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Doddavarapu B, Lata C, Shah JM. Epigenetic regulation influenced by soil microbiota and nutrients: Paving road to epigenome editing in plants. Biochim Biophys Acta Gen Subj 2024; 1868:130580. [PMID: 38325761 DOI: 10.1016/j.bbagen.2024.130580] [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: 06/16/2023] [Revised: 12/25/2023] [Accepted: 02/02/2024] [Indexed: 02/09/2024]
Abstract
Soil is a complex ecosystem that houses microbes and nutrients that are necessary for plant development. Edaphic properties of the soil and environmental conditions influence microbial growth and nutrient accessibility. Various environmental stimuli largely affect the soil microbes and ionic balance, in turn influencing plants. Soil microflora helps decompose organic matter and is involved in mineral uptake. The combination of soil microbes and mineral nutrients notably affects plant growth. Recent advancements have enabled a deeper understanding of plant genetic/molecular regulators. Deficiencies/sufficiencies of soil minerals and microbes also alter plant gene regulation. Gene regulation mediated by epigenetic mechanisms comprises conformational alterations in chromatin structure, DNA/histone modifications, or involvement of small RNAs. Epigenetic regulation is unique due to its potential to inherit without involving alteration of the DNA sequence. Thus, the compilation study of heritable epigenetic changes driven by nutrient imbalances and soil microbes would facilitate understanding this molecular phenomenon in plants. This information can aid in epigenome editing, which has recently emerged as a promising technology for plant non-transgenic/non-mutagenic modification. Potential epigenetic marks induced by biotic and abiotic stresses in plants could be explored as target sites for epigenome editing. This review discusses novel ways of epigenome editing to create epigenome edited plants with desirable and heritable phenotypes. As plants are sessile and in constant exposure to the soil microbiome and nutrients, epigenetic changes induced by these factors could provide more effective, stable and a sustainable molecular solution for crop improvement.
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Affiliation(s)
- Bhavya Doddavarapu
- Department of Plant Science, Central University of Kerala, Kerala, India
| | - Charu Lata
- Inclusive Health & Traditional Knowledge Studies Division, CSIR- National Institute of Science Communication and Policy Research, New Delhi, India
| | - Jasmine M Shah
- Department of Plant Science, Central University of Kerala, Kerala, India.
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Bajpai SK, Nisha, Pandita S, Bahadur A, Verma PC. Recent advancements in the role of histone acetylation dynamics to improve stress responses in plants. Mol Biol Rep 2024; 51:413. [PMID: 38472555 DOI: 10.1007/s11033-024-09300-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 01/30/2024] [Indexed: 03/14/2024]
Abstract
In eukaryotes, transcriptional regulation is determined by the DNA sequence and is facilitated through sophisticated and complex chromatin alterations and histone remodelling. Recent research has shown that the histone acetylation dynamic, an intermittent and reversible substitution, constitutes a prerequisite for chromatin modification. These changes in chromatin structure modulate genome-wide and specific changes in response to external and internal cues like cell differentiation, development, growth, light temperature, and biotic stresses. Histone acetylation dynamics also control the cell cycle. HATs and HDACs play a critical role in gene expression modulation during plant growth and response to environmental circumstances. It has been well established that HATs and HDACs interact with various distinct transcription factors and chromatin-remodelling proteins (CRPs) involved in the transcriptional regulation of several developmental processes. This review explores recent research on histone acyltransferases and histone deacetylases, mainly focusing on their involvement in plant biotic stress responses. Moreover, we also emphasized the research gaps that must be filled to fully understand the complete function of histone acetylation dynamics during biotic stress responses in plants. A thorough understanding of histone acetylation will make it possible to enhance tolerance against various kinds of stress and decrease yield losses in many crops.
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Affiliation(s)
- Sanjay Kumar Bajpai
- Molecular Biology & Biotechnology Division, CSIR-National Botanical Research Institute, (Council of Scientific and Industrial Research) Rana Pratap Marg, Lucknow, UP, 226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Nisha
- Molecular Biology & Biotechnology Division, CSIR-National Botanical Research Institute, (Council of Scientific and Industrial Research) Rana Pratap Marg, Lucknow, UP, 226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Shivali Pandita
- Molecular Biology & Biotechnology Division, CSIR-National Botanical Research Institute, (Council of Scientific and Industrial Research) Rana Pratap Marg, Lucknow, UP, 226001, India
- Department of Zoology, University of Lucknow, Lucknow, Uttar Pradesh, 226007, India
| | - Anand Bahadur
- Molecular Biology & Biotechnology Division, CSIR-National Botanical Research Institute, (Council of Scientific and Industrial Research) Rana Pratap Marg, Lucknow, UP, 226001, India
- Department of Botany, University of Lucknow, Lucknow, Uttar Pradesh, 226007, India
| | - Praveen C Verma
- Molecular Biology & Biotechnology Division, CSIR-National Botanical Research Institute, (Council of Scientific and Industrial Research) Rana Pratap Marg, Lucknow, UP, 226001, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India.
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Zhi P, Gao R, Chen W, Chang C. Wheat Transcriptional Corepressor TaTPR1 Suppresses Susceptibility Genes TaDND1/2 and Potentiates Post-Penetration Resistance against Blumeria graminis forma specialis tritici. Int J Mol Sci 2024; 25:1695. [PMID: 38338970 PMCID: PMC10855895 DOI: 10.3390/ijms25031695] [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: 12/26/2023] [Revised: 01/22/2024] [Accepted: 01/27/2024] [Indexed: 02/12/2024] Open
Abstract
The obligate biotrophic fungal pathogen Blumeria graminis forma specialis tritici (B.g. tritici) is the causal agent of wheat powdery mildew disease. The TOPLESS-related 1 (TPR1) corepressor regulates plant immunity, but its role in regulating wheat resistance against powdery mildew remains to be disclosed. Herein, TaTPR1 was identified as a positive regulator of wheat post-penetration resistance against powdery mildew disease. The transient overexpression of TaTPR1.1 or TaTPR1.2 confers wheat post-penetration resistance powdery mildew, while the silencing of TaTPR1.1 and TaTPR1.2 results in an enhanced wheat susceptibility to B.g. tritici. Furthermore, Defense no Death 1 (TaDND1) and Defense no Death 2 (TaDND2) were identified as wheat susceptibility (S) genes facilitating a B.g. tritici infection. The overexpression of TaDND1 and TaDND2 leads to an enhanced wheat susceptibility to B.g. tritici, while the silencing of wheat TaDND1 and TaDND2 leads to a compromised susceptibility to powdery mildew. In addition, we demonstrated that the expression of TaDND1 and TaDND2 is negatively regulated by the wheat transcriptional corepressor TaTPR1. Collectively, these results implicate that TaTPR1 positively regulates wheat post-penetration resistance against powdery mildew probably via suppressing the S genes TaDND1 and TaDND2.
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Affiliation(s)
| | | | | | - Cheng Chang
- College of Life Sciences, Qingdao University, Qingdao 266071, China
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Yung WS, Chan TF, Kong F, Lam HM. The Plant Genome special section: Epigenome and epitranscriptome in plant-environment interactions. THE PLANT GENOME 2023; 16:e20404. [PMID: 38124543 DOI: 10.1002/tpg2.20404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 10/12/2023] [Indexed: 12/23/2023]
Affiliation(s)
- Wai-Shing Yung
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, P. R. China
| | - Ting-Fung Chan
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, P. R. China
| | - Fanjiang Kong
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, P. R. China
| | - Hon-Ming Lam
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, P. R. China
- Institute of Environment, Energy, and Sustainability, The Chinese University of Hong Kong, Hong Kong SAR, P. R. China
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Zeng H, Xu H, Tan M, Zhang B, Shi H. LESION SIMULATING DISEASE 3 regulates disease resistance via fine-tuning histone acetylation in cassava. PLANT PHYSIOLOGY 2023; 193:2232-2247. [PMID: 37534747 DOI: 10.1093/plphys/kiad441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/16/2023] [Accepted: 07/16/2023] [Indexed: 08/04/2023]
Abstract
Bacterial blight seriously affects the growth and production of cassava (Manihot esculenta Crantz), but disease resistance genes and the underlying molecular mechanism remain unknown. In this study, we found that LESION SIMULATING DISEASE 3 (MeLSD3) is essential for disease resistance in cassava. MeLSD3 physically interacts with SIRTUIN 1 (MeSRT1), inhibiting MeSRT1-mediated deacetylation modification at the acetylation of histone 3 at K9 (H3K9Ac). This leads to increased H3K9Ac levels and transcriptional activation of SUPPRESSOR OF BIR1 (SOBIR1) and FLAGELLIN-SENSITIVE2 (FLS2) in pattern-triggered immunity, resulting in immune responses in cassava. When MeLSD3 was silenced, the release of MeSRT1 directly decreased H3K9Ac levels and inhibited the transcription of SOBIR1 and FLS2, leading to decreased disease resistance. Notably, DELLA protein GIBBERELLIC ACID INSENSITIVE 1 (MeGAI1) also interacted with MeLSD3, which enhanced the interaction between MeLSD3 and MeSRT1 and further strengthened the inhibition of MeSRT1-mediated deacetylation modification at H3K9Ac of defense genes. In summary, this study illustrates the mechanism by which MeLSD3 interacts with MeSRT1 and MeGAI1, thereby mediating the level of H3K9Ac and the transcription of defense genes and immune responses in cassava.
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Affiliation(s)
- Hongqiu Zeng
- Sanya Nanfan Research Institute of Hainan University, Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Nanfan, School of Tropical Agriculture and Forestry, Hainan University, 572025, Sanya, Hainan Province, China
- National Key Laboratory for Tropical Crop Breeding, Hainan University, 572025, Sanya, Hainan Province, China
- Hainan Yazhou Bay Seed Laboratory, 572025, Sanya, Hainan Province, China
| | - Haoran Xu
- Sanya Nanfan Research Institute of Hainan University, Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Nanfan, School of Tropical Agriculture and Forestry, Hainan University, 572025, Sanya, Hainan Province, China
| | - Mengting Tan
- Sanya Nanfan Research Institute of Hainan University, Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Nanfan, School of Tropical Agriculture and Forestry, Hainan University, 572025, Sanya, Hainan Province, China
| | - Bowen Zhang
- Sanya Nanfan Research Institute of Hainan University, Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Nanfan, School of Tropical Agriculture and Forestry, Hainan University, 572025, Sanya, Hainan Province, China
| | - Haitao Shi
- Sanya Nanfan Research Institute of Hainan University, Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Nanfan, School of Tropical Agriculture and Forestry, Hainan University, 572025, Sanya, Hainan Province, China
- National Key Laboratory for Tropical Crop Breeding, Hainan University, 572025, Sanya, Hainan Province, China
- Hainan Yazhou Bay Seed Laboratory, 572025, Sanya, Hainan Province, China
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Shan C, Zhang L, Chen L, Li S, Zhang Y, Ye L, Lin Y, Kuang W, Shi X, Ma J, Adnan M, Sun X, Cui R. Interaction of negative regulator OsWD40-193 with OseEF1A1 inhibits Oryza sativa resistance to Hirschmanniella mucronata infection. Int J Biol Macromol 2023; 248:125841. [PMID: 37479204 DOI: 10.1016/j.ijbiomac.2023.125841] [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: 04/08/2023] [Revised: 07/12/2023] [Accepted: 07/13/2023] [Indexed: 07/23/2023]
Abstract
Rice is a crucial food crop worldwide, but it is highly susceptible to Hirschmanniella mucronata, a migratory parasitic nematode. No rice variety has been identified that could resist H. mucronata infection. Therefore, it is very important to study the interaction between rice and H. mucronata to breed resistant rice varieties. Here, we demonstrated that protein OsWD40-193 interacted with the extension factor OseEF1A1 and both were negative regulators inhibiting rice resistance to H. mucronata infection. Overexpression of either OsWD40-193 or OseEF1A1 led to enhance susceptibility to H. mucronata, whereas the absence of OsWD40-193 or OseEF1A1 led to resistance. Further transcriptomic analysis showed that OseEF1A1 deletion altered the expression of genes association with salicylic acid, jasmonic acid and abolic acid signaling pathways and increased the accumulation of secondary metabolites to enhance resistance in rice. Our study showed that H. mucronata infection affected the expression of negative regulators in rice and inhibited rice resistance, which was conducive to the infection of nematode. Together, our data showed that H. mucronata affected the expression of negative regulators to facilitate its infection and provided potential target genes to engineering resistance germplasm via gene editing of the negative regulators.
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Affiliation(s)
- Chonglei Shan
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Lianhu Zhang
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China.
| | - Lanlan Chen
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Songyan Li
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Yifan Zhang
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Lifang Ye
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Yachun Lin
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Weigang Kuang
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Xugen Shi
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Jian Ma
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Muhammad Adnan
- College of Life Sciences and Oceanography, Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen 518060, China.
| | - Xiaotang Sun
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China; Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China.
| | - Ruqiang Cui
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China; Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China.
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7
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Guan Y, Wei Z, Zhou L, Wang K, Zhang M, Song P, Hu P, Hu H, Li C. Tae-miR397 Negatively Regulates Wheat Resistance to Blumeria graminis. PLANTS (BASEL, SWITZERLAND) 2023; 12:3096. [PMID: 37687344 PMCID: PMC10489981 DOI: 10.3390/plants12173096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/25/2023] [Accepted: 08/26/2023] [Indexed: 09/10/2023]
Abstract
MicroRNA (miRNA) plays a crucial role in the interactions between plants and pathogens, and identifying disease-related miRNAs could help us understand the mechanisms underlying plant disease pathogenesis and breed resistant varieties. However, the role of miRNA in wheat defense responses remains largely unexplored. The miR397 family is highly conserved in plants and involved in plant development and defense response. Therefore, the purpose of this study was to investigate the function of tae-miR397 in wheat resistance to powdery mildew. The expression pattern analysis revealed that tae-miR397 expression was higher in young leaves than in other tissues and was significantly decreased in wheat Bainong207 leaves after Blumeria graminis (Bgt) infection and chitin treatment. Additionally, the expression of tae-miR397 was significantly down-regulated by salicylic acid and induced under jasmonate treatment. The overexpression of tae-miR397 in common wheat Bainong207 enhanced the wheat's susceptibility to powdery mildew in the seedling and adult stages. The rate of Bgt spore germination and mycelial growth in transgenic wheat plants overexpressing tae-miR397 was faster than in the untransformed wild-type plants. The target gene of tae-miR397 was predicted to be a wound-induced protein (Tae-WIP), and the function was investigated. We demonstrated that silencing of Tae-WIP via barley-stripe-mosaic-virus-induced gene silencing enhanced wheat's susceptibility to powdery mildew. qRT-PCR indicated that tae-miR397 regulated wheat immunity by controlling pathogenesis-related gene expressions. Moreover, the transgenic plants overexpressing tae-miR397 exhibited more tillers than the wild-type plants. This work suggests that tae-miR397 is a negative regulator of resistance against powdery mildew and has great potential for breeding disease-resistant cultivars.
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Affiliation(s)
- Yuanyuan Guan
- School of Life Sciences, Henan Engineering Research Center of Crop Genome Editing, Henan International Joint Laboratory of Plant Genetic Improvement and Soil Remediation, Henan Institute of Science and Technology, Xinxiang 453003, China; (Y.G.); (Z.W.); (L.Z.); (K.W.)
| | - Zhiyuan Wei
- School of Life Sciences, Henan Engineering Research Center of Crop Genome Editing, Henan International Joint Laboratory of Plant Genetic Improvement and Soil Remediation, Henan Institute of Science and Technology, Xinxiang 453003, China; (Y.G.); (Z.W.); (L.Z.); (K.W.)
| | - Luyi Zhou
- School of Life Sciences, Henan Engineering Research Center of Crop Genome Editing, Henan International Joint Laboratory of Plant Genetic Improvement and Soil Remediation, Henan Institute of Science and Technology, Xinxiang 453003, China; (Y.G.); (Z.W.); (L.Z.); (K.W.)
| | - Kaige Wang
- School of Life Sciences, Henan Engineering Research Center of Crop Genome Editing, Henan International Joint Laboratory of Plant Genetic Improvement and Soil Remediation, Henan Institute of Science and Technology, Xinxiang 453003, China; (Y.G.); (Z.W.); (L.Z.); (K.W.)
| | - Meng Zhang
- School of Agriculture, Henan Engineering Research Center of Crop Genome Editing, Henan International Joint Laboratory of Plant Genetic Improvement and Soil Remediation, Henan Institute of Science and Technology, Xinxiang 453003, China; (M.Z.); (P.S.); (P.H.)
| | - Puwen Song
- School of Agriculture, Henan Engineering Research Center of Crop Genome Editing, Henan International Joint Laboratory of Plant Genetic Improvement and Soil Remediation, Henan Institute of Science and Technology, Xinxiang 453003, China; (M.Z.); (P.S.); (P.H.)
| | - Ping Hu
- School of Agriculture, Henan Engineering Research Center of Crop Genome Editing, Henan International Joint Laboratory of Plant Genetic Improvement and Soil Remediation, Henan Institute of Science and Technology, Xinxiang 453003, China; (M.Z.); (P.S.); (P.H.)
| | - Haiyan Hu
- School of Agriculture, Henan Engineering Research Center of Crop Genome Editing, Henan International Joint Laboratory of Plant Genetic Improvement and Soil Remediation, Henan Institute of Science and Technology, Xinxiang 453003, China; (M.Z.); (P.S.); (P.H.)
| | - Chengwei Li
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
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Jiang J, Xie X, Li X. Acetyl-Proteomic Profiling of Sorghum bicolor Seedlings after Chitin Treatment Reveals the Involvement of Acetylated Chlorophyll a/b Binding Proteins in the Innate Immune Response. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37384550 DOI: 10.1021/acs.jafc.3c00700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]
Abstract
Plant pathogen-associated molecular pattern-triggered immunity (PTI) is affected by post-translational modifications, but the role of acetylation in the PTI responses of Sorghum bicolor remains unclear. In this study, a comprehensive acetyl-proteomic analysis was performed on sorghum seedlings treated with chitin based on label-free protein quantification. Chitin rapidly induced 15 PTI-related genes and 5 defense enzymes. Acetylation was upregulated in sorghum after the chitin treatment, and 579, 895, and 929 acetylated proteins, peptides, and sites, respectively, were identified using high-performance liquid chromatography-tandem mass spectrometry. Acetylation and expression of chlorophyll a/b binding proteins (Lhcs) were significantly upregulated, and they were localized in chloroplasts. Additionally, we found that the expression of Lhcs in vivo enhanced chitin-mediated acetylation. The findings of this study provide a comprehensive assessment of the lysine acetylome in sorghum and a foundation for future study into the regulatory mechanisms of acetylation during chlorophyll synthesis.
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Affiliation(s)
- Junmei Jiang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, P. R. China
| | - Xin Xie
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, P. R. China
| | - Xiangyang Li
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, P. R. China
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Li M, Yang Z, Liu J, Chang C. Wheat Susceptibility Genes TaCAMTA2 and TaCAMTA3 Negatively Regulate Post-Penetration Resistance against Blumeria graminis forma specialis tritici. Int J Mol Sci 2023; 24:10224. [PMID: 37373370 DOI: 10.3390/ijms241210224] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/12/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
Blumeria graminis forma specialis tritici (B.g. tritici) is the airborne fungal pathogen that causes powdery mildew disease on hexaploid bread wheat. Calmodulin-binding transcription activators (CAMTAs) regulate plant responses to environments, but their potential functions in the regulation of wheat-B.g. tritici interaction remain unknown. In this study, the wheat CAMTA transcription factors TaCAMTA2 and TaCAMTA3 were identified as suppressors of wheat post-penetration resistance against powdery mildew. Transient overexpression of TaCAMTA2 and TaCAMTA3 enhanced the post-penetration susceptibility of wheat to B.g. tritici, while knockdown of TaCAMTA2 and TaCAMTA3 expression using transient- or virus-induced gene silencing compromised wheat post-penetration susceptibility to B.g. tritici. In addition, TaSARD1 and TaEDS1 were characterized as positive regulators of wheat post-penetration resistance against powdery mildew. Overexpressing TaSARD1 and TaEDS1 confers wheat post-penetration resistance against B.g. tritici, while silencing TaSARD1 and TaEDS1 enhances wheat post-penetration susceptibility to B.g. tritici. Importantly, we showed that expressions of TaSARD1 and TaEDS1 were potentiated by silencing of TaCAMTA2 and TaCAMTA3. Collectively, these results implicated that the Susceptibility genes TaCAMTA2 and TaCAMTA3 contribute to the wheat-B.g. tritici compatibility might via negative regulation of TaSARD1 and TaEDS1 expression.
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Affiliation(s)
- Mengmeng Li
- College of Life Sciences, Qingdao University, Qingdao 266071, China
| | - Zige Yang
- College of Life Sciences, Qingdao University, Qingdao 266071, China
| | - Jiao Liu
- College of Life Sciences, Qingdao University, Qingdao 266071, China
| | - Cheng Chang
- College of Life Sciences, Qingdao University, Qingdao 266071, China
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10
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Xie SS, Duan CG. Epigenetic regulation of plant immunity: from chromatin codes to plant disease resistance. ABIOTECH 2023; 4:124-139. [PMID: 37581024 PMCID: PMC10423193 DOI: 10.1007/s42994-023-00101-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/01/2023] [Indexed: 08/16/2023]
Abstract
Facing a deteriorating natural environment and an increasing serious food crisis, bioengineering-based breeding is increasing in importance. To defend against pathogen infection, plants have evolved multiple defense mechanisms, including pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) and effector-triggered immunity (ETI). A complex regulatory network acts downstream of these PTI and ETI pathways, including hormone signal transduction and transcriptional reprogramming. In recent years, increasing lines of evidence show that epigenetic factors act, as key regulators involved in the transcriptional reprogramming, to modulate plant immune responses. Here, we summarize current progress on the regulatory mechanism of DNA methylation and histone modifications in plant defense responses. In addition, we also discuss the application of epigenetic mechanism-based resistance strategies in plant disease breeding.
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Affiliation(s)
- Si-Si Xie
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
- University of the Chinese Academy of Sciences, Beijing, 100049 China
| | - Cheng-Guo Duan
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
- University of the Chinese Academy of Sciences, Beijing, 100049 China
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Moolhuijzen P, Ge C, Palmiero E, Ellwood SR. A unique resistance mechanism is associated with RBgh2 barley powdery mildew adult plant resistance. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:145. [PMID: 37253878 DOI: 10.1007/s00122-023-04392-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/20/2023] [Indexed: 06/01/2023]
Abstract
KEY MESSAGE Gene expression at the RBgh2 locus indicates involvement in cAMP/G-protein-coupled signalling and innate immunity in barley powdery mildew adult plant resistance. Barley powdery mildew is a globally significant disease, responsible for reduced grain yield and quality. A major effect adult plant resistance gene, RBgh2, was previously found in a landrace from Azerbaijan. The atypical phenotype suggested different underlying genetic factors compared to conventional resistance genes and to investigate this, genome-wide gene expression was compared between sets of heterogeneous doubled haploids. RBgh2 resistance is recessive and induces both temporary genome-wide gene expression changes during powdery mildew infection together with constitutive changes, principally at the RBgh2 locus. Defence-related genes significantly induced included homologues of genes associated with innate immunity and pathogen recognition. Intriguingly, RBgh2 resistance does not appear to be dependent on salicylic acid signalling, a key pathway in plant resistance to biotrophs. Constitutive co-expression of resistance gene homologues was evident at the 7HS RBgh2 locus, while no expression was evident for a 6-transmembrane gene, predicted in silico to contain both G-protein- and calmodulin-binding domains. The gene was disrupted at the 5' end, and G-protein-binding activity was suppressed. RBgh2 appears to operate through a unique mechanism that co-opts elements of innate immunity.
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Affiliation(s)
- Paula Moolhuijzen
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
| | - Cynthia Ge
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
| | - Elzette Palmiero
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
| | - Simon R Ellwood
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia.
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Kumar S, Saini DK, Jan F, Jan S, Tahir M, Djalovic I, Latkovic D, Khan MA, Kumar S, Vikas VK, Kumar U, Kumar S, Dhaka NS, Dhankher OP, Rustgi S, Mir RR. Comprehensive meta-QTL analysis for dissecting the genetic architecture of stripe rust resistance in bread wheat. BMC Genomics 2023; 24:259. [PMID: 37173660 PMCID: PMC10182688 DOI: 10.1186/s12864-023-09336-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUND Yellow or stripe rust, caused by the fungus Puccinia striiformis f. sp. tritici (Pst) is an important disease of wheat that threatens wheat production. Since developing resistant cultivars offers a viable solution for disease management, it is essential to understand the genetic basis of stripe rust resistance. In recent years, meta-QTL analysis of identified QTLs has gained popularity as a way to dissect the genetic architecture underpinning quantitative traits, including disease resistance. RESULTS Systematic meta-QTL analysis involving 505 QTLs from 101 linkage-based interval mapping studies was conducted for stripe rust resistance in wheat. For this purpose, publicly available high-quality genetic maps were used to create a consensus linkage map involving 138,574 markers. This map was used to project the QTLs and conduct meta-QTL analysis. A total of 67 important meta-QTLs (MQTLs) were identified which were refined to 29 high-confidence MQTLs. The confidence interval (CI) of MQTLs ranged from 0 to 11.68 cM with a mean of 1.97 cM. The mean physical CI of MQTLs was 24.01 Mb, ranging from 0.0749 to 216.23 Mb per MQTL. As many as 44 MQTLs colocalized with marker-trait associations or SNP peaks associated with stripe rust resistance in wheat. Some MQTLs also included the following major genes- Yr5, Yr7, Yr16, Yr26, Yr30, Yr43, Yr44, Yr64, YrCH52, and YrH52. Candidate gene mining in high-confidence MQTLs identified 1,562 gene models. Examining these gene models for differential expressions yielded 123 differentially expressed genes, including the 59 most promising CGs. We also studied how these genes were expressed in wheat tissues at different phases of development. CONCLUSION The most promising MQTLs identified in this study may facilitate marker-assisted breeding for stripe rust resistance in wheat. Information on markers flanking the MQTLs can be utilized in genomic selection models to increase the prediction accuracy for stripe rust resistance. The candidate genes identified can also be utilized for enhancing the wheat resistance against stripe rust after in vivo confirmation/validation using one or more of the following methods: gene cloning, reverse genetic methods, and omics approaches.
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Affiliation(s)
- Sandeep Kumar
- Division of Genetics and Plant Breeding, Faculty of Agriculture, SKUAST-Kashmir, Wadura, 193201, India
| | - Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Farkhandah Jan
- Division of Genetics and Plant Breeding, Faculty of Agriculture, SKUAST-Kashmir, Wadura, 193201, India
| | - Sofora Jan
- Division of Genetics and Plant Breeding, Faculty of Agriculture, SKUAST-Kashmir, Wadura, 193201, India
| | - Mohd Tahir
- Division of Genetics and Plant Breeding, Faculty of Agriculture, SKUAST-Kashmir, Wadura, 193201, India
| | - Ivica Djalovic
- Institute of Field and Vegetable Crops, National Institute of the Republic of Serbia, Maxim Gorki 30, Novi Sad, Serbia
| | - Dragana Latkovic
- Department of Field and Vegetable Crops, Faculty of Agriculture, University of Novi Sad, Trg Dositeja Obradovića 8, 21000, Novi Sad, Serbia
| | - Mohd Anwar Khan
- Division of Genetics and Plant Breeding, Faculty of Agriculture, SKUAST-Kashmir, Wadura, 193201, India
| | - Sundeep Kumar
- Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - V K Vikas
- ICAR-IARI, Regional Station, Wellington, 643 231, The Nilgiris, India
| | - Upendra Kumar
- Department of Molecular Biology & Biotechnology., CCS Haryana Agriculture University, Hisar, India
| | - Sundip Kumar
- Department of Molecular Biology and Genetic Engineering, Molecular Cytogenetics Laboratory, College of Basic Science and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar-263145, U.S. Nagar, Uttarakhand, India
| | - Narendra Singh Dhaka
- Department of Genetics and Plant Breeding, College of Agriculture, G. B. Pant, University of Agriculture & Technology, Pantnagar-263145, U. S. Nagar, Uttarakhand, India
| | - Om Parkash Dhankher
- School of Agriculture, University of Massachusetts Amherst, Stockbridge Amherst, MA, 01003, USA
| | - Sachin Rustgi
- Department of Plant and Environmental Sciences, Clemson University, 2200 Pocket Road, Florence, SC, 29506, USA
| | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Faculty of Agriculture, SKUAST-Kashmir, Wadura, 193201, India.
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Mapuranga J, Chang J, Yang W. Combating powdery mildew: Advances in molecular interactions between Blumeria graminis f. sp. tritici and wheat. FRONTIERS IN PLANT SCIENCE 2022; 13:1102908. [PMID: 36589137 PMCID: PMC9800938 DOI: 10.3389/fpls.2022.1102908] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
Wheat powdery mildew caused by a biotrophic fungus Blumeria graminis f. sp. tritici (Bgt), is a widespread airborne disease which continues to threaten global wheat production. One of the most chemical-free and cost-effective approaches for the management of wheat powdery mildew is the exploitation of resistant cultivars. Accumulating evidence has reported that more than 100 powdery mildew resistance genes or alleles mapping to 63 different loci (Pm1-Pm68) have been identified from common wheat and its wild relatives, and only a few of them have been cloned so far. However, continuous emergence of new pathogen races with novel degrees of virulence renders wheat resistance genes ineffective. An essential breeding strategy for achieving more durable resistance is the pyramiding of resistance genes into a single genotype. The genetics of host-pathogen interactions integrated with temperature conditions and the interaction between resistance genes and their corresponding pathogen a virulence genes or other resistance genes within the wheat genome determine the expression of resistance genes. Considerable progress has been made in revealing Bgt pathogenesis mechanisms, identification of resistance genes and breeding of wheat powdery mildew resistant cultivars. A detailed understanding of the molecular interactions between wheat and Bgt will facilitate the development of novel and effective approaches for controlling powdery mildew. This review gives a succinct overview of the molecular basis of interactions between wheat and Bgt, and wheat defense mechanisms against Bgt infection. It will also unleash the unsung roles of epigenetic processes, autophagy and silicon in wheat resistance to Bgt.
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Xu Y, Miao Y, Cai B, Yi Q, Tian X, Wang Q, Ma D, Luo Q, Tan F, Hu Y. A histone deacetylase inhibitor enhances rice immunity by derepressing the expression of defense-related genes. FRONTIERS IN PLANT SCIENCE 2022; 13:1041095. [PMID: 36407628 PMCID: PMC9667192 DOI: 10.3389/fpls.2022.1041095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 10/13/2022] [Indexed: 06/16/2023]
Abstract
Histone deacetylase (HDAC) inhibitors (HDACis) have been widely used in plants to investigate the role of histone acetylation, particularly the function of HDACs, in the regulation of development and stress response. However, how histone acetylation is involved in rice (Oryza sativa L.) disease resistance has hardly been studied. In this paper, four HDACis including Sodium butyrate (NaBT), Suberoylanilide Hydroxamic Acid (SAHA), LBH-589 and Trichostatin A (TSA) were used to treat rice seedlings at different concentrations before inoculation of Magnaporthe oryzae. We found that only 10mM NaBT treatment can significantly enhanced rice blast resistance. However, treatment of the four HDACis all increased global histone acetylation but at different sites, suggesting that the inhibition selectivity of these HDACis is different. Notably, the global H3K9ac level was dramatically elevated after both NaBT and LBH589 treatment although LBH589 could not enhance rice blast resistance. This indicates that the HDACs they inhibit target different genes. In accordance with the phenotype, transcriptomic analysis showed that many defense-related genes were up-regulated by NaBT treatment. Up-regulation of the four genes bsr-d1, PR10B, OsNAC4, OsKS4 were confirmed by RT-qPCR. ChIP-qPCR results revealed that H3K9ac level on these genes was increased after NaBT treatment, suggesting that these defense-related genes were repressed by HDACs. In addition, by promoter motif analysis of the genes that induced by both NaBT treatment and rice blast infection, we found that the motifs bound by ERF and AHL transcription factors (TFs) were the most abundant, which demonstrates that ERF and AHL proteins may act as the candidate TFs that recruit HDACs to defense-related genes to repress their expression when plants are not infected by rice blast.
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Affiliation(s)
- Yan Xu
- Hubei Engineering Research Center for Specialty Flowers Biological Breeding/College of Bioengineering, Jingchu University of Technology, Jingmen, China
| | - Yuanxin Miao
- Hubei Engineering Research Center for Specialty Flowers Biological Breeding/College of Bioengineering, Jingchu University of Technology, Jingmen, China
| | - Botao Cai
- Center for Science Popularization Jingmen, Science and Technology Museum, Jingmen, China
| | - Qingping Yi
- Hubei Engineering Research Center for Specialty Flowers Biological Breeding/College of Bioengineering, Jingchu University of Technology, Jingmen, China
| | - Xuejun Tian
- Hubei Engineering Research Center for Specialty Flowers Biological Breeding/College of Bioengineering, Jingchu University of Technology, Jingmen, China
| | - Qihai Wang
- Hubei Engineering Research Center for Specialty Flowers Biological Breeding/College of Bioengineering, Jingchu University of Technology, Jingmen, China
| | - Dan Ma
- Hubei Engineering Research Center for Specialty Flowers Biological Breeding/College of Bioengineering, Jingchu University of Technology, Jingmen, China
| | - Qiong Luo
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan/Ministry of Education Key Laboratory of Agricultural Biodiversity for Plant Disease Management, Yunnan Agricultural University, Kunming, China
| | - Feng Tan
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yongfeng Hu
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement, Biotechnology Research Center, China Three Gorges University, Yichang, China
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Song N, Lin J, Liu X, Liu Z, Liu D, Chu W, Li J, Chen Y, Chang S, Yang Q, Liu X, Guo W, Xin M, Yao Y, Peng H, Ni Z, Xie C, Sun Q, Hu Z. Histone acetyltransferase TaHAG1 interacts with TaPLATZ5 to activate TaPAD4 expression and positively contributes to powdery mildew resistance in wheat. THE NEW PHYTOLOGIST 2022; 236:590-607. [PMID: 35832009 PMCID: PMC9795918 DOI: 10.1111/nph.18372] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 07/06/2022] [Indexed: 05/24/2023]
Abstract
Plants have evolved a two-branched innate immune system to detect and cope with pathogen attack, which are initiated by cell-surface and intracellular immune receptors leading to pattern-triggered immunity (PTI) and effector-triggered immunity (ETI), respectively. A core transducer including PAD4-EDS1 node is proposed as the convergence point for a two-tiered immune system in conferring pathogen immunity. However, the transcriptional regulatory mechanisms controlling expression of these key transducers remain largely unknown. Here, we identified histone acetyltransferase TaHAG1 as a positive regulator of powdery mildew resistance in wheat. TaHAG1 regulates expression of key transducer gene TaPAD4 and promotes SA and reactive oxygen species accumulation to accomplish resistance to Bgt infection. Moreover, overexpression and CRISPR-mediated knockout of TaPAD4 validate its role in wheat powdery mildew resistance. Furthermore, TaHAG1 physically interacts with TaPLATZ5, a plant-specific zinc-binding protein. TaPLATZ5 directly binds to promoter of TaPAD4 and together with TaHAG1 to potentiate the expression of TaPAD4 by increasing the levels of H3 acetylation. Our study revealed a key transcription regulatory node in which TaHAG1 acts as an epigenetic modulator and interacts with TaPLATZ5 that confers powdery mildew resistance in wheat through activating a convergence point gene between PTI and ETI, which could be effective for genetic improvement of disease resistance in wheat and other crops.
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Affiliation(s)
- Na Song
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Jingchen Lin
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Xingbei Liu
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Zehui Liu
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Debiao Liu
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Wei Chu
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Jinpeng Li
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Yongming Chen
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Shumin Chang
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Qun Yang
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Xiaoyu Liu
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Mingming Xin
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Yingyin Yao
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Huiru Peng
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Chaojie Xie
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Zhaorong Hu
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
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Azevedo V, Daddiego L, Cardone MF, Perrella G, Sousa L, Santos RB, Malhó R, Bergamini C, Marsico AD, Figueiredo A, Alagna F. Transcriptomic and methylation analysis of susceptible and tolerant grapevine genotypes following Plasmopara viticola infection. PHYSIOLOGIA PLANTARUM 2022; 174:e13771. [PMID: 36053855 PMCID: PMC9826190 DOI: 10.1111/ppl.13771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/05/2022] [Accepted: 08/29/2022] [Indexed: 06/15/2023]
Abstract
Downy mildew, caused by the biotrophic oomycete Plasmopara viticola, is one of the most economically significant grapevine diseases worldwide. Current strategies to cope with this threat rely on the massive use of chemical compounds during each cultivation season. The economic costs and negative environmental impact associated with these applications increased the urge to search for sustainable strategies of disease control. Improved knowledge of plant mechanisms to counteract pathogen infection may allow the development of alternative strategies for plant protection. Epigenetic regulation, in particular DNA methylation, is emerging as a key factor in the context of plant-pathogen interactions associated with the expression modulation of defence genes. To improve our understanding of the genetic and epigenetic mechanisms underpinning grapevine response to P. viticola, we studied the modulation of both 5-mC methylation and gene expression at 6 and 24 h post-infection (hpi). Leaves of two table grape genotypes (Vitis vinifera), selected by breeding activities for their contrasting level of susceptibility to the pathogen, were analysed. Following pathogen infection, we found variations in the 5-mC methylation level and the gene expression profile. The results indicate a genotype-specific response to pathogen infection. The tolerant genotype (N23/018) at 6 hpi exhibits a lower methylation level compared to the susceptible one (N20/020), and it shows an early modulation (at 6 hpi) of defence and epigenetic-related genes during P. viticola infection. These data suggest that the timing of response is an important mechanism to efficiently counteract the pathogen attack.
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Affiliation(s)
- Vanessa Azevedo
- Faculdade de Ciências, Plant Biology Department, Biosystems & Integrative Sciences Institute (BioISI)Universidade de LisboaLisbonPortugal
| | - Loretta Daddiego
- Energy Technologies and Renewable Sources DepartmentNational Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Trisaia Research CentreRotondellaMateraItaly
| | - Maria Francesca Cardone
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and Economics (CREA)TuriBariItaly
| | | | - Lisete Sousa
- Department of Statistics and Operations Research, Faculdade de Ciências; Centre of Statistics and its Applications (CEAUL)Universidade de LisboaLisbonPortugal
| | - Rita B. Santos
- Faculdade de Ciências, Plant Biology Department, Biosystems & Integrative Sciences Institute (BioISI)Universidade de LisboaLisbonPortugal
| | - Rui Malhó
- Faculdade de Ciências, Plant Biology Department, Biosystems & Integrative Sciences Institute (BioISI)Universidade de LisboaLisbonPortugal
| | - Carlo Bergamini
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and Economics (CREA)TuriBariItaly
| | - Antonio Domenico Marsico
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and Economics (CREA)TuriBariItaly
| | - Andreia Figueiredo
- Faculdade de Ciências, Plant Biology Department, Biosystems & Integrative Sciences Institute (BioISI)Universidade de LisboaLisbonPortugal
| | - Fiammetta Alagna
- Energy Technologies and Renewable Sources DepartmentNational Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Trisaia Research CentreRotondellaMateraItaly
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Xu Y, Miao Y, Tian X, Wang Q, Hu Y, Luo Q. Transcriptomic and Epigenomic Assessment Reveals Epigenetic Regulation of WRKY Genes in Response to Magnaporthe oryzae Infection in Rice. Curr Genomics 2022; 23:182-194. [PMID: 36777006 PMCID: PMC9878826 DOI: 10.2174/1389202923666220510195910] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/07/2022] [Accepted: 03/28/2022] [Indexed: 11/22/2022] Open
Abstract
Background: Histone acetylations acting as active hallmarks for gene transcription is involved in regulating numerous developmental and stress-responsive gene expression. Methods: The data from chromatin immunoprecipitation sequencing (ChIP-seq) was performed by using histone H3 lysine 9 acetylation (H3K9ac) antibody, and RNA sequencing (RNA-seq) utilizing rice seedlings inoculated by Magnaporthe oryzae (M. oryzae) were integrated. Results: RNA-seq data revealed that 422, 460 and 466 genes were up-regulated at 12h, 24h and 48h after inoculation. ChIP-seq data showed that 60%-80% of blast up-regulated genes at different time points were marked with H3K9ac, which was prone to be enriched in both TSS and gene body region. However, the H3K9ac level at a rather small proportion of the up-regulated genes was elevated after M. oryzae inoculation. We found that seven WRKY genes induced by rice blast fungus harbor H3K9ac. For different WRKY genes, blast fungus induction led to the increase of H3K9ac in distinct regions, including promoter, TSS or gene body, indicating that histone acetylation may play diverse roles in the activation of defense-related genes. By searching DNA-binding motifs of transcription factors in the promoter of genes with increased H3K9ac after M. oryzae infection, we found that ERF family protein-binding motifs were enriched with high -log P-value (>20), including ERF1, DEAR3, DREB2C, RAP2.6, RRTF1_3ARY, all of which contain GCC-box (GCCGCC). Conclusion: In this study, we revealed that the vast majority of genes induced by fungus M. oryzae were marked with H3K9ac preferring both TSS and gene body regions. However, H3K9ac enrichment was increased, responding to M. oryzae inoculation only at a low proportion of these genes, including several WRKY genes. Besides, for different genes, the increment of H3K9ac occurred in different regions. Finally, ERF proteins that have been proved to bind GCC-box might be one of the potential transcription factors for recruiting histone acetyltransferases to deposit histone acetylation at defense-related genes in rice.
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Affiliation(s)
- Yan Xu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan/Ministry of Education, Key Labo-ratory of Agricultural Biodiversity for Plant Disease Management, Yunnan Agricultural University, 650201, Kunming, China;,College of Bioengineering, Jingchu University of Technology, 448000, Jingmen, China;,These authors contributed equally to this work.
| | - Yuanxin Miao
- College of Bioengineering, Jingchu University of Technology, 448000, Jingmen, China;,These authors contributed equally to this work.
| | - Xuejun Tian
- College of Bioengineering, Jingchu University of Technology, 448000, Jingmen, China
| | - Qihai Wang
- College of Bioengineering, Jingchu University of Technology, 448000, Jingmen, China
| | - Yongfeng Hu
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement, Biotechnology Research Center, China Three Gorges University, 443002, Yichang, Hubei, China,Address correspondence to these authors at the State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan/Ministry of Education Key Laboratory of Agricultural Biodiversity for Plant Disease Management, Yunnan Agricultural University, 650201, Kunming, China; Tel/Fax: 13769133718; E-mail: and Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement, Biotechnology Research Center, China Three Gorges University, 443002, Yichang, Hubei, China; Tel/Fax: 13677246318; E-mail:
| | - Qiong Luo
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan/Ministry of Education, Key Labo-ratory of Agricultural Biodiversity for Plant Disease Management, Yunnan Agricultural University, 650201, Kunming, China;,Address correspondence to these authors at the State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan/Ministry of Education Key Laboratory of Agricultural Biodiversity for Plant Disease Management, Yunnan Agricultural University, 650201, Kunming, China; Tel/Fax: 13769133718; E-mail: and Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement, Biotechnology Research Center, China Three Gorges University, 443002, Yichang, Hubei, China; Tel/Fax: 13677246318; E-mail:
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Hohenfeld CS, Passos AR, de Carvalho HWL, de Oliveira SAS, de Oliveira EJ. Genome-wide association study and selection for field resistance to cassava root rot disease and productive traits. PLoS One 2022; 17:e0270020. [PMID: 35709238 PMCID: PMC9202857 DOI: 10.1371/journal.pone.0270020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 06/02/2022] [Indexed: 12/04/2022] Open
Abstract
Cassava root rot disease is caused by a complex of soil-borne pathogens and has high economic impacts because it directly affects the tuberous roots, which are the main commercial product. This study aimed to evaluate cassava genotypes for resistance to root rot disease in a field with a previous history of high disease incidence. It also aimed to identify possible genomic regions associated with field resistance based on genome-wide association studies. A total of 148 genotypes from Embrapa Mandioca and Fruticultura were evaluated over two years, including improved materials and curated germplasms. Analysis of phenotypic data was conducted, as well as a genomic association analysis, based on the general linear model, mixed linear model, and fixed and random model circulating probability unification. The observed high disease index (ω) was directly correlated with genotype survival, affecting plant height, shoot yield, and fresh root yield. The genotypes were grouped into five clusters, which were classified according to level of root rot resistance (i.e., extremely susceptible, susceptible, moderately susceptible, moderately resistant, and resistant). The 10 genotypes with the best performance in the field were selected as potential progenitors for the development of segregating progenies. Estimates of genomic kinship between these genotypes ranged from -0.183 to 0.671. The genotypes BGM-1171 and BGM-1190 showed the lowest degree of kinship with the other selected sources of resistance. The genotypes BGM-0209, BGM-0398, and BGM-0659 showed negative kinship values with most elite varieties, while BGM-0659 presented negative kinship with all landraces. A genome-wide association analysis detected five significant single nucleotide polymorphisms related to defense mechanisms against biotic and abiotic stresses, with putative association with fresh root yield in soil infested with root rot pathogens. These findings can be utilized to develop molecular selection for root rot resistance in cassava.
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Liu J, Chang C. Concerto on Chromatin: Interplays of Different Epigenetic Mechanisms in Plant Development and Environmental Adaptation. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10122766. [PMID: 34961235 PMCID: PMC8705648 DOI: 10.3390/plants10122766] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/30/2021] [Accepted: 12/10/2021] [Indexed: 05/26/2023]
Abstract
Epigenetic mechanisms such as DNA methylation, histone post-translational modifications, chromatin remodeling, and noncoding RNAs, play important roles in regulating plant gene expression, which is involved in various biological processes including plant development and stress responses. Increasing evidence reveals that these different epigenetic mechanisms are highly interconnected, thereby contributing to the complexity of transcriptional reprogramming in plant development processes and responses to environmental stresses. Here, we provide an overview of recent advances in understanding the epigenetic regulation of plant gene expression and highlight the crosstalk among different epigenetic mechanisms in making plant developmental and stress-responsive decisions. Structural, physical, transcriptional and metabolic bases for these epigenetic interplays are discussed.
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Hou Q, Wan X. Epigenome and Epitranscriptome: Potential Resources for Crop Improvement. Int J Mol Sci 2021; 22:12912. [PMID: 34884725 PMCID: PMC8658206 DOI: 10.3390/ijms222312912] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/24/2021] [Accepted: 11/28/2021] [Indexed: 12/26/2022] Open
Abstract
Crop breeding faces the challenge of increasing food demand, especially under climatic changes. Conventional breeding has relied on genetic diversity by combining alleles to obtain desired traits. In recent years, research on epigenetics and epitranscriptomics has shown that epigenetic and epitranscriptomic diversity provides additional sources for crop breeding and harnessing epigenetic and epitranscriptomic regulation through biotechnologies has great potential for crop improvement. Here, we review epigenome and epitranscriptome variations during plant development and in response to environmental stress as well as the available sources for epiallele formation. We also discuss the possible strategies for applying epialleles and epitranscriptome engineering in crop breeding.
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Affiliation(s)
- Quancan Hou
- Zhongzhi International Institute of Agricultural Biosciences, Shunde Graduate School, Research Center of Biology and Agriculture, University of Science and Technology Beijing (USTB), Beijing 100024, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co., Ltd., Beijing 100192, China
| | - Xiangyuan Wan
- Zhongzhi International Institute of Agricultural Biosciences, Shunde Graduate School, Research Center of Biology and Agriculture, University of Science and Technology Beijing (USTB), Beijing 100024, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co., Ltd., Beijing 100192, China
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21
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Gutierrez N, Torres AM. QTL dissection and mining of candidate genes for Ascochyta fabae and Orobanche crenata resistance in faba bean (Vicia faba L.). BMC PLANT BIOLOGY 2021; 21:551. [PMID: 34809555 PMCID: PMC8607628 DOI: 10.1186/s12870-021-03335-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 11/08/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Ascochyta blight caused by Ascochyta fabae Speg. and broomrape (Orobanche crenata) are among the economically most significant pathogens of faba bean. Several QTLs conferring resistance against the two pathogens have been identified and validated in different genetic backgrounds. The aim of this study was to saturate the most stable QTLs for ascochyta and broomrape resistance in two Recombinant Inbred Line (RIL) populations, 29H x Vf136 and Vf6 x Vf136, to identify candidate genes conferring resistance against these two pathogens. RESULTS We exploited the synteny between faba bean and the model species Medicago truncatula by selecting a set of 219 genes encoding putative WRKY transcription factors and defense related proteins falling within the target QTL intervals, for genotyping and marker saturation in the two RIL populations. Seventy and 50 of the candidate genes could be mapped in 29H x Vf136 and Vf6 x Vf136, respectively. Besides the strong reduction of the QTL intervals, the mapping process allowed replacing previous dominant and pedigree-specific RAPD flanking markers with robust and transferrable SNP markers, revealing promising candidates for resistance against the two pathogens. CONCLUSIONS Although further efforts in association mapping and expression studies will be required to corroborate the candidate genes for resistance, the fine-mapping approach proposed here increases the genetic resolution of relevant QTL regions and paves the way for an efficient deployment of useful alleles for faba bean ascochyta and broomrape resistance through marker-assisted breeding.
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Affiliation(s)
- Natalia Gutierrez
- Área de Genómica y Biotecnología, IFAPA-Centro Alameda del Obispo, Apdo 3092, E-14080, Córdoba, Spain.
| | - Ana M Torres
- Área de Genómica y Biotecnología, IFAPA-Centro Alameda del Obispo, Apdo 3092, E-14080, Córdoba, Spain
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22
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Rashid MM, Vaishnav A, Verma RK, Sharma P, Suprasanna P, Gaur RK. Epigenetic regulation of salinity stress responses in cereals. Mol Biol Rep 2021; 49:761-772. [PMID: 34773178 DOI: 10.1007/s11033-021-06922-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/30/2021] [Indexed: 10/19/2022]
Abstract
Cereals are important crops and are exposed to various types of environmental stresses that affect the overall growth and yield. Among the various abiotic stresses, salt stress is a major environmental factor that influences the genetic, physiological, and biochemical responses of cereal crops. Epigenetic regulation which includes DNA methylation, histone modification, and chromatin remodelling plays an important role in salt stress tolerance. Recent studies in rice genomics have highlighted that the epigenetic changes are heritable and therefore can be considered as molecular signatures. An epigenetic mechanism under salinity induces phenotypic responses involving modulations in gene expression. Association between histone modification and altered DNA methylation patterns and differential gene expression has been evidenced for salt sensitivity in rice and other cereal crops. In addition, epigenetics also creates stress memory that helps the plant to better combat future stress exposure. In the present review, we have discussed epigenetic influences in stress tolerance, adaptation, and evolution processes. Understanding the epigenetic regulation of salinity could help for designing salt-tolerant varieties leading to improved crop productivity.
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Affiliation(s)
- Md Mahtab Rashid
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India.,Department of Plant Pathology, Bihar Agricultural University, Sabour, Bhagalpur, Bihar, India
| | - Anukool Vaishnav
- Department of Biotechnology, GLA University, Mathura, Uttar Pradesh, 281121, India.,Agroecology and Environment, Agroscope (Reckenholz), 8046, Zürich, Switzerland
| | - Rakesh Kumar Verma
- Department of Biosciences, Mody University of Science and Technology, Lakshmangarh, Sikar, Rajasthan, India
| | - Pradeep Sharma
- Department of Biotechnology, ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
| | - P Suprasanna
- Nuclear Agriculture & Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
| | - R K Gaur
- Department of Biotechnology, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur, Uttar Pradesh, India.
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Wang J, Liu C, Chen Y, Zhao Y, Ma Z. Protein acetylation and deacetylation in plant-pathogen interactions. Environ Microbiol 2021; 23:4841-4855. [PMID: 34398483 DOI: 10.1111/1462-2920.15725] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 12/12/2022]
Abstract
Protein acetylation and deacetylation catalysed by lysine acetyltransferases (KATs) and deacetylases (KDACs), respectively, are major mechanisms regulating various cellular processes. During the fight between microbial pathogens and host plants, both apply a set of measures, including acetylation interference, to strengthen themselves while suppressing the other. In this review, we first summarize KATs and KDACs in plants and their pathogens. Next, we introduce diverse acetylation and deacetylation mechanisms affecting protein functions, including the regulation of enzyme activity and specificity, protein-protein or protein-DNA interactions, subcellular localization and protein stability. We then focus on the current understanding of acetylation and deacetylation in plant-pathogen interactions. Additionally, we also discuss potential acetylation-related approaches for controlling plant diseases.
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Affiliation(s)
- Jing Wang
- State Key Laboratory of Rice Biology, and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Chao Liu
- State Key Laboratory of Rice Biology, and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yun Chen
- State Key Laboratory of Rice Biology, and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Youfu Zhao
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Zhonghua Ma
- State Key Laboratory of Rice Biology, and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China
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24
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Kumar V, Thakur JK, Prasad M. Histone acetylation dynamics regulating plant development and stress responses. Cell Mol Life Sci 2021; 78:4467-4486. [PMID: 33638653 PMCID: PMC11072255 DOI: 10.1007/s00018-021-03794-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/21/2021] [Accepted: 02/18/2021] [Indexed: 12/17/2022]
Abstract
Crop productivity is directly dependent on the growth and development of plants and their adaptation during different environmental stresses. Histone acetylation is an epigenetic modification that regulates numerous genes essential for various biological processes, including development and stress responses. Here, we have mainly discussed the impact of histone acetylation dynamics on vegetative growth, flower development, fruit ripening, biotic and abiotic stress responses. Besides, we have also emphasized the information gaps which are obligatory to be examined for understanding the complete role of histone acetylation dynamics in plants. A comprehensive knowledge about the histone acetylation dynamics will ultimately help to improve stress resistance and reduce yield losses in different crops due to climate changes.
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Affiliation(s)
- Verandra Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Jitendra K Thakur
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Zhi P, Chang C. Exploiting Epigenetic Variations for Crop Disease Resistance Improvement. FRONTIERS IN PLANT SCIENCE 2021; 12:692328. [PMID: 34149790 PMCID: PMC8212930 DOI: 10.3389/fpls.2021.692328] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 04/27/2021] [Indexed: 05/07/2023]
Abstract
Pathogen infections seriously threaten plant health and global crop production. Epigenetic processes such as DNA methylation, histone post-translational modifications, chromatin assembly and remodeling play important roles in transcriptional regulation of plant defense responses and could provide a new direction to drive breeding strategies for crop disease resistance improvement. Although past decades have seen unprecedented proceedings in understanding the epigenetic mechanism of plant defense response, most of these advances were derived from studies in model plants like Arabidopsis. In this review, we highlighted the recent epigenetic studies on crop-pathogen interactions and discussed the potentials, challenges, and strategies in exploiting epigenetic variations for crop disease resistance improvement.
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Genome-Wide Identification and Expression Analysis of the Histone Deacetylase Gene Family in Wheat ( Triticum aestivum L.). PLANTS 2020; 10:plants10010019. [PMID: 33374252 PMCID: PMC7823868 DOI: 10.3390/plants10010019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/20/2020] [Accepted: 12/22/2020] [Indexed: 12/16/2022]
Abstract
Histone acetylation is a dynamic modification process co-regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs). Although HDACs play vital roles in abiotic or biotic stress responses, their members in Triticumaestivum and their response to plant viruses remain unknown. Here, we identified and characterized 49 T. aestivumHDACs (TaHDACs) at the whole-genome level. Based on phylogenetic analyses, TaHDACs could be divided into 5 clades, and their protein spatial structure was integral and conserved. Chromosomal location and synteny analyses showed that TaHDACs were widely distributed on wheat chromosomes, and gene duplication has accelerated the TaHDAC gene family evolution. The cis-acting element analysis indicated that TaHDACs were involved in hormone response, light response, abiotic stress, growth, and development. Heatmaps analysis of RNA-sequencing data showed that TaHDAC genes were involved in biotic or abiotic stress response. Selected TaHDACs were differentially expressed in diverse tissues or under varying temperature conditions. All selected TaHDACs were significantly upregulated following infection with the barley stripe mosaic virus (BSMV), Chinese wheat mosaic virus (CWMV), and wheat yellow mosaic virus (WYMV), suggesting their involvement in response to viral infections. Furthermore, TaSRT1-silenced contributed to increasing wheat resistance against CWMV infection. In summary, these findings could help deepen the understanding of the structure and characteristics of the HDAC gene family in wheat and lay the foundation for exploring the function of TaHDACs in plants resistant to viral infections.
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27
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Histone Deacetylase TaHDT701 Functions in TaHDA6-TaHOS15 Complex to Regulate Wheat Defense Responses to Blumeria graminis f.sp. tritici. Int J Mol Sci 2020; 21:ijms21072640. [PMID: 32290114 PMCID: PMC7178159 DOI: 10.3390/ijms21072640] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/05/2020] [Accepted: 04/08/2020] [Indexed: 12/16/2022] Open
Abstract
Powdery mildew disease caused by Blumeria graminis f.sp. tritici (Bgt) leads to severe economic losses in bread wheat (Triticum aestivum L.). To date, only a few epigenetic modulators have been revealed to regulate wheat powdery mildew resistance. In this study, the histone deacetylase 2 (HD2) type histone deacetylase TaHDT701 was identified as a negative regulator of wheat defense responses to Bgt. Using multiple approaches, we demonstrated that TaHDT701 associates with the RPD3 type histone deacetylase TaHDA6 and the WD40-repeat protein TaHOS15 to constitute a histone deacetylase complex, in which TaHDT701 could stabilize the TaHDA6-TaHOS15 association. Furthermore, knockdown of TaHDT701, TaHDA6, and TaHOS15 resulted in enhanced wheat powdery mildew resistance, suggesting that the TaHDT701-TaHDA6-TaHOS15 histone deacetylase complex negatively regulates wheat defense responses to Bgt. Moreover, chromatin immunoprecipitation assays revealed that TaHDT701 could function in concert with TaHOS15 to recruit TaHDA6 to the promoters of defense-related genes such as TaPR1, TaPR2, TaPR5, and TaWRKY45. In addition, silencing of TaHDT701, TaHDA6, and TaHOS15 resulted in the up-regulation of TaPR1, TaPR2, TaPR5, and TaWRKY45 accompanied with increased histone acetylation and methylation, as well as reduced nucleosome occupancy, at their promoters, suggesting that the TaHDT701-TaHDA6-TaHOS15 histone deacetylase complex suppresses wheat powdery mildew resistance by modulating chromatin state at defense-related genes.
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28
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Yang L, Chen X, Wang Z, Sun Q, Hong A, Zhang A, Zhong X, Hua J. HOS15 and HDA9 negatively regulate immunity through histone deacetylation of intracellular immune receptor NLR genes in Arabidopsis. THE NEW PHYTOLOGIST 2020; 226:507-522. [PMID: 31854111 PMCID: PMC7080574 DOI: 10.1111/nph.16380] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 12/08/2019] [Indexed: 05/08/2023]
Abstract
Plant immune responses need to be tightly controlled for growth-defense balance. The mechanism underlying this tight control is not fully understood. Here we identify epigenetic regulation of nucleotide-binding leucine rich repeat or Nod-Like Receptor (NLR) genes as an important mechanism for immune responses. Through a sensitized genetic screen and molecular studies, we identified and characterized HOS15 and its associated protein HDA9 as negative regulators of immunity and NLR gene expression. The loss-of-function of HOS15 or HDA9 confers enhanced resistance to pathogen infection accompanied with increased expression of one-third of the 207 NLR genes in Arabidopsis thaliana. HOS15 and HDA9 are physically associated with some of these NLR genes and repress their expression likely through reducing the acetylation of H3K9 at these loci. In addition, these NLR genes are repressed by HOS15 under both pathogenic and nonpathogenic conditions but by HDA9 only under infection condition. Together, this study uncovers a previously uncharacterized histone deacetylase complex in plant immunity and highlights the importance of epigenetic regulation of NLR genes in modulating growth-defense balance.
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Affiliation(s)
- Leiyun Yang
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, 14853, USA
| | - Xiangsong Chen
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, 53706, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, 53706, USA
| | - Zhixue Wang
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, 14853, USA
| | - Qi Sun
- Cornell Computational Biology Service Unit, Cornell University, Ithaca, 14853, USA
| | - Anna Hong
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, 14853, USA
| | - Aiqin Zhang
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, 14853, USA
| | - Xuehua Zhong
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, 53706, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, 53706, USA
- For correspondence: Jian Hua: Tel (+1) 607-255-5554;; Xuehua Zhong: Tel (+1) 608-316-4421;
| | - Jian Hua
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, 14853, USA
- For correspondence: Jian Hua: Tel (+1) 607-255-5554;; Xuehua Zhong: Tel (+1) 608-316-4421;
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Kong L, Liu Y, Wang X, Chang C. Insight into the Role of Epigenetic Processes in Abiotic and Biotic Stress Response in Wheat and Barley. Int J Mol Sci 2020; 21:ijms21041480. [PMID: 32098241 PMCID: PMC7073019 DOI: 10.3390/ijms21041480] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/13/2020] [Accepted: 02/19/2020] [Indexed: 02/07/2023] Open
Abstract
Environmental stresses such as salinity, drought, heat, freezing, heavy metal and even pathogen infections seriously threaten the growth and yield of important cereal crops including wheat and barley. There is growing evidence indicating that plants employ sophisticated epigenetic mechanisms to fine-tune their responses to environmental stresses. Here, we provide an overview of recent developments in understanding the epigenetic processes and elements—such as DNA methylation, histone modification, chromatin remodeling, and non-coding RNAs—involved in plant responses to abiotic and biotic stresses in wheat and barley. Potentials of exploiting epigenetic variation for the improvement of wheat and barley are discussed.
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Affiliation(s)
- Lingyao Kong
- College of Life Sciences, Qingdao University, Qingdao 266071, China; (L.K.); (Y.L.); (X.W.)
| | - Yanna Liu
- College of Life Sciences, Qingdao University, Qingdao 266071, China; (L.K.); (Y.L.); (X.W.)
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaoyu Wang
- College of Life Sciences, Qingdao University, Qingdao 266071, China; (L.K.); (Y.L.); (X.W.)
| | - Cheng Chang
- College of Life Sciences, Qingdao University, Qingdao 266071, China; (L.K.); (Y.L.); (X.W.)
- Correspondence: ; Tel.: +86-532-85953227
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Ntoukakis V, Gifford ML. Plant-microbe interactions: tipping the balance. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:4583-4586. [PMID: 31306482 PMCID: PMC6760295 DOI: 10.1093/jxb/erz321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Affiliation(s)
- Vardis Ntoukakis
- School of Life Sciences and Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, UK
| | - Miriam L Gifford
- School of Life Sciences and Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, UK
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