Genome-wide identification and expression analyses of WRKY transcription factor family members from chickpea (Cicer arietinum L.) reveal their role in abiotic stress-responses

Waqas, Muhammad; Azhar, Muhammad Tehseen; Rana, İqrar Ahmad; Azeem, Farrukh; Ali, Muhammad Amjad; Nawaz, Muhammad Amjad; Chung, Gyuhwa; Atif, Rana Muhammad

doi:10.1007/s13258-018-00780-9

Cited by 78 publications

(65 citation statements)

References 80 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Both species displayed a number of WRKYs greater than that of barley (45) 46 , castor bean (58) 47 , cucumber (55) 48 , rapeseed (43) 49 and grapevine (59) 50 , and lower than that of cotton (120) 51 , maize (136) 52 , soybean (131) 53 and rice (100) 25 . From this comparison, it appears that the number of WRKY encoding genes is not proportional to the genome size of the respective plant species, as also reported by Waqas et al 54 . ScWRKY and SchWRKY proteins were primarily divided into three main phylogenetic Groups with Group II further classified into five subGroups (IIa-IIe).…”

Section: Structural Analysis Of Scwrkys and Schwrkys Revealed Interspsupporting

confidence: 82%

WRKY genes family study reveals tissue-specific and stress-responsive TFs in wild potato species

Villano

Esposito

D’Amelia

et al. 2020

Sci Rep

View full text Add to dashboard Cite

Wild potatoes, as dynamic resource adapted to various environmental conditions, represent a powerful and informative reservoir of genes useful for breeding efforts. WRKY transcription factors (TFs) are encoded by one of the largest families in plants and are involved in several biological processes such as growth and development, signal transduction, and plant defence against stress. In this study, 79 and 84 genes encoding putative WRKY TFs have been identified in two wild potato relatives, Solanum commersonii and S. chacoense. Phylogenetic analysis of WRKY proteins divided ScWRKYs and SchWRKYs into three Groups and seven subGroups. Structural and phylogenetic comparative analyses suggested an interspecific variability of WRKYs. Analysis of gene expression profiles in different tissues and under various stresses allowed to select ScWRKY045 as a good candidate in woundingresponse, ScWRKY055 as a bacterial infection triggered WRKY and ScWRKY023 as a multiple stressresponsive WRKY gene. Those WRKYs were further studied through interactome analysis allowing the identification of potential co-expression relationships between ScWRKYs/SchWRKYs and genes of various pathways. Overall, this study enabled the discrimination of WRKY genes that could be considered as potential candidates in both breeding programs and functional studies.Plants experience environmental constrains and pathogen attacks during their life. Being sessile organisms, their survival depends on the ability to properly and promptly reprogram cellular networks. Several and different classes of transcription factors (TFs) work as "master regulators" and "selector genes", being able to control processes that specify cell types and developmental patterning and modulate specific pathways. Among them, WRKY factors are drawing a great deal of interest in the scientific community due to their ability to simultaneously cope with multiple stresses 1,2 . They are notorious for coordinating signals in plant immunity response against several pathogens and pest attacks 3,4 . More recently, it has been confirmed that WRKYs also base defence mechanism to abiotic stresses and play a key role in cross-talk pathway networks between plant response and development 5,6 . Their involvement into multiple stress response and in plant growth regulation is evidenced by their W-box specific DNA binding 7,8 . Besides, WRKY binds sugar responsive elements and, very recently, it has been demonstrated that they activate sugar responsive genes through an epigenetic mechanism of control 9 . The systematic classification of components of the WRKY family is well organized. It is based on the WRKY binding domain (WD) characteristics along with those of the Zinc Finger (ZF) motif, which is typically present downstream the WD. WD consists of 60 amino acids structured as four-stranded β-sheets able to enter the major groove of B-form DNA. The highly conserved motif is "WRKYGQK". According to the number of WDs and the type of zinc finger motif, WRKY proteins can be classified into three Groups,...

show abstract

Section: Structural Analysis Of Scwrkys and Schwrkys Revealed Interspsupporting

confidence: 82%

WRKY genes family study reveals tissue-specific and stress-responsive TFs in wild potato species

Villano

Esposito

D’Amelia

et al. 2020

Sci Rep

View full text Add to dashboard Cite

show abstract

“…The higher proportion of group II members was also detected in other plant WRKY families such as 58% in Arabidopsis, 64% in Caragana intermedia [48] and 66% in Manihot esculenta [49]. For each group, CsWRKY members exhibited the similar structure, but members in different group showed speci c feature, which is in agreement with reports in other plants such as chickpea [50] and common bean [47].…”

Section: Conserved and Divergent Features Among Cswrky Family Memberssupporting

confidence: 88%

“…Increasing reports indicated that gene duplication (e.g. tandem duplication, segmental duplication, and genome duplication) was the key force for gene family expansion in plant genomes [50]. Here, genomewide identi cation and analysis of the WRKY gene family in C. sativa identi ed 137 segmental duplication events but no tandem duplication event.…”

Section: Segmental Duplication Contributed Critically To Expansion Ofmentioning

confidence: 88%

“…All these data demonstrate that segmental duplication is the major force for expansion of CsWRKY gene family. As the key factor, segmental duplication was detected to be related with expansion of WRKY gene family in Chickpea, Pineapple and Kiwifruit [24,27,50]. Therefore, we can speculate that segmental duplication events are the primary cause to drive CsWRKY gene family to expand so large members.…”

Section: Segmental Duplication Contributed Critically To Expansion Ofmentioning

confidence: 89%

“…Previous reports indicated that group I WRKY containing two WRKY domains was considered to be the ancient members during the WRKY evolution. The WRKYs in group IIa and IIb came from an algal single WRKY domain or the other Group 1-derived lineage [26,50]. The members of group IIc had been evolved from the lack of N-terminal domain of WRKYs in group II.…”

Section: Conserved and Divergent Features Among Cswrky Family Membersmentioning

confidence: 99%

See 2 more Smart Citations

Genome-wide identification and functional characterization of Camelina sativa WRKY gene family in response to abiotic stress

Song

Cui

She

et al. 2020

Preprint

View full text Add to dashboard Cite

Background: WRKY transcription factors are a superfamily of regulators involved in diverse biological processes and stress responses in plants. However, knowledge is limited for WRKY family in camelina (Camelina sativa), an important Brassicaceae oil crop with strong tolerance against various stresses. Here, genome-wide characterization of WRKY proteins is performed to examine their gene-structures, phylogenetics, expressions, conserved motif organizations, and functional annotation to identify candidate WRKYs mediating regulation of stress resistance in camelina. Results: Total of 242 CsWRKY proteins encoded by 224 gene loci distributed uneven on chromosomes were identified, and classified into three groups via phylogenetic analysis according to their WRKY domains and zinc finger motifs. 15 CsWRKY gene loci generated 33 spliced variants. Orthologous WRKY gene pairs were identified, with 173 pairs in C. sativa and Arabidopsis genomes as well as 282 pairs for C. sativa and B. napus, respectively. 137 segmental duplication events were observed but no tandem duplication in camelina genome. Ten major conserved motifs were examined, with WRKYGQK as the most conserved and several variants existed in many CsWRKYs. Expression analysis revealed that half more CsWRKY genes were expressed constitutively, and a set of them had a tissue-specific expression. Notably, 11 CsWRKY genes exhibited significantly expression changes in plant seedlings under cold, salt, and drought stress, respectively, having preferentially inducible expression pattern in response to the stress. Conclusions: The present described a detail analysis of CsWRKY gen family and their expression profiled in twelve tissues and under several stress conditions. Segmental duplication is the major force for large expansion of this gene family, and a strong purifying pressure happened for CsWRKY proteins evolutionally. CsWRKY proteins play important roles for plant development, with differential functions in different tissues. Exceptionally, eleven CsWRKYs, particularly five alternative spliced isoforms were found to be the key players possibly in mediating plant response to various stresses. Overall, our results provide a foundation for understanding roles of CsWRKYs and the precise mechanism through which CsWRKYs regulate high stress resistance to stress as well as development of stress tolerance cultivars for Cruciferae crops.

show abstract

Identification and expression analysis of WRKY superfamily genes under lychee downy blight stress in lychee

Liu,

Jiang,

Wen

et al. 2023

Agronomy Journal

View full text Add to dashboard Cite

WRKY proteins comprise a large family of transcription factors that play important roles in plant growth, development, and responses to stress, but little information is available about these genes in lychee (Litchi chinensis Sonn.). Despite being a popular fruit worldwide, lychee is highly vulnerable to lychee downy blight (LDB), a major disease affecting lychee. Based on lychee whole‐genome data, a total of 50 LcWRKY genes were identified across 15 chromosomes. According to a conserved domain and phylogenetic analysis, these 50 LcWRKYs were classified into three distinct subfamilies. Gene structure analysis revealed the presence of 2‐11 exons in the LcWRKYs. Cis‐acting regulatory element analysis identified many stress‐response elements in LcWRKY promoters. Moreover, a comprehensive two‐year investigation involving the screening of a lychee natural population led to the identification of Guiwei (GW) and Yurong 1 (YR1) as displaying stable susceptibility and resistance against LDB, respectively. Furthermore, expression patterns indicated that LcWRKY13, LcWRKY17, and LcWRKY34 were significantly upregulated in response to LDB induction, while LDB suppressed the expression of LcWRKY11. These findings suggest that these four genes may play a crucial role in lychee resistance to LDB. The present study has provided a foundation for future investigations of LcWRKY gene function in lychee.This article is protected by copyright. All rights reserved

show abstract

Genome-wide identification and expression analyses of WRKY transcription factor family members from chickpea (Cicer arietinum L.) reveal their role in abiotic stress-responses

Cited by 78 publications

References 80 publications

WRKY genes family study reveals tissue-specific and stress-responsive TFs in wild potato species

WRKY genes family study reveals tissue-specific and stress-responsive TFs in wild potato species

Genome-wide identification and functional characterization of Camelina sativa WRKY gene family in response to abiotic stress

Identification and expression analysis of WRKY superfamily genes under lychee downy blight stress in lychee

Contact Info

Product

Resources

About