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Spada M, Pugliesi C, Fambrini M, Pecchia S. Challenges and Opportunities Arising from Host- Botrytis cinerea Interactions to Outline Novel and Sustainable Control Strategies: The Key Role of RNA Interference. Int J Mol Sci 2024; 25:6798. [PMID: 38928507 PMCID: PMC11203536 DOI: 10.3390/ijms25126798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 06/18/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024] Open
Abstract
The necrotrophic plant pathogenic fungus Botrytis cinerea (Pers., 1794), the causative agent of gray mold disease, causes significant losses in agricultural production. Control of this fungal pathogen is quite difficult due to its wide host range and environmental persistence. Currently, the management of the disease is still mainly based on chemicals, which can have harmful effects not only on the environment and on human health but also because they favor the development of strains resistant to fungicides. The flexibility and plasticity of B. cinerea in challenging plant defense mechanisms and its ability to evolve strategies to escape chemicals require the development of new control strategies for successful disease management. In this review, some aspects of the host-pathogen interactions from which novel and sustainable control strategies could be developed (e.g., signaling pathways, molecules involved in plant immune mechanisms, hormones, post-transcriptional gene silencing) were analyzed. New biotechnological tools based on the use of RNA interference (RNAi) are emerging in the crop protection scenario as versatile, sustainable, effective, and environmentally friendly alternatives to the use of chemicals. RNAi-based fungicides are expected to be approved soon, although they will face several challenges before reaching the market.
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Affiliation(s)
- Maria Spada
- Department of Agriculture Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
| | - Claudio Pugliesi
- Department of Agriculture Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
| | - Marco Fambrini
- Department of Agriculture Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
| | - Susanna Pecchia
- Department of Agriculture Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
- Interdepartmental Research Center Nutrafood “Nutraceuticals and Food for Health”, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
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Chang Y, Liu Y, Wang L, Wang S, Wu J. Global transcriptome analysis reveals resistance genes in the early response of common bean (Phaseolus vulgaris L.) to Colletotrichum lindemuthianum. BMC Genomics 2024; 25:579. [PMID: 38858660 PMCID: PMC11165746 DOI: 10.1186/s12864-024-10497-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 06/05/2024] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND Disease can drastically impair common bean (Phaseolus vulgaris L.) production. Anthracnose, caused by the fungal pathogen Colletotrichum lindemuthianum (Sacc. and Magnus) Briosi and Cavara, is one of the diseases that are widespread and cause serious economic loss in common bean. RESULTS Transcriptome analysis of the early response of common bean to anthracnose was performed using two resistant genotypes, Hongyundou and Honghuayundou, and one susceptible genotype, Jingdou. A total of 9,825 differentially expressed genes (DEGs) responding to pathogen infection and anthracnose resistance were identified by differential expression analysis. By using weighted gene coexpression network analysis (WGCNA), 2,051 DEGs were found to be associated with two resistance-related modules. Among them, 463 DEGs related to anthracnose resistance were considered resistance-related candidate genes. Nineteen candidate genes were coexpressed with three resistance genes, Phvul.001G243600, Phvul.001G243700 and Phvul.001G243800. To further identify resistance genes, 46 candidate genes were selected for experimental validation using salicylic acid (SA) and methyl jasmonate (MeJA). The results indicated that 38 candidate genes that responded to SA/MeJA treatment may be involved in anthracnose resistance in common bean. CONCLUSIONS This study identified 38 resistance-related candidate genes involved in the early response of common bean, and 19 resistance-related candidate genes were coexpressed with anthracnose resistance genes. This study identified putative resistance genes for further resistance genetic investigation and provides an important reference for anthracnose resistance breeding in common bean.
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Affiliation(s)
- Yujie Chang
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yonghui Liu
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lanfen Wang
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shumin Wang
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jing Wu
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Zhu L, Zhang M, Yang X, Zi Y, Yin T, Li X, Wen K, Zhao K, Wan J, Zhang H, Luo X, Zhang H. Genome-wide identification of bZIP transcription factors in 12 Rosaceae species and modeling of novel mechanisms of EjbZIPs response to salt stress. THE PLANT GENOME 2024:e20468. [PMID: 38840305 DOI: 10.1002/tpg2.20468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 04/18/2024] [Accepted: 05/02/2024] [Indexed: 06/07/2024]
Abstract
In plantae, basic leucine zipper (bZIP) transcription factors (TFs) are widespread and regulate a variety of biological processes under abiotic stress. However, it has not been extensively studied in Rosaceae, and the functional effects of bZIP on Eriobotrya japonica under salt stress are still unknown. Therefore, in this study, the bZIP TF family of 12 species of Rosaceae was analyzed by bioinformatics method, and the expression profile and quantitative real-time polymerase chain reaction of E. japonica under salt stress were analyzed. The results showed that a total of 869 bZIP TFs were identified in 12 species of Rosaceae and divided into nine subfamilies. Differences in promoter cis-elements between subfamilies vary depending on their role. Species belonging to the same subfamily have a similar number of chromosomes and the number of genes contained on each chromosome. Gene duplication analysis has found segmental duplication to be a prime force in the evolution of Rosaceae species. In addition, nine EjbZIPs were significantly different, including seven up-regulated and two down-regulated in E. japonica under salt stress. Especially, EjbZIP13 was involved in the expression of SA-responsive proteins by binding to the NPR1 gene. EjbZIP27, EjbZIP30, and EjbZIP38 were highly expressed in E. japonica under salt stress, thus improving the salt tolerance capacity of the plants. These results can provide a theoretical basis for exploring the characteristics and functions of the bZIP TF family in more species and breeding salt-tolerant E. japonica varieties. It also provides a reference for resolving the response mechanism of bZIP TF in 12 Rosaceae species under salt stress.
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Affiliation(s)
- Ling Zhu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agriculture Sciences, Bao Shan, China
| | | | - Xiuyao Yang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
| | - Yinqiang Zi
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
| | - Tuo Yin
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
| | - Xulin Li
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
| | - Ke Wen
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
| | - Ke Zhao
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
| | - Jiaqiong Wan
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
| | - Huiyun Zhang
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agriculture Sciences, Bao Shan, China
| | - Xinping Luo
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agriculture Sciences, Bao Shan, China
| | - Hanyao Zhang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
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Chen L, Hu Y, Huang L, Chen L, Duan X, Wang G, Ou H. Comparative transcriptome revealed the molecular responses of Aconitum carmichaelii Debx. to downy mildew at different stages of disease development. BMC PLANT BIOLOGY 2024; 24:332. [PMID: 38664645 PMCID: PMC11044490 DOI: 10.1186/s12870-024-05048-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 04/19/2024] [Indexed: 04/29/2024]
Abstract
BACKGROUND Aconitum carmichaelii Debx. has been widely used as a traditional medicinal herb for a long history in China. It is highly susceptible to various dangerous diseases during the cultivation process. Downy mildew is the most serious leaf disease of A. carmichaelii, affecting plant growth and ultimately leading to a reduction in yield. To better understand the response mechanism of A. carmichaelii leaves subjected to downy mildew, the contents of endogenous plant hormones as well as transcriptome sequencing were analyzed at five different infected stages. RESULTS The content of 3-indoleacetic acid, abscisic acid, salicylic acid and jasmonic acid has changed significantly in A. carmichaelii leaves with the development of downy mildew, and related synthetic genes such as 9-cis-epoxycarotenoid dioxygenase and phenylalanine ammonia lyase were also significant for disease responses. The transcriptomic data indicated that the differentially expressed genes were primarily associated with plant hormone signal transduction, plant-pathogen interaction, the mitogen-activated protein kinase signaling pathway in plants, and phenylpropanoid biosynthesis. Many of these genes also showed potential functions for resisting downy mildew. Through weighted gene co-expression network analysis, the hub genes and genes that have high connectivity to them were identified, which could participate in plant immune responses. CONCLUSIONS In this study, we elucidated the response and potential genes of A. carmichaelii to downy mildew, and observed the changes of endogenous hormones content at different infection stages, so as to contribute to the further screening and identification of genes involved in the defense of downy mildew.
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Affiliation(s)
- Lijuan Chen
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Yiwen Hu
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Li Huang
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Long Chen
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Xianglei Duan
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Guangzhi Wang
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
| | - Hong Ou
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, China.
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Gao H, Ma J, Zhao Y, Zhang C, Zhao M, He S, Sun Y, Fang X, Chen X, Ma K, Pang Y, Gu Y, Dongye Y, Wu J, Xu P, Zhang S. The MYB Transcription Factor GmMYB78 Negatively Regulates Phytophthora sojae Resistance in Soybean. Int J Mol Sci 2024; 25:4247. [PMID: 38673832 PMCID: PMC11050205 DOI: 10.3390/ijms25084247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
Phytophthora root rot is a devastating disease of soybean caused by Phytophthora sojae. However, the resistance mechanism is not yet clear. Our previous studies have shown that GmAP2 enhances sensitivity to P. sojae in soybean, and GmMYB78 is downregulated in the transcriptome analysis of GmAP2-overexpressing transgenic hairy roots. Here, GmMYB78 was significantly induced by P. sojae in susceptible soybean, and the overexpressing of GmMYB78 enhanced sensitivity to the pathogen, while silencing GmMYB78 enhances resistance to P. sojae, indicating that GmMYB78 is a negative regulator of P. sojae. Moreover, the jasmonic acid (JA) content and JA synthesis gene GmAOS1 was highly upregulated in GmMYB78-silencing roots and highly downregulated in overexpressing ones, suggesting that GmMYB78 could respond to P. sojae through the JA signaling pathway. Furthermore, the expression of several pathogenesis-related genes was significantly lower in GmMYB78-overexpressing roots and higher in GmMYB78-silencing ones. Additionally, we screened and identified the upstream regulator GmbHLH122 and downstream target gene GmbZIP25 of GmMYB78. GmbHLH122 was highly induced by P. sojae and could inhibit GmMYB78 expression in resistant soybean, and GmMYB78 was highly expressed to activate downstream target gene GmbZIP25 transcription in susceptible soybean. In conclusion, our data reveal that GmMYB78 triggers soybean sensitivity to P. sojae by inhibiting the JA signaling pathway and the expression of pathogenesis-related genes or through the effects of the GmbHLH122-GmMYB78-GmbZIP25 cascade pathway.
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Affiliation(s)
- Hong Gao
- Soybean Research Institute of Northeast Agricultural University/Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin 150030, China; (H.G.); (J.M.); (Y.Z.); (C.Z.); (M.Z.); (S.H.); (Y.S.); (X.F.); (X.C.); (K.M.); (Y.P.); (Y.G.); (Y.D.)
| | - Jia Ma
- Soybean Research Institute of Northeast Agricultural University/Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin 150030, China; (H.G.); (J.M.); (Y.Z.); (C.Z.); (M.Z.); (S.H.); (Y.S.); (X.F.); (X.C.); (K.M.); (Y.P.); (Y.G.); (Y.D.)
| | - Yuxin Zhao
- Soybean Research Institute of Northeast Agricultural University/Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin 150030, China; (H.G.); (J.M.); (Y.Z.); (C.Z.); (M.Z.); (S.H.); (Y.S.); (X.F.); (X.C.); (K.M.); (Y.P.); (Y.G.); (Y.D.)
| | - Chuanzhong Zhang
- Soybean Research Institute of Northeast Agricultural University/Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin 150030, China; (H.G.); (J.M.); (Y.Z.); (C.Z.); (M.Z.); (S.H.); (Y.S.); (X.F.); (X.C.); (K.M.); (Y.P.); (Y.G.); (Y.D.)
| | - Ming Zhao
- Soybean Research Institute of Northeast Agricultural University/Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin 150030, China; (H.G.); (J.M.); (Y.Z.); (C.Z.); (M.Z.); (S.H.); (Y.S.); (X.F.); (X.C.); (K.M.); (Y.P.); (Y.G.); (Y.D.)
| | - Shengfu He
- Soybean Research Institute of Northeast Agricultural University/Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin 150030, China; (H.G.); (J.M.); (Y.Z.); (C.Z.); (M.Z.); (S.H.); (Y.S.); (X.F.); (X.C.); (K.M.); (Y.P.); (Y.G.); (Y.D.)
| | - Yan Sun
- Soybean Research Institute of Northeast Agricultural University/Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin 150030, China; (H.G.); (J.M.); (Y.Z.); (C.Z.); (M.Z.); (S.H.); (Y.S.); (X.F.); (X.C.); (K.M.); (Y.P.); (Y.G.); (Y.D.)
| | - Xin Fang
- Soybean Research Institute of Northeast Agricultural University/Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin 150030, China; (H.G.); (J.M.); (Y.Z.); (C.Z.); (M.Z.); (S.H.); (Y.S.); (X.F.); (X.C.); (K.M.); (Y.P.); (Y.G.); (Y.D.)
| | - Xiaoyu Chen
- Soybean Research Institute of Northeast Agricultural University/Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin 150030, China; (H.G.); (J.M.); (Y.Z.); (C.Z.); (M.Z.); (S.H.); (Y.S.); (X.F.); (X.C.); (K.M.); (Y.P.); (Y.G.); (Y.D.)
| | - Kexin Ma
- Soybean Research Institute of Northeast Agricultural University/Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin 150030, China; (H.G.); (J.M.); (Y.Z.); (C.Z.); (M.Z.); (S.H.); (Y.S.); (X.F.); (X.C.); (K.M.); (Y.P.); (Y.G.); (Y.D.)
| | - Yanjie Pang
- Soybean Research Institute of Northeast Agricultural University/Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin 150030, China; (H.G.); (J.M.); (Y.Z.); (C.Z.); (M.Z.); (S.H.); (Y.S.); (X.F.); (X.C.); (K.M.); (Y.P.); (Y.G.); (Y.D.)
| | - Yachang Gu
- Soybean Research Institute of Northeast Agricultural University/Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin 150030, China; (H.G.); (J.M.); (Y.Z.); (C.Z.); (M.Z.); (S.H.); (Y.S.); (X.F.); (X.C.); (K.M.); (Y.P.); (Y.G.); (Y.D.)
| | - Yaqun Dongye
- Soybean Research Institute of Northeast Agricultural University/Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin 150030, China; (H.G.); (J.M.); (Y.Z.); (C.Z.); (M.Z.); (S.H.); (Y.S.); (X.F.); (X.C.); (K.M.); (Y.P.); (Y.G.); (Y.D.)
| | - Junjiang Wu
- Soybean Research Institute of Heilongjiang Academy of Agricultural Sciences/Key Laboratory of Soybean Cultivation of Ministry of Agriculture, Harbin 150030, China;
| | - Pengfei Xu
- Soybean Research Institute of Northeast Agricultural University/Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin 150030, China; (H.G.); (J.M.); (Y.Z.); (C.Z.); (M.Z.); (S.H.); (Y.S.); (X.F.); (X.C.); (K.M.); (Y.P.); (Y.G.); (Y.D.)
| | - Shuzhen Zhang
- Soybean Research Institute of Northeast Agricultural University/Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin 150030, China; (H.G.); (J.M.); (Y.Z.); (C.Z.); (M.Z.); (S.H.); (Y.S.); (X.F.); (X.C.); (K.M.); (Y.P.); (Y.G.); (Y.D.)
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Li D, Li X, Wang Z, Wang H, Gao J, Liu X, Zhang Z. Transcription factors RhbZIP17 and RhWRKY30 enhance resistance to Botrytis cinerea by increasing lignin content in rose petals. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1633-1646. [PMID: 38180121 DOI: 10.1093/jxb/erad473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 01/04/2024] [Indexed: 01/06/2024]
Abstract
The petals of ornamental plants such as roses (Rosa spp.) are the most economically important organs. This delicate, short-lived plant tissue is highly susceptible to pathogens, in large part because the walls of petal cells are typically thinner and more flexible compared with leaf cells, allowing the petals to fold and bend without breaking. The cell wall is a dynamic structure that rapidly alters its composition in response to pathogen infection, thereby reinforcing its stability and boosting plant resistance against diseases. However, little is known about how dynamic changes in the cell wall contribute to resistance to Botrytis cinerea in rose petals. Here, we show that the B. cinerea-induced transcription factor RhbZIP17 is required for the defense response of rose petals. RhbZIP17 is associated with phenylpropanoid biosynthesis and binds to the promoter of the lignin biosynthesis gene RhCAD1, activating its expression. Lignin content showed a significant increase under gray mold infection compared with the control. RhCAD1 functions in the metabolic regulation of lignin production and, consequently, disease resistance, as revealed by transient silencing and overexpression in rose petals. The WRKY transcription factor RhWRKY30 is also required to activate RhCAD1 expression and enhance resistance against B. cinerea. We propose that RhbZIP17 and RhWRKY30 increase lignin biosynthesis, improve the resistance of rose petals to B. cinerea, and regulate RhCAD1 expression.
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Affiliation(s)
- Dandan Li
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China
| | - Xiaomei Li
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China
| | - Zicheng Wang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China
| | - Haochen Wang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China
| | - Junzhao Gao
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China
| | - Xintong Liu
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China
| | - Zhao Zhang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China
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Wang S, Zhao Y, Chen Y, Gao M, Wang Y. The Association between BZIP Transcription Factors and Flower Development in Litsea cubeba. Int J Mol Sci 2023; 24:16646. [PMID: 38068969 PMCID: PMC10705912 DOI: 10.3390/ijms242316646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/17/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
The basic leucine zipper (bZIP) family is one of the largest families of transcription factors among eukaryotic organisms. Members of the bZIP family play various roles in regulating the intricate process of flower development in plants. Litsea cubeba (Lour.) (family: Lauraceae) is an aromatic, dioecious plant used in China for a wide range of applications. However, no study to date has undertaken a comprehensive analysis of the bZIP gene family in L. cubeba. In this work, we identified 68 members of the bZIP gene family in L. cubeba and classified them into 12 subfamilies based on previous studies on Arabidopsis thaliana. Transcriptome data analysis revealed that multiple LcbZIP genes exhibit significantly high expression levels in the flowers of L. cubeba, while some also demonstrate distinct temporal specificity during L. cubeba flower development. In particular, some LcbZIP genes displayed specific and high expression levels during the stamen and pistil degradation process. Using differential gene expression analysis, weighted gene co-expression network analysis, and Gene Ontology enrichment analysis, we identified six candidate LcbZIP genes that potentially regulate stamen or pistil degradation during flower development. In summary, our findings provide a framework for future functional analysis of the LcbZIP gene family in L. cubeba and offer novel insights for investigating the mechanism underlying pistil and stamen degeneration in this plant.
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Affiliation(s)
- Siqi Wang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100000, China; (S.W.); (Y.Z.); (Y.C.)
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 310000, China
| | - Yunxiao Zhao
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100000, China; (S.W.); (Y.Z.); (Y.C.)
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 310000, China
| | - Yicun Chen
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100000, China; (S.W.); (Y.Z.); (Y.C.)
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 310000, China
| | - Ming Gao
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100000, China; (S.W.); (Y.Z.); (Y.C.)
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 310000, China
| | - Yangdong Wang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100000, China; (S.W.); (Y.Z.); (Y.C.)
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 310000, China
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Song J, Chen F, Lv B, Guo C, Yang J, Huang L, Guo J, Xiang F. Genome-Wide Identification and Expression Analysis of the TIR-NBS-LRR Gene Family and Its Response to Fungal Disease in Rose (Rosa chinensis). BIOLOGY 2023; 12:biology12030426. [PMID: 36979118 PMCID: PMC10045381 DOI: 10.3390/biology12030426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 03/12/2023]
Abstract
Roses, which are one of the world’s most important ornamental plants, are often damaged by pathogens, resulting in serious economic losses. As a subclass of the disease resistance gene family of plant nucleotide-binding oligomerization domain (NOD)-like receptors, TIR-NBS-LRR (TNL) genes play a vital role in identifying pathogen effectors and activating defense responses. However, a systematic analysis of the TNL gene family is rarely reported in roses. Herein, 96 intact TNL genes were identified in Rosa chinensis. Their phylogenies, physicochemical characteristics, gene structures, conserved domains and motifs, promoter cis-elements, microRNA binding sites, and intra- and interspecific collinearity relationships were analyzed. An expression analysis using transcriptome data revealed that RcTNL genes were dominantly expressed in leaves. Some RcTNL genes responded to gibberellin, jasmonic acid, salicylic acid, Botrytis cinerea, Podosphaera pannosa, and Marssonina rosae (M. rosae); the RcTNL23 gene responded significantly to three hormones and three pathogens, and exhibited an upregulated expression. Furthermore, the black spot pathogen was identified as M. rosae. After inoculating rose leaves, an expression pattern analysis of the RcTNL genes suggested that they act during different periods of pathogen infection. The present study lays the foundations for an in-depth investigation of the TNL gene function and the mining of disease resistance genes in roses.
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Li M, Hwarari D, Li Y, Ahmad B, Min T, Zhang W, Wang J, Yang L. The bZIP transcription factors in Liriodendron chinense: Genome-wide recognition, characteristics and cold stress response. FRONTIERS IN PLANT SCIENCE 2022; 13:1035627. [PMID: 36420021 PMCID: PMC9676487 DOI: 10.3389/fpls.2022.1035627] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 10/17/2022] [Indexed: 05/08/2023]
Abstract
The basic leucine zipper (bZIP) is a transcription factor family that plays critical roles in abiotic and biotic stress responses as well as plant development and growth. A comprehensive genome-wide study in Liriodendron chinense was conducted to identify 45 bZIP transcription factors (LchibZIPs), which were divided into 13 subgroups according the phylogenetic analysis. Proteins in the same subgroup shared similar gene structures and conserved domains, and a total of 20 conserved motifs were revealed in LchibZIP proteins. Gene localization analysis revealed that LchibZIP genes were unequally distributed across 16 chromosomes, and that 4 pairs of tandem and 9 segmental gene duplications existed. Concluding that segmental duplication events may be strongly associated with the amplification of the L. chinense bZIP gene family. We also assessed the collinearity of LchibZIPs between the Arabidopsis and Oryza and showed that the LchibZIP is evolutionarily closer to O. sativa as compared to the A. thaliana. The cis-regulatory element analysis showed that LchibZIPs clustered in one subfamily are involved in several functions. In addition, we gathered novel research suggestions for further exploration of the new roles of LchibZIPs from protein-protein interactions and gene ontology annotations of the LchibZIP proteins. Using the RNA-seq data and qRT-PCR we analyzed the gene expression patterns of LchibZIP genes, and showed that LchibZIP genes regulate cold stress, especially LchibZIP4 and LchibZIP7; and LchibZIP2 and LchibZIP28 which were up-regulated and down-regulated by cold stress, respectively. Studies of genetic engineering and gene function in L. chinense can benefit greatly from the thorough investigation and characterization of the L. chinense bZIP gene family.
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Affiliation(s)
- Mingyue Li
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
- Innovation Center of Excellence, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Delight Hwarari
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Yang Li
- Innovation Center of Excellence, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Baseer Ahmad
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Tian Min
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Wenting Zhang
- Innovation Center of Excellence, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Jinyan Wang
- Innovation Center of Excellence, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
- *Correspondence: Jinyan Wang, ; Liming Yang,
| | - Liming Yang
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
- *Correspondence: Jinyan Wang, ; Liming Yang,
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