Genome-wide identification and characterization of the WRKY gene family in potato ( Solanum tuberosum )

Liu, Qiu-Ning; Liu, Yu; Xin, Zhao-Zhe; Zhang, Dai-Zhen; Ge, Bao-Ming; Yang, Ruiping; Wang, Zheng-Fei; Yang, Li; Tang, Boping; Zhou, Chun-Lin

doi:10.1016/j.bse.2017.02.010

Cited by 25 publications

(22 citation statements)

References 29 publications

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“…ScWRKY and SchWRKY proteins were primarily divided into three main phylogenetic Groups with Group II further classified into five subGroups (IIa-IIe). Most of WRKYs found in the two wild species belonged to Group II and this is in line with results obtained in S. tuberosum 22 . As known, WRKY proteins are characterized by one or more WRKY domain.…”

Section: Structural Analysis Of Scwrkys and Schwrkys Revealed Interspsupporting

confidence: 90%

“…We detected 79 and 84 genes encoding putative WRKY TFs in S. commersonii and S. chacoense, respectively. These results indicate that, compared to the cultivated potato 22 , S. commersonii possesses a lower number and S. chacoense a higher number of WRKY genes. 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 .…”

Section: Structural Analysis Of Scwrkys and Schwrkys Revealed Interspmentioning

confidence: 76%

“…Due to its importance in the regulation of several processes in plants 5 , WRKY family has been studied in more than 60 plant species. In Solanaceae, data are available in some important crops, such as S. tuberosum (79 21 , 82 22 and 81 12 WRKYs), S. lycopersicum (83 WRKYs 41 ) and S. melongena (50 WRKYs 42 ). However, no information is available on the number and structural variability of WRKY TFs in Solanaceae wild species, which represent an important reservoir of genetic variation for breeding.…”

Section: Discussionmentioning

confidence: 99%

“…Identification of WRKY in S. commersonii and S. chacoense and phylogenetic analysis. The well-known WRKY protein sequences of S. tuberosum 22 and A. thaliana 25 were used as queries to build an HMM profile through HMMER as reported by Esposito et al 26 and to search orthologs in S. commersonii (cmm1T clone of PI243503) and S. chacoense (M6 clone) genomes. Only sequences with an e-value lower than 10 −5 and an identity higher than 55% were regarded as putative WRKYs and further analyzed.…”

Section: Methodsmentioning

confidence: 99%

“…Despite this, to date no studies have examined WRKY gene family components and their different characteristics in wild potato species. A few data on this gene family are available only in the cultivated potato, where Zhang et al 21 , Liu et al 22 and Cheng et al 12 identified 79, 82 and 81 StWRKYs, respectively. Previously, Dellagi et al 23 identified StWRKY1 as a good candidate for functional studies, and Shahzad et al 24 overexpressed it in potato.…”

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confidence: 99%

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

Villano

Esposito

D’Amelia

et al. 2020

Sci Rep

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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,...

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Section: Structural Analysis Of Scwrkys and Schwrkys Revealed Interspsupporting

confidence: 90%

Section: Structural Analysis Of Scwrkys and Schwrkys Revealed Interspmentioning

confidence: 76%

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

See 3 more Smart Citations

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

Villano

Esposito

D’Amelia

et al. 2020

Sci Rep

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show abstract

WRKY transcription factors: evolution, regulation, and functional diversity in plants

et al. 2022

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The sweet sorghum SbWRKY50 is negatively involved in salt response by regulating ion homeostasis

Song

Sui

et al. 2020

Plant Mol Biol

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Genome-wide identification and characterization of the WRKY gene family in potato ( Solanum tuberosum )

Cited by 25 publications

References 29 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

WRKY transcription factors: evolution, regulation, and functional diversity in plants

The sweet sorghum SbWRKY50 is negatively involved in salt response by regulating ion homeostasis

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