Genome-Wide Identification of WRKY Genes and Their Response to Cold Stress in Coffea canephora

Dong, Xiangshu; Yang, Yanan; Zhang, Ziying; Xiao, Ziwei; Bai, Xuehui; Gao, Jing; Hur, Yoonkang; Hao, Shumei; He, Feifei

doi:10.3390/f10040335

Cited by 22 publications

(15 citation statements)

References 54 publications

(140 reference statements)

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“…In contrast, sorghum contains fewer WRKY genes than maize, soybean, or rice [ 23 , 45 , 46 ]. The present findings in sorghum, an important cereal crop and a model plant for drought tolerance, add to the recent identification of WRKY genes in a variety of plant species, including chickpea [ 26 ], Chinese jujube ( Ziziphus jujube ) [ 47 ], sugar beet ( Beta vulgaris ) [ 48 ], coffee ( Coffea arabica ) [ 49 ], pepper [ 50 ], eggplant ( Solanum melongena ) [ 51 ], Asian legume crops [ 52 ], sweet potato ( Ipomoea batatas ) [ 53 ], and pearl millet ( Pennisetum glaucum ) [ 54 ].…”

Section: Discussionmentioning

confidence: 66%

Genome-wide Identification of WRKY transcription factor family members in sorghum (Sorghum bicolor (L.) moench)

et al. 2020

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WRKY transcription factors regulate diverse biological processes in plants, including abiotic and biotic stress responses, and constitute one of the largest transcription factor families in higher plants. Although the past decade has seen significant progress towards identifying and functionally characterizing WRKY genes in diverse species, little is known about the WRKY family in sorghum ( Sorghum bicolor (L.) moench). Here we report the comprehensive identification of 94 putative WRKY transcription factors ( Sb WRKYs). The Sb WRKYs were divided into three groups (I, II, and III), with those in group II further classified into five subgroups (IIa–IIe), based on their conserved domains and zinc finger motif types. WRKYs from the model plant Arabidopsis ( Arabidopsis thaliana ) were used for the phylogenetic analysis of all SbWRKY genes. Motif analysis showed that all Sb WRKYs contained either one or two WRKY domains and that Sb WRKYs within the same group had similar motif compositions. SbWRKY genes were located on all 10 sorghum chromosomes, and some gene clusters and two tandem duplications were detected. SbWRKY gene structure analysis showed that they contained 0–7 introns, with most SbWRKY genes consisting of two introns and three exons. Gene ontology (GO) annotation functionally categorized SbWRKYs under cellular components, molecular functions and biological processes. A cis -element analysis showed that all SbWRKYs contain at least one stress response-related cis -element. We exploited publicly available microarray datasets to analyze the expression profiles of 78 SbWRKY genes at different growth stages and in different tissues. The induction of SbWRKYs by different abiotic stresses hinted at their potential involvement in stress responses. qRT-PCR analysis revealed different expression patterns for SbWRKYs during drought stress. Functionally characterized WRKY genes in Arabidopsis and other species will provide clues for the functional characterization of putative orthologs in sorghum. Thus, the present study delivers a solid foundation for future functional studies of SbWRKY genes and their roles in the response to critical stresses such as drought.

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Section: Discussionmentioning

confidence: 66%

Genome-wide Identification of WRKY transcription factor family members in sorghum (Sorghum bicolor (L.) moench)

et al. 2020

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“…TFs are key regulators of gene expression and have a variety of important functions in the plant response to abiotic stress [30,31]. The identification of TFs involved in saline-alkaline stress is crucial to reveal the innate molecular mechanisms.…”

Section: Discussionmentioning

confidence: 99%

Comparative transcriptome analysis reveals gene expression differences between two peach cultivars under saline-alkaline stress

Sun

Song

et al. 2020

Hereditas

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Background: Saline-alkaline stress is a major abiotic stress that is harmful to plant growth worldwide. Two peach cultivars (GF677 and Maotao) display distinct phenotypes under saline-alkaline stress. The molecular mechanism explaining the differences between the two cultivars is still unclear. Results: In the present study, we systematically analysed the changes in GF677 and Maotao leaves upon salinealkaline stress by using cytological and biochemical technologies as well as comparative transcriptome analysis. Transmission electron microscopy (TEM) observations showed that the structure of granum was dispersive in Maotao chloroplasts. The biochemical analysis revealed that POD activity and the contents of chlorophyll a and chlorophyll b, as well as iron, were notably decreased in Maotao. Comparative transcriptome analysis detected 881 genes with differential expression (including 294 upregulated and 587 downregulated) under the criteria of |log2 Ratio| ≥ 1 and FDR ≤0.01. Gene ontology (GO) analysis showed that all differentially expressed genes (DEGs) were grouped into 30 groups. MapMan annotation of DEGs showed that photosynthesis, antioxidation, ion metabolism, and WRKY TF were activated in GF677, while cell wall degradation, secondary metabolism, starch degradation, MYB TF, and bHLH TF were activated in Maotao. Several iron and stress-related TFs (ppa024966m, ppa010295m, ppa0271826m, ppa002645m, ppa010846m, ppa009439m, ppa008846m, and ppa007708m) were further discussed from a functional perspective based on the phylogenetic tree integration of other species homologues. Conclusions: According to the cytological and molecular differences between the two cultivars, we suggest that the integrity of chloroplast structure and the activation of photosynthesis as well as stress-related genes are crucial for saline-alkaline resistance in GF677. The results presented in this report provide a theoretical basis for cloning saline-alkaline tolerance genes and molecular breeding to improve saline-alkaline tolerance in peach.

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“…In potato, the UDP-glucosyltransferase gene is highly correlated with glucose and gene expression under cold-induced sweetening [ 55 ]. Genome-wide identification of WRKY genes and their response to cold stress in Coffea canephora showed that UDP-glucosyltransferase activity is remarkably represented [ 56 ]. The overexpression of LTG5 increases the CT of rice at the germination stage.…”

Section: Disccussionmentioning

confidence: 99%

Transcriptomic profiling of germinating seeds under cold stress and characterization of the cold-tolerant gene LTG5 in rice

et al. 2020

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Background: Low temperature is a limiting factor of rice productivity and geographical distribution. Wild rice (Oryza rufipogon Griff.) is an important germplasm resource for rice improvement. It has superior tolerance to many abiotic stresses, including cold stress, but little is known about the mechanism underlying its resistance to cold. Results: This study elucidated the molecular genetic mechanisms of wild rice in tolerating low temperature. Comprehensive transcriptome profiles of two rice genotypes (cold-sensitive ce 253 and cold-tolerant Y12-4) at the germinating stage under cold stress were comparatively analyzed. A total of 42.44-68.71 million readings were obtained, resulting in the alignment of 29,128 and 30,131 genes in genotypes 253 and Y12-4, respectively. Many common and differentially expressed genes (DEGs) were analyzed in the cold-sensitive and cold-tolerant genotypes. Results showed more upregulated DEGs in the cold-tolerant genotype than in the cold-sensitive genotype at four stages under cold stress. Gene ontology enrichment analyses based on cellular process, metabolic process, response stimulus, membrane part, and catalytic activity indicated more upregulated genes than downregulated ones in the cold-tolerant genotype than in the cold-sensitive genotype. Quantitative real-time polymerase chain reaction was performed on seven randomly selected DEGs to confirm the RNA Sequencing (RNA-seq) data. These genes showed similar expression patterns corresponding with the RNA-Seq method. Weighted gene co-expression network analysis (WGCNA) revealed Y12-4 showed more positive genes than 253 under cold stress. We also explored the cold tolerance gene LTG5 (Low Temperature Growth 5) encoding a UDP-glucosyltransferase. The overexpression of the LTG5 gene conferred cold tolerance to indica rice. Conclusion: Gene resources related to cold stress from wild rice can be valuable for improving the cold tolerance of crops.

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Genome-Wide Identification of WRKY Genes and Their Response to Cold Stress in Coffea canephora

Cited by 22 publications

References 54 publications

Genome-wide Identification of WRKY transcription factor family members in sorghum (Sorghum bicolor (L.) moench)

Genome-wide Identification of WRKY transcription factor family members in sorghum (Sorghum bicolor (L.) moench)

Comparative transcriptome analysis reveals gene expression differences between two peach cultivars under saline-alkaline stress

Transcriptomic profiling of germinating seeds under cold stress and characterization of the cold-tolerant gene LTG5 in rice

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