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

Submission Deadline: 31 January 2023 (closed) Submit to Special Issue

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


  • Open Access

    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, DOI:10.32604/phyton.2022.023928
    (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 BnGA2ox genes were distributed in the A and C subgenomes. Subcellular localization predictions suggested that all BnGA2ox proteins were localized in the cytoplasm, and gene structure analysis showed that the BnGA2ox genes contained 2–4 exons. Phylogenetic analysis indicated that BnGA2ox family proteins in monocotyledons and dicotyledons can be divided into four groups, including… More >

  • Open Access

    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 >

  • Open Access

    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 >

  • Open Access

    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 >

  • Open Access

    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 >

  • Open Access

    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 >

  • Open Access

    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. cathayensisMore >

  • Open Access

    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 >

  • Open Access

    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 >

  • Open Access

    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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