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Identification of Genetic/Epigenetic Components Responding to Biotic and Abiotic Stresses in Crops

Submission Deadline: 31 January 2023 (closed)

Guest Editors

Dr. Dayong Zhang, Nanjing Agricultural University, China. dyzhang@njau.edu.cn
Dr. Zhiwei Chen, Shanghai Academy of Agricultural Sciences, China. chenzhiwei@saas.sh.cn
Dr. Zongkuan Wang, Nanjing Agricultural University, China. wangzkuan@njau.edu.cn

Summary

Crops, as human being main sources of food and clothes, are often endured diverse biotic and abiotic stresses, such as high salinity, drought, insect and disease. The genetic locus and epigenetic components play importance roles in responding to these stresses in crops. Accumulating evidences indicated that the proteins belong to classic genetic pathways could interact with the proteins from epigenetic components, and form complicated crosstalk or molecular regulatory network during the response to environmental factors in plants. Therefore, identification and functional analysis by transgenic or CRISPR/Cas9 technology of key components are urgent got sustainable modern agriculture in the future.

This issue highlights recent advances in the field of resistance to stress (biotic and abiotic) in crops. The topics are diverse: the identification of key components (genetic locus, key genes, small moleculars, proteins, secondary metabolites, etc.) from different crop species to response stresses (salt, drought, heat, insect, disease, etc.) and their functional mechanisms, plant-pathogens interactions, and plant-environmental factors acting on these interactions.

Keywords

Crop; Locus; Gene; stress; Molecular Mechanism; Interaction

Published Papers

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ARTICLE

Identification of the SERK Gene Family in Paulownia fortunei and Its Involvement in the Response to Biotic and Abiotic Stresses
Tongman Zhao, Yujie Fan, Yabing Cao, Xiaogai Zhao, Guoqiang Fan
Phyton-International Journal of Experimental Botany, Vol.92, No.9, pp. 2473-2488, 2023, DOI:10.32604/phyton.2023.029469
（This article belongs to this Special Issue: Identification of Genetic/Epigenetic Components Responding to Biotic and Abiotic Stresses in Crops)
Abstract Somatic embryogenesis receptor-like kinases (SERKs) are receptor-like proteins that contain leucine-rich repeats and are involved in various signaling pathways. This study identified SERK family members in the Paulownia fortunei genome and analyzed their characteristics and expression profiles using bioinformatics methods. We identified 12 SERK genes with relatively conserved gene structures and motifs that were distributed unevenly on eight Paulownia chromosomes. The gene promoters contained various cis-acting elements that regulated the expression of the PfSERK genes in response to hormones and abiotic stresses. Synteny analysis indicated that 10 segmental duplication events had occurred during evolution of the PfSERK family. The expression… More >

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Transcriptome and Metabolome Revealed the Mechanism of NtBRL3 Overexpression Tobacco (Nicotiana tabacum L. K326) in Response to Drought Stress
Jing Yang, Tianxiunan Pu, Ke Wan, Linqi Wang, Yuanshuai Shi, Xu Luo, Jie Tan, Dongmei Wang, Yang Liu
Phyton-International Journal of Experimental Botany, Vol.92, No.9, pp. 2555-2576, 2023, DOI:10.32604/phyton.2023.030301
（This article belongs to this Special Issue: Identification of Genetic/Epigenetic Components Responding to Biotic and Abiotic Stresses in Crops)
Abstract Drought has severely affected the yield and quality of commercial crops. The BRI1 family plays an important role in plant response to drought stress, and BRL3 gene plays an important role in the study of drought in Arabidopsis thaliana. In this study, NtBRL3 was constructed as a vector and genetically transformed to obtain ‘N. Tobacco K326’ overexpression of NtBRL3. The enzyme activities of transgenic tobacco and wild-type tobacco were measured and transcriptome and metabolome analyses were performed. The results showed that the antioxidant enzymes of transgenic tobacco were more active under drought conditions, and 85 significantly differentially metabolites and 106… More >

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ARTICLE

Identification and Expression Analysis of Abscisic Acid Signal Transduction Genes in Hemp Seeds
Cong Hou, Kang Ning, Xiuye Wei, Yufei Cheng, Huatao Yu, Haibin Yu, Xia Liu, Linlin Dong
Phyton-International Journal of Experimental Botany, Vol.92, No.7, pp. 2087-2103, 2023, DOI:10.32604/phyton.2023.029041
（This article belongs to this Special Issue: Identification of Genetic/Epigenetic Components Responding to Biotic and Abiotic Stresses in Crops)
Abstract Abscisic acid (ABA) is involved in regulating diverse biological processes, but its signal transduction genes and roles in hemp seed germination are not well known. Here, the ABA signaling pathway members, PYL, PP2C and SnRK2 gene families, were identified from the hemp reference genome, including 7 CsPYL (pyrab-actin resistance1-like, ABA receptor), 8 CsPP2CA (group A protein phosphatase 2c), and 7 CsSnRK2 (sucrose nonfermenting1-related protein kinase 2). The content of ABA in hemp seeds in germination stage is lower than that in non-germination stage. Exogenous ABA (1 or 10 μM) treatment had a significant regulatory effect on the selected PYL, PP2C,… More >

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Analysis of Subcellular Localization and Pathogenicity of Plum Bark Necrosis Stem-Pitting Associated Virus Protein P6
Yuanyuan Li, Jinze Mu, Qingliang Li, Huabing Liu, Xuefeng Yuan, Deya Wang
Phyton-International Journal of Experimental Botany, Vol.92, No.7, pp. 2079-2085, 2023, DOI:10.32604/phyton.2023.028237
（This article belongs to this Special Issue: Identification of Genetic/Epigenetic Components Responding to Biotic and Abiotic Stresses in Crops)
Abstract Infection of plum bark necrosis stem pitting associated virus (PBNSPaV) has been reported in many Prunus species in several countries, causing significant economic losses. The very small proteins encoded by plant viruses are often overlooked due to their short sequences and uncertain significance. However, numerous studies have indicated that they might play important roles in the pathogenesis of virus infection. The role of small hydrophobic protein P6, encoded by the open reading frame 2 of PBNSPaV, has not been well explored. In this study, we amplified the P6 fragment from a PBNSPaV isolate by RT-PCR using specific primers and found… More >

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Rice E3 Ligase-Like Protein OsPIAL1 Positively Regulated the Drought Stress Response but Negatively Regulated the Salt Stress Response
Sang Ik Song
Phyton-International Journal of Experimental Botany, Vol.92, No.7, pp. 2017-2034, 2023, DOI:10.32604/phyton.2023.027469
（This article belongs to this Special Issue: Identification of Genetic/Epigenetic Components Responding to Biotic and Abiotic Stresses in Crops)
Abstract Small ubiquitin-like modifier (SUMO) E3 ligases that facilitate the conjugation of SUMO proteins to target substrates contain an SP-RING domain which is like the RING domain found in ubiquitin E3 ligases. In this study, we isolated and characterized the Oryza sativa protein inhibitor of activated STAT like1 (OsPIAL1) containing SP-RING domains, as the rice homolog of Arabidopsis PIALs. OsPIAL1 interacts with OsSUMO proteins but does not interact with rice SUMO-conjugating enzymes (OsSCEs). An analysis of transgenic rice plant shows that OsPIAL1 is involved in SUMO conjugation to SCEs but not in SUMO conjugation to substrates. In addition, this OsPIAL1 activity… More >

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Identification of a Novel OsCYP2 Allele that Was Involved in Rice Response to Low Temperature Stress
Hongxiu Gao, Lin Zhu, Tianqi Liu, Xueyu Leng, Zhenxing Zhu, Wei Xie, Haitao Lv, Zhengxun Jin, Ping Wu, Zhongchen Zhang
Phyton-International Journal of Experimental Botany, Vol.92, No.6, pp. 1743-1763, 2023, DOI:10.32604/phyton.2023.026516
（This article belongs to this Special Issue: Identification of Genetic/Epigenetic Components Responding to Biotic and Abiotic Stresses in Crops)
Abstract Cyclophilin (CYP) plays an important role in plant response to stress, and OsCYP2, one gene of cyclophlilin family, is involved in auxin signal transduction and stress signaling in rice. However, the mechanism that OsCYP2 is involved in rice response to low temperature is still unclear. We identified a new OsCYP2 allelic mutant, lrl3, with fewer lateral roots, and the differences in shoot height, primary root length and adventitious root length increased with the growth process compared to the wild-type plant. Auxin signaling pathway was also affected and became insensitive to gravity. The transgenic rice plants with over-expression of OsCYP2 were… More >

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REVIEW

Application of Silicon and Selenium in Rice for Reducing Cadmium Stress
Mohammad Reza Boorboori, Husen Qiu, Jieyun Liu, Haiyang Zhang
Phyton-International Journal of Experimental Botany, Vol.92, No.6, pp. 1873-1886, 2023, DOI:10.32604/phyton.2023.027924
（This article belongs to this Special Issue: Identification of Genetic/Epigenetic Components Responding to Biotic and Abiotic Stresses in Crops)
Abstract Rice is an essential part of the human diet in most parts of the world; On the other hand, the industrialization of societies has led to pollution of the environment, including heavy metal contamination of soil and water, which negatively affects rice production and quality. Therefore, finding ways to increase the yield and quality of this strategic crop seems essential. Several studies have been conducted in recent decades to find effective and inexpensive solutions to reduce the adverse effects of heavy metals in rice fields. Due to the negative effect of cadmium pollution on rice quality and yield, the current… More >

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Comparative Non Participating Transcriptome Analysis Response to Low Phosphorus by CmPht1;2 in Chrysanthemum
Chen Liu , Xiaowei Tang, Xiaohui Qu , Fadi Chen, Jiafu Jiang and Sumei Chen
Phyton-International Journal of Experimental Botany, Vol.92, No.5, pp. 1391-1404, 2023, DOI:10.32604/phyton.2023.027231
（This article belongs to this Special Issue: Identification of Genetic/Epigenetic Components Responding to Biotic and Abiotic Stresses in Crops)
Abstract Chrysanthemum morifolium Ramat is one of the four major cut flowers in the world. Pht1 family is focus on the uptake and transport of phosphate in plants. In our previous studies, CmPht1;2 overexpression line (Oe1) had higher phosphate contents both in roots and shoots, and its root development was significantly enhanced than wild type (WT) at low phosphorus conditions in chrysanthemum. Metabolomics analysis showed that several metabolites had a change in pyruvate metabolism and tricarboxylic acid (TCA) cycle pathway. To explore the gene difference expression and the change of metabolic pathway between CmPht1;2-Oe1 and WT, we conducted the transcriptome analysis.… More >

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Cloning and Function Identification of a Phytoene Desaturase Gene from Eucommia ulmoides
Jiali Wang, Xiangmei Chen, Xiaozhen Huang, Yichen Zhao, Degang Zhao
Phyton-International Journal of Experimental Botany, Vol.92, No.5, pp. 1377-1389, 2023, DOI:10.32604/phyton.2023.026830
（This article belongs to this Special Issue: Identification of Genetic/Epigenetic Components Responding to Biotic and Abiotic Stresses in Crops)
Abstract The phytoene desaturase (PDS) encodes a crucial enzyme in the carotenoid biosynthesis pathway. Silencing or inhibiting PDS expression leads to the appearance of mottled, chlorosis, or albino leaves. In this study, the CDS sequence of EuPDS (Eucommia ulmoides Phytoene Desaturase) was first cloned and then PDS was silenced in Nicotiana benthamiana. Result showed the expression level of EuPDS in leaves was higher than that in the roots and stems. In N. benthamiana leaves, which were treated by Agrobacterium for 24 h, photo-bleaching was shown on the fresh leaves one week after injection and the transcript level of PDS was down-regulated… More >

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ARTICLE

Genome-Wide Identification and Characterisation of Abiotic Stress Responsive mTERF Gene Family in Amaranthus hypochondriacus
Mortaza Hajyzadeh
Phyton-International Journal of Experimental Botany, Vol.92, No.5, pp. 1649-1664, 2023, DOI:10.32604/phyton.2023.028028
（This article belongs to this Special Issue: Identification of Genetic/Epigenetic Components Responding to Biotic and Abiotic Stresses in Crops)
Abstract Abiotic stresses at different growth stages in the life of plants negatively affect yield productivity. Therefore, plants, including Amaranthus hypochondriacus, develop adaptive strategies to face the stresses and expand functional diversification. In plants, the mitochondrial transcription termination factors (mTERF) are essential functions in regulation, and organelles (mitochondria and chloroplasts) control gene expression (OGE) under several stress conditions. Based on the in-silico-wide genome and transcriptome analysis, twenty-four mTERF genes were detected in the main targeted mitochondria organelles clustered into three different main groups. The chromosomal location and gene duplication analysis indicated one segmental and one tandem duplication in the genome. The… More >

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ARTICLE

Proteomic Analyses of Three Inflorescence Styles of Castor (Ricinus communis L.) at Different Developmental Stages
Xue Lei, Yong Zhao, Rui Luo, Mingda Yin, Yanpeng Wen, Zhiyan Wang, Xuemei Hu, Fenglan Huang
Phyton-International Journal of Experimental Botany, Vol.92, No.5, pp. 1621-1632, 2023, DOI:10.32604/phyton.2023.027046
（This article belongs to this Special Issue: Identification of Genetic/Epigenetic Components Responding to Biotic and Abiotic Stresses in Crops)
Abstract Castor (Ricinus communis L.) is one of ten oil crops in the world and has complex inflorescence styles. Generally, castor has three inflorescence types: single female inflorescence (SiFF), standard female inflorescence (StFF) and bisexual inflorescence (BF). StFF is realized as a restorer line and as a maintainer line, which was applied to castor hybrid breeding. However, the developmental mechanism of the three inflorescences is not clear. Therefore, we used proteomic techniques to analyze different inflorescence styles. A total of 72 diferentially abundant protein species (DAPs) were detected. These DAPs are primarily involved in carbon and energy metabolism and carbon fixation… More >

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ARTICLE

Comparative Transcriptome Analyses Reveal Genes Related to Spine Development in Cucumber (Cucumis sativus)
Yue Chen, Huan Wang, Taibai Xu, Peng Zhou, Junsong Pan, Weiwei She, Weiwei Zhang
Phyton-International Journal of Experimental Botany, Vol.92, No.4, pp. 1059-1070, 2023, DOI:10.32604/phyton.2023.026486
（This article belongs to this Special Issue: Identification of Genetic/Epigenetic Components Responding to Biotic and Abiotic Stresses in Crops)
Abstract Fruit spine is an important quality trait of cucumber. To better understand the molecular basis of cucumber spine development and function, RNA-Seq was performed to identify differentially expressed genes (DEGs) in fruit spines of different development stages, namely, 8 days before anthesis (SpBA8), anthesis (SpA) and 8 days after anthesis (SpAA8). Stage-wise comparisons obtained 2,259 (SpBA8 vs. SpA), 4,551 (SpA vs. SpAA8), and 5,290 (SpBA8 vs. SpAA8) DEGs. All the DEGs were classified into eight expression clusters by trend analysis. Among these DEGs, in addition to the Mict, Tril, CsTTG1, CsMYB6, NS, and Tu genes that have been reported to… More >

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ARTICLE

Genetic Diversity and Population Structure Analysis of Barley Landraces from Shanghai Region Using Genotyping-by-Sequencing
Luli Li, Nigel G. Halford, Huihui Wang, Yingjie Zong, Zhenzhu Guo, Ruiju Lu, Chenghong Liu, Zhiwei Chen
Phyton-International Journal of Experimental Botany, Vol.92, No.4, pp. 1275-1287, 2023, DOI:10.32604/phyton.2023.026946
（This article belongs to this Special Issue: Identification of Genetic/Epigenetic Components Responding to Biotic and Abiotic Stresses in Crops)
Abstract Barley (Hordeum vulgare L.) is an important economic crop for food, feed and industrial raw materials. In the present research, 112 barley landraces from the Shanghai region were genotyped using genotyping-by-sequencing (GBS), and the genetic diversity and population structure were analyzed. The results showed that 210,268 Single Nucleotide Polymorphisms (SNPs) were present in total, and the average poly-morphism information content (PIC) was 0.1642. Genetic diversity and population structure analyses suggested that these barley landraces were differentiated and could be divided into three sub-groups, with morphological traits of row-type and adherence of the hulls the main distinguishing factors between groups. Genotypes… More >

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ARTICLE

VvAGAMOUS Affect Development of Four Different Grape Species Ovary
Pengfei Zhang, Yuqin Zhang, Qifeng Zhao, Tiequan Niu, Pengfei Wen, Jinjun Liang
Phyton-International Journal of Experimental Botany, Vol.92, No.4, pp. 1125-1138, 2023, DOI:10.32604/phyton.2023.026227
（This article belongs to this Special Issue: Identification of Genetic/Epigenetic Components Responding to Biotic and Abiotic Stresses in Crops)
Abstract Grape pistil has an important influence on fruit size and quality. However, there were few studies on grape ovary, and the development process of the ovary is still unclear. Therefore, in this paper, four different grape varieties with different lengths of small inflorescences, namely ‘Musct Hambourg’ grape (Vitis vinifera), ‘Concord’ grape (Vitis labrusca), ‘ShanPuTao’ grape (Vitis amurensis) and ‘GongNiang2Hao’ grape (Vitis amurensis × Vitis vinifera) were used as test materials. Four varieties ovary were significant differences by means of stereomicroscope, paraffin section. The expression of ovary determining gene VvAGAMOUS (VvAG) and its development related genes VvCRABS CLAW (VvCRC) and VvAGAMOUS-LIKE 11 … More >

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ARTICLE

Identification and Characterization of ZF-HD Genes in Response to Abscisic Acid and Abiotic Stresses in Maize
Xiaojie Jing, Chunyan Li, Chengjuan Luo, Chaonan Yao, Jiahao Zhang, Tingting Zhu, Jiuguang Wang, Chaoxian Liu
Phyton-International Journal of Experimental Botany, Vol.92, No.3, pp. 707-723, 2023, DOI:10.32604/phyton.2023.024338
（This article belongs to this Special Issue: Identification of Genetic/Epigenetic Components Responding to Biotic and Abiotic Stresses in Crops)
Abstract The zinc finger homeodomain (ZF-HD) genes belong to the homeobox gene family, playing critical roles in flower development and stress response. Despite their importance, however, to date there has been no genome-wide identification and characterization of the ZF-HD genes that are probably involved in stress responses in maize. In this study, 24 ZF-HD genes were identified, and their chromosomal locations, protein properties, duplication patterns, structures, conserved motifs and expression patterns were investigated. The results revealed that the ZF-HD genes are unevenly distributed on nine chromosomes and that most of these genes lack introns. Six and two ZF-HD genes have undergone… More >

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ARTICLE

Selection of Stable Reference Genes for Quantitative Real-Time PCR on Herbaceous Peony (Paeonia lactiflora Pall.) in Response to Drought Stress
Zhipeng Sheng, Yuting Luan, Cong Xu, Jun Tao, Daqiu Zhao
Phyton-International Journal of Experimental Botany, Vol.92, No.3, pp. 801-814, 2023, DOI:10.32604/phyton.2023.024953
（This article belongs to this Special Issue: Identification of Genetic/Epigenetic Components Responding to Biotic and Abiotic Stresses in Crops)
Abstract Herbaceous peony (Paeonia lactiflora Pall.), as a high-end cut flower in the international market, has high ornamental and medicinal values. But in Northern China, drought is a major environmental factor influencing the growth and development of P. lactiflora. Quantitative real-time polymerase chain reaction (qRT-PCR) can evaluate gene expression levels under different stress conditions, and stable internal reference is the key for qRT-PCR. At present, there is no systematic screening of internal reference for correcting gene expressions of P. lactiflora in response to drought stress. In this study, 10 candidate genes [ubiquitin (UBQ2), UBQ1, elongation factor 1-α (EF-1α), Histidine (His), eukaryotic… More >

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ARTICLE

Comparative Analysis of the Photosynthetic Characteristics and Active Compounds of Semiliquidambar cathayensis Chang Heteromorphic Leaves
Xiaoming Tian, Guangfeng Xiang, Hao Lv, Jing Peng, Lu Zhu
Phyton-International Journal of Experimental Botany, Vol.92, No.3, pp. 837-850, 2023, DOI:10.32604/phyton.2023.024408
（This article belongs to this Special Issue: Identification of Genetic/Epigenetic Components Responding to Biotic and Abiotic Stresses in Crops)
Abstract In the present study, the variation patterns of leaf shape in different populations of individual Semiliquidambar cathayensis plants were analyzed to investigate the relationship among leaf shape variation, photosynthetic properties, and active compounds to understand the genetic characteristics of S. cathayensis and screen elite germplasms. The leaf shape of 18 offspring from three natural S. cathayensis populations was analyzed to investigate the level of diversity and variation patterns of leaf shape. Furthermore, photosynthetic pigment content, physiological parameters of photosynthesis, and the active compounds in leaves of different shapes were determined. Statistical analysis showed that the leaf shape variation in S. cathayensis… More >

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ARTICLE

Genome-Wide Identification, Evolution and Expression Analyses of GA2ox Gene Family in Brassica napus L.
Yanhua Li, Hualei Huang, Youming Shi, Shuqin Huang, Tao Liu, Changming Xiao, Xiaoqing Tian, Ping Zhao, Xiaoyan Dai, Taocui Huang, Yan Zhou
Phyton-International Journal of Experimental Botany, Vol.92, No.3, pp. 815-835, 2023, DOI:10.32604/phyton.2023.023928
（This article belongs to this Special Issue: Identification of Genetic/Epigenetic Components Responding to Biotic and Abiotic Stresses in Crops)
Abstract Gibberellin 2-oxidases (GA2ox) are important enzymes that maintain the balance of bioactive GAs in plants. GA2ox genes have been identified and characterized in many plants, but these genes were not investigated in Brassica napus. Here, we identified 31 GA2ox genes in B. napus and 15 of these BnaGA2ox genes were distributed in the A and C subgenomes. Subcellular localization predictions suggested that all BnaGA2ox proteins were localized in the cytoplasm, and gene structure analysis showed that the BnaGA2ox genes contained 2–4 exons. Phylogenetic analysis indicated that BnGA2ox family proteins in monocotyledons and dicotyledons can be divided into four groups, including… More >

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ARTICLE

De Novo Transcriptome Analysis in Hevea brasiliensis to Unveil Genes Involved in Low Temperature Stress Response
Bingsong Yang, Xiaomeng Shi, Tingting Guo, Meixia Liang
Phyton-International Journal of Experimental Botany, Vol.92, No.2, pp. 559-575, 2023, DOI:10.32604/phyton.2022.024266
（This article belongs to this Special Issue: Identification of Genetic/Epigenetic Components Responding to Biotic and Abiotic Stresses in Crops)
Abstract Low temperature is one of the adversities threatening the growth and development and reduces the yield of rubber trees. However, molecular mechanisms toward rubber trees in response to low temperature are largely unclear. In this study, 7,159 and 7,600 differentially expressed genes (DEGs) were identified in ‘Reyan 73397’ rubber trees. Through GO analysis, the catalytic activity was the representative of the GO term in the only DEGs at the two studied temperatures (room temperature and 4°C, respectively), while KEGG analysis showed that carbon metabolism was the most important grouping under the comparison of these two temperatures. In addition, expression of… More >

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ARTICLE

Chickpea C2H2-Type Zinc Finger Protein ZF2 is a Positive Regulator in Drought Response in Arabidopsis
Sushuang Liu, Yanmin Liu, Chundong Liu, Xingwang Yu, Hao Ma
Phyton-International Journal of Experimental Botany, Vol.92, No.2, pp. 577-590, 2023, DOI:10.32604/phyton.2022.023738
（This article belongs to this Special Issue: Identification of Genetic/Epigenetic Components Responding to Biotic and Abiotic Stresses in Crops)
Abstract Drought is a major abiotic stress limiting agricultural crops production worldwide. In our study, we isolated a novel C2H2-type zinc finger protein gene ZF2 from chickpea. ZF2 consisted of 232 amino acids with two QALGGH motifs in Cys2/His2 zinc finger domain. Transient expression analysis of ZF2:GFP fusion protein showed that ZF2 was a nuclear localized protein. In the yeast assay system, the full-length of ZF2 did not show transcriptional activation. Expression of ZF2 gene was enhanced by treatments of several abiotic stresses and phytohormones. The promoter region of ZF2 contained multiple stress- and hormone-related cis-elements. Overexpression of ZF2 in Arabidopsis… More >

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Identification of Genetic/Epigenetic Components Responding to Biotic and Abiotic Stresses in Crops

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