soybean zinc finger protein). This transcription factor, however, was not responsive to drought or salinity stress. SCOF1 was a zinc finger nuclear localized protein but failed to bind directly to either CRT/DRE or ABRE elements. Yeast 2-hybrid study revealed that SCOF-1 interacted strongly with SGBF-1 (Soybean G-box bind-ing bZip transcription factor) and hi vitro DNA binding activity of SGBF-1 to ABRE elements was greatly unproved by the presence of SCOF-1. This study supported that protein-protein interaction is essential for the activation of ABRE-mediated cold responsive genes. Transcription factors like DREB2A and DREB2B gets activated in response to dehydration and confer tolerance by induction of genes involved in maintaining the osmotic equilibrium of the cell (Liu et al, 1998). Several basic leucine zipper (bZip) transcription factors (namely ABF/AREB) have been isolated which can specifically bind to ABRE element and activate the expression of stress genes (Choi et al, 2000). These AREB genes (AREB1 and AREB2) are ABA responsive and need ABA for their frill activation. These transcription factors exhibited reduced activity in the ABA-deficient mutant aba2 as well as in ABA insensitive mutant aba 1-1. Some of the stress responsive genes for example RD22 lack the typical CRT/DRE elements in their promoter indicating their regulation by other mechanisms. Transcription factor RD22BP1 (a MYC transcription factor) and AtMYB2 (a MYB transcription factor) could bind MYCRS (MYC recognition sequence) and MYBRS (MYB recognition sequence) elements, respectively, and could cooperatively activate the expression of RD22 gene (Abe et al, 1997). As cold, salinity and drought stress ultimately impair the osmotic equilibrium of the cell it is likely that these transcription factors as well as the major stress genes may cross talk with each other for their maximal response and help in reinstating the normal physiology of the plant. ABA is an important phytohormone and plays a critical role in response to various stress signals. The application of ABA to plant mimics the effect of a stress condition. As many abiotic stresses ultimately results in desiccation of the cell and osmotic imbalance, there is an overlap in the expression pattern of stress genes after cold, drought, high salt or ABA application. This suggests that various stress signals and ABA share common elements in their signaling pathways and these common elements cross talk with each other, to maintain cellular homeostasis (Finkelstein et ah, 2002). Functions of ABA include: 1) ABA causes seed dormancy and delays its germination. 2) ABA promotes stomatal closure.

ABA levels are induced in response to various stress signals. ABA actually helps the seeds to surpass the stress conditions and germinate only when the conditions are conducive for seed germination and growth. ABA also pre-vents the precocious germination of premature embryos. Stomatal closure under drought conditions prevents the intracellular water loss and thus ABA is aptly called as a stress hormone. The main function of ABA seems to be the regulation of plant water balance and osmotic stress tolerance. Several ABA deWcient mutants namely abal, aba2 and aba3 have been reported for Arabidopsis (Koomneef et ah, 1998).

There have been numerous efforts in enhancing tolerance towards multiple stresses such as cold, drought and salt stress in crops other than the model plants like Ar abidopsis, tobacco and alfalfa. An increased tolerance to freezing and drought in Arabidopsis was achieved by over expressing CBF4, a close CBF/ DREB1 homolog whose expression is rapidly induced during drought stress and by ABA treatment, but not by cold (Haake et ah, 2002). Similarly, a cis-acting element, dehydration responsive element (DRE) identified in A. thaliana, is also involved in ABA-independent gene expression under drought, low temperature and high salt stress conditions in many dehydration responsive genes like rd29A that are responsible for dehydration and cold-induced gene expression (Yamaguchi-Shinozaki and Shinozaki 1993; Iwasaki et ah, 1997; Nordin et ah, 1991). Several cDNAs encoding the DRE binding proteins, DREB1A and DREB2A have been isolated from A. thaliana and shown to specifically bind and activate the transcription of genes containing DRE sequences(Liu et ah, 1998). DREBl/CBFs are thought to function in cold-responsive gene expression, whereas DREB2s are involved in drought-responsive gene expression. The transcriptional activation of stress-induced genes has been possible in transgenic plants over-expressing one or more transcription factors that recognize regulatory elements of these genes. In Arabidopsis, the transcription factor DREB1A specifically interacts with the DRE and induces expression of stress tolerance genes (Shinozaki and Yamaguchi- Shinozaki 1997). DREB1A cDNA under the control of CaMY 35S promoter in transgenic plants elicits strong constitutive expression of the stress inducible genes and brings about increased tolerance to freezing, salt and drought stresses (Liu et ah, 1998). Strong tolerance to freezing stress was observed in transgenic Arabidopsis plants that over express CBF1 (DREB1B) cDNA under the control of the CaMV 35S promoter (Jaglo-Ottosen et ah, 1998). Subsequently, the over expression of DREB1A has been shown to improve the drought and low- temperature stress tolerance in tobacco, wheat and groundnut (Kasuga et al.,

Gene	Gene Action	Species	Phenotype	Reference
ABF3	Transcription factor	Rice	Drought resistance	Oh et al., 2005
ABP9	ABRE binding protein9	Arabidopsis	Regulation of plant photosynthesis under stress	Zhang et al., 2008
ABP9	ABRE binding protein9	Arabidopsis	drought and salt stress tolerance	Zhang et al., 2011
AISAP	Transcription factor	Tobacco	Drought, salinity and freezing tolerance	Ben Saad et al., 2010
ALDH3I1 & ALDH7B4	Aldehyde dehydrogenase	Arabidopsis	Salt and dehydration stress tolerance	Kotchoni et al., 2006
ZmALDH22A1	Aldehyde dehydrogenase	Tobacco	Salt and dehydration tolerance	Huang et al., 2008
Alx8	High APX2 and ABA	Arabidopsis	Drought tolerance	Rossel et al., 2006
AnnAtl	Annexin synthesis	Arabidopsis	Drought tolerance	Konopka-Postupolska et al., 2009
AnnBjl	Annexin synthesis	Cotton	Salt and osmotic resistance	Divya et al., 2010
AP37	Transcription factor	Rice	Drought tolerance in yield	Oh et al., 2009
S\|AREB1	ABA-responsive element binding protein	Tomato	Salinity and drought tolerance	Orellana et al., 2010
ASR1	Undetermined	Tobacco	Decreased water loss; salt tolerance	Kalifa etal., 2004
HvCBF4	Induced expression of COR genes	Rice	Drought resistance	Lourengo et al., 2011
AtCML9	Transcription factor	Arabidopsis	Drought and salt tolerance	Magnan et al., 2008
AtCPK6	Calcium-dependent protein kinase	Arabidopsis	Salt and drought tolerance	Xu etal., 2010
OSCPK21	Calcium-dependent protein kinase	Rice	Salt tolerance	Asano et al., 2011
AtGSKI	Homologue of GSK3/ shaggy like protein kinase	Arabidopsis	Salt tolerance in plant and root growth	Piao et al.,2001

Gene	Gene Action	Species	Phenotype	Reference
ATHB6	Transcription factor	Tomato	Drought resistance	Mishra et al., 2012
AtMYB102	Chimeric repressors	Arabidopsis, rice	Salt tolerance	Mito et al., 2011
GhMT3a	Metallothionein synthesis and ROS scavenging	Tobacco	Drought, salt, cold tolerance	Xue et al., 2009
AtNOAl	Nitric Oxide synthesis	Arabidopsis	Salt tolerance	Zhao et al., 2007
AtNOAl	Nitric Oxide synthesis	Arabidopsis	Salt tolerance	Qiao et al., 2009
OsPR4	Transcription factor	rice	Drought resistance	Wang et al., 2011
AtRabG3e	Intracellular vesicle trafficking	Arabidopsis	Salt and osmotic stress tolerance	Mazel eta!., 2004
GhDi19-1 GhDi19-2	Cys2/His2-Type Zinc-Finger Proteins	Arabidopsis	Salt and ABA sensitivity	Li et al., 2010
AtSZFI& AtSZF2	CCCH-type zinc finger proteins, involved in salt stress responses	Arabidopsis	Salt tolerance	Sun et al., 2007
StZFPI	TFIIIA-type zinc finger protein	Tobacco	Salt tolerance	Tian et al., 2010
At-SR05	Antioxidative action	Arabidopsis	Salt tolerance	Rabajani et al., 2009
BnPtdlns-PLC2	Phosphatidylinositol-specific phospholipase C	Canola	Drought resistance, early flowering	Georges et al., 2009
CAbZIPI	Plant development (dwarf phenotype)	Arabidopsis	Drought and salt tolerance	Lee et al., 2006
AtbZIP17	Transcription factor	Arabidopsis	Salt tolerance	lu et al., 2008
BAX	BCL2-associated x protein as the pro-PCD factor	Tobacco	Drought, salt and heat tolerance	Isbat et al., 2009

Gene	Gene Action	Species	Phenotype	Reference
bZIP23	Transcription factor	Rice	ABA sensitivity, drought and salt tolerance Xiang et al., 2008
ZIP72	Transcription factor	Rice	ABA sensitivity and drought resistance	Lu et al., 2009
ThbZIPI	Transcription factor	Tobacco	Salt tolerance and antioxidant activity	Wang et al., 2010
CAP2	Transcription factor	Tobacco	Drought and salt tolerance	Shukla et al., 2006
CBF3	Transcription factor	Rice	Drought and salt resistance	Oh et al., 2005
CBF4	Transcription factor	Arabidopsis	Drought and freezing tolerance (via activation of C-repeat/dehydration responsive element)	Haake et al., 2002
CBL1	Ca sensing protein	Arabidopsis	Salt and drought tolerance & cold sensitivity	Cheong et al., 2003
CBL1	Ca sensing protein	Arabidopsis	Salt and drought resistance - reduced transpiration	Albrecht et al., 2003
CBL1	Ca sensing protein	Arabidopsis	Salt tolerance	Wang et al., 2007
CBP20	cap binding complex	Arabidopsis	Loss of function (recessive) induces drought resistance	Papp et al., 2004
CcHyPRP	A hybrid-proline-rich protein encoding gene	Arabidopsis	Heat, salt and osmotic resistance	Priyanka et al., 2010
CpMYBIO	Glucose sensitive and ABA hypersensitive	Arabidopsis	Desiccation and salinity tolerance	Villalobos et al., 2004
DREB	Transcription factor	Arabidopsis	Increased tolerance to cold, drought and salinity	Kasuga et al., 1999
DREB	Transcription factor	Arabidopsis	Saliity tolerance	Xu et al., 2009
CgDREBa	Transcription factor	Chrysanthemum	Drought and salinity tolerance	Chen et al.,
GhDREBI	Transcription factor	Arabidopsis	Salt and osmotic tolerance	Huang et al., 2009

Gene	Gene Action	Species	Phenotype	Reference
DREB1A	Transcription factor	Paspalum grass	Salinity and dehydration tolerance	James et al., 2008
DREB1 or OsDREBI	Transcription factor	Rice	Drought, salt and cold tolerance with reduced growth under non-stress	Ito et al., 2006
DREB1A	Transcription factor	Tobacco	Drought and cold tolerance	Kasuga et al., 2004
DREB1A	Transcription factor	Tobacco	Salinity tolerance and dwarfing	Cong et al., 2008
DREB1A	Transcription factor	wheat	Delayed wilting under drought stress	Pellegrineschi et al., 2004
DREB1A; DREB2ATranscription factor		Arabidopsis	Drought-cold tolerance	Maruyama et al., 2009
DREB2A	Transcription factor	Arabidopsis	Drought tolerance	Sakuma et al., 2006
DREB2	Transcription factor	Rice	Improve yield under limited water	Bihani et al., 2011
MbDREBI	Transcription factor	Arabidopsis	Drought and salt tolerance	Yang etal., 2011
SIDREB2	Transcription factor	Foxtail millet	Salinity and osmotic stress resistance	Lata et al., 2011
TaDREB2-3	Transcription factor	Wheat, barley	Drought and frost resistance	Morran et al., 2011
ERA1	Farnesyltransferase	Canola	When down regulated promotes drought tolerance	Wang et al., 2009
FAD3&FAD8	Increased fatty acid desaturation	Tobacco	Drought tolerance	Zhang et al., 2005
FLD	Flavodoxin overexpression	Medicago truncatula	Salinity tolerance	Pena et al., 2010
FTL1/DDF1	Transcription factor	Arabidopsis	Resistance to cold, drought and heat	Kang et al., 2011
LeGPAT	glycerol-3-phosphate acyltransferase of chloroplasts	Tomato	Salt tolerance	Sun et al., 2010

Gene	Gene Action	Species	Phenotype	Reference
GsCBRLK	Calcium/calmodulin -independent kinase	Arabidopsis	Salt and ABA tolerance	Yang etal., 2010
HAL1	Promote K+/Na+ selectivity	Tomato	Salt tolerance in growth and fruit production	Rus et al., 2001
HAL1	Promote K+/Na+ selectivity	Watermelon	Salt tolerance in growth	Ellul et al., 2003
HAL2	Promote K+/Na+ selectivity	Tomato	Salt tolerance in calli and rooting	Arrillaga et al., 1998
HAL I or HAL II	Promote K+/Na+ selectivity	Tomato	Salt tolerance	Safdar et al., 2011
Hardy	AP2/ERF (APETALA2/ ethylene responsive element binding factors) transcription factor	Clover	Drought and salt tolerance	Abogadallah etal., 2011
HOT2	Encode a chitinase-like protein	Arabidopsis	Salt tolerance	Kwon et al., 2007
Hrf1	Harpin protein	Rice	Drought tolerance via ABA signaling and antioxidants	Zhang et al., 2011
HvCBF4	Transcription factor	Rice	Drought, salt chilling tolerance	Oh et al., 2007
lnsP3	Human type lnositol-(1,4,5) -trisphosphate	Tomato	Drought resistance	Khodakovskaya etal., 2010
ITN1	Transcription factor	Arabidopsis	Salt tolerance	Sakamoto et al., 2008
GmERF3	Jasmonate and ethylene -responsive factor 3	Tobacco	Drought, salt and disease resistance	Zhang et al., 2009
JERF3	Jasmonate and ethylene -responsive factor 3	Tobacco	Salinity tolerance	Wang et al., 2004
SodERF3	Ethylene-responsive factor 3	Tobacco	Drought tolerance	Trujillo et al., 2008

Gene	Gene Action	Species	Phenotype	Reference
JERF1	Jasmonate and ethylene -responsive factor 1	Tobacco	Salinity tolerance	Zhang et al., 2004
JERF1	Jasmonate and ethylene- responsive factor 1	Tobacco	Salt and cold tolerance	Wu eta!., 2007
JERF1	Jasmonate and ethylene- responsive factor 1	Rice	Drought tolerance	Zhang et a!., 2010
JERF1	Jasmonate and ethylene- responsive factor 1	Wheat	Multiple stress tolerance	Xu eta!., 2007
JERF3	Jasmonate and ethylene- responsive factor 3	Tobacco	Drought, salt and freezing tolerance	Wu eta!., 2008
TSRF1	Ethylene-responsive factor 1	Rice	Drought tolerance	Quan et at., 2010
КАРР	Kinase-associated protein phosphatase	Arabidopsis	Salt (Na+) tolerance	Manabe et al., 2008
Iew2	Wilting allele; cellulose synthesis complex	Arabidopsis	Drought tolerance	Chen et al., 2005
LOS5	Regulates ABA biosynthesis	Tobacco	Drought tolerance	Yue et al., 2011
LOS5	Molybdenum cofactor sulfurase (Metabolism of abscisic acid)	Soybean	Drought tolerance	Lief al., 2013.
MCM6	Transcription factor	Tobacco	Salinity tolerance	Dang et al., 2011
NADP-ME2	NADP-malic enzyme	Arabidopsis	Salt tolerance	Liu et al., 2007
MH1	DNA helicase	Arabidopsis	Drought and salt tolerance due to antioxidative action	Luo et al., 2009
MKK9	MAP Kinase	Arabidopsis	Salt tolerance in germination	Alzwiya eta!., 2007

Gene	Gene Action	Species	Phenotype	Reference
GhMPK2	MAP Kinase	Tobacco	Salt and drought tolerance	Zhang et at., 2011
PtrMAPK	MAP Kinase	Tobacco	Drought tolerance	Huang et at., 2011
ZmMKK4	MAP Kinase	Arabidopsis	Salt and cold resistance	Kong et at., 2011
MsPRP2	Transcription factor	Alfalfa	Increased salinity tolerance	Winicov and Bastola 1999
GmNAC11; GmNAC20	Transcription factors	Arabidopsis	Salt and cold tolerance	Hao et at., 2011
NDPK1	Nucleoside diphosphate kinase 2	Potato	Multiple stress tolerance	Tang et at., 2008
NEK6	NIMA-related kinase	Arabidopsis	Salinity tolerance	Zhang et at., 2011
NFYB2	Transcription factor	Maize	Drought resistance	Nelson et at., 2007
NahG	Salicylate hydroxylase expression	Arabidopsis	Reduced leaf necrosis under salt stress	Borsani et at., 2001
NPK1	Mitogen-activated protein kinase	Maize	Drought resistance of photosynthesis	Shou et at., 2004
OSCDPK7	Transcription factor	Rice	Increased cold salinity and drought tolerance	Saijo et at., 2000
OsCIPKOI- OSCIPK30	Calcineurin В-like proteininteracting protein kinases	Rice	Salt and drought tolerance	Xiang et at., 2007
OSCIPK03	Calcineurin В-like proteininteracting protein kinase	Rice	Salt tolerance	Rao et at., 2011
CIPK6	Calcineurin В-like proteininteracting protein kinase	Tobacco	Salt tolerance	Tripathi et at., 2009

Gene	Gene Action	Species	Phenotype	Reference
OrbHLH2	helix-loop-helix (bHLH) ncoding gene	Arabidopsis	Salt and osmotic tolerance	Zhu et al., 2009
OsCOIN	RING finger protein	Rice	Cold, salt and drought tolerance and overexpression of P5CS	Liu et al., 2007
OCPI1	Transcription factor	Rice	Drought resistance in yield	Huang et at., 2007
ocp3	Transcription factor	Arabidopsis	Drought resistance	Ramirez et at., 2009
OPBP1	Transcription factor	Tobacco	Salinity and disease tolerance	Guo et at., 2004
OsSbp	Calvin cycle enzyme sedoheptulose-1, 7- bisphosphatase	Rice	Tolerance of photosynthesis to salt	Feng eta!., 2007
OsDREBIA	Transcription factor	Arabidopsis	Drought, salt, freezing tolerance	Dubouz et al., 2003
OSDREB2A	Transcription factor	Rice	Drought tolerance	Cui et a/.,2011
OSMYB3R-2	MYB homeodomain, and zinc finger proteins	Arabidopsis	Drought, salt, freezing tolerance	Dai et al., 2007
OsiSAP8	Stress/zinc finger protein	Rice	Salt drought and cold tolerance	Kanneganti and Gupta, 200
OsNAC5	Transcription factor	Rice	Salt tolerance	Song et al., 2011
OsNACIO	Transcription factor	Rice	Drought tolerance in the field	Jeong et al. 2010
PARP1; PARP2	Poly(ADP-ribose) polymerase	Arabidopsis; Brassica	Silencing induces drought and heat tolerance	Block et al., 2004
PDH45	DNA helicase 45	Pea	Salinity tolerance in yield	Sanan-Mishra et al., 2005; Sahoo et al., 2012

Gene	Gene Action	Species	Phenotype	Reference
PeSCL7	Transcription factor	Arabidopsis	Salt and drought tolerance	Ma et al., 2010
PLD	Phospholipase D	Arabidopsis	Salt tolerance	Bargmann et al., 2009
RGS1	Regulation of G-protein signalling	Arabidopsis	ABA mediated root elongation and drought tolerance	Chen et al., 2006
SCABP8	Interacts with SOS2	Arabidopsis	Salt tolerance	Quan et al., 2007
smGTP	Encode small guanosine triphosphate binding protein	Lolium temulentum	Salt & dehydration tolerance	Dombrowski et al., 2008
SINAGS1	Ornithine accumulation	Arabidopsis	Drought and salt tolerance	Kalamaki et al., 2009
SIZ1	SUMO E3 ligase	Arabidopsis	Salt tolerance	Miura et al., 2011
SIZ1	SUMO E3 ligase	Arabidopsis	Heat tolerance	Chen et al., 2011
SNAC1	Transcription factor	Rice	Drought and salt tolerance	Hu et al., 2006
TaSnRK2.7	Transcription factor	Arabidopsis	Multi-abiotic stress tolerance	Zhang et al., 2011
ONAC063	Transcription factor	Arabidopsis	Salt tolerance	Yokotani et al., 2009
SQE1	Squalene epoxidase enzyme	Arabidopsis	Root sterol biosynthesis and drought tolerance	Pose et al., 2009
OsRDCPI	Transcription factor	Rice	Drought tolerance	Bae et al., 2011
SRK2C	Protein kinase	Arabidopsis	Osmotic stress/drought tolerance	Umezawa et al.,2004
OsSDIRI	RING-finger containing E3 ligase	Rice	Drought tolerance	Gao et al., 2011
StMYB1R-1	MYB-Like Domain Transcription Factor	Potato	Drought tolerance via reduced water loss Shin eta!., 2011
STO	Protein binds to a Myb transcription factor	Arabidopsis	Salt tolerance	Ngaoka and Takano, 20

Gene	Gene Action	Species	Phenotype	Reference
Sto1	Reduced ABA accumulation	Arabidopsis	Better growth under salt stress	Ruggiero et al., 2004
TaABCI	Protein kinase	Arabidopsis	Drought salt and cold tolerance	Wang et at., 2011
TaCHP	Cysteine, histidine, and proline rich zinc finger protei	Arabidopsis	Promotion of CBF3 and DREB2A expression and salt tolerance	Li etal., 2010
TaPP2Ac-1	catalytic subunit (c) of protein phosphatase 2A	Tobacco	Drought resistance; maintain RWC and membrane stability	Xu etal., 2007
TaSTK	serine/threonine protein kinase	Wheat	Salt tolerance	Ge et a!., 2007
TaSrg6	Transcription factor	Arabidopsis	Drought tolerance	Tong et al., 2007
TERF1	ERF transcription activator	Tobacco	ABA sensitivity and drought tolerance	Zhang et al., 2005
ThlPK2	Inositol polyphosphate kinase	Brassica	Salt and drought tolerance	Zhu et al., 2009
Tsi1	Transcription factor	Tobacco	Increase osmotic stress tolerance	Park et al., 2001
VuNCEDI	Involved in ABA biosynthesis	Creepingbent grass	Salinity and drought tolerance	Aswath et al., 2005
WAB15	Transcription factor	Tobacco	Freezing, osmotic and salt tolerance	Kobayashi et al., 2008
WIN1/SHN1	Wax inducer	Arabidopsis	Epicuticular wax, stomata number and drought tolerance	Yang etal., 2011
GmWNKI	(With No Lysine K) serine- threonine kinase	Arabidopsis	Seedling salt tolerance	Wang et al., 2011
WRKY25 & WRKY33	Transcription factor	Arabidopsis	Salt tolerance	Jiang and Deyholos, 2009
WRKY45	Transcription factor	Arabidopsis	Drought resistance	Qiu and Yu, 2009
OSWRKY45	Transcription factor	Rice	Drought and cold resistance	Tao et al., 2011

Gene	Gene Action	Species	Phenotype	Reference
AtWRKY63	Transcription factor	Arabidopsis	ABA response and drought tolerance	Ren et al., 2010
WXP1	Epicuticular wax accumulation	Alfalfa	Drought resistance in maintained leaf water status and delayed wilting	Zhang et al., 2005
WXP1	Epicuticular wax accumulation	White clover	Drought resistance	Jiang et al., 2010
WXP1 ;WXP2	Epicuticular wax accumulation	Arabidopsis	Drought and freezing tolerance	Zhang et al., 2007
WRSI5	Protease inhibitors	Arabidopsis	Salt tolerance	Shan et al.,2008
	Protease inhibitors	Tobacco	Salt tolerance	Srinivasan et al., 2009
ZmDREB2A	Encodes HSP &LEA proteins	Arabidopsis	Drought and heat tolerance	Qin et al., 2007
ThZFL	zinc finger protein	Tobacco	Salinity tolerance	An eta!., 2011
MtZpt2	zinc finger protein	Medicao	Recover Root growth under salt stress	Merchan et al., 2007

Source: (www.plantstress.com1

Gene	Gene Action	Species	Phenotype	Reference
AIABCG36/ AtPDR8	ATP-binding cassette (ABC) transporter	Arabidopsis	Salt tolerance due to sodium exclusion	Kim et at., 2010
Atchx21	Putative Na+/H+ antiporter	Arabidopsis	Sodium concentrations in plant, root growth, plant size	Hall et ai, 2006
AtCNGCW	Plasma membrane cation transport	Arabidopsis	Salt tolerance	Guo et ai, 2008
AtCLC	Chloride channel	Arabidopsis	Salt tolerance	Jossier et ai, 2010
AtHKTI	Reduction in Sodium in root	Arabidopsis	Salt tolerance	Horie etai, 2006
AtHKTI	Sodium and Potassium transporter	cells	Reduced sodium accumulation	Sunarpi et ai, 2005
GmHKTI	Sodium and Potassium transporter	Tobacco	Salinity tolerance	Chen et ai, 2011
HKT2;1	Sodium and Potassium transporter	Barley	Salinity tolerance	Mian et at., 2011
AtMRP4	Stomatal guard cell plasma membrane ABCC-type ABC transporter,	Arabidopsis	Drought susceptibility due to loss of stomatal control	Markus et at., 2004
AtNHXI	Vacuolar Na⁺/H⁺ antiporter	Arabidopsis	Salt tolerance	Yokoi et ai, 2002
AtNHXI	Vacuolar Na⁺/H⁺ antiporter	Brassicanapus	Salt tolerance, growth, seed yield and seed oil quality	Zhang et at., 2001
AtNHXI	Vacuolar Na⁺/H⁺ antiporter	Buckwheat	Salt tolerance	Chen et at., 2008
AtNHXI	Vacuolar Na⁺/H⁺ antiporter	Cotton	Salt tolerance in photosynthesis and yield	He etai, 2005
AtNHXI	Vacuolar Na⁺/H⁺ antiporter	Tall fwscue	Salt tolerance	Zhao etai., 2007

Gene	Gene Action Species	Phenotype	Reference
AtNHXI	Vacuolar Na⁺/H⁺ antiporter Tomato	Salt tolerance, growth, fruit yield	Apse et al., 1999
AtNHXI	Vacuolar Na⁺/H⁺ antiporter Wheat	Salt tolerance for grain yield in the field	Xue et al., 2004
AtNHXI	Vacuolar Na⁺/H⁺ antiporter Sugar beet	Salt tolerance, sugar accumulation	Liu et al., 2008
LnNHX2	Vacuolar Na⁺/H⁺ antiporter Arabidopsis	K+ accumulation, salt tolerance	Rodriguez-Rosales eta!., 2008
AtNHX5	Vacuolar Na⁺/H⁺ antiporter Torenia	Salt tolerance	Shi et al., 2008
AtNHX5	Vacuolar Na⁺/H⁺ antiporter Paper Mulberry	Salt and drought resistance	Li eta!., 2011
AtNHX2 AtNHX5	Vacuolar Na⁺/H⁺ antiporter Arabidopsis	Salt tolerance	Yokoi et al., 2002
AVP1	Vacuolar H⁺-pyrophosphatase Arabidopsis (H⁺-PPase) gene	Salt tolerance in growth and sustained plant water status	Gaxiola et al., 2001
AVP1	Vacuolar H⁺-pyrophosphatase Alfalfa (H⁺-PPase) gene	Drought and salt tolerance	Bao et al., 2009
AVP1	Vacuolar H⁺-pyrophosphatase Agrostis (H⁺-PPase) gene stolonifera L	Salt tolerance	Li eta!., 2010
AVP1	Vacuolar H⁺-pyrophosphatase Cotton (H⁺-PPase) gene	Drought and salt resistance and yield in the field	Pasapula et al., 2011
MdVHPI	Vacuolar H⁺-pyrophosphatase Tomato (H⁺-PPase) gene	Drought and salinity resistance	Dong et al., 2011
AVP1 + PgNHXI	H⁺-PPase + Vacuolar Tomato Na⁺/H⁺ antiporter	Salinity tolerance	Bhaskaran & Savithramma 2011
TsVP	H⁺-PPase gene Cotton	Drought resistance (yield)	Lv et al., 2009
GhNHXI	Vacuolar Na⁺/H⁺ Arabidopsis antiporter (cotton)	Salt tolerance	Wu et al., 2004

Gene	Gene Action	Species	Phenotype	Reference
GmCAXI	Cation/proton antiporter	Arabidopsis	Salt tolerance	Luo et al., 2005
HKT1	Potassium transporter	Wheat	Salt tolerance in growth and improved K+/Na+ ratio	Laurie et al., 2002
NtAQPI	PIP1 plasma membrane aquaporin	Tobacco	High root hydraulic conductance and reduced plant water deficit under drought stress	Siefritz et al., 2002
OsARP	Antiporter-regulating protein	Tobacco	Salt tolerance by Na+ compartmentation	Uddin et al., 2006
OsNHXI	Vacuolar Na⁺/H⁺ antiporter	Rice	Salt tolerance	Fukuda et al., 2004
OsSOSI	Plasma membrane Na⁺/H⁺exchanger	Rice	Salt tolerance et at., 2007	Martinez-Atienza
SISOS1	Plasma membrane Na⁺/H⁺exchanger	Tomato	Salt tolerance	Olias et al., 2009
PcSrp	Serine rich protein (enhancing ion homeostasis?)	Finger millet	Salt tolerance	Mahalakshmi eta!., 2006
PgTIPI	Tonoplast intrinsic protein	Arabidopsis	Salt tolerance; root dependant drought tolerance	Peng et al., 2007
PpENA1	Plasma membrane Na⁺pumping ATPase	Rice	Salt tolerance	Jacobs et al., 2011
PIP1 (VfPIPI)	Plasma membrane aquaporin overexression	Arabidopsis	Faster growth, stomatal closure under drought stress	Cui et al., 2008
PIP1;4 & PIP2;5	Plasma membrane aquaporin overexression	Tobacco	Excessive water loss and retarded seedling growth under drought stress	Jang et al., 2007

Table Contd.

Gene	Gene Action	Species	Phenotype	Reference
TdPIP1;1 or TdPIP2;1	Plasma membrane aquaporin overexression	Tobacco	Salt and osmotic tolerance	Ayadi et al., 2011
SAT32	Enhanced vacuolar H⁺- pyrophosphatase (H⁺-PPase	Arabidopsis	Salt tolerance	Park et at., 2009
SITIP2;2	Tonoplast aquaporin	Tomato	Enhanced transpiration and f yield under drought and control	Sade et at., 2009
SOD2	Vacuolar Na⁺/H⁺ antiporter	Arabidopsis	Salt tolerance; higher plant K/Na ratio	Gao et at., 2004
SOD2	Vacuolar Na⁺/H⁺ antiporter	Rice	Salt tolerance	Zhao et at., 2006
SOS1	Na⁺/H⁺ antiporter	Arabidopsis	Protect K+ permeability during salt stress	Qi and Spalding, 2004
SOS3	Sodium accumulation in roots	Arabidopsis	Salt tolerance	Horie et at., 2006
SOS4	Involved in the synthesis of pyridoxal-5-phosphate which modulates ion transporters	Arabidopsis	Salt tolerance through Na+/K+ homeostasis	Shi et at.,2002
SsNHXI	Vacuolar Na⁺/H⁺ antiporter	Rice	Salt tolerance	Zhao et at., 2006
SsVP-2	Vacuolar Na⁺/H⁺ antiporter	Arabidopsis	Salt tolerance	Guo et at., 2006
TNHX1 and H+- PPase TVP1	Vacuolar Na⁺/H⁺ antiporter	Arabidopsis	Salt tolerance	Brini et at., 2007
TaVB	H⁺-ATPases (V-ATPase) subunit В	Arabidopsis	Salt tolerance	Wang et at., 2011
TsVP	Vacuolar Na⁺/H⁺ antiporter	Tobacco	Salt tolerance	Gao et at., 2006
TsVP	Vacuolar Na⁺/H⁺ antiporter	Cotton	Salt tolerance	Lv etal., 2008
YCF1	Sequester glutathione- chelates of heavy metals into vacuoles	Arabidopsis	Heavy metal and salt tolerance	Koh et at., 2006

Source: (www.plantstress.com)

2004; Pellegrineschi et al, 2004; Behnam et al., 2006; Bhatnagar-Mathur et al, 2004, 2006). The use of stress inducible rd29A promoter minimized the negative effects on plant growth in these crop species. However, over expression of DREB2 in transgenic plants did not improve stress tolerance, suggesting involvement of post-translational activation of DREB2 proteins (Liu et al, 1998). Recently, an active form of DREB2 was shown to trails activate target stress-inducible genes and improve drought tolerance in transgenic Arabidopsis (Sakuma et al., 2006). The DREB2 protein is expressed under normal growth conditions and activated by osmotic stress through post-translational modification in the early stages of the osmotic stress response. Another ABA-independent, stress-responsive and senescence-activated gene expression involves ERD gene, the promoter analysis of which further identified two different novel cis acting elements involved with dehydration stress induction and in dark-induced senescence (Simpson et al., 2003). Similarly, transgenic plants developed by expressing a drought-responsive AP2- type TF, SHNl-3orWXPl, induced several wax-related genes resulting hi enhanced cuticular wax accumulation and increased drought tolerance (Aharoni et al., 2004; Zhang et al., 2005). Thus, clearly, the over expression of some drought-responsive transcription factors can lead to the expression of downstream genes and the enhancement of abiotic stress tolerance in plants (see review, Zhang et al., 2004). The regulatory genes/factors reported so far not only playa significant role in drought and salinity stresses, but also in submergence tolerance. More recently, an ethylene response-factor-like gene SublA, one of the cluster of three genes at the Subl locus have been identified in rice and the over expression of SublA-1 in a submergence-intolerant variety conferred enhanced submergence tolerance to the plants (Xu et al.,2006),thus confirming the role of this gene in submergence tolerance in rice.