The WRKY Transcription Factor Family in Model Plants and Crops

Critical Reviews in Plant Sciences
ISSN: 0735-2689 (Print) 1549-7836 (Online) Journal homepage: http://www.tandfonline.com/loi/bpts20
The WRKY Transcription Factor Family in Model

Plants and Crops
Fei Chen, Yue Hu, Alessandro Vannozzi, Kangcheng Wu, Hanyang Cai, Yuan
Qin, Alison Mullis, Zhenguo Lin & Liangsheng Zhang
To cite this article: Fei Chen, Yue Hu, Alessandro Vannozzi, Kangcheng Wu, Hanyang
Cai, Yuan Qin, Alison Mullis, Zhenguo Lin & Liangsheng Zhang (2018): The WRKY
Transcription Factor Family in Model Plants and Crops, Critical Reviews in Plant Sciences, DOI:
10.1080/07352689.2018.1441103
To link to this article: https://doi.org/10.1080/07352689.2018.1441103
Published online: 05 Mar 2018.
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CRITICAL REVIEWS IN PLANT SCIENCES
https://doi.org/10.1080/07352689.2018.1441103
The WRKY Transcription Factor Family in Model Plants and Crops

Fei Chena, Yue Hua, Alessandro Vannozzib, Kangcheng Wua, Hanyang Caia, Yuan Qina, Alison Mullisc, Zhenguo Linc,
and Liangsheng Zhanga
a
State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; Key Laboratory of Ministry of Education for Genetics, Breeding and
Multiple Utilization of Crops; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology; Fujian Agriculture and Forestry
University, Fuzhou, China; bDepartment of Agronomy, Food, Natural Resources, Animals, and Environment (DAFNAE), University of Padova,
Legnaro, Italy; cDepartment of Biology, Saint Louis University, St Louis, Missouri, USA
ABSTRACT KEYWORDS
The WRKY gene family in flowering plants encodes a large group of transcription factors (TFs) that environmental stress; gene
play essential roles in diverse stress responses, developmental, and physiological processes. In this family; growth and
review, we provided a comprehensive screenshot about the studies on WRKY TFs in model plants development; transcription
and in crops of economical relevance. Specifically, we discussed the history of discovery and factor; WRKY
functional characterization, classification, and evolutionary history, 3D structure and physiological
functions of WRKY transcription factors. Based on the previous functional studies of WRKY genes in
model plants such as Arabidopsis and rice, we summarized various roles of WRKY TFs in a broad
range of biological processes as well as their degradation process. We also discussed the
characterization and functional studies of WRKY TFs in important crops. Considering the rapid
progress of high-throughput techniques, especially genomics and transcriptomics, which have been
instrumental in advancing our understanding of the crop genomes, we comment one-by-one on
the applications of a suite of new and high-throughput techniques to accelerate the studies of
WRKY genes in crops.
I. Studies on WRKY transcription factor family in families based on their DNA binding domains (Zhang
model plants et al., 2011). The WRKY gene family is the 7th largest TF
family in flowering plants following basic helix-loop-
A. A brief discovery history of the wrky genes
helix (bHLH), myeloblastosis (MYB), Ethylene respon-
Transcription factors (TFs) play essential roles in plants, sive factor (ERF), NAM (no apical meristem), ATAF1/2
as well as in all other living organisms, by controlling the and CUC2 (cup-shaped cotyledon) (NAC), basic leucine
expression of genes involved in various cellular processes Zipper (bZIP), and C2H2 families (Jin et al., 2014).
(Riechmann and Ratcliffe, 2000; Amor et al., 2004; Han WRKYs have attracted a lot of attention because they are
et al., 2014). TFs also play a central role in the process of involved in a broad range of biological processes, includ-
crop domestication and are targets of molecular breeding ing diverse biotic/abiotic stress responses, developmen-
of crops (Doebley et al., 2006; Century et al., 2008). For tal, and physiological processes (Birkenbihl et al., 2017b;
example, five of the six major genes controlling morpho- Jiang et al., 2017). The WRKY TFs are defined by the
logical and structural changes during crop domestication presence of a WRKY domain, a »60-residue DNA-bind-
are TFs (Doebley et al., 2006). The accumulation of ing domain containing a highly conserved heptapeptide
completely sequenced plant genomes and the develop- motif WRKYGQK. The first WRKY gene was identified
ment of bioinformatics tools have largely facilitated the in 1994 from eudicot crop sweet potato (Ipomoea bata-
identification, functional characterization, and evolu- tas), encoding a 549 amino acid protein called SPF1
tionary studies of TF families in plants. (SWEET POTATO FACTOR1) (Ishiguro and Naka-
Angiosperm genomes are predicted to contain more mura, 1994). The SPF1 protein binds to the promoter of
than 1,000 TF genes, which were classified into 58 two genes coding for sporamin (protease inhibitor) and
CONTACT Liangsheng Zhang fafuzhang@163.com State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; Key Laboratory of
Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology; Fujian
Agriculture and Forestry University, Fuzhou, China 350002; Zhenguo Lin zhenguo.lin@slu.edu Department of Biology, Saint Louis University, St Louis, MO
63103, USA.
Color versions of one or more of the figures in this article can be found online at www.tandfonline.com/bpts.
© 2018 Taylor & Francis
2 F. CHEN ET AL.
one beta-amylase gene in tuberous roots (Ishiguro and structure display (Li et al., 2017a). Various tools, such as
Nakamura, 1994). In 1995, two WRKY proteins, ABF1 Trinity (github.com/trinityrnaseq) and SOAPdenovo (Li
and ABF2, were isolated from a monocot plant wild oat, et al., 2010), are very popular in expressional quantifica-
Avena fatua. Both proteins have a zinc finger structure tion of WRKY genes. BLAST, Jbrowse, and complicated
(C-X4-5-C-X22-23-HXH) within the DNA binding search systems (such as Phytomine and Biomart) have
domain following the WRKYGQK sequence, and are been developed and integrated into comprehensive data-
involved in the regulation of seed germination (Rushton bases such as Phytozome (phytozome.jgi.doe.gov) and
et al., 1995). In 1996, three WRKY members, WRKY1, EsemblPlants (plants.ensembl.org). Many gene family-
WRKY2, and WRKY3 were identified in parsley (Petro- specific databases have also been constructed, including
selinum crispum). The three WRKY genes can be those for rice kinase genes (http://kinase.com/web/cur
induced by elicitors, and all the three WRKYs regulate rent/#) (Dardick et al., 2006) and the homeobox gene
ribosomal protein gene expression (Rushton et al., 1996). family (Zhong et al., 2008). However, a WKRY-specific
database is still not yet available. We believe that a
WKRY-specific database would facilitate the studies of
B. Updates of research tools
WKRY genes through providing access to the sequence,
The first WRKY gene was cloned by means of southwest- structure, expression patterns of WRKY genes, and
ern screening of the cDNA library (Ishiguro and Naka- related publications for WRKY genes.
mura, 1994). The same method was used to identify and
clone WRKY genes in the 1990s (Rushton et al., 1995;
C. Classification of the wrky gene family
Pater et al., 1996; Eulgem et al., 1999; Yang et al., 1999).
After completion of the first sequenced plant genome The current and widely accepted system of WRKY clas-
Arabidopsis thaliana, 68 WRKY genes were identified sification was established in 2000 based on the genomic
based on homology search using BLAST (Altschul et al., characterization of this gene family in Arabidopsis
1990; The Arabidopsis Genome Initiative, 2000). In (Eulgem et al., 2000). According to this classification,
another study, 75 WRKY genes were identified from the WRKY genes in plants were hitherto classified into the
Arabidopsis genome (Riechmann and Ratcliffe, 2000). In following three groups: I, II, and III based on the number
the rice genome, 83 WRKYs were identified using of WRKY domains and the features of their zinc-finger-
BLAST-based search (Goff et al., 2002). Protein homolog like motif (Eulgem et al., 2000), with group II WRKYs
searches have been greatly facilitated by (i) the develop- further divided into the following five subgroups: IIa,
ment of the hidden Markov model (HMM), (ii) the IIb, IIc, IId, and IIe based on their phylogenetic relation-
implementation of HMMER software (Eddy, 2009), and ships (Eulgem et al., 2000). Group I WRKY proteins har-
(iii) the availability of HMM seeds for various gene fami- bor two WRKY domains, whereas groups II and III
lies (Eddy, 1996), which were designed to increase the WRKY proteins contain only one WRKY domain.
sensitivity of homology searches. HMM method was first Group II and III WRKY proteins differed by the type of
employed to identify the WRKY genes in the rice zinc finger motif. The zinc finger motif in group II is
genome (Xie, 2005). The rapid accumulation of WRKY same as group I, which is C-X4-5-C-X22-23-H-X1-H,
gene sequences (6,320 sequences from 89 species) in the whereas the zinc finger in group III is C-X7-C-X23-H-
Pfam database (Finn et al., 2014) makes it possible to X1-C (Bakshi and Oelm€ uller, 2014). To illustrate evolu-
screen genomes for WRKY sequences by means of tionary relationships of WRKY proteins, we built a phy-
HMM-based searches without using BLAST or other logenetic tree based on members from four
computationally expensive bioinformatics tools. representative land plants, including Arabidopsis thali-
The implementation of other bioinformatics tools has ana, Vitis vinifera, Oryza sativa, and Selaginella moellen-
strongly accelerated researches on WRKYs. A plant tran- dorffii (Figure 1). The phylogenetic tree supports the
scription factor database, PlantTFDB, recorded 58 TF previous classifications. The groupings of WRKY genes
gene families from 165 plant species, including 14,549 are further supported by their conserved intron–exon
WRKY genes (Jin et al., 2017). An online database structures (Figure 1). Each of the subgroup or subfami-
(www.mpipz.mpg.de/20985/WRKY_References) has lies contains a characteristic intron insertion in the cod-
been developed reporting all the WRKY-related publica- ing region. A highly conserved phase-2 intron is present
tions. Phylogenetic tree reconstruction tool MEGA between the WRKYGQK motif and the zinc finger motif
(Tamura et al., 2013; Kumar et al., 2018) and multiple in the subfamily I’s C-terminal WRKY domain, and sub-
sequence alignment tools have been extensively used for family IIc, IIdCIIe, and III (Figure 1). In contrast, both
phylogenetic analyses. The Gene Structure Displayer subfamilies IIa and IIb contain the same conserved
Server (http://gsds.cbi.pku.edu.cn/) is useful for WRKY intron within the zinc finger motif (Zhang and Wang,
CRITICAL REVIEWS IN PLANT SCIENCES 3
Figure 1. Classification of land plant WRKY gene family. The phylogenetic tree was reconstructed using both near maximum-likelihood
(ML) and ML method based on the WRKY amino acid sequences from four representative land plants: A. thaliana, V. vinifera, Oryza sat-
iva, and S. moellendorffii. The WRKY gene family is classified into I, IIa, IIb, IIc, IId, IIe, and III subfamilies with evidence of tree topology
and conserved intron insertion patterns.
2005). This pattern suggests that the phase-2 intron D. Origin and diversification of WRKY genes
between WRKYGQK and the zinc finger motifs was
WRKY genes were initially believed to be plant-specific
probably present in the common ancestor of WRKY
(Eulgem et al., 2000). Sampling from broader taxonomic
family, but was subsequently lost in subfamilies IIa and
groups revealed that WRKY genes are also present in
IIb. Because both the split of IIa and IIb and split of IId
other eukaryotic lineages, such as fungi, Amoebozoa,
and IIe have occurred in the ancestor of land plants
diplomonads, and slime molds (Zhang and Wang, 2005;
(Zhang and Wang, 2005), much later than other groups,
Rinerson et al., 2015). Based on the distribution patterns
we thereby propose that IIa and IIb should be merged as
of WRKYs, it was speculated that nonplant WRKYs orig-
a single subfamily, and merge the IId and IIe subfamilies
inated from multiple ancient gene transfer events (Riner-
(Figure 1).
son et al., 2015). However, it seems large-scale sampling
Challenges are arising since rapid accumulation of
will be required to elucidate the gene transfer details.
genome sequencing data will lead to discovery of many
new members and even novel WRKY subfamily. For Zhang and Wang (2005) showed that only subfamily I
example, four Arabidopsis WRKYs have been found fused WRKYs are present in green algae, whereas subfamilies
with additional domains, (i) Leucine-rich repeat (LRR) IIaCIIb, IIc, and IIdCIIe evolved in the common ances-
domains at the N-terminal (At4G12020, At5g45050, tor of land plants, and subfamily III emerged in the com-
At5G45260), and (ii) BDP1 domain at the N-terminal mon ancestor of seed plants. Based on a larger number
(At1G55600). Although the tandem duplicated gene pair of sequences from more algal species and more detailed
At5g45050 and At5G45260 were grouped into the IIe sub- analyses, it was found that subfamily IId could be traced
family, phylogenetic places of At4G12020 and At1G55600 back to an ancestral sequence in Charophyte alga Kleb-
were uncertain (Figure 1). Recruitment of novel domains/ sormidium flaccidum (aka K. nitens) (Rinerson et al.,
genes will lead to the birth of novel subfamilies, such as the 2015). Also, subfamily III members were found in moss,
subfamily I with two WRKY domains. The future of but IIa were originated in seed plants. In the latter study,
WRKY classification will obviously be challenged in facing two alternative hypotheses regarding the evolution of the
the tremendous WRKYs from various plants. WRKY gene family were proposed (Rinerson et al.,
4 F. CHEN ET AL.
2015): (i) all WRKY genes were originated from Group I the N-terminus and at the C-terminus in the WRKY
C-terminal WRKY domains; (ii) subfamilies IIa and IIb domains (Figure 2A) (Eulgem et al., 2000). Some WRKY
evolved directly from an ancestral algal WRKY gene genes encode triple or tetrad WRKY domains in which
with a single domain that was separated from the sub- some are fused genes encoding novel domains such as
family I-derived lineage. ZF-SBP, CBS, kinase, PAH, ULP_PROTEASE, TIR,
The classification of the WRKY gene family is sup- NAC, LRR, ATP_GRASP, B3 (Figure 2A) (Mohanta
posed to change as far as a higher number of sequences et al., 2016). According to the current version of Pfam
from different organisms are considered. Currently, the database (Version 31), 69 domain architectures have
most comprehensive study of the WRKY gene family been identified based on 6320 WRKY proteins from 89
only includes 43 plant species and other eukaryotes species (http://pfam.xfam.org/family/PF03106#tabview
(Mohanta et al., 2016), without considering any species D tab1). Subfamily I of WRKY proteins contain two
from glaucophyta, rhodophyta, pteridophyta, chloro- WRKY domains. The C-terminal WRKY domain func-
phyta, and charophyta, which are important for evolu- tions in DNA binding, but the function of the N-termi-
tionary inferences. This study (Mohanta et al., 2016) nal WRKY domain remains unclear (Duan et al., 2007).
refreshed and challenged the current classification, intro- Only the C-terminal WRKY domain is present in the
ducing a differential classification of WRKYs in dicots members of subfamily II and III.
and monocots. However, such classification will proba- The WRKY domain includes a positively charged
bly change again as far as more genomes are be available. b strand that binds to the cis-acting element designed as
W-box (C/T)TGAC(C/T). In a genome-wide investigation,
W-box is the predominant binding motif for three
E. Structure of WRKY genes and proteins Arabidopsis WRKYs, namely WRKY18, WRKY33, and
Although WRKY proteins can greatly vary in size, all of WRKY40 (Birkenbihl et al., 2017a). W-box elements are
them harbor a conserved WRKY domain consisting of prevalent in plant genomes. For example, 32,162
two parts, the DNA-binding heptapeptide WRKYGQK, TTGACY, 60,612 TTGAC, and 14,857 TTTGACY were
and the zinc-finger binding motif. The two motifs identified in Arabidopsis. Recent work (Brand et al., 2013)
together span approximately 60 amino acids in length at suggests that the W-box has a degenerated/core TGAC
Figure 2. Domain structure of WRKY family and the working mechanism of a typical WRKY protein. (A) Representative domain organiza-
tions of WRKY proteins. (B) 3D structure of a WRKY protein and its binding to a W-box on the gene promoter.
motif, composed of an ultra-conserved GAC core and the sativa. Therefore, the roles of WRKYs in diverse cell sig-
upstream thymine and downstream pyrimidine (C/T). The naling and physiological processes discussed here are
GAC core interacts with the WRKY proteins whereas the based mainly on studies from the two model organisms.
flanking residues help dictate recognition by specific
WRKY factors. These motifs are widely found in genes 1. Abiotic stress
with various functions (Jiang et al., 2017). Multiple W-box Harsh environmental factors such as drought, flooding,
elements could form a cluster in promoter regions, for salinity, heat, low temperature, and strong ultraviolet
example, the barley WRKY38 requires two neighboring (UV) radiation, adversely affect the growth and develop-
W-boxes for efficient binding (Mare et al., 2004). ment of plants. It was projected that elevated global CO2
WRKY proteins also bind to non-W-box DNA cis ele- would also bring more unexpected abiotic stresses for
ments. For example, the WT-box (GGACTTTC) is plant growth (Feng et al., 2014). Therefore, it is impor-
required for binding of Arabidopsis WRKY26 and tant to study the molecular mechanism of abiotic stresses
WRKY41 (Kanofsky et al., 2017) and WRKY70 and to identify important genes responsible for stress-
(Machens et al., 2014). However, not all WT-box can be tolerance (Chen et al., 2013a). In plant cell signaling,
bound by WRKYs based on yeast one-hybrid screens WRKY TFs have been regarded as a jack of many trades
(Kanofsky et al., 2017). In rice, the OsWRKY13 protein (Bakshi and Oelm€ uller, 2014) from plant growth and
binds to both W-box and PRE4 element (Cai et al., various stress responses, providing an important basis
2008). NtWRKY12 from tobacco binds specifically to the for genetic improvement of crops.
WK box (TTTTCCAC) (van Verk et al., 2008). Future
chromatin immunoprecipitation (ChIP)-seq studies are Drought and salt stresses. Drought stress and salt stress
needed to unravel the diversity of sequences that are rec- both cause cellular dehydration and are key environmen-
ognized by WRKYs. tal factors influencing plant yield and spatial distribution
The three-dimensional (3D) structure of a TF is valu- (Bartels and Sunkar, 2005). At the molecular level,
able for studying its binding and activation mechanism. responses to drought and salt stresses usually share the
Currently, three 3D structure models related to Arabi- same signal transduction pathways, causing reactive oxy-
dopsis WRKY proteins are available in the PDB database gen species (ROS) and abscisic acid (ABA) accumulation
(www.rcsb.org), namely 1WJ2 and 2LEX for the C-ter- (Bartels and Sunkar, 2005; Miller et al., 2010). All
minal WRKY domain of AtWRKY1, 2AYD for the C- WRKY subfamilies have members involved in response
terminal WRKY domain of AtWRKY1. 2AYD has the to drought and salt stresses (Figure 3). AtWRKY18,

best resolution at 1.6 A. A typical WRKY domain com- AtWRKY40, and AtWRKY60, which are subfamily IIa/
prises five parallel b-strands (Figure 2B). The core IIb members, negatively regulate the transcription of
WRKYGQK motif locates on the second, and the outer- receptor-like kinase CRK5. AtWRKY18 and
most b-strand, enabling its interaction with the major AtWRKY40, but not AtWRKY60, directly bind to the
DNA groove. The WRKY domain is similar to the glial promoter of CRK5. Knock-out of all the three genes led
cell missing (GCM) and the NAC domains in terms of to the significantly increased expression of CRK5, but no
sequence and structure (Babu et al., 2006). The WRKY change of CRK5 expression was observed if only one or
and GCM domains share the zinc finger domain, but the two of them were knocked out, suggesting a close inter-
WRKY domain contains a conserved DNA-binding action between the three WRKY genes (Lu et al., 2016).
motif WRKYGQK. Several WRKY genes involved in the drought stress
Variants of the WRKYGQK motif have been found in response are ABA-dependent. In Arabidopsis, AtWRKY1
various plant lineages (Mohanta et al., 2016), including is involved in the stomatal closure via the regulation of
WRKYGEK, WRKYGKK, WSKYEQK, WRKYSEK. membrane transporters to maintain moisture (Qiao
Some variants have differences only in the WRKY pat- et al., 2016). Also, AtWRKY1 TF binds to the promoter
tern, such as WRRY, WSKY, WKRY, WVKY, WKKY, of MYB2, ABCG40, DREB1A, and ABI5, thus regulating
WRIC, WRMC, WIKY, and WKRY (Jiang et al., 2017). the drought response. AtWRKY1 knockout mutant
Because changes in WRKYGQK pattern could alter their showed a higher sensitivity to ABA and lower drought
DNA binding affinity, some of these variants might lack resistance than wild type, suggesting a negative regula-
DNA-binding affinity and even ability. tory role of AtWRKY1 in ABA signaling pathway of
guard cells (Qiao et al., 2016). Compared with wild-type,
the AtWRKY63 knockout mutant had decreased toler-
F. Functions and regulatory network of WRKYs
ance to drought stress (Ren et al., 2010). AtWRKY46,
WRKY genes have been extensively studied in the eudi- AtWRKY54, and AtWRKY70 all belong to the group III
cot model plant A. thaliana and monocot model plant O. and are engaged in BR signaling to regulate both growth
6 F. CHEN ET AL.
and osmotic stress (Chen et al., 2017). Drought leads to are involved in osmotic stress. Thus, the IIc members
high expression of ABA, which induces high expression may be the key TFs involved in response to drought and
of AtWRKY57 that binds to W-box in the promoter salt stress.
region of the downstream response genes (RD29A,
NCED3 are both VQ motif-containing genes). This acti- Temperature-induced stresses. Temperature changes
vates gene expression, resulting in a high seed germina- have broad effects on plant physiology. WRKY transcrip-
tion rate in drought environment (Jiang et al., 2012). In tion factors play an important role in the response to
addition, AtWRKY63 binds to the ABF2 promoter and temperature stress. AtWRKY25, AtWRKY26, and
activates expression of RD29A and COR47 (Ren et al., AtWRKY33 participated in heat-induced signal trans-
2010). duction. The heat shock transcription factors, HsfA2,
In rice, overexpression of OsWRKY30 dramatically HsfB1, heat shock protein 101 (Hsp101), and zinc finger
enhances drought resistance, which is a signal hub to protein 10 (Zat10), are the master regulators in the acti-
downstream of proteins OsMAK3, OsMPK4, OsMPK7, vation of transcriptional networks (Ohama et al., 2016).
OsMPK14, OsMPK20-4, and OsMPK20-5 (Shen et al., These proteins contained W-box sequences that were
2012). Drought-induced senescence could increase the recognized by the three WRKY proteins (Li et al., 2011).
expression level of OsWRKY80, which is putatively regu- AtWRKY39 is induced by heat stress, positively regulat-
lated by ABA (Ricachenevsky et al., 2010). OsWRKY47 ing the crosstalk of jasmonate (JA) and salicylic acid
binds to the W-box in the promoters of Cys Rich Repeat (SA) pathways that mediate the heat response (Jqw et al.,
Secretory Protein 55 Precursor and Calmodulin-Binding 2010). Under the control of the HSP101 promoter, over-
Protein. Knockout mutants of OsWRKY47 are highly expressing OsWRKY11 enhances heat and drought toler-
susceptible to drought and have reduced yield, whereas ance in transgenic rice seedlings (Wu et al., 2009).
mutants with overexpression of OsWRKY47 are more AtWRKY34, a pollen-specific gene, receives cold sig-
resistant to drought (Raineri et al., 2015). Furthermore, nals and transmits to the C-repeat/DRE-Binding Factor ,
OsWRKY45 was also found involved in ABA signaling effectively alleviating the pollen’s cold stress (Zou et al.,
and salt stress in rice (Tao et al., 2011). 2010). OsWRKY71 is controlled by hypothermia, which
Salt stress is another important negative factor of activates the expression of downstream genes OsTGFR,
plant growth and development. Salt stress usually produ- OsDREB1A, TPP1, and WSI76, thereby enhancing plant
ces ROS, which are one of the primary signal transduc- cold tolerance (Kim et al., 2016). In addition,
tion signals. AtWRKY8 is highly expressed in plant roots OsWRKY76 leads to the increased expression of abiotic
and is significantly upregulated under salt stress. The stress-associated genes such as peroxidase and lipid
knockout mutant of AtWRKY8 is more sensitive to salt metabolism genes to alleviate cold stress (Yokotani et al.,
with seed germination and subsequent inhibited growth. 2013).
AtWRKY8 regulates NaC / KC balance by binding to a
VQ motif in the promoter of RD29A (Chen et al., 2010; Waterlogging stress. WRKY transcription factors were
Hu et al., 2013). AtWRKY28 acts synergistically with involved in the response of waterlogging stress. The
AtHBH17 (AtAIB), a member of the bHLH family, to expression of AtWRKY22 was rapidly and strongly
increase tolerance to salt stress and oxidative stress in induced upon submergence (Hsu et al., 2013).
the presence of high salt concentrations. Under the high AtWRKY22 protein binds to TRE1’s promoter and
mannitol concentration, AtWRKY28 causes the plant represses its expression, affecting the plant’s resistance to
roots to elongate, and effectively enhances plant toler- flooding by influencing plant stomatal activity. In addi-
ance to drought stress (Babitha et al., 2013; Chen et al., tion, AtWRKY22 also regulates the expression of
2013b). Another WRKY family member, AtWRKY75, is MYB15, PUB24, and ACS7, which are related to the plant
also found involved in the response of plants to salt stress immune response (Cai et al., 2013). Thus, waterlogging
(Chen et al., 2013b; Hossain et al., 2016). AtWRKY15 is induced the expression of AtWRKY22 that triggered the
induced by ROS. The increased expression of immune response in Arabidopsis, and contributed to
AtWRKY15 makes Arabidopsis more susceptible to plant resistance to pathogen infection during waterlog-
osmotic stress and oxidative stress (Vanderauwera et al., ging (Hsu et al., 2013).
2012). OsWRKY30 and OsWRKY72 from subfamily III
are activated by ROS, and overexpression of them makes Ultraviolet stress. Visible light is an essential factor for
plants more susceptible to salt stress (Yu et al., 2010; plant growth, whereas the relationship between UV and
Scarpeci et al., 2013). In general, as shown in Figure 3, plant growth and development is still insufficient. UV-B
five members of the IIc population (AtWRKY57, is a wavelength of 280–315 nm moderate wavelength UV
AtWRKY28, AtWRKY8, AtWRKY75, and OsWRKY72) light that may damage DNA bases. Overexpression of
Figure 3. WRKYs in plant abiotic stress signaling network. References were mentioned in the main text.
OsWRKY89 significantly increased the resistance of subfamilies of WRKYs have been found to be involved in
plants to UV-B (Wang et al., 2007). However, whether the microbe-associated molecular pattern-triggered
or not other WRKYs are involved in response to UV- immunity, PAMP-triggered immunity, effector-triggered
induced stress or how WRKYs regulate UV-induced sig- immunity, or system acquired resistance (SAR).
nal transduction remains to be elucidated. AtWRKY33 and AtWRKY25 proteins (members of
In summary, molecular studies have identified many subfamily I) bind to the activated MKS1p. This pathway
WRKY genes that are involved in various abiotic stress is required for both repression of SA-dependent resis-
responses. However, there is a need in the future for tance as well as activation of JA-dependent defense
more extensive field studies of WRKY genes to test the (Andreasson et al., 2005). AtWRKY3 enhances the resis-
applications of these genes in agriculture. tance to the necrotrophic pathogen, whereas AtWRKY4
enhances the resistance to both necrotrophic pathogen
2. Biotic stress and biotrophic pathogen. Overexpression of AtWRKY3
WRKYs are known to play important roles in plant and AtWRKY4 inhibit pathogen-induced PR1 (Lai et al.,
immune responses to various biotic stresses. Summa- 2008). OsWRKY3 is light-dependent and binds to the
rized from various publications, members from all upstream sequence of OsNPR1 and is involved in
8 F. CHEN ET AL.
immune regulation through SA or JA-induced immune immune response by increasing the susceptibility of
signaling cascade systems. Overexpression of OsWRKY3 plants to Botrytis cinerea. AtWRKY57 competes with
upregulated OsPR1b, phenylalanine ammonialyase ZB8 AtWRKY33 for binding to the promoters of SIGMA
and peroxidase POX22.3 (Liu et al., 2005). OsWRKY71 is FACTOR BINDING PROTEIN1 (SIB1), SIB2, JASMO-
upregulated by SA, methyl jasmonate (MeJA), and path- NATE ZIM-DOMAIN 1 (JAZ1), and JAZ5, thus affecting
ogen infection. OsWRKY71 overexpression mutant the JA-mediated defense signal pathway (Jiang and Yu,
showed enhanced resistance to Xanthomonas oryzae 2016). Overexpression of OsWRKY13 enhances the resis-
(Xoo), and OsPR1b and OsNPR1were also upregulated in tance of rice to bacterial blight and rice blast. OsWRKY13
the mutant, indicating that they may be regulated by plays a negative regulatory role in the JA-induced
OsWRKY71 (Liu et al., 2007). defense signaling pathway, and plays a positive role in
Ten WRKY genes of subfamily IIc are involved in the SA-induced defense signaling pathway (Qiu et al.,
plant immunity (Figure 4). AtWRKY28 and AtWRKY75 2007). OsWRKY89 could be induced by MeJA to
are detected to be upregulated by oxalic acid and Scleroti- enhance the resistance to Magnaporthe grisea and Soga-
nia sclerotiorum infection using microarray screening. tella furcifera (Wang et al., 2007).
These genes are TFs involved in SA and JA/ET-depen- In Arabidopsis and rice, ten members from the IIa-
dent defense signaling pathways, suggesting that CIIb group are involved in the plant immune response
AtWRKY28 and AtWRKY75 may enhance plant resis- (Figure 4). AtWRKY18, AtWRKY40, and AtWRKY60 are
tance to oxalic acid and fungal infection through the JA/ partially functionally redundant. In the AtWRKY18 and
ET pathway (Chen et al., 2013b). In the AtWRKY48 AtWRKY40 double knockout mutant, a series of
overexpression mutant, the expression of PR1 is downre- immune-related genes such as camalexin are detected
gulated, indicating that AtWRKY48 could regulate plant and showed higher tolerance to the powdery mildew
immunity by negative regulation of Pathogenesis-Related organism, Golovinomyces orontii (Sch€on et al., 2013). In
(PR) genes (Xing et al., 2008). In the AtWRKY50 and vitro experiments, AtWRKY40 regulates immune
AtWRKY51 double knockout mutant, both the SA con- responses through binding to the promoter of
tent and the JA pathway-related PDF1.2 gene expression ENHANCED DISEASE SUSCEPTIBILITY1, AP2-type
levels are reduced, suggesting that AtWRKY50 and TF redox-responsive transcription factor 1, and a JA-sig-
AtWRKY51 mediate SA- and low-oleic acid-dependent naling repressor gene JAZ8 (Pandey et al., 2010). Overex-
repression of JA signaling (Gao et al., 2011). AtWRKY57 pression of AtWRKY18-AtWRKY40 and AtWRKY18-
also plays a regulatory role in the process of plant AtWRKY60 leads to a higher susceptibility to
Figure 4. WRKYs in plant abiotic stress signaling network.

Pseudomonas syringae and Botrytis cinerea, suggesting which it binds (Sarris et al., 2015). The flagellin
that they have functional or physical interactions in the receptor FLS2 is a LRR receptor kinase. It activates
regulation of plant immunity, and this effect is mediated the Mitogen-activated protein kinase (MAPK) signal-
by regulation of the JA and SA pathways (Xu et al., ing cascade and thereby activates the AtWRKY22 and
2006). The AtWRKY6 knockdown mutant has a greater AtWRKY29, involved in regulating the immune
leaf infection area than the wild type, suggesting that responses to bacteria and fungi (Asai et al., 2002).
AtWRKY6 might be involved in the regulation in a spe- Knockout experiments showed that AtWRKY11 and
cific cell layer in the region surrounding the infected area AtWRKY17 are partially functionally redundant. The
(Robatzek and Somssich, 2002). AtWRKY61 enhances double knockout mutant of AtWRKY11 and
plant resistance to Turnip Crimp Virus, and AtWRKY61 AtWRKY17, genes activated by the JA signaling path-
may have similar regulatory effects on SAR and PR gene way, is more resistant to P. syringae than any of the
regulation (Gao et al., 2016). AtWRKY72 has a positive single knockout mutants (Journot-Catalino et al.,
regulatory effect on the induction of root-knot nema- 2006). AtWRKY7 plays a negative regulatory role in
tode, Meloidogyne species and the downy mildew, Hya- the immunization of P. syringae infection and is upre-
loperonospora arabidopsidis. This process is not related gulated by SA induction. Expression of the PR1 gene
to the SA signaling pathway, but may be related to the regulated by SA is increased in the knockout mutant,
expression of R gene Mi-1 (Bhattarai et al., 2010). whereas in the overexpressed mutant PR-related gene
OsWRKY62 and OsWRKY76 proteins form homo- expression it is significantly lower, suggesting that
dimers and heterodimers, and overexpression of the two PR1 may be the target of AtWRKY7 (Kim et al.,
genes increases susceptibility to Magnaporthe oryzae and 2006). OsMKK4 activates OsMPK3/OsMPK6, then the
Xoo. In the double-knockout mutant of OsWRKY62 and latter recognizes SP cluster located in OsWRKY53.
OsWRKY76, phytoalexin and the expression levels of Plants overexpressing phosphorylated OsWRKY53
many resistance genes increases, suggesting that the two show higher resistance to rice blast than plants over-
genes have a negative regulatiory effect on plant disease expressing unphosphorylated OsWRKY53 itself, indi-
resistance (Liu et al., 2016). Overexpression of cating that the modified status of the WRKY gene is
OsWRKY28 could enhance the susceptibility of M. ory- responsible for its function (Chujo et al., 2014). By
zae to rice blast, and OsWRKY28 could negatively regu- binding to the cis-element W-box and WLE1 on the
late the resistance gene to maintain the dynamic balance promoter of the defense gene OsPR10a, OsWRKY51
(Chujo et al., 2013). OsWRKY22 is found to be involved enhances plant resistance to Xoo by activating the
in defense of M. oryzae, M. grisea, and Blumeria grami- expression of this gene (Hwang et al., 2016). In addi-
nis. Interestingly, OsWRKY22 does not show any interaction, OsWRKY51 has a negative regulatory role in the
tion with other OsWRKYs in coregulatory assays, GA signaling pathway (Zhang et al., 2009).
suggesting that this gene may have a unique role in plant OsWRKY31 could be induced by M. grisea, and lots
defense (Abbruscato et al., 2012). of defense genes such as PBZ1 and OsSci2 could be
Eleven members of IIdCIIe subfamily are involved upregulated in the overexpression mutant of
in immune regulation (Figure 4). AtWRKY27 has a OsWRKY31. At the same time, the sensitivity of this
negative effect on plant immunity, and its knockout mutant to indolebutyric acid (IBA), 1-naphthaleneace-
mutant shows symptoms of Ralstonia solanacearum tic acid (NAA), and 2,4-D decreased, indicating that
infection. The expression levels of Nitrate Reductase 2 OsWRKY31 may be involved in multiple signal trans-
(NR2/NIA2) and Asparagine Synthase 2 (ASN2) duction systems (Zhang et al., 2008). OsWRKY68
increase in the AtWRKY27 mutant. As the promoter binds to the W-boxes of the PR1b promoter region
region of these two genes contains W-box, they may and, by activating the gene, participates in Xa21-regu-
be regulated by AtWRKY27 (Mukhtar et al., 2008). lated Xoo-related resistance expression (Shuo et al.,
AtWRKY52 (aka Resistance to Ralstonia solanacearum 2016).
1, RRS1) is a receptor of the nucleotide-binding, LRR Nine WRKYs have been reported to participate in
(NB-LRR). AtWRKY52 interacts with resistance gene the immune response to subfamily III, including five
RPS4 (Resistance to Pseudomonas syringae 4, a mem- AtWRKYs and four OsWRKYs (Figure 4). AtWRKY38
ber of NB-LRR), bacterial response factors AvrRps4 and AtWRKY62 are induced by P. syringae or SA; they
and PopP2 to form complexes to coactivate immune then negatively control the expression of the defense
response. AvrRps4 and PopP2 bind directly to the gene Nonexpressor of PR Gene1 (NPR1). In a single
WRKY motif of AtWRKY52. AtWRKY52 together WRKY knockout mutant, the expression of the PR1
with RPS4 form a bait region that allows the bacterial and disease resistance are both enhanced and to a
effector to more easily detect the WRKY motif to greater extent in the double knockout mutants.
10 F. CHEN ET AL.
AtWRKY38 and AtWRKY62 interact with Histone have evolved the functions in plant immunity, and (ii) a
Deacetylase 19, which plays a positive role in plant dosage of WRKYs is a critical element for the environ-
immunity and inhibits the activity of AtWRKY38 and mental adaptation of plants.
AtWRKY62 (Kc et al., 2008). In general, AtWRKY38
and AtWRKY62 play negative roles in plant defense. 3. Growth and development
AtWRKY46, AtWRKY53, and AtWRKY70 are function- The WRKY genes are involved in a wide-range of plant
ally redundant and play a synergistic role in the growth and developmental processes (Table 1). Six Ara-
immune process. AtWRKY46 can be induced by SA bidopsis WRKY genes and one rice WRKY gene have
and P. syringae. AtWRKY46-AtWRKY53 or been reported to participate in the process of seed growth
AtWRKY46-AtWRKY70 double-knockout mutants, as and maturation (Table 1). AtWRKY28 participates in the
well as AtWRKY46-AtWRKY53-AtWRKY70 three-gene megasporocyte cell fate (Zhao et al., 2017). AtWRKY2
knockout mutants increase sensitivity to P. syringae, and AtWRKY34 are redundantly involved in pollen for-
and show lower PR1 gene expression. The expression mation, pollen tube elongation, seed germination, and
profiles show that AtWRKY46, AtWRKY53, and early growth after germination. AtWRKY2 knockout
AtWRKY70 may play a role in SA signaling pathway mutant showed high sensitivity to ABA, suggesting that
(Hu et al., 2012). In rice, OsWRKY4 and OsWRKY45 AtWRKY2 regulates seed germination (Jiang and Yu,
are involved in controlling rice sheath blight resistance. 2009). In the AtMPK3-AtMPK6 double knockout
The OsWRKY4 expression level is rapidly upregulated mutant, AtWRKY34 cannot be phosphorylated; thereby,
in plants infected with the fungal pathogen Rhizoctonia its function is inhibited (Guan et al., 2014). The homozy-
solani. Additional experiments show that overexpres- gous AtWRKY10 (also called as MINISEED3, MINI3)
sion of OsWRKY4 increases the resistance of plants to knockout mutants have a smaller seed size, are slower in
R.a solani infection. In the overexpression mutants, the development, and have early cellularization of the endo-
expression levels of the resistance genes PR1a, PR1b, sperm (Luo et al., 2005). The OsWRKY78 knockout
PR5, and PR10/PBZ1 are enhanced. As these down- mutant showed semidwarf and small kernel phenotype
stream genes are involved in JA and ET-mediated and produced smaller seeds, suggesting that OsWRKY78
response pathway, OsWRKY4 may regulate JA and ET plays an important role in stem elongation and seed
signaling pathway in immune regulation. Furthermore, development regulator in rice (Zhang et al., 2011). The
W-box and TG-like (TGAC [C/T]) cis-elements are AtWRKY41 protein binds to three adjacent W-boxes in
found in the promoter regions of PR1b and PR5, sug- the promoter of the ABSCISIC ACID INSENSITIVE 3
gesting that they may be target genes for OsWRKY4 (ABI3). Knockout of AtWRKY41 m significantly down-
(Wang et al., 2015). OsWRKY45-1 (from japonica) and regulated ABI3 and influenced the seed dormancy (Ding
OsWRKY45-2 (from indica) are two alleles of et al., 2014).
OsWRKY45, and they have opposite effects in plant In addition to regulation of seed growth, the WRKY
immunoregulation. OsWRKY45-1 and OsWRKY45-2 genes are involved in regulation of seed coloration
have negative and positive regulatory effects on the (Table 1). AtWRKY44 (also known as transparent testa
infection of Xoo and Xoo pv oryzicola (Xoc), respec- glabra, TTG2) regulates the epidermal color of Arabidop-
tively. The expression of OsWRKY45-1 could lead to sis seeds by participating in transcriptional regulation.
the increase of JA and SA content in tissues and AtWRKY44 binds directly to the upstream regulatory
defense-related genes. In plants overexpressing region of TT12. TTG1, TT2, and TT8 are involved in the
OsWRKY45-2, the expression of JA is also upregulated, biosynthesis of proanthocyanidins in Arabidopsis and the
while the expression of SA is downregulated, accompa- pigmentation, thus, making Arabidopsis seeds brown-col-
nied by the increased expression of downstream defense ored skin (Gonzalez et al., 2016; Johnson et al., 2002).
genes. In addition, overexpression of both WRKYs can The WRKY genes are also involved in plant root
enhance plant resistance to M. grisea (Tao et al., 2009; development (Table 1). Auxin induces the expression of
Cheng et al., 2015). OsWRKY77 could regulate the AtWRKY23, AUXIN RESPONSE FACTOR7 (ARF7), and
expression level of PR1, PR2, and PR5 in rice, and thus ARF19, serving as part of the auxin feedback loop, to reg-
enhance the resistance of plants to P. syringae (Lan ulate the proper growth of plant roots and the local syn-
et al., 2013). Overexpression of OsWRKY23 activates a thesis of flavonoids (Grunewald et al., 2012). AtWRKY44
series of PR genes, thereby increasing plant resistance and AtWRKY75 both regulate the development of root
to P. syringae (Jing et al., 2009). hairs. AtWRKY44 is the downstream gene of TTG1 and
In summary, each subfamily of WRKY has been GLABROUS1. It expresses continuously in the root hairs
shown to be involved in the biotic stress response, sug- and can cooperate with GLABRA2 to control the growth
gesting that (i) the ancestor of WRKYs might already of root hairs on plants (Johnson et al., 2002). In the
Table 1. WRKY as key regulators in plant growth and development.

Name Gene Locus ID Function References
AtWRKY28 At4G18170 Ovule development Zhao et al., 2017

AtWRKY2 AT5G56270 Seed germination, postgermination growth Jiang et al., 2009
AtWRKY10 AT1G55600 Seed size Luo et al., 2005
AtWRKY34 AT4G26440 Seed germination, postgermination growth Guan et al., 2014
AtWRKY41 AT4G11070 Seed dormancy Ding et al., 2014
AtWRKY44 AT2G37260 Seed coat tannins in the proanthocy Gonzalez et al., 2016
OsWRKY78 LOC_Os01g54600 Seed development; stem elongation Zhang et al., 2011 Planta
AtWRKY23 AT2G47260 Root growth; biosynthesis of flavonols Grunewald et al., 2011
AtWRKY44 AT2G37260 Root hair growth Verweij et al., 2016
AtWRKY75 AT5G13080 Root hair growth Devaiah et al., 2007
OsWRKY31 LOC_Os06g30860 Root formation and elongation Zhang et al., 2008
AtWRKY75 AT5G13080 Leaf senescence Li et al., 2012
AtWRKY6 AT1G62300 Leaf senescence Robatzek et al., 2016
AtWRKY54 AT2G40750 Leaf senescence Besseau et al., 2012
AtWRKY70 AT3G56400 Leaf senescence Besseau et al., 2012
AtWRKY53 AT4G23810 Leaf senescence Zentgraf et al., 2009; Miao and
Zentgraf, 2010
AtWRKY57 AT1G69310 Leaf senescence Jiang et al., 2014
AtWRKY22 AT4G01250 Leaf senescence Zhou et al., 2011
AtWRKY26 AT5G07100 Leaf senescence Li et al., 2017
OsWRKY42 LOC_Os05g46020 Leaf senescence Liu et al., 2016
OsWRKY23 LOC_Os01g53260 Leaf senescence Jing et al., 2009
OsWRKY80 LOC_Os09g30400 Leaf senescence Ricachenevsky et al., 2010
OsWRKY14 LOC_Os01g53040 Leaf senescence Kang et al., 2011
AtWRKY12 AT2G44745 Flowering time Li et al., 2016
AtWRKY13 AT4G39410 Flowering time Li et al., 2016
AtWRKY71 AT1G29860 Flowering time Yu et al., 2016
OsWRKY11 LOC_Os01g43650 Flowering time; plant height Cai et al., 2014
AtWRKY45 AT3G01970 Phosphate uptake Wang et al., 2014
AtWRKY42 AT4G04450 Phosphate uptake Su et al., 2015
AtWRKY75 AT5G13080 Phosphate uptake Devaiah et al., 2007
AtWRKY6 AT1G62300 Phosphate uptake; Boron uptake Chen et al., 2009; Kawajima et al.,
2010
OsWRKY74 LOC_Os09g16510 Phosphate uptake Dai et al., 2016
AtWRKY75 knockout mutant, the number and length of crosstalk of JA and auxin, and mediates the leaf senes-
the root hairs show an increase compared with the wild- cence (Jiang et al., 2014). AtWRKY22 is promoted by
type, suggesting that AtWRKY75 is a negative regulator darkness and suppressed by light and involved in dark-
of root hair development (Devaiah et al., 2007). ness-induced leaf senescence (Zhou et al., 2011).
OsWRKY31 was also found induced by auxin. Compared AtWRKY26 is also a positive regulator of leaf senescence
with the wild-type, plant lateral root formation and elon- (Li et al., 2017b). In rice, OsWRKY14 is involved in
gation are inhibited in the OsWRKY31 overexpression methanol-induced tryptophan biosynthesis as well as
mutant. This mutant also shows tolerance to high con- tryptophan-induced secondary metabolites (Kang et al.,
centrations of plant growth regulators IBA, NAA, and 2011). Overexpression of OsWRKY23 could accelerate
2,4-D, suggesting that overexpression of OsWRKY31 leaf senescence under dark induction (Jing et al., 2009).
may affect the transport process of auxin (Zhang et al., Using an overexpression mutant, OsWRKY42 shows
2008). early leaf senescence, accumulation of ROS, and
Twelve WRKY genes from rice and Arabidopsis have decreased chlorophyll content (Han et al., 2014).
been reported to participate in senescence (Table 1). OsWRKY80 showed a high level of expression in dark-
AtWRKY6 binds to a receptor-like kinase Senescence- induced senescent plant leaves, which was induced by 6-
induced receptor-like serine/threonine-protein kinase and Benzylaminopurine and ABA, suggesting that it is a typi-
regulates the leaf senescence process (Robatzek and cal senescence-related gene (Ricachenevsky et al., 2010).
Somssich, 2002). AtWRKY75 mutant showed leaf senes- Control of flowering time is an important part of the
cence inhibition, suggesting that AtWRKY75 has a posi- development process of angiosperm plants (Table 1).
tive effect on leaf senescence (Li et al., 2012). AtWRKY53 AtWRKY12, AtWRKY13, and AtWRKY71 are involved
has a positive effect on plant senescence (Miao and in this process (Table 1). AtWRKY12 and AtWRKY13
Zentgraf, 2010), whereas AtWRKY54 and AtWRKY70 have opposite regulatory effects on the flowering time
function redundantly, and potentially interact with under short daylight conditions. The flowering time of
AtWRKY30, negatively regulating the plant senescence the AtWRKY12 knockout mutant is delayed compared
(Besseau et al., 2012). AtWRKY57 acts as a node in the with wild-type, whereas AtWRKY13 induces flowering.
12 F. CHEN ET AL.
FRUITFULL (FUL), a direct downstream target gene of (Yamada and Sato, 2016). In Arabidopsis, AtWRKY6 is
AtWRKY12 and AtWRKY13, is the signaling pathway ubiquitinated through interacting with Really Interesting
hub of these two WRKY genes. In addition, AtWRKY12 New Gene (RING)-type finger E3 ubiquitin ligase
and AtWRKY13 can also affect plant flowering by par- (At1g74410), and this degradation process could be ter-
tially regulating GA3 (Li et al., 2016). AtWRKY71 has a minated by the 26S proteosome inhibitor MG132 (Chen
positive effect on plant flowering, both the active target et al., 2009). Similar to AtWRKY6, AtWRKY53 is also
mutant and the overexpression mutant has earlier flow- degraded by the action of a Homologous to the E6-AP
ering time than the wild type. In specific, promoter Carboxyl Terminus (HECT) E3 ubiquitin ligase, which
sequences of FT, LFY, AP1, and CAL (but not FUL) har- can accelerate the senescence of plant leaf (Miao and
bor W-boxes (TTTGACT/C), AtWRKY71 affects the Zentgraf, 2010). In Chinese wild grapevine (Vitis pseu-
flowering time of plants by directly regulating these doreticulata), VpWRKY11 interacts with Erysiphe neca-
genes (Yu et al., 2016). OsWRKY11 acts as a trans-regu- tor-induced RING finger protein 1 (EIRP1) through the
latory factor, delaying the flowering time of plants by RING domain, and degraded by the latter. Through this
downregulating gene expression of Early Heading date way, EIRP1 can enhance plant resistance to pathogens
Ehd2/ROOT INITIATION DEFECTIVE RID1//Indeter- (Yu et al., 2013). In rice, OsWRKY53 was able to bind to
minate 1 (Osld1); also, its downstream genes include the leucine zipper domain of the ubiquitin ligase
Heading date1 (Hd1), Ehd1, and Hd3a (Cai et al., 2014). OsUPL5, negatively affecting leaf senescence (Miao and
Four WRKYs and one rice WRKY are involved in Zentgraf, 2010). OsWRKY45 was also degraded through
plant nutrient utilization in Arabidopsis (Table 1). Plant ubiquitination, playing an important role in rice defense
growth and development process require a large amount responses (Matsushita et al., 2013).
of phosphorus and boron, and lacking these elements
will significantly impact gene regulations. AtWRKY42,
II. Studies of WRKY genes in crops
AtWRKY45, and AtWRKY75 participate in the regula-
tion of phosphorus deficiency signaling, in which Most crops originated from seed plants including
AtWRKY42 knockout mutant is more sensitive to low- gymnosperms and angiosperms (Feuillet et al., 2011).
phosphorus stress, and their shoots contained less phos- Unlike the model plant Arabidopsis, crops usually
phorus than wild-type (Su et al., 2015). AtWRKY45 can have large and complex genomes. For example, maize
bind to two W-boxes in the promoter region of the (Zea mays) has a genome of 2,106 Mb, the wheat
PHOSPHATE TRANSPORTER 1; 1 (PHT1; 1), and upre- variety Chinese Spring has an allooctoploid genome
gulates the taking up of phosphorus (Wang et al., 2014). of 10.2 Gb (www.wheatgenome.org), and sugarcane
AtWRKY75 has a positive regulatory effect on plant tol- (Saccharum officinarum) has a basic ploidy unit of 40
erance to phosphorus deficiency, and AtWRKY75 is sig- chromosomes (http://ccdb.tau.ac.il). As of December 31,
nificantly upregulated in the condition of insufficient 2017, the genomes of 270 angiosperm species have been
phosphorus in the environment (Devaiah et al., 2007). released (www.angiosperms.org). Seventy percent or 168
Besides its role in regulating leaf senescence, AtWRKY6 of the sequenced angiosperm plants are crops and most
is involved in responses to low-phosphorus stress via of the other sequenced plants are the wild relatives of
regulating PHOSPHATE1 (PHO1) expression (Chen crops with important evolutionary positions.
et al., 2009). AtWRKY6 is the first characterized TF that
is involved in response to boron deficiency (Kasajima
A. Genome-wide identification of WRKY genes in
et al., 2010). OsWRKY74 modulates the phosphorus
crops
homeostasis and the potential crosstalk between ion and
phosphorus starvation (Dai et al., 2017). OsWRKY80 Genome-wide identification and characterizations of
responds to Fe-excess in rice leaves, stems and roots, sug- WRKY genes have been carried-out in several crop
gesting a role in Fe signaling (Klein et al., 2010). plants (Table 2). For example, sized duckweed Spirodela
polyrhiza, which has a small genome, has 43 WRKY
genes (Table 2). More than 100 WRKY genes have been
G. Degradation of WRKY Proteins
identified from crops with large genomes, such as soy-
Similar to other eukaryotes, the ubiquitin-proteosome bean, cotton, and napa (Table 2). Compared to other
system (UPS) mediated degradation of TFs plays an plants, the Poaceae plants (Oryza sativa, Zea mays, and
important role in the regulation of gene expression Sorghum bicolor) are enriched with subfamily III mem-
(Jakoby et al., 2002; Allen et al., 2008). The degradation bers. Subfamily IIc and subfamily IIa C IIb were specifi-
of a WRKY transcription factor in Japanese goldthread, cally amplified in cruciferous and legumes, respectively
Coptis japonica, CjWRKY, was regulated by UPS (Table 2). Since the first release of Arabidopsis genome
Table 2. WRKY gene family characterizations in representative crops.

Type Species I IIa C IIb IIc IId C IIe III Undefined Total Number Reported total number/Reference
Vegetable Solanum tuberosum 35 19 18 33 20 0 80 75 / Schluttenhofer et al., 2014

Vegetable Solanum lycopersicum 17 13 16 23 11 1 81 81 / Huang et al., 2012
Vegetable Capsicum annuum 15 10 13 14 9 1 62 71 / Diao et al., 2016
Drink Coffea arabica 10 9 14 10 5 1 49 49 / Schluttenhofer et al., 2015
Fruit Fragaria vesca 9 10 10 12 15 1 58 62 / Wei et al., 2016
Fruit Prunus persica 10 11 14 14 8 1 56 58 / Chen et al., 2016
Fruit Malus domestica 31 24 33 31 17 5 141 127 / Meng et al., 2016
Vegetable Cucumis sativus 15 9 19 16 7 1 62 55 / Xu et al., 2015
Economic Glycine max 37 45 37 38 24 4 182 197 / Rushton et al., 2010
Vegetable Phaseolus vulgaris 19 21 19 18 14 1 90 90 / Wang et al., 2016
Economic Populus trichocarpa 22 14 25 30 10 2 103 104 / He et al., 2012
Drink Theobroma cacao 12 11 15 12 6 6 59 18 / Borrone et al., 2007
Economic Gossypium raimondii 18 23 35 31 12 2 120 116 / Dou et al., 2014
Fruit Carica papaya 10 10 11 11 7 1 49 52 / Pan et al., 2014
Vegetable Brassica rapa 28 22 37 26 24 4 141 145 / Kayum et al., 2015
Model Arabidopsis thaliana 15 11 17 16 13 2 72 72 / Rushton et al., 2010
Fruit Vitis vinifera 12 11 15 14 6 1 59 59 / Wang et al., 2014
Fruit Musa acuminata 24 34 30 41 14 0 152 147 / Goel et al., 2016
Food Oryza sativa 19 13 17 18 27 7 103 103 / Ramamoorthy et al., 2008
Food Zea mays 28 15 22 28 30 0 132 116 / Wei et al., 2012
Food Sorghum bicolor 18 14 17 17 24 7 97 68 / Pandey et al., 2009
Economic Spirodela polyrhiza 11 8 6 13 3 2 43 34 / Yang et al., 2015
Wild Amborella trichopoda 7 6 7 7 4 1 32 29 / Yang et al., 2015
in 2000, 205 crop genome sequences have been released, (sugar-responsive) and W-box in the promoter of iso1,
whereas only 79 crops have their WRKY genes reported involved in the sugar signaling and the biosynthesis of
(Figure 5 and Table 3). Considering the importance of starch. In the chili pepper, Capsicum annuum,
crop plants in global economy and human life, further CaWRKY1 is a negative regulator influencing pathogen
characterizations of the functions of WRKY genes using infections, and expression was detected after only one-
newly developed techniques will become a necessity. half hour after the infection by Pseudomonas syringe.
CaWRKY1 is an ortholog to the Arabidopsis WRKY50
and WRKY51 TFs, and therefore might target the same
B. Functional characterization of WRKYs in crops
kinds of genes (Oh et al., 2007). In cotton (Gossypium
Although the studies of WRKY in most crops are not as hirsutum), plants with overexpression of GhWRKY44
extensive as in those model plants, the WRKY mediated were more resistant to fungal pathogen R. solanacearum
signaling pathway/network has been studied in some and R. solani. The expression of PR-1, PR-2, PR-5, NPR1,
crops. Sun et al. (2003) identified a WRKY gene SUS- and PR-4 was also upregulated in overexpressed plants,
IBA2 in barley that interacts with cis element SURE suggesting that these genes may be involved in the
Figure 5. Crop genome decoding progress and WRKY gene family research advances. Statistic resource data could be found at www.
angiosperms.org.
14 F. CHEN ET AL.
Table 3. WRKY research in 205 crop species genomes.

Species Genome_release WRKY report Taxonomy Crop_attribute
Capsella bursa-pastoris 2017 — Brassicales Vegetable

Barbarea vulgaris 2017 — Brassicales Vegetable
Momordica charantia 2016 — Cucurbitales Vegetable
Brassica juncea 2016 — Brassicales Vegetable
Vigna unguiculata 2016 — Fabales Vegetable
Zizania latifolia 2015 — Poales Vegetable
Moringa oleifera 2015 — Brassicales Vegetable
Vicia faba 2015 — Fabales Vegetable
Vigna angularis 2015 — Fabales Vegetable
Thlaspi arvense 2015 — Brassicales Vegetable
Vigna radiata 2014 — Fabales Vegetable
Phaseolus vulgaris 2014 — Fabales Vegetable
Spinacia oleracea 2013 — Caryophyllales Vegetable
Lagenaria siceraria 2013 — Cucurbitales Vegetable
Capsella rubella 2013 — Brassicales Vegetable
Beta vulgaris 2013 — Caryophyllales Vegetable
Cajanus cajan 2011 — Fabales Vegetable
Lactuca sativa 2011 — Asterales Vegetable
Raphanus sativus 2014 2016 Brassicales Vegetable
Daucus carota 2016 2015 Apiales Vegetable
Solanum melongena 2014 2015 Solanales Vegetable
Brassica oleracea 2014 2015 Brassicales Vegetable
Solanum pimpinellifolium 2012 2014 Solanales Vegetable
Cicer arietinum 2013 2013 Fabales Vegetable
Cucumis sativus 2009 2011 Cucurbitales Vegetable
Brassica napus 2014 2009 Brassicales Vegetable
Solanum lycopersicum 2012 2008 Solanales Vegetable
Medicago truncatula 2011 2008 Fabales Vegetable
Glycine max 2010 2008 Fabales Vegetable
Capsicum annuum 2014 2006 Solanales Vegetable
Brassica rapa 2011 2006 Brassicales Vegetable
Solanum tuberosum 2011 2000 Solanales Vegetable
Capsella bursa-pastoris 2017 — Brassicales Vegetable
Asparagus officinalis 2017 2017 Asparagales Vegetable
Momordica charantia 2017 — Cucurbitales Vegetable
Cephalotus follicularis 2017 — Oxalidales Ornamental
Zoysia pacifica 2016 — Poales Ornamental
Fraxinus excelsior 2016 — Lamiales Ornamental
Hibiscus syriacus 2016 — Malvales Ornamental
Drosera capensis 2016 — Caryophyllales Ornamental
Rosa x damascena 2016 — Rosales Ornamental
Petunia inflata 2016 — Solanales Ornamental
Zoysia japonica 2016 — Poales Ornamental
Rosa roxburghii 2016 — Rosales Ornamental
Cynara cardunculus 2016 — Asterales Ornamental
Nymphaea colorata 2016 — Nymphaeales Ornamental
Kalanchoe marnieriana 2016 — Saxifragales Ornamental
Kalanchoe laxiflora 2016 — Saxifragales Ornamental
Lolium perenne 2015 — Poales Ornamental
Phalaenopsis equestris 2014 — Asparagales Ornamental
Amaranthus hypochondriacus 2014 — Caryophyllales Ornamental
Erythranthe guttata 2014 — Lamiales Ornamental
Ensete ventricosum 2014 — Zingiberales Ornamental
Petunia integrifolia 2014 — Solanales Ornamental
Dianthus caryophyllus 2013 — Caryophyllales Ornamental
Tarenaya hassleriana 2013 — Brassicales Ornamental
Nicotiana sylvestris 2013 — Solanales Ornamental
Lupinus angustifolius 2013 — Fabales Ornamental
Nelumbo nucifera 2013 — Proteales Ornamental
Mimulus guttatus 2013 — Lamiales Ornamental
Kalanchoe fedtschenkoi 2013 — Saxifragales Ornamental
Prunus mume 2012 — Rosales Ornamental
Aquilegia caerulea 2012 — Ranunculales Ornamental
Musa acuminata 2012 2016 Zingiberales Ornamental
Dendrobium catenatum 2016 2015 Asparagales Ornamental
Zoysia matrella 2016 2013 Poales Ornamental
Ipomoea nil 2016 2000 Solanales Ornamental
Carnegiea gigantea 2017 — Caryophyllales Ornamental
Rhododendron delavayi 2017 — Ericales Ornamental
(Continued on next page)
Table 3. (Continued )
Fraxinus excelsior 2017 — Lamiales Ornamental

Panax ginseng 2017 2016 Apiales Medical
Calotropis gigantea 2017 — Gentianales Medical
Camptotheca acuminata 2017 — Cornales Medical
Rhodiola crenulata 2017 — Saxifragales Medicinal
Panax notoginseng 2017 — Apiales Medicinal
Erigeron breviscapus 2017 — Asterales Medicinal
Citrus medica 2017 — Sapindales Medicinal
Mentha longifolia 2016 — Lamiales Medicinal
Glycyrrhiza uralensis 2016 — Fabales Medicinal
Rhazya stricta 2016 — Gentianales Medicinal
Pogostemon cablin 2016 — Lamiales Medicinal
Lepidium meyenii 2016 — Brassicales Medicinal
Silybum marianum 2016 — Asterales Medicinal
Dorcoceras hygrometricum 2016 — Coleoptera Medicinal
Ocimum tenuiflorum 2015 — Lamiales Medicinal
Ocimum sanctum 2015 — Lamiales Medicinal
Azadirachta indica 2012 — Sapindales Medicinal
Salix suchowensis 2014 2016 Malpighiales Medicinal
Salvia miltiorrhiza 2015 2014 Lamiales Medicinal
Catharanthus roseus 2015 2011 Gentianales Medicinal
Ficus carica 2017 — Rosales Fruit
Dimocarpus longan 2017 — Sapindales Fruit
Durio zibethinus 2017 — Malvales Fruit
Punica granatum L 2017 2017 Myrtales Fruit
Fagopyrum tataricum 2017 — Caryophyllales Fruit
Ficus carica L. 2017 2017 Rosales Fruit
Citrus ichangensis 2017 — Sapindales Fruit
Citrus grandis 2017 — Sapindales Fruit
Macadamia integrifolia 2016 — Proteales Fruit
Siraitia grosvenorii 2016 — Cucurbitales Fruit
Musa itinerans 2016 — Zingiberales Fruit
Olea europaea 2016 — Lamiales Fruit
Vitis aestivalis 2016 — Vitales Fruit
Artocarpus camansi 2016 — Rosales Fruit
Ananas comosus 2015 — Poales Fruit
Vaccinium corymbosum 2015 — Ericales Fruit
Fragaria orientalis 2015 — Rosales Fruit
Fragaria nipponica 2015 — Rosales Fruit
Castanea mollissima 2015 — Fagales Fruit
Diospyros lotus 2014 — Ericales Fruit
Ziziphus jujuba 2014 — Rosales Fruit
Vaccinium macrocarpon 2014 — Ericales Fruit
Citrus clementina 2014 — Sapindales Fruit
Pyrus communis 2014 — Rosales Fruit
Actinidia chinensis 2013 — Ericales Fruit
Prunus persica 2013 — Rosales Fruit
Citrus sinensis 2012 — Sapindales Fruit
Cucumis melo 2012 — Cucurbitales Fruit
Phoenix dactylifera 2011 — Arecales Fruit
Juglans regia 2016 2016 Fagales Fruit
Musa balbisiana 2013 2016 Zingiberales Fruit
Morus notabilis 2013 2016 Rosales Fruit
Juglans regia 2012 2016 Fagales Fruit
Ginkgo biloba 2016 2015 Gymnosperm Fruit
Pyrus bretschneideri 2012 2015 Rosales Fruit
Juglans sigillata 2016 2014 Fagales Fruit
Malus domestica 2010 2014 Rosales Fruit
Carica papaya 2008 2014 Brassicales Fruit
Citrullus lanatus 2012 2012 Cucurbitales Fruit
Fragaria vesca 2010 2012 Rosales Fruit
Fragaria x ananassa 2015 2010 Rosales Fruit
Vitis vinifera 2007 2006 Vitales Fruit
Citrus parasisi x Poncirus trifoliata 2016 2003 Sapindales Fruit
Rubus occidentalis 2016 Rosales Fruit
Secale cereale 2017 — Poales Food
Chenopodium pallidicaule 2016 — Caryophyllales Food
Fagopyrum esculentum 2016 — Caryophyllales Food
(Continued on next page)
16 F. CHEN ET AL.
Table 3. (Continued )
Manihot esculenta ssp.flabellirolia 2014 2016 Malpighiales Food

Chenopodium quinoa 2016 2015 Caryophyllales Food
Setaria italica 2012 2015 Poales Food
Glycine soja 2014 2013 Fabales Food
Zea mays 2009 2012 Poales Food
Sorghum bicolor 2009 2009 Poales Food
Triticum aestivum 2014 2008 Poales Food
Oryza sativa 2002 2004 Poales Food
Hordeum vulgare 2015 2000 Poales Food
Cucurbita pepo 2017 2012 Cucurbitales Food
Capsicum baccatum 2017 — Solanales Food
Ipomoea batatas 2017 1994 Solanales Food
Cucurbita moschata 2017 — Cucurbitales Food
Cenchrus americanus 2017 — Poales Food
Dioscorea rotundata 2017 — Dioscoreales Food
Secale cereale L. 2017 — Poales Food
Corchorus capsularis 2017 — Malvales Economic
Corchirus olitorius 2017 — Malvales Economic
Betula pendula 2017 — Fagales Economic
Atalantia buxifolia 2017 — Sapindales Economic
Quercus lobata 2016 — Fagales Economic
Brassica nigra 2016 — Brassicales Economic
Eichhornia paniculata 2016 — Commelinales Economic
Carthamus tinctorius 2016 — Asterales Economic
Pseudotsuga menziesii 2015 — Economic
Lemna minor 2015 — Alismatales Economic
Vitis cinerea x Vitis riparia 2015 — Vitales Economic
Aquilaria agallocha 2014 — Malvales Economic
Eucalyptus grandis 2014 — Myrtales Economic
Camelina sativa 2014 — Brassicales Economic
Eragrostis tef 2014 — Poales Economic
Picea abies 2013 — Economic
Picea glauca 2013 — Pinales Economic
Phyllostachys heterocycla 2013 2017 Poales Economic
Linum usitatissimum 2012 — Malpighiales Economic
Eucalyptus camaldulensis 2011 — Myrtales Economic
Sesamum indicum 2014 2016 Lamiales Economic
Cannabis sativa 2011 2016 Brassicales Economic
Spirodela polyrhiza 2014 2014 Alismatales Economic
Hevea brasiliensis 2013 2014 Malpighiales Economic
Gossypium raimondii 2012 2014 Malvales Economic
Lotus japonicus 2008 2014 Fabales Economic
Jatropha curcas 2010 2013 Malpighiales Economic
Helianthus annuus 2017 2012 Asterales Economic
Gossypium barbadense 2015 2012 Malvales Economic
Brachypodium distachyon 2010 2012 Poales Economic
Populus trichocarpa 2006 2012 Malpighiales Economic
Gossypium hirsutum 2015 2011 Malvales Economic
Populus tremulaxPopulus tremuloides-T89x 2015 2009 Malpighiales Economic
Populus tremula 2015 2009 Malpighiales Economic
Pinus taeda 2014 2009 Economic
Elaeis guineensis 2013 2009 Arecales Economic
Nicotiana benthamiana 2012 2009 Solanales Economic
Ricinus communis 2010 2009 Malpighiales Economic
Gossypium arboreum 2014 2004 Malvales Economic
Nicotiana tabacum 2014 2000 Solanales Economic
Boehmeria nivea 2017 2013 Rosales Economic
Eucommia ulmoides 2017 — Garryales Economic
Handroanthus impetiginosus 2017 — Lamiales Economic
Populus pruinosa 2017 2014 Malpighiales Economic
Corchorus olitorius 2017 — Malvales Economic
Corchorus capsularis 2017 2014 Malvales Economic
Trifolium pratense 2015 — Fabales Drink
Camellia sinensis 2017 2016 Ericales Drink
Humulus lupulus 2014 2016 Rosales Drink
Coffea arabica 2017 2013 Gentianales Drink
Coffea canephora 2014 2010 Gentianales Drink
Theobroma cacao 2010 2004 Malvales Drink
immune process as GhWRKY44 target genes (Li et al., A. Evo-devo based functional inference
2015). Summer waterlogging can seriously affect the
Newly duplicated genes usually retain similar functions
quality of grape fruit, and grape WRKY11 has been con-
(Guth and Wegner, 2008). Therefore, phylogenetic anal-
firmed to improve the resistance of grapes to waterlog-
ysis of the plant WRKY genes is an effective way to infer
ging. This process is through the regulation of Atrisne
the functions of uncharacterized WRKY members based
29A and AtRD29B, two stress response genes (Liu et al.,
on their evolutionary history and sequence similarity.
2011). In maize, ZmWRKY33 can be induced in high
Such studies could be a convenient way to infer the func-
salt and drought conditions. Transgenic experiments
tions of WRKY genes in crops. Figure 6 shows a phyloge-
show that ZmWRKY33 overexpression can activate mul-
netic tree constructed using WRKYs from the 23 plants
tiple stress response genes, including RD29A, thereby
listed in Table 2, in which the genes designated by the
enhancing plant tolerance to salt stress (Li et al., 2013).
color dots present those which have been identified, and
In apple (Malus domestica), MdWRKY13 overexpressing
the hollow circles represent the functional-unknown
plants showed a higher susceptibility to drought, suggest-
genes in Arabidopsis and O. sativa. Most of the subfamily
ing that this gene may be a negative regulator of apple
IIa genes are involved in both biotic and abiotic pro-
stress on drought stress, and further testing suggests that
cesses, suggesting that this subfamily is largely engaged
this regulation may be related to the proline degradation
in stress signaling and those IIa genes in crop may share
gene p5cs1 (Duan et al., 2014).
similar functions. Similarly, the subfamily IId genes are
not involved in the regulation of growth and develop-
ment, suggesting that this subfamily may have evolved to
C. WRKYs in crop domestication and breeding become stress-specific genes. Although genes in subfam-
ily I cover the three functions with most stress-related,
TFs are suitable candidates for plant domestication
when further divided, the small branches of these genes
and molecular breeding, because they are linked to
have only one or two functions. Compared to other well-
the recognition of domestication gene to affect spatial
characterized subfamilies, the functions of most subfam-
and temporal gene expression (Swinnen et al., 2016).
ily III genes are unknown.
Gu et al. (2017) reported that a WRKY gene from
Whole genome sequencing data make it possible for
soybean, SoyWRKY15a, was related to seed size and
rapid prediction and retrieval of WRKY genes in a spe-
weight variation in wild soybean. The diverged
cies. Although the numbers of WRKY genes and their
expression levels of SoyWRKY15a could distinguish
wild soybeans from cultivated soybeans, suggesting a
critical role of WRKY genes in the domestication pro-
cesses of soybean. Because of their critical roles in
various signaling pathways, WRKY genes have a very
promising potential in plant breeding. Silencing or
knockout WRKY genes in feedback inhibition of
stress signaling pathways or immune pathways are
potential potent targets in molecular breeding of
novel crops.
III. Applications of high throughput

technologies to accelerate the exploration of
crop WRKY genes
Researches based on model plants are instrumental to
advance our understandings of the functional roles of
the WRKY genes, but it also has limitations. For exam-
ple, Arabidopsis and rice are not ideal study systems for
the study of color, floral, nitrogen fixation, perennial, Figure 6. Functional similarity in the phylogenetic view of WRKY
gene family in Arabidopsis and rice. The phylogenetic tree using
fruit development. The new and improved techniques
by Arabidopsis and rice WRKY gene family. The genes designated
that have been used in model plants, especially Arabidop- by the color dots have been identified, and the hollow circles rep-
sis, would significantly facilitate the studies of WRKY resent the function-unknown genes, which came from Arabidop-
genes in crops. sis and O. sativa.
18 F. CHEN ET AL.
classification in many species have been studied, com- deletions (indels) in specific target genes and has been
parative analysis between multiple species will be helpful applied to many organisms. Relying on these convenient
to understand the evolutionary patterns of WRKY subfa- characters, some CRISPR/Cas9 mutant libraries have
milies and members. Because there are more than 100 been developed for genome-wide mutation screens in
copies in many crops, detailed structural and functional cultured eukaryotic cells (Shalem et al., 2015). In rice,
studies of every WRKY gene of each crop species is chal- the CRISPR/Cas9 system has been successfully applied
lenging and time-consuming. It is necessary to establish in the construction of a genome-wide mutant library
a public database to include all WRKY genes found in (Meng et al., 2017). The future application of the
crops that have completed genome sequencing. Second, CRISPR/Cas9 system in other crops, such as soybean or
analytical tools such as sequence retrieval, gene structure oilseed plant or other crops, would significantly acceler-
and expression analysis, and gene phylogenetic tree con- ate the identification and characterization of WRKY
struction should be integrated. genes and have potential use for genetic improvement.
B. The temporal and spatial expression patterns of D. Identification of WRKY target genes using
WRKY genes ChIP-seq
RNA-seq is a powerful tool to study the temporal and ChIP-sequencing, also known as ChIP-seq, a powerful
spatial expression patterns of the whole WRKY gene tool for studying the interaction between chromatin and
family of a plant. Based on RNA-seq data of samples of DNA, is widely used to determine how TFs
mock and pathogen inoculated plants, the expression influence phenotype-affecting mechanisms. In Arabidop-
pattern of all the WRKY family members in plant sis, AtWRKY18, AtWRKY33, and AtWRKY40 have
immune responses have been determined (Okay et al., been demonstrated to modulate pathogen-triggered cel-
2014). Similar researches were conducted for WRKYs in lular responses (Walker, 2011). Chip-seq study on Arabi-
wheat drought stress responses (Okay et al., 2014; Sata- dopsis revealed that each of the three WRKY proteins
pathy et al., 2014). The expression atlas of WRKYs in the bind to more than 1,000 W-box elements, which mainly
American cotton G. aridum under drought stress treat- locate in the 500 bp promoter region. Bioinformatics
ment have also been generated (Fan et al., 2015). The analyses of these genes identified not only the genes
newly developed third generation sequencing platforms, involved in defense signal perception and transduction,
such as Pacific Biosciences and Oxford Nanopore Tech- but also numerous TFs encoding ethylene response fac-
nologies, are able to generate full-length transcriptome, tors. The detailed protocol of WRKY-oriented Chip-seq
which offers an opportunity to identify the members of has been developed to study its genome-wide targets
WRKY gene family from highly polyploid crops, such as (Walker, 2011). ChIP-seq has also been applied in
the sugarcane (Hoang et al., 2017), providing unprece- research of the related TF genes, such as NAC and
dented knowledge of WRKY gene evolution. YABBY (Walker, 2011). Therefore, ChIP-seq techniques
will be instrumental for global identification of WRKY
targets, contributing to a better understanding of the
C. Functional characterization of WRKY genes using
WRKY signaling network.
CRISPR
Gene editing tools such as CRISPR (Clustered Regularly
E. Online data analysis and visualization
Interspaced Palindromic Repeats)-Cas9 (Songstad et al.,
2017; Zhang et al., 2017) have been rapidly developed in Large-scale sequencing of genomes, transcriptomes, epi-
the past years. The CRISPR/Cas9 system becomes an genomes, and specific sequencing such as ChIP-seq, has
important tool in plant molecular biology research due produced a large amount of heterogeneous data. How to
to the precise editing or excision of genes. Liu et al. integrate and analyze different types of ome data
2016b reported the introduction of a special carrier con- becomes the focus of bioinformatics research. For a large
taining CRISPR/Cas9 into tobacco, which successfully gene family such as WRKY, a database/webserver can
knocked out a tobacco’s NbWRKY70 gene. Many share and update the latest -ome data, providing power-
WRKYs can be served as good targets because of their ful and fast computational resources, making it possible
roles in the signaling pathways in model plants. to analyze the basic features of the WRKY gene family
The CRISPR/Cas9 system could create a mutant online. On the other hand, scientists have accumulated
library in a fast and convenient way, making functional 1,001 Arabidopsis genome sequences (Weigel and Mott,
genomics possible for various crops. Recently, the 2009), 3,000 rice genome sequences (The 3,000 rice
CRISPR/Cas9 system can create small insertions and genomes project, 2014), and will sequence even more
crop genomes. A main challenge is how to compare the Science Foundation of China (81502437), and a start-up fund
difference of WRKYs as fast as possible. from Fujian Agriculture and Forestry University.
Although there is no WRKY-centered database at
present, we propose the conceptional structure of such References
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The WRKY Transcription Factor Family in Model Plants and Crops

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Critical Reviews in Plant Sciences

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The WRKY Transcription Factor Family in Model

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The WRKY Transcription Factor Family in Model Plants and Crops

Figure 4. WRKYs in plant abiotic stress signaling network.

Table 1. WRKY as key regulators in plant growth and development.

AtWRKY28 At4G18170 Ovule development Zhao et al., 2017

Table 2. WRKY gene family characterizations in representative crops.

Vegetable Solanum tuberosum 35 19 18 33 20 0 80 75 / Schluttenhofer et al., 2014

Table 3. WRKY research in 205 crop species genomes.

Capsella bursa-pastoris 2017 — Brassicales Vegetable

Fraxinus excelsior 2017 — Lamiales Ornamental

Manihot esculenta ssp.ﬂabellirolia 2014 2016 Malpighiales Food

III. Applications of high throughput

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