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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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Srikakulam N, Guria A, Karanthamalai J, Murugesan V, Krishnan V, Sundaramoorthy K, Saha S, Singh R, Victorathisayam T, Rajapriya V, Sridevi G, Pandi G. An Insight Into Pentatricopeptide-Mediated Chloroplast Necrosis via microRNA395a During Rhizoctonia solani Infection. Front Genet 2022; 13:869465. [PMID: 35706449 PMCID: PMC9189367 DOI: 10.3389/fgene.2022.869465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
Sheath blight (ShB) disease, caused by Rhizoctonia solani, is one of the major biotic stress-oriented diseases that adversely affect the rice productivity worldwide. However, the regulatory mechanisms are not understood yet comprehensively. In the current study, we had investigated the potential roles of miRNAs in economically important indica rice variety Pusa Basmati-1 upon R. solani infection by carrying out in-depth, high-throughput small RNA sequencing with a total data size of 435 million paired-end raw reads from rice leaf RNA samples collected at different time points. Detailed data analysis revealed a total of 468 known mature miRNAs and 747 putative novel miRNAs across all the libraries. Target prediction and Gene Ontology functional analysis of these miRNAs were found to be unraveling various cellular, molecular, and biological functions by targeting various plant defense-related genes. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) was performed to validate the miRNAs and their putative target genes. Out of the selected miRNA-specific putative target genes, miR395a binding and its cleavage site on pentatricopeptide were determined by 5’ RACE-PCR. It might be possible that R. solani instigated chloroplast degradation by modulating the pentatricopeptide which led to increased susceptibility to fungal infection.
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Campo S, Sánchez‐Sanuy F, Camargo‐Ramírez R, Gómez‐Ariza J, Baldrich P, Campos‐Soriano L, Soto‐Suárez M, San Segundo B. A novel Transposable element-derived microRNA participates in plant immunity to rice blast disease. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1798-1811. [PMID: 33780108 PMCID: PMC8428829 DOI: 10.1111/pbi.13592] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 02/15/2021] [Accepted: 03/02/2021] [Indexed: 05/04/2023]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that direct post-transcriptional gene silencing in plant development and stress responses through cleavage or translational repression of target mRNAs. Here, we report the identification and functional characterization of a new member of the miR812 family in rice (named as miR812w) involved in disease resistance. miR812w is present in cultivated Oryza species, both japonica and indica subspecies, and wild rice species within the Oryza genus, but not in dicotyledonous species. miR812w is a 24nt-long that requires DCL3 for its biogenesis and is loaded into AGO4 proteins. Whereas overexpression of miR812w increased resistance to infection by the rice blast fungus Magnaporthe oryzae, CRISPR/Cas9-mediated MIR812w editing enhances disease susceptibility, supporting that miR812w plays a role in blast resistance. We show that miR812w derives from the Stowaway type of rice MITEs (Miniature Inverted-Repeat Transposable Elements). Moreover, miR812w directs DNA methylation in trans at target genes that have integrated a Stowaway MITE copy into their 3' or 5' untranslated region (ACO3, CIPK10, LRR genes), as well as in cis at the MIR812w locus. The target genes of miR812 were found to be hypo-methylated around the miR812 recognition site, their expression being up-regulated in transgene-free CRISPR/Cas9-edited miR812 plants. These findings further support that, in addition to post-transcriptional regulation of gene expression, miRNAs can exert their regulatory function at the transcriptional level. This relationship between miR812w and Stowaway MITEs integrated into multiple coding genes might eventually create a network for miR812w-mediated regulation of gene expression with implications in rice immunity.
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Affiliation(s)
- Sonia Campo
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés)C/ de la Vall Moronta, CRAG BuildingBarcelona08193Spain
| | - Ferran Sánchez‐Sanuy
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés)C/ de la Vall Moronta, CRAG BuildingBarcelona08193Spain
| | - Rosany Camargo‐Ramírez
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés)C/ de la Vall Moronta, CRAG BuildingBarcelona08193Spain
| | - Jorge Gómez‐Ariza
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés)C/ de la Vall Moronta, CRAG BuildingBarcelona08193Spain
| | - Patricia Baldrich
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés)C/ de la Vall Moronta, CRAG BuildingBarcelona08193Spain
- Present address:
Donald Danforth Plant Science Center975 N Warson RoadSt. LouisMO63132USA
| | - Lidia Campos‐Soriano
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés)C/ de la Vall Moronta, CRAG BuildingBarcelona08193Spain
| | - Mauricio Soto‐Suárez
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés)C/ de la Vall Moronta, CRAG BuildingBarcelona08193Spain
- Present address:
Corporación Colombiana de Investigación Agropecuaria. AGROSAVIAKm 14 vía Mosquera‐BogotáMosquera250047Colombia
| | - Blanca San Segundo
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés)C/ de la Vall Moronta, CRAG BuildingBarcelona08193Spain
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Chen JF, Zhao ZX, Li Y, Li TT, Zhu Y, Yang XM, Zhou SX, Wang H, Zhao JQ, Pu M, Feng H, Fan J, Zhang JW, Huang YY, Wang WM. Fine-Tuning Roles of Osa-miR159a in Rice Immunity Against Magnaporthe oryzae and Development. RICE (NEW YORK, N.Y.) 2021; 14:26. [PMID: 33677712 PMCID: PMC7937009 DOI: 10.1186/s12284-021-00469-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 02/24/2021] [Indexed: 05/04/2023]
Abstract
BACKGROUND Rice blast caused by Magnaporthe oryzae is one of the most destructive diseases of rice. An increasing number of microRNAs (miRNAs) have been reported to fine-tune rice immunity against M. oryzae and coordinate with growth and development. RESULTS Here, we showed that rice microRNA159a (Osa-miR159a) played a positive role in rice resistance to M. oryzae. The expression of Osa-miR159a was suppressed in a susceptible accession at 12, 24, and 48 h post-inoculation (hpi); it was upregulated in a resistant accession of M. oryzae at 24 hpi. The transgenic rice lines overexpressing Osa-miR159a were highly resistant to M. oryzae. In contrast, the transgenic lines expressing a short tandem target mimic (STTM) to block Osa-miR159a showed enhanced susceptibility. Knockout mutations of the target genes of Osa-miR159a, including OsGAMYB, OsGAMYBL, and OsZF, led to resistance to M. oryzae. Alteration of the expression of Osa-miR159a impacted yield traits including pollen and grain development. CONCLUSIONS Our results indicated that Osa-miR159a positively regulated rice immunity against M. oryzae by downregulating its target genes. Proper expression of Osa-miR159a was critical for coordinating rice blast resistance with grain development.
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Affiliation(s)
- Jin-Feng Chen
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhi-Xue Zhao
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yan Li
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ting-Ting Li
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yong Zhu
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xue-Mei Yang
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shi-Xin Zhou
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University, Chengdu, 611130, China
| | - He Wang
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ji-Qun Zhao
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University, Chengdu, 611130, China
| | - Mei Pu
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hui Feng
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jing Fan
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ji-Wei Zhang
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yan-Yan Huang
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wen-Ming Wang
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University, Chengdu, 611130, China.
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Arora K, Rai AK, Devanna BN, Dubey H, Narula A, Sharma TR. Deciphering the role of microRNAs during Pi54 gene mediated Magnaporthe oryzae resistance response in rice. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:633-647. [PMID: 33854289 PMCID: PMC7981355 DOI: 10.1007/s12298-021-00960-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/14/2021] [Accepted: 02/15/2021] [Indexed: 05/08/2023]
Abstract
The broad-spectrum resistance gene Pi54 confers resistance to multiple isolates of Magnaporthe oryzae in rice. In order to decipher the molecular mechanism underlying the Pi54 mediated resistance in rice line Taipei309 Pi54 (carrying Pi54), miRNAome study was performed at 24 h post-inoculation (hpi) with M. oryzae. A total of 222 known miRNAs representing 101 miRNA families were found in this study. Of these, 29 and 24 miRNAs were respectively up- and down-regulated in the resistant Taipei309 Pi54 . Defence response (DR) genes, like, NBSGO35, and OsWAK129b, and genes related to transcription factors were up-regulated in Taipei309 Pi54 line. The vast array of miRNA candidates identified here are miR159c, miR167c, miR2100, miR2118o, miR2118l, miR319a, miR393, miR395l, miR397a, miR397b, miR398, miR439g, miR531b, miR812f, and miR815c, and they manifest their role in balancing the interplay between various DR genes during Pi54 mediated resistance. We also validated miRNA/target gene pairs involved in hormone signalling, and cross-talk among hormone pathways regulating the rice immunity. This study suggests that the Pi54 gene mediated blast resistance is influenced by several microRNAs through PTI and ETI components in the rice line Taipei309 Pi54 , leading to incompatible host-pathogen interaction.
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Affiliation(s)
- Kirti Arora
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
- Department of Biotechnology, Jamia Hamdard, New Delhi, 110062 India
| | - Amit Kumar Rai
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
| | - B. N. Devanna
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
- ICAR-National Rice Research Institute, Cuttack, 753006 India
| | - Himanshu Dubey
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
| | - Alka Narula
- Department of Biotechnology, Jamia Hamdard, New Delhi, 110062 India
| | - Tilak Raj Sharma
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
- Division of Crop Science, Indian Council of Agricultural Research, Krishi Bhavan, New Delhi, 110 001 India
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A Comprehensive Analysis of MicroRNAs Expressed in Susceptible and Resistant Rice Cultivars during Rhizoctonia solani AG1-IA Infection Causing Sheath Blight Disease. Int J Mol Sci 2020; 21:ijms21217974. [PMID: 33120987 PMCID: PMC7662745 DOI: 10.3390/ijms21217974] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/08/2020] [Accepted: 10/08/2020] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs regulate plant responses to fungal infections and immunity. In this study, miRNAs were identified in six rice cultivars during a Rhizoctonia solani Kühn AG1-IA infection using a deep sequencing approach. Known and novel miRNAs were analyzed in these rice cultivars, and a set of fungal infection/immunity-associated miRNAs and target genes were quantified by reverse transcription (RT)-qPCR in six rice cultivars. Additionally, the relative expression of these miRNAs was analyzed in different time points of the infection, wild species of rice, and in response to different strains of R. solani. Osa-miR1320-5p showed preferential expression during the fungal infection in all the six rice genotypes, while Osa-miR156d, Osa-miR159b, Osa-miR820c, and Osa-miR1876 were differentially regulated in susceptible and resistant genotypes. A greater degree of downregulation of miRNAs was observed during the initial time points of infection (24-72 h), suggesting a maximum molecular activity of rice-R. solani interaction and resistance response of the host during the early phase of infection. After R. solani infection, the expression of Osa-miR820c and Osa-miR156d was downregulated in Oryza rufipogon, O. alta, O. latifolia, and O. minuta, while Osa-miR397b was downregulated in all the wild rice species except O. officinalis. This study provided comprehensive information on the repertoire of miRNAs expressed in six sheath blight disease-susceptible and resistant indica and aus rice cultivars.
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Campos‐Soriano L, Bundó M, Bach‐Pages M, Chiang S, Chiou T, San Segundo B. Phosphate excess increases susceptibility to pathogen infection in rice. MOLECULAR PLANT PATHOLOGY 2020; 21:555-570. [PMID: 32072745 PMCID: PMC7060143 DOI: 10.1111/mpp.12916] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 12/18/2019] [Accepted: 01/10/2020] [Indexed: 05/08/2023]
Abstract
Phosphorus (P) is an essential nutrient for plant growth and productivity. Due to soil fixation, however, phosphorus availability in soil is rarely sufficient to sustain high crop yields. The overuse of fertilizers to circumvent the limited bioavailability of phosphate (Pi) has led to a scenario of excessive soil P in agricultural soils. Whereas adaptive responses to Pi deficiency have been deeply studied, less is known about how plants adapt to Pi excess and how Pi excess might affect disease resistance. We show that high Pi fertilization, and subsequent Pi accumulation, enhances susceptibility to infection by the fungal pathogen Magnaporthe oryzae in rice. This fungus is the causal agent of the blast disease, one of the most damaging diseases of cultivated rice worldwide. Equally, MIR399f overexpression causes an increase in Pi content in rice leaves, which results in enhanced susceptibility to M. oryzae. During pathogen infection, a weaker activation of defence-related genes occurs in rice plants over-accumulating Pi in leaves, which is in agreement with the phenotype of blast susceptibility observed in these plants. These data support that Pi, when in excess, compromises defence mechanisms in rice while demonstrating that miR399 functions as a negative regulator of rice immunity. The two signalling pathways, Pi signalling and defence signalling, must operate in a coordinated manner in controlling disease resistance. This information provides a basis to understand the molecular mechanisms involved in immunity in rice plants under high Pi fertilization, an aspect that should be considered in management of the rice blast disease.
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Affiliation(s)
- Lidia Campos‐Soriano
- Centre for Research in Agricultural GenomicsCSIC‐IRTA‐UAB‐UBUniversitat Autònoma de BarcelonaBellaterra (Cerdanyola del Vallés)BarcelonaSpain
| | - Mireia Bundó
- Centre for Research in Agricultural GenomicsCSIC‐IRTA‐UAB‐UBUniversitat Autònoma de BarcelonaBellaterra (Cerdanyola del Vallés)BarcelonaSpain
| | - Marcel Bach‐Pages
- Centre for Research in Agricultural GenomicsCSIC‐IRTA‐UAB‐UBUniversitat Autònoma de BarcelonaBellaterra (Cerdanyola del Vallés)BarcelonaSpain
- Present address:
Department of Plant SciencesUniversity of OxfordOxfordUK
| | - Su‐Fen Chiang
- Agricultural Biotechnology Research CenterAcademia SinicaTaipeiTaiwan
| | - Tzyy‐Jen Chiou
- Agricultural Biotechnology Research CenterAcademia SinicaTaipeiTaiwan
| | - Blanca San Segundo
- Centre for Research in Agricultural GenomicsCSIC‐IRTA‐UAB‐UBUniversitat Autònoma de BarcelonaBellaterra (Cerdanyola del Vallés)BarcelonaSpain
- Consejo Superior de Investigaciones CientíficasBarcelonaSpain
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Fan J, Quan W, Li GB, Hu XH, Wang Q, Wang H, Li XP, Luo X, Feng Q, Hu ZJ, Feng H, Pu M, Zhao JQ, Huang YY, Li Y, Zhang Y, Wang WM. circRNAs Are Involved in the Rice- Magnaporthe oryzae Interaction. PLANT PHYSIOLOGY 2020; 182:272-286. [PMID: 31628150 PMCID: PMC6945833 DOI: 10.1104/pp.19.00716] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 10/07/2019] [Indexed: 05/03/2023]
Abstract
Circular RNAs (circRNAs) play roles in various biological processes, but their functions in the rice (Oryza sativa) response to Magnaporthe oryzae remain elusive. Here, we demonstrate that circRNAs are involved in the rice-M. oryzae interaction using comparative circRNA-sequencing and transgenic approaches. We identified 2932 high-confidence circRNAs from young leaves of the blast-resistant accession International Rice Blast Line Pyricularia-Kanto51-m-Tsuyuake (IR25) and the blast-susceptible accession Lijiangxin Tuan Heigu (LTH) under M oryzae-infected or uninfected conditions; 636 were detected specifically upon M oryzae infection. The circRNAs in IR25 were significantly more diverse than those in LTH, especially under M. oryzae infection. Particularly, the number of circRNAs generated per parent gene was much higher in IR25 than in LTH and increased in IR25 but decreased in LTH upon M. oryzae infection. The higher diversity of circRNAs in IR25 was further associated with more frequent 3' and 5' alternative back-splicing and usage of complex splice sites. Moreover, a subset of circRNAs was differentially responsive to M oryzae in IR25 and LTH. We further confirmed that circR5g05160 promotes rice immunity against M oryzae Therefore, our data indicate that circRNA diversity is associated with different responses to M oryzae infection in rice and provide a starting point to investigate a new layer of regulation in the rice-M oryzae interaction.
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Affiliation(s)
- Jing Fan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Weili Quan
- Center for Genome Analysis, ABLife Inc., Wuhan 430075, Hubei, China
| | - Guo-Bang Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Xiao-Hong Hu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Qi Wang
- Center for Genome Analysis, ABLife Inc., Wuhan 430075, Hubei, China
| | - He Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Xu-Pu Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Xiaotian Luo
- Laboratory for Genome Regulation and Human Health, ABLife Inc., Wuhan 430075, Hubei, China
| | - Qin Feng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Zi-Jin Hu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Hui Feng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Mei Pu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Ji-Qun Zhao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Yan-Yan Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Yan Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Yi Zhang
- Center for Genome Analysis, ABLife Inc., Wuhan 430075, Hubei, China
| | - Wen-Ming Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
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9
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Sánchez-Sanuy F, Peris-Peris C, Tomiyama S, Okada K, Hsing YI, San Segundo B, Campo S. Osa-miR7695 enhances transcriptional priming in defense responses against the rice blast fungus. BMC PLANT BIOLOGY 2019; 19:563. [PMID: 31852430 PMCID: PMC6921540 DOI: 10.1186/s12870-019-2156-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 11/21/2019] [Indexed: 05/14/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression at the post-transcriptional level in eukaryotes. In rice, MIR7695 expression is regulated by infection with the rice blast fungus Magnaporthe oryzae with subsequent down-regulation of an alternatively spliced transcript of natural resistance-associated macrophage protein 6 (OsNramp6). NRAMP6 functions as an iron transporter in rice. RESULTS Rice plants grown under high iron supply showed blast resistance, which supports that iron is a factor in controlling blast resistance. During pathogen infection, iron accumulated in the vicinity of M. oryzae appressoria, the sites of pathogen entry, and in cells surrounding infected regions of the rice leaf. Activation-tagged MIR7695 rice plants (MIR7695-Ac) exhibited enhanced iron accumulation and resistance to M. oryzae infection. RNA-seq analysis revealed that blast resistance in MIR7695-Ac plants was associated with strong induction of defense-related genes, including pathogenesis-related and diterpenoid biosynthetic genes. Levels of phytoalexins during pathogen infection were higher in MIR7695-Ac than wild-type plants. Early phytoalexin biosynthetic genes, OsCPS2 and OsCPS4, were also highly upregulated in wild-type rice plants grown under high iron supply. CONCLUSIONS Our data support a positive role of miR7695 in regulating rice immunity that further underpin links between defense and iron signaling in rice. These findings provides a basis to better understand regulatory mechanisms involved in rice immunity in which miR7695 participates which has a great potential for the development of strategies to improve blast resistance in rice.
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Affiliation(s)
- Ferran Sánchez-Sanuy
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), Barcelona, Spain
| | - Cristina Peris-Peris
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), Barcelona, Spain
| | - Shiho Tomiyama
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
| | - Kazunori Okada
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
| | - Yue-Ie Hsing
- Institute of Plant and Microrbial Biology, Academia Sinica, Taipei, Taiwan
| | - Blanca San Segundo
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), Barcelona, Spain
- Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Sonia Campo
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), Barcelona, Spain
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10
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Deciphering signalling network in broad spectrum Near Isogenic Lines of rice resistant to Magnaporthe oryzae. Sci Rep 2019; 9:16939. [PMID: 31729398 PMCID: PMC6858299 DOI: 10.1038/s41598-019-50990-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 08/27/2019] [Indexed: 01/21/2023] Open
Abstract
Disease resistance (R) genes like Pi9, Pita, Pi21, Pi54 are playing important role for broad spectrum blast resistance in rice. Development of near isogenic lines (NILs) using these type of broad spectrum genes and understanding their signalling networks is essential to cope up with highly evolving Magnaporthe oryzae strains for longer duration. Here, transcriptional-level changes were studied in three near-isogenic lines (PB1 + Pi1, PB1 + Pi9 and PB1 + Pi54) of rice resistant to blast infection, to find the loci that are unique to resistant lines developed in the background of Pusa Basmati 1 (PB1). The pathway analysis of loci, unique to resistant NILs compared to susceptible control revealed that plant secondary metabolite synthesis was the common mechanism among all NILs to counter against M. oryzae infection. Comparative transcriptome analysis helped to find out common clusters of co-expressed significant differentially expressed loci (SDEL) in both PB1 + Pi9 and PB1 + Pi54 NILs. SDELs from these clusters were involved in the synthesis and degradation of starch; synthesis and elongation of fatty acids; hydrolysis of phospholipids; synthesis of phenylpropanoid; and metabolism of ethylene and jasmonic acid. Through detailed analysis of loci specific to each resistant NIL, we identified a network of signalling pathways mediated by each blast resistance gene. The study also offers insights into transcriptomic dynamics, points to a set of important candidate genes that serve as module to regulate the changes in resistant NILs. We suggest that pyramiding of the blast resistance gene Pi9 with Pi54 will lead to maximum broad spectrum resistance to M. oryzae.
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Gabriel AF, Costa MC, Enguita FJ, Leitão AL. Si vis pacem para bellum: A prospective in silico analysis of miRNA-based plant defenses against fungal infections. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 288:110241. [PMID: 31521215 DOI: 10.1016/j.plantsci.2019.110241] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 07/31/2019] [Accepted: 08/25/2019] [Indexed: 06/10/2023]
Abstract
Fungal pathogens are an important threat for plant crops, being responsible for important reductions of production yields and a consequent economic impact. Among the molecular mediators of fungal infections of plant crops, non-coding RNAs (ncRNAs) have been described as relevant players either in the plant immune responses and mechanism of defense or in the colonization of plant tissues by fungi. Acting as a mechanism of defense, some plant small ncRNAs such as miRNAs and tasiRNAs can be secreted by cells and directed to target the transcriptome of pathogenic fungi, triggering an RNAi-like interference mechanism able to silence the expression of specific fungal genes. The detailed knowledge of this mechanism of defense against fungal pathogens could open new possibilities for the protection of human important crops. To infer putative functional relationships mediated by ncRNA communication, we performed a prospective analysis to determine potential plant miRNAs able to target the genome of fungal pathogens, which resulted in the description of enriched specific plant miRNA families and their putative fungal targets that could be further studied in the context of plant-fungi interactions. The expression profile of specific members of the enriched miRNAs families showed an infection-dependent behavior in laboratory models of infection. Plant miRNAs showed sequence complementarity with coding genes of their cognate fungal pathogens. Plant miRNAs could potentially target fungal genes belonging to functional families related to stress response, membrane architecture, vacuolar transport, membrane traffic, and anabolic processes. Families of specific infection-responsive miRNAs are included in the putative plant defense mechanism.
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Affiliation(s)
- André F Gabriel
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisboa, Portugal
| | - Marina C Costa
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisboa, Portugal
| | - Francisco J Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisboa, Portugal.
| | - Ana Lúcia Leitão
- Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516, Caparica, Portugal; MEtRICs, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, Caparica, 2829-516, Portugal.
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12
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Salvador-Guirao R, Baldrich P, Tomiyama S, Hsing YI, Okada K, San Segundo B. OsDCL1a activation impairs phytoalexin biosynthesis and compromises disease resistance in rice. ANNALS OF BOTANY 2019; 123:79-93. [PMID: 30032201 PMCID: PMC6344094 DOI: 10.1093/aob/mcy141] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 06/30/2018] [Indexed: 05/09/2023]
Abstract
BACKGROUND AND AIMS MicroRNAs (miRNAs) are small non-coding RNAs that act as post-transcriptional regulators of gene expression via sequence-specific cleavage or translational repression of target transcripts. They are transcribed as long single-stranded RNA precursors with unique stem-loop structures that are processed by a DICER-Like (DCL) ribonuclease, typically DCL1, to produce mature miRNAs. Although a plethora of miRNAs have been found to be regulated by pathogen infection in plants, the biological function of most miRNAs remains largely unknown. Here, the contribution of OsDCL1 to rice immunity was investigated. METHODS Activation-tagged Osdcl1a (Osdcl1a-Ac) rice mutants were examined for resistance to pathogen infection. mRNA and small RNA deep sequencing, quantitative real-time PCR (RT-qPCR) and stem-loop reverse tanscripion-PCR (RT-PCR) were used to examine DCL1a-mediated alterations in the rice transcriptome. Rice diterpene phytoalexins were quantified by liquid chromatography-tandem mass spectrometry (LC-MSMS). Accumulation of O2·- was determined by nitroblue tetrazolium (NBT) staining. KEY RESULTS dcl1a-Ac mutants exhibit enhanced susceptibility to infection by fungal pathogens which was associated with a weaker induction of defence gene expression. Comparison of the mRNA and miRNA transcriptomes of dcl1a-Ac and wild-type plants revealed misregulation of genes involved in detoxification of reactive oxygen species. Consequently, dcl1a-Ac plants accumulated O2·- in their leaves and were more sensitive to methyl viologen-induced oxidative stress. Furthermore, dcl1a-Ac plants showed downregulation of diterpenoid phytoalexin biosynthetic genes, these genes also being weakly induced during pathogen infection. Upon pathogen challenge, dcl1a-Ac plants failed to accumulate major diterpenoid phytoalexins. OsDCL1a activation resulted in marked alterations in the rice miRNAome, including both upregulation and downregulation of miRNAs. CONCLUSIONS OsDCL1a activation enhances susceptibility to infection by fungal pathogens in rice. Activation of OsDCL1a represses the pathogen-inducible host defence response and negatively regulates diterpenoid phytoalexin production. These findings provide a basis to understand the molecular mechanisms through which OsDCL1a mediates rice immunity.
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Affiliation(s)
- Raquel Salvador-Guirao
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), Barcelona, Spain
| | - Patricia Baldrich
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), Barcelona, Spain
- Donald Danforth Plant Science Center, St Louis, MO, USA
| | - Shiho Tomiyama
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
| | - Yue-Ie Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Kazunori Okada
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
| | - Blanca San Segundo
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), Barcelona, Spain
- Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
- For correspondence. E-mail
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13
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Li WQ, Jia YL, Liu FQ, Wang FQ, Fan FJ, Wang J, Zhu JY, Xu Y, Zhong WG, Yang J. Genome-wide identification and characterization of long non-coding RNAs responsive to Dickeya zeae in rice. RSC Adv 2018; 8:34408-34417. [PMID: 35548658 PMCID: PMC9087051 DOI: 10.1039/c8ra04993a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 09/09/2018] [Indexed: 11/26/2022] Open
Abstract
Plant long non-coding RNA (lncRNA) is a type of newly emerging epigenetic regulator playing a critical role in plant growth, development, and biotic stress responses. However, it is unknown whether lncRNAs are involved in resistance responses between rice and Dickeya zeae, a bacterial agent causing rice foot rot disease. In this study, RNA-seq was performed to uncover the co-expression regulating networks mediated by D. zeae responsive lncRNAs and their candidate target genes. Of the 4709 lncRNAs identified, 2518 and 2191 were up- and down-regulated in response to D. zeae infection, respectively. Expression changes of 17 selected lncRNAs and their predicted targets with a potential role in defense response were investigated by qPCR. The expression levels of five lncRNAs were up-regulated while their cognate candidate target genes were down-regulated upon D. zeae infection. In addition, several lncRNAs were predicted to be target mimics of osa-miR396 and osa-miR156. These results suggest that lncRNAs might play a role in response to D. zeae infection by regulating the transcript levels of their targets and miRNAs in rice.
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Affiliation(s)
- Wen Qi Li
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Branch of Chinese National Center for Rice Improvement, Jiangsu High Quality Rice R&D Center Nanjing 210014 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University Yangzhou 225009 China
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences Nanjing 210014 China
| | - Yu Lin Jia
- United States Department of Agriculture-Agriculture Research Service, Dale Bumpers National Rice Research Center Stuttgart 72160 USA
| | - Feng Quan Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences Nanjing 210014 China
| | - Fang Quan Wang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Branch of Chinese National Center for Rice Improvement, Jiangsu High Quality Rice R&D Center Nanjing 210014 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University Yangzhou 225009 China
| | - Fang Jun Fan
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Branch of Chinese National Center for Rice Improvement, Jiangsu High Quality Rice R&D Center Nanjing 210014 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University Yangzhou 225009 China
| | - Jun Wang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Branch of Chinese National Center for Rice Improvement, Jiangsu High Quality Rice R&D Center Nanjing 210014 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University Yangzhou 225009 China
| | - Jin Yan Zhu
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Branch of Chinese National Center for Rice Improvement, Jiangsu High Quality Rice R&D Center Nanjing 210014 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University Yangzhou 225009 China
| | - Yang Xu
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Branch of Chinese National Center for Rice Improvement, Jiangsu High Quality Rice R&D Center Nanjing 210014 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University Yangzhou 225009 China
| | - Wei Gong Zhong
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Branch of Chinese National Center for Rice Improvement, Jiangsu High Quality Rice R&D Center Nanjing 210014 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University Yangzhou 225009 China
| | - Jie Yang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Branch of Chinese National Center for Rice Improvement, Jiangsu High Quality Rice R&D Center Nanjing 210014 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University Yangzhou 225009 China
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14
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Singh PK, Nag A, Arya P, Kapoor R, Singh A, Jaswal R, Sharma TR. Prospects of Understanding the Molecular Biology of Disease Resistance in Rice. Int J Mol Sci 2018; 19:E1141. [PMID: 29642631 PMCID: PMC5979409 DOI: 10.3390/ijms19041141] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 03/03/2018] [Accepted: 03/05/2018] [Indexed: 12/11/2022] Open
Abstract
Rice is one of the important crops grown worldwide and is considered as an important crop for global food security. Rice is being affected by various fungal, bacterial and viral diseases resulting in huge yield losses every year. Deployment of resistance genes in various crops is one of the important methods of disease management. However, identification, cloning and characterization of disease resistance genes is a very tedious effort. To increase the life span of resistant cultivars, it is important to understand the molecular basis of plant host-pathogen interaction. With the advancement in rice genetics and genomics, several rice varieties resistant to fungal, bacterial and viral pathogens have been developed. However, resistance response of these varieties break down very frequently because of the emergence of more virulent races of the pathogen in nature. To increase the durability of resistance genes under field conditions, understanding the mechanismof resistance response and its molecular basis should be well understood. Some emerging concepts like interspecies transfer of pattern recognition receptors (PRRs) and transgenerational plant immunitycan be employed to develop sustainable broad spectrum resistant varieties of rice.
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Affiliation(s)
- Pankaj Kumar Singh
- National Agri-Food Biotechnology Institute, Mohali 140 306, Punjab, India.
| | - Akshay Nag
- National Agri-Food Biotechnology Institute, Mohali 140 306, Punjab, India.
| | - Preeti Arya
- National Agri-Food Biotechnology Institute, Mohali 140 306, Punjab, India.
| | - Ritu Kapoor
- National Agri-Food Biotechnology Institute, Mohali 140 306, Punjab, India.
| | - Akshay Singh
- National Agri-Food Biotechnology Institute, Mohali 140 306, Punjab, India.
| | - Rajdeep Jaswal
- National Agri-Food Biotechnology Institute, Mohali 140 306, Punjab, India.
| | - Tilak Raj Sharma
- National Agri-Food Biotechnology Institute, Mohali 140 306, Punjab, India.
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15
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Salvador-Guirao R, Hsing YI, San Segundo B. The Polycistronic miR166k-166h Positively Regulates Rice Immunity via Post-transcriptional Control of EIN2. FRONTIERS IN PLANT SCIENCE 2018; 9:337. [PMID: 29616057 PMCID: PMC5869255 DOI: 10.3389/fpls.2018.00337] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 02/28/2018] [Indexed: 05/18/2023]
Abstract
MicroRNAs (miRNAs) are small RNAs acting as regulators of gene expression at the post-transcriptional level. In plants, most miRNAs are generated from independent transcriptional units, and only a few polycistronic miRNAs have been described. miR166 is a conserved miRNA in plants targeting the HD-ZIP III transcription factor genes. Here, we show that a polycistronic miRNA comprising two miR166 family members, miR166k and miR166h, functions as a positive regulator of rice immunity. Rice plants with activated MIR166k-166h expression showed enhanced resistance to infection by the fungal pathogens Magnaporthe oryzae and Fusarium fujikuroi, the causal agents of the rice blast and bakanae disease, respectively. Disease resistance in rice plants with activated MIR166k-166h expression was associated with a stronger expression of defense responses during pathogen infection. Stronger induction of MIR166k-166h expression occurred in resistant but not susceptible rice cultivars. Notably, the ethylene-insensitive 2 (EIN2) gene was identified as a novel target gene for miR166k. The regulatory role of the miR166h-166k polycistron on the newly identified target gene results from the activity of the miR166k-5p specie generated from the miR166k-166h precursor. Collectively, our findings support a role for miR166k-5p in rice immunity by controlling EIN2 expression. Because rice blast is one of the most destructive diseases of cultivated rice worldwide, unraveling miR166k-166h-mediated mechanisms underlying blast resistance could ultimately help in designing appropriate strategies for rice protection.
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Affiliation(s)
- Raquel Salvador-Guirao
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Yue-ie Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Blanca San Segundo
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Barcelona, Spain
- Consejo Superior de Investigaciones Científicas, Barcelona, Spain
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16
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17
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Current understanding of pattern-triggered immunity and hormone-mediated defense in rice (Oryza sativa) in response to Magnaporthe oryzae infection. Semin Cell Dev Biol 2017; 83:95-105. [PMID: 29061483 DOI: 10.1016/j.semcdb.2017.10.020] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 09/21/2017] [Accepted: 10/20/2017] [Indexed: 11/22/2022]
Abstract
Plant pathogens represent a huge threat to world food security, affecting both crop production and quality. Although significant progress has been made in improving plant immunity by expressing key, defense-related genes and proteins from different species in transgenic crops, a challenge remains for molecular breeders and biotechnologists to successfully engineer elite, transgenic crop varieties with improved resistance against critical plant pathogens. Upon pathogen attack, including infection of rice (Oryza sativa) by Magnaporthe oryzae, host plants initiate a complex defense response at molecular, biochemical and physiological levels. Plants perceive the presence of pathogens by detecting microbe-associated molecular patterns via pattern recognition receptors, and initiate a first line of innate immunity, the so-called pattern-triggered immunity (PTI). This results in a series of downstream defense responses, including the production of hormones, which collectively function to fend off pathogen attacks. A variety of studies have demonstrated that many genes are involved in the defense response of rice to M. oryzae. In this review, the current understanding of mechanisms that improve rice defense response to M. oryzae will be discussed, with special focus on PTI and the phytohormones ethylene, jasmonic acid, salicylic acid, and abscisic acid; as well as on the mediation of defense signaling mechanisms by PTI and these hormones. Potential target genes that may serve as promising candidates for improving rice immunity against M. oryzae will also be discussed.
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18
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Wu Y, Lv W, Hu L, Rao W, Zeng Y, Zhu L, He Y, He G. Identification and analysis of brown planthopper-responsive microRNAs in resistant and susceptible rice plants. Sci Rep 2017; 7:8712. [PMID: 28821824 PMCID: PMC5562839 DOI: 10.1038/s41598-017-09143-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 07/20/2017] [Indexed: 11/27/2022] Open
Abstract
The brown planthopper (BPH) is the most devastating insect pest of rice. The rice gene BPH15 confers resistance to BPH. MicroRNAs (miRNAs) regulate a spectrum of development and defense response processes in plants. In this study, we analyzed six miRNA profiles of a BPH15 introgression line (P15) and a susceptible recipient line (PC) at three time points (0 h, 6 h and 48 h) after BPH attack, and identified 464 known miRNAs and 183 potential novel miRNAs. Before the BPH feeding, we identified 23 miRNAs differentially expressed in P15 and PC. We speculated that the resistant plant is in a priming state by the regulation of miRNAs. After the BPH feeding, 104 miRNAs were found to be expressed differentially in P15 (68 in P15-6/P15-0, 36 in P15-48/P15-0), and 80 miRNAs were found expressed differentially in PC (32 in PC-6/PC-0, 48 in PC-48/PC-0), which illustrated that miRNA expression is activated upon attack. These miRNAs regulate different pathways that contribute to the basal defense and specific resistance of rice to the BPH. Our study provides additional data for scientists to further explore the mechanism of plant defense against insect attack and to find a way for efficient insect control.
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Affiliation(s)
- Yan Wu
- National Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Wentang Lv
- National Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
- Shandong Rice Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Liang Hu
- National Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Weiwei Rao
- National Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Ya Zeng
- National Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Lili Zhu
- National Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yuqing He
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guangcun He
- National Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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19
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Liu H, Guo Z, Gu F, Ke S, Sun D, Dong S, Liu W, Huang M, Xiao W, Yang G, Liu Y, Guo T, Wang H, Wang J, Chen Z. 4-Coumarate-CoA Ligase-Like Gene OsAAE3 Negatively Mediates the Rice Blast Resistance, Floret Development and Lignin Biosynthesis. FRONTIERS IN PLANT SCIENCE 2017; 7:2041. [PMID: 28119718 PMCID: PMC5222848 DOI: 10.3389/fpls.2016.02041] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 12/20/2016] [Indexed: 05/23/2023]
Abstract
Although adenosine monophosphate (AMP) binding domain is widely distributed in multiple plant species, detailed molecular functions of AMP binding proteins (AMPBPs) in plant development and plant-pathogen interaction remain unclear. In the present study, we identified an AMPBP OsAAE3 from a previous analysis of early responsive genes in rice during Magnaporthe oryzae infection. OsAAE3 is a homolog of Arabidopsis AAE3 in rice, which encodes a 4-coumarate-Co-A ligase (4CL) like protein. A phylogenetic analysis showed that OsAAE3 was most likely 4CL-like 10 in an independent group. OsAAE3 was localized to cytoplasm, and it could be expressed in various tissues. Histochemical staining of transgenic plants carrying OsAAE3 promoter-driven GUS (β-glucuronidase) reporter gene suggested that OsAAE3 was expressed in all tissues of rice. Furthermore, OsAAE3-OX plants showed increased susceptibility to M. Oryzae, and this finding was attributable to decreased expression of pathogen-related 1a (PR1) and low level of peroxidase (POD) activity. Moreover, OsAAE3 over-expression resulted in increased content of H2O2, leading to programmed cell-death induced by reactive oxygen species (ROS). In addition, OsAAE3 over-expression repressed the floret development, exhibiting dramatically twisted glume and decreased fertility rate of anther. Meanwhile, the expressions of lignin biosynthesis genes were significantly decreased in OsAAE3-OX plants, thereby leading to reduced lignin content. Taken together, OsAAE3 functioned as a negative regulator in rice blast resistance, floret development, and lignin biosynthesis. Our findings further expanded the knowledge in functions of AMBPs in plant floret development and the regulation of rice-fungus interaction.
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Affiliation(s)
- Hao Liu
- National Engineering Research Center of Plant Space Breeding, South China Agricultural UniversityGuangzhou, China
| | - Zhenhua Guo
- Department of Rice Breeding, Jiamusi Rice Research Institute of Heilongjiang Academy of Agricultural SciencesJiamusi, China
| | - Fengwei Gu
- National Engineering Research Center of Plant Space Breeding, South China Agricultural UniversityGuangzhou, China
| | - Shanwen Ke
- Department of Plant Breeding, College of Agricultural, South China Agricultural UniversityGuangzhou, China
| | - Dayuan Sun
- Plant Protection Research Institute Guangdong Academy of Agricultural Sciences/Guangdong Provincial key Laboratory of High Technology for Plant ProtectionGuangzhou, China
| | - Shuangyu Dong
- National Engineering Research Center of Plant Space Breeding, South China Agricultural UniversityGuangzhou, China
| | - Wei Liu
- National Engineering Research Center of Plant Space Breeding, South China Agricultural UniversityGuangzhou, China
| | - Ming Huang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural UniversityGuangzhou, China
| | - Wuming Xiao
- National Engineering Research Center of Plant Space Breeding, South China Agricultural UniversityGuangzhou, China
| | - Guili Yang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural UniversityGuangzhou, China
| | - Yongzhu Liu
- National Engineering Research Center of Plant Space Breeding, South China Agricultural UniversityGuangzhou, China
| | - Tao Guo
- National Engineering Research Center of Plant Space Breeding, South China Agricultural UniversityGuangzhou, China
| | - Hui Wang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural UniversityGuangzhou, China
| | - Jiafeng Wang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural UniversityGuangzhou, China
| | - Zhiqiang Chen
- National Engineering Research Center of Plant Space Breeding, South China Agricultural UniversityGuangzhou, China
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Li Y, Zhao SL, Li JL, Hu XH, Wang H, Cao XL, Xu YJ, Zhao ZX, Xiao ZY, Yang N, Fan J, Huang F, Wang WM. Osa-miR169 Negatively Regulates Rice Immunity against the Blast Fungus Magnaporthe oryzae. FRONTIERS IN PLANT SCIENCE 2017; 8:2. [PMID: 28144248 PMCID: PMC5239796 DOI: 10.3389/fpls.2017.00002] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 01/03/2017] [Indexed: 05/18/2023]
Abstract
miR169 is a conserved microRNA (miRNA) family involved in plant development and stress-induced responses. However, how miR169 functions in rice immunity remains unclear. Here, we show that miR169 acts as a negative regulator in rice immunity against the blast fungus Magnaporthe oryzae by repressing the expression of nuclear factor Y-A (NF-YA) genes. The accumulation of miR169 was significantly increased in a susceptible accession but slightly fluctuated in a resistant accession upon M. oryzae infection. Consistently, the transgenic lines overexpressing miR169a became hyper-susceptible to different M. oryzae strains associated with reduced expression of defense-related genes and lack of hydrogen peroxide accumulation at the infection site. Consequently, the expression of its target genes, the NF-YA family members, was down-regulated by the overexpression of miR169a at either transcriptional or translational level. On the contrary, overexpression of a target mimicry that acts as a sponge to trap miR169a led to enhanced resistance to M. oryzae. In addition, three of miR169's target genes were also differentially up-regulated in the resistant accession upon M. oryzae infection. Taken together, our data indicate that miR169 negatively regulates rice immunity against M. oryzae by differentially repressing its target genes and provide the potential to engineer rice blast resistance via a miRNA.
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Affiliation(s)
- Yan Li
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University at WenjiangChengdu, China
- Collaborative Innovation Center for Hybrid Rice in Yangtze River Basin, Sichuan Agricultural University at WenjiangChengdu, China
| | - Sheng-Li Zhao
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University at WenjiangChengdu, China
| | - Jin-Lu Li
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University at WenjiangChengdu, China
| | - Xiao-Hong Hu
- College of Agronomy, Sichuan Agricultural University at WenjiangChengdu, China
| | - He Wang
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University at WenjiangChengdu, China
| | - Xiao-Long Cao
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University at WenjiangChengdu, China
| | - Yong-Ju Xu
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University at WenjiangChengdu, China
| | - Zhi-Xue Zhao
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University at WenjiangChengdu, China
| | - Zhi-Yuan Xiao
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University at WenjiangChengdu, China
| | - Nan Yang
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University at WenjiangChengdu, China
| | - Jing Fan
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University at WenjiangChengdu, China
- Collaborative Innovation Center for Hybrid Rice in Yangtze River Basin, Sichuan Agricultural University at WenjiangChengdu, China
| | - Fu Huang
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University at WenjiangChengdu, China
- College of Agronomy, Sichuan Agricultural University at WenjiangChengdu, China
| | - Wen-Ming Wang
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University at WenjiangChengdu, China
- Collaborative Innovation Center for Hybrid Rice in Yangtze River Basin, Sichuan Agricultural University at WenjiangChengdu, China
- *Correspondence: Wen-Ming Wang,
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