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Rodrigues JCM, Carrijo J, Anjos RM, Cunha NB, Grynberg P, Aragão FJL, Vianna GR. The role of microRNAs in NBS-LRR gene expression and its implications for plant immunity and crop development. Transgenic Res 2024:10.1007/s11248-024-00387-9. [PMID: 38856866 DOI: 10.1007/s11248-024-00387-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 05/15/2024] [Indexed: 06/11/2024]
Abstract
Plants evolved, over millions of years, complex defense systems against pathogens. Once infected, the interaction between pathogen effector molecules and host receptors triggers plant immune responses, which include apoptosis, systemic immune response, among others. An important protein family responsible for pathogen effector recognition is the nucleotide binding site-leucine repeat rich (NBS-LRR) proteins. The NBS-LRR gene family is the largest disease resistance gene class in plants. These proteins are widely distributed in vascular plants and have a complex multigenic cluster distribution in plant genomes. To counteract the genetic load of such a large gene family on fitness cost, plants evolved a mechanism using post transcriptional gene silencing induced by small RNAs, particularly microRNAs. For the NBS-LRR gene family, the small RNAs involved in this silencing mechanism are mainly the microRNA482/2118 superfamily. This suppression mechanism is relieved upon pathogen infection, thus allowing increased NBS-LRR expression and triggering plant immunity. In this review, we will discuss the biogenesis of microRNAs and secondary RNAs involved in this silencing mechanism, biochemical and structural features of NBS-LRR proteins in response to pathogen effectors and the evolution of microRNA-based silencing mechanism with a focus on the miR482/2118 family. Furthermore, the biotechnological manipulation of microRNA expression, using both transgenic or genome editing approaches to improve cultivated plants will be discussed, with a focus on the miR482/2118 family in soybean.
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Affiliation(s)
- J C M Rodrigues
- Embrapa Genetic Resources and Biotechnology, Brasília, Brazil.
| | - J Carrijo
- Embrapa Genetic Resources and Biotechnology, Brasília, Brazil
| | - R M Anjos
- University of Brasília, Brasília, Brazil
| | - N B Cunha
- University of Brasília, Brasília, Brazil
| | - P Grynberg
- Embrapa Genetic Resources and Biotechnology, Brasília, Brazil
| | - F J L Aragão
- Embrapa Genetic Resources and Biotechnology, Brasília, Brazil
| | - G R Vianna
- Embrapa Genetic Resources and Biotechnology, Brasília, Brazil
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2
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Wang H, Wang X, Li Y, Cui Y, Yan X, Gao J, Ouyang J, Li S. Pleiotropic Effects of miR5504 Underlying Plant Height, Grain Yield and Quality in Rice. PLANT & CELL PHYSIOLOGY 2024; 65:781-789. [PMID: 38447119 DOI: 10.1093/pcp/pcae015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 02/13/2024] [Indexed: 03/08/2024]
Abstract
MicroRNAs (miRNAs) are known to play critical roles in regulating rice agronomic traits through mRNA cleavage or translational repression. Our previous study indicated that miR5504 regulates plant height by affecting cell proliferation and expansion. Here, the two independent homozygous mir5504 mutants (CR1 and CR2) and overexpression lines (OE1 and OE2) were further used to investigate the functions of miR5504. The panicle length, 1000-grain weight and grain yield per plant of miR5504-OE lines were identical to those of Nipponbare (NIP), but the 1000-grain weight of mir5504 mutants was reduced by about 10% and 9%, respectively. Meanwhile, the grain width and thickness of mir5504 mutants decreased significantly by approximately 10% and 11%, respectively. Moreover, the cytological results revealed a significant decrease in cell number along grain width direction and cell width in spikelet in mir5504, compared with those in NIP. In addition, several major storage substances of the rice seeds were measured. Compared to NIP, the amylose content of the mir5504 seeds was noticeably decreased, leading to an increase of nearly 10 mm in gel consistency (GC) in mir5504 lines. Further investigation confirmed that LOC_Os08g16914 was the genuine target of miR5504: LOC_Os08g16914 over-expression plants phenocopied the mir5504 mutants. This study provides insights into the role of miR5504 in rice seed development.
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Affiliation(s)
- Huihui Wang
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang 330031, China
| | - Xin Wang
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang 330031, China
| | - Yangyang Li
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang 330031, China
| | - Ying Cui
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang 330031, China
| | - Xin Yan
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang 330031, China
| | - Jiadong Gao
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Guangzhou 510640, China
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510555, China
| | - Jiexiu Ouyang
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang 330031, China
| | - Shaobo Li
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang 330031, China
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Gao M, Hao Z, Ning Y, He Z. Revisiting growth-defence trade-offs and breeding strategies in crops. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1198-1205. [PMID: 38410834 PMCID: PMC11022801 DOI: 10.1111/pbi.14258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/02/2023] [Accepted: 11/20/2023] [Indexed: 02/28/2024]
Abstract
Plants have evolved a multi-layered immune system to fight off pathogens. However, immune activation is costly and is often associated with growth and development penalty. In crops, yield is the main breeding target and is usually affected by high disease resistance. Therefore, proper balance between growth and defence is critical for achieving efficient crop improvement. This review highlights recent advances in attempts designed to alleviate the trade-offs between growth and disease resistance in crops mediated by resistance (R) genes, susceptibility (S) genes and pleiotropic genes. We also provide an update on strategies for optimizing the growth-defence trade-offs to breed future crops with desirable disease resistance and high yield.
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Affiliation(s)
- Mingjun Gao
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science and Institute of Eco‐Chongming, School of Life SciencesFudan UniversityShanghaiChina
| | - Zeyun Hao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Yuese Ning
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Zuhua He
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
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Xu C, Huang X, Ma N, Liu Y, Xu A, Zhang X, Li D, Li Y, Zhang W, Wang K. MicroRNA164 Affects Plant Responses to UV Radiation in Perennial Ryegrass. PLANTS (BASEL, SWITZERLAND) 2024; 13:1242. [PMID: 38732457 PMCID: PMC11085334 DOI: 10.3390/plants13091242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/13/2024]
Abstract
Increasing the ultraviolet radiation (UV) level, particularly UV-B due to damage to the stratospheric ozone layer by human activities, has huge negative effects on plant and animal metabolism. As a widely grown cool-season forage grass and turfgrass in the world, perennial ryegrass (Lolium perenne) is UV-B-sensitive. To study the effects of miR164, a highly conserved microRNA in plants, on perennial ryegrass under UV stress, both OsmiR164a overexpression (OE164) and target mimicry (MIM164) transgenic perennial ryegrass plants were generated using agrobacterium-mediated transformation, and UV-B treatment (~600 μw cm-2) of 7 days was imposed. Morphological and physiological analysis showed that the miR164 gene affected perennial ryegrass UV tolerance negatively, demonstrated by the more scorching leaves, higher leaf electrolyte leakage, and lower relative water content in OE164 than the WT and MIM164 plants after UV stress. The increased UV sensitivity could be partially due to the reduction in antioxidative capacity and the accumulation of anthocyanins. This study indicated the potential of targeting miR164 and/or its targeted genes for the genetic manipulation of UV responses in forage grasses/turfgrasses; further research to reveal the molecular mechanism underlying how miR164 affects plant UV responses is needed.
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Affiliation(s)
- Chang Xu
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China; (C.X.); (X.H.); (N.M.); (Y.L.); (A.X.); (Y.L.)
| | - Xin Huang
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China; (C.X.); (X.H.); (N.M.); (Y.L.); (A.X.); (Y.L.)
| | - Ning Ma
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China; (C.X.); (X.H.); (N.M.); (Y.L.); (A.X.); (Y.L.)
| | - Yanrong Liu
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China; (C.X.); (X.H.); (N.M.); (Y.L.); (A.X.); (Y.L.)
| | - Aijiao Xu
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China; (C.X.); (X.H.); (N.M.); (Y.L.); (A.X.); (Y.L.)
| | - Xunzhong Zhang
- School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA;
| | - Dayong Li
- Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China;
| | - Yue Li
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China; (C.X.); (X.H.); (N.M.); (Y.L.); (A.X.); (Y.L.)
| | - Wanjun Zhang
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China; (C.X.); (X.H.); (N.M.); (Y.L.); (A.X.); (Y.L.)
| | - Kehua Wang
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China; (C.X.); (X.H.); (N.M.); (Y.L.); (A.X.); (Y.L.)
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Zhong Q, Yu J, Wu Y, Yao X, Mao C, Meng X, Ming F. Rice transcription factor OsNAC2 maintains the homeostasis of immune responses to bacterial blight. PLANT PHYSIOLOGY 2024; 195:785-798. [PMID: 38159040 DOI: 10.1093/plphys/kiad683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 11/03/2023] [Accepted: 11/24/2023] [Indexed: 01/03/2024]
Abstract
Rice (Oryza sativa) bacterial blight, caused by Xanthomonas oryzae pv. Oryzae (Xoo), threatens plant growth and yield. However, the molecular mechanisms underlying rice immunity against Xoo remain elusive. Here, we identified a NAC (NAM-ATAF-CUC) transcription factor OsNAC2 as a negative regulator in the resistance to bacterial blight disease in rice. Constitutive overexpression of OsNAC2 inhibited the expression of salicylic acid (SA) biosynthesis-related genes (i.e. isochorismate synthase 1 (OsICS1), phenylalanine ammonia lyase 3 (OsPAL3), etc.) with adverse impacts on the pathogenesis-related proteins (PRs) responses and compromised blight resistance. Moreover, OsNAC2 interacted with APETALA2/ethylene-responsive element binding protein (AP2/EREBP) transcription factor OsEREBP1 and possibly threatened its protein stability, destroying the favorable interaction of OsEREBP1-Xa21-binding protein OsXb22a in the cytoplasm during Xoo-induced infection. On the contrary, downregulation of OsNAC2 resulted in enhanced resistance to bacterial blight in rice without any growth or yield penalties. Our results demonstrated that OsNAC2 inhibits SA signaling and stably interacted with OsEREBP1 to impair disease resistance. This OsNAC2-OsEREBP1-based homeostatic mechanism provided insights into the competition between rice and bacterial pathogens, and it will be useful to improve the disease resistance of important crops through breeding.
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Affiliation(s)
- Qun Zhong
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
- The Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Jiangtao Yu
- Institute of Future Agriculture, Northwest Agriculture & Forestry University, Shaanxi 712100, China
| | - Yiding Wu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
- The Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Xuefeng Yao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Chanjuan Mao
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
- The Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Xiangzong Meng
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
- The Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Feng Ming
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
- The Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
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Kou Y, Shi H, Qiu J, Tao Z, Wang W. Effectors and environment modulating rice blast disease: from understanding to effective control. Trends Microbiol 2024:S0966-842X(24)00072-6. [PMID: 38580607 DOI: 10.1016/j.tim.2024.03.006] [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: 01/16/2024] [Revised: 03/08/2024] [Accepted: 03/13/2024] [Indexed: 04/07/2024]
Abstract
Rice blast is a highly destructive crop disease that requires the interplay of three essential factors: the virulent blast fungus, the susceptible rice plant, and favorable environmental conditions. Although previous studies have focused mainly on the pathogen and rice, recent research has shed light on the molecular mechanisms by which the blast fungus and environmental conditions regulate host resistance and contribute to blast disease outbreaks. This review summarizes significant achievements in understanding the sophisticated modulation of blast resistance by Magnaporthe oryzae effectors and the dual regulatory mechanisms by which environmental conditions influence rice resistance and virulence of the blast fungus. Furthermore, it emphasizes potential strategies for developing blast-resistant rice varieties to effectively control blast disease.
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Affiliation(s)
- Yanjun Kou
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China.
| | - Huanbin Shi
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
| | - Jiehua Qiu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
| | - Zeng Tao
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
| | - Wenming Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China.
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Asadi M, Millar AA. Review: Plant microRNAs in pathogen defense: A panacea or a piece of the puzzle? PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 341:111993. [PMID: 38266718 DOI: 10.1016/j.plantsci.2024.111993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/11/2024] [Accepted: 01/16/2024] [Indexed: 01/26/2024]
Abstract
Plant microRNAs (miRNAs) control key agronomic traits that are associated with their conserved role(s) in development. However, despite a multitude of studies, the utility of miRNAs in plant-pathogen resistance remains less certain. Reviewing the literature identifies three general classes of miRNAs regarding plant pathogen defense. Firstly, a number of evolutionary dynamic 22 nucleotide miRNA families that repress large numbers of plant immunity genes, either directly, or through triggering the biogenesis of secondary siRNAs. However, understanding of their role in defense and of their manipulation to enhance pathogen resistance are still lacking. Secondly, highly conserved miRNAs that indirectly impact disease resistance through their targets that are primarily regulating development or hormone signaling. Any alteration of these miRNAs usually results in pleiotropic impacts, which may alter disease resistance in some plant species, and against some pathogens. Thirdly, are the comparatively diverse and evolutionary dynamic set of non-conserved miRNAs, some of which contribute to pathogen resistance, but whose narrow evolutionary presence will likely restrict their utility. Therefore, reflecting the diverse and evolving nature of plant-pathogen interactions, a complex interplay of plant miRNAs with pathogen responses exists. Any miRNA-based solution for pathogen resistance will likely be highly specific, rather than a general panacea.
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Affiliation(s)
- Mohsen Asadi
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran; Department of Agricultural Science, Technical and Vocational University (TVU), Tehran, Iran
| | - Anthony A Millar
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra, Australia; ARC Training Centre for Accelerated Future Crop development, ANU, Canberra, Australia.
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Zaheer U, Munir F, Salum YM, He W. Function and regulation of plant ARGONAUTE proteins in response to environmental challenges: a review. PeerJ 2024; 12:e17115. [PMID: 38560454 PMCID: PMC10979746 DOI: 10.7717/peerj.17115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 02/26/2024] [Indexed: 04/04/2024] Open
Abstract
Environmental stresses diversely affect multiple processes related to the growth, development, and yield of many crops worldwide. In response, plants have developed numerous sophisticated defense mechanisms at the cellular and subcellular levels to react and adapt to biotic and abiotic stressors. RNA silencing, which is an innate immune mechanism, mediates sequence-specific gene expression regulation in higher eukaryotes. ARGONAUTE (AGO) proteins are essential components of the RNA-induced silencing complex (RISC). They bind to small noncoding RNAs (sRNAs) and target complementary RNAs, causing translational repression or triggering endonucleolytic cleavage pathways. In this review, we aim to illustrate the recently published molecular functions, regulatory mechanisms, and biological roles of AGO family proteins in model plants and cash crops, especially in the defense against diverse biotic and abiotic stresses, which could be helpful in crop improvement and stress tolerance in various plants.
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Affiliation(s)
- Uroosa Zaheer
- Plant Protection, State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Plant Protection, International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Plant Protection, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Faisal Munir
- Plant Protection, State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Plant Protection, International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Plant Protection, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yussuf Mohamed Salum
- Plant Protection, State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Plant Protection, International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Plant Protection, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Weiyi He
- Plant Protection, State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Plant Protection, International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Plant Protection, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
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Zhou J, Han H, Liu S, Ji C, Jiao B, Yang Y, Xi D. miRNAs are involved in regulating the formation of recovery tissues in virus infected Nicotiana tabacum. Mol Genet Genomics 2024; 299:10. [PMID: 38376608 DOI: 10.1007/s00438-024-02106-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 01/11/2024] [Indexed: 02/21/2024]
Abstract
MiRNAs play an important role in regulating plant growth and immune response. Mosaic diseases are recognized as the most important plant diseases in the world, and mosaic symptoms are recovery tissues formed by plants against virus infection. However, the mechanism of the formation of mosaic symptoms remains elusive. In this study, two typical mosaic systems consisting of Nicotiana tabacum-cucumber mosaic virus (CMV) and N. tabacum-tobacco mosaic virus (TMV) were used to investigate the relevance of miRNAs to the appearance of mosaic symptoms. The results of miRNA-seq showed that there were significant differences in miRNA abundance between dark green tissues and chlorotic tissues in mosaic leaves caused by the infection of CMV or TMV. Compared with healthy tissues, miRNA expression was significantly increased in chlorotic tissues, but slightly increased in dark green tissues. Three miRNAs, namely miR1919, miR390a, and miR6157, were identified to be strongly up-regulated in chlorotic tissues of both mosaic systems. Results of overexpressing or silencing of the three miRNAs proved that they were related to chlorophyll synthesis, auxin response, and small GTPase-mediated immunity pathway, which were corresponding to the phenotype, physiological parameters and susceptibility of the chlorotic tissues in mosaic leaves. Besides, the newly identified novel-miRNA48, novel-miRNA96 and novel-miRNA103 may also be involved in this formation of mosaic symptoms. Taken together, our results demonstrated that miR1919, miR390a and miR6157 are involved in the formation of mosaic symptoms and plant antiviral responses, providing new insight into the role of miRNAs in the formation of recovery tissue and plant immunity.
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Affiliation(s)
- Jingya Zhou
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Hongyan Han
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, 637009, China
| | - Sucen Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Chenglong Ji
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Bolei Jiao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Yiting Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Dehui Xi
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China.
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Zhong C, Smith NA, Zhang D, Gou X, Greaves IK, Millar AA, Walsh TK, Shan W, Wang MB. G-U base-paired hpRNA confers potent inhibition of small RNA function in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1206-1222. [PMID: 38038953 DOI: 10.1111/tpj.16555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 10/31/2023] [Accepted: 11/06/2023] [Indexed: 12/02/2023]
Abstract
MicroRNA (miRNA) target mimicry technologies, utilizing naturally occurring miRNA decoy molecules, represent a potent tool for analyzing miRNA function. In this study, we present a highly efficient small RNA (sRNA) target mimicry design based on G-U base-paired hairpin RNA (hpG:U), which allows for the simultaneous targeting of multiple sRNAs. The hpG:U constructs consistently generate high amounts of intact, polyadenylated stem-loop (SL) RNA outside the nuclei, in contrast to traditional hairpin RNA designs with canonical base pairing (hpWT), which were predominantly processed resulting in a loop. By incorporating a 460-bp G-U base-paired double-stranded stem and a 312-576 nt loop carrying multiple miRNA target mimicry sites (GUMIC), the hpG:U construct displayed effective repression of three Arabidopsis miRNAs, namely miR165/166, miR157, and miR160, both individually and in combination. Additionally, a GUMIC construct targeting a prominent cluster of siRNAs derived from cucumber mosaic virus (CMV) Y-satellite RNA (Y-Sat) effectively inhibited Y-Sat siRNA-directed silencing of the chlorophyll biosynthetic gene CHLI, thereby reducing the yellowing symptoms in infected Nicotiana plants. Therefore, the G-U base-paired hpRNA, characterized by differential processing compared to traditional hpRNA, acts as an efficient decoy for both miRNAs and siRNAs. This technology holds great potential for sRNA functional analysis and the management of sRNA-mediated diseases.
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Affiliation(s)
- Chengcheng Zhong
- CSIRO Agriculture and Food, Canberra, 2601, ACT, Australia
- Stake Key Laboratory for Crop Stress Resistance and High-Efficiency Production and College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Neil A Smith
- CSIRO Agriculture and Food, Canberra, 2601, ACT, Australia
| | - Daai Zhang
- CSIRO Agriculture and Food, Canberra, 2601, ACT, Australia
| | - Xiuhong Gou
- Stake Key Laboratory for Crop Stress Resistance and High-Efficiency Production and College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Ian K Greaves
- CSIRO Agriculture and Food, Canberra, 2601, ACT, Australia
| | - Anthony A Millar
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra, 2601, ACT, Australia
| | - Tom K Walsh
- CSIRO Environment, Canberra, 2601, ACT, Australia
| | - Weixing Shan
- Stake Key Laboratory for Crop Stress Resistance and High-Efficiency Production and College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Ming-Bo Wang
- CSIRO Agriculture and Food, Canberra, 2601, ACT, Australia
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Luo H, Li T, Guan Y, Zhang Z, Zhang Z, Zhang Z, Li H. FvemiR160-FveARF18A-FveAP1/FveFUL module regulates flowering time in woodland strawberry. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1130-1147. [PMID: 37967025 DOI: 10.1111/tpj.16544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 10/31/2023] [Indexed: 11/17/2023]
Abstract
Flowering is an indicator of plant transformation from vegetative to reproductive growth. miR160 has been shown to have a significant effect on the growth and development of fruits, leaves, and roots of plants or their stress response to environment, but the participation of miR160 in regulating flowering time in plants is unclear. In this study, we found that two FvemiR160s (FvemiR160a/FvemiR160b) mature sequences in strawberry (Fragaria vesca) were consistent. It was displayed that the miR160 mature sequence is highly conserved in various species, and the miR160 mature sequence formed by the 5' arm of the MIR160 precursor was more conserved. Three FveARFs in woodland strawberry were negatively regulated by FvemiR160a, among which FveARF18A was the most significant. Phylogenetic analysis indicated that FvemiR160 is closely related to apple (Malus domestica), grape (Vitis vinifera), and Arabidopsis thaliana, while FveARF18A is closely related to RcARF18. Subsequently, we demonstrated that FvemiR160a can target cutting FveARF18A to negatively regulate its expression by RLM-5' RACE, cleavage site mutation, and GFP fluorescence assay. Moreover, we observed that FveMIR160a overexpressed plants have advanced flowering, while mFveARF18A overexpressed plants have delayed flowering. We also verified that FveARF18A negatively regulates the expression of FveAP1 and FveFUL by binding their promoters by yeast one-hybrid, LUC, and GUS assay, and FveAP1 and FveFUL transgenic Arabidopsis showed early flowering phenotype. In addition, the expression level of FvemiR160a was decreased obviously while that of FveARF18A was increased obviously by MeJA, GA and IAA. In conclusion, our study reveals the important role of the FvemiR160-FveARF18A-FveAP1/FveFUL module in the flowering process of woodland strawberry and provides a new pathway for studying flowering.
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Affiliation(s)
- He Luo
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Tianyu Li
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yuhan Guan
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Zhuo Zhang
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Zihui Zhang
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Zhihong Zhang
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - He Li
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
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12
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Cai X, Chen Y, Wang Y, Shen Y, Yang J, Jia B, Sun X, Sun M. A comprehensive investigation of the regulatory roles of OsERF096, an AP2/ERF transcription factor, in rice cold stress response. PLANT CELL REPORTS 2023; 42:2011-2022. [PMID: 37812280 DOI: 10.1007/s00299-023-03079-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/20/2023] [Indexed: 10/10/2023]
Abstract
KEY MESSAGE OsERF096 negatively regulates rice cold tolerance and mediates IAA biosynthesis and signaling under cold stress. The APETALA2/ethylene-responsive factor (AP2/ERF) transcription factors play important roles in regulating plant tolerance to abiotic stress. OsERF096 was previously identified as a direct target of miR1320, and was suggested to negatively regulate rice cold tolerance. In this study, we performed RNA-sequencing and targeted metabolomics assays to reveal the regulatory roles of OsERF096 in cold stress response. GO and KEGG analysis of differentially expressed genes showed that the starch and sucrose metabolism, plant-pathogen interaction, and plant hormone signal transduction pathways were significantly enriched. Quantification analysis confirmed a significant difference in sugar contents among WT and OsERF096 transgenic lines under cold treatment. Targeted metabolomics analysis uncovered that IAA accumulation and signaling were modified by OsERF096 in response to cold stress. Expectedly, qRT-PCR assays confirmed significant OsIAAs and OsARFs expression changes in OsERF096 transgenic lines. Finally, we identified three targets of OsERF096 based on RNA-seq, qRT-PCR, and dual-LUC assays. In summary, these results revealed the multiple regulatory roles of OsERF096 in cold stress response.
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Affiliation(s)
- Xiaoxi Cai
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Yue Chen
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Yan Wang
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Yang Shen
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Junkai Yang
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Bowei Jia
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Xiaoli Sun
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing, 163319, China.
| | - Mingzhe Sun
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing, 163319, China.
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13
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Liu Y, Zhu QF, Li WY, Chen P, Xue J, Yu Y, Feng YZ. The Pivotal Role of Noncoding RNAs in Flowering Time Regulation. Genes (Basel) 2023; 14:2114. [PMID: 38136936 PMCID: PMC10742506 DOI: 10.3390/genes14122114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023] Open
Abstract
Noncoding RNAs constitute a substantial portion of the transcriptome and play pivotal roles in plant growth and development. Among these processes, flowering stands out as a crucial trait, ensuring reproductive success and seed set, and is meticulously controlled by genetic and environmental factors. With remarkable advancements in the identification and characterization of noncoding RNAs in plants, it has become evident that noncoding RNAs are intricately linked to the regulation of flowering time. In this article, we present an overview of the classification of plant noncoding RNAs and delve into their functions in the regulation of flowering time. Furthermore, we review their molecular mechanisms and their involvement in flowering pathways. Our comprehensive review enhances the understanding of how noncoding RNAs contribute to the regulation of flowering time and sheds light on their potential implications in crop breeding.
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Affiliation(s)
| | | | | | | | | | - Yang Yu
- Guangdong Key Laboratory of Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (Y.L.); (Q.-F.Z.); (W.-Y.L.); (P.C.); (J.X.)
| | - Yan-Zhao Feng
- Guangdong Key Laboratory of Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (Y.L.); (Q.-F.Z.); (W.-Y.L.); (P.C.); (J.X.)
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14
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Wang Q, Wan J, Dang K, Meng S, Hu D, Lin Y, Qiu X, Guo Z, Fu Z, Ding D, Tang J. zma-miR159 targets ZmMYB74 and ZmMYB138 transcription factors to regulate grain size and weight in maize. PLANT PHYSIOLOGY 2023; 193:2430-2441. [PMID: 37590954 DOI: 10.1093/plphys/kiad455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 06/15/2023] [Accepted: 07/01/2023] [Indexed: 08/19/2023]
Abstract
Endosperm cell number is critical in determining grain size in maize (Zea mays). Here, zma-miR159 overexpression led to enlarged grains in independent transgenic lines, suggesting that zma-miR159 contributes positively to maize grain size. Targeting of ZmMYB74 and ZmMYB138 transcription factor genes by zma-miR159 was validated using 5' RACE and dual-luciferase assay. Lines in which ZmMYB74 was knocked out using clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) presented a similar enlarged grain phenotype as those with zma-miR159 overexpression. Downstream genes regulating cell division were identified through DNA affinity purification sequencing using ZmMYB74 and ZmMYB138. Our results suggest that zma-miR159-ZmMYB modules act as an endosperm development hub, participating in the division and proliferation of endosperm cells.
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Affiliation(s)
- Qiyue Wang
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China
- Maize Research Department, Hebi Academy of Agricultural Sciences, Hebi, Henan 458030, China
| | - Jiong Wan
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Kuntai Dang
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Shujun Meng
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Desheng Hu
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Yuan Lin
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China
- Maize Research Department, Hebi Academy of Agricultural Sciences, Hebi, Henan 458030, China
| | - Xiaoqian Qiu
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Zhanyong Guo
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Zhiyuan Fu
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Dong Ding
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China
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15
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Gao S, Hou Y, Huang Q, Wu P, Han Z, Wei D, Xie H, Gu F, Chen C, Wang J. Osa-miR11117 Targets OsPAO4 to Regulate Rice Immunity against the Blast Fungus Magnaporthe oryzae. Int J Mol Sci 2023; 24:16052. [PMID: 38003241 PMCID: PMC10670930 DOI: 10.3390/ijms242216052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/03/2023] [Accepted: 11/04/2023] [Indexed: 11/26/2023] Open
Abstract
The intricate regulatory process governing rice immunity against the blast fungus Magnaporthe oryzae remains a central focus in plant-pathogen interactions. In this study, we investigated the important role of Osa-miR11117, an intergenic microRNA, in regulating rice defense mechanisms. Stem-loop qRT-PCR analysis showed that Osa-miR11117 is responsive to M. oryzae infection, and overexpression of Osa-miR11117 compromises blast resistance. Green fluorescent protein (GFP)-based reporter assay indicated OsPAO4 is one direct target of Osa-miR11117. Furthermore, qRT-PCR analysis showed that OsPAO4 reacts to M. oryzae infection and polyamine (PA) treatment. In addition, OsPAO4 regulates rice resistance to M. oryzae through the regulation of PA accumulation and the expression of the ethylene (ETH) signaling genes. Taken together, these results suggest that Osa-miR11117 is targeting OsPAO4 to regulate blast resistance by adjusting PA metabolism and ETH signaling pathways.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Jiafeng Wang
- National Plant Space Breeding Engineering Technology Research Center, Guangdong Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China; (S.G.); (Y.H.); (Q.H.); (P.W.); (Z.H.); (D.W.); (H.X.); (F.G.); (C.C.)
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16
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Li M, Li W, Zhao M, Li Z, Wang GL, Liu W, Liang C. Transcriptome analysis reveals a lncRNA-miRNA-mRNA regulatory network in OsRpp30-mediated disease resistance in rice. BMC Genomics 2023; 24:643. [PMID: 37884868 PMCID: PMC10604448 DOI: 10.1186/s12864-023-09748-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 10/17/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) play critical roles in various biological processes in plants. Extensive studies utilizing high-throughput RNA sequencing have revealed that many lncRNAs are involved in plant disease resistance. Oryza sativa RNase P protein 30 (OsRpp30) has been identified as a positive regulator of rice immunity against fungal and bacterial pathogens. Nevertheless, the specific functions of lncRNAs in relation to OsRpp30-mediated disease resistance in rice remain elusive. RESULTS We conducted a comprehensive analysis of lncRNAs, miRNAs, and mRNAs expression patterns in wild type (WT), OsRpp30 overexpression (OsRpp30-OE), and OsRpp30 knockout (OsRpp30-KO) rice plants. In total, we identified 91 differentially expressed lncRNAs (DElncRNAs), 1671 differentially expressed mRNAs (DEmRNAs), and 41 differentially expressed miRNAs (DEmiRNAs) across the different rice lines. To gain further insights, we investigated the interaction between DElncRNAs and DEmRNAs, leading to the discovery of 10 trans- and 27 cis-targeting pairs specific to the OsRpp30-OE and OsRpp30-KO samples. In addition, we constructed a competing endogenous RNA (ceRNA) network comprising differentially expressed lncRNAs, miRNAs, and mRNAs to elucidate their intricate interplay in rice disease resistance. The ceRNA network analysis uncovered a set of gene targets regulated by lncRNAs and miRNAs, which were found to be involved in pathogen recognition, hormone pathways, transcription factor activation, and other biological processes related to plant immunity. CONCLUSIONS Our study provides a comprehensive expression profiling of lncRNAs, miRNAs, and mRNAs in a collection of defense mutants in rice. To decipher the putative functional significance of lncRNAs, we constructed trans- and cis-targeting networks involving differentially expressed lncRNAs and mRNAs, as well as a ceRNA network incorporating differentially expressed lncRNAs, miRNAs, and mRNAs. Together, the findings from this study provide compelling evidence supporting the pivotal roles of lncRNAs in OsRpp30-mediated disease resistance in rice.
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Affiliation(s)
- Minghua Li
- Department of Biology, Miami University, Oxford, OH, 45056, USA
| | - Wei Li
- Department of Plant Pathology, Ohio State University, Columbus, OH, 43210, USA
| | - Meixia Zhao
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA
| | - Zhiqiang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Guo-Liang Wang
- Department of Plant Pathology, Ohio State University, Columbus, OH, 43210, USA.
| | - Wende Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Chun Liang
- Department of Biology, Miami University, Oxford, OH, 45056, USA.
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17
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Escolà G, González-Miguel VM, Campo S, Catala-Forner M, Domingo C, Marqués L, San Segundo B. Development and Genome-Wide Analysis of a Blast-Resistant japonica Rice Variety. PLANTS (BASEL, SWITZERLAND) 2023; 12:3536. [PMID: 37896000 PMCID: PMC10667994 DOI: 10.3390/plants12203536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 10/06/2023] [Accepted: 10/08/2023] [Indexed: 10/29/2023]
Abstract
Rice is one of the most important crops in the world, and its production is severely affected by the rice blast disease caused by the fungus Magnaporthe oryzae. Several major blast resistance genes and QTLs associated with blast resistance have been described and mostly identified in indica rice varieties. In this work, we report the obtention of a blast-resistant rice breeding line derived from crosses between the resistant indica variety CT13432 and the japonica elite cultivar JSendra (highly susceptible to blast). The breeding line, named COPSEMAR9, was found to exhibit resistance to leaf blast and panicle blast, as demonstrated by disease assays under controlled and field conditions. Furthermore, a high-quality genome sequence of the blast-resistant breeding line was obtained using a strategy that combines short-read sequencing (Illumina sequencing) and long-read sequencing (Pacbio sequencing). The use of a whole-genome approach allowed the fine mapping of DNA regions of indica and japonica origin present in the COPSEMAR9 genome and the identification of parental gene regions potentially contributing to blast resistance in the breeding line. Rice blast resistance genes (including Pi33 derived from the resistant parent) and defense-related genes in the genome of COPSEMAR9 were identified. Whole-genome analyses also revealed the presence of microRNAs (miRNAs) with a known function in the rice response to M. oryzae infection in COPSEMAR9, which might also contribute to its phenotype of blast resistance. From this study, the genomic information and analysis methods provide valuable knowledge that will be useful in breeding programs for blast resistance in japonica rice cultivars.
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Affiliation(s)
- Glòria Escolà
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), C/de la Vall Moronta, CRAG Building, 08193 Barcelona, Spain; (G.E.); (V.M.G.-M.); (S.C.)
| | - Víctor M. González-Miguel
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), C/de la Vall Moronta, CRAG Building, 08193 Barcelona, Spain; (G.E.); (V.M.G.-M.); (S.C.)
| | - Sonia Campo
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), C/de la Vall Moronta, CRAG Building, 08193 Barcelona, Spain; (G.E.); (V.M.G.-M.); (S.C.)
| | - Mar Catala-Forner
- Institute of Agrifood Research and Technology (IRTA), Field Crops, Ctra. Balada km. 1, 43870 Tarragona, Spain;
| | - Concha Domingo
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Departamento del Arroz and Centro de Genómica. Ctra Moncada-Náquera km 10.7, 46113 Moncada, Spain;
| | - Luis Marqués
- Cooperativa de Productores de Semillas de Arroz, S.C.L. (COPSEMAR) Avda del Mar 1, 46410 Sueca, Spain;
| | - Blanca San Segundo
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), C/de la Vall Moronta, CRAG Building, 08193 Barcelona, Spain; (G.E.); (V.M.G.-M.); (S.C.)
- Consejo Superior de Investigaciones Científicas (CSIC), 08193 Barcelona, Spain
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18
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Samynathan R, Venkidasamy B, Shanmugam A, Ramalingam S, Thiruvengadam M. Functional role of microRNA in the regulation of biotic and abiotic stress in agronomic plants. Front Genet 2023; 14:1272446. [PMID: 37886688 PMCID: PMC10597799 DOI: 10.3389/fgene.2023.1272446] [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: 08/04/2023] [Accepted: 09/25/2023] [Indexed: 10/28/2023] Open
Abstract
The increasing demand for food is the result of an increasing population. It is crucial to enhance crop yield for sustainable production. Recently, microRNAs (miRNAs) have gained importance because of their involvement in crop productivity by regulating gene transcription in numerous biological processes, such as growth, development and abiotic and biotic stresses. miRNAs are small, non-coding RNA involved in numerous other biological functions in a plant that range from genomic integrity, metabolism, growth, and development to environmental stress response, which collectively influence the agronomic traits of the crop species. Additionally, miRNA families associated with various agronomic properties are conserved across diverse plant species. The miRNA adaptive responses enhance the plants to survive environmental stresses, such as drought, salinity, cold, and heat conditions, as well as biotic stresses, such as pathogens and insect pests. Thus, understanding the detailed mechanism of the potential response of miRNAs during stress response is necessary to promote the agronomic traits of crops. In this review, we updated the details of the functional aspects of miRNAs as potential regulators of various stress-related responses in agronomic plants.
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Affiliation(s)
- Ramkumar Samynathan
- Department of Oral and Maxillofacial Surgery, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, India
| | - Baskar Venkidasamy
- Department of Oral and Maxillofacial Surgery, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, India
| | - Ashokraj Shanmugam
- Plant Physiology and Biotechnology Division, UPASI Tea Research Foundation, Coimbatore, Tamil Nadu, India
| | - Sathishkumar Ramalingam
- Plant Genetic Engineering Lab, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India
| | - Muthu Thiruvengadam
- Department of Crop Science, College of Sanghuh Life Science, Konkuk University, Seoul, Republic of Korea
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Lai T, Yu Q, Pan J, Wang J, Tang Z, Bai X, Shi L, Zhou T. The Identification and Comparative Analysis of Non-Coding RNAs in Spores and Mycelia of Penicillium expansum. J Fungi (Basel) 2023; 9:999. [PMID: 37888255 PMCID: PMC10607695 DOI: 10.3390/jof9100999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/28/2023] Open
Abstract
Penicillium expansum is the most popular post-harvest pathogen and causes blue mold disease in pome fruit and leads to significant economic losses worldwide every year. However, the fundamental regulation mechanisms of growth in P. expansum are unclear. Recently, non-coding RNAs (ncRNAs) have attracted more attention due to critical roles in normalizing gene expression and maintaining cellular genotypes in organisms. However, the research related to ncRNAs in P. expansum have not been reported. Therefore, to provide an overview of ncRNAs on composition, distribution, expression changes, and potential targets in the growth process, a comparative transcriptomic analysis was performed on spores and mycelia of P. expansum in the present study. A total of 2595 novel mRNAs, 3362 long non-coding RNAs (lncRNAs), 10 novel microRNAs (miRNAs), 86 novel small interfering RNAs (siRNAs), and 11,238 circular RNAs (circRNAs) were predicted and quantified. Of these, 1482 novel mRNAs, 5987 known mRNAs, 2047 lncRNAs, 40 miRNAs, 38 novel siRNAs, and 9235 circRNAs were differentially expressed (DE) in response to the different development stages. Afterward, the involved functions and pathways of DE RNAs were revealed via Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) database enrichment analysis. The interaction networks between mRNAs, lncRNAs, and miRNAs were also predicted based on their correlation coefficient of expression profiles. Among them, it was found that miR168 family members may play important roles in fungal growth due to their central location in the network. These findings will contribute to a better understanding on regulation machinery at the RNA level on fungal growth and provide a theoretical basis to develop novel control strategies against P. expansum.
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Affiliation(s)
- Tongfei Lai
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (T.L.); (Q.Y.); (J.P.); (J.W.); (X.B.); (L.S.)
| | - Qinru Yu
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (T.L.); (Q.Y.); (J.P.); (J.W.); (X.B.); (L.S.)
| | - Jingjing Pan
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (T.L.); (Q.Y.); (J.P.); (J.W.); (X.B.); (L.S.)
| | - Jingjing Wang
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (T.L.); (Q.Y.); (J.P.); (J.W.); (X.B.); (L.S.)
| | - Zhenxing Tang
- School of Culinary Arts, Tourism College of Zhejiang, Hangzhou 311231, China;
| | - Xuelian Bai
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (T.L.); (Q.Y.); (J.P.); (J.W.); (X.B.); (L.S.)
| | - Lue Shi
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (T.L.); (Q.Y.); (J.P.); (J.W.); (X.B.); (L.S.)
| | - Ting Zhou
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (T.L.); (Q.Y.); (J.P.); (J.W.); (X.B.); (L.S.)
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20
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Zhao H, Huang X, Yang Z, Li F, Ge X. Synergistic optimization of crops by combining early maturation with other agronomic traits. TRENDS IN PLANT SCIENCE 2023; 28:1178-1191. [PMID: 37208203 DOI: 10.1016/j.tplants.2023.04.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 04/16/2023] [Accepted: 04/24/2023] [Indexed: 05/21/2023]
Abstract
Many newly created early maturing varieties exhibit poor stress resistance and low yield, whereas stress-resistant varieties are typically late maturing. For this reason, the polymerization of early maturity and other desired agronomic qualities requires overcoming the negative connection between early maturity, multi-resistance, and yield, which presents a formidable challenge in current breeding techniques. We review the most salient constraints of early maturity breeding in current crop planting practices and the molecular mechanisms of different maturation timeframes in diverse crops from their origin center to production areas. We explore current breeding tactics and the future direction of crop breeding and the issues that must be resolved to accomplish the polymerization of desirable traits in light of the current obstacles and limitations.
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Affiliation(s)
- Hang Zhao
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China; National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; College of Life Sciences, Qufu Normal University, Qufu, 273165, China
| | - Xianzhong Huang
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Chuzhou, China
| | - Zhaoen Yang
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China; National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Fuguang Li
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China; National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100 Xinjiang, China; Hainan Yazhou Bay Seed Lab, Sanya 572000, Hainan, China.
| | - Xiaoyang Ge
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China; National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100 Xinjiang, China; Hainan Yazhou Bay Seed Lab, Sanya 572000, Hainan, China.
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21
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Wang D, Sarsaiya S, Qian X, Jin L, Shu F, Zhang C, Chen J. Analysis of the response mechanisms of Pinellia ternata to terahertz wave stresses using transcriptome and metabolic data. FRONTIERS IN PLANT SCIENCE 2023; 14:1227507. [PMID: 37771489 PMCID: PMC10522861 DOI: 10.3389/fpls.2023.1227507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/01/2023] [Indexed: 09/30/2023]
Abstract
Pinellia ternata (Thunb.) Breit. (Araceae), a significant medicinal plant, has been used to treat various diseases for centuries. Terahertz radiation (THZ) is located between microwaves and infrared rays on the electromagnetic spectrum. THZ possesses low single-photon energy and a spectral fingerprint, but its effects on plant growth have not yet been investigated. The study's primary objective was to examine the transcriptome and metabolome databases of the SY line to provide a new perspective for identifying genes associated with resistance and growth promotion and comprehending the underlying molecular mechanism. Variations in the biological characteristics of P. ternata grown under control and experimental conditions were analyzed to determine the effect of THZ. Compared with the control group, phenotypic variables such as leaf length, petiole length, number of leaves, leaf petiole diameter, and proliferation coefficient exhibited significant differences. P. ternata response to THZ was analyzed regarding the effects of various coercions on root exudation. The experimental group contained considerably more sugar alcohol than the control group. The transcriptome analysis revealed 1,695 differentially expressed genes (DEGs), including 509 upregulated and 1,186 downregulated genes. In the KEGG-enriched plant hormone signaling pathway, there were 19 differentially expressed genes, 13 of which were downregulated and six of which were upregulated. In the metabolomic analysis, approximately 416 metabolites were uncovered. There were 112 DEMs that were downregulated, whereas 148 were upregulated. The P. ternata leaves displayed significant differences in phytohormone metabolites, specifically in brassinolide (BR) and abscisic acid (ABA). The rise in BR triggers alterations in internal plant hormones, resulting in faster growth and development of P. ternata. Our findings demonstrated a link between THZ and several metabolic pathway processes, which will enhance our understanding of P. ternata mechanisms.
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Affiliation(s)
- Dongdong Wang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu, China
| | - Surendra Sarsaiya
- Bioresource Institute for Healthy Utilization, Zunyi Medical University, Zunyi, Guizhou, China
| | - Xu Qian
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu, China
| | - Leilei Jin
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu, China
| | - Fuxing Shu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu, China
| | | | - Jishuang Chen
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu, China
- Bioresource Institute for Healthy Utilization, Zunyi Medical University, Zunyi, Guizhou, China
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22
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Chandra T, Jaiswal S, Iquebal MA, Singh R, Gautam RK, Rai A, Kumar D. Revitalizing miRNAs mediated agronomical advantageous traits improvement in rice. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 202:107933. [PMID: 37549574 DOI: 10.1016/j.plaphy.2023.107933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 07/04/2023] [Accepted: 08/02/2023] [Indexed: 08/09/2023]
Abstract
One of the key enigmas in conventional and modern crop improvement programmes is how to introduce beneficial traits without any penalty impairment. Rice (Oryza sativa L.), among the essential staple food crops grown and utilized worldwide, needs to improve genotypes in multifaceted ways. With the global view to feed ten billion under the climatic perturbation, only a potent functional master regulator can withstand with hope for the next green revolution and food security. miRNAs are such, miniature, fine tuners for crop improvement and provide a value addition in emerging technologies, namely large-scale genotyping, phenotyping, genome editing, marker-assisted selection, and genomic selection, to make rice production feasible. There has been surplus research output generated since the last decade on miRNAs in rice, however, recent functional knowledge is limited to reaping the benefits for conventional and modern improvements in rice to avoid ambiguity and redundancy in the generated data. Here, we present the latest functional understanding of miRNAs in rice. In addition, their biogenesis, intra- and inter-kingdom signaling and communication, implication of amiRNAs, and consequences upon integration with CRISPR-Cas9. Further, highlights refer to the application of miRNAs for rice agronomical trait improvements, broadly classified into three functional domains. The majority of functionally established miRNAs are responsible for growth and development, followed by biotic and abiotic stresses. Tabular cataloguing reveals and highlights two multifaceted modules that were extensively studied. These belong to miRNA families 156 and 396, orchestrate multifarious aspects of advantageous agronomical traits. Moreover, updated and exhaustive functional aspects of different supplemental miRNA modules that would strengthen rice improvement are also being discussed.
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Affiliation(s)
- Tilak Chandra
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Sarika Jaiswal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Mir Asif Iquebal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India.
| | - Rakesh Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - R K Gautam
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India.
| | - Anil Rai
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Dinesh Kumar
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India; Department of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana, India
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Guang H, Xiaoyang G, Zhian W, Ye W, Peng W, Linfang S, Bingting W, Anhong Z, Fuguang L, Jiahe W. The cotton MYB33 gene is a hub gene regulating the trade-off between plant growth and defense in Verticillium dahliae infection. J Adv Res 2023:S2090-1232(23)00233-3. [PMID: 37648022 DOI: 10.1016/j.jare.2023.08.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 08/16/2023] [Accepted: 08/26/2023] [Indexed: 09/01/2023] Open
Abstract
INTRODUCTION Sessile plants engage in trade-offs between growth and defense capacity in response to fluctuating environmental cues. MYB is an important transcription factor that plays many important roles in controlling plant growth and defense. However, the mechanism behind how it keeps a balance between these two physiological processes is still largely unknown. OBJECTIVES Our work focuses on the dissection of the molecular mechanism by which GhMYB33 regulates plant growth and defense. METHODS The CRISPR/Cas9 technique was used to generate mutants for deciphering GhMYB33 functions. Yeast two-hybrid, luciferase complementary imaging, and co-immunoprecipitation assays were used to prove that proteins interact with each other. We used the electrophoretic mobility shift assay, yeast one-hybrid, and luciferase activity assays to analyze GhMYB33 acting as a promoter. A β-glucuronidase fusion reporter and 5' RNA ligase mediated amplification of cDNA ends analysis showed that ghr-miR319c directedly cleaved the GhMYB33 mRNA. RESULTS Overexpressing miR319c-resistant GhMYB33 (rGhMYB33) promoted plant growth, accompanied by a significant decline in resistance against Verticillium dahliae. Conversely, its knockout mutant, ghmyb33, demonstrated growth restriction and concomitant augmentation of V. dahliae resistance. GhMYB33 was found to couple with the DELLA protein GhGAI1 and bind to the specific cis-elements of GhSPL9 and GhDFR1 promoters, thereby modulating internode elongation and plant resistance in V. dahliae infection. The ghr-miR319c was discovered to target and suppress GhMYB33 expression. The overexpression of ghr-miR319c led to enhanced plant resistance and a simultaneous reduction in plant height. CONCLUSION Our findings demonstrate that GhMYB33 encodes a hub protein and controls the expression of GhSPL9 and GhDFR1, implicating a pivotal role for the miR319c-MYB33 module to regulate the trade-offs between plant growth and defense.
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Affiliation(s)
- Hu Guang
- National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ge Xiaoyang
- National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Wang Zhian
- Institute of Cotton Research, Shanxi Agricultural University, Yuncheng 044000, China
| | - Wang Ye
- National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Wang Peng
- National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Shi Linfang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wang Bingting
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhang Anhong
- Institute of Cotton Research, Shanxi Agricultural University, Yuncheng 044000, China
| | - Li Fuguang
- National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Wu Jiahe
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
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Yue E, Rong F, Liu Z, Ruan S, Lu T, Qian H. Cadmium induced a non-coding RNA microRNA535 mediates Cd accumulation in rice. J Environ Sci (China) 2023; 130:149-162. [PMID: 37032032 DOI: 10.1016/j.jes.2022.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/03/2022] [Accepted: 10/05/2022] [Indexed: 06/19/2023]
Abstract
Identifying key regulators related to cadmium (Cd) tolerance and accumulation is the main factor for genetic engineering to improve plants for bioremediation and ensure crop food safety. MicroRNAs (miRNAs), as fine-tuning regulators of genes, participate in various abiotic stress processes. MiR535 is an ancient conserved non-coding small RNA in land plants, positively responding to Cd stress. We investigated the effects of knocking out (mir535) and overexpressing miR535 (mir535 and OE535) under Cd stress in rice plants in this study. The mir535 plants showed better Cd tolerance than wild type (WT), whereas the OE535 showed the opposite effect. Cd accumulated approximately 71.9% and 127% in the roots of mir535 and OE535 plants, respectively, compared to WT, after exposure to 2 µmol/L Cd. In brown rice, the total Cd accumulation of OE535 and mir535 was about 78% greater and 35% lower than WT. When growing in 2 mg/kg Cd of soil, the Cd concentration was significantly lower in mir535 and higher in OE535 than in the WT; afterward, we further revealed the most possible target gene SQUAMOSA promoter binding-like transcription factor 7(SPL7) and it negatively regulates Nramp5 expression, which in turn regulates Cd metabolism. Therefore, the CRISPR/Cas9 technology may be a valuable strategy for creating new rice varieties to ensure food safety.
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Affiliation(s)
- Erkui Yue
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China; Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Institute of Crops, Hangzhou Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Fuxi Rong
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zhen Liu
- Hainan Institute, Zhejiang University, Hainan 572000, China
| | - Songlin Ruan
- Institute of Crops, Hangzhou Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China.
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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: 5] [Impact Index Per Article: 5.0] [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.
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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.
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26
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Liu K, Ma X, Zhao L, Lai X, Chen J, Lang X, Han Q, Wan X, Li C. Comprehensive transcriptomic analysis of three varieties with different brown planthopper-resistance identifies leaf sheath lncRNAs in rice. BMC PLANT BIOLOGY 2023; 23:367. [PMID: 37480003 PMCID: PMC10362764 DOI: 10.1186/s12870-023-04374-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 07/12/2023] [Indexed: 07/23/2023]
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) have been brought great attention for their crucial roles in diverse biological processes. However, systematic identification of lncRNAs associated with specialized rice pest, brown planthopper (BPH), defense in rice remains unexplored. RESULTS In this study, a genome-wide high throughput sequencing analysis was performed using leaf sheaths of susceptible rice Taichung Native 1 (TN1) and resistant rice IR36 and R476 with and without BPH feeding. A total of 2283 lncRNAs were identified, of which 649 lncRNAs were differentially expressed. During BPH infestation, 84 (120 in total), 52 (70 in total) and 63 (94 in total) of differentially expressed lncRNAs were found only in TN1, IR36 and R476, respectively. Through analyzing their cis-, trans-, and target mimic-activities, not only the lncRNAs targeting resistance genes (NBS-LRR and RLKs) and transcription factors, but also the lncRNAs acting as the targets of the well-studied stress-related miRNAs (miR2118, miR528, and miR1320) in each variety were identified. Before the BPH feeding, 238 and 312 lncRNAs were found to be differentially expressed in TN1 vs. IR36 and TN1 vs. R476, respectively. Among their putative targets, the plant-pathogen interaction pathway was significantly enriched. It is speculated that the resistant rice was in a priming state by the regulation of lncRNAs. Furthermore, the lncRNAs extensively involved in response to BPH feeding were identified by Weighted Gene Co-expression Network Analysis (WGCNA), and the possible regulation networks of the key lncRNAs were constructed. These lncRNAs regulate different pathways that contribute to the basal defense and specific resistance of rice to the BPH. CONCLUSION In summary, we identified the specific lncRNAs targeting the well-studied stress-related miRNAs, resistance genes, and transcription factors in each variety during BPH infestation. Additionally, the possible regulating network of the lncRNAs extensively responding to BPH feeding revealed by WGCNA were constructed. These findings will provide further understanding of the regulatory roles of lncRNAs in BPH defense, and lay a foundation for functional research on the candidate lncRNAs.
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Affiliation(s)
- Kai Liu
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests & Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Xiaozhi Ma
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510642, China
| | - Luyao Zhao
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests & Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Xiaofeng Lai
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests & Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Jie Chen
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests & Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Xingxuan Lang
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests & Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Qunxin Han
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests & Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Xiaorong Wan
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests & Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China.
| | - Chunmei Li
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests & Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China.
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Yadav R, Ramakrishna W. MicroRNAs Involved in Nutritional Regulation During Plant-Microbe Symbiotic and Pathogenic Interactions with Rice as a Model. Mol Biotechnol 2023:10.1007/s12033-023-00822-y. [PMID: 37468736 DOI: 10.1007/s12033-023-00822-y] [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: 05/08/2023] [Accepted: 07/04/2023] [Indexed: 07/21/2023]
Abstract
Plants are constantly challenged with numerous adverse environmental conditions, including biotic and abiotic stresses. Coordinated regulation of plant responses requires crosstalk between regulatory pathways initiated by different external cues. Stress induced by excessiveness or deficiency of nutrients has been shown to positively or negatively interact with pathogen-induced immune responses. Also, colonization by arbuscular mycorrhizal (AM) fungi can improve plant nutrition, mainly phosphorus and resistance to pathogen infection. The proposed review addresses these issues about a new question that integrates adaptation to nutrient stress and disease resistance. The main goal of the current review is to provide insights into the interconnected regulation between nutrient signaling and immune signaling pathways in rice, focusing on phosphate, potassium and iron signaling. The underpinnings of plant/pathogen/AM fungus interaction concerning rice/M. oryzae/R. irregularis is highlighted. The role of microRNAs (miRNAs) involved in Pi (miR399, miR827) and Fe (miR7695) homeostasis in pathogenic/symbiotic interactions in rice is discussed. The intracellular dynamics of membrane proteins that function in nutrient transport transgenic rice lines expressing fluorescent protein fusion genes are outlined. Integrating functional genomic, nutritional and metal content, molecular and cell biology approaches to understand how disease resistance is regulated by nutrient status leading to novel concepts in fundamental processes underlying plant disease resistance will help to devise novel strategies for crop protection with less input of pesticides and fertilizers.
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Affiliation(s)
- Radheshyam Yadav
- Department of Biochemistry, Central University of Punjab, VPO Ghudda, Bathinda, Punjab, India
| | - Wusirika Ramakrishna
- Department of Biochemistry, Central University of Punjab, VPO Ghudda, Bathinda, Punjab, India.
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28
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Li L, Li Q, Chen B, Wang J, Ding F, Wang P, Zhang X, Hou J, Luo R, Li X, Zheng J, Yang S, Yang L, Zhu L, Sun S, Ma C, Li Q, Li Y, Hu J. Identification of candidate genes that regulate the trade-off between seedling cold tolerance and fruit quality in melon ( Cucumis melo L.). HORTICULTURE RESEARCH 2023; 10:uhad093. [PMID: 37416729 PMCID: PMC10321389 DOI: 10.1093/hr/uhad093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 05/01/2023] [Indexed: 07/08/2023]
Abstract
Trade-offs between survival and growth are widely observed in plants. Melon is an annual, trailing herb that produces economically valuable fruits that are traditionally cultivated in early spring in China. Melon seedlings are sensitive to low temperatures, and thus usually suffer from cold stress during the early growth period. However, little is known about the mechanism behind the trade-offs between seedling cold tolerance and fruit quality in melon. In this study, a total of 31 primary metabolites were detected from the mature fruits of eight melon lines that differ with respect to seedling cold tolerance; these included 12 amino acids, 10 organic acids, and 9 soluble sugars. Our results showed that concentrations of most of the primary metabolites in the cold-resistant melons were generally lower than in the cold-sensitive melons; the greatest difference in metabolite levels was observed between the cold-resistant line H581 and the moderately cold-resistant line HH09. The metabolite and transcriptome data for these two lines were then subjected to weighted correlation network analysis, resulting in the identification of five key candidate genes underlying the balancing between seedling cold tolerance and fruit quality. Among these genes, CmEAF7 might play multiple roles in regulating chloroplast development, photosynthesis, and the ABA pathway. Furthermore, multi-method functional analysis showed that CmEAF7 can certainly improve both seedling cold tolerance and fruit quality in melon. Our study identified an agriculturally important gene, CmEAF7, and provides a new insight into breeding methods to develop melon cultivars with seedling cold tolerance and high fruit quality.
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Affiliation(s)
- Lili Li
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Qiong Li
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Bin Chen
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Jiyu Wang
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Fei Ding
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Panqiao Wang
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Xiuyue Zhang
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Juan Hou
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Renren Luo
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Xiang Li
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Jingwen Zheng
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Sen Yang
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Luming Yang
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Lei Zhu
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Shouru Sun
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Changsheng Ma
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Qin Li
- The Seed Management Station of Zhengzhou City, Zhengzhou 450001, China
| | - Ying Li
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Jianbin Hu
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
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Balyan S, Kansal S, Jajo R, Behere PR, Chatterjee R, Raghuvanshi S. Delineating the tissue-mediated drought stress governed tuning of conserved miR408 and its targets in rice. Funct Integr Genomics 2023; 23:187. [PMID: 37243818 DOI: 10.1007/s10142-023-01111-2] [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: 12/30/2022] [Revised: 05/13/2023] [Accepted: 05/16/2023] [Indexed: 05/29/2023]
Abstract
Engineering drought tolerance in rice needs to focus on regulators that enhance tolerance while boosting plant growth and vigor. The present study delineated the concealed function and tissue-mediated interplay of the miR408/target module in imparting drought stress tolerance in rice. The plant miR408 family comprises three dominant mature forms (21 nt), including a distinct monocot variant (F-7 with 5' C) and is divided into six groups. miR408 majorly cleaves genes belonging to the blue copper protein in addition to several other species-specific targets in plants. Comparative sequence analysis in 4726 rice accessions identified 22 sequence variants (SNP and InDELs) in its promoter (15) and pre-miR408 region. Haplotype analysis of the sequence variants indicated eight haplotypes (three: Japonica-specific and five: Indica-specific) of the miR408 promoter. In drought-tolerant Nagina 22, miR408 follows flag leaf preferential expression. Under drought conditions, its levels are upregulated in flag leaf and roots which seems to be regulated by a differential fraction of methylated cytosines (mCs) in the precursor region. The active pool of miR408 regulated targets under control and drought conditions is impacted by the tissue type. Comparative expression analysis of the miR408/target module under different sets of conditions features 83 targets exhibiting antagonistic expression in rice, out of which 12 genes, including four PLANTACYANINS (OsUCL6, 7, 9 and 30), PIRIN, OsLPR1, OsCHUP1, OsDOF12, OsBGLU1, glycine-rich cell wall gene, OsDUT, and OsERF7, are among the high confidence targets. Further, overexpression of MIR408 in drought-sensitive rice cultivar (PB1) leads to the massive enhancement of vegetative growth in rice with improved ETR and Y(II) and enhanced dehydration stress tolerance. The above results suggest that miR408 is likely to act as a positive regulator of growth and vigor, as well as dehydration stress, making it a potential candidate for engineering drought tolerance in rice.
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Affiliation(s)
- Sonia Balyan
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Shivani Kansal
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Ringyao Jajo
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Pratyush Rajiv Behere
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Rishika Chatterjee
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Saurabh Raghuvanshi
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India.
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Sheng C, Li X, Xia S, Zhang Y, Yu Z, Tang C, Xu L, Wang Z, Zhang X, Zhou T, Nie P, Baig A, Niu D, Zhao H. An OsPRMT5-OsAGO2/miR1875-OsHXK1 module regulates rice immunity to blast disease. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:1077-1095. [PMID: 36511124 DOI: 10.1111/jipb.13430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
Rice ARGONAUTE2 (OsAGO2) is a core component of the rice RNA-induced silencing complex (RISC), which is repressed by Magnaporthe oryzae (M. oryzae) infection. Whether and how OsAGO2-mediated gene silencing plays a role in rice blast resistance and which sRNAs participate in this process are unknown. Our results indicate that OsAGO2 is a key immune player that manipulates rice defense responses against blast disease. OsAGO2 associates with the 24-nt miR1875 and binds to the promoter region of HEXOKINASE1 (OsHXK1), which causes DNA methylation and leads to gene silencing. Our multiple genetic evidence showed that, without M. oryzae infection, OsAGO2/miR1875 RISC promoted OsHXK1 promoter DNA methylation and OsHXK1 silencing; after M. oryzae infection, the reduced OsAGO2/miR1875 led to a relatively activated OsHXK1 expression. OsHXK1 acts as a positive regulator of blast disease resistance that OsHXK1-OE rice exhibited enhanced resistance, whereas Cas9-Oshxk1 rice showed reduced resistance against M. oryzae infection. OsHXK1 may function through its sugar sensor activity as glucose induced defense-related gene expression and reactive oxygen species (ROS) accumulation in Nipponbare and OsHXK1-OE but not in Cas9-Oshxk1 rice. OsAGO2 itself is delicately regulated by OsPRMT5, which senses M. oryzae infection and attenuates OsAGO2-mediated gene silencing through OsAGO2 arginine methylation. Our study reveals an OsPRMT5-OsAGO2/miR1875-OsHXK1 regulatory module that fine tunes the rice defense response to blast disease.
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Affiliation(s)
- Cong Sheng
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xuan Li
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shengge Xia
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yimai Zhang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ze Yu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, China
| | - Cheng Tang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, China
| | - Le Xu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhaoyun Wang
- Key Laboratory of Food Quality and Safety, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210095, China
| | - Xin Zhang
- Institute of Industrial Crops, Shanxi Agricultural University, Taiyuan, 030000, China
| | - Tong Zhou
- Key Laboratory of Food Quality and Safety, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210095, China
| | - Pingping Nie
- College of Life Sciences, Zaozhuang University, Zaozhuang, 277000, China
| | - Ayesha Baig
- Department of Biotechnology, COMSATS University Islamabad Abbottabad Campus, Abbottabad, Pakistan
| | - Dongdong Niu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hongwei Zhao
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, China
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A Novel miRNA in Rice Associated with the Low Seed Setting Rate Symptom of Rice Stripe Virus. Int J Mol Sci 2023; 24:ijms24043675. [PMID: 36835087 PMCID: PMC9967548 DOI: 10.3390/ijms24043675] [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: 12/31/2022] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
MicroRNAs play key regulatory roles in plant development. The changed pattern of miRNA expression is involved in the production of viral symptoms. Here, we showed that a small RNA, Seq119, a putative novel microRNA, is associated with the low seed setting rate, a viral symptom of rice stripe virus (RSV)-infected rice. The expression of Seq 119 was downregulated in RSV-infected rice. The overexpression of Seq119 in transgenic rice plants did not cause any obvious phenotypic changes in plant development. When the expression of Seq119 was suppressed in rice plants either by expressing a mimic target or by CRISPR/Cas editing, seed setting rates were extremely low, similar to the effects of RSV infection. The putative targets of Seq119 were then predicted. The overexpression of the target of Seq119 in rice caused a low seed setting rate, similar to that in Seq119-suppressed or edited rice plants. Consistently, the expression of the target was upregulated in Seq119-suppressed and edited rice plants. These results suggest that downregulated Seq119 is associated with the low seed setting rate symptom of the RSV in rice.
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Zhang L, Yang B, Zhang C, Chen H, Xu J, Qu C, Lu K, Li J. Genome-Wide Identification and Posttranscriptional Regulation Analyses Elucidate Roles of Key Argonautes and Their miRNA Triggers in Regulating Complex Yield Traits in Rapeseed. Int J Mol Sci 2023; 24:ijms24032543. [PMID: 36768865 PMCID: PMC9916703 DOI: 10.3390/ijms24032543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 01/21/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023] Open
Abstract
Argonautes (AGOs) interact with microRNAs (miRNAs) to form the RNA-induced silencing complex (RISC), which can posttranscriptionally regulate the expression of targeted genes. To date, however, the AGOs and their miRNA triggers remain elusive in rapeseed (Brassica napus). Here, we systematically performed a phylogenetic analysis and examined the collinear relationships of the AGOs among four Brassicaceae species. Their physicochemical properties, gene structures, and expression patterns among 81 tissues from multiple materials and developmental stages were further analyzed. Additionally, their posttranscriptional regulation was analyzed using psRNATarget prediction, miRNA-/mRNA-Seq analyses, and a qRT-PCR verification. We finally identified 10 AtAGOs, 13 BolAGOs, 11 BraAGOs, and 24 BnaAGOs. An expression analysis of the BnaAGOs in the B. napus cultivar ZS11, as well as genotypes with extreme phenotypes in various yield-related traits, revealed the conservation and diversity of these genes. Furthermore, we speculated the posttranscriptional regulation of the B. napus miR168a-AGO1s and miR403-AGO2s modules. Combining miRNA-Seq and mRNA-Seq analyses, we found that the B. napus miR168a-AGO1s module may play an essential role in negatively regulating yield traits, whereas the miR403-AGO2s module positively impacts yield. This is the first attempt to comprehensively analyze the AGOs and their miRNA triggers in B. napus and provides a theoretical basis for breeding high-yielding varieties through the manipulation of the miRNA-AGOs modules.
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Affiliation(s)
- Liyuan Zhang
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Bo Yang
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Chao Zhang
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Huan Chen
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Jinxiong Xu
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Cunmin Qu
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Kun Lu
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Jiana Li
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Correspondence: ; Tel.: +86-23-68250642
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Xia K, Pan X, Chen H, Xu X, Zhang M. Rice miR168a-5p regulates seed length, nitrogen allocation and salt tolerance by targeting OsOFP3, OsNPF2.4 and OsAGO1a, respectively. JOURNAL OF PLANT PHYSIOLOGY 2023; 280:153905. [PMID: 36580705 DOI: 10.1016/j.jplph.2022.153905] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/19/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Rice microRNA168a (osa-miR168a) plays important roles in mediating flowering time, grain yield and vigor, seeding growth, and immunity by targeting the RNA-induced silencing complex component Argonaute 1 (AGO1). However, the functions of miR168a exerted by targeting other genes require further clarification before it could be used in rice molecular breeding. In this study, we identified a new target gene of osa-miR168a-5p (miR168a-5p) in rice called OsOFP3 (ovate family protein 3) and investigated the roles of miR168a-5p in response to brassinosteroids (BRs), salt stress, and nitrogen allocation. Up- and downregulated miR168a-5p expression respectively decreased and increased the expression of the BR-negative regulator OsOPF3. The results of RNA ligase-mediated rapid amplification of cDNA ends (5'RLM-RACE) revealed cleavage sites in OsOPF3 and OsNPF2.4 mRNAs. The phenotype of miR168a-5p transgenic rice was BR-associated and included the lamina bending response to BR, short seeds, and low 1000-grain weight. MicroRNA 168a-5p also regulated the expression of the nitrate transporter, OsNPF2.4, which affected nitrogen allocation, and regulated OsAGO1a expression in response to salt stress. Taken together, rice miR168a-5p regulates BR-associated pathways, nitrogen transport, and stress by targeting OsOFP3, OsNPF2.4, and OsAGO1a, respectively, resulting in a series of important agronomic traits for rice breeding.
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Affiliation(s)
- Kuaifei Xia
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, Guangdong, China
| | - Xiaoqin Pan
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, Guangdong, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huaping Chen
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, Guangdong, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xinlan Xu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, Guangdong, China
| | - Mingyong Zhang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, Guangdong, China.
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Lu H, Chen L, Du M, Lu H, Liu J, Ye S, Tao B, Li R, Zhao L, Wen J, Yi B, Tu J, Fu T, Shen J. miR319 and its target TCP4 involved in plant architecture regulation in Brassica napus. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 326:111531. [PMID: 36343867 DOI: 10.1016/j.plantsci.2022.111531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/21/2022] [Accepted: 11/02/2022] [Indexed: 06/16/2023]
Abstract
Plant architecture is a collection of genetically controlled crop productivity and adaptation. MicroRNAs (miRNAs) have been proved to function in various biological processes, but little is known about how miRNA regulates plant architecture in rapeseed (Brassica napus L.). In this study, four small RNA libraries and two degradome libraries from shoot apex of normal and rod-like plants were sequenced. A total of 639 miRNA precursors and 16 differentially expressed miRNAs were identified in this study. In addition, 322 targets were identified through degradome sequencing. Among them, 14 targets were further validated via RNA ligase-mediated 5' rapid amplification of cDNA ends. Transgenic approach showed that increased TCP4 activity in Arabidopsis resulted in premature onset of maturation and reduced plant size along with early flowering and shortened flowering time. miR319-OE lines in Brassica napus exhibited serrated leaves and abnormal development of shoot apical meristem (SAM), which led to the deformed growth of stem and reduced plant height. In conclusion, our study lays the foundation for elucidating miRNA regulate plant architecture and provides new insight into the miR319/TCP4 module regulates plant architecture in rapeseed.
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Affiliation(s)
- Hongchen Lu
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, China
| | - Li Chen
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, China; School of Advanced Agriculture and Bioengineering, Yangtze Normal University, Chongqing, China
| | - Mengjie Du
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, China
| | - Haiqin Lu
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, China
| | - Jie Liu
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, China
| | - Shenhua Ye
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, China
| | - Baolong Tao
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, China
| | - Rihui Li
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, China
| | - Lun Zhao
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, China
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, China.
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Mapuranga J, Chang J, Zhang L, Zhang N, Yang W. Fungal Secondary Metabolites and Small RNAs Enhance Pathogenicity during Plant-Fungal Pathogen Interactions. J Fungi (Basel) 2022; 9:jof9010004. [PMID: 36675825 PMCID: PMC9862911 DOI: 10.3390/jof9010004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/16/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Fungal plant pathogens use proteinaceous effectors as well as newly identified secondary metabolites (SMs) and small non-coding RNA (sRNA) effectors to manipulate the host plant's defense system via diverse plant cell compartments, distinct organelles, and many host genes. However, most molecular studies of plant-fungal interactions have focused on secreted effector proteins without exploring the possibly equivalent functions performed by fungal (SMs) and sRNAs, which are collectively known as "non-proteinaceous effectors". Fungal SMs have been shown to be generated throughout the plant colonization process, particularly in the early biotrophic stages of infection. The fungal repertoire of non-proteinaceous effectors has been broadened by the discovery of fungal sRNAs that specifically target plant genes involved in resistance and defense responses. Many RNAs, particularly sRNAs involved in gene silencing, have been shown to transmit bidirectionally between fungal pathogens and their hosts. However, there are no clear functional approaches to study the role of these SM and sRNA effectors. Undoubtedly, fungal SM and sRNA effectors are now a treasured land to seek. Therefore, understanding the role of fungal SM and sRNA effectors may provide insights into the infection process and identification of the interacting host genes that are targeted by these effectors. This review discusses the role of fungal SMs and sRNAs during plant-fungal interactions. It will also focus on the translocation of sRNA effectors across kingdoms, the application of cross-kingdom RNA interference in managing plant diseases and the tools that can be used to predict and study these non-proteinaceous effectors.
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Guo L, Li Y, Zhang C, Wang Z, Carlson JE, Yin W, Zhang X, Hou X. Integrated analysis of miRNAome transcriptome and degradome reveals miRNA-target modules governing floral florescence development and senescence across early- and late-flowering genotypes in tree peony. FRONTIERS IN PLANT SCIENCE 2022; 13:1082415. [PMID: 36589111 PMCID: PMC9795019 DOI: 10.3389/fpls.2022.1082415] [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: 10/28/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
As a candidate national flower of China, tree peony has extremely high ornamental, medicinal and oil value. However, the short florescence and rarity of early-flowering and late-flowering varieties restrict further improvement of the economic value of tree peony. Specific miRNAs and their target genes engaged in tree peony floral florescence, development and senescence remain unknown. This report presents the integrated analysis of the miRNAome, transcriptome and degradome of tree peony petals collected from blooming, initial flowering, full blooming and decay stages in early-flowering variety Paeonia ostii 'Fengdan', an early-flowering mutant line of Paeonia ostii 'Fengdan' and late-flowering variety Paeonia suffruticosa 'Lianhe'. Transcriptome analysis revealed a transcript ('psu.G.00014095') which was annotated as a xyloglucan endotransglycosylase/hydrolase precursor XTH-25 and found to be differentially expressed across flower developmental stages in Paeonia ostii 'Fengdan' and Paeonia suffruticosa 'Lianhe'. The miRNA-mRNA modules were presented significant enrichment in various pathways such as plant hormone signal transduction, indole alkaloid biosynthesis, arachidonic acid metabolism, folate biosynthesis, fatty acid elongation, and the MAPK signaling pathway. Multiple miRNA-mRNA-TF modules demonstrated the potential functions of MYB-related, bHLH, Trihelix, NAC, GRAS and HD-ZIP TF families in floral florescence, development, and senescence of tree peony. Comparative spatio-temporal expression investigation of eight floral-favored miRNA-target modules suggested that transcript 'psu.T.00024044' and microRNA mtr-miR166g-5p are involved in the floral florescence, development and senescence associated agronomic traits of tree peony. The results might accelerate the understanding of the potential regulation mechanism in regards to floral florescence, development and abscission, and supply guidance for tree peony breeding of varieties with later and longer florescence characteristics.
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Affiliation(s)
- Lili Guo
- College of Tree Peony, Henan University of Science and Technology, Luoyang, Henan, China
| | - Yuying Li
- College of Tree Peony, Henan University of Science and Technology, Luoyang, Henan, China
| | - Chenjie Zhang
- College of Tree Peony, Henan University of Science and Technology, Luoyang, Henan, China
| | - Zhanying Wang
- Department of Horticulture, Luoyang Academy of Agricultural and Forestry Sciences, Luoyang, Henan, China
| | - John E. Carlson
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA, United States
| | - Weinlun Yin
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xiuxin Zhang
- Center of Peony, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing, China
| | - Xiaogai Hou
- Center of Peony, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing, China
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Wan J, Meng S, Wang Q, Zhao J, Qiu X, Wang L, Li J, Lin Y, Mu L, Dang K, Xie Q, Tang J, Ding D, Zhang Z. Suppression of microRNA168 enhances salt tolerance in rice (Oryza sativa L.). BMC PLANT BIOLOGY 2022; 22:563. [PMID: 36460977 PMCID: PMC9719116 DOI: 10.1186/s12870-022-03959-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Rice is a salt-sensitive crop. Complex gene regulatory cascades are likely involved in salinity stress in rice roots. microRNA168 (miR168) is a conserved miRNA among different plant species. It in-directly regulates the expression of all miRNAs by targeting gene ARGONAUTE1(AGO1). Short Tandem Target Mimic (STTM) technology is an ideal approach to study miRNA functions by in-activating mature miRNA in plants. RESULTS In this study, rice miR168 was inactivated by STTM. The T3 generation seedlings of STTM168 exhibited significantly enhanced salt resistance. Direct target genes of rice miR168 were obtained by in silico prediction and further confirmed by degradome-sequencing. PINHEAD (OsAGO1), which was previously suggested to be a plant abiotic stress response regulator. RNA-Seq was performed in root samples of 150mM salt-treated STTM168 and control seedlings. Among these screened 481 differentially expressed genes within STTM168 and the control, 44 abiotic stress response related genes showed significant difference, including four known salt-responsive genes. CONCLUSION Based on sequencing and qRT-PCR, a "miR168-AGO1-downstream" gene regulation model was proposed to be responsible for rice salt stress response. The present study proved miR168-AGO1 cascade to play important role in rice salinity stress responding, as well as to be applied in agronomic improvement in further.
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Affiliation(s)
- Jiong Wan
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, 450002, Zhengzhou, China
| | - Shujun Meng
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, 450002, Zhengzhou, China
| | - Qiyue Wang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, 450002, Zhengzhou, China
| | - Jiawen Zhao
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, 450002, Zhengzhou, China
| | - Xiaoqian Qiu
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, 450002, Zhengzhou, China
| | - Liangfa Wang
- Hebi Academy of Agricultural Sciences, 458030, Hebi, China
| | - Juan Li
- Institute of Crop Germplasm Resources, Guizhou Academy of Agricultural Sciences, 550006, Guiyang, China
| | - Yuan Lin
- Hebi Academy of Agricultural Sciences, 458030, Hebi, China
| | - Liqin Mu
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, 450002, Zhengzhou, China
| | - Kuntai Dang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, 450002, Zhengzhou, China
| | - Qiankun Xie
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, 450002, Zhengzhou, China
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, 450002, Zhengzhou, China
- The Shennong laboratory, 450002, Zhengzhou, China
| | - Dong Ding
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, 450002, Zhengzhou, China.
| | - Zhanhui Zhang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, 450002, Zhengzhou, China.
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Li H, Zhang Y, Wu C, Bi J, Chen Y, Jiang C, Cui M, Chen Y, Hou X, Yuan M, Xiong L, Yang Y, Xie K. Fine-tuning OsCPK18/OsCPK4 activity via genome editing of phosphorylation motif improves rice yield and immunity. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:2258-2271. [PMID: 35984919 PMCID: PMC9674324 DOI: 10.1111/pbi.13905] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 07/27/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
Plants have evolved complex signalling networks to regulate growth and defence responses under an ever-changing environment. However, the molecular mechanisms underlying the growth-defence tradeoff are largely unclear. We previously reported that rice CALCIUM-DEPENDENT PROTEIN KINASE 18 (OsCPK18) and MITOGEN-ACTIVATED PROTEIN KINASE 5 (OsMPK5) mutually phosphorylate each other and that OsCPK18 phosphorylates and positively regulates OsMPK5 to suppress rice immunity. In this study, we found that OsCPK18 and its paralog OsCPK4 positively regulate plant height and yield-related traits. Further analysis reveals that OsCPK18 and OsMPK5 synergistically regulate defence-related genes but differentially regulate development-related genes. In vitro and in vivo kinase assays demonstrated that OsMPK5 phosphorylates C-terminal threonine (T505) and serine (S512) residues of OsCPK18 and OsCPK4, respectively. The kinase activity of OsCPK18T505D , in which T505 was replaced by aspartic acid to mimic T505 phosphorylation, displayed less calcium sensitivity than that of wild-type OsCPK18. Interestingly, editing the MAPK phosphorylation motif in OsCPK18 and its paralog OsCPK4, which deprives OsMPK5-mediated phosphorylation but retains calcium-dependent activation of kinase activity, simultaneously increases rice yields and immunity. This editing event also changed the last seven amino acid residues of OsCPK18 and attenuated its binding with OsMPK5. This study presents a new regulatory circuit that fine tunes the growth-defence tradeoff by modulating OsCPK18/4 activity and suggests that CRISPR/Cas9-mediated engineering phosphorylation pathways could simultaneously improve crop yield and immunity.
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Affiliation(s)
- Hong Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
- Hubei Key Laboratory of Plant PathologyHuazhong Agricultural UniversityWuhanChina
- Shenzhen Institute of Nutrition and HealthHuazhong Agricultural UniversityWuhanChina
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Yun Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
- Hubei Key Laboratory of Plant PathologyHuazhong Agricultural UniversityWuhanChina
| | - Caiyun Wu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
- Hubei Key Laboratory of Plant PathologyHuazhong Agricultural UniversityWuhanChina
| | - Jinpeng Bi
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
- Hubei Key Laboratory of Plant PathologyHuazhong Agricultural UniversityWuhanChina
| | - Yache Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
- Hubei Key Laboratory of Plant PathologyHuazhong Agricultural UniversityWuhanChina
| | - Changjin Jiang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
- Hubei Key Laboratory of Plant PathologyHuazhong Agricultural UniversityWuhanChina
| | - Miaomiao Cui
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
- Hubei Key Laboratory of Plant PathologyHuazhong Agricultural UniversityWuhanChina
| | - Yuedan Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
- Hubei Key Laboratory of Plant PathologyHuazhong Agricultural UniversityWuhanChina
| | - Xin Hou
- State Key Laboratory of Hybrid RiceWuhan UniversityWuhanChina
| | - Meng Yuan
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Lizhong Xiong
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Yinong Yang
- Department of Plant Pathology and Environmental Microbiology, The Huck Institutes of Life SciencesThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Kabin Xie
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
- Hubei Key Laboratory of Plant PathologyHuazhong Agricultural UniversityWuhanChina
- Shenzhen Institute of Nutrition and HealthHuazhong Agricultural UniversityWuhanChina
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
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Feng Q, Wang H, Yang X, Hu Z, Zhou X, Xiang L, Xiong X, He X, Zhu Y, Li G, Zhao J, Ji Y, Hu X, Pu M, Zhou S, Zhao Z, Zhang J, Huang Y, Fan J, Wang W, Li Y. Osa-miR160a confers broad-spectrum resistance to fungal and bacterial pathogens in rice. THE NEW PHYTOLOGIST 2022; 236:2216-2232. [PMID: 36101507 PMCID: PMC9828417 DOI: 10.1111/nph.18491] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/27/2022] [Indexed: 06/15/2023]
Abstract
Rice production is threatened by multiple pathogens. Breeding cultivars with broad-spectrum disease resistance is necessary to maintain and improve crop production. Previously we found that overexpression of miR160a enhanced rice blast disease resistance. However, it is unclear whether miR160a also regulates resistance against other pathogens, and what the downstream signaling pathways are. Here, we demonstrate that miR160a positively regulates broad-spectrum resistance against the causative agents of blast, leaf blight and sheath blight in rice. Mutations of miR160a-targeted Auxin Response Factors result in different alteration of resistance conferred by miR160a. miR160a enhances disease resistance partially by suppressing ARF8, as mutation of ARF8 in MIM160 background partially restores the compromised resistance resulting from MIM160. ARF8 protein binds directly to the promoter and suppresses the expression of WRKY45, which acts as a positive regulator of rice immunity. Mutation of WRKY45 compromises the enhanced blast resistance and bacterial leaf blight resistance conferred by arf8 mutant. Overall, our results reveal that a microRNA coordinates rice broad-spectrum disease resistance by suppressing multiple target genes that play different roles in disease resistance, and uncover a new regulatory pathway mediated by the miR160a-ARF8 module. These findings provide new resources to potentially improve disease resistance for breeding in rice.
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Affiliation(s)
- Qin Feng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengdu611130China
| | - He Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengdu611130China
| | - Xue‐Mei Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengdu611130China
| | - Zhang‐Wei Hu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengdu611130China
| | - Xin‐Hui Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengdu611130China
| | - Ling Xiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengdu611130China
| | - Xiao‐Yu Xiong
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengdu611130China
| | - Xiao‐Rong He
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengdu611130China
| | - Yong Zhu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengdu611130China
| | - Guo‐Bang Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengdu611130China
| | - Jing‐Hao Zhao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengdu611130China
| | - Yun‐Peng Ji
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengdu611130China
| | - Xiao‐Hong Hu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengdu611130China
| | - Mei Pu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengdu611130China
| | - Shi‐Xin Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengdu611130China
| | - Zhi‐Xue Zhao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengdu611130China
| | - Ji‐Wei Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengdu611130China
| | - Yan‐Yan Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengdu611130China
| | - Jing Fan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengdu611130China
| | - Wen‐Ming Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengdu611130China
| | - Yan Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengdu611130China
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Dong L, Hou Z, Li H, Li Z, Fang C, Kong L, Li Y, Du H, Li T, Wang L, He M, Zhao X, Cheng Q, Kong F, Liu B. Agronomical selection on loss-of-function of GIGANTEA simultaneously facilitates soybean salt tolerance and early maturity. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:1866-1882. [PMID: 35904035 DOI: 10.1111/jipb.13332] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
Salt stress and flowering time are major factors limiting geographic adaptation and yield productivity in soybean (Glycine max). Although improving crop salt tolerance and latitude adaptation are essential for efficient agricultural production, whether and how these two traits are integrated remains largely unknown. Here, we used a genome-wide association study to identify a major salt-tolerance locus controlled by E2, an ortholog of Arabidopsis thaliana GIGANTEA (GI). Loss of E2 function not only shortened flowering time and maturity, but also enhanced salt-tolerance in soybean. E2 delayed soybean flowering by enhancing the transcription of the core flowering suppressor gene E1, thereby repressing Flowering Locus T (FT) expression. An E2 knockout mutant e2CR displayed reduced accumulation of reactive oxygen species (ROS) during the response to salt stress by releasing peroxidase, which functions in ROS scavenging to avoid cytotoxicity. Evolutionary and population genetic analyses also suggested that loss-of-function e2 alleles have been artificially selected during breeding for soybean adaptation to high-latitude regions with greater salt stress. Our findings provide insights into the coupled selection for adaptation to both latitude and salt stress in soybean; and offer an ideal target for molecular breeding of early-maturing and salt-tolerant cultivars.
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Affiliation(s)
- Lidong Dong
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, 510006, China
| | - Zhihong Hou
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, 510006, China
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 510062, China
| | - Haiyang Li
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, 510006, China
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhaobo Li
- College of Agriculture, Jilin Agricultural Science and Technology University, Jilin, 132101, China
| | - Chao Fang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, 510006, China
| | - Lingping Kong
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, 510006, China
| | - Yongli Li
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, 510006, China
| | - Hao Du
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, 510006, China
| | - Tai Li
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, 510006, China
| | - Lingshuang Wang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, 510006, China
| | - Milan He
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, 510006, China
| | - Xiaohui Zhao
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, 510006, China
| | - Qun Cheng
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, 510006, China
| | - Fanjiang Kong
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, 510006, China
- The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Baohui Liu
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, 510006, China
- The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
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He J, Xu C, You C, Mo B, Chen X, Gao L, Liu L. Parallel analysis of RNA ends reveals global microRNA-mediated target RNA cleavage in maize. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:268-283. [PMID: 35962593 PMCID: PMC9804894 DOI: 10.1111/tpj.15943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/29/2022] [Accepted: 08/07/2022] [Indexed: 06/15/2023]
Abstract
MicroRNAs (miRNAs) are endogenous 20-24-nucleotide non-coding RNAs that play important regulatory roles in many biological processes in eukaryotes. miRNAs modulate the expression of target genes at the post-transcriptional level by transcript cleavage or translational inhibition. The identification of miRNA target genes has been extensively investigated in Arabidopsis and rice, but an in-depth global analysis of miRNA-mediated target regulation is still lacking in maize. Here, we report a transcriptome-wide identification of miRNA targets by analyzing parallel analysis of RNA ends (PARE) datasets derived from nine different tissues at five developmental stages of the maize (Zea mays L.) B73 cultivar. In total, 246 targets corresponding to 60 miRNAs from 25 families were identified, including transcription factors and other genes. In addition, PARE analysis revealed that miRNAs guide specific target transcript cleavage in a tissue-preferential manner. Primary transcripts of MIR159c and MIR169e were found to be cleaved by mature miR159 and miR169, respectively, indicating a negative-feedback regulatory mechanism in miRNA biogenesis. Moreover, several miRNA-target gene pairs involved in seed germination were identified and experimentally validated. Our PARE analyses generated a wide and detailed miRNA-target interaction atlas, which provides a valuable resource for investigating the roles of miRNAs and their targets in maize.
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Affiliation(s)
- Juan He
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdong518060China
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Molecular Plant Sciences, School of Life SciencesDivision of Life Sciences and Medicine, University of Science and Technology of ChinaHefei230027China
| | - Chi Xu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdong518060China
| | - Chenjiang You
- Department of Botany and Plant Sciences, Institute for Integrative Genome BiologyUniversity of CaliforniaRiversideCA92521USA
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life SciencesFudan UniversityShanghai200438China
| | - Beixin Mo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdong518060China
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute for Integrative Genome BiologyUniversity of CaliforniaRiversideCA92521USA
| | - Lei Gao
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdong518060China
| | - Lin Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdong518060China
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Wang M, Wang J. Non-coding RNA expression analysis revealed the molecular mechanism of flag leaf heterosis in inter-subspecific hybrid rice. FRONTIERS IN PLANT SCIENCE 2022; 13:990656. [PMID: 36226282 PMCID: PMC9549252 DOI: 10.3389/fpls.2022.990656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 08/31/2022] [Indexed: 06/16/2023]
Abstract
Heterosis has been used widespread in agriculture, but its molecular mechanism is inadequately understood. Plants have a large number of non-coding RNAs (ncRNAs), among them, functional ncRNAs that have been studied widely containing long non-coding RNA (lncRNA) and circular RNA (circRNA) that play a role in varied biological processes, as well as microRNA (miRNA), which can not only regulate the post-transcriptional expression of target genes, but also target lncRNA and circRNA then participate the competing endogenous RNA (ceRNA) regulatory network. However, the influence of these three ncRNAs and their regulatory relationships on heterosis is unknown in rice. In this study, the expression profile of ncRNAs and the ncRNA regulatory network related to heterosis were comprehensively analyzed in inter-subspecific hybrid rice. A total of 867 miRNAs, 3,278 lncRNAs and 2,521 circRNAs were identified in the hybrid and its parents. Analysis of the global profiles of these three types of ncRNAs indicated that significant differences existed in the distribution and sequence characteristics of the corresponding genes. The numbers of miRNA and lncRNA in hybrid were higher than those in its parents. A total of 784 ncRNAs (169 miRNAs, 573 lncRNAs and 42 circRNAs) showed differentially expressed in the hybrid, and their target/host genes were vital in stress tolerance, growth and development in rice. These discoveries suggested that the expression plasticity of ncRNA has an important role of inter-subspecific hybrid rice heterosis. It is worth mentioning that miRNAs exhibited substantially more variations between hybrid and parents compared with observed variation for lncRNA and circRNA. Non-additive expression ncRNAs and allele-specific expression genes-related ncRNAs in hybrid were provided in this study, and multiple sets of ncRNA regulatory networks closely related to heterosis were obtained. Meanwhile, heterosis-related regulatory networks of ceRNA (lncRNA and circRNA) and miRNA were also demonstrated.
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Sun M, Shen Y, Chen Y, Wang Y, Cai X, Yang J, Jia B, Dong W, Chen X, Sun X. Osa-miR1320 targets the ERF transcription factor OsERF096 to regulate cold tolerance via JA-mediated signaling. PLANT PHYSIOLOGY 2022; 189:2500-2516. [PMID: 35522026 PMCID: PMC9342977 DOI: 10.1093/plphys/kiac208] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/09/2022] [Indexed: 05/08/2023]
Abstract
MicroRNAs play key roles in abiotic stress response. Rice (Oryza sativa L.) miR1320 is a species-specific miRNA that contributes to miR168-regulated immunity. However, it is still unknown whether miR1320 is involved in rice response to abiotic stress. In this study, we illustrated that the miR1320 precursor generated two mature miR1320s, miR1320-3p, and miR1320-5p, and they both displayed decreased expression under cold stress. Genetic evidence showed that miR1320 overexpression resulted in increased cold tolerance, while miR1320 knock down (KD) reduced cold tolerance. Furthermore, an APETALA2/ethylene-responsive factor (ERF) transcription factor OsERF096 was identified as a target of miR1320 via 5'-RACE and dual luciferase assays. OsERF096 expression was altered by miR1320 overexpression and KD and exhibited an opposite pattern to that of miR1320 in different tissues and under cold stress. Consistently, OsERF096 negatively regulated cold stress tolerance. Furthermore, we suggested that OsERF096 could bind to the GCC and DRE cis-elements and act as a transcriptional activator in the nucleus. Based on RNA-sequencing and targeted metabolomics assays, we found that OsERF096 modified hormone content and signaling pathways. Finally, phenotypic and reverse transcription-quantitative PCR assays showed that jasmonic acid (JA) methyl ester application recovered the cold-sensitive phenotype and JA-activated expression of three Dehydration Responsive Element Binding genes in the OsERF096-OE line. Taken together, our results strongly suggest that the miR1320-OsERF096 module regulates cold tolerance by repressing the JA-mediated cold signaling pathway.
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Affiliation(s)
| | | | | | - Yan Wang
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Xiaoxi Cai
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Junkai Yang
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Bowei Jia
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Weifeng Dong
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Xi Chen
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Xiaoli Sun
- Authors for correspondence: (X.S.), (M.S.)
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Iwamoto M. In-frame editing of transcription factor gene RDD1 to suppress miR166 recognition influences nutrient uptake, photosynthesis, and grain quality in rice. Sci Rep 2022; 12:10795. [PMID: 35750704 PMCID: PMC9232572 DOI: 10.1038/s41598-022-14768-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 06/13/2022] [Indexed: 11/09/2022] Open
Abstract
The transcription factor-encoding gene RDD1 increases the uptake of nutrient ions, photosynthetic activity under ambient and high CO2 conditions, and grain productivity, and microRNA166 (miR166) regulates its transcript levels. This study found that CRISPR/Cas9 genome editing of rice plants to inhibit miR166-RDD1 transcript pairing (R1-Cas plants) increased RDD1 transcript levels, NH4+ and PO43- uptake, and photosynthetic activity under high CO2 conditions in rice. However, the panicle weight of the R1-Cas plants decreased compared with the wild-type (WT) plants. Adversely, changes in environmental conditions, such as high CO2 or high temperatures, showed insignificant differences in the panicle weight between the WT and R1-Cas plants despite a largely increased panicle weight observed in the transgenic RDD1-overexpressing plants. Moreover, both the R1-Cas and transgenic RDD1-overexpressing plants that were matured in a growth chamber demonstrated an improved grain appearance quality or a decrease in the number of chalky grains compared with the WT plants. These results suggest that the in-frame mutagenesis of RDD1 to suppress miR166-RDD1 transcript pairing contributes to the improved grain appearance of rice.
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Affiliation(s)
- Masao Iwamoto
- Division of Crop Genome Editing, Institute of Agrobiological Sciences, NARO, Tsukuba Ibaraki, 305-8604, Japan.
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45
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Zhao Y, Zhu X, Chen X, Zhou JM. From plant immunity to crop disease resistance. J Genet Genomics 2022; 49:693-703. [PMID: 35728759 DOI: 10.1016/j.jgg.2022.06.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/07/2022] [Accepted: 06/08/2022] [Indexed: 11/28/2022]
Abstract
Plant diseases caused by diverse pathogens lead to serious reduction in crop yield and threaten food security worldwide. Genetic improvement of plant immunity is considered as the most effective and sustainable approach to control crop diseases. In the last decade, our understanding of plant immunity at both molecular and genomic levels has improved greatly. Combined with advances in biotechnologies, particularly CRISPR/Cas9-based genome editing, we can now rapidly identify new resistance genes and engineer disease resistance crop plants like never before. In this review, we summarize the current knowledge of plant immunity and outline existing and new strategies for disease resistance improvement in crop plants. We also discuss existing challenges in this field and suggest directions for future studies.
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Affiliation(s)
- Yan Zhao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaobo Zhu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Wenjiang, Chengdu Sichuan 611130, China
| | - Xuewei Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Wenjiang, Chengdu Sichuan 611130, China.
| | - Jian-Min Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China; Hainan Yazhou Bay Seed Laboratory, Sanya, Hainai 572025, China.
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Sheng M, Ma X, Wang J, Xue T, Li Z, Cao Y, Yu X, Zhang X, Wang Y, Xu W, Su Z. KNOX II transcription factor HOS59 functions in regulating rice grain size. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:863-880. [PMID: 35167131 DOI: 10.1111/tpj.15709] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 01/30/2022] [Accepted: 02/10/2022] [Indexed: 06/14/2023]
Abstract
Plant Knotted1-like homeobox (KNOX) genes encode homeodomain-containing transcription factors. In rice (Oryza sativa L.), little is known about the downstream target genes of KNOX Class II subfamily proteins. Here we generated chromatin immunoprecipitation (ChIP)-sequencing datasets for HOS59, a member of the rice KNOX Class II subfamily, and characterized the genome-wide binding sites of HOS59. We conducted trait ontology (TO) analysis of 9705 identified downstream target genes, and found that multiple TO terms are related to plant structure morphology and stress traits. ChIP-quantitative PCR (qPCR) was conducted to validate some key target genes. Meanwhile, our IP-MS datasets showed that HOS59 was closely associated with BELL family proteins, some grain size regulators (OsSPL13, OsSPL16, OsSPL18, SLG, etc.), and some epigenetic modification factors such as OsAGO4α and OsAGO4β, proteins involved in small interfering RNA-mediated gene silencing. Furthermore, we employed CRISPR/Cas9 editing and transgenic approaches to generate hos59 mutants and overexpression lines, respectively. Compared with wild-type plants, the hos59 mutants have longer grains and increased glume cell length, a loose plant architecture, and drooping leaves, while the overexpression lines showed smaller grain size, erect leaves, and lower plant height. The qRT-PCR results showed that mutation of the HOS59 gene led to upregulation of some grain size-related genes such as OsSPL13, OsSPL18, and PGL2. In summary, our results indicate that HOS59 may be a repressor of the downstream target genes, negatively regulating glume cell length, rice grain size, plant architecture, etc. The identified downstream target genes and possible interaction proteins of HOS59 improve our understanding of the KNOX regulatory networks.
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Affiliation(s)
- Minghao Sheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xuelian Ma
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jiyao Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tianxi Xue
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Zhongqiu Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yaxin Cao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xinyue Yu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xinyi Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yonghong Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wenying Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Zhen Su
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
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Zhang L, Huang Y, Zheng Y, Liu X, Zhou S, Yang X, Liu S, Li Y, Li J, Zhao S, Wang H, Ji Y, Zhang J, Pu M, Zhao Z, Fan J, Wang W. Osa-miR535 targets SQUAMOSA promoter binding protein-like 4 to regulate blast disease resistance in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:166-178. [PMID: 34997660 PMCID: PMC9305248 DOI: 10.1111/tpj.15663] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 01/02/2022] [Indexed: 06/14/2023]
Abstract
Many rice microRNAs have been identified as fine-tuning factors in the regulation of agronomic traits and immunity. Among them, Osa-miR535 targets SQUAMOSA promoter binding protein-like 14 (OsSPL14) to positively regulate tillers but negatively regulate yield and immunity. Here, we uncovered that Osa-miR535 targets another SPL gene, OsSPL4, to suppress rice immunity against Magnaporthe oryzae. Overexpression of Osa-miR535 significantly decreased the accumulation of the fusion protein SPL4TBS -YFP that contains the target site of Osa-miR535 in OsSPL4. Consistently, Osa-miR535 mediated the cleavage of OsSPL4 mRNA between the 10th and 11th base pair of the predicted binding site at the 3' untranslated region. Transgenic rice lines overexpressing OsSPL4 (OXSPL4) displayed enhanced blast disease resistance accompanied by enhanced immune responses, including increased expression of defense-relative genes and up-accumulated H2 O2 . By contrast, the knockout mutant osspl4 exhibited susceptibility. Moreover, OsSPL4 binds to the promoter of GH3.2, an indole-3-acetic acid-amido synthetase, and promotes its expression. Together, these data indicate that Os-miR535 targets OsSPL4 and OsSPL4-GH3.2, which may parallel the OsSPL14-WRKY45 module in rice blast disease resistance.
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Affiliation(s)
- Ling‐Li Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural University at Wenjiang211 Huimin RoadChengduSichuan611130China
- College of Environmental Science & EngineeringChina West Normal University1 Shida RoadNanchongSichuan637002China
| | - Yan‐Yan Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural University at Wenjiang211 Huimin RoadChengduSichuan611130China
| | - Ya‐Ping Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural University at Wenjiang211 Huimin RoadChengduSichuan611130China
| | - Xin‐Xian Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural University at Wenjiang211 Huimin RoadChengduSichuan611130China
| | - Shi‐Xin Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural University at Wenjiang211 Huimin RoadChengduSichuan611130China
| | - Xue‐Mei Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural University at Wenjiang211 Huimin RoadChengduSichuan611130China
| | - Shou‐Lan Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural University at Wenjiang211 Huimin RoadChengduSichuan611130China
| | - Yan Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural University at Wenjiang211 Huimin RoadChengduSichuan611130China
| | - Jin‐Lu Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural University at Wenjiang211 Huimin RoadChengduSichuan611130China
- Present address:
College of Plant ProtectionYunnan Agricultural University95 Jinhei RoadKunmingYunnan650201China
| | - Sheng‐Li Zhao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural University at Wenjiang211 Huimin RoadChengduSichuan611130China
- Institute of South Subtropical CropsChinese Academy of Tropical Agricultural SciencesZhanjiangGuangdong524013China
| | - He Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural University at Wenjiang211 Huimin RoadChengduSichuan611130China
| | - Yun‐Peng Ji
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural University at Wenjiang211 Huimin RoadChengduSichuan611130China
| | - Ji‐Wei Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural University at Wenjiang211 Huimin RoadChengduSichuan611130China
| | - Mei Pu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural University at Wenjiang211 Huimin RoadChengduSichuan611130China
| | - Zhi‐Xue Zhao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural University at Wenjiang211 Huimin RoadChengduSichuan611130China
| | - Jing Fan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural University at Wenjiang211 Huimin RoadChengduSichuan611130China
| | - Wen‐Ming Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural University at Wenjiang211 Huimin RoadChengduSichuan611130China
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Li Y, Li T, He X, Zhu Y, Feng Q, Yang X, Zhou X, Li G, Ji Y, Zhao J, Zhao Z, Pu M, Zhou S, Zhang J, Huang Y, Fan J, Wang W. Blocking Osa-miR1871 enhances rice resistance against Magnaporthe oryzae and yield. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:646-659. [PMID: 34726307 PMCID: PMC8989506 DOI: 10.1111/pbi.13743] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 07/31/2021] [Accepted: 10/24/2021] [Indexed: 05/04/2023]
Abstract
MicroRNAs (miRNAs) play vital roles in plant development and defence responses against various stresses. Here, we show that blocking miR1871 improves rice resistance against Magnaporthe oryzae and enhances grain yield simultaneously. The transgenic lines overexpressing miR1871 (OX1871) exhibit compromised resistance, suppressed defence responses and reduced panicle number resulting in slightly decreased yield. In contrast, the transgenic lines blocking miR1871 (MIM1871) show improved resistance, enhanced defence responses and significantly increased panicle number leading to enhanced yield per plant. The RNA-seq assay and defence response assays reveal that blocking miR1871 resulted in the enhancement of PAMP-triggered immunity (PTI). Intriguingly, miR1871 suppresses the expression of LOC_Os06g22850, which encodes a microfibrillar-associated protein (MFAP1) locating nearby the cell wall and positively regulating PTI responses. The mutants of MFAP1 resemble the phenotype of OX1871. Conversely, the transgenic lines overexpressing MFAP1 (OXMFAP1) or overexpressing both MFAP1 and miR1871 (OXMFAP1/OX1871) resemble the resistance of MIM1871. The time-course experiment data reveal that the expression of miR1871 and MFAP1 in rice leaves, panicles and basal internode is dynamic during the whole growth period to manipulate the resistance and yield traits. Our results suggest that miR1871 regulates rice yield and immunity via MFAP1, and the miR8171-MFAP1 module could be used in rice breeding to improve both immunity and yield.
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Affiliation(s)
- Yan Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Ting‐Ting Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Xiao‐Rong He
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Yong Zhu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Qin Feng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Xue‐Mei Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Xin‐Hui Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Guo‐Bang Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Yun‐Peng Ji
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Jing‐Hao Zhao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Zhi‐Xue Zhao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Mei Pu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Shi‐Xin Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Ji‐Wei Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Yan‐Yan Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Jing Fan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Wen‐Ming Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
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49
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Han H, Wang Y, Zheng T, Peng Q, Qiu L, Hu X, Lin H, Xi D. NtAGO1 positively regulates the generation and viral resistance of dark green islands in Nicotiana tabacum. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 174:1-10. [PMID: 35121480 DOI: 10.1016/j.plaphy.2022.01.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 01/20/2022] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
Dark green islands (DGIs) are the outcome of post-transcriptional gene silencing (PTGS) in antiviral immunity, but their characteristics related to PTGS remain largely unknown. In this study, the cucumber mosaic virus (CMV) was inoculated on Nicotiana tabacum plants to explore the PTGS features of DGIs. Our results showed that higher expressions of PTGS-associated genes, especially NtAGO1, present in DGIs. To investigate the role of NtAGO1 in the generation and the antiviral effect of DGIs, NtAGO1 was then over-expressed or knocked out in N. tabacum plants through agrobacterium-mediated genetic transformation. The results showed that more DGIs with larger areas appeared on NtAGO1 over-expressed plants, accompanied by less virus accumulation, less reactive oxygen species production, and seldom membrane damage, whereas fewer DGIs appeared on NtAGO1 knockout plants with more damage on infected plants. In addition, the NtAGO1-participated antiviral process could promote the transduction of the salicylic acid-mediated defense pathway. Taken together, our results indicate that DGIs are maintained by a stronger PTGS mechanism, and NtAGO1 positively regulates the generation and viral resistance of DGIs in N. tabacum.
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Affiliation(s)
- Hongyan Han
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Yunru Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Tianrui Zheng
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Qiding Peng
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Long Qiu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Xinyue Hu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Honghui Lin
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Dehui Xi
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China.
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50
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Dong Q, Hu B, Zhang C. microRNAs and Their Roles in Plant Development. FRONTIERS IN PLANT SCIENCE 2022; 13:824240. [PMID: 35251094 PMCID: PMC8895298 DOI: 10.3389/fpls.2022.824240] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/27/2022] [Indexed: 05/26/2023]
Abstract
Small RNAs are short non-coding RNAs with a length ranging between 20 and 24 nucleotides. Of these, microRNAs (miRNAs) play a distinct role in plant development. miRNAs control target gene expression at the post-transcriptional level, either through direct cleavage or inhibition of translation. miRNAs participate in nearly all the developmental processes in plants, such as juvenile-to-adult transition, shoot apical meristem development, leaf morphogenesis, floral organ formation, and flowering time determination. This review summarizes the research progress in miRNA-mediated gene regulation and its role in plant development, to provide the basis for further in-depth exploration regarding the function of miRNAs and the elucidation of the molecular mechanism underlying the interaction of miRNAs and other pathways.
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Affiliation(s)
- Qingkun Dong
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Binbin Hu
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Cui Zhang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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