1
|
Patil BL, Tripathi S. Differential expression of microRNAs in response to Papaya ringspot virus infection in differentially responding genotypes of papaya ( Carica papaya L.) and its wild relative. FRONTIERS IN PLANT SCIENCE 2024; 15:1398437. [PMID: 38966149 PMCID: PMC11222417 DOI: 10.3389/fpls.2024.1398437] [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: 03/09/2024] [Accepted: 05/29/2024] [Indexed: 07/06/2024]
Abstract
Papaya ringspot virus (PRSV) is one of the most devastating viruses of papaya that has significantly hampered papaya production across the globe. Although PRSV resistance is known in some of its wild relatives, such as Vasconcellea cauliflora and in some of the improved papaya genotypes, the molecular basis of this resistance mechanism has not been studied and understood. Plant microRNAs are an important class of small RNAs that regulate the gene expression in several plant species against the invading plant pathogens. These miRNAs are known to manifest the expression of genes involved in resistance against plant pathogens, through modulation of the plant's biochemistry and physiology. In this study we made an attempt to study the overall expression pattern of small RNAs and more specifically the miRNAs in different papaya genotypes from India, that exhibit varying levels of tolerance or resistance to PRSV. Our study found that the expression of some of the miRNAs was differentially regulated in these papaya genotypes and they had entirely different miRNA expression profile in healthy and PRSV infected symptomatic plants. This data may help in improvement of papaya cultivars for resistance against PRSV through new breeding initiatives or biotechnological approaches such as genome editing.
Collapse
Affiliation(s)
| | - Savarni Tripathi
- ICAR-Indian Agricultural Research Institute, Regional Station, Pune, India
| |
Collapse
|
2
|
Raza A, Charagh S, Karikari B, Sharif R, Yadav V, Mubarik MS, Habib M, Zhuang Y, Zhang C, Chen H, Varshney RK, Zhuang W. miRNAs for crop improvement. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107857. [PMID: 37437345 DOI: 10.1016/j.plaphy.2023.107857] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 07/14/2023]
Abstract
Climate change significantly impacts crop production by inducing several abiotic and biotic stresses. The increasing world population, and their food and industrial demands require focused efforts to improve crop plants to ensure sustainable food production. Among various modern biotechnological tools, microRNAs (miRNAs) are one of the fascinating tools available for crop improvement. miRNAs belong to a class of small non-coding RNAs playing crucial roles in numerous biological processes. miRNAs regulate gene expression by post-transcriptional target mRNA degradation or by translation repression. Plant miRNAs have essential roles in plant development and various biotic and abiotic stress tolerance. In this review, we provide propelling evidence from previous studies conducted around miRNAs and provide a one-stop review of progress made for breeding stress-smart future crop plants. Specifically, we provide a summary of reported miRNAs and their target genes for improvement of plant growth and development, and abiotic and biotic stress tolerance. We also highlight miRNA-mediated engineering for crop improvement and sequence-based technologies available for the identification of miRNAs associated with stress tolerance and plant developmental events.
Collapse
Affiliation(s)
- Ali Raza
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China
| | - Sidra Charagh
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Hangzhou, China
| | - Benjamin Karikari
- Department of Agricultural Biotechnology, Faculty of Agriculture, Food and Consumer Sciences, University for Development Studies, Tamale, Ghana
| | - Rahat Sharif
- Department of Horticulture, College of Horticulture and Landscape Architecture, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu 225009, China
| | - Vivek Yadav
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, Shanxi, 712100, China
| | | | - Madiha Habib
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Park Rd., Islamabad 45500, Pakistan
| | - Yuhui Zhuang
- College of Life Science, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Chong Zhang
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China
| | - Hua Chen
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China
| | - Rajeev K Varshney
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China; WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia.
| | - Weijian Zhuang
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China.
| |
Collapse
|
3
|
Li B, Karthikeyan A, Wang L, Yin J, Jin T, Liu H, Li K, Gai J, Zhi H. Discovery and characterization of differentially expressed soybean miRNAs and their targets during soybean mosaic virus infection unveils novel insight into Soybean-SMV interaction. BMC Genomics 2022; 23:171. [PMID: 35236286 PMCID: PMC8889786 DOI: 10.1186/s12864-022-08385-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 02/07/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Soybean mosaic virus (SMV) is one of the most devastating pathogens of soybean. MicroRNAs (miRNAs) are a class of non-coding RNAs (21-24 nucleotides) which are endogenously produced by the plant host as part of a general gene expression regulatory mechanisms, but also play roles in regulating plant defense against pathogens. However, miRNA-mediated plant response to SMV in soybean is not as well documented. RESULT In this study, we analyzed 18 miRNA libraries, including three biological replicates from two soybean lines (Resistant and susceptible lines to SMV strain SC3 selected from the near-isogenic lines of Qihuang No. 1 × Nannong1138-2) after virus infection at three different time intervals (0 dpi, 7 dpi and 14 dpi). A total of 1,092 miRNAs, including 608 known miRNAs and 484 novel miRNAs were detected. Differential expression analyses identified the miRNAs profile changes during soybean-SMV interaction. Then, miRNAs potential target genes were predicted via data mining, and functional annotation was done by Gene Ontology (GO) analysis. The expression patterns of several miRNAs were validated by quantitative real-time PCR. We also validated the miRNA-target gene interaction by agrobacterium-mediated transient expression in Nicotiana benthamiana. CONCLUSION We have identified a large number of miRNAs and their target genes and also functional annotations. We found that multiple miRNAs were differentially expressed in the two lines and targeted a series of NBS-LRR resistance genes. It is worth mentioning that many of these genes exist in the previous fine-mapping interval of the resistance gene locus. Our study provides additional information on soybean miRNAs and an insight into the role of miRNAs during SMV-infection in soybean.
Collapse
Affiliation(s)
- Bowen Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Adhimoolam Karthikeyan
- Subtropical Horticulture Research Institute, Jeju National University, Jeju, 63243, South Korea
| | - Liqun Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Jinlong Yin
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Tongtong Jin
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Hui Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Kai Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Junyi Gai
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
| | - Haijian Zhi
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
| |
Collapse
|
4
|
Nithin C, Mukherjee S, Basak J, Bahadur RP. NCodR: A multi-class support vector machine classification to distinguish non-coding RNAs in Viridiplantae. QUANTITATIVE PLANT BIOLOGY 2022; 3:e23. [PMID: 37077974 PMCID: PMC10095871 DOI: 10.1017/qpb.2022.18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/22/2022] [Accepted: 08/24/2022] [Indexed: 05/02/2023]
Abstract
Non-coding RNAs (ncRNAs) are major players in the regulation of gene expression. This study analyses seven classes of ncRNAs in plants using sequence and secondary structure-based RNA folding measures. We observe distinct regions in the distribution of AU content along with overlapping regions for different ncRNA classes. Additionally, we find similar averages for minimum folding energy index across various ncRNAs classes except for pre-miRNAs and lncRNAs. Various RNA folding measures show similar trends among the different ncRNA classes except for pre-miRNAs and lncRNAs. We observe different k-mer repeat signatures of length three among various ncRNA classes. However, in pre-miRs and lncRNAs, a diffuse pattern of k-mers is observed. Using these attributes, we train eight different classifiers to discriminate various ncRNA classes in plants. Support vector machines employing radial basis function show the highest accuracy (average F1 of ~96%) in discriminating ncRNAs, and the classifier is implemented as a web server, NCodR.
Collapse
Affiliation(s)
- Chandran Nithin
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology, Kharagpur721302, India
- Laboratory of Computational Biology, Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 02-089Warsaw, Poland
| | - Sunandan Mukherjee
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology, Kharagpur721302, India
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, PL-02-109Warsaw, Poland
| | - Jolly Basak
- Department of Biotechnology, Visva-Bharati, Santiniketan, 731235, India
| | - Ranjit Prasad Bahadur
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology, Kharagpur721302, India
- Author for correspondence: R. P. Bahadur, E-mail:
| |
Collapse
|
5
|
Gupta N, Reddy K, Bhattacharyya D, Chakraborty✉ S. Plant responses to geminivirus infection: guardians of the plant immunity. Virol J 2021; 18:143. [PMID: 34243802 PMCID: PMC8268416 DOI: 10.1186/s12985-021-01612-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 06/29/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Geminiviruses are circular, single-stranded viruses responsible for enormous crop loss worldwide. Rapid expansion of geminivirus diversity outweighs the continuous effort to control its spread. Geminiviruses channelize the host cell machinery in their favour by manipulating the gene expression, cell signalling, protein turnover, and metabolic reprogramming of plants. As a response to viral infection, plants have evolved to deploy various strategies to subvert the virus invasion and reinstate cellular homeostasis. MAIN BODY Numerous reports exploring various aspects of plant-geminivirus interaction portray the subtlety and flexibility of the host-pathogen dynamics. To leverage this pool of knowledge towards raising antiviral resistance in host plants, a comprehensive account of plant's defence response against geminiviruses is required. This review discusses the current knowledge of plant's antiviral responses exerted to geminivirus in the light of resistance mechanisms and the innate genetic factors contributing to the defence. We have revisited the defence pathways involving transcriptional and post-transcriptional gene silencing, ubiquitin-proteasomal degradation pathway, protein kinase signalling cascades, autophagy, and hypersensitive responses. In addition, geminivirus-induced phytohormonal fluctuations, the subsequent alterations in primary and secondary metabolites, and their impact on pathogenesis along with the recent advancements of CRISPR-Cas9 technique in generating the geminivirus resistance in plants have been discussed. CONCLUSIONS Considering the rapid development in the field of plant-virus interaction, this review provides a timely and comprehensive account of molecular nuances that define the course of geminivirus infection and can be exploited in generating virus-resistant plants to control global agricultural damage.
Collapse
Affiliation(s)
- Neha Gupta
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Kishorekumar Reddy
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Dhriti Bhattacharyya
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Supriya Chakraborty✉
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
| |
Collapse
|
6
|
Chand Jha U, Nayyar H, Mantri N, Siddique KHM. Non-Coding RNAs in Legumes: Their Emerging Roles in Regulating Biotic/Abiotic Stress Responses and Plant Growth and Development. Cells 2021; 10:cells10071674. [PMID: 34359842 PMCID: PMC8306516 DOI: 10.3390/cells10071674] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/24/2021] [Accepted: 06/28/2021] [Indexed: 12/28/2022] Open
Abstract
Noncoding RNAs, including microRNAs (miRNAs), small interference RNAs (siRNAs), circular RNA (circRNA), and long noncoding RNAs (lncRNAs), control gene expression at the transcription, post-transcription, and translation levels. Apart from protein-coding genes, accumulating evidence supports ncRNAs playing a critical role in shaping plant growth and development and biotic and abiotic stress responses in various species, including legume crops. Noncoding RNAs (ncRNAs) interact with DNA, RNA, and proteins, modulating their target genes. However, the regulatory mechanisms controlling these cellular processes are not well understood. Here, we discuss the features of various ncRNAs, including their emerging role in contributing to biotic/abiotic stress response and plant growth and development, in addition to the molecular mechanisms involved, focusing on legume crops. Unravelling the underlying molecular mechanisms and functional implications of ncRNAs will enhance our understanding of the coordinated regulation of plant defences against various biotic and abiotic stresses and for key growth and development processes to better design various legume crops for global food security.
Collapse
MESH Headings
- Fabaceae/genetics
- Fabaceae/growth & development
- Fabaceae/metabolism
- Food Security
- Gene Expression Regulation, Developmental
- Gene Expression Regulation, Plant
- Humans
- MicroRNAs/classification
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Organ Specificity
- Protein Biosynthesis
- RNA, Circular/classification
- RNA, Circular/genetics
- RNA, Circular/metabolism
- RNA, Long Noncoding/classification
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA, Plant/classification
- RNA, Plant/genetics
- RNA, Plant/metabolism
- RNA, Small Interfering/classification
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- Species Specificity
- Stress, Physiological/genetics
- Transcription, Genetic
Collapse
Affiliation(s)
- Uday Chand Jha
- ICAR—Indian Institute of Pulses Research (IIPR), Kanpur 208024, India
- Correspondence: (U.C.J.); (K.H.M.S.)
| | - Harsh Nayyar
- Department of Botany, Panjab University, Chandigarh 160014, India;
| | - Nitin Mantri
- School of Science, RMIT University, Melbourne 3083, Australia;
| | - Kadambot H. M. Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth 6001, Australia
- Correspondence: (U.C.J.); (K.H.M.S.)
| |
Collapse
|
7
|
Parreira JR, Cappuccio M, Balestrazzi A, Fevereiro P, Araújo SDS. MicroRNAs expression dynamics reveal post-transcriptional mechanisms regulating seed development in Phaseolus vulgaris L. HORTICULTURE RESEARCH 2021; 8:18. [PMID: 33436559 PMCID: PMC7804330 DOI: 10.1038/s41438-020-00448-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 11/24/2020] [Accepted: 11/27/2020] [Indexed: 05/04/2023]
Abstract
The knowledge on post-transcriptional regulation mechanisms implicated in seed development (SD) is still limited, particularly in one of the most consumed grain legumes, Phaseolus vulgaris L. We explore for the first time the miRNA expression dynamics in P. vulgaris developing seeds. Seventy-two known and 39 new miRNAs were found expressed in P. vulgaris developing seeds. Most of the miRNAs identified were more abundant at 10 and 40 days after anthesis, suggesting that late embryogenesis/early filling and desiccation were SD stages in which miRNA action is more pronounced. Degradome analysis and target prediction identified targets for 77 expressed miRNAs. While several known miRNAs were predicted to target HD-ZIP, ARF, SPL, and NF-Y transcription factors families, most of the predicted targets for new miRNAs encode for functional proteins. MiRNAs-targets expression profiles evidenced that these miRNAs could tune distinct seed developmental stages. MiRNAs more accumulated at early SD stages were implicated in regulating the end of embryogenesis, postponing the seed maturation program, storage compound synthesis and allocation. MiRNAs more accumulated at late SD stages could be implicated in seed quiescence, desiccation tolerance, and longevity with still uncovered roles in germination. The miRNAs herein described represent novel P. vulgaris resources with potential application in future biotechnological approaches to modulate the expression of genes implicated in legume seed traits with impact in horticultural production systems.
Collapse
Affiliation(s)
- José Ricardo Parreira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal
| | - Michela Cappuccio
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Alma Balestrazzi
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Pedro Fevereiro
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal
- InnovPlantProtect Collaborative Laboratory, Estrada de Gil Vaz, 7351-901, Elvas, Portugal
| | - Susana de Sousa Araújo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
- Association BLC3-Technology and Innovation Campus, Centre Bio R&D Unit, Rua Nossa Senhora da Conceição 2, Lagares da Beira, 3405-155, Oliveira do Hospital, Portugal.
| |
Collapse
|
8
|
Kankanala P, Nandety RS, Mysore KS. Genomics of Plant Disease Resistance in Legumes. FRONTIERS IN PLANT SCIENCE 2019; 10:1345. [PMID: 31749817 PMCID: PMC6842968 DOI: 10.3389/fpls.2019.01345] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 09/27/2019] [Indexed: 05/15/2023]
Abstract
The constant interactions between plants and pathogens in the environment and the resulting outcomes are of significant importance for agriculture and agricultural scientists. Disease resistance genes in plant cultivars can break down in the field due to the evolution of pathogens under high selection pressure. Thus, the protection of crop plants against pathogens is a continuous arms race. Like any other type of crop plant, legumes are susceptible to many pathogens. The dawn of the genomic era, in which high-throughput and cost-effective genomic tools have become available, has revolutionized our understanding of the complex interactions between legumes and pathogens. Genomic tools have enabled a global view of transcriptome changes during these interactions, from which several key players in both the resistant and susceptible interactions have been identified. This review summarizes some of the large-scale genomic studies that have clarified the host transcriptional changes during interactions between legumes and their plant pathogens while highlighting some of the molecular breeding tools that are available to introgress the traits into breeding programs. These studies provide valuable insights into the molecular basis of different levels of host defenses in resistant and susceptible interactions.
Collapse
|