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Cao Y, Yang W, Ma J, Cheng Z, Zhang X, Liu X, Wu X, Zhang J. An Integrated Framework for Drought Stress in Plants. Int J Mol Sci 2024; 25:9347. [PMID: 39273296 PMCID: PMC11395155 DOI: 10.3390/ijms25179347] [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: 08/02/2024] [Revised: 08/27/2024] [Accepted: 08/27/2024] [Indexed: 09/15/2024] Open
Abstract
With global warming, drought stress is becoming increasingly severe, causing serious impacts on crop yield and quality. In order to survive under adverse conditions such as drought stress, plants have evolved a certain mechanism to cope. The tolerance to drought stress is mainly improved through the synergistic effect of regulatory pathways, such as transcription factors, phytohormone, stomatal movement, osmotic substances, sRNA, and antioxidant systems. This study summarizes the research progress on plant drought resistance, in order to provide a reference for improving plant drought resistance and cultivating drought-resistant varieties through genetic engineering technology.
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Affiliation(s)
- Yanyong Cao
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, The Shennong Laboratory, Zhengzhou 450002, China
| | - Wenbo Yang
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, The Shennong Laboratory, Zhengzhou 450002, China
| | - Juan Ma
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, The Shennong Laboratory, Zhengzhou 450002, China
| | - Zeqiang Cheng
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, The Shennong Laboratory, Zhengzhou 450002, China
| | - Xuan Zhang
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Xueman Liu
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Xiaolin Wu
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Jinghua Zhang
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
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Malwattage NR, Wone B, Wone BWM. A CAM-Related NF-YB Transcription Factor Enhances Multiple Abiotic Stress Tolerance in Arabidopsis. Int J Mol Sci 2024; 25:7107. [PMID: 39000218 PMCID: PMC11241642 DOI: 10.3390/ijms25137107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 06/19/2024] [Accepted: 06/26/2024] [Indexed: 07/16/2024] Open
Abstract
Abiotic stresses often occur simultaneously, and the tolerance mechanisms of plants to combined multiple abiotic stresses remain poorly studied. Extremophytes, adapted to abiotic stressors, might possess stress-adaptive or -responsive regulators that could enhance multiple abiotic stress resistance in crop plants. We identified an NF-YB transcription factor (TF) from the heat-tolerant obligate Crassulacean acid metabolism (CAM) plant, Kalanchoe fedtschenkoi, as a potential regulator of multiple abiotic stresses. The KfNF-YB3 gene was overexpressed in Arabidopsis to determine its role in multiple abiotic stress responses. Transgenic lines exhibited accelerated flowering time, increased biomass, larger rosette size, higher seed yield, and more leaves. Transgenic lines had higher germination rates under combined NaCl, osmotic, and water-deficit stress treatments compared to control plants. They also showed enhanced root growth and survival under simultaneous NaCl, osmotic, water-deficit, and heat stress conditions in vitro. Interestingly, potted transgenic lines had higher survival rates, yield, and biomass under simultaneous heat, water-deficit, and light stresses compared to control plants. Altogether, these results provide initial insights into the functions of a CAM-related TF and its potential roles in regulating multiple abiotic stress responses. The CAM abiotic stress-responsive TF-based approach appears to be an ideal strategy to enhance multi-stress resilience in crop plants.
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Affiliation(s)
| | | | - Bernard W. M. Wone
- Department of Biology, University of South Dakota, Vermillion, SD 57069, USA
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Luo G, Li L, Yang X, Yu Y, Gao L, Mo B, Chen X, Liu L. MicroRNA1432 regulates rice drought stress tolerance by targeting the CALMODULIN-LIKE2 gene. PLANT PHYSIOLOGY 2024; 195:1954-1968. [PMID: 38466155 DOI: 10.1093/plphys/kiae127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/31/2024] [Accepted: 01/31/2024] [Indexed: 03/12/2024]
Abstract
Due to climate change, drought has become a major threat to rice (Oryza sativa L.) growth and yield worldwide. Understanding the genetic basis of drought tolerance in rice is therefore of great importance. Here, we identified a microRNA, miR1432, which regulates rice drought tolerance by targeting the CALMODULIN-LIKE2 (OsCaML2) gene. Mutation of MIR1432 or suppression of miR1432 expression significantly impaired seed germination and seedling growth under drought-stress conditions. Molecular analysis demonstrated that miR1432 affected rice drought tolerance by directly targeting OsCaML2, which encodes an EF-hand chiral calcium-binding protein. Overexpression of a miR1432-resistant form of OsCaML2 (OEmCaML2) phenocopied the mir1432 mutant and miR1432 suppression plants. Furthermore, the suppression of miR1432 severely affected the expression of genes involved in responses to stimulation, metabolism and signal transduction, especially the mitogen-activated protein kinase (MAPK) pathway and hormone transduction pathway in rice under drought stress. Thus, our findings show that the miR1432-OsCaML2 module plays an important role in the regulation of rice drought tolerance, suggesting its potential utilization in developing molecular breeding strategies that improve crop drought tolerance.
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Affiliation(s)
- Guangyu Luo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Lin Li
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Xiaoyu Yang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Yu Yu
- School of Life Sciences, Peking-Tsinghua Joint Center for Life Sciences, Peking University, Beijing 100871, China
| | - Lei Gao
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Beixin Mo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Xuemei Chen
- School of Life Sciences, Peking-Tsinghua Joint Center for Life Sciences, Peking University, Beijing 100871, China
| | - Lin Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China
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Yan W, Sharif R, Sohail H, Zhu Y, Chen X, Xu X. Surviving a Double-Edged Sword: Response of Horticultural Crops to Multiple Abiotic Stressors. Int J Mol Sci 2024; 25:5199. [PMID: 38791235 PMCID: PMC11121501 DOI: 10.3390/ijms25105199] [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: 03/31/2024] [Revised: 05/04/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Climate change-induced weather events, such as extreme temperatures, prolonged drought spells, or flooding, pose an enormous risk to crop productivity. Studies on the implications of multiple stresses may vary from those on a single stress. Usually, these stresses coincide, amplifying the extent of collateral damage and contributing to significant financial losses. The breadth of investigations focusing on the response of horticultural crops to a single abiotic stress is immense. However, the tolerance mechanisms of horticultural crops to multiple abiotic stresses remain poorly understood. In this review, we described the most prevalent types of abiotic stresses that occur simultaneously and discussed them in in-depth detail regarding the physiological and molecular responses of horticultural crops. In particular, we discussed the transcriptional, posttranscriptional, and metabolic responses of horticultural crops to multiple abiotic stresses. Strategies to breed multi-stress-resilient lines have been presented. Our manuscript presents an interesting amount of proposed knowledge that could be valuable in generating resilient genotypes for multiple stressors.
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Affiliation(s)
- Wenjing Yan
- School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (W.Y.); (R.S.); (H.S.); (Y.Z.); (X.C.)
| | - Rahat Sharif
- School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (W.Y.); (R.S.); (H.S.); (Y.Z.); (X.C.)
| | - Hamza Sohail
- School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (W.Y.); (R.S.); (H.S.); (Y.Z.); (X.C.)
| | - Yu Zhu
- School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (W.Y.); (R.S.); (H.S.); (Y.Z.); (X.C.)
| | - Xuehao Chen
- School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (W.Y.); (R.S.); (H.S.); (Y.Z.); (X.C.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Xuewen Xu
- School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (W.Y.); (R.S.); (H.S.); (Y.Z.); (X.C.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
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Yuan J, Wang X, Qu S, Shen T, Li M, Zhu L. The roles of miR156 in abiotic and biotic stresses in plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 204:108150. [PMID: 37922645 DOI: 10.1016/j.plaphy.2023.108150] [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: 08/02/2023] [Revised: 10/09/2023] [Accepted: 10/27/2023] [Indexed: 11/07/2023]
Abstract
MicroRNAs (miRNAs), known as a kind of non-coding RNA, can negatively regulate its target genes. To date, the roles of various miRNAs in plant development and resistance to abiotic and biotic stresses have been widely explored. The present review summarized and discussed the functions of miR156 or miR156-SPL module in abiotic and biotic stresses, such as drought, salt, heat, cold stress, UV-B radiation, heavy mental hazards, nutritional starvation, as well as plant viruses, plant diseases, etc. Based on this, the regulation of miR156-involved stress tolerance was better understood, thus, it would be much easier for plant biologists to carry out suitable strategies to help plants suffer from unfavorable living environments.
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Affiliation(s)
- Jing Yuan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xi Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Shengtao Qu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Tian Shen
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Mingjun Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Lingcheng Zhu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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Liu J, Wei L, Feng S. Research progress of non-coding RNAs in vegetable responses to abiotic stresses. Gene 2023:147537. [PMID: 37301448 DOI: 10.1016/j.gene.2023.147537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 05/25/2023] [Accepted: 06/01/2023] [Indexed: 06/12/2023]
Abstract
Vegetable crops play a crucial role in agricultural production, providing essential vitamins and minerals necessary for a healthy diet. Recently, there has been growing interest in cultivating vegetable varieties with outstanding agricultural and economic traits. However, vegetable production is often exposed to various abiotic stresses like soil drought, temperature fluctuations, and heavy metal stress, which can negatively impact yield and quality. While previous research has investigated the physiological responses of vegetable crops to such stressors, less attention has been given to genetic networks. Plants respond to environmental stress mainly by adapting first and then reacting, thereby enhancing their resistance to stress. Typically, different abiotic stresses trigger epigenetic changes, which can regulate non-coding RNAs. Therefore, studying the epigenetic mechanisms of vegetable crop responses to abiotic stress can provide insights into the molecular response mechanisms of plants under stress. This knowledge has practical applications in breeding vegetable crops for resistance. This article summarizes the primary research findings on the regulation of non-coding RNAs and their expression levels in vegetable crops exposed to abiotic stresses to guide molecular breeding approaches for vegetable crops.
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Affiliation(s)
- Jipeng Liu
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou 311300, Zhejiang, China
| | - Liang Wei
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou 311300, Zhejiang, China
| | - Shengjun Feng
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou 311300, Zhejiang, China.
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Verma D, Kaushal N, Balhara R, Singh K. Genome-wide analysis of Catalase gene family reveal insights into abiotic stress response mechanism in Brassica juncea and B. rapa. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 330:111620. [PMID: 36738937 DOI: 10.1016/j.plantsci.2023.111620] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/19/2023] [Accepted: 01/28/2023] [Indexed: 06/18/2023]
Abstract
Environmental stresses affect the yield and productivity of Brassica crops. Catalases are important antioxidant enzymes involved in reducing excess hydrogen peroxide produced by environmental stresses. In the present study, nine and seven CAT family members in two oilseed Brassica species (B. juncea and B. rapa) were identified with complete characterization based on gene and protein structure. Phylogenetic classification categorized CAT proteins into three classes and differentiated the monocot and dicot-specific CAT proteins. Further, the gene and protein characterizations revealed a high degree of conservation across the CAT family members. Differences were observed in the CAT-HEME binding affinity in CAT1, CAT2, and CAT3 isozymes, which could suggest their differential enzyme activities in different conditions. Furthermore, protein-protein interaction with other antioxidant proteins suggested their coordinated role in ROS scavenging mechanisms. Notably, the differential gene expression of BjuCATs and BraCATs and CAT enzyme activities suggested their crucial roles in major abiotic stresses faced by Brassica species. Promoter analysis in BjuCATs and BraCATs suggested the presence of abiotic-stress responsive cis-regulatory elements. Gene regulatory network analysis suggested miRNA and TF mediated stress response in BjuCATs and BraCATs. CAT family screening and characterization in Brassica sp. has established a basic ground for further functional validation in abiotic and heavy-metal stresses which can help in developing stress tolerant crops.
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Affiliation(s)
- Deepika Verma
- Department of Biotechnology, BMS Block I, Panjab University, Sector 25, Chandigarh 160014, India
| | - Nishant Kaushal
- Department of Biotechnology, BMS Block I, Panjab University, Sector 25, Chandigarh 160014, India
| | - Rinku Balhara
- Department of Biotechnology, BMS Block I, Panjab University, Sector 25, Chandigarh 160014, India
| | - Kashmir Singh
- Department of Biotechnology, BMS Block I, Panjab University, Sector 25, Chandigarh 160014, India.
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Tsai WA, Sung PH, Kuo YW, Chen MC, Jeng ST, Lin JS. Involvement of microRNA164 in responses to heat stress in Arabidopsis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 329:111598. [PMID: 36657663 DOI: 10.1016/j.plantsci.2023.111598] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 12/28/2022] [Accepted: 01/14/2023] [Indexed: 06/17/2023]
Abstract
MicroRNAs (miRNAs) are considered to be integral parts of plant stress regulatory networks. Under long-term heat stress, miR164 is induced. Conversely, its targets are repressed. Transgenic overexpressors (164OE) and mutants of MIR164 (mir164) were used to study miR164's functions during heat responses. Target gene expression decreased in 164OE transgenic plants and increased in mir164a-4 and mir164b mutants. Under heat stress, the mir164 mutants presented heat-sensitive phenotypes, while 164OE transgenic plants showed better thermotolerance than wild-type (WT) plants. Overexpression of miR164 decreased heat-inhibition of hypocotyl lengths. Under heat stress, miR164 target genes modulated the expression of chlorophyll b reductase and chlorophyll catabolic genes, reducing the chlorophyll a/b ratio. More H2O2 accumulated in the mir164 mutants under heat stress, which may have caused oxidative damage. In addition, expression of HSPs was altered in the experimental plants compared to that of the WT. Overall, miR164 influenced target gene expression, altering development, chlorophyll a/b ratio, H2O2-caused damage, and HSPs expression under long-term heat stress. These phenomena, in turn, likely influence the thermotolerance of plants.
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Affiliation(s)
- Wei-An Tsai
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia.
| | - Po-Han Sung
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan.
| | - Yun-Wei Kuo
- Department of Agronomy, National Chung Hsing University, Taichung 40227, Taiwan; Institute of Flowers, Sanming Academy of Agricultural Sciences, Sanming 365000, Fujian, China.
| | - Ming-Cheng Chen
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan.
| | - Shih-Tong Jeng
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei 10617, Taiwan.
| | - Jeng-Shane Lin
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan.
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Megha S, Wang Z, Kav NNV, Rahman H. Genome-wide identification of biotin carboxyl carrier subunits of acetyl-CoA carboxylase in Brassica and their role in stress tolerance in oilseed Brassica napus. BMC Genomics 2022; 23:707. [PMID: 36253756 PMCID: PMC9578262 DOI: 10.1186/s12864-022-08920-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 09/23/2022] [Indexed: 11/22/2022] Open
Abstract
Background Biotin carboxyl carrier protein (BCCP) is a subunit of Acetyl CoA-carboxylase (ACCase) which catalyzes the conversion of acetyl-CoA to malonyl-CoA in a committed step during the de novo biosynthesis of fatty acids. Lipids, lipid metabolites, lipid-metabolizing and -modifying enzymes are known to play a role in biotic and abiotic stress tolerance in plants. In this regard, an understanding of the Brassica napus BCCP genes will aid in the improvement of biotic and abiotic stress tolerance in canola. Results In this study, we identified 43 BCCP genes in five Brassica species based on published genome data. Among them, Brassica rapa, Brassica oleracea, Brassica nigra, Brassica napus and Brassica juncea had six, seven, seven, 10 and 13 BCCP homologs, respectively. Phylogenetic analysis categorized them into five classes, each with unique conserved domains. The promoter regions of all BCCP genes contained stress-related cis-acting elements as determined by cis-element analysis. We identified four and three duplicated gene pairs (segmental) in B. napus and B. juncea respectively, indicating the role of segmental duplication in the expansion of this gene family. The Ka/Ks ratios of orthologous gene pairs between Arabidopsis thaliana and five Brassica species were mostly less than 1.0, implying that purifying selection, i.e., selective removal of deleterious alleles, played a role during the evolution of Brassica genomes. Analysis of 10 BnaBCCP genes using qRT-PCR showed a different pattern of expression because of exposure of the plants to biotic stresses, such as clubroot and sclerotinia diseases, and abiotic stresses such as drought, low temperature and salinity stresses. Conclusions The identification and functional analysis of the Brassica BCCPs demonstrated that some of these genes might play important roles in biotic and abiotic stress responses. Results from this study could lay the foundation for a better understanding of these genes for the improvement of Brassica crops for stress tolerance. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08920-y.
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Affiliation(s)
- Swati Megha
- Department of Agricultural Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Zhengping Wang
- Department of Agricultural Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Nat N V Kav
- Department of Agricultural Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Habibur Rahman
- Department of Agricultural Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
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Mohsenzadeh Golfazani M, Taghvaei MM, Samizadeh Lahiji H, Ashery S, Raza A. Investigation of proteins' interaction network and the expression pattern of genes involved in the ABA biogenesis and antioxidant system under methanol spray in drought-stressed rapeseed. 3 Biotech 2022; 12:217. [PMID: 35965657 PMCID: PMC9365922 DOI: 10.1007/s13205-022-03290-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 07/26/2022] [Indexed: 01/29/2023] Open
Abstract
Drought is one of the most critical abiotic stresses, which significantly impair rapeseed (Brassica napus L.) productivity. Several factors can regulate the stress response, including changes in gene expression in biological pathways, extensive protein interaction networks, and post-translational regulatory factors like microRNAs. External factors can also affect the intensity of the stress response. Therefore, this study investigated protein-protein interactions of some essential genes involved in abscisic acid (ABA) production, antioxidant system, and Krebs cycle. The expression of phyton synthase (PSY), 9-cis-epoxycarotenoid dioxygenase (NCED3), aldehyde oxidase (AAO3), thioredoxin reductase (NTRC), and glutathione reductase (GR) genes in two rapeseed genotypes, i.e., Hyola308 (drought-sensitive) and SLM046 (drought-tolerant) were evaluated using qRT-PCR technique under 72 h of drought stress and methanol foliar application. In the SLM046 (tolerant) genotype, the expression levels of PYS, NCED, AAO3, and GR genes were increased after 8 h of foliar application. The expression level of the NTR gene was increased 8 and 24 h after stress and methanol treatment. In the Hyola308 genotype, PYS, AAO3, NTR, and GR genes' expression level was increased 8 h after methanol foliar application, and the NCED gene was increased 24 h after stress with methanol treatment. In general, methanol foliar application increased the expression levels of several genes. Particularly, the gene expression was considerably higher in the SLM046 genotype than in Hyola308. Bioinformatics prediction of microRNAs targeting PSY, NCED, GR, NTRC, and AAO3 genes was performed, and 38, 38, 13, 11, and 11 microRNAs were predicted for these genes, respectively. The study of effective microRNAs showed that sometimes more than one type of microRNA could affect the desired gene, and in some cases, a conserved family of microRNAs caused the main effect on gene expression. Overall, our results lay the foundation for functional characterization of these genes or gene-miRNA modules in regulating drought stress tolerance in rapeseed.
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Affiliation(s)
| | - Mohammad Mahdi Taghvaei
- Department of Agricultural Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
| | - Habibollah Samizadeh Lahiji
- Department of Agricultural Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
| | - Seddigheh Ashery
- Department of Agricultural Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
| | - Ali Raza
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
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Tan M, Niu J, Peng DZ, Cheng Q, Luan MB, Zhang ZQ. Clone and Function Verification of the OPR gene in Brassica napus Related to Linoleic Acid Synthesis. BMC PLANT BIOLOGY 2022; 22:192. [PMID: 35410118 PMCID: PMC9003975 DOI: 10.1186/s12870-022-03549-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 03/16/2022] [Indexed: 05/30/2023]
Abstract
BACKGROUND Fatty acid composition and content affect rapeseed oil quality. Fatty acid synthesis-related genes in rapeseed have been studied globally by researchers. Nevertheless, rapeseed oil is mainly composed of seven different fatty acids (FA), and each fatty acid was regulated by different genes. Furthermore, different FA affect each other, which needs continuous and in-depth research to obtain more clear results in Brassica napus. RESULTS In this paper, broad-scale miRNA expression profiles were constructed and 21 differentially expressed miRNAs were detected. GO enrichment analysis showed that most up-regulated proteins were involved in transcription factor activity and catalytic activity. KEGG pathway enrichment analysis indicated that 20 pathways involving 36 target genes were enriched, of which the bna00592 pathway may be involved in fatty acid metabolism. The results were verified using a quantitative real-time PCR (RT-qPCR) analysis, we found that the target gene of bna-miR156b > c > g was the OPR (12-oxo-phytodienoic acid reductase). Four copies of OPR gene were found, and the over-expression vectors (pCAMBIA1300-35 s-OPR and pCAMBIA1300-RNAi-OPR) were constructed to verify their functions. In T1 and T2 generation, the content of linoleic acid (LA) increased significantly in OE but deceased in OPRi. CONCLUSIONS This is the first study to provide four copies of the OPR gene that regulates LA metabolism, can be used for the molecular mechanism of LA and optimizing fatty acid profiles in oilseed for breeding programs.
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Affiliation(s)
- Min Tan
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Juan Niu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, Hunan, China
| | - Duo Zi Peng
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Qian Cheng
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Ming Bao Luan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, Hunan, China.
| | - Zhen Qian Zhang
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China.
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Shen X, He J, Ping Y, Guo J, Hou N, Cao F, Li X, Geng D, Wang S, Chen P, Qin G, Ma F, Guan Q. The positive feedback regulatory loop of miR160-Auxin Response Factor 17-HYPONASTIC LEAVES 1 mediates drought tolerance in apple trees. PLANT PHYSIOLOGY 2022; 188:1686-1708. [PMID: 34893896 PMCID: PMC8896624 DOI: 10.1093/plphys/kiab565] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 11/10/2021] [Indexed: 05/25/2023]
Abstract
Drought stress tolerance is a complex trait regulated by multiple factors. Here, we demonstrate that the miRNA160-Auxin Response Factor 17 (ARF17)-HYPONASTIC LEAVES 1 module is crucial for apple (Malus domestica) drought tolerance. Using stable transgenic plants, we found that drought tolerance was improved by higher levels of Mdm-miR160 or MdHYL1 and by decreased levels of MdARF17, whereas reductions in MdHYL1 or increases in MdARF17 led to greater drought sensitivity. Further study revealed that modulation of drought tolerance was achieved through regulation of drought-responsive miRNA levels by MdARF17 and MdHYL1; MdARF17 interacted with MdHYL1 and bound to the promoter of MdHYL1. Genetic analysis further suggested that MdHYL1 is a direct downstream target of MdARF17. Importantly, MdARF17 and MdHYL1 regulated the abundance of Mdm-miR160. In addition, the Mdm-miR160-MdARF17-MdHYL1 module regulated adventitious root development. We also found that Mdm-miR160 can move from the scion to the rootstock in apple and tomato (Solanum lycopersicum), thereby improving root development and drought tolerance of the rootstock. Our study revealed the mechanisms by which the positive feedback loop of Mdm-miR160-MdARF17-MdHYL1 influences apple drought tolerance.
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Affiliation(s)
- Xiaoxia Shen
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Life Science, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jieqiang He
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yikun Ping
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Junxing Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Nan Hou
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fuguo Cao
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xuewei Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Dali Geng
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Shicong Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Pengxiang Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Gege Qin
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qingmei Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
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Wu B, Li Y, Li J, Xie Z, Luan M, Gao C, Shi Y, Chen S. Genome-Wide Analysis of Alternative Splicing and Non-Coding RNAs Reveal Complicated Transcriptional Regulation in Cannabis sativa L. Int J Mol Sci 2021; 22:ijms222111989. [PMID: 34769433 PMCID: PMC8584933 DOI: 10.3390/ijms222111989] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/21/2021] [Accepted: 10/26/2021] [Indexed: 12/26/2022] Open
Abstract
It is of significance to mine the structural genes related to the biosynthetic pathway of fatty acid (FA) and cellulose as well as explore the regulatory mechanism of alternative splicing (AS), microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) in the biosynthesis of cannabinoids, FA and cellulose, which would enhance the knowledge of gene expression and regulation at post-transcriptional level in Cannabis sativa L. In this study, transcriptome, small RNA and degradome libraries of hemp 'Yunma No.1' were established, and comprehensive analysis was performed. As a result, a total of 154, 32 and 331 transcripts encoding key enzymes involved in the biosynthesis of cannabinoids, FA and cellulose were predicted, respectively, among which AS occurred in 368 transcripts. Moreover, 183 conserved miRNAs, 380 C. sativa-specific miRNAs and 7783 lncRNAs were predicted. Among them, 70 miRNAs and 17 lncRNAs potentially targeted 13 and 17 transcripts, respectively, encoding key enzymes or transporters involved in the biosynthesis of cannabinoids, cellulose or FA. Finally, the crosstalk between AS and miRNAs or lncRNAs involved in cannabinoids and cellulose was also predicted. In summary, all these results provided insights into the complicated network of gene expression and regulation in C. sativa.
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Affiliation(s)
- Bin Wu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; (B.W.); (Y.L.); (J.L.); (Z.X.)
| | - Yanni Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; (B.W.); (Y.L.); (J.L.); (Z.X.)
| | - Jishuang Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; (B.W.); (Y.L.); (J.L.); (Z.X.)
| | - Zhenzhen Xie
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; (B.W.); (Y.L.); (J.L.); (Z.X.)
| | - Mingbao Luan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (M.L.); (C.G.)
| | - Chunsheng Gao
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (M.L.); (C.G.)
| | - Yuhua Shi
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China;
| | - Shilin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China;
- Correspondence:
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14
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Mbinda W, Mukami A. A Review of Recent Advances and Future Directions in the Management of Salinity Stress in Finger Millet. FRONTIERS IN PLANT SCIENCE 2021; 12:734798. [PMID: 34603359 PMCID: PMC8481900 DOI: 10.3389/fpls.2021.734798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 08/16/2021] [Indexed: 06/13/2023]
Abstract
Salinity stress is a major environmental impediment affecting the growth and production of crops. Finger millet is an important cereal grown in many arid and semi-arid areas of the world characterized by erratic rainfall and scarcity of good-quality water. Finger millet salinity stress is caused by the accumulation of soluble salts due to irrigation without a proper drainage system, coupled with the underlying rocks having a high salt content, which leads to the salinization of arable land. This problem is projected to be exacerbated by climate change. The use of new and efficient strategies that provide stable salinity tolerance across a wide range of environments can guarantee sustainable production of finger millet in the future. In this review, we analyze the strategies that have been used for salinity stress management in finger millet production and discuss potential future directions toward the development of salt-tolerant finger millet varieties. This review also describes how advanced biotechnological tools are being used to develop salt-tolerant plants. The biotechnological techniques discussed in this review are simple to implement, have design flexibility, low cost, and highly efficient. This information provides insights into enhancing finger millet salinity tolerance and improving production.
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Affiliation(s)
- Wilton Mbinda
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
- Pwani University Biosciences Research Centre (PUBReC), Pwani University, Kilifi, Kenya
| | - Asunta Mukami
- Department of Life Sciences, South Eastern Kenya University, Kitui, Kenya
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15
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Northern Blotting Technique for Detection and Expression Analysis of mRNAs and Small RNAs. Methods Mol Biol 2021; 2170:155-183. [PMID: 32797458 DOI: 10.1007/978-1-0716-0743-5_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Northern analysis is a conventional but gold standard method for detection and quantification of gene expression changes. It not only detects the presence of a transcript but also indicates size and relative comparison of transcript abundance on a single membrane. In recent years it has been aptly adapted to validate and study the size and expression of small noncoding RNAs. Here, we describe protocols employed in our laboratory for conventional northern analysis with total RNA/mRNA to study gene expression and validation of small noncoding RNAs using low molecular weight fraction of RNAs. A brief account on the recent advancements for improving the sensitivity and efficiency of northern blot detection is also included in this chapter.
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16
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Lee JS, Adams KL. Global insights into duplicated gene expression and alternative splicing in polyploid Brassica napus under heat, cold, and drought stress. THE PLANT GENOME 2020; 13:e20057. [PMID: 33043636 DOI: 10.1002/tpg2.20057] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 07/26/2020] [Accepted: 08/20/2020] [Indexed: 05/21/2023]
Abstract
Polyploidy has been a prevalent process during plant evolution and it has made a major impact on the structure and evolution of plant genomes. Many important crop plants are polyploid. There is considerable interest in expression patterns of duplicated genes in polyploids. Alternative splicing (AS) is a fundamental aspect of gene expression that produces multiple final transcript types from a single type of mRNAs. The effects of abiotic stress conditions on AS in polyploids has received little attention. We conducted a global transcriptome analysis of Brassica napus, an allotetraploid derived from B. rapa (AT ) and B. oleracea (CT ), by RNA-Seq of plants subjected to cold, heat, and drought stress treatments. Analyses of 27,360 pairs of duplicated genes revealed overall AT subgenome biases in gene expression and CT subgenome biases in the extent of alternative splicing under all three stress treatments. More genes increased in expression than decreased in response to the stresses. Negative correlations were found between expression levels and AS frequency for each type of AS. Cold stress produced the greatest changes in gene expression and AS. Cold-induced AS changes were more likely to be shared with those generated by drought than by heat stress. We used homeologs of FLC and CCA1 as case studies to show the dynamics of how duplicates in a polyploid respond to cold stress. Our results suggest that divergence in gene expression and AS patterns between duplicated genes may increase the flexibility of polyploids when responding to abiotic stressors.
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Affiliation(s)
- Joon Seon Lee
- Department of Botany, University of British Columbia, 6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
| | - Keith L Adams
- Department of Botany, University of British Columbia, 6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
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17
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Ahmed W, Li R, Xia Y, Bai G, Siddique KHM, Zhang H, Zheng Y, Yang X, Guo P. Comparative Analysis of miRNA Expression Profiles Between Heat-Tolerant and Heat-Sensitive Genotypes of Flowering Chinese Cabbage Under Heat Stress Using High-Throughput Sequencing. Genes (Basel) 2020; 11:E264. [PMID: 32121287 PMCID: PMC7140848 DOI: 10.3390/genes11030264] [Citation(s) in RCA: 12] [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: 01/20/2020] [Revised: 02/19/2020] [Accepted: 02/19/2020] [Indexed: 12/19/2022] Open
Abstract
Heat stress disturbs cellular homeostasis, thus usually impairs yield of flowering Chinese cabbage (Brassica campestris L. ssp. chinensis var. utilis Tsen et Lee). MicroRNAs (miRNAs) play a significant role in plant responses to different stresses by modulating gene expression at the post-transcriptional level. However, the roles that miRNAs and their target genes may play in heat tolerance of flowering Chinese cabbage remain poorly characterized. The current study sequenced six small RNA libraries generated from leaf tissues of flowering Chinese cabbage collected at 0, 6, and 12 h after 38 °C heat treatment, and identified 49 putative novel miRNAs and 43 known miRNAs that differentially expressed between heat-tolerant and heat-sensitive flowering Chinese cabbage. Among them, 14 novel and nine known miRNAs differentially expressed only in the heat-tolerant genotype under heat-stress, therefore, their target genes including disease resistance protein TAO1-like, RPS6, reticuline oxidase-like protein, etc. might play important roles in enhancing heat-tolerance. Gene Ontology (GO) analysis revealed that targets of these differentially expressed miRNAs may play key roles in responses to temperature stimulus, cell part, cellular process, cell, membrane, biological regulation, binding, and catalytic activities. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis identified their important functions in signal transduction, environmental adaptation, global and overview maps, as well as in stress adaptation and in MAPK signaling pathways such as cell death. These findings provide insight into the functions of the miRNAs in heat stress tolerance of flowering Chinese cabbage.
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Affiliation(s)
- Waqas Ahmed
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Ronghua Li
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Yanshi Xia
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Guihua Bai
- United States Department of Agriculture - Agricultural Research Service, Hard Winter Wheat Genetics Research Unit, Manhattan, Kansas 66506, United States of America
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture and School of Agriculture & Environment, The University of Western Australia, LB 5005, Perth WA 6001, Australia
| | - Hua Zhang
- Guangzhou Academy of Agricultural Sciences, Guangzhou 510308, China
| | - Yansong Zheng
- Guangzhou Academy of Agricultural Sciences, Guangzhou 510308, China
| | - Xinquan Yang
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Peiguo Guo
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou 510006, China
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18
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Influence of Mixed Substrate and Arbuscular Mycorrhizal Fungi on Photosynthetic Efficiency, Nutrient and Water Status and Yield in Tomato Plants Irrigated with Saline Reclaimed Waters. WATER 2020. [DOI: 10.3390/w12020438] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The use of reclaimed water (RW) is considered as a means of maintaining agricultural productivity under drought conditions. However, RW may contain high concentrations of salts. The use of some practices, such as biofertilizers and organic substrates, is also becoming increasingly important in agricultural. production. The aim of this study was to evaluate the application of a mixed substrate (with coconut fibre) and arbuscular mycorrhizal fungi (AMF) on water relations, nutrient uptake and productivity in tomato plants irrigated with saline RW in a commercial greenhouse. Saline RW on its own caused a nutrient imbalance and negatively affected several physiological parameters. However, the high water-holding capacity of coconut fibre in the mixed substrate increased water and nutrient availability for the plants. As a consequence, leaf water potential, gas exchange, some fluorescence parameters (PhiPSII, Fv’/Fm’, qP and ETR) and fruit size and weight improved, even in control irrigation conditions. The use of AMF improved only some parameters because of the low percentage of colonization, suggesting that AMF effectiveness in commercial field conditions is slower and dependent of several factors.
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19
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Kang T, Yu CY, Liu Y, Song WM, Bao Y, Guo XT, Li B, Zhang HX. Subtly Manipulated Expression of ZmmiR156 in Tobacco Improves Drought and Salt Tolerance Without Changing the Architecture of Transgenic Plants. FRONTIERS IN PLANT SCIENCE 2020; 10:1664. [PMID: 31998347 PMCID: PMC6965348 DOI: 10.3389/fpls.2019.01664] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 11/26/2019] [Indexed: 05/23/2023]
Abstract
Plants in the juvenile state are more tolerant to adverse conditions. Constitutive expression of MicroRNA156 (miR156) prolonged the juvenile phase and increased resistance to abiotic stress, but also affected the architecture of transgenic plants. In this study, we investigated the possibility of subtle manipulation of miR156 expression in flowering plants, with the goal to increase tolerance to abiotic stress without altering the normal growth and development of transgenic plants. Transgenic tobacco plants expressing ZmmiR156 from maize were generated, driven either by the cauliflower mosaic virus (CaMV) 35S promoter or the stress-inducible ZmRab17 promoter. Expression of ZmmiR156 led to improved drought and salt tolerance in both 35S::MIR156 and Rab17::MIR156 transgenic plants, as shown by more vigorous growth, greater biomass production and higher antioxidant enzyme expression after a long period of drought or salt treatment, when compared to wild type and transgenic vector control plants. However, constitutive expression of ZmmiR156 also resulted in retarded growth, increased branching and delayed flowering of transgenic plants. These undesirable developmental changes could be mitigated by using the stress-inducible ZmRab17 promoter. Furthermore, under drought or salt stress conditions, expression of ZmmiR156 reduced the transcript level of NtSPL2 and NtSPL9, the genes potentially targeted by ZmmiR156, as well as that of CP1, CP2, and SAG12, the senescence-associated genes in tobacco. Collectively, our results indicate that ZmmiR156 can be temporally manipulated for the genetic improvement of plants resistant to various abiotic stresses.
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Affiliation(s)
- Tao Kang
- College of Agriculture, Ludong University, Yantai, China
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chun-Yan Yu
- College of Agriculture, Ludong University, Yantai, China
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong (Ludong University), Yantai, China
| | - Yue Liu
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong (Ludong University), Yantai, China
- College of Life Sciences, Qingdao University, Qingdao, China
| | - Wei-Meng Song
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yan Bao
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiao-Tong Guo
- College of Agriculture, Ludong University, Yantai, China
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong (Ludong University), Yantai, China
| | - Bei Li
- College of Agriculture, Ludong University, Yantai, China
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong (Ludong University), Yantai, China
| | - Hong-Xia Zhang
- College of Agriculture, Ludong University, Yantai, China
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong (Ludong University), Yantai, China
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20
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Ahmed W, Xia Y, Zhang H, Li R, Bai G, Siddique KHM, Guo P. Identification of conserved and novel miRNAs responsive to heat stress in flowering Chinese cabbage using high-throughput sequencing. Sci Rep 2019; 9:14922. [PMID: 31624298 PMCID: PMC6797766 DOI: 10.1038/s41598-019-51443-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 10/01/2019] [Indexed: 12/12/2022] Open
Abstract
Plant microRNAs (miRNAs) are noncoding and endogenous key regulators that play significant functions in regulating plant responses to stress, and plant growth and development. Heat stress is a critical abiotic stress that reduces the yield and quality of flowering Chinese cabbage (Brassica campestris L. ssp. chinensis var. utilis Tsen et Lee). However, limited information is available on whether miRNAs are involved in the regulation of heat stress in B. campestris. A high-throughput sequencing approach was used to identify novel and conserved heat-responsive miRNAs in four small RNA libraries of flowering Chinese cabbage using leaves collected at 0 h, 1 h, 6 h and 12 h after a 38 °C heat-stress treatment. The analysis identified 41 conserved miRNAs (belonging to 19 MIR families), of which MIR156, MIR159, MIR168, MIR171 and MIR1885 had the most abundant molecules. Prediction and evaluation of novel miRNAs using the unannotated reads resulted in 18 candidate miRNAs. Differential expression analysis showed that most of the identified miRNAs were downregulated in heat-treated groups. To better understand functional importance, bioinformatic analysis predicted 432 unique putative target miRNAs involved in cells, cell parts, catalytic activity, cellular processes and abiotic stress responses. Furthermore, the Kyoto Encyclopedia of Genes and Genomes maps of flowering Chinese cabbage identified the significant role of miRNAs in stress adaptation and stress tolerance, and in several mitogen-activated protein kinases signaling pathways including cell death. This work presents a comprehensive study of the miRNAs for understanding the regulatory mechanisms and their participation in the heat stress of flowering Chinese cabbage.
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Affiliation(s)
- Waqas Ahmed
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Yanshi Xia
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Hua Zhang
- Guangzhou Academy of Agricultural Sciences, Guangzhou, 510308, China
| | - Ronghua Li
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Guihua Bai
- United States Department of Agriculture - Agricultural Research Service, Hard Winter Wheat Genetics Research Unit, Manhattan, Kansas, 66506, United States of America
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture and School of Agriculture & Environment, The University of Western Australia, LB 5005, Perth, WA, 6001, Australia
| | - Peiguo Guo
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, 510006, China.
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21
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Jeyaraj A, Wang X, Wang S, Liu S, Zhang R, Wu A, Wei C. Identification of Regulatory Networks of MicroRNAs and Their Targets in Response to Colletotrichum gloeosporioides in Tea Plant ( Camellia sinensis L.). FRONTIERS IN PLANT SCIENCE 2019; 10:1096. [PMID: 31572415 PMCID: PMC6751461 DOI: 10.3389/fpls.2019.01096] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 08/09/2019] [Indexed: 05/21/2023]
Abstract
Anthracnose disease is caused by Colletotrichum gloeosporioides, and is common in leaves of the tea plant (Camellia sinensis). MicroRNAs (miRNAs) have been known as key modulators of gene expression in response to environmental stresses, disease resistance, defense responses, and plant immunity. However, the role of miRNAs in responses to C. gloeosporioides remains unexplored in tea plant. Therefore, in the present study, six miRNA sequencing data sets and two degradome data sets were generated from C. gloeosporioides-inoculated and control tea leaves. A total of 485 conserved and 761 novel miRNAs were identified. Of those, 239 known and 369 novel miRNAs exhibited significantly differential expression under C. gloeosporioides stress. One thousand one hundred thirty-four and 596 mRNAs were identified as targets of 389 conserved and 299 novel miRNAs by degradome analysis, respectively. Based on degradome analysis, most of the predicted targets are negatively correlated with their corresponding conserved and novel miRNAs. The expression levels of 12 miRNAs and their targets were validated by quantitative real-time PCR. A negative correlation between expression profiles of five miRNAs (PC-5p-80764_22, csn-miR160c, csn-miR828a, csn-miR164a, and csn-miR169e) and their targets (WRKY, ARF, MYB75, NAC, and NFY transcription factor) was observed. The predicted targets of five interesting miRNAs were further validated through 5'RLM-RACE. Furthermore, Gene Ontology and metabolism pathway analysis revealed that most of the target genes were involved in the regulation of auxin pathway, ROS scavenging pathway, salicylic acid mediated pathway, receptor kinases, and transcription factors for plant growth and development as well as stress responses in tea plant against C. gloeosporioides stress. This study enriches the resources of stress-responsive miRNAs and their targets in C. sinensis and thus provides novel insights into the miRNA-mediated regulatory mechanisms, which could contribute to the enhanced susceptibility of C. gloeosporioides in tea plant.
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Affiliation(s)
- Anburaj Jeyaraj
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
- Department of Biotechnology, Karpagam Academy of Higher Education, Coimbatore, India
| | - Xuewen Wang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
- Department of Genetics, University of Georgia, Athens, United States
| | - Shuangshuang Wang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Shengrui Liu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Ran Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Ailin Wu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Chaoling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
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22
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Ahmed W, Xia Y, Li R, Bai G, Siddique KHM, Guo P. Non-coding RNAs: Functional roles in the regulation of stress response in Brassica crops. Genomics 2019; 112:1419-1424. [PMID: 31430515 DOI: 10.1016/j.ygeno.2019.08.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 07/03/2019] [Accepted: 08/16/2019] [Indexed: 12/22/2022]
Abstract
Brassica crops face a combination of different abiotic and biotic stresses in the field that can reduce plant growth and development by affecting biochemical and morpho-physiological processes. Emerging evidence suggests that non-coding RNAs (ncRNAs), especially microRNAs (miRNAs) and long ncRNAs (lncRNAs), play a significant role in the modulation of gene expression in response to plant stresses. Recent advances in computational and experimental approaches are of great interest for identifying and functionally characterizing ncRNAs. While progress in this field is limited, numerous ncRNAs involved in the regulation of gene expression in response to stress have been reported in Brassica. In this review, we summarize the modes of action and functions of stress-related miRNAs and lncRNAs in Brassica as well as the approaches used to identify ncRNAs.
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Affiliation(s)
- Waqas Ahmed
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, China
| | - Yanshi Xia
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, China
| | - Ronghua Li
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, China
| | - Guihua Bai
- United States Department of Agriculture - Agricultural Research Service, Hard Winter Wheat Genetics Research Unit, Manhattan, Kansas 66506, United States
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture and School of Agriculture & Environment, The University of Western Australia, LB 5005, Perth, WA 6001, Australia
| | - Peiguo Guo
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, China.
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Gahlaut V, Baranwal VK, Khurana P. miRNomes involved in imparting thermotolerance to crop plants. 3 Biotech 2018; 8:497. [PMID: 30498670 PMCID: PMC6261126 DOI: 10.1007/s13205-018-1521-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 11/17/2018] [Indexed: 12/20/2022] Open
Abstract
Thermal stress is one of the challenges to crop plants that negatively impacts crop yield. To overcome this ever-growing problem, utilization of regulatory mechanisms, especially microRNAs (miRNAs), that provide efficient and precise regulation in a targeted manner have been found to play determining roles. Besides their roles in plant growth and development, many recent studies have shown differential regulation of several miRNAs during abiotic stresses including heat stress (HS). Thus, understanding the underlying mechanism of miRNA-mediated gene expression during HS will enable researchers to exploit this regulatory mechanism to address HS responses. This review focuses on the miRNAs and regulatory networks that were involved in physiological, metabolic and morphological adaptations during HS in plant, specifically in crops. Illustrated examples including, the miR156-SPL, miR169-NF-YA5, miR395-APS/AST, miR396-WRKY, etc., have been discussed in specific relation to the crop plants. Further, we have also discussed the available plant miRNA databases and bioinformatics tools useful for miRNA identification and study of their regulatory role in response to HS. Finally, we have briefly discussed the future prospects about the miRNA-related mechanisms of HS for improving thermotolerance in crop plants.
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Affiliation(s)
- Vijay Gahlaut
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021 India
| | - Vinay Kumar Baranwal
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021 India
- Department of Botany, Swami Devanand Post Graduate College, Math-lar, Lar, Deoria, Uttar Pradesh 274502 India
| | - Paramjit Khurana
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021 India
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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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Singh I, Smita S, Mishra DC, Kumar S, Singh BK, Rai A. Abiotic Stress Responsive miRNA-Target Network and Related Markers (SNP, SSR) in Brassica juncea. FRONTIERS IN PLANT SCIENCE 2017; 8:1943. [PMID: 29209340 PMCID: PMC5702422 DOI: 10.3389/fpls.2017.01943] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 10/30/2017] [Indexed: 05/30/2023]
Abstract
Abiotic stress is one of the major factors responsible for huge yield loss in crop plants. MicroRNAs play a key role in adaptive responses of plants under abiotic stress conditions through post-transcriptional gene regulations. In present study, 95 potential miRNAs were predicted in Brassica juncea using comparative genomics approach. It was noted that these miRNAs, target several transcription factors (TFs), transporter family proteins, signaling related genes, and protease encoding genes. Nineteen distinct miRNA-target regulatory networks were observed with significant involvement in regulation of transcription, response to stimulus, hormone and auxin mediated signaling pathway related gene ontology (GO) term. The sucrose-starch metabolism and pentose-gluconate interconversion pathways were found significantly enriched for these target genes. Molecular markers such as Simple Sequence Repeats (SSR) and Single Nucleotide Polymorphism (SNPs) were identified on miRNAs (miR-SSRs and miR-SNPs) and their target genes in B. juncea. Notably, one of the miR-SNP (C/T) was found at the 5th position on mature region of miR2926. This C/T transition led to the distorted and unstable hairpin structure of miR2926, consequently complete loss of target function. Hence, findings from this study will lay a foundation for marker assisted breeding for abiotic stress tolerant varieties of B. juncea.
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Affiliation(s)
- Indra Singh
- Centre for Agricultural Bio-Informatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Shuchi Smita
- Centre for Agricultural Bio-Informatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dwijesh C. Mishra
- Centre for Agricultural Bio-Informatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sanjeev Kumar
- Centre for Agricultural Bio-Informatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Binay K. Singh
- ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, India
| | - Anil Rai
- Centre for Agricultural Bio-Informatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
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Jeyaraj A, Zhang X, Hou Y, Shangguan M, Gajjeraman P, Li Y, Wei C. Genome-wide identification of conserved and novel microRNAs in one bud and two tender leaves of tea plant (Camellia sinensis) by small RNA sequencing, microarray-based hybridization and genome survey scaffold sequences. BMC PLANT BIOLOGY 2017; 17:212. [PMID: 29157210 PMCID: PMC5697157 DOI: 10.1186/s12870-017-1169-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 11/10/2017] [Indexed: 05/19/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) are important for plant growth and responses to environmental stresses via post-transcriptional regulation of gene expression. Tea, which is primarily produced from one bud and two tender leaves of the tea plant (Camellia sinensis), is one of the most popular non-alcoholic beverages worldwide owing to its abundance of secondary metabolites. A large number of miRNAs have been identified in various plants, including non-model species. However, due to the lack of reference genome sequences and/or information of tea plant genome survey scaffold sequences, discovery of miRNAs has been limited in C. sinensis. RESULTS Using small RNA sequencing, combined with our recently obtained genome survey data, we have identified and analyzed 175 conserved and 83 novel miRNAs mainly in one bud and two tender leaves of the tea plant. Among these, 93 conserved and 18 novel miRNAs were validated using miRNA microarray hybridization. In addition, the expression pattern of 11 conserved and 8 novel miRNAs were validated by stem-loop-qRT-PCR. A total of 716 potential target genes of identified miRNAs were predicted. Further, Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that most of the target genes were primarily involved in stress response and enzymes related to phenylpropanoid biosynthesis. The predicted targets of 4 conserved miRNAs were further validated by 5'RLM-RACE. A negative correlation between expression profiles of 3 out of 4 conserved miRNAs (csn-miR160a-5p, csn-miR164a, csn-miR828 and csn-miR858a) and their targets (ARF17, NAC100, WER and MYB12 transcription factor) were observed. CONCLUSION In summary, the present study is one of few such studies on miRNA detection and identification in the tea plant. The predicted target genes of majority of miRNAs encoded enzymes, transcription factors, and functional proteins. The miRNA-target transcription factor gene interactions may provide important clues about the regulatory mechanism of these miRNAs in the tea plant. The data reported in this study will make a huge contribution to knowledge on the potential miRNA regulators of the secondary metabolism pathway and other important biological processes in C. sinensis.
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Affiliation(s)
- Anburaj Jeyaraj
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui Province 230036 People’s Republic of China
| | - Xiao Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui Province 230036 People’s Republic of China
| | - Yan Hou
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui Province 230036 People’s Republic of China
| | - Mingzhu Shangguan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui Province 230036 People’s Republic of China
| | - Prabu Gajjeraman
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui Province 230036 People’s Republic of China
- Department of Biotechnology, Karpagam University, Coimbatore, India
| | - Yeyun Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui Province 230036 People’s Republic of China
| | - Chaoling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui Province 230036 People’s Republic of China
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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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Ma Z, Jiang J, Hu Z, Lyu T, Yang Y, Jiang J, Cao J. Over-expression of miR158 causes pollen abortion in Brassica campestris ssp. chinensis. PLANT MOLECULAR BIOLOGY 2017; 93:313-326. [PMID: 27909970 DOI: 10.1007/s11103-016-0563-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 11/12/2016] [Indexed: 06/06/2023]
Abstract
We identified and cloned the two precursors of miR158 and its target gene in Brassica campestris ssp. chinensis, which both had high relative expression in the inflorescences. Further study revealed that over-expression of miR158 caused reduced pollen varbility, which was caused by the degradation of pollen contents from the binucleate microspore stage. These results first suggest the role of miR158 in pollen development of Brassica campestris ssp. chinensis. MicroRNAs (miRNAs) play crucial roles in many important growth and development processes both in plants and animals by regulating the expression of their target genes via mRNA cleavage or translational repression. In this study, miR158, a Brassicaceae specific miRNA, was functionally characterized with regard to its role in pollen development of non-heading Chinese cabbage (Brassica campestris ssp. chinensis). Two family members of miR158 in B. campestris, namely bra-miR158a1 and bra-miR158a2, and their target gene bra027656, which encodes a pentatricopeptide repeat (PPR) containing protein, were identified. Then, qRT-PCR analysis and GUS-reporter system revealed that both bra-miR158 and its target gene had relatively high expression levels in the inflorescences. Further study revealed that over-expression of miR158 caused reduced pollen varbility and pollen germination ratio, and the degradation of pollen contents from the binucleate microspore stage was also found in those deformed pollen grains, which led to pollen shrinking and collapse in later pollen development stage. These results first shed light on the importance of miR158 in pollen development of Brassica campestris ssp. chinensis.
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Affiliation(s)
- Zhiming Ma
- Lab of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
| | - Jianxia Jiang
- Lab of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
| | - Ziwei Hu
- Lab of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
| | - Tianqi Lyu
- Lab of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
| | - Yang Yang
- Lab of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
| | - Jingjing Jiang
- State Key Lab of Agrobiotechnology, Shenzhen Base, Shenzhen Research Institute, Chinese University of Hong Kong, Shenzhen, 518057, China
| | - Jiashu Cao
- Lab of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China.
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Liu SC, Xu YX, Ma JQ, Wang WW, Chen W, Huang DJ, Fang J, Li XJ, Chen L. Small RNA and degradome profiling reveals important roles for microRNAs and their targets in tea plant response to drought stress. PHYSIOLOGIA PLANTARUM 2016; 158:435-451. [PMID: 27282332 DOI: 10.1111/ppl.12477] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 04/25/2016] [Accepted: 05/22/2016] [Indexed: 06/06/2023]
Abstract
Tea (Camellia sinensis) is a popular beverage worldwide. Drought stress (DS) is a major constraint on the growth, yield and quality of tea plants. MicroRNAs (miRNAs) play important roles in plant responses to DS. We constructed eight small RNA libraries from the drought-tolerant 'Ningzhou 2' (NZ2) and drought-susceptible 'Zhuyeqi' (ZYQ) cultivars during four stages [control (CK), the fourth day of DS, the eighth day of DS and after recovery (RC)]. A total of 268 conserved and 62 novel miRNAs were identified using small RNA sequencing. In total, 139 (52.9%) and 96 (36.0%) conserved miRNAs were differentially expressed during the four stages (P ≤ 0.05) in NZ2 and ZYQ, respectively. A total of 814 predicted target genes were identified as differentially regulated by 199 miRNAs through degradome sequencing. Among them, 201 and 218 genes were specific to the NZ2 and ZYQ cultivars, respectively, and 395 were common to both cultivars. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed the biological roles of these targets and showed that some of the targets responded to DS in a stress- and cultivar-dependent manner. Correlated expression patterns between miRNA and their targets showed that specific miRNAs target the miRNA effector Argonaute 1 (AGO1), drought signaling-related receptors and enzymes, transcription factors, and other structural and functional proteins. The predicted regulatory networks provide insights into a potential miRNA-mediated regulatory mechanism. These results will contribute to the breeding of drought-tolerant tea plants and to elucidating miRNA regulation in response to drought.
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Affiliation(s)
- Sheng-Chuan Liu
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008, China
- Tea Research Institute, Guizhou Academy of Agricultrural Sciences, Guiyang, 550006, China
| | - Yan-Xia Xu
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008, China
| | - Jian-Qiang Ma
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008, China
| | - Wei-Wei Wang
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008, China
| | - Wei Chen
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008, China
| | - Dan-Juan Huang
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008, China
| | - Jie Fang
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008, China
| | - Xiao-Jie Li
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008, China
| | - Liang Chen
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008, China
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Wu Y, Guo J, Cai Y, Gong X, Xiong X, Qi W, Pang Q, Wang X, Wang Y. Genome-wide identification and characterization of Eutrema salsugineum microRNAs for salt tolerance. PHYSIOLOGIA PLANTARUM 2016; 157:453-68. [PMID: 26806325 DOI: 10.1111/ppl.12419] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 11/12/2015] [Accepted: 12/10/2015] [Indexed: 05/23/2023]
Abstract
Eutrema salsugineum, a close relative of Arabidopsis thaliana, is a valuable halophytic model plant that has extreme tolerance to salinity. As posttranscriptional gene regulators, microRNAs (miRNAs) control gene expression and a variety of biological processes, including plant-stress responses. To identify salt-stress responsive miRNAs in E. salsugineum and reveal their possible roles in the adaptive response to salt stress, we chose the Solexa sequencing platform to screen the miRNAs in 4-week-old E. salsugineum seedlings under salt treatment. A total of 82 conserved miRNAs belonging to 27 miRNA families and 17 novel miRNAs were identified and 11 conserved miRNA families and 4 novel miRNAs showed a significant response to salt stress. To investigate the possible biological roles of miRNAs, 1060 potential targets were predicted. Moreover, 35 gene ontology (GO) categories and 1 pathway, including a few terms that were directly and indirectly related to salt stress, were significantly enriched in the salt-stress-responsive miRNAs targets. The relative expression analysis of six target genes was analyzed using quantitative real-time polymerase chain reaction (PCR) and showed a negative correlation with their corresponding miRNAs. Many stress regulatory and phytohormone regulatory cis-regulatory elements were widely present in the promoter region of the salt-responsive miRNA precursors. This study describes the large-scale characterization of E. salsugineum miRNAs and provides a useful resource for further understanding of miRNA functions in the regulation of the E. salsugineum salt-stress response.
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Affiliation(s)
- Ying Wu
- Alkali Soil Natural Environmental Science Center, Northeast Forestry University/Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin, 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Jing Guo
- Alkali Soil Natural Environmental Science Center, Northeast Forestry University/Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin, 150040, China
| | - Yimei Cai
- CAS Key Laboratory of Genome Sciences and Information, BeGenomics, Chinese Academy of Sciences, Beijing, 100029, China
| | - Xiaolin Gong
- Alkali Soil Natural Environmental Science Center, Northeast Forestry University/Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin, 150040, China
| | - Xuemei Xiong
- Alkali Soil Natural Environmental Science Center, Northeast Forestry University/Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin, 150040, China
| | - Wenwen Qi
- Alkali Soil Natural Environmental Science Center, Northeast Forestry University/Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin, 150040, China
| | - Qiuying Pang
- Alkali Soil Natural Environmental Science Center, Northeast Forestry University/Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin, 150040, China
| | - Xumin Wang
- CAS Key Laboratory of Genome Sciences and Information, BeGenomics, Chinese Academy of Sciences, Beijing, 100029, China
| | - Yang Wang
- Alkali Soil Natural Environmental Science Center, Northeast Forestry University/Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin, 150040, China
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Bakhshi B, Mohseni Fard E, Nikpay N, Ebrahimi MA, Bihamta MR, Mardi M, Salekdeh GH. MicroRNA Signatures of Drought Signaling in Rice Root. PLoS One 2016; 11:e0156814. [PMID: 27276090 PMCID: PMC4898717 DOI: 10.1371/journal.pone.0156814] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 05/19/2016] [Indexed: 11/21/2022] Open
Abstract
Background Drought stress is one of the most important abiotic stresses and the main constraint to rice agriculture. MicroRNA-mediated post-transcriptional gene regulation is one of the ways to establish drought stress tolerance in plants. MiRNAs are 20–24-nt regulatory RNAs that play an important role in regulating plant gene expression upon exposure to biotic and abiotic stresses. Methodology/Principal Findings In this study, we applied a partial root drying system as well as a complete root drying system to identify miRNAs involved in conditions of drought stress, drought signaling and wet signaling using high-throughput sequencing. To this end, we produced four small RNA libraries: (1) fully-watered (WW), (2) fully-droughted (WD), and split-root systems where (3) one-half was well watered (SpWW) and (4) the other half was water-deprived (SpWD). Our analysis revealed 10,671 and 783 unique known and novel miRNA reads in all libraries, respectively. We identified, 65 (52 known + 13 novel), 72 (61 known + 11 novel) and 51 (38 known + 13 novel) miRNAs that showed differential expression under conditions of drought stress, drought signaling and wet signaling, respectively. The results of quantitative real-time PCR showed expression patterns similar to the high-throughput sequencing results. Furthermore, our target prediction led to the identification of 244, 341 and 239 unique target genes for drought-stress-, drought-signaling- and wet-signaling-responsive miRNAs, respectively. Conclusions/Significance Our results suggest that miRNAs that are responsive under different conditions could play different roles in the regulation of abscisic acid signaling, calcium signaling, detoxification and lateral root formation.
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Affiliation(s)
- Behnam Bakhshi
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Iran
- Department of Plant Breeding, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Ehsan Mohseni Fard
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Zanjan, Zanjan, Iran
| | - Nava Nikpay
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Iran
| | | | - Mohammad Reza Bihamta
- Department of Agronomy and Plant Breeding, Faculty of Agricultural Science and Engineering, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Mohsen Mardi
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Iran
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Iran
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- * E-mail:
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Liu H, Searle IR, Watson-Haigh NS, Baumann U, Mather DE, Able AJ, Able JA. Genome-Wide Identification of MicroRNAs in Leaves and the Developing Head of Four Durum Genotypes during Water Deficit Stress. PLoS One 2015; 10:e0142799. [PMID: 26562166 PMCID: PMC4643036 DOI: 10.1371/journal.pone.0142799] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 10/27/2015] [Indexed: 11/19/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that play critical roles in plant development and abiotic stress responses. The miRNA transcriptome (miRNAome) under water deficit stress has been investigated in many plant species, but is poorly characterised in durum wheat (Triticum turgidum L. ssp. durum). Water stress during early reproductive stages can result in significant yield loss in durum wheat and this study describes genotypic differences in the miRNAome between water deficit tolerant and sensitive durum genotypes. Small RNA libraries (96 in total) were constructed from flag leaf and developing head tissues of four durum genotypes, with or without water stress to identify differentially abundant miRNAs. Illumina sequencing detected 110 conserved miRNAs and 159 novel candidate miRNA hairpins with 66 conserved miRNAs and five novel miRNA hairpins differentially abundant under water deficit stress. Ten miRNAs (seven conserved, three novel) were validated through qPCR. Several conserved and novel miRNAs showed unambiguous inverted regulatory profiles between the durum genotypes. Several miRNAs also showed differential abundance between two tissue types regardless of treatment. Predicted mRNA targets (130) of four novel durum miRNAs were characterised using Gene Ontology (GO) which revealed functions common to stress responses and plant development. Negative correlation was observed between several target genes and the corresponding miRNA under water stress. For the first time, we present a comprehensive study of the durum miRNAome under water deficit stress. The identification of differentially abundant miRNAs provides molecular evidence that miRNAs are potential determinants of water stress tolerance in durum wheat. GO analysis of predicted targets contributes to the understanding of genotypic physiological responses leading to stress tolerance capacity. Further functional analysis of specific stress responsive miRNAs and their interaction with targets is ongoing and will assist in developing future durum wheat varieties with enhanced water deficit stress tolerance.
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Affiliation(s)
- Haipei Liu
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, South Australia, Australia
| | - Iain R. Searle
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, South Australia, Australia
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
- The University of Adelaide-Shanghai Jiao Tong University Joint International Centre for Agriculture & Health, School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Nathan S. Watson-Haigh
- Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Adelaide, South Australia, Australia
| | - Ute Baumann
- Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Adelaide, South Australia, Australia
| | - Diane E. Mather
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, South Australia, Australia
| | - Amanda J. Able
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, South Australia, Australia
| | - Jason A. Able
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, South Australia, Australia
- * E-mail:
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Yuan S, Li Z, Li D, Yuan N, Hu Q, Luo H. Constitutive Expression of Rice MicroRNA528 Alters Plant Development and Enhances Tolerance to Salinity Stress and Nitrogen Starvation in Creeping Bentgrass. PLANT PHYSIOLOGY 2015; 169:576-593. [PMID: 26224802 PMCID: PMC4577425 DOI: 10.1104/pp.15.00899] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 07/29/2015] [Indexed: 05/20/2023]
Abstract
MicroRNA528 (miR528) is a conserved monocot-specific small RNA that has the potential of mediating multiple stress responses. So far, however, experimental functional studies of miR528 are lacking. Here, we report that overexpression of a rice (Oryza sativa) miR528 (Osa-miR528) in transgenic creeping bentgrass (Agrostis stolonifera) alters plant development and improves plant salt stress and nitrogen (N) deficiency tolerance. Morphologically, miR528-overexpressing transgenic plants display shortened internodes, increased tiller number, and upright growth. Improved salt stress resistance is associated with increased water retention, cell membrane integrity, chlorophyll content, capacity for maintaining potassium homeostasis, CATALASE activity, and reduced ASCORBIC ACID OXIDASE (AAO) activity; while enhanced tolerance to N deficiency is associated with increased biomass, total N accumulation and chlorophyll synthesis, nitrite reductase activity, and reduced AAO activity. In addition, AsAAO and COPPER ION BINDING PROTEIN1 are identified as two putative targets of miR528 in creeping bentgrass. Both of them respond to salinity and N starvation and are significantly down-regulated in miR528-overexpressing transgenics. Our data establish a key role that miR528 plays in modulating plant growth and development and in the plant response to salinity and N deficiency and indicate the potential of manipulating miR528 in improving plant abiotic stress resistance.
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Affiliation(s)
- Shuangrong Yuan
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29634
| | - Zhigang Li
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29634
| | - Dayong Li
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29634
| | - Ning Yuan
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29634
| | - Qian Hu
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29634
| | - Hong Luo
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29634
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Root precursors of microRNAs in wild emmer and modern wheats show major differences in response to drought stress. Funct Integr Genomics 2015; 15:587-98. [PMID: 26174050 DOI: 10.1007/s10142-015-0453-0] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 06/26/2015] [Accepted: 07/01/2015] [Indexed: 01/09/2023]
Abstract
MicroRNAs, small regulatory molecules with significant impacts on the transcriptional network of all living organisms, have been the focus of several studies conducted mostly on modern wheat cultivars. In this study, we investigated miRNA repertoires of modern durum wheat and its wild relatives, with differing degrees of drought tolerance, to identify miRNA candidates and their targets involved in drought stress response. Root transcriptomes of Triticum turgidum ssp. durum variety Kızıltan and two Triticum turgidum ssp. dicoccoides genotypes TR39477 and TTD-22 under control and drought conditions were assembled from individual RNA-Seq reads and used for in silico identification of miRNAs. A total of 66 miRNAs were identified from all species, across all conditions, of which 46 and 38 of the miRNAs identified from modern durum wheat and wild genotypes, respectively, had not been previously reported. Genotype- and/or stress-specific miRNAs provide insights into our understanding of the complex drought response. Particularly, miR1435, miR5024, and miR7714, identified only from drought-stress roots of drought-tolerant genotype TR39477, can be candidates for future studies to explore and exploit the drought response to develop tolerant varieties.
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36
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Construction of regulatory networks mediated by small RNAs responsive to abiotic stresses in rice (Oryza sativa). Comput Biol Chem 2015; 58:69-80. [PMID: 26057839 DOI: 10.1016/j.compbiolchem.2015.05.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 04/16/2015] [Accepted: 05/22/2015] [Indexed: 11/21/2022]
Abstract
Plants have evolved exquisite molecular mechanisms to adapt to diverse abiotic stresses. MicroRNAs play an important role in stress response in plants. However, whether the other small RNAs (sRNAs) possess stress-related roles remains elusive. In this study, thousands of sRNAs responsive to cold, drought and salt stresses were identified in rice seedlings and panicles by using high-throughput sequencing data. These sRNAs were classified into 12 categories, including "Panicle_Cold_Down", "Panicle_Cold_Up", "Panicle_Drought_Down", "Panicle_Drought_Up", "Panicle_Salt_Down", "Panicle_Salt_Up", "Seedling_Cold_Down", "Seedling_Cold_Up", "Seedling_Drought_Down", "Seedling_Drought_Up", "Seedling_Salt_Down" and "Seedling_Salt_Up". The stress-responsive sRNAs enriched in Argonaute 1 were extracted for target prediction and degradome sequencing data-based validation, which enabled network construction. Within certain subnetworks, some target genes were further supported by microarray data. Literature mining indicated that certain targets were potentially involved in stress response. These results demonstrate that the established networks are biologically meaningful. We discovered that in some cases, one sRNA sequence could be assigned to two or more categories. Moreover, within certain target-centered subnetworks, one transcript was regulated by several stress-responsive sRNAs assigned to different categories. It implies that these subnetworks are potentially implicated in stress signal crosstalk. Together, our results could advance the current understanding of the biological role of plant sRNAs in stress signaling.
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Lee WS, Gudimella R, Wong GR, Tammi MT, Khalid N, Harikrishna JA. Transcripts and MicroRNAs Responding to Salt Stress in Musa acuminata Colla (AAA Group) cv. Berangan Roots. PLoS One 2015; 10:e0127526. [PMID: 25993649 PMCID: PMC4439137 DOI: 10.1371/journal.pone.0127526] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 04/15/2015] [Indexed: 12/03/2022] Open
Abstract
Physiological responses to stress are controlled by expression of a large number of genes, many of which are regulated by microRNAs. Since most banana cultivars are salt-sensitive, improved understanding of genetic regulation of salt induced stress responses in banana can support future crop management and improvement in the face of increasing soil salinity related to irrigation and climate change. In this study we focused on determining miRNA and their targets that respond to NaCl exposure and used transcriptome sequencing of RNA and small RNA from control and NaCl-treated banana roots to assemble a cultivar-specific reference transcriptome and identify orthologous and Musa-specific miRNA responding to salinity. We observed that, banana roots responded to salinity stress with changes in expression for a large number of genes (9.5% of 31,390 expressed unigenes) and reduction in levels of many miRNA, including several novel miRNA and banana-specific miRNA-target pairs. Banana roots expressed a unique set of orthologous and Musa-specific miRNAs of which 59 respond to salt stress in a dose-dependent manner. Gene expression patterns of miRNA compared with those of their predicted mRNA targets indicated that a majority of the differentially expressed miRNAs were down-regulated in response to increased salinity, allowing increased expression of targets involved in diverse biological processes including stress signaling, stress defence, transport, cellular homeostasis, metabolism and other stress-related functions. This study may contribute to the understanding of gene regulation and abiotic stress response of roots and the high-throughput sequencing data sets generated may serve as important resources related to salt tolerance traits for functional genomic studies and genetic improvement in banana.
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Affiliation(s)
- Wan Sin Lee
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Kuala Lumpur, Malaysia
| | - Ranganath Gudimella
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Kuala Lumpur, Malaysia
| | - Gwo Rong Wong
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Kuala Lumpur, Malaysia
| | - Martti Tapani Tammi
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Kuala Lumpur, Malaysia
- Bioinformatics, Sime Darby Technology Centre Sdn Bhd, Serdang, Selangor, Malaysia
| | - Norzulaani Khalid
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Kuala Lumpur, Malaysia
| | - Jennifer Ann Harikrishna
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Kuala Lumpur, Malaysia
- * E-mail:
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Zheng C, Zhao L, Wang Y, Shen J, Zhang Y, Jia S, Li Y, Ding Z. Integrated RNA-Seq and sRNA-Seq Analysis Identifies Chilling and Freezing Responsive Key Molecular Players and Pathways in Tea Plant (Camellia sinensis). PLoS One 2015; 10:e0125031. [PMID: 25901577 PMCID: PMC4406609 DOI: 10.1371/journal.pone.0125031] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 03/19/2015] [Indexed: 12/17/2022] Open
Abstract
Tea [Camellia sinensis (L) O. Kuntze, Theaceae] is one of the most popular non-alcoholic beverages worldwide. Cold stress is one of the most severe abiotic stresses that limit tea plants’ growth, survival and geographical distribution. However, the genetic regulatory network and signaling pathways involved in cold stress responses in tea plants remain unearthed. Using RNA-Seq, DGE and sRNA-Seq technologies, we performed an integrative analysis of miRNA and mRNA expression profiling and their regulatory network of tea plants under chilling (4℃) and freezing (-5℃) stress. Differentially expressed (DE) miRNA and mRNA profiles were obtained based on fold change analysis, miRNAs and target mRNAs were found to show both coherent and incoherent relationships in the regulatory network. Furthermore, we compared several key pathways (e.g., ‘Photosynthesis’), GO terms (e.g., ‘response to karrikin’) and transcriptional factors (TFs, e.g., DREB1b/CBF1) which were identified as involved in the early chilling and/or freezing response of tea plants. Intriguingly, we found that karrikins, a new group of plant growth regulators, and β-primeverosidase (BPR), a key enzyme functionally relevant with the formation of tea aroma might play an important role in both early chilling and freezing response of tea plants. Quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) analysis further confirmed the results from RNA-Seq and sRNA-Seq analysis. This is the first study to simultaneously profile the expression patterns of both miRNAs and mRNAs on a genome-wide scale to elucidate the molecular mechanisms of early responses of tea plants to cold stress. In addition to gaining a deeper insight into the cold resistant characteristics of tea plants, we provide a good case study to analyse mRNA/miRNA expression and profiling of non-model plant species using next-generation sequencing technology.
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Affiliation(s)
- Chao Zheng
- Tea Research Institute, Qingdao Agricultural University, Qingdao, Shandong, China
- Key Laboratory of Genetic Improvement and Breeding for Horticultural Plants, Qingdao, Shandong, China
| | - Lei Zhao
- Tea Research Institute, Qingdao Agricultural University, Qingdao, Shandong, China
- Key Laboratory of Genetic Improvement and Breeding for Horticultural Plants, Qingdao, Shandong, China
| | - Yu Wang
- Tea Research Institute, Qingdao Agricultural University, Qingdao, Shandong, China
- Key Laboratory of Genetic Improvement and Breeding for Horticultural Plants, Qingdao, Shandong, China
| | - Jiazhi Shen
- Tea Research Institute, Qingdao Agricultural University, Qingdao, Shandong, China
- Key Laboratory of Genetic Improvement and Breeding for Horticultural Plants, Qingdao, Shandong, China
| | - Yinfei Zhang
- Tea Research Institute, Qingdao Agricultural University, Qingdao, Shandong, China
- Key Laboratory of Genetic Improvement and Breeding for Horticultural Plants, Qingdao, Shandong, China
| | - Sisi Jia
- Tea Research Institute, Qingdao Agricultural University, Qingdao, Shandong, China
- Key Laboratory of Genetic Improvement and Breeding for Horticultural Plants, Qingdao, Shandong, China
| | - Yusheng Li
- Fruit and Tea Technology Extension Station, Jinan, Shandong, China
| | - Zhaotang Ding
- Tea Research Institute, Qingdao Agricultural University, Qingdao, Shandong, China
- Key Laboratory of Genetic Improvement and Breeding for Horticultural Plants, Qingdao, Shandong, China
- * E-mail:
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39
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Correction: a genome-wide perspective of miRNAome in response to high temperature, salinity and drought stresses in Brassica juncea (Czern) L. PLoS One 2015; 10:e0125644. [PMID: 25874851 PMCID: PMC4395156 DOI: 10.1371/journal.pone.0125644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Feng J, Wang J, Fan P, Jia W, Nie L, Jiang P, Chen X, Lv S, Wan L, Chang S, Li S, Li Y. High-throughput deep sequencing reveals that microRNAs play important roles in salt tolerance of euhalophyte Salicornia europaea. BMC PLANT BIOLOGY 2015; 15:63. [PMID: 25848810 PMCID: PMC4349674 DOI: 10.1186/s12870-015-0451-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 02/06/2015] [Indexed: 05/07/2023]
Abstract
BACKGROUND microRNAs (miRNAs) are implicated in plant development processes and play pivotal roles in plant adaptation to environmental stresses. Salicornia europaea, a salt mash euhalophyte, is a suitable model plant to study salt adaptation mechanisms. S. europaea is also a vegetable, forage, and oilseed that can be used for saline land reclamation and biofuel precursor production on marginal lands. Despite its importance, no miRNA has been identified from S. europaea thus far. RESULTS Deep sequencing was performed to investigate small RNA transcriptome of S. europaea. Two hundred and ten conserved miRNAs comprising 51 families and 31 novel miRNAs (including seven miRNA star sequences) belonging to 30 families were identified. About half (13 out of 31) of the novel miRNAs were only detected in salt-treated samples. The expression of 43 conserved and 13 novel miRNAs significantly changed in response to salinity. In addition, 53 conserved and 13 novel miRNAs were differentially expressed between the shoots and roots. Furthermore, 306 and 195 S. europaea unigenes were predicted to be targets of 41 conserved and 29 novel miRNA families, respectively. These targets encoded a wide range of proteins, and genes involved in transcription regulation constituted the largest category. Four of these genes encoding laccase, F-box family protein, SAC3/GANP family protein, and NADPH cytochrome P-450 reductase were validated using 5'-RACE. CONCLUSIONS Our results indicate that specific miRNAs are tightly regulated by salinity in the shoots and/or roots of S. europaea, which may play important roles in salt tolerance of this euhalophyte. The S. europaea salt-responsive miRNAs and miRNAs that target transcription factors, nucleotide binding site-leucine-rich repeat proteins and enzymes involved in lignin biosynthesis as well as carbon and nitrogen metabolism may be applied in genetic engineering of crops with high stress tolerance, and genetic modification of biofuel crops with high biomass and regulatable lignin biosynthesis.
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Affiliation(s)
- Juanjuan Feng
- />Institute of Botany, Key Laboratory of Plant Molecular Physiology, Chinese Academy of Sciences, Beijing, 100093 China
| | - Jinhui Wang
- />Institute of Botany, Key Laboratory of Plant Molecular Physiology, Chinese Academy of Sciences, Beijing, 100093 China
| | - Pengxiang Fan
- />Institute of Botany, Key Laboratory of Plant Molecular Physiology, Chinese Academy of Sciences, Beijing, 100093 China
- />Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson road, East Lansing, MI 48824 USA
| | - Weitao Jia
- />Institute of Botany, Key Laboratory of Plant Molecular Physiology, Chinese Academy of Sciences, Beijing, 100093 China
| | - Lingling Nie
- />Institute of Botany, Key Laboratory of Plant Molecular Physiology, Chinese Academy of Sciences, Beijing, 100093 China
| | - Ping Jiang
- />Institute of Botany, Key Laboratory of Plant Molecular Physiology, Chinese Academy of Sciences, Beijing, 100093 China
| | - Xianyang Chen
- />Institute of Botany, Key Laboratory of Plant Molecular Physiology, Chinese Academy of Sciences, Beijing, 100093 China
| | - Sulian Lv
- />Institute of Botany, Key Laboratory of Plant Molecular Physiology, Chinese Academy of Sciences, Beijing, 100093 China
| | - Lichuan Wan
- />Institute of Botany, Key Laboratory of Plant Molecular Physiology, Chinese Academy of Sciences, Beijing, 100093 China
| | - Sandra Chang
- />Beijing Engineering Research Center for Biofuels, Tsinghua University, Beijing, 100084 China
- />Institute of Nuclear and New Energy Technology, Tsinghua University, Beijing, 100084 China
| | - Shizhong Li
- />Beijing Engineering Research Center for Biofuels, Tsinghua University, Beijing, 100084 China
- />Institute of Nuclear and New Energy Technology, Tsinghua University, Beijing, 100084 China
| | - Yinxin Li
- />Institute of Botany, Key Laboratory of Plant Molecular Physiology, Chinese Academy of Sciences, Beijing, 100093 China
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Yaish MW, Sunkar R, Zheng Y, Ji B, Al-Yahyai R, Farooq SA. A genome-wide identification of the miRNAome in response to salinity stress in date palm (Phoenix dactylifera L.). FRONTIERS IN PLANT SCIENCE 2015; 6:946. [PMID: 26594218 PMCID: PMC4633500 DOI: 10.3389/fpls.2015.00946] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 10/17/2015] [Indexed: 05/22/2023]
Abstract
Although date palm is relatively salt-tolerant, little is known about the underlying molecular mechanisms that contribute to its salt tolerance. Only recently, investigators have uncovered microRNA-mediated post-transcriptional gene regulation, which is critical for typical plant development and adaptation to stress conditions such as salinity. To identify conserved and novel miRNAs in date palm and to characterize miRNAs that could play a role in salt tolerance, we have generated sRNA libraries from the leaves and roots of NaCl-treated and untreated seedlings of date palm. Deep sequencing of these four sRNA libraries yielded approximately 251 million reads. The bioinformatics analysis has identified 153 homologs of conserved miRNAs, 89 miRNA variants, and 180 putative novel miRNAs in date palm. Expression profiles under salinity revealed differential regulation of some miRNAs in date palm. In leaves, 54 of the identified miRNAs were significantly affected and the majority (70%) of them were upregulated, whereas in roots, 25 of the identified miRNAs were significantly affected and 76% of them were upregulated by the salinity stress. The salt-responsiveness of some of these miRNAs was further validated using semi-quantitative PCR (qPCR). Some of the predicted targets for the identified miRNA include genes with known functions in plant salt tolerance, such as potassium channel AKT2-like proteins, vacuolar protein sorting-associated protein, calcium-dependent and mitogen-activated proteins. As one of the first cultivated trees in the world that can tolerate a wide range of abiotic stresses, date palm contains a large population of conserved and non-conserved miRNAs that function at the post-transcriptional level. This study provided insights into miRNA-mediated gene expression that are important for adaptation to salinity in date palms.
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Affiliation(s)
- Mahmoud W. Yaish
- Department of Biology, College of Science, Sultan Qaboos UniversityMuscat, Oman
- *Correspondence: Mahmoud W. Yaish
| | - Ramanjulu Sunkar
- Department of Biochemistry and Molecular Biology, Oklahoma State UniversityStillwater, OK, USA
| | - Yun Zheng
- Faculty of Life Science and Technology, Kunming University of Science and TechnologyKunming, China
| | - Bo Ji
- Faculty of Life Science and Technology, Kunming University of Science and TechnologyKunming, China
| | - Rashid Al-Yahyai
- Department of Crop Science, College of Agriculture, Sultan Qaboos UniversityMuscat, Oman
| | - Sardar A. Farooq
- Department of Biology, College of Science, Sultan Qaboos UniversityMuscat, Oman
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