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Bravo-Vázquez LA, García-Ortega M, Medina-Feria S, Srivastava A, Paul S. Identification and expression profiling of microRNAs in leaf tissues of Foeniculum vulgare Mill. under salinity stress. PLANT SIGNALING & BEHAVIOR 2024; 19:2361174. [PMID: 38825852 DOI: 10.1080/15592324.2024.2361174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Accepted: 05/24/2024] [Indexed: 06/04/2024]
Abstract
Foeniculum vulgare Mill. commonly known as fennel, is a globally recognized aromatic medicinal plant and culinary herb with widespread popularity due to its antimicrobial, antioxidant, carminative, and diuretic properties, among others. Although the phenotypic effects of salinity stress have been previously explored in fennel, the molecular mechanisms underlying responses to elevated salinity in this plant remain elusive. MicroRNAs (miRNAs) are tiny, endogenous, and extensively conserved non-coding RNAs (ncRNAs) typically ranging from 20 to 24 nucleotides (nt) in length that play a major role in a myriad of biological functions. In fact, a number of miRNAs have been extensively associated with responses to abiotic stress in plants. Consequently, employing computational methodologies and rigorous filtering criteria, 40 putative miRNAs belonging to 25 different families were characterized from fennel in this study. Subsequently, employing the psRNATarget tool, a total of 67 different candidate target transcripts for the characterized fennel miRNAs were predicted. Additionally, the expression patterns of six selected fennel miRNAs (i.e. fvu-miR156a, fvu-miR162a-3p, fvu-miR166a-3p, fvu-miR167a-5p, fvu-miR171a-3p, and fvu-miR408-3p) were analyzed under salinity stress conditions via qPCR. This article holds notable significance as it identifies not only 40 putative miRNAs in fennel, a non-model plant, but also pioneers the analysis of their expression under salinity stress conditions.
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Affiliation(s)
| | - Mariana García-Ortega
- School of Engineering and Sciences, Tecnologico de Monterrey, San Pablo, Queretaro, Mexico
| | - Sara Medina-Feria
- School of Engineering and Sciences, Tecnologico de Monterrey, San Pablo, Queretaro, Mexico
| | | | - Sujay Paul
- School of Engineering and Sciences, Tecnologico de Monterrey, San Pablo, Queretaro, Mexico
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Sabouri H, Pezeshkian Z, Taliei F, Akbari M, Kazerani B. Detection of closely linked QTLs and candidate genes controlling germination indices in response to drought and salinity stresses in barley. Sci Rep 2024; 14:15656. [PMID: 38977885 PMCID: PMC11231201 DOI: 10.1038/s41598-024-66452-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 07/01/2024] [Indexed: 07/10/2024] Open
Abstract
The aim of current study was to identify closely linked QTLs and candidate genes related to germination indices under control, salinity and drought conditions in barley. A total of nine (a major), 28 (eight major) and 34 (five major) closely linked QTLs were mapped on the seven chromosomes in response to control, drought and salinity conditions using genome-wide composite interval mapping, respectively. The major QTLs can be used in marker-assisted selection (MAS) projects to increase tolerance to drought and salinity stresses during the germination. Overall, 422 unique candidate genes were associated with most major QTLs. Moreover, gene ontology analysis showed that candidate genes mostly involved in biological process related to signal transduction and response to stimulus in the pathway of resistance to drought and salinity stresses. Also, the protein-protein interaction network was identified 10 genes. Furthermore, 10 genes were associated with receptor-like kinase family. In addition, 16 transcription factors were detected. Three transcription factors including B3, bHLH, and FAR1 had the most encoding genes. Totally, 60 microRNAs were traced to regulate the target genes. Finally, the key genes are a suitable and reliable source for future studies to improve resistance to abiotic stress during the germination of barley.
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Affiliation(s)
- Hossein Sabouri
- Department of Plant Production, College of Agriculture Science and Natural Resource, Gonbad Kavous University, Gonbad, Iran.
| | - Zahra Pezeshkian
- Department of Animal Sciences, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
- BioGenTAC Inc., Technology Incubator of Agricultural Biotechnology Research Institute of Iran-North Branch (ABRII), Rasht, Iran
| | - Fakhtak Taliei
- Department of Plant Production, College of Agriculture Science and Natural Resource, Gonbad Kavous University, Gonbad, Iran
| | - Mahjoubeh Akbari
- Department of Plant Production, College of Agriculture Science and Natural Resource, Gonbad Kavous University, Gonbad, Iran
| | - Borzo Kazerani
- Department of Plant Breeding and Biotechnology, Faculty of Plant Production, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
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Samynathan R, Venkidasamy B, Shanmugam A, Ramalingam S, Thiruvengadam M. Functional role of microRNA in the regulation of biotic and abiotic stress in agronomic plants. Front Genet 2023; 14:1272446. [PMID: 37886688 PMCID: PMC10597799 DOI: 10.3389/fgene.2023.1272446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 09/25/2023] [Indexed: 10/28/2023] Open
Abstract
The increasing demand for food is the result of an increasing population. It is crucial to enhance crop yield for sustainable production. Recently, microRNAs (miRNAs) have gained importance because of their involvement in crop productivity by regulating gene transcription in numerous biological processes, such as growth, development and abiotic and biotic stresses. miRNAs are small, non-coding RNA involved in numerous other biological functions in a plant that range from genomic integrity, metabolism, growth, and development to environmental stress response, which collectively influence the agronomic traits of the crop species. Additionally, miRNA families associated with various agronomic properties are conserved across diverse plant species. The miRNA adaptive responses enhance the plants to survive environmental stresses, such as drought, salinity, cold, and heat conditions, as well as biotic stresses, such as pathogens and insect pests. Thus, understanding the detailed mechanism of the potential response of miRNAs during stress response is necessary to promote the agronomic traits of crops. In this review, we updated the details of the functional aspects of miRNAs as potential regulators of various stress-related responses in agronomic plants.
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Affiliation(s)
- Ramkumar Samynathan
- Department of Oral and Maxillofacial Surgery, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, India
| | - Baskar Venkidasamy
- Department of Oral and Maxillofacial Surgery, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, India
| | - Ashokraj Shanmugam
- Plant Physiology and Biotechnology Division, UPASI Tea Research Foundation, Coimbatore, Tamil Nadu, India
| | - Sathishkumar Ramalingam
- Plant Genetic Engineering Lab, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India
| | - Muthu Thiruvengadam
- Department of Crop Science, College of Sanghuh Life Science, Konkuk University, Seoul, Republic of Korea
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Kusch S, Singh M, Thieron H, Spanu PD, Panstruga R. Site-specific analysis reveals candidate cross-kingdom small RNAs, tRNA and rRNA fragments, and signs of fungal RNA phasing in the barley-powdery mildew interaction. MOLECULAR PLANT PATHOLOGY 2023; 24:570-587. [PMID: 36917011 DOI: 10.1111/mpp.13324] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 05/18/2023]
Abstract
The establishment of host-microbe interactions requires molecular communication between both partners, which may involve the mutual transfer of noncoding small RNAs. Previous evidence suggests that this is also true for powdery mildew disease in barley, which is caused by the fungal pathogen Blumeria hordei. However, previous studies lacked spatial resolution regarding the accumulation of small RNAs upon host infection by B. hordei. Here, we analysed site-specific small RNA repertoires in the context of the barley-B. hordei interaction. To this end, we dissected infected leaves into separate fractions representing different sites that are key to the pathogenic process: epiphytic fungal mycelium, infected plant epidermis, isolated haustoria, a vesicle-enriched fraction from infected epidermis, and extracellular vesicles. Unexpectedly, we discovered enrichment of specific 31-33-base 5'-terminal fragments of barley 5.8S ribosomal RNA in extracellular vesicles and infected epidermis, as well as particular B. hordei transfer RNA fragments in haustoria. We describe canonical small RNAs from both the plant host and the fungal pathogen that may confer cross-kingdom RNA interference activity. Interestingly, we found first evidence of phased small interfering RNAs in B. hordei, a feature usually attributed to plants, which may be associated with the posttranscriptional control of fungal coding genes, pseudogenes, and transposable elements. Our data suggest a key and possibly site-specific role for cross-kingdom RNA interference and noncoding RNA fragments in the host-pathogen communication between B. hordei and its host barley.
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Affiliation(s)
- Stefan Kusch
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Aachen, Germany
| | - Mansi Singh
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Aachen, Germany
| | - Hannah Thieron
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Aachen, Germany
| | - Pietro D Spanu
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Aachen, Germany
| | - Ralph Panstruga
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Aachen, Germany
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5
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What Do We Know about Barley miRNAs? Int J Mol Sci 2022; 23:ijms232314755. [PMID: 36499082 PMCID: PMC9740008 DOI: 10.3390/ijms232314755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/09/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
Plant miRNAs are powerful regulators of gene expression at the post-transcriptional level, which was repeatedly proved in several model plant species. miRNAs are considered to be key regulators of many developmental, homeostatic, and immune processes in plants. However, our understanding of plant miRNAs is still limited, despite the fact that an increasing number of studies have appeared. This systematic review aims to summarize our current knowledge about miRNAs in spring barley (Hordeum vulgare), which is an important agronomical crop worldwide and serves as a common monocot model for studying abiotic stress responses as well. This can help us to understand the connection between plant miRNAs and (not only) abiotic stresses in general. In the end, some future perspectives and open questions are summarized.
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Sánchez-Bermúdez M, del Pozo JC, Pernas M. Effects of Combined Abiotic Stresses Related to Climate Change on Root Growth in Crops. FRONTIERS IN PLANT SCIENCE 2022; 13:918537. [PMID: 35845642 PMCID: PMC9284278 DOI: 10.3389/fpls.2022.918537] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Climate change is a major threat to crop productivity that negatively affects food security worldwide. Increase in global temperatures are usually accompanied by drought, flooding and changes in soil nutrients composition that dramatically reduced crop yields. Against the backdrop of climate change, human population increase and subsequent rise in food demand, finding new solutions for crop adaptation to environmental stresses is essential. The effects of single abiotic stress on crops have been widely studied, but in the field abiotic stresses tend to occur in combination rather than individually. Physiological, metabolic and molecular responses of crops to combined abiotic stresses seem to be significantly different to individual stresses. Although in recent years an increasing number of studies have addressed the effects of abiotic stress combinations, the information related to the root system response is still scarce. Roots are the underground organs that directly contact with the soil and sense many of these abiotic stresses. Understanding the effects of abiotic stress combinations in the root system would help to find new breeding tools to develop more resilient crops. This review will summarize the current knowledge regarding the effects of combined abiotic stress in the root system in crops. First, we will provide a general overview of root responses to particular abiotic stresses. Then, we will describe how these root responses are integrated when crops are challenged to the combination of different abiotic stress. We will focus on the main changes on root system architecture (RSA) and physiology influencing crop productivity and yield and convey the latest information on the key molecular, hormonal and genetic regulatory pathways underlying root responses to these combinatorial stresses. Finally, we will discuss possible directions for future research and the main challenges needed to be tackled to translate this knowledge into useful tools to enhance crop tolerance.
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Guo S, Liao X, Chen S, Liao B, Guo Y, Cheng R, Xiao S, Hu H, Chen J, Pei J, Chen Y, Xu J, Chen S. A Comparative Analysis of the Chloroplast Genomes of Four Polygonum Medicinal Plants. Front Genet 2022; 13:764534. [PMID: 35547259 PMCID: PMC9084321 DOI: 10.3389/fgene.2022.764534] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 03/11/2022] [Indexed: 12/12/2022] Open
Abstract
Polygonum is a generalized genus of the Polygonaceae family that includes various herbaceous plants. In order to provide aid in understanding the evolutionary and phylogenetic relationship in Polygonum at the chloroplast (cp) genome-scale level, we sequenced and annotated the complete chloroplast genomes of four Polygonum species using next-generation sequencing technology and CpGAVAS. Then, repeat sequences, IR contractions, and expansion and transformation sites of chloroplast genomes of four Polygonum species were studied, and a phylogenetic tree was built using the chloroplast genomes of Polygonum. The results indicated that the chloroplast genome construction of Polygonum also displayed characteristic four types of results, comparable to the published chloroplast genome of recorded angiosperms. The chloroplast genomes of the four Polygonum plants are highly consistent in genome size (159,015 bp-163,461 bp), number of genes (112 genes, including 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes), gene types, gene order, codon usage, and repeat sequence distribution, which identifies the high preservation among the Polygonum chloroplast genomes. The Polygonum phylogenetic tree was recreated by a full sequence of the chloroplast genome, which illustrates that the P. bistorta, P. orientale, and P. perfoliatum are divided into the same branch, and P. aviculare belongs to Fallopia. The precise system site of lots base parts requires further verification, but the study would provide a basis for developing the available genetic resources and evolutionary relationships of Polygonum.
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Affiliation(s)
- Shuai Guo
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, China.,Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xuejiao Liao
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, China.,Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Shiyu Chen
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, China.,Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Baosheng Liao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yiming Guo
- Kenneth P. Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA, United States
| | - Ruiyang Cheng
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Shuiming Xiao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Haoyu Hu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jun Chen
- Beijing Engineering Research Center of Pediatric Surgery, Engineering and Transformation Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Jin Pei
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yangjin Chen
- Department of City and Regional Planning, Nanjing University, Nanjing, China
| | - Jiang Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Shilin Chen
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, China.,Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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Singh A, Jain D, Pandey J, Yadav M, Bansal KC, Singh IK. Deciphering the role of miRNA in reprogramming plant responses to drought stress. Crit Rev Biotechnol 2022; 43:613-627. [PMID: 35469523 DOI: 10.1080/07388551.2022.2047880] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Drought is the most prevalent environmental stress that affects plants' growth, development, and crop productivity. However, plants have evolved adaptive mechanisms to respond to the harmful effects of drought. They reprogram their: transcriptome, proteome, and metabolome that alter their cellular and physiological processes and establish cellular homeostasis. One of the crucial regulatory processes that govern this reprogramming is post-transcriptional regulation by microRNAs (miRNAs). miRNAs are small non-coding RNAs, involved in the downregulation of the target mRNA via translation inhibition/mRNA degradation/miRNA-mediated mRNA decay/ribosome drop off/DNA methylation. Many drought-inducible miRNAs have been identified and characterized in plants. Their main targets are regulatory genes that influence growth, development, osmotic stress tolerance, antioxidant defense, phytohormone-mediated signaling, and delayed senescence during drought stress. Overexpression of drought-responsive miRNAs (Osa-miR535, miR160, miR408, Osa-miR393, Osa-miR319, and Gma-miR394) in certain plants has led to tolerance against drought stress indicating their vital role in stress mitigation. Similarly, knock down (miR166/miR398c) or deletion (miR169 and miR827) of miRNAs has also resulted in tolerance to drought stress. Likewise, engineered Arabidopsis plants with miR165, miR166 using short tandem target mimic strategy, exhibited drought tolerance. Since miRNAs regulate the expression of an array of drought-responsive genes, they can act as prospective targets for genetic manipulations to enhance drought tolerance in crops and achieve sustainable agriculture. Further investigations toward functional characterization of diverse miRNAs, and understanding stress-responses regulated by these miRNAs and their utilization in biotechnological applications is highly recommended.
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Affiliation(s)
- Archana Singh
- Department of Botany, Hansraj College, University of Delhi, New Delhi, India
| | - Deepti Jain
- Department of Plant Molecular Biology, Interdisciplinary Centre for Plant Genomics, Delhi University South Campus, New Delhi, India
| | - Jyotsna Pandey
- Department of Botany, Hansraj College, University of Delhi, New Delhi, India
| | - Manisha Yadav
- Department of Botany, Hansraj College, University of Delhi, New Delhi, India
| | - Kailash C Bansal
- The Alliance of Bioversity International and CIAT (CGIAR), New Delhi, India
| | - Indrakant K Singh
- Department of Zoology, Molecular Biology Research Lab, Deshbandhu College, University of Delhi, New Delhi, India.,DBC i4 Center, Deshbandhu College, University of Delhi, New Delhi, India
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Zeeshan M, Qiu CW, Naz S, Cao F, Wu F. Genome-Wide Discovery of miRNAs with Differential Expression Patterns in Responses to Salinity in the Two Contrasting Wheat Cultivars. Int J Mol Sci 2021; 22:ijms222212556. [PMID: 34830438 PMCID: PMC8621374 DOI: 10.3390/ijms222212556] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 01/16/2023] Open
Abstract
Salinity is a serious environmental issue. It has a substantial effect on crop yield, as many crop species are sensitive to salinity due to climate change, and it impact is continuing to increase. Plant microRNAs (miRNAs) contribute to salinity stress response in bread wheat. However, the underlying molecular mechanisms by which miRNAs confer salt tolerance in wheat are unclear. We conducted a genome-wide discovery study using Illumina high throughput sequencing and comprehensive in silico analysis to obtain insight into the underlying mechanisms by which small RNAs confer tolerance to salinity in roots of two contrasting wheat cvv., namely Suntop (salt-tolerant) and Sunmate (salt-sensitive). A total of 191 microRNAs were identified in both cultivars, consisting of 110 known miRNAs and 81 novel miRNAs; 181 miRNAs were shared between the two cultivars. The known miRNAs belonged to 35 families consisted of 23 conserved and 12 unique families. Salinity stress induced 43 and 75 miRNAs in Suntop and Sunmate, respectively. Among them, 14 and 29 known and novel miRNAs were expressed in Suntop and 37 and 38 in Sunmate. In silico analysis revealed 861 putative target mRNAs for the 75 known miRNAs and 52 putative target mRNAs for the 15 candidate novel miRNAs. Furthermore, seven miRNAs including tae-miR156, tae-miR160, tae-miR171a-b, tae-miR319, tae-miR159a-b, tae-miR9657 and novel-mir59 that regulate auxin responsive-factor, SPL, SCL6, PCF5, R2R3 MYB, and CBL-CIPK, respectively, were predicted to contribute to salt tolerance in Suntop. This information helps further our understanding of how the molecular mechanisms of salt tolerance are mediated by miRNAs and may facilitate the genetic improvement of wheat cultivars.
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Affiliation(s)
- Muhammad Zeeshan
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; (M.Z.); (C.-W.Q.); (S.N.); (F.C.)
- Key Laboratory of Crop Cultivation and Tillage, Agricultural College of Guangxi University, Nanning 530004, China
| | - Cheng-Wei Qiu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; (M.Z.); (C.-W.Q.); (S.N.); (F.C.)
| | - Shama Naz
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; (M.Z.); (C.-W.Q.); (S.N.); (F.C.)
| | - Fangbin Cao
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; (M.Z.); (C.-W.Q.); (S.N.); (F.C.)
| | - Feibo Wu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; (M.Z.); (C.-W.Q.); (S.N.); (F.C.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
- Correspondence: ; Tel./Fax: +86-571-8898-2827
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10
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Werner BT, Koch A, Šečić E, Engelhardt J, Jelonek L, Steinbrenner J, Kogel KH. Fusarium graminearum DICER-like-dependent sRNAs are required for the suppression of host immune genes and full virulence. PLoS One 2021; 16:e0252365. [PMID: 34351929 PMCID: PMC8341482 DOI: 10.1371/journal.pone.0252365] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/19/2021] [Indexed: 11/18/2022] Open
Abstract
In filamentous fungi, gene silencing by RNA interference (RNAi) shapes many biological processes, including pathogenicity. Recently, fungal small RNAs (sRNAs) have been shown to act as effectors that disrupt gene activity in interacting plant hosts, thereby undermining their defence responses. We show here that the devastating mycotoxin-producing ascomycete Fusarium graminearum (Fg) utilizes DICER-like (DCL)-dependent sRNAs to target defence genes in two Poaceae hosts, barley (Hordeum vulgare, Hv) and Brachypodium distachyon (Bd). We identified 104 Fg-sRNAs with sequence homology to host genes that were repressed during interactions of Fg and Hv, while they accumulated in plants infected by the DCL double knock-out (dKO) mutant PH1-dcl1/2. The strength of target gene expression correlated with the abundance of the corresponding Fg-sRNA. Specifically, the abundance of three tRNA-derived fragments (tRFs) targeting immunity-related Ethylene overproducer 1-like 1 (HvEOL1) and three Poaceae orthologues of Arabidopsis thaliana BRI1-associated receptor kinase 1 (HvBAK1, HvSERK2 and BdSERK2) was dependent on fungal DCL. Additionally, RNA-ligase-mediated Rapid Amplification of cDNA Ends (RLM-RACE) identified infection-specific degradation products for the three barley gene transcripts, consistent with the possibility that tRFs contribute to fungal virulence via targeted gene silencing.
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Affiliation(s)
- Bernhard Timo Werner
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Aline Koch
- Institute for Phytomedicine, University of Hohenheim, Stuttgart, Germany
| | - Ena Šečić
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Jonas Engelhardt
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Lukas Jelonek
- Institute of Bioinformatics and Systems Biology, Justus Liebig University, Giessen, Germany
| | - Jens Steinbrenner
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Karl-Heinz Kogel
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
- * E-mail:
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11
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Abdellatef E, Kamal NM, Tsujimoto H. Tuning Beforehand: A Foresight on RNA Interference (RNAi) and In Vitro-Derived dsRNAs to Enhance Crop Resilience to Biotic and Abiotic Stresses. Int J Mol Sci 2021; 22:ijms22147687. [PMID: 34299307 PMCID: PMC8306419 DOI: 10.3390/ijms22147687] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/12/2021] [Accepted: 07/14/2021] [Indexed: 11/23/2022] Open
Abstract
Crop yield is severely affected by biotic and abiotic stresses. Plants adapt to these stresses mainly through gene expression reprogramming at the transcriptional and post-transcriptional levels. Recently, the exogenous application of double-stranded RNAs (dsRNAs) and RNA interference (RNAi) technology has emerged as a sustainable and publicly acceptable alternative to genetic transformation, hence, small RNAs (micro-RNAs and small interfering RNAs) have an important role in combating biotic and abiotic stresses in plants. RNAi limits the transcript level by either suppressing transcription (transcriptional gene silencing) or activating sequence-specific RNA degradation (post-transcriptional gene silencing). Using RNAi tools and their respective targets in abiotic stress responses in many crops is well documented. Many miRNAs families are reported in plant tolerance response or adaptation to drought, salinity, and temperature stresses. In biotic stress, the spray-induced gene silencing (SIGS) provides an intelligent method of using dsRNA as a trigger to silence target genes in pests and pathogens without producing side effects such as those caused by chemical pesticides. In this review, we focus on the potential of SIGS as the most recent application of RNAi in agriculture and point out the trends, challenges, and risks of production technologies. Additionally, we provide insights into the potential applications of exogenous RNAi against biotic stresses. We also review the current status of RNAi/miRNA tools and their respective targets on abiotic stress and the most common responsive miRNA families triggered by stress conditions in different crop species.
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Affiliation(s)
- Eltayb Abdellatef
- Commission for Biotechnology and Genetic Engineering, National Center for Research, P.O. Box 2404, Khartoum 11111, Sudan;
- Arid Land Research Center, Tottori University, 1390 Hamasaka, Tottori 680-0001, Japan;
- Behavioural and Chemical Ecology Unit, International Centre of Insect Physiology and Ecology, P.O. Box 30772, Nairobi 00100, Kenya
| | - Nasrein Mohamed Kamal
- Arid Land Research Center, Tottori University, 1390 Hamasaka, Tottori 680-0001, Japan;
- Agricultural Research Corporation, P.O. Box 30, Khartoum North 11111, Sudan
| | - Hisashi Tsujimoto
- Arid Land Research Center, Tottori University, 1390 Hamasaka, Tottori 680-0001, Japan;
- Correspondence:
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Chaudhary S, Grover A, Sharma PC. MicroRNAs: Potential Targets for Developing Stress-Tolerant Crops. Life (Basel) 2021; 11:life11040289. [PMID: 33800690 PMCID: PMC8066829 DOI: 10.3390/life11040289] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 12/24/2022] Open
Abstract
Crop yield is challenged every year worldwide by changing climatic conditions. The forecasted climatic scenario urgently demands stress-tolerant crop varieties to feed the ever-increasing global population. Molecular breeding and genetic engineering approaches have been frequently exploited for developing crops with desired agronomic traits. Recently, microRNAs (miRNAs) have emerged as powerful molecules, which potentially serve as expression markers during stress conditions. The miRNAs are small non-coding endogenous RNAs, usually 20-24 nucleotides long, which mediate post-transcriptional gene silencing and fine-tune the regulation of many abiotic- and biotic-stress responsive genes in plants. The miRNAs usually function by specifically pairing with the target mRNAs, inducing their cleavage or repressing their translation. This review focuses on the exploration of the functional role of miRNAs in regulating plant responses to abiotic and biotic stresses. Moreover, a methodology is also discussed to mine stress-responsive miRNAs from the enormous amount of transcriptome data available in the public domain generated using next-generation sequencing (NGS). Considering the functional role of miRNAs in mediating stress responses, these molecules may be explored as novel targets for engineering stress-tolerant crop varieties.
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Affiliation(s)
- Saurabh Chaudhary
- Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AT, UK
- Correspondence: (S.C.); (P.C.S.)
| | - Atul Grover
- Defence Institute of Bio-Energy Research, Defence Research and Development Organisation (DRDO), Haldwani 263139, India;
| | - Prakash Chand Sharma
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi 110078, India
- Correspondence: (S.C.); (P.C.S.)
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Waseem M, Aslam MM, Shaheen I. The DUF221 domain-containing (DDP) genes identification and expression analysis in tomato under abiotic and phytohormone stress. GM CROPS & FOOD 2021; 12:586-599. [PMID: 34379048 PMCID: PMC8820248 DOI: 10.1080/21645698.2021.1962207] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The domain of unknown function (DUF221 domain-containing) proteins regulates various aspects of plant growth, development, responses to abiotic stresses, and hormone transduction pathways. To understand the role of DDP proteins in tomato, a comprehensive genome-wide analysis was performed in the tomato genome. A total of 12 DDP genes were identified and distributed in 8 chromosomes in the tomato genome. Phylogenetically all SlDDPs were clustered into four clades, subsequently supported by their gene structure and conserved motifs distribution. The SlDDPs contained various cis-acting elements involved in plant responses to abiotic and various phytohormones stresses. The tissue-specific expression profile analysis revealed the constitutive expression of SlDDPs in roots, leaves, and developmental phases of fruit. It was found that SlDDP1, SlDDP3, SlDDP4, SlDDP9, SlDDP10, and SlDDP12 exhibited high expression levels in fruits at different development stages. Of these genes, SlDDP12 contained ethylene (ERE) responsive elements in their promoter regions, suggesting its role in ethylene-dependent fruit ripening. It was found that a single SlDDP induced by two or more abiotic and phytohormone stresses. These include, SlDDP1, SlDDP2, SlDDP3, SlDDP4, SlDDP7, SlDDP8, and SlDDP10 was induced under salt, drought, ABA, and IAA stresses. Moreover, tomato SlDDPs were targeted by multiple miRNA gene families as well. In conclusion, this study predicted that the putative DDP genes might help improve abiotic and phytohormone tolerance in plants, particularly tomato, rice, and other economically important crop plant species.
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Affiliation(s)
- Muhammad Waseem
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | | | - Iffat Shaheen
- Faculty of Agriculture Science and Technology, Bahauddin Zakariya University, Multan, Pakistan
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Xu T, Zhang L, Yang Z, Wei Y, Dong T. Identification and Functional Characterization of Plant MiRNA Under Salt Stress Shed Light on Salinity Resistance Improvement Through MiRNA Manipulation in Crops. FRONTIERS IN PLANT SCIENCE 2021; 12:665439. [PMID: 34220888 PMCID: PMC8247772 DOI: 10.3389/fpls.2021.665439] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/29/2021] [Indexed: 05/07/2023]
Abstract
Salinity, as a major environmental stressor, limits plant growth, development, and crop yield remarkably. However, plants evolve their own defense systems in response to salt stress. Recently, microRNA (miRNA) has been broadly studied and considered to be an important regulator of the plant salt-stress response at the post-transcription level. In this review, we have summarized the recent research progress on the identification, functional characterization, and regulatory mechanism of miRNA involved in salt stress, have discussed the emerging manipulation of miRNA to improve crop salt resistance, and have provided future direction for plant miRNA study under salt stress, suggesting that the salinity resistance of crops could be improved by the manipulation of microRNA.
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Affiliation(s)
- Tao Xu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- *Correspondence: Tao Xu,
| | - Long Zhang
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Zhengmei Yang
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea
| | - Yiliang Wei
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Tingting Dong
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Tingting Dong,
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15
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Chang B, Ma K, Lu Z, Lu J, Cui J, Wang L, Jin B. Physiological, Transcriptomic, and Metabolic Responses of Ginkgo biloba L. to Drought, Salt, and Heat Stresses. Biomolecules 2020; 10:E1635. [PMID: 33287405 PMCID: PMC7761781 DOI: 10.3390/biom10121635] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/02/2020] [Accepted: 12/02/2020] [Indexed: 02/01/2023] Open
Abstract
Ginkgo biloba L. is highly adaptable and resistant to a range of abiotic stressors, allowing its growth in various environments. However, it is unclear how G. biloba responds to common environmental stresses. We explored the physiological, transcriptomic, and metabolic responses of G. biloba to short-term drought, salt, and heat stresses. Proline, H2O2, and ABA contents, along with CAT activity, increased under all three types of stress. SOD activity increased under salt and heat stresses, while soluble protein and IAA contents decreased under drought and salt stresses. With respect to metabolites, D-glyceric acid increased in response to drought and salt stresses, whereas isomaltose 1, oxalamide, and threonine 2 increased under drought. Piceatannol 2,4-hydroxybutyrate and 1,3-diaminopropane increased under salt stress, whereas 4-aminobutyric acid 1 and galactonic acid increased in response to heat stress. Genes regulating nitrogen assimilation were upregulated only under drought, while the GRAS gene was upregulated under all three types of stressors. ARF genes were downregulated under heat stress, whereas genes encoding HSF and SPL were upregulated. Additionally, we predicted that miR156, miR160, miR172, and their target genes participate in stress responses. Our study provides valuable data for studying the multilevel response to drought, salinity, and heat in G. biloba.
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Affiliation(s)
| | | | | | | | | | | | - Biao Jin
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (B.C.); (K.M.); (Z.L.); (J.L.); (J.C.); (L.W.)
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Xu J, Shen X, Liao B, Xu J, Hou D. Comparing and phylogenetic analysis chloroplast genome of three Achyranthes species. Sci Rep 2020; 10:10818. [PMID: 32616875 PMCID: PMC7331806 DOI: 10.1038/s41598-020-67679-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 06/12/2020] [Indexed: 11/29/2022] Open
Abstract
In this study, the chloroplast genome sequencing of the Achyranthes longifolia, Achyranthes bidentata and Achyranthes aspera were performed by Next-generation sequencing technology. The results revealed that there were a length of 151,520 bp (A. longifolia), 151,284 bp (A. bidentata), 151,486 bp (A. aspera), respectively. These chloroplast genome have a highly conserved structure with a pair of inverted repeat (IR) regions (25,150 bp; 25,145 bp; 25,150 bp), a large single copy (LSC) regions (83,732 bp; 83,933 bp; 83,966 bp) and a small single copy (SSC) regions (17,252 bp; 17,263 bp; 17,254 bp) in A. bidentate, A. aspera and A. longifolia. There were 127 genes were annotated, which including 8 rRNA genes, 37 tRNA genes and 82 functional genes. The phylogenetic analysis strongly revealed that Achyranthes is monophyletic, and A. bidentata was the closest relationship with A. aspera and A. longifolia. A. bidentata and A. longifolia were clustered together, the three Achyranthes species had the same origin, then the gunes of Achyranthes is the closest relative to Alternanthera, and that forms a group with Alternanthera philoxeroides. The research laid a foundation and provided relevant basis for the identification of germplasm resources in the future.
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Affiliation(s)
- Jingya Xu
- Agricultural College, Henan University of Science and Technology, Luoyang, China
- The Luoyang Engineering Research Center of Breeding and Utilization of Dao-Di Herbs, Luoyang, China
- Institute of Chinese Materia Medical, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xiaofeng Shen
- Institute of Chinese Materia Medical, China Academy of Chinese Medical Sciences, Beijing, China
| | - Baosheng Liao
- Institute of Chinese Materia Medical, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jiang Xu
- Institute of Chinese Materia Medical, China Academy of Chinese Medical Sciences, Beijing, China.
| | - Dianyun Hou
- Agricultural College, Henan University of Science and Technology, Luoyang, China.
- The Luoyang Engineering Research Center of Breeding and Utilization of Dao-Di Herbs, Luoyang, China.
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Smoczynska A, Pacak AM, Nuc P, Swida-Barteczka A, Kruszka K, Karlowski WM, Jarmolowski A, Szweykowska-Kulinska Z. A Functional Network of Novel Barley MicroRNAs and Their Targets in Response to Drought. Genes (Basel) 2020; 11:genes11050488. [PMID: 32365647 PMCID: PMC7290300 DOI: 10.3390/genes11050488] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/17/2020] [Accepted: 04/21/2020] [Indexed: 12/27/2022] Open
Abstract
The regulation of mRNA (messenger RNA) levels by microRNA-mediated activity is especially important in plant responses to environmental stresses. In this work, we report six novel barley microRNAs, including two processed from the same precursor that are severely downregulated under drought conditions. For all analyzed microRNAs, we found target genes that were upregulated under drought conditions and that were known to be involved in a plethora of processes from disease resistance to chromatin–protein complex formation and the regulation of transcription in mitochondria. Targets for novel barley microRNAs were confirmed through degradome data analysis and RT-qPCR using primers flanking microRNA-recognition site. Our results show a broad transcriptional response of barley to water deficiency conditions through microRNA-mediated gene regulation and facilitate further research on drought tolerance in crops.
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Affiliation(s)
- Aleksandra Smoczynska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland; (A.S.); (A.M.P.); (P.N.); (A.S.-B.); (K.K.); (A.J.)
| | - Andrzej M. Pacak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland; (A.S.); (A.M.P.); (P.N.); (A.S.-B.); (K.K.); (A.J.)
| | - Przemysław Nuc
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland; (A.S.); (A.M.P.); (P.N.); (A.S.-B.); (K.K.); (A.J.)
| | - Aleksandra Swida-Barteczka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland; (A.S.); (A.M.P.); (P.N.); (A.S.-B.); (K.K.); (A.J.)
| | - Katarzyna Kruszka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland; (A.S.); (A.M.P.); (P.N.); (A.S.-B.); (K.K.); (A.J.)
| | - Wojciech M. Karlowski
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-712 Poznan, Poland;
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland; (A.S.); (A.M.P.); (P.N.); (A.S.-B.); (K.K.); (A.J.)
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland; (A.S.); (A.M.P.); (P.N.); (A.S.-B.); (K.K.); (A.J.)
- Correspondence: ; Tel.: +48-61-829-5950
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Yin X, Liao B, Guo S, Liang C, Pei J, Xu J, Chen S. The chloroplasts genomic analyses of Rosa laevigata, R. rugosa and R. canina. Chin Med 2020; 15:18. [PMID: 32082412 PMCID: PMC7020376 DOI: 10.1186/s13020-020-0298-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 02/05/2020] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Many species of the genus Rosa have been used as ornamental plants and traditional medicines. However, industrial development of roses is hampered due to highly divergent characteristics. METHODS We analyzed the chloroplast (cp) genomes of Rosa laevigata, R. rugosa and R. canina, including the repeat sequences, inverted-repeat (IR) contractions and expansions, and mutation sites. RESULTS The size of the cp genome of R. laevigata, R. rugosa and R. canina was between 156 333 bp and 156 533 bp, and contained 113 genes (30 tRNA genes, 4 rRNA genes and 79 protein-coding genes). The regions with a higher degree of variation were screened out (trnH-GUU, trnS-GCU, trnG-GCC, psbA-trnH, trnC-GCA,petN, trnT-GGU, psbD, petA, psbJ, ndhF, rpl32,psaC and ndhE). Such higher-resolution loci lay the foundation of barcode-based identification of cp genomes in Rosa genus. A phylogenetic tree of the genus Rosa was reconstructed using the full sequences of the cp genome. These results were largely in accordance with the current taxonomic status of Rosa. CONCLUSIONS Our data: (i) reveal that cp genomes can be used for the identification and classification of Rosa species; (ii) can aid studies on molecular identification, genetic transformation, expression of secondary metabolic pathways and resistant proteins; (iii) can lay a theoretical foundation for the discovery of disease-resistance genes and cultivation of Rosa species.
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Affiliation(s)
- Xianmei Yin
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611130 China
| | - Baosheng Liao
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institution of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 China
| | - Shuai Guo
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institution of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 China
| | - Conglian Liang
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, 250355 China
| | - Jin Pei
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611130 China
| | - Jiang Xu
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institution of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 China
| | - Shilin Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institution of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 China
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20
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Xu J, Chen Q, Liu P, Jia W, Chen Z, Xu Z. Integration of mRNA and miRNA Analysis Reveals the Molecular Mechanism Underlying Salt and Alkali Stress Tolerance in Tobacco. Int J Mol Sci 2019; 20:E2391. [PMID: 31091777 PMCID: PMC6566703 DOI: 10.3390/ijms20102391] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/07/2019] [Accepted: 05/09/2019] [Indexed: 12/24/2022] Open
Abstract
Salinity is one of the most severe forms of abiotic stress and affects crop yields worldwide. Plants respond to salinity stress via a sophisticated mechanism at the physiological, transcriptional and metabolic levels. However, the molecular regulatory networks involved in salt and alkali tolerance have not yet been elucidated. We developed an RNA-seq technique to perform mRNA and small RNA (sRNA) sequencing of plants under salt (NaCl) and alkali (NaHCO3) stress in tobacco. Overall, 8064 differentially expressed genes (DEGs) and 33 differentially expressed microRNAs (DE miRNAs) were identified in response to salt and alkali stress. A total of 1578 overlapping DEGs, which exhibit the same expression patterns and are involved in ion channel, aquaporin (AQP) and antioxidant activities, were identified. Furthermore, genes involved in several biological processes, such as "photosynthesis" and "starch and sucrose metabolism," were specifically enriched under NaHCO3 treatment. We also identified 15 and 22 miRNAs that were differentially expressed in response to NaCl and NaHCO3, respectively. Analysis of inverse correlations between miRNAs and target mRNAs revealed 26 mRNA-miRNA interactions under NaCl treatment and 139 mRNA-miRNA interactions under NaHCO3 treatment. This study provides new insights into the molecular mechanisms underlying the response of tobacco to salinity stress.
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Affiliation(s)
- Jiayang Xu
- National Tobacco Cultivation and Physiology and Biochemistry Research Center, College of Tobacco Science, Henan Agricultural University, Zhengzhou 450002, China.
| | - Qiansi Chen
- Zhengzhou Tobacco Research Institute, Zhengzhou 450001, China.
| | - Pingping Liu
- Zhengzhou Tobacco Research Institute, Zhengzhou 450001, China.
| | - Wei Jia
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China.
| | - Zheng Chen
- National Tobacco Cultivation and Physiology and Biochemistry Research Center, College of Tobacco Science, Henan Agricultural University, Zhengzhou 450002, China.
| | - Zicheng Xu
- National Tobacco Cultivation and Physiology and Biochemistry Research Center, College of Tobacco Science, Henan Agricultural University, Zhengzhou 450002, China.
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Alzahrani SM, Alaraidh IA, Khan MA, Migdadi HM, Alghamdi SS, Alsahli AA. Identification and Characterization of Salt-Responsive MicroRNAs in Vicia faba by High-Throughput Sequencing. Genes (Basel) 2019; 10:E303. [PMID: 30999691 PMCID: PMC6523927 DOI: 10.3390/genes10040303] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 04/02/2019] [Accepted: 04/11/2019] [Indexed: 02/07/2023] Open
Abstract
Salt stress has detrimental effects on plant growth and development. MicroRNAs (miRNAs) are a class of noncoding RNAs that are involved in post-transcriptional gene expression regulation. In this study, small RNA sequencing was employed to identify the salt stress-responsive miRNAs of the salt-sensitive Hassawi-3 and the salt-tolerant ILB4347 genotypes of faba bean, growing under salt stress. A total of 527 miRNAs in Hassawi-3 plants, and 693 miRNAs in ILB4347 plants, were found to be differentially expressed. Additionally, 284 upregulated and 243 downregulated miRNAs in Hassawi-3, and 298 upregulated and 395 downregulated miRNAs in ILB4347 plants growing in control and stress conditions were recorded. Target prediction and annotation revealed that these miRNAs regulate specific salt-responsive genes, which primarily included genes encoding transcription factors and laccases, superoxide dismutase, plantacyanin, and F-box proteins. The salt-responsive miRNAs and their targets were functionally enriched by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, which showed that the miRNAs were involved in salt stress-related biological pathways, including the ABC transporter pathway, MAPK signaling pathway, plant hormone signal transduction, and the phosphatidylinositol signaling system, among others, suggesting that the miRNAs play an important role in the salt stress tolerance of the ILB4347 genotype. These results offer a novel understanding of the regulatory role of miRNAs in the salt response of the salt-tolerant ILB4347 and the salt-sensitive Hassawi-3 faba bean genotypes.
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Affiliation(s)
- Saud M Alzahrani
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia.
| | - Ibrahim A Alaraidh
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia.
| | - Muhammad A Khan
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, Riyadh 11451, Saudi Arabia.
| | - Hussein M Migdadi
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, Riyadh 11451, Saudi Arabia.
- Plant Biotechnology Department, National Agricultural Research Center, Baq'a 19381, Jordan.
| | - Salem S Alghamdi
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, Riyadh 11451, Saudi Arabia.
| | - Abdluaziz A Alsahli
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia.
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Matthews C, Arshad M, Hannoufa A. Alfalfa response to heat stress is modulated by microRNA156. PHYSIOLOGIA PLANTARUM 2019; 165:830-842. [PMID: 29923601 DOI: 10.1111/ppl.12787] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 06/14/2018] [Accepted: 06/15/2018] [Indexed: 05/09/2023]
Abstract
Heat stress and extreme temperatures negatively affect plant development by disrupting regular cellular and biochemical functions, ultimately leading to reduced crop production. Alfalfa (Medicago sativa) is an important forage crop grown worldwide as forage for livestock feed. Limiting the effects of abiotic stress by developing alfalfa cultivars that are stress tolerant would help mitigate losses to crop production. Members of the microRNA156 (miR156) family regulate the Squamosa Promoter-Binding Protein-Like (SPL) genes that in turn impact plant growth and development by regulating downstream genes in response to various abiotic stresses. In this study, alfalfa with miR156 overexpression and SPL13 RNAi knockdown show increased tolerance to heat stress (40°C). Transgenic plants show high water potential and increased non-enzymatic antioxidant content under heat stress. Moreover, anthocyanin content and chlorophyll abundance were increased under stress. Expression of some important transcription factors and downstream genes involved in abiotic stress response were altered in miR156-overexpressing genotypes under heat. Taken together, our results demonstrate that the miR156/SPL13 network contributes to improving heat stress tolerance in alfalfa.
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Affiliation(s)
- Craig Matthews
- Agriculture and Agri-Food Canada, London, Ontario, N5V 4T3, Canada
- Biology Department, University of Western Ontario, London, Ontario, N6A 5B7, Canada
| | - Muhammad Arshad
- Agriculture and Agri-Food Canada, London, Ontario, N5V 4T3, Canada
- Centre for Agriculture Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Abdelali Hannoufa
- Agriculture and Agri-Food Canada, London, Ontario, N5V 4T3, Canada
- Biology Department, University of Western Ontario, London, Ontario, N6A 5B7, Canada
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Xu J, Hou QM, Khare T, Verma SK, Kumar V. Exploring miRNAs for developing climate-resilient crops: A perspective review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 653:91-104. [PMID: 30408672 DOI: 10.1016/j.scitotenv.2018.10.340] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 10/24/2018] [Accepted: 10/25/2018] [Indexed: 05/21/2023]
Abstract
Climate changes and environmental stresses have significant implications on global crop production and necessitate developing crops that can withstand an array of climate changes and environmental perturbations such as irregular water-supplies leading to drought or water-logging, hyper soil-salinity, extreme and variable temperatures, ultraviolet radiations and metal stress. Plants have intricate molecular mechanisms to cope with these dynamic environmental changes, one of the most common and effective being the reprogramming of expression of stress-responsive genes. Plant microRNAs (miRNAs) have emerged as key post-transcriptional and translational regulators of gene-expression for modulation of stress implications. Recent reports are establishing their key roles in epigenetic regulations of stress/adaptive responses as well as in providing plants genome-stability. Several stress responsive miRNAs are being identified from different crop plants and miRNA-driven RNA-interference (RNAi) is turning into a technology of choice for improving crop traits and providing phenotypic plasticity in challenging environments. Here we presents a perspective review on exploration of miRNAs as potent targets for engineering crops that can withstand multi-stress environments via loss-/gain-of-function approaches. This review also shed a light on potential roles plant miRNAs play in genome-stability and their emergence as potent target for genome-editing. Current knowledge on plant miRNAs, their biogenesis, function, their targets, and latest developments in bioinformatics approaches for plant miRNAs are discussed. Though there are recent reviews discussing primarily the individual miRNAs responsive to single stress factors, however, considering practical limitation of this approach, special emphasis is given in this review on miRNAs involved in responses and adaptation of plants to multi-stress environments including at epigenetic and/or epigenomic levels.
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Affiliation(s)
- Jin Xu
- School of Environmental Science and Safety Engineering, Tianjin University of Technology, Tianjin 300384, China
| | - Qin-Min Hou
- School of Environmental Science and Safety Engineering, Tianjin University of Technology, Tianjin 300384, China.
| | - Tushar Khare
- Department of Biotechnology, Modern College of Arts, Science and Commerce (Savitribai Phule Pune University), Ganeshkhind, Pune 411016, India
| | - Sandeep Kumar Verma
- Biotechnology Laboratory (TUBITAK Fellow), Department of Biology, Bolu Abant Izeet Baysal University, 14030 Bolu, Turkey
| | - Vinay Kumar
- Department of Biotechnology, Modern College of Arts, Science and Commerce (Savitribai Phule Pune University), Ganeshkhind, Pune 411016, India; Department of Environmental Science, Savitribai Phule Pune University, Pune 411007, India.
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Ünlü ES, Bataw S, Aslan Şen D, Şahin Y, Zencirci N. Identification of conserved miRNA molecules in einkorn wheat (Triticum monococcum subsp. monococcum) by using small RNA sequencing analysis. Turk J Biol 2018; 42:527-536. [PMID: 30983871 PMCID: PMC6451844 DOI: 10.3906/biy-1802-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Triticum monococcum subsp. monococcum as a first cultivated diploid wheat species possesses desirable agronomic and quality characteristics. Drought and salinity are the most dramatic environmental stress factors that have serious impact on yield and quality of crops; however, plants can use alternative defense mechanisms against these stresses. The posttranscriptional alteration of gene expression by microRNAs (miRNAs) is one of the most conserved mechanisms. In plant species including wheat genomes, miRNAs have been implicated in the management of salt and drought stress; however, studies on einkorn wheat (Triticum monococcum subsp. monococcum) are not yet available. In this study, we aimed to identify conserved miRNAs in einkorn wheat using next generation sequencing technology and bioinformatics analysis. In order to include a larger set of miRNAs, small RNA molecules from pooled plant samples grown under normal, drought, and salinity conditions were used for the library preparation and sequence analysis. After bioinformatics analysis, we identified 167 putative mature miRNA sequences belonging to 140 distinct miRNA families. We also presented a comparative analysis to propose that miRNAs and their target genes were involved in salt and drought stress control in addition to a comprehensive analysis of the scanned target genes in the T. aestivum genome.
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Affiliation(s)
- Ercan Selçuk Ünlü
- Department of Chemistry, Faculty of Arts and Science, Abant İzzet Baysal University , Bolu , Turkey
| | - Sara Bataw
- Department of Biology, Faculty of Arts and Science, Abant İzzet Baysal University , Bolu , Turkey
| | - Didem Aslan Şen
- Department of Biology, Faculty of Arts and Science, Abant İzzet Baysal University , Bolu , Turkey
| | - Yunus Şahin
- Department of Biochemistry, School of Medicine, Altınbaş University , İstanbul , Turkey.,Department of Biology, Faculty of Arts and Science, Abant İzzet Baysal University , Bolu , Turkey
| | - Nusret Zencirci
- Department of Biology, Faculty of Arts and Science, Abant İzzet Baysal University , Bolu , Turkey
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Świda-Barteczka A, Krieger-Liszkay A, Bilger W, Voigt U, Hensel G, Szweykowska-Kulinska Z, Krupinska K. The plastid-nucleus located DNA/RNA binding protein WHIRLY1 regulates microRNA-levels during stress in barley (Hordeum vulgare L.). RNA Biol 2018; 15:886-891. [PMID: 29947287 DOI: 10.1080/15476286.2018.1481695] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
In this article a novel mechanism of retrograde signaling by chloroplasts during stress is described. This mechanism involves the DNA/RNA binding protein WHIRLY1 as a regulator of microRNA levels. By virtue of its dual localization in chloroplasts and the nucleus of the same cell, WHIRLY1 was proposed as an excellent candidate coordinator of chloroplast function and nuclear gene expression. Comparison of wild-type and transgenic plants with an RNAi-mediated knockdown of WHIRLY1 showed, that the transgenic plants were unable to cope with continuous high light conditions. They were impaired in production of several microRNAs mediating post-transcriptional responses during stress. The results support a central role of WHIRLY1 in retrograde signaling and also underpin a so far underestimated role of microRNAs in this process.
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Affiliation(s)
- Aleksandra Świda-Barteczka
- a Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology , Adam Mickiewicz University , Poznań , Poland
| | - Anja Krieger-Liszkay
- b Institute for Integrative Biology of the Cell, Commissariat à l'Energie Atomique et aux Energies Alternatives Saclay, Centre National de la Recherche Scientifique , Université Paris-Sud, Université Paris-Saclay , Gif-sur-Yvette , France
| | - Wolfgang Bilger
- c Institute of Botany , Christian-Albrechts-University , Kiel , Germany
| | - Ulrike Voigt
- c Institute of Botany , Christian-Albrechts-University , Kiel , Germany
| | - Götz Hensel
- d Department of Physiology and Cell Biology , Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) , Seeland OT Gatersleben , Germany
| | - Zofia Szweykowska-Kulinska
- a Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology , Adam Mickiewicz University , Poznań , Poland
| | - Karin Krupinska
- c Institute of Botany , Christian-Albrechts-University , Kiel , Germany
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Zhang L, Yao L, Zhang N, Yang J, Zhu X, Tang X, Calderón-Urrea A, Si H. Lateral Root Development in Potato Is Mediated by Stu-mi164 Regulation of NAC Transcription Factor. FRONTIERS IN PLANT SCIENCE 2018; 9:383. [PMID: 29651294 PMCID: PMC5884874 DOI: 10.3389/fpls.2018.00383] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 03/08/2018] [Indexed: 05/23/2023]
Abstract
The NAC designation is derived from petunia (Petunia hybrida) gene NO APICAL MERISTEM (NAM) and Arabidopsis genes ATAF1/ATAF2 and CUP-SHAPED COTYLEDON2 (CUC2), which belongs to the family of plant-specific transcription factors (TFs), and plays important role in plant development processes, such as response to biotic and abiotic stress, and hormone signaling. MicroRNAs (miRNAs) are a class of small, non-coding endogenous RNAs which play versatile and significant role in plant stress response and development via negatively affecting gene expression at a post-transcriptional level. Here, we showed that Stu-mi164 had a complementary sequence in the CDS sequence of potato NAC TFs, and that NAC expression exhibited significant differences under osmotic stress. We measured expression levels of the Stu-mi164 target gene StNAC262 between control and PEG-treated plants using real-time PCR, and the results demonstrated that they had inverse relationship. We suggested that Stu-miR164 might drive overexpression of NAC gene under osmotic stress in potato. To confirm the regulation of NAC TFs by Stu-mi164, we developed transgenic plants, using Agrobacterium tumefaciens-mediated transformation, of the potato cultivars "Gannongshu 2" and "Kexin 3" overexpressing the Stu-mi164 or the TF StNAC262. Real-time PCR analysis of transgenic potato plants under osmotic (PEG) stress, showed that potato plants overexpressing Stu-mi164 had reduced expression of StNAC262 and their osmotic resistance decreased. Furthermore, these plants had low number of lateral roots although the same length as the control. Our findings support the regulatory role of Stu-miRNAs in controlling plant response to osmotic stress via StNAC262.
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Affiliation(s)
- Li Zhang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Lei Yao
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Ning Zhang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jiangwei Yang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xi Zhu
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xun Tang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Alejandro Calderón-Urrea
- College of Plant Protection, Gansu Agricultural University, Lanzhou, China
- Department of Biology, California State University, Fresno, CA, United States
| | - Huaijun Si
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
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Identification of Blueberry miRNAs and Their Targets Based on High-Throughput Sequencing and Degradome Analyses. Int J Mol Sci 2018; 19:ijms19040983. [PMID: 29587414 PMCID: PMC5979386 DOI: 10.3390/ijms19040983] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 02/24/2018] [Accepted: 03/02/2018] [Indexed: 01/06/2023] Open
Abstract
miRNAs are important regulators of plant gene expression. To better characterize their functions, we applied high-throughput sequencing and degradome analyses to investigate three blueberry (Vaccinium ashei) tissues. A total of 127 known and 101 novel miRNAs were identified. Moreover, 141 targets for 42 known and 19 novel miRNAs were experimentally validated by degradome sequencing. A functional analysis of these miRNA targets revealed they were associated with diverse biological activities and several pathways, e.g., anthocyanin biosynthesis and cytokinin signal transduction. The data presented herein expand our understanding of the regulation of blueberry miRNAs during floral and fruit development stages. They may also provide new insights into the roles of miRNAs during anthocyanin biosynthesis in blueberry fruits.
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Guo S, Guo L, Zhao W, Xu J, Li Y, Zhang X, Shen X, Wu M, Hou X. Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Paeonia ostii. Molecules 2018; 23:molecules23020246. [PMID: 29373520 PMCID: PMC6017096 DOI: 10.3390/molecules23020246] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 01/20/2018] [Accepted: 01/24/2018] [Indexed: 01/21/2023] Open
Abstract
Paeonia ostii, a common oil-tree peony, is important ornamentally and medicinally. However, there are few studies on the chloroplast genome of Paeonia ostii. We sequenced and analyzed the complete chloroplast genome of P. ostii. The size of the P. ostii chloroplast genome is 152,153 bp, including a large single-copy region (85,373 bp), a small single-copy region (17,054 bp), and a pair of inverted repeats regions (24,863 bp). The P. ostii chloroplast genome encodes 111 genes, including 77 protein-coding genes, four ribosomal RNA genes, and 30 transfer RNA genes. The genome contains forward repeats (22), palindromic repeats (28), and tandem repeats (24). The presence of rich simple-sequence repeat loci in the genome provides opportunities for future population genetics work for breeding new varieties. A phylogenetic analysis showed that P. ostii is more closely related to Paeonia delavayi and Paeonialudlowii than to Paeoniaobovata and Paeoniaveitchii. The results of this study provide an assembly of the whole chloroplast genome of P. ostii, which may be useful for future breeding and further biological discoveries. It will provide a theoretical basis for the improvement of peony yield and the determination of phylogenetic status.
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Affiliation(s)
- Shuai Guo
- College of Agricultural (College of Tree Peony), Henan University of Science and Technology, Luoyang 471023, Henan, China; (S.G.); (L.G.); (W.Z.); (Y.L.)
- Institute of Chinese Materia Medical, China Academy of Chinese Medical Sciences, Beijing 100700, China; (J.X.); (X.Z); (X.S.); (M.W.)
| | - Lili Guo
- College of Agricultural (College of Tree Peony), Henan University of Science and Technology, Luoyang 471023, Henan, China; (S.G.); (L.G.); (W.Z.); (Y.L.)
| | - Wei Zhao
- College of Agricultural (College of Tree Peony), Henan University of Science and Technology, Luoyang 471023, Henan, China; (S.G.); (L.G.); (W.Z.); (Y.L.)
| | - Jiang Xu
- Institute of Chinese Materia Medical, China Academy of Chinese Medical Sciences, Beijing 100700, China; (J.X.); (X.Z); (X.S.); (M.W.)
| | - Yuying Li
- College of Agricultural (College of Tree Peony), Henan University of Science and Technology, Luoyang 471023, Henan, China; (S.G.); (L.G.); (W.Z.); (Y.L.)
| | - Xiaoyan Zhang
- Institute of Chinese Materia Medical, China Academy of Chinese Medical Sciences, Beijing 100700, China; (J.X.); (X.Z); (X.S.); (M.W.)
- College of Life Science, Huaibei Normal University, Huaibei 235000, Anhui, China
| | - Xiaofeng Shen
- Institute of Chinese Materia Medical, China Academy of Chinese Medical Sciences, Beijing 100700, China; (J.X.); (X.Z); (X.S.); (M.W.)
| | - Mingli Wu
- Institute of Chinese Materia Medical, China Academy of Chinese Medical Sciences, Beijing 100700, China; (J.X.); (X.Z); (X.S.); (M.W.)
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, Hubei China
| | - Xiaogai Hou
- College of Agricultural (College of Tree Peony), Henan University of Science and Technology, Luoyang 471023, Henan, China; (S.G.); (L.G.); (W.Z.); (Y.L.)
- Correspondence: ; Tel: +86-0379-6998-0776
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Świda-Barteczka A, Krieger-Liszkay A, Bilger W, Voigt U, Hensel G, Szweykowska-Kulinska Z, Krupinska K. The plastid-nucleus located DNA/RNA binding protein WHIRLY1 regulates microRNA-levels during stress in barley (Hordeum vulgare L.). RNA Biol 2018. [PMID: 29947287 DOI: 10.1101/197202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023] Open
Abstract
In this article a novel mechanism of retrograde signaling by chloroplasts during stress is described. This mechanism involves the DNA/RNA binding protein WHIRLY1 as a regulator of microRNA levels. By virtue of its dual localization in chloroplasts and the nucleus of the same cell, WHIRLY1 was proposed as an excellent candidate coordinator of chloroplast function and nuclear gene expression. Comparison of wild-type and transgenic plants with an RNAi-mediated knockdown of WHIRLY1 showed, that the transgenic plants were unable to cope with continuous high light conditions. They were impaired in production of several microRNAs mediating post-transcriptional responses during stress. The results support a central role of WHIRLY1 in retrograde signaling and also underpin a so far underestimated role of microRNAs in this process.
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Affiliation(s)
- Aleksandra Świda-Barteczka
- a Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology , Adam Mickiewicz University , Poznań , Poland
| | - Anja Krieger-Liszkay
- b Institute for Integrative Biology of the Cell, Commissariat à l'Energie Atomique et aux Energies Alternatives Saclay, Centre National de la Recherche Scientifique , Université Paris-Sud, Université Paris-Saclay , Gif-sur-Yvette , France
| | - Wolfgang Bilger
- c Institute of Botany , Christian-Albrechts-University , Kiel , Germany
| | - Ulrike Voigt
- c Institute of Botany , Christian-Albrechts-University , Kiel , Germany
| | - Götz Hensel
- d Department of Physiology and Cell Biology , Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) , Seeland OT Gatersleben , Germany
| | - Zofia Szweykowska-Kulinska
- a Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology , Adam Mickiewicz University , Poznań , Poland
| | - Karin Krupinska
- c Institute of Botany , Christian-Albrechts-University , Kiel , Germany
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Kumar V, Khare T, Shriram V, Wani SH. Plant small RNAs: the essential epigenetic regulators of gene expression for salt-stress responses and tolerance. PLANT CELL REPORTS 2018; 37:61-75. [PMID: 28951953 DOI: 10.1007/s00299-017-2210-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 09/12/2017] [Indexed: 05/07/2023]
Abstract
Saline environment cues distort the plant growth, development and crop yield. Epigenetics has emerged as one of the prime themes in plant functional genomics for molecular-stress-physiology research, as copious studies have provided new visions into the epigenetic control of stress adaptations. The epigenetic control is associated with the regulation of the expression of stress-related genes which also comprises many steady alterations inherited in next cellular generation as stress memory. These epigenetic amendments also implicate induction of small RNA (sRNA)-mediated fine-tuning of transcriptional and post-transcriptional regulations of gene expression. These tiny (19-24 nt) RNA species, particularly microRNAs (miRNAs) besides endogenous small interfering RNA (siRNA) have emerged as important responsive entities for epigenetic modulation of salt-stress effects on plants. There is a recent upsurge in development of tools and databases useful for prediction, identification and validation of small RNAs (sRNAs) and their target messenger RNAs (mRNAs). Therefore, these small but key regulatory molecules have received a wide attention in post-genomic era as potential targets for engineering stress tolerance in major glycophytic crops, though it is yet to be explored optimally. This review aims to provide critical updates on plant sRNAs as key epigenetic regulators of plant salt-stress responses, their target prediction and validation, computational tools and databases available for plant small RNAs, besides discussing their roles in salt-stress regulatory networks and adaptive mechanisms in plants, with special emphasis on their exploration for engineering salinity tolerance in plants.
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Affiliation(s)
- Vinay Kumar
- Department of Biotechnology, Modern College of Arts, Science and Commerce (Savitribai Phule Pune University), Ganeshkhind, Pune, 411016, India.
- Department of Environmental Science, Savitribai Phule Pune University, Ganeshkhind, Pune, 411007, India.
| | - Tushar Khare
- Department of Biotechnology, Modern College of Arts, Science and Commerce (Savitribai Phule Pune University), Ganeshkhind, Pune, 411016, India
| | - Varsha Shriram
- Department of Botany, Prof. Ramkrishna More College (Savitribai Phule Pune University), Akurdi, Pune, 411044, India
| | - Shabir H Wani
- Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Khudwani, Anantnag, Jammu and Kashmir, 192101, India.
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA.
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Sahito ZA, Wang L, Sun Z, Yan Q, Zhang X, Jiang Q, Ullah I, Tong Y, Li X. The miR172c-NNC1 module modulates root plastic development in response to salt in soybean. BMC PLANT BIOLOGY 2017; 17:229. [PMID: 29191158 PMCID: PMC5709930 DOI: 10.1186/s12870-017-1161-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Accepted: 11/08/2017] [Indexed: 05/23/2023]
Abstract
BACKGROUND Plant roots are highly plastic to high salinity. However, the molecular mechanism by which root developmental plasticity is regulated remains largely unknown. Previously we reported that miR172c-NNC1 module plays a key role in soybean-rhizobial symbiosis. The fact that the miR172c promoter contains several stress-related cis elements indicates that miR172c may have a role in root response to abiotic stress. RESULTS Here we showed that miR172c is greatly induced by salt stress in soybean. Overexpression of miR172c and knockdown of miR172c activity resulted in substantially increased and reduced root sensitivity to salt stress, respectively. Furthermore, we show that the target gene NNC1 (Nodule Number Control 1) of miR172c was downregulated by salt stress. The transgenic roots overexpressing or knocking down NNC1 expression also exhibited the altered root sensitivity to salt stress. CONCLUSION The study reveals the crucial role of miR172c-NNC1 module in root stress tolerance to salt stress in soybean.
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Affiliation(s)
- Zulfiqar Ali Sahito
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang, Hebei 050021 People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Lixiang Wang
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang, Hebei 050021 People’s Republic of China
| | - Zhengxi Sun
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Qiqi Yan
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Xingke Zhang
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Qiong Jiang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang, Hebei 050021 People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Ihteram Ullah
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang, Hebei 050021 People’s Republic of China
| | - Yiping Tong
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Xia Li
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
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Bai B, Shi B, Hou N, Cao Y, Meng Y, Bian H, Zhu M, Han N. microRNAs participate in gene expression regulation and phytohormone cross-talk in barley embryo during seed development and germination. BMC PLANT BIOLOGY 2017; 17:150. [PMID: 28877679 PMCID: PMC5586051 DOI: 10.1186/s12870-017-1095-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Accepted: 08/22/2017] [Indexed: 05/09/2023]
Abstract
BACKGROUND Small RNA and degradome sequencing have identified a large number of miRNA-target pairs in plant seeds. However, detailed spatial and temporal studies of miRNA-mediated regulation, which can reflect links between seed development and germination are still lacking. RESULTS In this study, we extended our investigation on miRNAs-involved gene regulation by a combined analysis of seed maturation and germination in barley. Through bioinformatics analysis of small RNA sequencing data, a total of 1324 known miRNA families and 448 novel miRNA candidates were identified. Of those, 16 known miRNAs with 40 target genes, and three novel miRNAs with four target genes were confirmed based on degradome sequencing data. Conserved miRNA families such as miR156, miR168, miR166, miR167, and miR894 were highly expressed in embryos of developing and germinating seeds. A barley-specific miRNA, miR5071, which was predicted to target an OsMLA10-like gene, accumulated at a high level, suggesting its involvement in defence response during these two developmental stages. Based on target prediction and Kyoto Encyclopedia of Genes and Genomes analysis of putative targets, nine highly expressed miRNAs were found to be related to phytohormone signalling and hormone cross-talk. Northern blot and qRT-PCR analysis showed that these miRNAs displayed differential expression patterns during seed development and germination, indicating their different roles in hormone signalling pathways. In addition, we showed that miR393 affected seed development through targeting two genes encoding the auxin receptors TIR1/AFBs in barley, as over-expression of miR393 led to an increased length-width ratio of seeds, whereas target mimic (MIM393)-mediated inhibition of its activity decreased the 1000-grain weight of seeds. Furthermore, the expression of auxin-responsive genes, abscisic acid- and gibberellic acid-related genes was altered in miR393 misexpression lines during germination and early seedling growth. CONCLUSIONS Our work indicates that miRNA-target pairs participate in gene expression regulation and hormone interaction in barley embryo and provides evidence that miR393-mediated auxin response regulation affects grain development and influences gibberellic acid and abscisic acid homeostasis during germination.
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Affiliation(s)
- Bin Bai
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou 310058 China
| | - Bo Shi
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou 310058 China
| | - Ning Hou
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou 310058 China
| | - Yanli Cao
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou 310058 China
| | - Yijun Meng
- College of Life and Environmental Sciences, Hangzhou Normal University, Zhejiang, Hangzhou 310036 China
| | - Hongwu Bian
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou 310058 China
| | - Muyuan Zhu
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou 310058 China
| | - Ning Han
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou 310058 China
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Banerjee S, Sirohi A, Ansari AA, Gill SS. Role of small RNAs in abiotic stress responses in plants. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.plgene.2017.04.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Ganie SA, Pani DR, Mondal TK. Genome-wide analysis of DUF221 domain-containing gene family in Oryza species and identification of its salinity stress-responsive members in rice. PLoS One 2017; 12:e0182469. [PMID: 28846681 PMCID: PMC5573286 DOI: 10.1371/journal.pone.0182469] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/19/2017] [Indexed: 11/20/2022] Open
Abstract
DUF221 domain-containing genes (DDP genes) play important roles in developmental biology, hormone signalling transduction, and responses to abiotic stress. Therefore to understand their structural and evolutionary relationship, we did a genome-wide analysis of this important gene family in rice. Further, through comparative genomics, DDP genes from Oryza sativa subsp. (indica), nine different wild species of rice and Arabidopsis were also identified. We also found an expansion of the DDP gene families in rice and Arabidopsis which is due to the segmental duplication events in some of the gene family members. In general, a highly purifying selection was found acting on all the deduced paralogous and orthologous DDP gene pairs. The data from microarray and subsequent qRT-PCR analysis revealed that although several OsDDPs were differentially regulated under salinity stress, yet OsDDP6 was upregulated at all the developmental stages in salt tolerant rice genotype, FL478. Interestingly, OsDDP6 was found to be involved in proline metabolism pathway as indicated by protein network analysis. The diverse gene structures, varied transmembrane topologies and the differential expression patterns implied the functional diversity in DDP genes. Therefore, the comprehensive evolutionary analysis of DDP genes from different Oryza species and Arabidopsis performed in this study will provide the basis for further functional validation studies vis-à-vis DDP genes of rice and other plant species.
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Affiliation(s)
- Showkat Ahmad Ganie
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | - Dipti Ranjan Pani
- NBPGR Base Centre, ICAR-National Rice Research Institute Campus, Cuttack, Orissa, India
| | - Tapan Kumar Mondal
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
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Shen X, Wu M, Liao B, Liu Z, Bai R, Xiao S, Li X, Zhang B, Xu J, Chen S. Complete Chloroplast Genome Sequence and Phylogenetic Analysis of the Medicinal Plant Artemisia annua. Molecules 2017; 22:molecules22081330. [PMID: 28800082 PMCID: PMC6152406 DOI: 10.3390/molecules22081330] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 07/31/2017] [Accepted: 08/08/2017] [Indexed: 12/17/2022] Open
Abstract
The complete chloroplast genome of Artemisia annua (Asteraceae), the primary source of artemisinin, was sequenced and analyzed. The A. annua cp genome is 150,995 bp, and harbors a pair of inverted repeat regions (IRa and IRb), of 24,850 bp each that separate large (LSC, 82,988 bp) and small (SSC, 18,267 bp) single-copy regions. Our annotation revealed that the A. annua cp genome contains 113 genes and 18 duplicated genes. The gene order in the SSC region of A. annua is inverted; this fact is consistent with the sequences of chloroplast genomes from three other Artemisia species. Fifteen (15) forward and seventeen (17) inverted repeats were detected in the genome. The existence of rich SSR loci in the genome suggests opportunities for future population genetics work on this anti-malarial medicinal plant. In A. annua cpDNA, the rps19 gene was found in the LSC region rather than the IR region, and the rps19 pseudogene was absent in the IR region. Sequence divergence analysis of five Asteraceae species indicated that the most highly divergent regions were found in the intergenic spacers, and that the differences between A. annua and A. fukudo were very slight. A phylogenetic analysis revealed a sister relationship between A. annua and A. fukudo. This study identified the unique characteristics of the A. annua cp genome. These results offer valuable information for future research on Artemisia species identification and for the selective breeding of A. annua with high pharmaceutical efficacy.
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Affiliation(s)
- Xiaofeng Shen
- Institute of Chinese Materia Medica, Artemisinin Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China.
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 300193, China.
| | - Mingli Wu
- Institute of Chinese Materia Medica, Artemisinin Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China.
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, Hubei, China.
| | - Baosheng Liao
- Institute of Chinese Materia Medica, Artemisinin Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Zhixiang Liu
- Institute of Chinese Materia Medica, Artemisinin Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Rui Bai
- College of Pharmacy and Chemistry, Dali University, Dali 671000, Yunnan, China.
| | - Shuiming Xiao
- Institute of Chinese Materia Medica, Artemisinin Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Xiwen Li
- Institute of Chinese Materia Medica, Artemisinin Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Boli Zhang
- Institute of Chinese Materia Medica, Artemisinin Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China.
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 300193, China.
| | - Jiang Xu
- Institute of Chinese Materia Medica, Artemisinin Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Shilin Chen
- Institute of Chinese Materia Medica, Artemisinin Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China.
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Genome-Wide Identification and Characterization of Salinity Stress-Responsive miRNAs in Wild Emmer Wheat (Triticum turgidum ssp. dicoccoides). Genes (Basel) 2017; 8:genes8060156. [PMID: 28587281 PMCID: PMC5485520 DOI: 10.3390/genes8060156] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 05/26/2017] [Accepted: 05/26/2017] [Indexed: 12/17/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of endogenous small noncoding RNAs which regulate diverse molecular and biochemical processes at a post-transcriptional level in plants. As the ancestor of domesticated wheat, wild emmer wheat (Triticum turgidum ssp. dicoccoides) has great genetic potential for wheat improvement. However, little is known about miRNAs and their functions on salinity stress in wild emmer. To obtain more information on miRNAs in wild emmer, we systematically investigated and characterized the salinity-responsive miRNAs using deep sequencing technology. A total of 88 conserved and 124 novel miRNAs were identified, of which 50 were proven to be salinity-responsive miRNAs, with 32 significantly up-regulated and 18 down-regulated. miR172b and miR1120a, as well as mi393a, were the most significantly differently expressed. Targets of these miRNAs were computationally predicted, then Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis found that the targets of salinity-responsive miRNAs were enriched in transcription factors and stress-related proteins. Finally, we investigated the expression profiles of seven miRNAs ranging between salt-tolerant and sensitive genotypes, and found that they played critical roles in salinity tolerance in wild emmer. Our results systematically identified the salinity-responsive miRNAs in wild emmer, not only enriching the miRNA resource but also laying the foundation for further study on the biological functions and evolution of miRNAs in wild wheat and beyond.
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Alptekin B, Langridge P, Budak H. Abiotic stress miRNomes in the Triticeae. Funct Integr Genomics 2017; 17:145-170. [PMID: 27665284 PMCID: PMC5383695 DOI: 10.1007/s10142-016-0525-9] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 09/02/2016] [Accepted: 09/09/2016] [Indexed: 12/14/2022]
Abstract
The continued growth in world population necessitates increases in both the quantity and quality of agricultural production. Triticeae members, particularly wheat and barley, make an important contribution to world food reserves by providing rich sources of carbohydrate and protein. These crops are grown over diverse production environments that are characterized by a range of environmental or abiotic stresses. Abiotic stresses such as drought, heat, salinity, or nutrient deficiencies and toxicities cause large yield losses resulting in economic and environmental damage. The negative effects of abiotic stresses have increased at an alarming rate in recent years and are predicted to further deteriorate due to climate change, land degradation, and declining water supply. New technologies have provided an important tool with great potential for improving crop tolerance to the abiotic stresses: microRNAs (miRNAs). miRNAs are small regulators of gene expression that act on many different molecular and biochemical processes such as development, environmental adaptation, and stress tolerance. miRNAs can act at both the transcriptional and post-transcriptional levels, although post-transcriptional regulation is the most common in plants where miRNAs can inhibit the translation of their mRNA targets via complementary binding and cleavage. To date, expression of several miRNA families such as miR156, miR159, and miR398 has been detected as responsive to environmental conditions to regulate stress-associated molecular mechanisms individually and/or together with their various miRNA partners. Manipulation of these miRNAs and their targets may pave the way to improve crop performance under several abiotic stresses. Here, we summarize the current status of our knowledge on abiotic stress-associated miRNAs in members of the Triticeae tribe, specifically in wheat and barley, and the miRNA-based regulatory mechanisms triggered by stress conditions. Exploration of further miRNA families together with their functions under stress will improve our knowledge and provide opportunities to enhance plant performance to help us meet global food demand.
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Affiliation(s)
- Burcu Alptekin
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA
| | - Peter Langridge
- School of Agriculture, Food and Wine, University of Adelaide, Adelaide, Australia
| | - Hikmet Budak
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA.
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Djami-Tchatchou AT, Sanan-Mishra N, Ntushelo K, Dubery IA. Functional Roles of microRNAs in Agronomically Important Plants-Potential as Targets for Crop Improvement and Protection. FRONTIERS IN PLANT SCIENCE 2017; 8:378. [PMID: 28382044 PMCID: PMC5360763 DOI: 10.3389/fpls.2017.00378] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 03/06/2017] [Indexed: 05/18/2023]
Abstract
MicroRNAs (miRNAs) are a class of small non-coding RNAs that have recently emerged as important regulators of gene expression, mainly through cleavage and/or translation inhibition of the target mRNAs during or after transcription. miRNAs play important roles by regulating a multitude of biological processes in plants which include maintenance of genome integrity, development, metabolism, and adaptive responses toward environmental stresses. The increasing population of the world and their food demands requires focused efforts for the improvement of crop plants to ensure sustainable food production. Manipulation of mRNA transcript abundance via miRNA control provides a unique strategy for modulating differential plant gene expression and miRNAs are thus emerging as the next generation targets for genetic engineering for improvement of the agronomic properties of crops. However, a deeper understanding of its potential and the mechanisms involved will facilitate the design of suitable strategies to obtain the desirable traits with minimum trade-offs in the modified crops. In this regard, this review highlights the diverse roles of conserved and newly identified miRNAs in various food and industrial crops and recent advances made in the uses of miRNAs to improve plants of agronomically importance so as to significantly enhance crop yields and increase tolerance to various environmental stress agents of biotic-or abiotic origin.
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Affiliation(s)
- Arnaud T. Djami-Tchatchou
- Department of Agriculture and Animal Health, University of South Africa (Florida Campus)Pretoria, South Africa
| | - Neeti Sanan-Mishra
- Plant RNAi Biology Group, International Centre for Genetic Engineering and BiotechnologyNew Delhi, India
| | - Khayalethu Ntushelo
- Department of Agriculture and Animal Health, University of South Africa (Florida Campus)Pretoria, South Africa
| | - Ian A. Dubery
- Department of Biochemistry, University of Johannesburg (Auckland Park Kingsway Campus)Johannesburg, South Africa
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Liu H, Able AJ, Able JA. SMARTER De-Stressed Cereal Breeding. TRENDS IN PLANT SCIENCE 2016; 21:909-925. [PMID: 27514453 DOI: 10.1016/j.tplants.2016.07.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 06/30/2016] [Accepted: 07/05/2016] [Indexed: 05/06/2023]
Abstract
In cereal breeding programs, improved yield potential and stability are ultimate goals when developing new varieties. To facilitate achieving these goals, reproductive success under stressful growing conditions is of the highest priority. In recent times, small RNA (sRNA)-mediated pathways have been associated with the regulation of genes involved in stress adaptation and reproduction in both model plants and several cereals. Reproductive and physiological traits such as flowering time, reproductive branching, and root architecture can be manipulated by sRNA regulatory modules. We review sRNA-mediated pathways that could be exploited to expand crop diversity with adaptive traits and, in particular, the development of high-yielding stress-tolerant cereals: SMARTER cereal breeding through 'Small RNA-Mediated Adaptation of Reproductive Targets in Epigenetic Regulation'.
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Affiliation(s)
- Haipei Liu
- School of Agriculture, Food and Wine, University of Adelaide, Waite Research Institute, PMB 1, Glen Osmond, South Australia 5064, Australia
| | - Amanda J Able
- School of Agriculture, Food and Wine, University of Adelaide, Waite Research Institute, PMB 1, Glen Osmond, South Australia 5064, Australia
| | - Jason A Able
- School of Agriculture, Food and Wine, University of Adelaide, Waite Research Institute, PMB 1, Glen Osmond, South Australia 5064, Australia.
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Deng P, Bian J, Yue H, Feng K, Wang M, Du X, Weining S, Nie X. Characterization of microRNAs and their targets in wild barley (Hordeum vulgare subsp. spontaneum) using deep sequencing. Genome 2016; 59:339-48. [PMID: 27100818 DOI: 10.1139/gen-2015-0224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
MicroRNAs (miRNA) are a class of small, endogenous RNAs that play a negative regulatory role in various developmental and metabolic processes of plants. Wild barley (Hordeum vulgare subsp. spontaneum), as the progenitor of cultivated barley (Hordeum vulgare subsp. vulgare), has served as a valuable germplasm resource for barley genetic improvement. To survey miRNAs in wild barley, we sequenced the small RNA library prepared from wild barley using the Illumina deep sequencing technology. A total of 70 known miRNAs and 18 putative novel miRNAs were identified. Sequence analysis revealed that all of the miRNAs identified in wild barley contained the highly conserved hairpin sequences found in barley cultivars. MiRNA target predictions showed that 12 out of 52 miRNA families were predicted to target transcription factors, including 8 highly conserved miRNA families in plants and 4 wheat-barley conserved miRNA families. In addition to transcription factors, other predicted target genes were involved in diverse physiological and metabolic processes and stress defense. Our study for the first time reported the large-scale investigation of small RNAs in wild barley, which will provide essential information for understanding the regulatory role of miRNAs in wild barley and also shed light on future practical utilization of miRNAs for barley improvement.
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Affiliation(s)
- Pingchuan Deng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, Shaanxi 712100, China.,State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jianxin Bian
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, Shaanxi 712100, China.,State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hong Yue
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, Shaanxi 712100, China.,State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Kewei Feng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, Shaanxi 712100, China.,State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mengxing Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, Shaanxi 712100, China.,State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xianghong Du
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, Shaanxi 712100, China.,State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Song Weining
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, Shaanxi 712100, China.,State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, Shaanxi 712100, China.,State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, Shaanxi 712100, China
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Shriram V, Kumar V, Devarumath RM, Khare TS, Wani SH. MicroRNAs As Potential Targets for Abiotic Stress Tolerance in Plants. FRONTIERS IN PLANT SCIENCE 2016; 7:817. [PMID: 27379117 PMCID: PMC4906921 DOI: 10.3389/fpls.2016.00817] [Citation(s) in RCA: 174] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/25/2016] [Indexed: 05/19/2023]
Abstract
The microRNAs (miRNAs) are small (20-24 nt) sized, non-coding, single stranded riboregulator RNAs abundant in higher organisms. Recent findings have established that plants assign miRNAs as critical post-transcriptional regulators of gene expression in sequence-specific manner to respond to numerous abiotic stresses they face during their growth cycle. These small RNAs regulate gene expression via translational inhibition. Usually, stress induced miRNAs downregulate their target mRNAs, whereas, their downregulation leads to accumulation and function of positive regulators. In the past decade, investigations were mainly aimed to identify plant miRNAs, responsive to individual or multiple environmental factors, profiling their expression patterns and recognizing their roles in stress responses and tolerance. Altered expressions of miRNAs implicated in plant growth and development have been reported in several plant species subjected to abiotic stress conditions such as drought, salinity, extreme temperatures, nutrient deprivation, and heavy metals. These findings indicate that miRNAs may hold the key as potential targets for genetic manipulations to engineer abiotic stress tolerance in crop plants. This review is aimed to provide recent updates on plant miRNAs, their biogenesis and functions, target prediction and identification, computational tools and databases available for plant miRNAs, and their roles in abiotic stress-responses and adaptive mechanisms in major crop plants. Besides, the recent case studies for overexpressing the selected miRNAs for miRNA-mediated enhanced abiotic stress tolerance of transgenic plants have been discussed.
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Affiliation(s)
- Varsha Shriram
- Department of Botany, Prof. Ramkrishna More Arts, Commerce and Science College, Savitribai Phule Pune UniversityPune, India
| | - Vinay Kumar
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune UniversityPune, India
- *Correspondence: Vinay Kumar
| | - Rachayya M. Devarumath
- Molecular Biology and Genetic Engineering Section, Vasantdada Sugar InstitutePune, India
| | - Tushar S. Khare
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune UniversityPune, India
| | - Shabir H. Wani
- Division of Genetics and Plant Breeding, Faculty of Agriculture WADURA, Sher-e-Kashmir University of Agricultural Sciences and TechnologyKashmir, India
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