WRKY transcription factors

Bakshi, Madhunita; Oelmüller, Ralf

doi:10.4161/psb.27700

Cited by 516 publications

(278 citation statements)

References 144 publications

(256 reference statements)

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“…The copy number of the WRKY cisacting elements in the upstream region of OsAPx8 (Ascorbate peroxidase 8) gene in the Godawee genome as compared to the reference was significantly high depicting the possible upregulation of OsAPx8 gene expression in Godawee. This is comparable with the previous findings where Hong and Kao [55] showed that the expression of OsAPx8 is enhanced by the accumulation of ABA (Abscisic acid) which in turn enhances the expression of WRKY transcription factors [56]. Additionally, higher numbers of WRKY cisacting elements were also observed in OsMSR2, OsTIR1, OsHKT2;3, OsHKT1;4 and OsSOS1 genes compared to their counterparts in the reference genome.…”

Section: Discussionsupporting

confidence: 90%

Whole Genome Sequencing and Analysis of Godawee, a Salt Tolerant Indica Rice Variety

Singhabahu¹,

Wijesinghe²,

Gunawardana³

et al. 2017

J Rice Res

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Godawee is a cultivated salt tolerant Oryza sativa rice variety indigenous to Sri Lanka, but its genetic basis is unknown. The whole genome of Godawee was sequenced using Illumina paired-end technology. The reads were mapped to Oryza sativa Nipponbare reference genome. Investigation of genome wide variation patterns resulted in the identification of 2,231,717 SNPs and 480,460 InDels. In silico analysis identified 192,249 non-synonymous SNPs in 31,287 genes. Variants in 28 Salt Tolerance Related Genes (STRGs) were examined. The OsHKT 2;1 gene had the largest number of SNPs in comparison to the reference genome. 16 non-synonymous SNPs that were predicted to have functional effects either by SIFT, Provean or SNAP algorithms were detected in the STRGs. The upstream regions of the STRGs were examined for cis-regulatory elements found in STIFDB, Plant CARE and PLACE databases. The most striking of this was the WRKY cis-acting family of elements which were found in abundance in the upstream regions of OsAPx8, OsMSR2, OsTIR1, OsHKT2;3, OsHKT14 and OsSOS1 genes. Sequencing and whole genome analysis of Godawee helped to understand the genetic basis of its salinity tolerance which is a complex trait involving multiple factors.

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Section: Discussionsupporting

confidence: 90%

Whole Genome Sequencing and Analysis of Godawee, a Salt Tolerant Indica Rice Variety

Singhabahu¹,

Wijesinghe²,

Gunawardana³

et al. 2017

J Rice Res

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“…For this, we focused a hot spot QTL region on chromosome 1H (122.17 cM) associated commonly with shoot and root variation which accounted the highest LOD score for Til. In silico analysis of the associated marker BOPA1_7381_1292 with barley Genome Zipper found an essential WRKY transcription factor (WRKY29) gene known for its role in the development of shoot and root (Bakshi and Oelmüller, 2014). Hence, we made full length sequencing of WRKY29 gene in selected genotypes having minor and major QTL alleles for QRdw.1H and QTil.1H.…”

Section: Resultsmentioning

confidence: 99%

Genome-Wide Association Mapping in the Global Diversity Set Reveals New QTL Controlling Root System and Related Shoot Variation in Barley

et al. 2016

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The fibrous root system is a visible sign of ecological adaptation among barley natural populations. In the present study, we utilized rich barley diversity to dissect the genetic basis of root system variation and its link with shoot attributes under well-water and drought conditions. Genome-wide association mapping of phenotype data using a dense genetic map (5892 SNP markers) revealed 17 putative QTL for root and shoot traits. Among these, at 14 loci the preeminence of exotic QTL alleles resulted in trait improvements. The most promising QTL were quantified using haplotype analysis at local and global genome levels. The strongest QTL was found on chromosome 1H which accounted for root dry weight and tiller number simultaneously. Candidate gene analysis across the targeted region detected a crucial amino acid substitution mutation in the conserved domain of a WRKY29 transcription factor among genotypes bearing major and minor QTL alleles. Similarly, the drought inducible QTL QRdw.5H (5H, 95.0 cM) seems to underlie 37 amino acid deletion and substitution mutations in the conserved domain of two related genes CBF10B and CBF10A, respectively. The identification and further characterization of these candidate genes will be essential to decipher genetics behind developmental and natural adaptation mechanisms of barley.

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“…The fact that MYB4 and MYB12 contain highly conserved W-boxes in their promoters suggests that both might be a target for flg22-induced WRKY TFs as shown in Figure 2. Since WRKYs comprise positive (activating) and negative (repressing) regulators, 35 36 it cannot be predicted in how far the arrangement and location of W-boxes within a given promoter has an impact on binding of positively or negatively acting WRKYs (Imre Somssich, MPIPZ Cologne, personal communication). To evidence this, CHIP-qPCR experiments with anti-all WRKY antibodies should be conducted to prove WRKY binding at the promoters of these two MYB TFs.…”

Section: Resultsmentioning

confidence: 99%

The interplay of transcription factors in suppression of UV-B induced flavonol accumulation by flg22

Schenke¹,

Cai

2014

Plant Signaling & Behavior

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WRKY transcription factors

Cited by 516 publications

References 144 publications

Whole Genome Sequencing and Analysis of Godawee, a Salt Tolerant Indica Rice Variety

Whole Genome Sequencing and Analysis of Godawee, a Salt Tolerant Indica Rice Variety

Genome-Wide Association Mapping in the Global Diversity Set Reveals New QTL Controlling Root System and Related Shoot Variation in Barley

The interplay of transcription factors in suppression of UV-B induced flavonol accumulation by flg22

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