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Zhang M, Chen D, Tian J, Cao J, Xie K, He Y, Yuan M. OsGELP77, a QTL for broad-spectrum disease resistance and yield in rice, encodes a GDSL-type lipase. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1352-1371. [PMID: 38100249 PMCID: PMC11022805 DOI: 10.1111/pbi.14271] [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: 10/09/2023] [Revised: 11/15/2023] [Accepted: 11/29/2023] [Indexed: 12/17/2023]
Abstract
Lipids and lipid metabolites have essential roles in plant-pathogen interactions. GDSL-type lipases are involved in lipid metabolism modulating lipid homeostasis. Some plant GDSLs modulate lipid metabolism altering hormone signal transduction to regulate host-defence immunity. Here, we functionally characterized a rice lipase, OsGELP77, promoting both immunity and yield. OsGELP77 expression was induced by pathogen infection and jasmonic acid (JA) treatment. Overexpression of OsGELP77 enhanced rice resistance to both bacterial and fungal pathogens, while loss-of-function of osgelp77 showed susceptibility. OsGELP77 localizes to endoplasmic reticulum and is a functional lipase hydrolysing universal lipid substrates. Lipidomics analyses demonstrate that OsGELP77 is crucial for lipid metabolism and lipid-derived JA homeostasis. Genetic analyses confirm that OsGELP77-modulated resistance depends on JA signal transduction. Moreover, population genetic analyses indicate that OsGELP77 expression level is positively correlated with rice resistance against pathogens. Three haplotypes were classified based on nucleotide polymorphisms in the OsGELP77 promoter where OsGELP77Hap3 is an elite haplotype. Three OsGELP77 haplotypes are differentially distributed in wild and cultivated rice, while OsGELP77Hap3 has been broadly pyramided for hybrid rice development. Furthermore, quantitative trait locus (QTL) mapping and resistance evaluation of the constructed near-isogenic line validated OsGELP77, a QTL for broad-spectrum disease resistance. In addition, OsGELP77-modulated lipid metabolism promotes JA accumulation facilitating grain yield. Notably, the hub defence regulator OsWRKY45 acts upstream of OsGELP77 by initiating the JA-dependent signalling to trigger immunity. Together, OsGELP77, a QTL contributing to immunity and yield, is a candidate for breeding broad-spectrum resistant and high-yielding rice.
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Affiliation(s)
- Miaojing Zhang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Dan Chen
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Jingjing Tian
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Jianbo Cao
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Kabin Xie
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Yuqing He
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Meng Yuan
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
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Hui S, Ke Y, Chen D, Wang L, Li Q, Yuan M. Rice microRNA156/529-SQUAMOSA PROMOTER BINDING PROTEIN-LIKE7/14/17 modules regulate defenses against bacteria. PLANT PHYSIOLOGY 2023; 192:2537-2553. [PMID: 36994827 PMCID: PMC10315298 DOI: 10.1093/plphys/kiad201] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/01/2023] [Accepted: 03/07/2023] [Indexed: 06/19/2023]
Abstract
Rice (Oryza sativa L.) microRNA156/529-SQUAMOSA PROMOTER BINDING PROTEIN-LIKE7/14/17 (miR156/529-SPL7/14/17) modules have pleiotropic effects on many biological pathways. OsSPL7/14 can interact with DELLA protein SLENDER RICE1 (SLR1) to modulate gibberellin acid (GA) signal transduction against the bacterial pathogen Xanthomonas oryzae pv. oryzae. However, whether the miR156/529-OsSPL7/14/17 modules also regulate resistance against other pathogens is unclear. Notably, OsSPL7/14/17 functioning as transcriptional activators, their target genes, and the corresponding downstream signaling pathways remain largely unexplored. Here, we demonstrate that miR156/529 play negative roles in plant immunity and that miR156/529-regulated OsSPL7/14/17 confer broad-spectrum resistance against 2 devastating bacterial pathogens. Three OsSPL7/14/17 proteins directly bind to the promoters of rice Allene Oxide Synthase 2 (OsAOS2) and NONEXPRESSOR OF PATHOGENESIS-RELATED GENES1 (OsNPR1) and activate their transcription, regulating jasmonic acid (JA) accumulation and the salicylic acid (SA) signaling pathway, respectively. Overexpression of OsAOS2 or OsNPR1 impairs the susceptibility of the osspl7/14/17 triple mutant. Exogenous application of JA enhances resistance of the osspl7/14/17 triple mutant and the miR156 overexpressing plants. In addition, genetic evidence confirms that bacterial pathogen-activated miR156/529 negatively regulate pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) responses, such as pattern recognition receptor Xa3/Xa26-initiated PTI. Our findings demonstrate that bacterial pathogens modulate miR156/529-OsSPL7/14/17 modules to suppress OsAOS2-catalyzed JA accumulation and the OsNPR1-promoted SA signaling pathway, facilitating pathogen infection. The uncovered miR156/529-OsSPL7/14/17-OsAOS2/OsNPR1 regulatory network provides a potential strategy to genetically improve rice disease resistance.
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Affiliation(s)
- Shugang Hui
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Yinggen Ke
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Dan Chen
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Lei Wang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Qingqing Li
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Meng Yuan
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
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Tian J, Wang L, Hui S, Yang D, He Y, Yuan M. Cadmium accumulation regulated by a rice heavy-metal importer is harmful for host plant and leaf bacteria. J Adv Res 2023; 45:43-57. [PMID: 35640876 PMCID: PMC10006513 DOI: 10.1016/j.jare.2022.05.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/07/2022] [Accepted: 05/25/2022] [Indexed: 10/18/2022] Open
Abstract
INTRODUCTION Cadmium (Cd), one of the major toxic heavy metals, causes severe deleterious effects on all living organisms from prokaryotes to eukaryotes. Cadmium deposition affects bacterial diversity and bacterial population in soil. Cadmium accumulation in plants is mainly controlled by transporters and the resulting Cd enrichment gives rise to phytotoxicity. OBJECTIVE This study aimed to mine transporters that control Cd import or accumulation in rice and uncover the underlying mechanisms that how accumulated Cd poses risks to host plant and leaf bacteria. METHODS RNA-seq analysis, histochemical assays, and elemental quantification were carried out to reveal the biological roles of OsABCG43 for Cd import. Pathogen inoculation, IC50 value, and bacterial virulence assays were conducted to disclose the effects of Cd on leaf bacteria. RESULTS OsABCG43 is characterized as a Cd importer controlling Cd accumulation in rice. OsABCG43 was induced under Cd stress and specifically expressed in the vasculature of leaves and roots. Overexpression of OsABCG43 caused Cd accumulation which inhibits photosynthesis and development and alters the antioxidant system, resulting in phytotoxicity. Moreover, overexpression of OsABCG43 resulted in retarded plant growth and enhanced rice sensitivity to Cd stress. Numerous differentially expressed genes were identified via RNA-seq analysis between the OsABCG43-overexpressing plants and wild type, which functioned in Cd or reactive oxygen species (ROS) homeostasis. In addition, OsABCG43 transcripts were induced by leaf bacteria Xanthomonas oryzae pv. oryzicola (Xoc) and X. oryzae pv. oryzae (Xoo). The enriched Cd directly impaired the formation of virulence factors for the leaf bacteria, preventing colonization or proliferation of Xoc or Xoo in rice leaves. CONCLUSION This work reveals that OsABCG43 is expressed specifically in the vascular and plasma membrane-localized OsABCG43 functions as a Cd importer. OsABCG43-mediated import of Cd is harmful for both rice and the corresponding leaf bacteria.
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Affiliation(s)
- Jingjing Tian
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Li Wang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Shugang Hui
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Dan Yang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Yuqing He
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Meng Yuan
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China.
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Yang Z, Hui S, Lv Y, Zhang M, Chen D, Tian J, Zhang H, Liu H, Cao J, Xie W, Wu C, Wang S, Yuan M. miR395-regulated sulfate metabolism exploits pathogen sensitivity to sulfate to boost immunity in rice. MOLECULAR PLANT 2022; 15:671-688. [PMID: 34968734 DOI: 10.1016/j.molp.2021.12.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 11/30/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
MicroRNAs (miRNAs) play important roles in plant physiological activities. However, their roles and molecular mechanisms in boosting plant immunity, especially through the modulation of macronutrient metabolism in response to pathogens, are largely unknown. Here, we report that an evolutionarily conserved miRNA, miR395, promotes resistance to Xanthomonas oryzae pv. oryzae (Xoo) and X. oryzae pv. oryzicola (Xoc), two destructive bacterial pathogens, by regulating sulfate accumulation and distribution in rice. Specifically, miR395 targets and suppresses the expression of the ATP sulfurylase gene OsAPS1, which functions in sulfate assimilation, and two sulfate transporter genes, OsSULTR2;1 and OsSULTR2;2, which function in sulfate translocation, to promote sulfate accumulation, resulting in broad-spectrum resistance to bacterial pathogens in miR395-overexpressing plants. Genetic analysis revealed that miR395-triggered resistance is involved in both pathogen-associated molecular pattern-triggered immunity and R gene-mediated resistance. Moreover, we found that accumulated sulfate but not S-metabolites inhibits proliferation of pathogenic bacteria, revealing a sulfate-mediated antibacterial defense mechanism that differs from sulfur-induced resistance. Furthermore, compared with other bacteria, Xoo and Xoc, which lack the sulfate transporter CysZ, are sensitive to high levels of extracellular sulfate. Accordingly, miR395-regulated sulfate accumulation impaired the virulence of Xoo and Xoc by decreasing extracellular polysaccharide production and biofilm formation. Taken together, these results suggest that rice miR395 modulates sulfate metabolism to exploit pathogen sensitivity to sulfate and thereby promotes broad-spectrum resistance.
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Affiliation(s)
- Zeyu Yang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Shugang Hui
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Yan Lv
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Miaojing Zhang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Dan Chen
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Jingjing Tian
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Haitao Zhang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Hongbo Liu
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Jianbo Cao
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenya Xie
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Changyin Wu
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Shiping Wang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China.
| | - Meng Yuan
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China.
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Chu C, Huang R, Liu L, Tang G, Xiao J, Yoo H, Yuan M. The rice heavy-metal transporter OsNRAMP1 regulates disease resistance by modulating ROS homoeostasis. PLANT, CELL & ENVIRONMENT 2022; 45:1109-1126. [PMID: 35040151 DOI: 10.1111/pce.14263] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/04/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
Crop diseases threaten food security and sustainable agriculture. Consumption of crops containing nonessential toxic metals leads to health risks for humans. Therefore, cultivation of disease-resistant and toxic metal-safe crops is a double-gain strategy that can contribute to food security. Here, we show that rice heavy-metal transporter OsNRAMP1 plays an important role in plant immunity by modulating metal ion and reactive oxygen species (ROS) homoeostasis. OsNRAMP1 expression was induced after pathogenic bacteria and fungi infections. The osnramp1 mutants had an increased content of H2 O2 and activity of superoxide dismutase, but decreased activity of catalase, showing enhanced broad-spectrum resistance against bacterial and fungal pathogens. RNA-seq analysis identified a number of differentially expressed genes that were involved in metal ion and ROS homoeostasis. Altered expression of metal ion-dependent ROS-scavenging enzymes genes and lower accumulation of cations such as Mn together induced compromised metal ion-dependent enzyme-catalysing activity and modulated ROS homoeostasis, which together contributed towards disease resistance in osnramp1 mutants. Furthermore, the osnramp1 mutants contained lower levels of toxic heavy metals Cd and Pb and micronutrients Ni and Mn in leaves and grains. Taken together, a proof of concept was achieved that broad-spectrum disease-resistant and toxic heavy-metal-safe rice was engineered by removal of the OsNRAMP1 gene.
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Affiliation(s)
- Chuanliang Chu
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Renyan Huang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Liping Liu
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Guilin Tang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Jinghua Xiao
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Heejin Yoo
- Department of Plant Biology, Ecology, and Evolution, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Meng Yuan
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
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Rashid MM, Vaishnav A, Verma RK, Sharma P, Suprasanna P, Gaur RK. Epigenetic regulation of salinity stress responses in cereals. Mol Biol Rep 2021; 49:761-772. [PMID: 34773178 DOI: 10.1007/s11033-021-06922-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/30/2021] [Indexed: 10/19/2022]
Abstract
Cereals are important crops and are exposed to various types of environmental stresses that affect the overall growth and yield. Among the various abiotic stresses, salt stress is a major environmental factor that influences the genetic, physiological, and biochemical responses of cereal crops. Epigenetic regulation which includes DNA methylation, histone modification, and chromatin remodelling plays an important role in salt stress tolerance. Recent studies in rice genomics have highlighted that the epigenetic changes are heritable and therefore can be considered as molecular signatures. An epigenetic mechanism under salinity induces phenotypic responses involving modulations in gene expression. Association between histone modification and altered DNA methylation patterns and differential gene expression has been evidenced for salt sensitivity in rice and other cereal crops. In addition, epigenetics also creates stress memory that helps the plant to better combat future stress exposure. In the present review, we have discussed epigenetic influences in stress tolerance, adaptation, and evolution processes. Understanding the epigenetic regulation of salinity could help for designing salt-tolerant varieties leading to improved crop productivity.
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Affiliation(s)
- Md Mahtab Rashid
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India.,Department of Plant Pathology, Bihar Agricultural University, Sabour, Bhagalpur, Bihar, India
| | - Anukool Vaishnav
- Department of Biotechnology, GLA University, Mathura, Uttar Pradesh, 281121, India.,Agroecology and Environment, Agroscope (Reckenholz), 8046, Zürich, Switzerland
| | - Rakesh Kumar Verma
- Department of Biosciences, Mody University of Science and Technology, Lakshmangarh, Sikar, Rajasthan, India
| | - Pradeep Sharma
- Department of Biotechnology, ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
| | - P Suprasanna
- Nuclear Agriculture & Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
| | - R K Gaur
- Department of Biotechnology, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur, Uttar Pradesh, India.
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Jia Y, Li Q, Li Y, Zhai W, Jiang G, Li C. Inducible Enrichment of Osa-miR1432 Confers Rice Bacterial Blight Resistance through Suppressing OsCaML2. Int J Mol Sci 2021; 22:ijms222111367. [PMID: 34768797 PMCID: PMC8583624 DOI: 10.3390/ijms222111367] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 10/14/2021] [Accepted: 10/14/2021] [Indexed: 01/20/2023] Open
Abstract
MicroRNAs (miRNAs) handle immune response to pathogens by adjusting the function of target genes in plants. However, the experimentally documented miRNA/target modules implicated in the interplay between rice and Xanthomonas oryzae pv. oryzae (Xoo) are still in the early stages. Herein, the expression of osa-miR1432 was induced in resistant genotype IRBB5, but not susceptible genotype IR24, under Xoo strain PXO86 attack. Overexpressed osa-miR1432 heightened rice disease resistance to Xoo, indicated by enhancive enrichment of defense marker genes, raised reactive oxygen species (ROS) levels, repressed bacterial growth and shortened leaf lesion length, whilst the disruptive accumulation of osa-miR1432 accelerated rice susceptibility to Xoo infection. Noticeably, OsCaML2 (LOC_Os03g59770) was experimentally confirmed as a target gene of osa-miR1432, and the overexpressing OsCaML2 transgenic plants exhibited compromised resistance to Xoo infestation. Our results indicate that osa-miR1432 and OsCaML2 were differently responsive to Xoo invasion at the transcriptional level and fine-tune rice resistance to Xoo infection, which may be referable in resistance gene discovery and valuable in the pursuit of improving Xoo resistance in rice breeding.
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Li J, Zhang H, Yang R, Zeng Q, Han G, Du Y, Yang J, Yang G, Luo Q. Identification of miRNAs Contributing to the Broad-Spectrum and Durable Blast Resistance in the Yunnan Local Rice Germplasm. FRONTIERS IN PLANT SCIENCE 2021; 12:749919. [PMID: 34721478 PMCID: PMC8551726 DOI: 10.3389/fpls.2021.749919] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/13/2021] [Indexed: 06/13/2023]
Abstract
MicroRNAs are 20-24 nucleotide non-coding RNAs and play important roles in plant-environment interactions. In recent years, many microRNAs (miRNAs) have been found to regulate rice immunity against rice blast fungus. However, there are limited studies about miRNAs that directly target resistance (R) genes to regulate rice immunity. In this study, by deep sequencing, small RNA libraries were constructed from four-leaf stage seedlings of the resistant variety Ziyu44 and susceptible variety Jiangnanxiangnuo (JNXN) upon Magnaporthe oryzae infection, we found that much more miRNAs were significantly differentially expressed in Ziyu44 than in JNXN. Among these miRNAs, we focused on miR9664, a newly identified rice miRNA in our sequencing, which was upregulated lightly in Ziyu44 and drastically in JNXN at 24-48 h post-inoculation (hpi). The transgenic plants overexpressing miR9664 (miR9664-oe) displayed reduced defense responses to M. oryzae, while those knocking down miR9664 (miR9664-m) displayed enhanced defense responses to M. oryzae. Most of the detected miR9664 predicted target genes were reduced in the miR9664-oe lines while increased in the miR9664-m lines. The cleavage site of LOC_Os08g07774 was confirmed by RLM-RACE. Meanwhile, after being inoculated with M. oryzae, the genes were expressed differently between Ziyu44 and JNXN. The results suggest that miR9664-mediated R gene turnover contributes to Ziyu44 broad-spectrum resistance to rice blast fungus. Taken together, our research identified a new rice miRNA that directly targets R genes to regulate rice immunity against rice blast fungus, adding significant information to the study of rice-M. oryzae interaction.
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Affiliation(s)
- Jinlu Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan/Ministry of Education Key Laboratory of Agricultural Biodiversity for Plant Disease Management, Yunnan Agricultural University, Kunming, China
| | - Hui Zhang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Rui Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan/Ministry of Education Key Laboratory of Agricultural Biodiversity for Plant Disease Management, Yunnan Agricultural University, Kunming, China
| | - Qianchun Zeng
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Guangyu Han
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan/Ministry of Education Key Laboratory of Agricultural Biodiversity for Plant Disease Management, Yunnan Agricultural University, Kunming, China
| | - Yunlong Du
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan/Ministry of Education Key Laboratory of Agricultural Biodiversity for Plant Disease Management, Yunnan Agricultural University, Kunming, China
| | - Jing Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan/Ministry of Education Key Laboratory of Agricultural Biodiversity for Plant Disease Management, Yunnan Agricultural University, Kunming, China
| | - Genhua Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan/Ministry of Education Key Laboratory of Agricultural Biodiversity for Plant Disease Management, Yunnan Agricultural University, Kunming, China
| | - Qiong Luo
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan/Ministry of Education Key Laboratory of Agricultural Biodiversity for Plant Disease Management, Yunnan Agricultural University, Kunming, China
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Musavizadeh Z, Najafi-Zarrini H, Kazemitabar SK, Hashemi SH, Faraji S, Barcaccia G, Heidari P. Genome-Wide Analysis of Potassium Channel Genes in Rice: Expression of the OsAKT and OsKAT Genes under Salt Stress. Genes (Basel) 2021; 12:784. [PMID: 34065373 PMCID: PMC8160896 DOI: 10.3390/genes12050784] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 05/09/2021] [Accepted: 05/18/2021] [Indexed: 12/21/2022] Open
Abstract
Potassium (K+), as a vital element, is involved in regulating important cellular processes such as enzyme activity, cell turgor, and nutrient movement in plant cells, which affects plant growth and production. Potassium channels are involved in the transport and release of potassium in plant cells. In the current study, three OsKAT genes and two OsAKT genes, along with 11 nonredundant putative potassium channel genes in the rice genome, were characterized based on their physiochemical properties, protein structure, evolution, duplication, in silico gene expression, and protein-protein interactions. In addition, the expression patterns of OsAKTs and OsKATs were studied in root and shoot tissues under salt stress using real-time PCR in three rice cultivars. K+ channel genes were found to have diverse functions and structures, and OsKATs showed high genetic divergence from other K+ channel genes. Furthermore, the Ka/Ks ratios of duplicated gene pairs from the K+ channel gene family in rice suggested that these genes underwent purifying selection. Among the studied K+ channel proteins, OsKAT1 and OsAKT1 were identified as proteins with high potential N-glycosylation and phosphorylation sites, and LEU, VAL, SER, PRO, HIS, GLY, LYS, TYR, CYC, and ARG amino acids were predicted as the binding residues in the ligand-binding sites of K+ channel proteins. Regarding the coexpression network and KEGG ontology results, several metabolic pathways, including sugar metabolism, purine metabolism, carbon metabolism, glycerophospholipid metabolism, monoterpenoid biosynthesis, and folate biosynthesis, were recognized in the coexpression network of K+ channel proteins. Based on the available RNA-seq data, the K+ channel genes showed differential expression levels in rice tissues in response to biotic and abiotic stresses. In addition, the real-time PCR results revealed that OsAKTs and OsKATs are induced by salt stress in root and shoot tissues of rice cultivars, and OsKAT1 was identified as a key gene involved in the rice response to salt stress. In the present study, we found that the repression of OsAKTs, OsKAT2, and OsKAT2 in roots was related to salinity tolerance in rice. Our findings provide valuable insights for further structural and functional assays of K+ channel genes in rice.
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Affiliation(s)
- Zahra Musavizadeh
- Department of Biochemical Sciences, Sapienza University of Rome, 00185 Rome, Italy;
| | - Hamid Najafi-Zarrini
- Department of Plant Breeding, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari 4818166996, Iran; (H.N.-Z.); (S.K.K.); (S.F.)
| | - Seyed Kamal Kazemitabar
- Department of Plant Breeding, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari 4818166996, Iran; (H.N.-Z.); (S.K.K.); (S.F.)
| | - Seyed Hamidreza Hashemi
- Genetics and Agricultural Biotechnology Institute of Tabarestan, Sari Agricultural Sciences and Natural Resources University, Sari 4818166996, Iran;
| | - Sahar Faraji
- Department of Plant Breeding, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari 4818166996, Iran; (H.N.-Z.); (S.K.K.); (S.F.)
| | - Gianni Barcaccia
- Laboratory of Genomics for Breeding, DAFNAE, Campus of Agripolis, University of Padova, Legnaro, 35020 Padova, Italy;
| | - Parviz Heidari
- Faculty of Agriculture, Shahrood University of Technology, Shahrood 3619995161, Iran
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10
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Feng Q, Li Y, Zhao ZX, Wang WM. Contribution of Small RNA Pathway to Interactions of Rice with Pathogens and Insect Pests. RICE (NEW YORK, N.Y.) 2021; 14:15. [PMID: 33547972 PMCID: PMC7867673 DOI: 10.1186/s12284-021-00458-z] [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: 09/12/2020] [Accepted: 01/28/2021] [Indexed: 05/20/2023]
Abstract
Small RNAs (sRNAs) are mainly classified into microRNAs (miRNAs) and small interfering RNAs (siRNAs) according to their origin. miRNAs originate from single-stranded RNA precursors, whereas siRNAs originate from double-stranded RNA precursors that are synthesized by RNA-dependent RNA polymerases. Both of single-stranded and double-stranded RNA precursors are processed into sRNAs by Dicer-like proteins. Then, the sRNAs are loaded into ARGONAUTE proteins, forming RNA-induced silencing complexes (RISCs). The RISCs repress the expression of target genes with sequences complementary to the sRNAs through the cleavage of transcripts, the inhibition of translation or DNA methylation. Here, we summarize the recent progress of sRNA pathway in the interactions of rice with various parasitic organisms, including fungi, viruses, bacteria, as well as insects. Besides, we also discuss the hormone signal in sRNA pathway, and the emerging roles of circular RNAs and long non-coding RNAs in rice immunity. Obviously, small RNA pathway may act as a part of rice innate immunity to coordinate with growth and development.
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Affiliation(s)
- Qin Feng
- Rice Research Institute and Research Center for Crop Disease and Insect Pests, Sichuan Agricultural University at Wenjiang, 211 Huimin Road, Wenjiang District, Chengdu, 611130 China
| | - Yan Li
- Rice Research Institute and Research Center for Crop Disease and Insect Pests, Sichuan Agricultural University at Wenjiang, 211 Huimin Road, Wenjiang District, Chengdu, 611130 China
| | - Zhi-Xue Zhao
- Rice Research Institute and Research Center for Crop Disease and Insect Pests, Sichuan Agricultural University at Wenjiang, 211 Huimin Road, Wenjiang District, Chengdu, 611130 China
| | - Wen-Ming Wang
- Rice Research Institute and Research Center for Crop Disease and Insect Pests, Sichuan Agricultural University at Wenjiang, 211 Huimin Road, Wenjiang District, Chengdu, 611130 China
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11
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Lu Y, Zhou DX, Zhao Y. Understanding epigenomics based on the rice model. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1345-1363. [PMID: 31897514 DOI: 10.1007/s00122-019-03518-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 12/18/2019] [Indexed: 05/26/2023]
Abstract
The purpose of this paper provides a comprehensive overview of the recent researches on rice epigenomics, including DNA methylation, histone modifications, noncoding RNAs, and three-dimensional genomics. The challenges and perspectives for future research in rice are discussed. Rice as a model plant for epigenomic studies has much progressed current understanding of epigenetics in plants. Recent results on rice epigenome profiling and three-dimensional chromatin structure studies reveal specific features and implication in gene regulation during rice plant development and adaptation to environmental changes. Results on rice chromatin regulator functions shed light on mechanisms of establishment, recognition, and resetting of epigenomic information in plants. Cloning of several rice epialleles associated with important agronomic traits highlights importance of epigenomic variation in rice plant growth, fitness, and yield. In this review, we summarize and analyze recent advances in rice epigenomics and discuss challenges and directions for future research in the field.
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Affiliation(s)
- Yue Lu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dao-Xiu Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Institute of Plant Science of Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University Paris-Saclay, 91405, Orsay, France
| | - Yu Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
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12
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Yu Y, Zhou Y, Feng Y, He H, Lian J, Yang Y, Lei M, Zhang Y, Chen Y. Transcriptional landscape of pathogen-responsive lncRNAs in rice unveils the role of ALEX1 in jasmonate pathway and disease resistance. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:679-690. [PMID: 31419052 PMCID: PMC7004900 DOI: 10.1111/pbi.13234] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 08/02/2019] [Accepted: 08/09/2019] [Indexed: 05/16/2023]
Abstract
Plant defence is multilayered and is essential for surviving in a changing environment. The discovery of long noncoding RNAs (lncRNAs) has dramatically extended our understanding of post-transcriptional gene regulation in diverse biological processes. However, the expression profile and function of lncRNAs in disease resistance are still largely unknown, especially in monocots. Here, we performed strand-specific RNA sequencing of rice leaves infected by Xanthomonas oryzae pv. Oryzae (Xoo) in different time courses and systematically identified 567 disease-responsive rice lncRNAs. Target analyses of these lncRNAs showed that jasmonate (JA) pathway was significantly enriched. To reveal the interaction between lncRNAs and JA-related genes, we studied the coexpression of them and found 39 JA-related protein-coding genes to be interplayed with 73 lncRNAs, highlighting the potential modulation of lncRNAs in JA pathway. We subsequently identified an lncRNA, ALEX1, whose expression is highly induced by Xoo infection. A T-DNA insertion line constructed using enhancer trap system showed a higher expression of ALEX1 and exerted a significant resistance to rice bacterial blight. Functional study revealed that JA signalling is activated and the endogenous content of JA and JA-Ile is increased. Overexpressing ALEX1 in rice further confirmed the activation of JA pathway and resistance to bacterial blight. Our findings reveal the expression of pathogen-responsive lncRNAs in rice and provide novel insights into the connection between lncRNAs and JA pathway in the regulation of plant disease resistance.
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Affiliation(s)
- Yang Yu
- Guangdong Provincial Key Laboratory of Plant ResourcesState Key Laboratory for BiocontrolSchool of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Yan‐Fei Zhou
- Guangdong Provincial Key Laboratory of Plant ResourcesState Key Laboratory for BiocontrolSchool of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Yan‐Zhao Feng
- Guangdong Provincial Key Laboratory of Plant ResourcesState Key Laboratory for BiocontrolSchool of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Huang He
- Guangdong Provincial Key Laboratory of Plant ResourcesState Key Laboratory for BiocontrolSchool of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Jian‐Ping Lian
- Guangdong Provincial Key Laboratory of Plant ResourcesState Key Laboratory for BiocontrolSchool of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Yu‐Wei Yang
- Guangdong Provincial Key Laboratory of Plant ResourcesState Key Laboratory for BiocontrolSchool of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Meng‐Qi Lei
- Guangdong Provincial Key Laboratory of Plant ResourcesState Key Laboratory for BiocontrolSchool of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Yu‐Chan Zhang
- Guangdong Provincial Key Laboratory of Plant ResourcesState Key Laboratory for BiocontrolSchool of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Yue‐Qin Chen
- Guangdong Provincial Key Laboratory of Plant ResourcesState Key Laboratory for BiocontrolSchool of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
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13
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Characteristic Dissection of Xanthomonas oryzae pv. o ryzae Responsive MicroRNAs in Rice. Int J Mol Sci 2020; 21:ijms21030785. [PMID: 31991765 PMCID: PMC7037501 DOI: 10.3390/ijms21030785] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 01/19/2020] [Accepted: 01/23/2020] [Indexed: 12/03/2022] Open
Abstract
MicroRNAs (miRNAs) are crucial player in plant-pathogen interaction. While the evidence has demonstrated that rice miRNAs mediate immune response to pathogens invasion, the roles of miRNAs on Xanthomonas oryzae pv. oryzae (Xoo) attack remain be in place. Herein, we monitored the responsive changes of rice miRNAs at 0, 8, 24 h across Xoo strain PXO86 infection in its compatible rice variety IR24 and incompatible variety IRBB5 by small RNA sequencing, and the genes targeted by miRNAs were also detected via degradome technology. The faithfulness of sequencing data was validated through quantitative real-time stem-loop reverse transcription-polymerase chain reaction assay. Bioinformatic analysis showed that the differentially expressed miRNAs could be divided into three immunity-related clusters, and 80 regulatory units were emerged in infection process, which comprises 29 differentially expressed known miRNAs and 38 cleaved targets. Furthermore, the miRNA presumptive function of separate immunity cluster in rice-Xoo interplay was confirmed through overexpressing osa-miR164a, osa-miR167d and osa-miR159b, and the disruption of regulatory units, osa-miR164a/OsNAC60, osa-miR167d-5p/OsWD40-174 and osa-miR159b/OsMYBGA, OsLRR-RLK2, OsMPK20-4, may reset rice defense response to Xoo infestation in a controllable manner. These findings provide new insights into the complex roles of characteristic miRNAs and their targets in rice-Xoo interactions.
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Li W, Jia Y, Liu F, Wang F, Fan F, Wang J, Zhu J, Xu Y, Zhong W, Yang J. Integration Analysis of Small RNA and Degradome Sequencing Reveals MicroRNAs Responsive to Dickeya zeae in Resistant Rice. Int J Mol Sci 2019; 20:E222. [PMID: 30626113 PMCID: PMC6337123 DOI: 10.3390/ijms20010222] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 12/26/2018] [Accepted: 12/31/2018] [Indexed: 12/20/2022] Open
Abstract
Rice foot rot disease caused by the pathogen Dickeya zeae (formerly known as Erwinia chrysanthemi pv. zeae), is a newly emerging damaging bacterial disease in China and the southeast of Asia, resulting in the loss of yield and grain quality. However, the genetic resistance mechanisms mediated by miRNAs to D. zeae are unclear in rice. In the present study, 652 miRNAs including osa-miR396f predicted to be involved in multiple defense responses to D. zeae were identified with RNA sequencing. A total of 79 differentially expressed miRNAs were detected under the criterion of normalized reads ≥10, including 51 known and 28 novel miRNAs. Degradome sequencing identified 799 targets predicted to be cleaved by 168 identified miRNAs. Among them, 29 differentially expressed miRNA and target pairs including miRNA396f-OsGRFs were identified by co-expression analysis. Overexpression of the osa-miR396f precursor in a susceptible rice variety showed enhanced resistance to D. zeae, coupled with significant accumulation of transcripts of osa-miR396f and reduction of its target the Growth-Regulating Factors (OsGRFs). Taken together, these findings suggest that miRNA and targets including miR396f-OsGRFs have a role in resisting the infections by bacteria D. zeae.
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Affiliation(s)
- Wenqi Li
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing 210014, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China.
| | - Yulin Jia
- United States Department of Agriculture-Agriculture Research Service, Dale Bumpers National Rice Research Center, Stuttgart, AR 72160, USA.
| | - Fengquan Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
| | - Fangquan Wang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing 210014, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China.
| | - Fangjun Fan
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, 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, Nanjing 210014, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China.
| | - Jinyan Zhu
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, 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, Nanjing 210014, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China.
| | - Weigong Zhong
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, 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, Nanjing 210014, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China.
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15
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Chen G, Zou Y, Hu J, Ding Y. Genome-wide analysis of the rice PPR gene family and their expression profiles under different stress treatments. BMC Genomics 2018; 19:720. [PMID: 30285603 PMCID: PMC6167770 DOI: 10.1186/s12864-018-5088-9] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 09/18/2018] [Indexed: 01/30/2023] Open
Abstract
Background Pentatricopeptide-repeat proteins (PPRs) are characterized by tandem arrays of a degenerate 35-amino-acid (PPR motifs), which can bind RNA strands and participate in post-transcription. PPR proteins family is one of the largest families in land plants and play important roles in organelle RNA metabolism and plant development. However, the functions of PPR genes involved in biotic and abiotic stresses of rice (Oryza sativa L.) remain largely unknown. Results In the present study, a comprehensive genome-wide analysis of PPR genes was performed. A total of 491 PPR genes were found in the rice genome, of which 246 PPR genes belong to the P subfamily, and 245 genes belong to the PLS subfamily. Gene structure analysis showed that most PPR genes lack intron. Chromosomal location analysis indicated that PPR genes were widely distributed in all 12 rice chromosomes. Phylogenetic relationship analysis revealed the distinct difference between the P and PLS subfamilies. Many PPR proteins are predicted to target chloroplasts or mitochondria, and a PPR protein (LOC_Os10g34310) was verified to localize in mitochondria. Furthermore, three PPR genes (LOC_Os03g17634,LOC_Os07g40820,LOC_Os04g51350) were verified as corresponding miRNA targets. The expression pattern analysis showed that many PPR genes could be induced under biotic and abiotic stresses. Finally, seven PPR genes were confirmed with their expression patterns under salinity or drought stress. Conclusions We found 491 PPR genes in the rice genome, and our genes structure analysis and syntenic analysis indicated that PPR genes might be derived from amplification by retro-transposition. The expression pattern present here suggested that PPR proteins have crucial roles in response to different abiotic stresses in rice. Taken together, our study provides a comprehensive analysis of the PPR gene family and will facilitate further studies on their roles in rice growth and development. Electronic supplementary material The online version of this article (10.1186/s12864-018-5088-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Guanglong Chen
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yu Zou
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jihong Hu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Yi Ding
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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16
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microRNA-mediated R gene regulation: molecular scabbards for double-edged swords. SCIENCE CHINA-LIFE SCIENCES 2018; 61:138-147. [DOI: 10.1007/s11427-017-9237-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Accepted: 12/04/2017] [Indexed: 11/27/2022]
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17
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Gao F, Nan F, Feng J, Lv J, Liu Q, Xie S. Identification of conserved and novel microRNAs in Porphyridium purpureum via deep sequencing and bioinformatics. BMC Genomics 2016; 17:612. [PMID: 27516065 PMCID: PMC4981961 DOI: 10.1186/s12864-016-2985-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 08/01/2016] [Indexed: 11/22/2022] Open
Abstract
Background Porphyridium purpureum has been utilized in important industrial and pharmaceutical fields. The identification of microRNAs (miRNAs) in this unique species is of great importance: such identification can help fill gaps in the small RNA (sRNA) studies of this organism and help to elucidate essential biological processes and their regulation mechanisms in this special micro alga. Results In this study, 254 high-confidence miRNAs (203 conserved miRNAs and 51 novel miRNAs) were identified by sRNA deep sequencing (sRNA-seq) combined with bioinformatics. A total of 235 putative miRNA families were predicted, including 192 conserved families and 43 species-specific families. The conservation and diversity of predicted miRNA families were analysed in different plant species. Both the 100 % northern blot validation rate (VR) of four randomly selected miRNAs and the results of stem-loop quantitative real time RT-PCR (qRT-PCR) assays of 25 randomly selected miRNAs demonstrated that the majority of the miRNAs identified in this study are credible. A total of 14,958 and 2184 genes were predicted to be targeted by the 186 conserved and 41 novel miRNAs. Gene ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that some target genes likely provide valuable references for further understanding of vital functions in P. purpureum. In addition, a cytoscape network will provide some clues for research into the complex biological processes that occur in this unique alga. Conclusions We first identified a large set of conserved and novel miRNAs in P. purpureum. The characteristic and validation analysis on miRNAs demonstrated authenticity of identification data. Functional annotation of target genes and metabolic pathways they involved in illuminated the direction for further utilization and development this micro alga based on its unique properties. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2985-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fan Gao
- School of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Fangru Nan
- School of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Jia Feng
- School of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Junping Lv
- School of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Qi Liu
- School of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Shulian Xie
- School of Life Science, Shanxi University, Taiyuan, 030006, China.
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