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Li G, Gao Q, Li B, Wang J, Cheng B, Wang D, Gao H, Xu W, Wang W, Zhang W, Zhang G, Qi Z, Ji J, Liu Y. Comparative transcriptome profiling reveals the key genes and molecular mechanisms involved in rice under blast infection. Gene 2024; 933:148942. [PMID: 39278376 DOI: 10.1016/j.gene.2024.148942] [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: 01/26/2024] [Revised: 09/08/2024] [Accepted: 09/10/2024] [Indexed: 09/18/2024]
Abstract
The aim of this study was to analyze the resistance genes and molecular mechanisms involved in rice blast infection. The contents of seven hormones and eight biochemical indicators in the leaves and spikes were at dynamic levels after inoculation with rice blast strains over time. The mRNA and protein expression of the six genes were consistent with the transcriptome analysis results. In addition, KEGG enrichment analysis showed that Os03g0132000, Os06g0215600, and Os06g0215500 were significantly enriched in the alpha-linolenic acid metabolism KEGG pathway, whereas Os05g0311801 was significantly enriched in the zeatin biosynthesis KEGG pathway. Furthermore, Os03g0180900 and Os09g0439200 were significantly enriched in the plant hormone signal transduction KEGG pathways. Therefore, blast infection could alter the hormones, biochemical indicators, and traits of rice. Moreover, genes including Os03g0132000, Os03g0180900, and Os05g0311801 were identified as rice blast resistance genes, and the mechanism might involve alpha-linolenic acid metabolism, zeatin biosynthesis, and plant hormone signal transduction KEGG pathways.
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Affiliation(s)
- Gang Li
- Huaiyin Institute of Agricultural Science in Xuhuai region of Jiangsu/Huai'an Key Laboratory of Agricultural Biotechnology, Huai'an 223001,China.
| | - Qingsong Gao
- Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection Co-constructed by the Province and Ministry, Huaiyin Normal University, Huai'an 223300, China
| | - Bianhao Li
- School of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, China
| | - Jian Wang
- Huaiyin Institute of Agricultural Science in Xuhuai region of Jiangsu/Huai'an Key Laboratory of Agricultural Biotechnology, Huai'an 223001,China
| | - Baoshan Cheng
- Huaiyin Institute of Agricultural Science in Xuhuai region of Jiangsu/Huai'an Key Laboratory of Agricultural Biotechnology, Huai'an 223001,China
| | - Di Wang
- Huaiyin Institute of Agricultural Science in Xuhuai region of Jiangsu/Huai'an Key Laboratory of Agricultural Biotechnology, Huai'an 223001,China
| | - Hao Gao
- Huaiyin Institute of Agricultural Science in Xuhuai region of Jiangsu/Huai'an Key Laboratory of Agricultural Biotechnology, Huai'an 223001,China
| | - Weijun Xu
- Huaiyin Institute of Agricultural Science in Xuhuai region of Jiangsu/Huai'an Key Laboratory of Agricultural Biotechnology, Huai'an 223001,China
| | - Wei Wang
- Huaiyin Institute of Agricultural Science in Xuhuai region of Jiangsu/Huai'an Key Laboratory of Agricultural Biotechnology, Huai'an 223001,China
| | - Wenxia Zhang
- Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection Co-constructed by the Province and Ministry, Huaiyin Normal University, Huai'an 223300, China
| | - Guoliang Zhang
- School of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, China
| | - Zhongqiang Qi
- Institute of Plant Protection, Jiangsu Academy of Agricultural Science, Nanjing 210014, China
| | - Jianhui Ji
- Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection Co-constructed by the Province and Ministry, Huaiyin Normal University, Huai'an 223300, China.
| | - Yongfeng Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Science, Nanjing 210014, China.
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2
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Antony A, Veerappapillai S, Karuppasamy R. Deciphering early responsive signature genes in rice blast disease: an integrated temporal transcriptomic study. J Appl Genet 2024:10.1007/s13353-024-00901-z. [PMID: 39180632 DOI: 10.1007/s13353-024-00901-z] [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: 02/23/2024] [Revised: 06/03/2024] [Accepted: 08/06/2024] [Indexed: 08/26/2024]
Abstract
Rice blast disease, caused by Magnaporthe oryzae, reigns as the top-most cereal killer, jeopardizing global food security. This necessitates the timely scouting of pathogen stress-responsive genes during the early infection stages. Thus, we integrated time-series microarray (GSE95394) and RNA-Seq (GSE131641) datasets to decipher rice transcriptome responses at 12- and 24-h post-infection (Hpi). Our analysis revealed 1580 differentially expressed genes (DEGs) overlapped between datasets. We constructed a protein-protein interaction (PPI) network for these DEGs and identified significant subnetworks using the MCODE plugin. Further analysis with CytoHubba highlighted eight plausible hub genes for pathogenesis: RPL8 (upregulated) and RPL27, OsPRPL3, RPL21, RPL9, RPS5, OsRPS9, and RPL17 (downregulated). We validated the expression levels of these hub genes in response to infection, finding that RPL8 exhibited significantly higher expression compared with other downregulated genes. Remarkably, RPL8 formed a distinct cluster in the co-expression network, whereas other hub genes were interconnected, with RPL9 playing a central role, indicating its pivotal role in coordinating gene expression during infection. Gene Ontology highlighted the enrichment of hub genes in the ribosome and protein translation processes. Prior studies suggested that plant immune defence activation diminishes the energy pool by suppressing ribosomes. Intriguingly, our study aligns with this phenomenon, as the identified ribosomal proteins (RPs) were suppressed, while RPL8 expression was activated. We anticipate that these RPs could be targeted to develop new stress-resistant rice varieties, beyond their housekeeping role. Overall, integrating transcriptomic data revealed more common DEGs, enhancing the reliability of our analysis and providing deeper insights into rice blast disease mechanisms.
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Affiliation(s)
- Ajitha Antony
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, 632014, Tamil Nadu, India
| | - Shanthi Veerappapillai
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, 632014, Tamil Nadu, India
| | - Ramanathan Karuppasamy
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, 632014, Tamil Nadu, India.
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Sinha A, Narula K, Bhola L, Sengupta A, Choudhary P, Nalwa P, Kumar M, Elagamey E, Chakraborty N, Chakraborty S. Proteomic signatures uncover phenotypic plasticity of susceptible and resistant genotypes by wall remodelers in rice blast. PLANT, CELL & ENVIRONMENT 2024. [PMID: 38825969 DOI: 10.1111/pce.14973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 05/06/2024] [Accepted: 05/15/2024] [Indexed: 06/04/2024]
Abstract
Molecular communication between macromolecules dictates extracellular matrix (ECM) dynamics during pathogen recognition and disease development. Extensive research has shed light on how plant immune components are activated, regulated and function in response to pathogen attack. However, two key questions remain largely unresolved: (i) how does ECM dynamics govern susceptibility and disease resistance, (ii) what are the components that underpin these phenomena? Rice blast, caused by Magnaporthe oryzae adversely affects rice productivity. To understand ECM regulated genotype-phenotype plasticity in blast disease, we temporally profiled two contrasting rice genotypes in disease and immune state. Morpho-histological, biochemical and electron microscopy analyses revealed that increased necrotic lesions accompanied by electrolyte leakage governs disease state. Wall carbohydrate quantification showed changes in pectin level was more significant in blast susceptible compared to blast resistant cultivar. Temporally resolved quantitative disease- and immune-responsive ECM proteomes identified 308 and 334 proteins, respectively involved in wall remodelling and integrity, signalling and disease/immune response. Pairwise comparisons between time and treatment, messenger ribonucleic acid expression, diseasome and immunome networks revealed novel blast-related functional modules. Data demonstrated accumulation of α-galactosidase and phosphatase were associated with disease state, while reactive oxygen species, induction of Lysin motif proteins, CAZymes and extracellular Ca-receptor protein govern immune state.
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Affiliation(s)
- Arunima Sinha
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Kanika Narula
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Latika Bhola
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Atreyee Sengupta
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Pooja Choudhary
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Pragya Nalwa
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Mohit Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Eman Elagamey
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Niranjan Chakraborty
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Subhra Chakraborty
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
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Xiao N, Wu Y, Zhang X, Hao Z, Chen Z, Yang Z, Cai Y, Wang R, Yu L, Wang Z, Lu Y, Shi W, Pan C, Li Y, Zhou C, Liu J, Huang N, Liu G, Ji H, Zhu S, Fang S, Ning Y, Li A. Pijx confers broad-spectrum seedling and panicle blast resistance by promoting the degradation of ATP β subunit and OsRbohC-mediated ROS burst in rice. MOLECULAR PLANT 2023; 16:1832-1846. [PMID: 37798878 DOI: 10.1016/j.molp.2023.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 04/11/2023] [Accepted: 10/01/2023] [Indexed: 10/07/2023]
Abstract
Rice blast, caused by the fungal pathogen Magnaporthe oryzae, is one of the most important diseases of rice. Utilization of blast-resistance genes is the most economical, effective, and environmentally friendly way to control the disease. However, genetic resources with broad-spectrum resistance (BSR) that is effective throughout the rice growth period are rare. In this work, using a genome-wide association study, we identify a new blast-resistance gene, Pijx, which encodes a typical CC-NBS-LRR protein. Pijx is derived from a wild rice species and confers BSR to M. oryzae at both the seedling and panicle stages. The functions of the resistant haplotypes of Pijx are confirmed by gene knockout and overexpression experiments. Mechanistically, the LRR domain in Pijx interacts with and promotes the degradation of the ATP synthase β subunit (ATPb) via the 26S proteasome pathway. ATPb acts as a negative regulator of Pijx-mediated panicle blast resistance, and interacts with OsRbohC to promote its degradation. Consistently, loss of ATPb function causes an increase in NAPDH content and ROS burst. Remarkably, when Pijx is introgressed into two japonica rice varieties, the introgression lines show BSR and increased yields that are approximately 51.59% and 79.31% higher compared with those of their parents in a natural blast disease nursery. In addition, we generate PPLPijx Pigm and PPLPijx Piz-t pyramided lines and these lines also have higher BSR to panicle blast compared with Pigm- or Piz-t-containing rice plants. Collectively, this study demonstrates that Pijx not only confers BSR to M. oryzae but also maintains high and stable rice yield, providing new genetic resources and molecular targets for breeding rice varieties with broad-spectrum blast resistance.
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Affiliation(s)
- Ning Xiao
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou Rice Experiment Station of the China Agricultural Research System, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou 225009, China
| | - Yunyu Wu
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou Rice Experiment Station of the China Agricultural Research System, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou 225009, China
| | - Xiaoxiang Zhang
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou Rice Experiment Station of the China Agricultural Research System, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou 225009, China
| | - Zeyun Hao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zichun Chen
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou Rice Experiment Station of the China Agricultural Research System, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou 225009, China
| | - Zefeng Yang
- Key Laboratory of Plant Functional Genomics, Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, China
| | - Yue Cai
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou Rice Experiment Station of the China Agricultural Research System, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou 225009, China
| | - Ruyi Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ling Yu
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou Rice Experiment Station of the China Agricultural Research System, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou 225009, China
| | - Zhiping Wang
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou Rice Experiment Station of the China Agricultural Research System, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou 225009, China
| | - Yue Lu
- Key Laboratory of Plant Functional Genomics, Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, China
| | - Wei Shi
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou Rice Experiment Station of the China Agricultural Research System, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou 225009, China
| | - Cunhong Pan
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou Rice Experiment Station of the China Agricultural Research System, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou 225009, China
| | - Yuhong Li
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou Rice Experiment Station of the China Agricultural Research System, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou 225009, China
| | - Changhai Zhou
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou Rice Experiment Station of the China Agricultural Research System, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou 225009, China
| | - Jianju Liu
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou Rice Experiment Station of the China Agricultural Research System, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou 225009, China
| | - Niansheng Huang
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou Rice Experiment Station of the China Agricultural Research System, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou 225009, China
| | - Guangqing Liu
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou Rice Experiment Station of the China Agricultural Research System, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou 225009, China
| | - Hongjuan Ji
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou Rice Experiment Station of the China Agricultural Research System, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou 225009, China
| | - Shuhao Zhu
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou Rice Experiment Station of the China Agricultural Research System, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou 225009, China
| | - Shuai Fang
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou Rice Experiment Station of the China Agricultural Research System, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou 225009, China
| | - Yuese Ning
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Aihong Li
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou Rice Experiment Station of the China Agricultural Research System, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou 225009, China.
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Banakar SN, Prasannakumar MK, Parivallal PB, Pramesh D, Mahesh HB, Sarangi AN, Puneeth ME, Patil SS. Rice- Magnaporthe transcriptomics reveals host defense activation induced by red seaweed-biostimulant in rice plants. Front Genet 2023; 14:1132561. [PMID: 37424731 PMCID: PMC10327602 DOI: 10.3389/fgene.2023.1132561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 05/30/2023] [Indexed: 07/11/2023] Open
Abstract
Red seaweed extracts have been shown to trigger the biotic stress tolerance in several crops. However, reports on transcriptional modifications in plants treated with seaweed biostimulant are limited. To understand the specific response of rice to blast disease in seaweed-biostimulant-primed and non-primed plants, transcriptomics of a susceptible rice cultivar IR-64 was carried out at zero and 48 h post inoculation with Magnaporthe oryzae (strain MG-01). A total of 3498 differentially expressed genes (DEGs) were identified; 1116 DEGs were explicitly regulated in pathogen-inoculated treatments. Functional analysis showed that most DEGs were involved in metabolism, transport, signaling, and defense. In a glass house, artificial inoculation of MG-01 on seaweed-primed plants resulted in the restricted spread of the pathogen leading to the confined blast disease lesions, primarily attributed to reactive oxygen species (ROS) accumulation. The DEGs in the primed plants were defense-related transcription factors, kinases, pathogenesis-related genes, peroxidases, and growth-related genes. The beta-D-xylosidase, a putative gene that helps in secondary cell wall reinforcement, was downregulated in non-primed plants, whereas it upregulated in the primed plants indicating its role in the host defense. Additionally, Phenylalanine ammonia-lyase, pathogenesis-related Bet-v-I family protein, chalcone synthase, chitinases, WRKY, AP2/ERF, and MYB families were upregulated in seaweed and challenge inoculated rice plants. Thus, our study shows that priming rice plants with seaweed bio-stimulants resulted in the induction of the defense in rice against blast disease. This phenomenon is contributed to early protection through ROS, protein kinase, accumulation of secondary metabolites, and cell wall strengthening.
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Affiliation(s)
- Sahana N. Banakar
- Plant PathoGenOmics Laboratory, Department of Plant Pathology, University of Agricultural Sciences, Bengaluru, India
| | - M. K. Prasannakumar
- Plant PathoGenOmics Laboratory, Department of Plant Pathology, University of Agricultural Sciences, Bengaluru, India
| | - P. Buela Parivallal
- Plant PathoGenOmics Laboratory, Department of Plant Pathology, University of Agricultural Sciences, Bengaluru, India
| | - D. Pramesh
- Rice Pathology Laboratory, All India Coordinated Rice Improvement Programme, University of Agricultural Sciences, Raichur, India
| | - H. B. Mahesh
- Department of Genetics and Plant Breeding, College of Agriculture, Mandya, India
| | | | - M. E. Puneeth
- Plant PathoGenOmics Laboratory, Department of Plant Pathology, University of Agricultural Sciences, Bengaluru, India
| | - Swathi S. Patil
- Plant PathoGenOmics Laboratory, Department of Plant Pathology, University of Agricultural Sciences, Bengaluru, India
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Kumari M, Kapoor R, Devanna BN, Varshney S, Kamboj R, Rai AK, Sharma TR. iTRAQ based proteomic analysis of rice lines having single or stacked blast resistance genes: Pi54/ Pi54rh during incompatible interaction with Magnaporthe oryzae. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:871-887. [PMID: 37520805 PMCID: PMC10382468 DOI: 10.1007/s12298-023-01327-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 05/12/2023] [Accepted: 06/08/2023] [Indexed: 08/01/2023]
Abstract
Deployment of single or multiple blast resistance (R) genes in rice plant is considered to be the most promising approach to enhance resistance against blast disease caused by fungus Magnaporthe oryzae. At the proteome level, relatively little information about R gene mediated defence mechanisms for single and stacking resistance characteristics is available. The overall objective of this study is to look at the proteomics of rice plants that have R genes; Pi54, Pi54rh and stacked Pi54 + Pi54rh in response to rice blast infection. In this study 'isobaric tag for relative and absolute quantification' (iTRAQ)-based proteomics analysis was performed in rice plants at 72-h post inoculation with Magnaporthe oryzae and various differentially expressed proteins were identified in these three transgenic lines in comparison to wild type during resistance response to blast pathogen. Through STRING analysis, the observed proteins were further examined to anticipate their linked partners, and it was shown that several defense-related proteins were co-expressed. These proteins can be employed as targets in future rice resistance breeding against Magnaporthe oryzae. The current study is the first to report a proteomics investigation of rice lines that express single blast R gene Pi54, Pi54rh and stacked (Pi54 + Pi54rh) during incompatible interaction with Magnaporthe oryzae. The differentially expressed proteins indicated that secondary metabolites, reactive oxygen species-related proteins, phenylpropanoid, phytohormones and pathogenesis-related proteins have a substantial relationship with the defense response against Magnaporthe oryzae. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01327-3.
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Affiliation(s)
- Mandeep Kumari
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, Vanasthali, Rajasthan India
| | - Ritu Kapoor
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab India
| | - B. N. Devanna
- ICAR-National Rice Research Institute, Cuttack, Odisha India
| | - Swati Varshney
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, Delhi India
| | - Richa Kamboj
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, Vanasthali, Rajasthan India
| | - Amit Kumar Rai
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - T. R. Sharma
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
- Division of Crop Science, Indian Council of Agricultural Research, Krishi Bhavan, New Delhi, India
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7
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Liu J, Tang X, Guan X. Grain protein function prediction based on self-attention mechanism and bidirectional LSTM. Brief Bioinform 2023; 24:6886418. [PMID: 36567619 DOI: 10.1093/bib/bbac493] [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: 06/09/2022] [Revised: 10/13/2022] [Accepted: 10/18/2022] [Indexed: 12/27/2022] Open
Abstract
With the development of genome sequencing technology, using computing technology to predict grain protein function has become one of the important tasks of bioinformatics. The protein data of four grains, soybean, maize, indica and japonica are selected in this experimental dataset. In this paper, a novel neural network algorithm Chemical-SA-BiLSTM is proposed for grain protein function prediction. The Chemical-SA-BiLSTM algorithm fuses the chemical properties of proteins on the basis of amino acid sequences, and combines the self-attention mechanism with the bidirectional Long Short-Term Memory network. The experimental results show that the Chemical-SA-BiLSTM algorithm is superior to other classical neural network algorithms, and can more accurately predict the protein function, which proves the effectiveness of the Chemical-SA-BiLSTM algorithm in the prediction of grain protein function. The source code of our method is available at https://github.com/HwaTong/Chemical-SA-BiLSTM.
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Affiliation(s)
- Jing Liu
- College of Information Engineering, Shanghai Maritime University, 201306, Shanghai, China
| | - Xinghua Tang
- College of Information Engineering, Shanghai Maritime University, 201306, Shanghai, China
| | - Xiao Guan
- School of Health Science and Engineering, University of Shanghai for Science and Technology, 200093, Shanghai, China
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8
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Zhang L, Shan C, Zhang Y, Miao W, Bing X, Kuang W, Wang Z, Cui R, Olsson S. Transcriptome Analysis of Protein Kinase MoCK2, which Affects Acetyl-CoA Metabolism and Import of CK2-Interacting Mitochondrial Proteins into Mitochondria in the Rice Blast Fungus Magnaporthe oryzae. Microbiol Spectr 2022; 10:e0304222. [PMID: 36255296 PMCID: PMC9769659 DOI: 10.1128/spectrum.03042-22] [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: 08/04/2022] [Accepted: 09/21/2022] [Indexed: 01/09/2023] Open
Abstract
The rice pathogen Magnaporthe oryzae causes severe losses to rice production. Previous studies have shown that the protein kinase MoCK2 is essential for pathogenesis, and this ubiquitous eukaryotic protein kinase might affect several processes in the fungus that are needed for infection. To better understand which cellular processes are affected by MoCK2 activity, we performed a detailed transcriptome sequencing analysis of deletions of the MoCK2 b1 and b2 components in relation to the background strain Ku80 and connected this analysis with the abundance of substrates for proteins in a previous pulldown of the essential CKa subunit of CK2 to estimate the effects on proteins directly interacting with CK2. The results showed that MoCK2 seriously affected carbohydrate metabolism, fatty acid metabolism, amino acid metabolism, and the related transporters and reduced acetyl-CoA production. CK2 phosphorylation can affect the folding of proteins and especially the effective formation of protein complexes by intrinsically disordered or mitochondrial import by destabilizing soluble alpha helices. The upregulated genes found in the pulldown of the b1 and b2 mutants indicate that proteins directly interacting with CK2 are compensatorily upregulated depending on their pulldown. A similar correlation was found for mitochondrial proteins. Taken together, the classes of proteins and the changes in regulation in the b1 and b2 mutants suggest that CK2 has a central role in mitochondrial metabolism, secondary metabolism, and reactive oxygen species (ROS) resistance, in addition to its previously suggested role in the formation of new ribosomes, all of which are processes central to efficient nonself responses as innate immunity. IMPORTANCE The protein kinase CK2 is highly expressed and essential for plants, animals, and fungi, affecting fatty acid-related metabolism. In addition, it directly affects the import of essential mitochondrial proteins into mitochondria. These effects mean that CK2 is essential for lipid metabolism and mitochondrial function and, as shown previously, is crucial for making new translation machinery proteins. Taken together, our new results combined with previously reported results indicate that CK2 is an essential protein necessary for the capacities to launch efficient innate immunity responses and withstand the negative effects of such responses necessary for general resistance against invading bacteria and viruses as well as to interact with plants, withstand plant immunity responses, and kill plant cells.
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Affiliation(s)
- Lianhu Zhang
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi, China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Chonglei Shan
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Yifan Zhang
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Wenjing Miao
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Xiaoli Bing
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Weigang Kuang
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Zonghua Wang
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Ruqiang Cui
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi, China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Stefan Olsson
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
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9
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Tan Q, He H, Chen W, Huang L, Zhao D, Chen X, Li J, Yang X. Integrated genetic analysis of leaf blast resistance in upland rice: QTL mapping, bulked segregant analysis and transcriptome sequencing. AOB PLANTS 2022; 14:plac047. [PMID: 36567764 PMCID: PMC9773827 DOI: 10.1093/aobpla/plac047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 10/13/2022] [Indexed: 06/17/2023]
Abstract
Elite upland rice cultivars have the advantages of less water requirement along with high yield but are usually susceptible to various diseases. Rice blast caused by Magnaporthe oryzae is the most devastating disease in rice. Identification of new sources of resistance and the introgression of major resistance genes into elite cultivars are required for sustainable rice production. In this study, an upland rice genotype UR0803 was considered an emerging source of blast resistance. An F2 mapping population was developed from a cross between UR0803 and a local susceptible cultivar Lijiang Xintuan Heigu. The individuals from the F2 population were evaluated for leaf blast resistance in three trials 7 days after inoculation. Bulked segregant analysis (BSA) by high-throughput sequencing and SNP-index algorithm was performed to map the candidate region related to disease resistance trait. A major quantitative trait locus (QTL) for leaf blast resistance was identified on chromosome 11 in an interval of 1.61-Mb genomic region. The candidate region was further shortened to a 108.9-kb genomic region by genotyping the 955 individuals with 14 SNP markers. Transcriptome analysis was further performed between the resistant and susceptible parents, yielding a total of 5044 differentially expressed genes (DEGs). There were four DEGs in the candidate QTL region, of which, two (Os11g0700900 and Os11g0704000) were upregulated and the remaining (Os11g0702400 and Os11g0703600) were downregulated in the susceptible parent after inoculation. These novel candidate genes were functionally annotated to catalytic response against disease stimulus in cellular membranes. The results were further validated by a quantitative real-time PCR analysis. The fine-mapping of a novel QTL for blast resistance by integrative BSA mapping and transcriptome sequencing enhanced the genetic understanding of the mechanism of blast resistance in upland rice. The most suitable genotypes with resistance alleles would be useful genetic resources in rice blast resistance breeding.
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Affiliation(s)
| | | | - Wen Chen
- Guizhou Institute of Plant Protection, Guizhou Academy of Agricultural Sciences, Guiyang 550009, China
| | - Lu Huang
- Guizhou Institute of Plant Protection, Guizhou Academy of Agricultural Sciences, Guiyang 550009, China
| | - Dailin Zhao
- Guizhou Institute of Plant Protection, Guizhou Academy of Agricultural Sciences, Guiyang 550009, China
| | - Xiaojun Chen
- Guizhou Institute of Plant Protection, Guizhou Academy of Agricultural Sciences, Guiyang 550009, China
| | - Jiye Li
- Guizhou Institute of Plant Protection, Guizhou Academy of Agricultural Sciences, Guiyang 550009, China
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10
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Zhu Z, Wang T, Lan J, Ma J, Xu H, Yang Z, Guo Y, Chen Y, Zhang J, Dou S, Yang M, Li L, Liu G. Rice MPK17 Plays a Negative Role in the Xa21-Mediated Resistance Against Xanthomonas oryzae pv. oryzae. RICE (NEW YORK, N.Y.) 2022; 15:41. [PMID: 35920921 PMCID: PMC9349333 DOI: 10.1186/s12284-022-00590-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
Rice bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is one of the most serious diseases affecting rice production worldwide. Xa21 was the first disease resistance gene cloned in rice, which encodes a receptor kinase and confers broad resistance against Xoo stains. Dozens of components in the Xa21-mediated pathway have been identified in the past decades, however, the involvement of mitogen-activated protein kinase (MAPK) genes in the pathway has not been well described. To identify MAPK involved in Xa21-mediated resistance, the level of MAPK proteins was profiled using Western blot analysis. The abundance of OsMPK17 (MPK17) was found decreased during the rice-Xoo interaction in the background of Xa21. To investigate the function of MPK17, MPK17-RNAi and over-expression (OX) transgenic lines were generated. The RNAi lines showed an enhanced resistance, while OX lines had impaired resistance against Xoo, indicating that MPK17 plays negative role in Xa21-mediated resistance. Furthermore, the abundance of transcription factor WRKY62 and pathogenesis-related proteins PR1A were changed in the MPK17 transgenic lines when inoculated with Xoo. We also observed that the MPK17-RNAi and -OX rice plants showed altered agronomic traits, indicating that MPK17 also plays roles in the growth and development. On the basis of the current study and published results, we propose a "Xa21-MPK17-WRKY62-PR1A" signaling that functions in the Xa21-mediated disease resistance pathway. The identification of MPK17 advances our understanding of the mechanism underlying Xa21-mediated immunity, specifically in the mid- and late-stages.
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Affiliation(s)
- Zheng Zhu
- College of Life Sciences, Hebei Agricultural University, 2596 Lekai South Street, West Campus, Baoding, 071001, Hebei, China
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Baoding, 071001, China
| | - Tianxingzi Wang
- College of Life Sciences, Hebei Agricultural University, 2596 Lekai South Street, West Campus, Baoding, 071001, Hebei, China
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Baoding, 071001, China
| | - Jinping Lan
- College of Life Sciences, Hebei Agricultural University, 2596 Lekai South Street, West Campus, Baoding, 071001, Hebei, China
- Research Center for Life Sciences, Hebei North University, Zhangjiakou, 075000, Hebei, China
| | - Jinjiao Ma
- College of Life Sciences, Hebei Agricultural University, 2596 Lekai South Street, West Campus, Baoding, 071001, Hebei, China
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Baoding, 071001, China
| | - Haiqing Xu
- College of Life Sciences, Hebei Agricultural University, 2596 Lekai South Street, West Campus, Baoding, 071001, Hebei, China
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Baoding, 071001, China
| | - Zexi Yang
- College of Life Sciences, Hebei Agricultural University, 2596 Lekai South Street, West Campus, Baoding, 071001, Hebei, China
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Baoding, 071001, China
| | - Yalu Guo
- College of Life Sciences, Hebei Agricultural University, 2596 Lekai South Street, West Campus, Baoding, 071001, Hebei, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518116, Guangdong, China
| | - Yue Chen
- College of Life Sciences, Hebei Agricultural University, 2596 Lekai South Street, West Campus, Baoding, 071001, Hebei, China
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Baoding, 071001, China
| | - Jianshuo Zhang
- College of Life Sciences, Hebei Agricultural University, 2596 Lekai South Street, West Campus, Baoding, 071001, Hebei, China
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Baoding, 071001, China
| | - Shijuan Dou
- College of Life Sciences, Hebei Agricultural University, 2596 Lekai South Street, West Campus, Baoding, 071001, Hebei, China
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Baoding, 071001, China
| | - Ming Yang
- College of Life Sciences, Hebei Agricultural University, 2596 Lekai South Street, West Campus, Baoding, 071001, Hebei, China
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Baoding, 071001, China
| | - Liyun Li
- College of Life Sciences, Hebei Agricultural University, 2596 Lekai South Street, West Campus, Baoding, 071001, Hebei, China.
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Baoding, 071001, China.
| | - Guozhen Liu
- College of Life Sciences, Hebei Agricultural University, 2596 Lekai South Street, West Campus, Baoding, 071001, Hebei, China.
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Baoding, 071001, China.
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11
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Understanding the Dynamics of Blast Resistance in Rice-Magnaporthe oryzae Interactions. J Fungi (Basel) 2022; 8:jof8060584. [PMID: 35736067 PMCID: PMC9224618 DOI: 10.3390/jof8060584] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/03/2022] [Accepted: 05/10/2022] [Indexed: 01/09/2023] Open
Abstract
Rice is a global food grain crop for more than one-third of the human population and a source for food and nutritional security. Rice production is subjected to various stresses; blast disease caused by Magnaporthe oryzae is one of the major biotic stresses that has the potential to destroy total crop under severe conditions. In the present review, we discuss the importance of rice and blast disease in the present and future global context, genomics and molecular biology of blast pathogen and rice, and the molecular interplay between rice–M. oryzae interaction governed by different gene interaction models. We also elaborated in detail on M. oryzae effector and Avr genes, and the role of noncoding RNAs in disease development. Further, rice blast resistance QTLs; resistance (R) genes; and alleles identified, cloned, and characterized are discussed. We also discuss the utilization of QTLs and R genes for blast resistance through conventional breeding and transgenic approaches. Finally, we review the demonstrated examples and potential applications of the latest genome-editing tools in understanding and managing blast disease in rice.
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12
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Dauda WP, Shanmugam V, Tyagi A, Solanke AU, Kumar V, Krishnan SG, Bashyal BM, Aggarwal R. Genome-Wide Identification and Characterisation of Cytokinin-O-Glucosyltransferase (CGT) Genes of Rice Specific to Potential Pathogens. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11070917. [PMID: 35406897 PMCID: PMC9002877 DOI: 10.3390/plants11070917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/25/2022] [Accepted: 03/25/2022] [Indexed: 05/12/2023]
Abstract
Cytokinin glucosyltransferases (CGTs) are key enzymes of plants for regulating the level and function of cytokinins. In a genomic identification of rice CGTs, 41 genes with the plant secondary product glycosyltransferases (PSPG) motif of 44-amino-acid consensus sequence characteristic of plant uridine diphosphate (UDP)-glycosyltransferases (UGTs) were identified. In-silico physicochemical characterisation revealed that, though the CGTs belong to the same subfamily, they display varying molecular weights, ranging from 19.6 kDa to 59.7 kDa. The proteins were primarily acidic (87.8%) and hydrophilic (58.6%) and were observed to be distributed in the plastids (16), plasma membrane (13), mitochondria (5), and cytosol (4). Phylogenetic analysis of the CGTs revealed that their evolutionary relatedness ranged from 70-100%, and they aligned themselves into two major clusters. In a comprehensive analysis of the available transcriptomics data of rice samples representing different growth stages only the CGT, Os04g25440.1 was significantly expressed at the vegetative stage, whereas 16 other genes were highly expressed only at the reproductive growth stage. On the contrary, six genes, LOC_Os07g30610.1, LOC_Os04g25440.1, LOC_Os07g30620.1, LOC_Os04g25490.1, LOC_Os04g37820.1, and LOC_Os04g25800.1, were significantly upregulated in rice plants inoculated with Rhizoctonia solani (RS), Xoo (Xanthomonas oryzae pv. oryzae) and Mor (Magnaporthe oryzae). In a qRT-PCR analysis of rice sheath tissue susceptible to Rhizoctonia solani, Mor, and Xoo pathogens, compared to the sterile distilled water control, at 24 h post-infection only two genes displayed significant upregulation in response to all the three pathogens: LOC_Os07g30620.1 and LOC_Os04g25820.1. On the other hand, the expression of genes LOC_Os07g30610.1, LOC_Os04g25440, LOC_Os04g25490, and LOC_Os04g25800 were observed to be pathogen-specific. These genes were identified as the candidate-responsive CGT genes and could serve as potential susceptibility genes for facilitating pathogen infection.
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Affiliation(s)
- Wadzani Palnam Dauda
- ICAR-Indian Agricultural Research Institute, New Delhi 110012, India; (W.P.D.); (A.T.); (S.G.K.); (B.M.B.); (R.A.)
- Crop Science Unit, Department of Agronomy, Federal University, Gashua 1005, Nigeria
| | - Veerubommu Shanmugam
- ICAR-Indian Agricultural Research Institute, New Delhi 110012, India; (W.P.D.); (A.T.); (S.G.K.); (B.M.B.); (R.A.)
- Correspondence:
| | - Aditya Tyagi
- ICAR-Indian Agricultural Research Institute, New Delhi 110012, India; (W.P.D.); (A.T.); (S.G.K.); (B.M.B.); (R.A.)
| | - Amolkumar U. Solanke
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India; (A.U.S.); (V.K.)
| | - Vishesh Kumar
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India; (A.U.S.); (V.K.)
| | - Subbaiyan Gopala Krishnan
- ICAR-Indian Agricultural Research Institute, New Delhi 110012, India; (W.P.D.); (A.T.); (S.G.K.); (B.M.B.); (R.A.)
| | - Bishnu Maya Bashyal
- ICAR-Indian Agricultural Research Institute, New Delhi 110012, India; (W.P.D.); (A.T.); (S.G.K.); (B.M.B.); (R.A.)
| | - Rashmi Aggarwal
- ICAR-Indian Agricultural Research Institute, New Delhi 110012, India; (W.P.D.); (A.T.); (S.G.K.); (B.M.B.); (R.A.)
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13
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Kumar V, Singh PK, Karkute SG, Tasleem M, Bhagat S, Abdin MZ, Sevanthi AM, Rai A, Sharma TR, Singh NK, Solanke AU. Identification of novel resources for panicle blast resistance from wild rice accessions and mutants of cv. Nagina 22 by syringe inoculation under field conditions. 3 Biotech 2022; 12:53. [PMID: 35127308 PMCID: PMC8804147 DOI: 10.1007/s13205-022-03122-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 01/16/2022] [Indexed: 02/03/2023] Open
Abstract
Panicle blast is the most severe type of rice blast disease. Screening of rice genotypes for panicle blast resistance at the field level requires an efficient and robust method of inoculation. Here, we standardized a method that can be utilized for both small- and large-scale screening and assessment of panicle blast infection and disease reaction. The method involves inoculation of Magnaporthe oryzae spore culture in the neck of the rice panicle using a syringe and covering the inoculation site with wet cotton wrapped with aluminum foil to provide the required humidity for spore germination. The method was standardized using panicle blast-resistant cv. Tetep and susceptible cv. HP2216 inoculated with Mo-ni-025 isolate of M. oryzae. The method was evaluated at phenotypic as well as molecular level by expression analysis of disease responsive pathogenesis-related (PR) genes. We found this method simple, robust, reliable, and highly efficient for screening of large germplasm sets of rice for panicle blast. This was validated by screening the wild rice germplasm for panicle blast response in the field using three M. oryzae strains and subsequently with the most virulent strain in 45 EMS-induced mutants of Nagina 22 shortlisted based on field screening in a blast hotspot region. We identified five novel blast disease-resistant wild rice genotypes and 15 Nagina 22 mutants that can be used in breeding programmes.
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Affiliation(s)
- Vishesh Kumar
- ICAR-National Institute for Plant Biotechnology, LBS Building, New Delhi, Delhi 110012 India
- Department of Biotechnology, Jamia Hamdard, Hamdard Nagar, New Delhi, 110062 India
| | - Pankaj K. Singh
- ICAR-National Institute for Plant Biotechnology, LBS Building, New Delhi, Delhi 110012 India
| | - Suhas Gorakh Karkute
- ICAR-National Institute for Plant Biotechnology, LBS Building, New Delhi, Delhi 110012 India
| | - Mohd. Tasleem
- ICAR-National Institute for Plant Biotechnology, LBS Building, New Delhi, Delhi 110012 India
| | - Someshwar Bhagat
- ICAR-NRRI-Central Rainfed Upland Rice Research Station (CRURRS), Hazaribagh, Jharkhand 825302 India
| | - M. Z. Abdin
- Department of Biotechnology, Jamia Hamdard, Hamdard Nagar, New Delhi, 110062 India
| | - Amitha Mithra Sevanthi
- ICAR-National Institute for Plant Biotechnology, LBS Building, New Delhi, Delhi 110012 India
| | - Anil Rai
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012 India
| | - Tilak Raj Sharma
- ICAR-National Institute for Plant Biotechnology, LBS Building, New Delhi, Delhi 110012 India
- Division of Crop Science, Indian Council of Agricultural Research, New Delhi, 110001 India
| | - Nagendra K. Singh
- ICAR-National Institute for Plant Biotechnology, LBS Building, New Delhi, Delhi 110012 India
| | - Amolkumar U. Solanke
- ICAR-National Institute for Plant Biotechnology, LBS Building, New Delhi, Delhi 110012 India
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14
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Wu Y, Xiao N, Li Y, Gao Q, Ning Y, Yu L, Cai Y, Pan C, Zhang X, Huang N, Zhou C, Ji H, Liu J, Shi W, Chen Z, Liang C, Li A. Identification and fine mapping of qPBR10-1, a novel locus controlling panicle blast resistance in Pigm-containing P/TGMS line. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:75. [PMID: 37309514 PMCID: PMC10236096 DOI: 10.1007/s11032-021-01268-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 11/15/2021] [Indexed: 06/14/2023]
Abstract
Rice blast is one of the most widespread and devastating diseases in rice production. Tremendous success has been achieved in the identification and characterization of genes and quantitative trait loci (QTLs) conferring seedling blast resistance, however, genetic studies on panicle blast resistance have lagged far behind. In this study, two advanced backcross inbred sister lines (MSJ13 and MSJ18) were obtained in the process of introducing Pigm into C134S and showed significant differences in the panicle blast resistance. One F2 population derived from the crossing MSJ13/MSJ18 was used to QTL mapping for panicle blast resistance using genotyping by sequencing (GBS) method. A total of seven QTLs were identified, including a major QTL qPBR10-1 on chromosome 10 that explains 24.21% of phenotypic variance with LOD scores of 6.62. Furthermore, qPBR10-1 was verified using the BC1F2 and BC1F3 population and narrowed to a 60.6-kb region with six candidate genes predicted, including two genes encoding exonuclease family protein, two genes encoding hypothetical protein, and two genes encoding transposon protein. The nucleotide variations and the expression patterns of the candidate genes were identified and analyzed between MSJ13 and MSJ18 through sequence comparison and RT-PCR approach, and results indicated that ORF1 and ORF2 encoding exonuclease family protein might be the causal candidate genes for panicle blast resistance in the qPBR10-1 locus. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01268-3.
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Affiliation(s)
- Yunyu Wu
- Lixiahe Agricultural Research Institute of Jiangsu Province, Jiangsu Collaborative Innovation Center for Modern Crop Production, Yangzhou, 225009 China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, 210095 China
| | - Ning Xiao
- Lixiahe Agricultural Research Institute of Jiangsu Province, Jiangsu Collaborative Innovation Center for Modern Crop Production, Yangzhou, 225009 China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, 210095 China
| | - Yuhong Li
- Lixiahe Agricultural Research Institute of Jiangsu Province, Jiangsu Collaborative Innovation Center for Modern Crop Production, Yangzhou, 225009 China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, 210095 China
| | - Qiang Gao
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Yuese Ning
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Ling Yu
- Lixiahe Agricultural Research Institute of Jiangsu Province, Jiangsu Collaborative Innovation Center for Modern Crop Production, Yangzhou, 225009 China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, 210095 China
| | - Yue Cai
- Lixiahe Agricultural Research Institute of Jiangsu Province, Jiangsu Collaborative Innovation Center for Modern Crop Production, Yangzhou, 225009 China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, 210095 China
| | - Cunhong Pan
- Lixiahe Agricultural Research Institute of Jiangsu Province, Jiangsu Collaborative Innovation Center for Modern Crop Production, Yangzhou, 225009 China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, 210095 China
| | - Xiaoxiang Zhang
- Lixiahe Agricultural Research Institute of Jiangsu Province, Jiangsu Collaborative Innovation Center for Modern Crop Production, Yangzhou, 225009 China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, 210095 China
| | - Niansheng Huang
- Lixiahe Agricultural Research Institute of Jiangsu Province, Jiangsu Collaborative Innovation Center for Modern Crop Production, Yangzhou, 225009 China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, 210095 China
| | - Changhai Zhou
- Lixiahe Agricultural Research Institute of Jiangsu Province, Jiangsu Collaborative Innovation Center for Modern Crop Production, Yangzhou, 225009 China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, 210095 China
| | - Hongjuan Ji
- Lixiahe Agricultural Research Institute of Jiangsu Province, Jiangsu Collaborative Innovation Center for Modern Crop Production, Yangzhou, 225009 China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, 210095 China
| | - Jianju Liu
- Lixiahe Agricultural Research Institute of Jiangsu Province, Jiangsu Collaborative Innovation Center for Modern Crop Production, Yangzhou, 225009 China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, 210095 China
| | - Wei Shi
- Lixiahe Agricultural Research Institute of Jiangsu Province, Jiangsu Collaborative Innovation Center for Modern Crop Production, Yangzhou, 225009 China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, 210095 China
| | - Zichun Chen
- Lixiahe Agricultural Research Institute of Jiangsu Province, Jiangsu Collaborative Innovation Center for Modern Crop Production, Yangzhou, 225009 China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, 210095 China
| | - Chengzhi Liang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Aihong Li
- Lixiahe Agricultural Research Institute of Jiangsu Province, Jiangsu Collaborative Innovation Center for Modern Crop Production, Yangzhou, 225009 China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, 210095 China
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15
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Polko JK, Potter KC, Burr CA, Schaller GE, Kieber JJ. Meta-analysis of transcriptomic studies of cytokinin-treated rice roots defines a core set of cytokinin response genes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1387-1402. [PMID: 34165836 DOI: 10.1111/tpj.15386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/06/2021] [Accepted: 06/19/2021] [Indexed: 05/25/2023]
Abstract
Cytokinins regulate diverse aspects of plant growth and development, primarily through modulation of gene expression. The cytokinin-responsive transcriptome has been thoroughly described in dicots, especially Arabidopsis, but much less so in monocots. Here, we present a meta-analysis of five different transcriptomic analyses of rice (Oryza sativa) roots treated with cytokinin, including three previously unpublished experiments. We developed a treatment method in which hormone is added to the media of rice seedlings grown in sterile hydroponic culture under a continuous airflow, which resulted in minimal perturbation of the seedlings, thus greatly reducing changes in gene expression in the absence of exogenous hormone. We defined a core set of 205 upregulated and 86 downregulated genes that were differentially expressed in at least three of the transcriptomic datasets. This core set includes genes encoding the type-A response regulators (RRs) and cytokinin oxidases/dehydrogenases, which have been shown to be primary cytokinin response genes. GO analysis revealed that the upregulated genes were enriched for terms related to cytokinin/hormone signaling and metabolism, while the downregulated genes were significantly enriched for genes encoding transporters. Variations of type-B RR binding motifs were significantly enriched in the promoters of the upregulated genes, as were binding sites for other potential partner transcription factors. The promoters of the downregulated genes were generally enriched for distinct cis-acting motifs and did not include the type-B RR binding motif. This analysis provides insight into the molecular mechanisms underlying cytokinin action in a monocot and provides a useful foundation for future studies of this hormone in rice and other cereals.
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Affiliation(s)
- Joanna K Polko
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Kevin C Potter
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Christian A Burr
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - G Eric Schaller
- Department of Biological Sciences, Dartmouth College, Hanover, NH, 03755, USA
| | - Joseph J Kieber
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
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16
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Kampire MG, Sanglou RK, Wang H, Kazeem BB, Wu JL, Zhang X. A Novel Allele Encoding 7-Hydroxymethyl Chlorophyll a Reductase Confers Bacterial Blight Resistance in Rice. Int J Mol Sci 2021; 22:ijms22147585. [PMID: 34299202 PMCID: PMC8303675 DOI: 10.3390/ijms22147585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 11/28/2022] Open
Abstract
Rice spotted leaf mutants are helpful to investigate programmed cell death (PCD) and defense response pathways in plants. Using a map-based cloning strategy, we characterized novel rice spotted leaf mutation splHM143 that encodes a 7-hydroxymethyl chlorophyll a reductase (OsHCAR). The wild-type (WT) allele could rescue the mutant phenotype, as evidenced by complementation analysis. OsHCAR was constitutively expressed at all rice tissues tested and its expression products localized to chloroplasts. The mutant exhibited PCD and leaf senescence with increased H2O2 (hydrogen peroxide) accumulation, increased of ROS (reactive oxygen species) scavenging enzymes activities and TUNEL (terminal deoxyribonucleotidyl transferase-mediated dUTP nick-end labeling) -positive nuclei, upregulation of PCD related genes, decreased chlorophyll (Chl) contents, downregulation of photosynthesis-related genes, and upregulation of senescence-associated genes. Besides, the mutant exhibited enhanced bacterial blight resistance with significant upregulation of defense response genes. Knockout lines of OsHCAR exhibited spotted leaf phenotype, cell death, leaf senescence, and showed increased resistance to the bacterial pathogen Xanthomonas oryzae pv. oryzae (Xoo) coupled with upregulation of five pathogenesis-related marker genes. The overexpression of OsHCAR resulted in increased susceptibility to Xoo with decreased expression of pathogenesis-related marker genes. Altogether, our findings revealed that OsHCAR is involved in regulating cell death and defense response against bacterial blight pathogen in rice.
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Affiliation(s)
- Marie Gorette Kampire
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; (M.G.K.); (R.K.S.); (H.W.)
| | - Ringki Kuinamei Sanglou
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; (M.G.K.); (R.K.S.); (H.W.)
| | - Huimei Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; (M.G.K.); (R.K.S.); (H.W.)
| | | | - Jian-li Wu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; (M.G.K.); (R.K.S.); (H.W.)
- Correspondence: (J.-l.W.); (X.Z.); Tel.: +86-571-63370326 (J.-l.W.); +86-571-63370295 (X.Z.)
| | - Xiaobo Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; (M.G.K.); (R.K.S.); (H.W.)
- Correspondence: (J.-l.W.); (X.Z.); Tel.: +86-571-63370326 (J.-l.W.); +86-571-63370295 (X.Z.)
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