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Ullah I, Kamel EAR, Shah ST, Basit A, Mohamed HI, Sajid M. Application of RNAi technology: a novel approach to navigate abiotic stresses. Mol Biol Rep 2022; 49:10975-10993. [PMID: 36057876 DOI: 10.1007/s11033-022-07871-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 08/15/2022] [Indexed: 11/26/2022]
Abstract
BACKGROUND Due to the rising population globally, and the demand for food, it is critical to significantly increase crop production by 2050. However, climate change estimates show that droughts and heatwaves will become more prevalent in many parts of the world, posing a severe danger to food output. METHODS Selective breeding based on genetic diversity is falling short of meeting the expanding need for food and feed. However, the advent of modern plant genetic engineering, genome editing, and synthetic biology provides precise techniques for producing crops capable of sustaining yield under stress situations. RESULTS As a result, crop varieties with built-in genetic tolerance to environmental challenges are desperately needed. In the recent years, small RNA (sRNA) data has progressed to become one of the most effective approaches for the improvement of crops. So many sRNAs (18-30nt) have been found with the use of hi-tech bioinformatics and sequencing techniques which are involved in the regulation of sequence specific gene noncoding RNAs (short ncRNAs) i.e., microRNA (miRNA) and small interfering RNA (siRNA). Such research outcomes may advance our understanding of the genetic basis of adaptability of plants to various environmental challenges and the genetic variation of plant's tolerance to a number of abiotic stresses. CONCLUSION The review article highlights current trends and advances in sRNAs' critical role in responses of plants to drought, heat, cold, and salinity, and also the potential technology that identifies the abiotic stress-regulated sRNAs, and techniques for analyzing and validating the target genes.
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Affiliation(s)
- Izhar Ullah
- Department of Horticulture, Faculty of Crop Production Sciences, The University of Agriculture, Peshawar, 25120, Pakistan
| | - Ehab A R Kamel
- Department of Biological and Geological Sciences, Faculty of Education, Ain Shams University, Cairo, Egypt
| | - Syed Tanveer Shah
- Department of Horticulture, Faculty of Crop Production Sciences, The University of Agriculture, Peshawar, 25120, Pakistan
| | - Abdul Basit
- Department of Horticulture, Faculty of Crop Production Sciences, The University of Agriculture, Peshawar, 25120, Pakistan
| | - Heba I Mohamed
- Department of Biological and Geological Sciences, Faculty of Education, Ain Shams University, Cairo, Egypt.
| | - Muhammad Sajid
- Department of Horticulture, Faculty of Crop Production Sciences, The University of Agriculture, Peshawar, 25120, Pakistan
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Hu Y, Chen X, Shen X. Regulatory network established by transcription factors transmits drought stress signals in plant. STRESS BIOLOGY 2022; 2:26. [PMID: 37676542 PMCID: PMC10442052 DOI: 10.1007/s44154-022-00048-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 06/20/2022] [Indexed: 09/08/2023]
Abstract
Plants are sessile organisms that evolve with a flexible signal transduction system in order to rapidly respond to environmental changes. Drought, a common abiotic stress, affects multiple plant developmental processes especially growth. In response to drought stress, an intricate hierarchical regulatory network is established in plant to survive from the extreme environment. The transcriptional regulation carried out by transcription factors (TFs) is the most important step for the establishment of the network. In this review, we summarized almost all the TFs that have been reported to participate in drought tolerance (DT) in plant. Totally 466 TFs from 86 plant species that mostly belong to 11 families are collected here. This demonstrates that TFs in these 11 families are the main transcriptional regulators of plant DT. The regulatory network is built by direct protein-protein interaction or mutual regulation of TFs. TFs receive upstream signals possibly via post-transcriptional regulation and output signals to downstream targets via direct binding to their promoters to regulate gene expression.
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Affiliation(s)
- Yongfeng Hu
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement, Biotechnology Research Center, China Three Gorges University, Yichang, 443002 Hubei China
| | - Xiaoliang Chen
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement, Biotechnology Research Center, China Three Gorges University, Yichang, 443002 Hubei China
| | - Xiangling Shen
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement, Biotechnology Research Center, China Three Gorges University, Yichang, 443002 Hubei China
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3
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Zhu Y, Liu Q, Xu W, Yao L, Wang X, Wang H, Xu Y, Li L, Duan C, Yi Z, Lin C. Identification of novel drought-responsive miRNA regulatory network of drought stress response in common vetch ( Vicia sativa). Open Life Sci 2021; 16:1111-1121. [PMID: 34712821 PMCID: PMC8511966 DOI: 10.1515/biol-2021-0109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 08/06/2021] [Accepted: 08/19/2021] [Indexed: 11/15/2022] Open
Abstract
Drought is among the most important natural disasters with severe effects on animals and plants. MicroRNAs are a class of noncoding RNAs that play a crucial role in plant growth, development, and response to stress factors, including drought. However, the microRNAs in drought responses in common vetch (Vicia sativa), an annual herbaceous leguminous plant commonly used for forage by including it in mixed seeding during winter and spring, have not been characterized. To explore the microRNAs’ response to drought in common vetch, we sequenced 10 small RNA (sRNA) libraries by the next-generation sequencing technology. We obtained 379 known miRNAs belonging to 38 families and 47 novel miRNAs. The two groups had varying numbers of differentially expressed miRNAs: 85 in the comparison group D5 vs C5 and 38 in the comparison group D3 vs C3. Combined analysis of mRNA and miRNA in the same samples under drought treatment identified 318 different target genes of 123 miRNAs. Functional annotation of the target genes revealed that the miRNAs regulate drought-responsive genes, such as leucine-rich repeat receptor-like kinase-encoding genes (LRR-RLKs), ABC transporter G family member 1 (ABCG1), and MAG2-interacting protein 2 (MIP2). The genes were involved in various pathways, including cell wall biosynthesis, reactive oxygen removal, and protein transport. The findings in this study provide new insights into the miRNA-mediated regulatory networks of drought stress response in common vetch.
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Affiliation(s)
- Yongqun Zhu
- Soil and Fertilizer Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610066, People's Republic of China
| | - Qiuxu Liu
- Soil and Fertilizer Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610066, People's Republic of China
| | - Wenzhi Xu
- Soil and Fertilizer Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610066, People's Republic of China
| | - Li Yao
- Soil and Fertilizer Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610066, People's Republic of China
| | - Xie Wang
- Soil and Fertilizer Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610066, People's Republic of China
| | - Hong Wang
- Soil and Fertilizer Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610066, People's Republic of China
| | - Yalin Xu
- Soil and Fertilizer Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610066, People's Republic of China
| | - Linxiang Li
- Bazhong Green Agriculture Innovation and Development Research Institute, Sichuan Academy of Agricultural Sciences, Bazhong, Sichuan 636000, People's Republic of China
| | - Chunhua Duan
- Soil and Fertilizer Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610066, People's Republic of China
| | - Zhixin Yi
- Bazhong Green Agriculture Innovation and Development Research Institute, Sichuan Academy of Agricultural Sciences, Bazhong, Sichuan 636000, People's Republic of China
| | - Chaowen Lin
- Soil and Fertilizer Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610066, People's Republic of China
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Pagano L, Rossi R, Paesano L, Marmiroli N, Marmiroli M. miRNA regulation and stress adaptation in plants. ENVIRONMENTAL AND EXPERIMENTAL BOTANY 2021. [PMID: 0 DOI: 10.1016/j.envexpbot.2020.104369] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
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Rosero A, Granda L, Berdugo-Cely JA, Šamajová O, Šamaj J, Cerkal R. A Dual Strategy of Breeding for Drought Tolerance and Introducing Drought-Tolerant, Underutilized Crops into Production Systems to Enhance Their Resilience to Water Deficiency. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1263. [PMID: 32987964 PMCID: PMC7600178 DOI: 10.3390/plants9101263] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/19/2020] [Accepted: 09/22/2020] [Indexed: 02/06/2023]
Abstract
Water scarcity is the primary constraint on crop productivity in arid and semiarid tropical areas suffering from climate alterations; in accordance, agricultural systems have to be optimized. Several concepts and strategies should be considered to improve crop yield and quality, particularly in vulnerable regions where such environmental changes cause a risk of food insecurity. In this work, we review two strategies aiming to increase drought stress tolerance: (i) the use of natural genes that have evolved over time and are preserved in crop wild relatives and landraces for drought tolerance breeding using conventional and molecular methods and (ii) exploiting the reservoir of neglected and underutilized species to identify those that are known to be more drought-tolerant than conventional staple crops while possessing other desired agronomic and nutritive characteristics, as well as introducing them into existing cropping systems to make them more resilient to water deficiency conditions. In the past, the existence of drought tolerance genes in crop wild relatives and landraces was either unknown or difficult to exploit using traditional breeding techniques to secure potential long-term solutions. Today, with the advances in genomics and phenomics, there are a number of new tools available that facilitate the discovery of drought resistance genes in crop wild relatives and landraces and their relatively easy transfer into advanced breeding lines, thus accelerating breeding progress and creating resilient varieties that can withstand prolonged drought periods. Among those tools are marker-assisted selection (MAS), genomic selection (GS), and targeted gene editing (clustered regularly interspaced short palindromic repeat (CRISPR) technology). The integration of these two major strategies, the advances in conventional and molecular breeding for the drought tolerance of conventional staple crops, and the introduction of drought-tolerant neglected and underutilized species into existing production systems has the potential to enhance the resilience of agricultural production under conditions of water scarcity.
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Affiliation(s)
- Amparo Rosero
- Corporación Colombiana de Investigación Agropecuaria–AGROSAVIA, Centro de Investigación Turipaná, Km 13 vía Montería, 250047 Cereté, Colombia;
| | - Leiter Granda
- Department of Crop Science, Breeding and Plant Medicine, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic; (L.G.); (R.C.)
| | - Jhon A. Berdugo-Cely
- Corporación Colombiana de Investigación Agropecuaria–AGROSAVIA, Centro de Investigación Turipaná, Km 13 vía Montería, 250047 Cereté, Colombia;
| | - Olga Šamajová
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic; (O.Š.); (J.Š.)
| | - Jozef Šamaj
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic; (O.Š.); (J.Š.)
| | - Radim Cerkal
- Department of Crop Science, Breeding and Plant Medicine, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic; (L.G.); (R.C.)
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Liu ZW, Li H, Liu JX, Wang Y, Zhuang J. Integrative transcriptome, proteome, and microRNA analysis reveals the effects of nitrogen sufficiency and deficiency conditions on theanine metabolism in the tea plant ( Camellia sinensis). HORTICULTURE RESEARCH 2020; 7:65. [PMID: 32377356 PMCID: PMC7192918 DOI: 10.1038/s41438-020-0290-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/13/2020] [Accepted: 03/02/2020] [Indexed: 05/18/2023]
Abstract
Nitrogen (N) is associated with amino acid metabolism in higher plants. Theanine is an important amino acid in tea plants. To explore the relationship between theanine metabolism and N conditions, we examined the differentially expressed genes (DEGs), proteins (DEPs), and microRNAs (DEMs) involved in theanine metabolism in tea plant shoots and roots under N sufficiency and deficiency conditions. Transcriptome, proteome, and microRNA analyses were performed on tea plant shoots and roots under N sufficiency and deficiency conditions. The contents of theanine, expression levels of genes involved in theanine metabolism, contents of proteinogenic amino acids, and activity of enzymes were analyzed. The DEP-DEG correlation pairs and negative DEM-DEG interactions related to theanine metabolism were identified based on correlation analyses. The expression profiles of DEGs and negative DEM-DEG pairs related to theanine biosynthesis were consistent with the sequencing results. Our results suggest that the molecular and physiological mechanism of theanine accumulation is significantly affected by N sufficiency and deficiency conditions. The DEGs, DEPs, and DEMs and the activity of the enzymes involved in theanine biosynthesis might play vital roles in theanine accumulation under N sufficiency and deficiency conditions in the shoots and roots of tea plants.
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Affiliation(s)
- Zhi-Wei Liu
- Tea Science Research Institute, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Hui Li
- Tea Science Research Institute, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Jie-Xia Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095 Nanjing, China
| | - Yu Wang
- Tea Science Research Institute, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Jing Zhuang
- Tea Science Research Institute, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
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Liu J, Fan H, Wang Y, Han C, Wang X, Yu J, Li D, Zhang Y. Genome-Wide microRNA Profiling Using Oligonucleotide Microarray Reveals Regulatory Networks of microRNAs in Nicotiana benthamiana During Beet Necrotic Yellow Vein Virus Infection. Viruses 2020; 12:E310. [PMID: 32178444 PMCID: PMC7150760 DOI: 10.3390/v12030310] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/05/2020] [Accepted: 03/10/2020] [Indexed: 01/15/2023] Open
Abstract
Beet necrotic yellow vein virus (BNYVV) infections induce stunting and leaf curling, as well as root and floral developmental defects and leaf senescence in Nicotiana benthamiana. A microarray analysis with probes capable of detecting 1596 candidate microRNAs (miRNAs) was conducted to investigate differentially expressed miRNAs and their targets upon BNYVV infection of N. benthamiana plants. Eight species-specific miRNAs of N. benthamiana were identified. Comprehensive characterization of the N. benthamiana microRNA profile in response to the BNYVV infection revealed that 129 miRNAs were altered, including four species-specific miRNAs. The targets of the differentially expressed miRNAs were predicted accordingly. The expressions of miR164, 160, and 393 were up-regulated by BNYVV infection, and those of their target genes, NAC21/22, ARF17/18, and TIR, were down-regulated. GRF1, which is a target of miR396, was also down-regulated. Further genetic analysis of GRF1, by Tobacco rattle virus-induced gene silencing, assay confirmed the involvement of GRF1 in the symptom development during BNYVV infection. BNYVV infection also induced the up-regulation of miR168 and miR398. The miR398 was predicted to target umecyanin, and silencing of umecyanin could enhance plant resistance against viruses, suggesting the activation of primary defense response to BNYVV infection in N. benthamiana. These results provide a global profile of miRNA changes induced by BNYVV infection and enhance our understanding of the mechanisms underlying BNYVV pathogenesis.
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Affiliation(s)
- Junying Liu
- State Key Laboratory for Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China; (J.L.); (H.F.); (Y.W.)
- Laboratory of Phytopathology, College of Chemistry Biology and Environment, Yuxi Normal University, Yuxi 653100, China
| | - Huiyan Fan
- State Key Laboratory for Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China; (J.L.); (H.F.); (Y.W.)
| | - Ying Wang
- State Key Laboratory for Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China; (J.L.); (H.F.); (Y.W.)
| | - Chenggui Han
- State Key Laboratory for Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China; (J.L.); (H.F.); (Y.W.)
| | - Xianbing Wang
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China; (X.W.); (J.Y.); (D.L.)
| | - Jialin Yu
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China; (X.W.); (J.Y.); (D.L.)
| | - Dawei Li
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China; (X.W.); (J.Y.); (D.L.)
| | - Yongliang Zhang
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China; (X.W.); (J.Y.); (D.L.)
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Chen P, Chen J, Sun M, Yan H, Feng G, Wu B, Zhang X, Wang X, Huang L. Comparative transcriptome study of switchgrass ( Panicum virgatum L.) homologous autopolyploid and its parental amphidiploid responding to consistent drought stress. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:170. [PMID: 33072185 PMCID: PMC7559793 DOI: 10.1186/s13068-020-01810-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 10/06/2020] [Indexed: 05/09/2023]
Abstract
BACKGROUND Newly formed polyploids may experience short-term adaptative changes in their genome that may enhance the resistance of plants to stress. Considering the increasingly serious effects of drought on biofuel plants, whole genome duplication (WGD) may be an efficient way to proceed with drought resistant breeding. However, the molecular mechanism of drought response before/after WGD remains largely unclear. RESULT We found that autoploid switchgrass (Panicum virgatum L.) 8X Alamo had higher drought tolerance than its parent amphidiploid 4X Alamo using physiological tests. RNA and microRNA sequencing at different time points during drought were then conducted on 8X Alamo and 4X Alamo switchgrass. The specific differentially expressed transcripts (DETs) that related to drought stress (DS) in 8X Alamo were enriched in ribonucleoside and ribonucleotide binding, while the drought-related DETs in 4X Alamo were enriched in structural molecule activity. Ploidy-related DETs were primarily associated with signal transduction mechanisms. Weighted gene co-expression network analysis (WGCNA) detected three significant DS-related modules, and their DETs were primarily enriched in biosynthesis process and photosynthesis. A total of 26 differentially expressed microRNAs (DEmiRs) were detected, and among them, sbi-microRNA 399b was only expressed in 8X Alamo. The targets of microRNAs that were responded to polyploidization and drought stress all contained cytochrome P450 and superoxide dismutase genes. CONCLUSIONS This study explored the drought response of 8X and 4X Alamo switchgrass on both physiological and transcriptional levels, and provided experimental and sequencing data basis for a short-term adaptability study and drought-resistant biofuel plant breeding.
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Affiliation(s)
- Peilin Chen
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 China
- Institute for Biology, Plant Cell and Molecular Biology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Jing Chen
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 China
| | - Min Sun
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 China
| | - Haidong Yan
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 China
- Department of Horticulture, Virginia Tech, Blacksburg, VA 24061 USA
| | - Guangyan Feng
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 China
| | - Bingchao Wu
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 China
| | - Xinquan Zhang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 China
| | - Xiaoshan Wang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 China
| | - Linkai Huang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 China
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Liu X, Zhang X, Sun B, Hao L, Liu C, Zhang D, Tang H, Li C, Li Y, Shi Y, Xie X, Song Y, Wang T, Li Y. Genome-wide identification and comparative analysis of drought-related microRNAs in two maize inbred lines with contrasting drought tolerance by deep sequencing. PLoS One 2019; 14:e0219176. [PMID: 31276526 PMCID: PMC6611575 DOI: 10.1371/journal.pone.0219176] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 06/18/2019] [Indexed: 11/19/2022] Open
Abstract
Drought has become one of the most serious abiotic stresses influencing crop production worldwide. Understanding the molecular regulatory networks underlying drought adaption and tolerance in crops is of great importance for future breeding. microRNAs (miRNAs), as important components of post-transcriptional regulation, play crucial roles in drought response and adaptation in plants. Here, we report a miRNome analysis of two maize inbred lines with contrasting levels of drought tolerance under soil drought in the field. Differential expression analysis showed 11 and 34 miRNAs were uniquely responded to drought in H082183 (drought tolerant) and Lv28 (drought sensitive), respectively, in leaves. In roots, 19 and 23 miRNAs uniquely responded to drought in H082183 and Lv28, respectively. Expression analysis of these drought-responsive miRNA-mRNA modules revealed miR164-MYB, miR164-NAC, miR159-MYB, miR156-SPL and miR160-ARF showed a negative regulatory relationship. Further analysis showed that the miR164-MYB and miR164-NAC modules in the tolerant line modulated the stress response in an ABA (abscisic acid)-dependent manner, while the miR156-SPL and miR160-ARF modules in the sensitive line participated in the inhibition of metabolism in drought-exposed leaves. Together, our results provide new insight into not only drought-tolerance-related miRNA regulation networks in maize but also key miRNAs for further characterization and improvement of maize drought tolerance.
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Affiliation(s)
- Xuyang Liu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaojing Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Baocheng Sun
- Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Luyang Hao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Cheng Liu
- Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Dengfeng Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huaijun Tang
- Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Chunhui Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongxiang Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunsu Shi
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoqing Xie
- Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Yanchun Song
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tianyu Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yu Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
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Xu J, Chen Q, Liu P, Jia W, Chen Z, Xu Z. Integration of mRNA and miRNA Analysis Reveals the Molecular Mechanism Underlying Salt and Alkali Stress Tolerance in Tobacco. Int J Mol Sci 2019; 20:E2391. [PMID: 31091777 PMCID: PMC6566703 DOI: 10.3390/ijms20102391] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/07/2019] [Accepted: 05/09/2019] [Indexed: 12/24/2022] Open
Abstract
Salinity is one of the most severe forms of abiotic stress and affects crop yields worldwide. Plants respond to salinity stress via a sophisticated mechanism at the physiological, transcriptional and metabolic levels. However, the molecular regulatory networks involved in salt and alkali tolerance have not yet been elucidated. We developed an RNA-seq technique to perform mRNA and small RNA (sRNA) sequencing of plants under salt (NaCl) and alkali (NaHCO3) stress in tobacco. Overall, 8064 differentially expressed genes (DEGs) and 33 differentially expressed microRNAs (DE miRNAs) were identified in response to salt and alkali stress. A total of 1578 overlapping DEGs, which exhibit the same expression patterns and are involved in ion channel, aquaporin (AQP) and antioxidant activities, were identified. Furthermore, genes involved in several biological processes, such as "photosynthesis" and "starch and sucrose metabolism," were specifically enriched under NaHCO3 treatment. We also identified 15 and 22 miRNAs that were differentially expressed in response to NaCl and NaHCO3, respectively. Analysis of inverse correlations between miRNAs and target mRNAs revealed 26 mRNA-miRNA interactions under NaCl treatment and 139 mRNA-miRNA interactions under NaHCO3 treatment. This study provides new insights into the molecular mechanisms underlying the response of tobacco to salinity stress.
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Affiliation(s)
- Jiayang Xu
- National Tobacco Cultivation and Physiology and Biochemistry Research Center, College of Tobacco Science, Henan Agricultural University, Zhengzhou 450002, China.
| | - Qiansi Chen
- Zhengzhou Tobacco Research Institute, Zhengzhou 450001, China.
| | - Pingping Liu
- Zhengzhou Tobacco Research Institute, Zhengzhou 450001, China.
| | - Wei Jia
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China.
| | - Zheng Chen
- National Tobacco Cultivation and Physiology and Biochemistry Research Center, College of Tobacco Science, Henan Agricultural University, Zhengzhou 450002, China.
| | - Zicheng Xu
- National Tobacco Cultivation and Physiology and Biochemistry Research Center, College of Tobacco Science, Henan Agricultural University, Zhengzhou 450002, China.
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Bioinformatic Exploration of the Targets of Xylem Sap miRNAs in Maize under Cadmium Stress. Int J Mol Sci 2019; 20:ijms20061474. [PMID: 30909604 PMCID: PMC6470939 DOI: 10.3390/ijms20061474] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/12/2019] [Accepted: 03/14/2019] [Indexed: 11/17/2022] Open
Abstract
Cadmium (Cd) has the potential to be chronically toxic to humans through contaminated crop products. MicroRNAs (miRNAs) can move systemically in plants. To investigate the roles of long-distance moving xylem miRNAs in regulating maize response to Cd stress, three xylem sap small RNA (sRNA) libraries were constructed for high-throughput sequencing to identify potential mobile miRNAs in Cd-stressed maize seedlings and their putative targets in maize transcriptomes. In total, about 199 miRNAs (20–22 nucleotides) were identified in xylem sap from maize seedlings, including 97 newly discovered miRNAs and 102 known miRNAs. Among them, 10 miRNAs showed differential expression in xylem sap after 1 h of Cd treatment. Two miRNAs target prediction tools, psRNAtarget (reporting the inhibition pattern of cleavage) and DPMIND (discovering Plant MiRNA-Target Interaction with degradome evidence), were used in combination to identify, via bioinformatics, the targets of 199 significantly expressed miRNAs in maize xylem sap. The integrative results of these two bioinformatic tools suggested that 27 xylem sap miRNAs inhibit 34 genes through cleavage with degradome evidence. Moreover, nearly 300 other genes were also the potential miRNAs cleavable targets without available degradome data support, and the majority of them were enriched in abiotic stress response, cell signaling, transcription regulation, as well as metal handling. These approaches and results not only enhanced our understanding of the Cd-responsive long-distance transported miRNAs from the view of xylem sap, but also provided novel insights for predicting the molecular genetic mechanisms mediated by miRNAs.
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Ji Y, Chen P, Chen J, Pennerman KK, Liang X, Yan H, Zhou S, Feng G, Wang C, Yin G, Zhang X, Hu Y, Huang L. Combinations of Small RNA, RNA, and Degradome Sequencing Uncovers the Expression Pattern of microRNA⁻mRNA Pairs Adapting to Drought Stress in Leaf and Root of Dactylis glomerata L. Int J Mol Sci 2018; 19:E3114. [PMID: 30314311 PMCID: PMC6213654 DOI: 10.3390/ijms19103114] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 10/05/2018] [Accepted: 10/08/2018] [Indexed: 11/17/2022] Open
Abstract
Drought stress is a global problem, and the lack of water is a key factor that leads to agricultural shortages. MicroRNAs play a crucial role in the plant drought stress response; however, the microRNAs and their targets involved in drought response have not been well elucidated. In the present study, we used Illumina platform (https://www.illumina.com/) and combined data from miRNA, RNA, and degradome sequencing to explore the drought- and organ-specific miRNAs in orchardgrass (Dactylis glomerata L.) leaf and root. We aimed to find potential miRNA⁻mRNA regulation patterns responding to drought conditions. In total, 519 (486 conserved and 33 novel) miRNAs were identified, of which, 41 miRNAs had significant differential expression among the comparisons (p < 0.05). We also identified 55,366 unigenes by RNA-Seq, where 12,535 unigenes were differently expressed. Finally, our degradome analysis revealed that 5950 transcripts were targeted by 487 miRNAs. A correlation analysis identified that miRNA ata-miR164c-3p and its target heat shock protein family A (HSP70) member 5 gene comp59407_c0 (BIPE3) may be essential in organ-specific plant drought stress response and/or adaptation in orchardgrass. Additionally, Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) analyses found that "antigen processing and presentation" was the most enriched downregulated pathway in adaptation to drought conditions. Taken together, we explored the genes and miRNAs that may be involved in drought adaptation of orchardgrass and identified how they may be regulated. These results serve as a valuable genetic resource for future studies focusing on how plants adapted to drought conditions.
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Affiliation(s)
- Yang Ji
- Sichuan Animal Science Academy, Chengdu 610066, China.
| | - Peilin Chen
- Department of Grassland Science, Faculty of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Jing Chen
- Department of Grassland Science, Faculty of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Kayla K Pennerman
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA.
| | - Xiaoyu Liang
- Sichuan Animal Science Academy, Chengdu 610066, China.
| | - Haidong Yan
- Department of Horticulture, Virginia Tech, Blacksburg, VA 24061, USA.
| | - Sifan Zhou
- Department of Grassland Science, Faculty of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Guangyan Feng
- Department of Grassland Science, Faculty of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Chengran Wang
- Department of Grassland Science, Faculty of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Guohua Yin
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA.
| | - Xinquan Zhang
- Department of Grassland Science, Faculty of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Yuanbin Hu
- Sichuan Animal Science Academy, Chengdu 610066, China.
| | - Linkai Huang
- Department of Grassland Science, Faculty of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
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Wang L, Zhu C, Jin L, Xiao A, Duan J, Ma L. A novel gene of Kalanchoe daigremontiana confers plant drought resistance. Sci Rep 2018; 8:2547. [PMID: 29416051 PMCID: PMC5803263 DOI: 10.1038/s41598-018-20687-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 01/23/2018] [Indexed: 11/09/2022] Open
Abstract
Kalanchoe (K.) daigremontiana is important for studying asexual reproduction under different environmental conditions. Here, we describe a novel KdNOVEL41 (KdN41) gene that may confer drought resistance and could thereby affect K. daigremontiana development. The detected subcellular localization of a KdN41/Yellow Fluorescent Protein (YFP) fusion protein was in the nucleus and cell membrane. Drought, salt, and heat stress treatment in tobacco plants containing the KdN41 gene promoter driving β-glucuronidase (GUS) gene transcription revealed that only drought stress triggered strong GUS staining in the vascular tissues. Overexpression (OE) of the KdN41 gene conferred improved drought resistance in tobacco plants compared to wild-type and transformed with empty vector plants by inducing higher antioxidant enzyme activities, decreasing cell membrane damage, increasing abscisic acid (ABA) content, causing reinforced drought resistance related gene expression profiles. The 3,3'-diaminobenzidine (DAB) and nitroblue tetrazolium (NBT) staining results also showed less relative oxygen species (ROS) content in KdN41-overexpressing tobacco leaf during drought stress. Surprisingly, by re-watering after drought stress, KdN41-overexpressing tobacco showed earlier flowering. Overall, the KdN41 gene plays roles in ROS scavenging and osmotic damage reduction to improve tobacco drought resistance, which may increase our understanding of the molecular network involved in developmental manipulation under drought stress in K. daigremontiana.
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Affiliation(s)
- Li Wang
- Key Laboratory for Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China
| | - Chen Zhu
- Shanghai Center for Plant Stress Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lin Jin
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing, China
| | - Aihua Xiao
- Key Laboratory for Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China
| | - Jie Duan
- Key Laboratory for Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China.
- National Energy R&D Center for Non-food Biomass, Beijing, China.
| | - Luyi Ma
- Key Laboratory for Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China.
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14
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Li Y, Wan L, Bi S, Wan X, Li Z, Cao J, Tong Z, Xu H, He F, Li X. Identification of Drought-Responsive MicroRNAs from Roots and Leaves of Alfalfa by High-Throughput Sequencing. Genes (Basel) 2017; 8:genes8040119. [PMID: 28406444 PMCID: PMC5406866 DOI: 10.3390/genes8040119] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 04/05/2017] [Accepted: 04/06/2017] [Indexed: 12/13/2022] Open
Abstract
Alfalfa, an important forage legume, is an ideal crop for sustainable agriculture and a potential crop for bioenergy resources. Drought, one of the most common environmental stresses, substantially affects plant growth, development, and productivity. MicroRNAs (miRNAs) are newly discovered gene expression regulators that have been linked to several plant stress responses. To elucidate the role of miRNAs in drought stress regulation of alfalfa, a high-throughput sequencing approach was used to analyze 12 small RNA libraries comprising of four samples, each with three biological replicates. From the 12 libraries, we identified 348 known miRNAs belonging to 80 miRNA families, and 281 novel miRNAs, using Mireap software. Eighteen known miRNAs in roots and 12 known miRNAs in leaves were screened as drought-responsive miRNAs. With the exception of miR319d and miR157a which were upregulated under drought stress, the expression pattern of drought-responsive miRNAs was different between roots and leaves in alfalfa. This is the first study that has identified miR3512, miR3630, miR5213, miR5294, miR5368 and miR6173 as drought-responsive miRNAs. Target transcripts of drought-responsive miRNAs were computationally predicted. All 447 target genes for the known miRNAs were predicted using an online tool. This study provides a significant insight on understanding drought-responsive mechanisms of alfalfa.
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Affiliation(s)
- Yue Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Liqiang Wan
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Shuyi Bi
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Xiufu Wan
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Zhenyi Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Jing Cao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Zongyong Tong
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Hongyu Xu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Feng He
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Xianglin Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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15
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Chen Q, Li M, Zhang Z, Tie W, Chen X, Jin L, Zhai N, Zheng Q, Zhang J, Wang R, Xu G, Zhang H, Liu P, Zhou H. Integrated mRNA and microRNA analysis identifies genes and small miRNA molecules associated with transcriptional and post-transcriptional-level responses to both drought stress and re-watering treatment in tobacco. BMC Genomics 2017; 18:62. [PMID: 28068898 PMCID: PMC5223433 DOI: 10.1186/s12864-016-3372-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 12/02/2016] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Drought stress is one of the most severe problem limited agricultural productivity worldwide. It has been reported that plants response to drought-stress by sophisticated mechanisms at both transcriptional and post-transcriptional levels. However, the precise molecular mechanisms governing the responses of tobacco leaves to drought stress and water status are not well understood. To identify genes and miRNAs involved in drought-stress responses in tobacco, we performed both mRNA and small RNA sequencing on tobacco leaf samples from the following three treatments: untreated-control (CL), drought stress (DL), and re-watering (WL). RESULTS In total, we identified 798 differentially expressed genes (DEGs) between the DL and CL (DL vs. CL) treatments and identified 571 DEGs between the WL and DL (WL vs. DL) treatments. Further analysis revealed 443 overlapping DEGs between the DL vs. CL and WL vs. DL comparisons, and, strikingly, all of these genes exhibited opposing expression trends between these two comparisons, strongly suggesting that these overlapping DEGs are somehow involved in the responses of tobacco leaves to drought stress. Functional annotation analysis showed significant up-regulation of genes annotated to be involved in responses to stimulus and stress, (e.g., late embryogenesis abundant proteins and heat-shock proteins) antioxidant defense (e.g., peroxidases and glutathione S-transferases), down regulation of genes related to the cell cycle pathway, and photosynthesis processes. We also found 69 and 56 transcription factors (TFs) among the DEGs in, respectively, the DL vs. CL and the WL vs. DL comparisons. In addition, small RNA sequencing revealed 63 known microRNAs (miRNA) from 32 families and 368 novel miRNA candidates in tobacco. We also found that five known miRNA families (miR398, miR390, miR162, miR166, and miR168) showed differential regulation under drought conditions. Analysis to identify negative correlations between the differentially expressed miRNAs (DEMs) and DEGs revealed 92 mRNA-miRNA interactions between CL and DL plants, and 32 mRNA-miRNA interactions between DL and WL plants. CONCLUSIONS This study provides a global view of the transcriptional and the post-transcriptional responses of tobacco under drought stress and re-watering conditions. Our results establish an empirical foundation that should prove valuable for further investigations into the molecular mechanisms through which tobacco, and plants more generally, respond to drought stress at multiple molecular genetic levels.
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Affiliation(s)
- Qiansi Chen
- Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
| | - Meng Li
- Key Laboratory of Cultivation and Protection for Non-wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, 410000, China
- College of Life Science and Technology, Central South University of Forestry and Technology, Changsha, 410000, China
| | - Zhongchun Zhang
- School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Weiwei Tie
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Xia Chen
- Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
| | - Lifeng Jin
- Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
| | - Niu Zhai
- Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
| | - Qingxia Zheng
- Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
| | - Jianfeng Zhang
- Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
| | - Ran Wang
- Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
| | - Guoyun Xu
- Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
| | - Hui Zhang
- Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
| | - Pingping Liu
- Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China.
| | - Huina Zhou
- Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China.
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16
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Cao X, Fan G, Cao L, Deng M, Zhao Z, Niu S, Wang Z, Wang Y. Drought stress-induced changes of microRNAs in diploid and autotetraploid Paulownia tomentosa. Genes Genomics 2016; 39:77-86. [PMID: 28090264 PMCID: PMC5196014 DOI: 10.1007/s13258-016-0473-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 10/08/2016] [Indexed: 12/24/2022]
Abstract
Drought stress adversely affects plant productivity. Growth and timber production of Paulownia trees are limited under drought stress. Changes in gene expression patterns and miRNA in different ploidy of Paulownia tomentosa have been investigated. However, the responses of P. tomentosa to drought stress at the microRNA (miRNA) level have not been reported so far. To identify miRNA candidates and their target genes involved in the drought stress response in diploid and tetraploid P. tomentosa, four small RNA and four degradome libraries from diploid and autotetraploid P. tomentosa under normal and drought stress conditions were constructed and sequenced. A total of 41 conserved and 90 novel miRNAs were identified. Among these miRNAs, 67 (26 conserved and 41 novel) and 53 (six conserved and 47 novel) were significantly differentially expressed in response to drought stress in diploid and autotetraploid P. tomentosa, respectively. Degradome analysis identified 356 candidate miRNA target genes that encoded proteins with functions that included plant defense, transcriptional regulation, and hormone metabolism. In particular, miR4 and miR156 were identified only in autotetraploid P. tomentosa under drought stress. These results will help us build a foundation for future studies of the biological functions of miRNA-mediated gene regulation in P. tomentosa.
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Affiliation(s)
- Xibing Cao
- Institute of Paulownia, Henan Agricultural University, No 95 Wenhua Road, Jinshui Area, Zhengzhou, 450002 Henan People’s Republic of China
- College of Forestry, Henan Agricultural University, No 95 Wenhua Road, Jinshui Area, Zhengzhou, 450002 Henan People’s Republic of China
| | - Guoqiang Fan
- Institute of Paulownia, Henan Agricultural University, No 95 Wenhua Road, Jinshui Area, Zhengzhou, 450002 Henan People’s Republic of China
- College of Forestry, Henan Agricultural University, No 95 Wenhua Road, Jinshui Area, Zhengzhou, 450002 Henan People’s Republic of China
| | - Lin Cao
- Institute of Paulownia, Henan Agricultural University, No 95 Wenhua Road, Jinshui Area, Zhengzhou, 450002 Henan People’s Republic of China
- College of Forestry, Henan Agricultural University, No 95 Wenhua Road, Jinshui Area, Zhengzhou, 450002 Henan People’s Republic of China
| | - Minjie Deng
- Institute of Paulownia, Henan Agricultural University, No 95 Wenhua Road, Jinshui Area, Zhengzhou, 450002 Henan People’s Republic of China
- College of Forestry, Henan Agricultural University, No 95 Wenhua Road, Jinshui Area, Zhengzhou, 450002 Henan People’s Republic of China
| | - Zhenli Zhao
- Institute of Paulownia, Henan Agricultural University, No 95 Wenhua Road, Jinshui Area, Zhengzhou, 450002 Henan People’s Republic of China
- College of Forestry, Henan Agricultural University, No 95 Wenhua Road, Jinshui Area, Zhengzhou, 450002 Henan People’s Republic of China
| | - Suyan Niu
- Institute of Paulownia, Henan Agricultural University, No 95 Wenhua Road, Jinshui Area, Zhengzhou, 450002 Henan People’s Republic of China
- College of Forestry, Henan Agricultural University, No 95 Wenhua Road, Jinshui Area, Zhengzhou, 450002 Henan People’s Republic of China
| | - Zhe Wang
- Institute of Paulownia, Henan Agricultural University, No 95 Wenhua Road, Jinshui Area, Zhengzhou, 450002 Henan People’s Republic of China
- College of Forestry, Henan Agricultural University, No 95 Wenhua Road, Jinshui Area, Zhengzhou, 450002 Henan People’s Republic of China
| | - Yuanlong Wang
- Institute of Paulownia, Henan Agricultural University, No 95 Wenhua Road, Jinshui Area, Zhengzhou, 450002 Henan People’s Republic of China
- College of Forestry, Henan Agricultural University, No 95 Wenhua Road, Jinshui Area, Zhengzhou, 450002 Henan People’s Republic of China
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17
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Candar-Cakir B, Arican E, Zhang B. Small RNA and degradome deep sequencing reveals drought-and tissue-specific micrornas and their important roles in drought-sensitive and drought-tolerant tomato genotypes. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1727-46. [PMID: 26857916 PMCID: PMC5067666 DOI: 10.1111/pbi.12533] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 12/15/2015] [Accepted: 12/26/2015] [Indexed: 05/03/2023]
Abstract
Drought stress has adverse impacts on plant production and productivity. MicroRNAs (miRNAs) are one class of noncoding RNAs regulating gene expression post-transcriptionally. In this study, we employed small RNA and degradome sequencing to systematically investigate the tissue-specific miRNAs responsible to drought stress, which are understudied in tomato. For this purpose, root and upground tissues of two different drought-responsive tomato genotypes (Lycopersicon esculentum as sensitive and L. esculentum var. cerasiforme as tolerant) were subjected to stress with 5% polyethylene glycol for 7 days. A total of 699 conserved miRNAs belonging to 578 families were determined and 688 miRNAs were significantly differentially expressed between different treatments, tissues and genotypes. Using degradome sequencing, 44 target genes were identified associated with 36 miRNA families. Drought-related miRNAs and their targets were enriched functionally by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Totally, 53 miRNAs targeted 23 key drought stress- and tissue development-related genes, including DRP (dehydration-responsive protein), GTs (glycosyltransferases), ERF (ethylene responsive factor), PSII (photosystem II) protein, HD-ZIP (homeodomain-leucine zipper), MYB and NAC-domain transcription factors. miR160, miR165, miR166, miR171, miR398, miR408, miR827, miR9472, miR9476 and miR9552 were the key miRNAs functioning in regulation of these genes and involving in tomato response to drought stress. Additionally, plant hormone signal transduction pathway genes were differentially regulated by miR169, miR172, miR393, miR5641, miR5658 and miR7997 in both tissues of both sensitive and tolerant genotypes. These results provide new insight into the regulatory role of miRNAs in drought response with plant hormone signal transduction and drought-tolerant tomato breeding.
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Affiliation(s)
- Bilgin Candar-Cakir
- Programme of Molecular Biology and Genetics, Institute of Science, Istanbul University, Vezneciler, Istanbul, Turkey
- Department of Biology, East Carolina University, Greenville, NC, USA
| | - Ercan Arican
- Department of Molecular Biology and Genetics, Faculty of Science, Istanbul University, Vezneciler, Istanbul, Turkey
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC, USA
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18
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Zhang L, Xuan H, Zuo Y, Xu G, Wang P, Song Y, Zhang S. Topological characteristics of target genes regulated by abiotic-stress-responsible miRNAs in a rice interactome network. Funct Integr Genomics 2016; 16:243-51. [PMID: 26830287 DOI: 10.1007/s10142-016-0481-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 01/18/2016] [Accepted: 01/20/2016] [Indexed: 10/22/2022]
Abstract
A great number of microRNAs (miRNAs) have been identified in responding and acting in gene regulatory networks associated with plant tolerance to abiotic stress conditions, such as drought, salinity, and high temperature. The topological exploration of target genes regulated by abiotic-stress-responsible miRNAs (ASRmiRs) in a network facilitates to discover the molecular basis of plant abiotic stress response. This study was based on the staple food rice (Oryza sativa) in which ASRmiRs were manually curated. After having compared the topological properties of target genes (stress-miR-targets) with those (non-stress-miR-targets) not regulated by ASRmiRs in a rice interactome network, we found that stress-miR-targets exhibited distinguishable topological properties. The interaction probability analysis and k-core decomposition showed that stress-miR-targets preferentially interacted with non-stress-miR-targets and located at the peripheral positions in the network. Our results indicated an obvious topological distinction between the two types of genes, reflecting the specific mechanisms of action of stress-miR-targets in rice abiotic stress response. Also, the results may provide valuable clues to elucidate molecular mechanisms of crop response to abiotic stress.
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Affiliation(s)
- Linzhong Zhang
- School of Science, Anhui Agricultural University, Hefei, 230036, China
| | - Hongdong Xuan
- College of Information and Computer Science, Anhui Agricultural University, Hefei, 230036, China
| | - Yongchun Zuo
- College of Life Sciences, Inner Mongolia University, Hohhot, 010021, China
| | - Gaojian Xu
- College of Information and Computer Science, Anhui Agricultural University, Hefei, 230036, China
| | - Ping Wang
- School of Science, Anhui Agricultural University, Hefei, 230036, China
| | - Youhong Song
- School of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Shihua Zhang
- School of Science, Anhui Agricultural University, Hefei, 230036, China. .,State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China.
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19
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Zhang Y, Nan J, Yu B. OMICS Technologies and Applications in Sugar Beet. FRONTIERS IN PLANT SCIENCE 2016; 7:900. [PMID: 27446130 PMCID: PMC4916227 DOI: 10.3389/fpls.2016.00900] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/07/2016] [Indexed: 05/08/2023]
Abstract
Sugar beet is a species of the Chenopodiaceae family. It is an important sugar crop that supplies approximately 35% of the sugar in the world. Sugar beet M14 line is a unique germplasm that contains genetic materials from Beta vulgaris L. and Beta corolliflora Zoss. And exhibits tolerance to salt stress. In this review, we have summarized OMICS technologies and applications in sugar beet including M14 for identification of novel genes, proteins related to biotic and abiotic stresses, apomixes and metabolites related to energy and food. An OMICS overview for the discovery of novel genes, proteins and metabolites in sugar beet has helped us understand the complex mechanisms underlying many processes such as apomixes, tolerance to biotic and abiotic stresses. The knowledge gained is valuable for improving the tolerance of sugar beet and other crops to biotic and abiotic stresses as well as for enhancing the yield of sugar beet for energy and food production.
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Affiliation(s)
- Yongxue Zhang
- Key Laboratory of Molecular Biology of Heilongjiang Province, College of Life Sciences, Heilongjiang UniversityHarbin, China
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang UniversityHarbin, China
| | - Jingdong Nan
- Key Laboratory of Molecular Biology of Heilongjiang Province, College of Life Sciences, Heilongjiang UniversityHarbin, China
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang UniversityHarbin, China
| | - Bing Yu
- Key Laboratory of Molecular Biology of Heilongjiang Province, College of Life Sciences, Heilongjiang UniversityHarbin, China
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang UniversityHarbin, China
- *Correspondence: Bing Yu
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20
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Ganie SA, Dey N, Mondal TK. Promoter methylation regulates the abundance of osa-miR393a in contrasting rice genotypes under salinity stress. Funct Integr Genomics 2015; 16:1-11. [PMID: 26319531 DOI: 10.1007/s10142-015-0460-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 07/28/2015] [Accepted: 08/02/2015] [Indexed: 01/03/2023]
Abstract
MicroRNAs (miRNAs) are important molecules that regulate gene expression under salinity stress. Despite their evolutionary conservation, these regulatory elements have been shown to behave differently in different plant species under a particular environmental stress. In this study, we investigated the behavior of salt responsive osa-miR393a and its target gene (TIR1, LOC_Os05g05800) in salt-tolerant (FL478) and salt-sensitive (IR29) rice genotypes. It was found that the mature and precursor sequences of osa-miR393a as well as its cleavage site in TIR1 were conserved among salt tolerant and sensitive genotypes. Promoters of different salt-responsive miRNAs were also found to be less variable between salt-tolerant and salt-susceptible genotypes. Analysis of gene expression, promoter methylation, and cis-element abundance showed that osa-miR393a behaves differently in FL478 and IR29. Salt stress altered the expression pattern of osa-miR393a-TIR1 module in a time-dependent manner in the roots and shoots of two genotypes. Promoter methylation of this regulatory module was also altered at different time points under salt stress. Expression analysis in two genotypes indicated the overall down-regulation of osa-miR393a and up-regulation of TIR1 in FL478 and their reciprocal regulation in IR29. The expression results were complemented by the differential promoter methylation and cis-element abundance of this regulatory module. Together, the results of transcript abundance and promoter methylation of osa-miR393a-TIR1 module signified the association between these two processes which is reported for the first time in plants to the best of our knowledge.
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Affiliation(s)
- Showkat Ahmad Ganie
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, IARI Campus, New Delhi, 110012, India
| | - Narottam Dey
- Department of Biotechnology, Visva-Bharati, Santiniketan, 731 235, West Bengal, India
| | - Tapan Kumar Mondal
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, IARI Campus, New Delhi, 110012, India.
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Yin F, Qin C, Gao J, Liu M, Luo X, Zhang W, Liu H, Liao X, Shen Y, Mao L, Zhang Z, Lin H, Lübberstedt T, Pan G. Genome-wide identification and analysis of drought-responsive genes and microRNAs in tobacco. Int J Mol Sci 2015; 16:5714-40. [PMID: 25775154 PMCID: PMC4394501 DOI: 10.3390/ijms16035714] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Revised: 01/19/2015] [Accepted: 01/29/2015] [Indexed: 01/16/2023] Open
Abstract
Drought stress response is a complex trait regulated at transcriptional and post-transcriptional levels in tobacco. Since the 1990s, many studies have shown that miRNAs act in many ways to regulate target expression in plant growth, development and stress response. The recent draft genome sequence of Nicotiana benthamiana has provided a framework for Digital Gene Expression (DGE) and small RNA sequencing to understand patterns of transcription in the context of plant response to environmental stress. We sequenced and analyzed three Digital Gene Expression (DGE) libraries from roots of normal and drought-stressed tobacco plants, and four small RNA populations from roots, stems and leaves of control or drought-treated tobacco plants, respectively. We identified 276 candidate drought responsive genes (DRGs) with sequence similarities to 64 known DRGs from other model plant crops, 82 were transcription factors (TFs) including WRKY, NAC, ERF and bZIP families. Of these tobacco DRGs, 54 differentially expressed DRGs included 21 TFs, which belonged to 4 TF families such as NAC (6), MYB (4), ERF (10), and bZIP (1). Additionally, we confirmed expression of 39 known miRNA families (122 members) and five conserved miRNA families, which showed differential regulation under drought stress. Targets of miRNAs were further surveyed based on a recently published study, of which ten targets were DRGs. An integrated gene regulatory network is proposed for the molecular mechanisms of tobacco root response to drought stress using differentially expressed DRGs, the changed expression profiles of miRNAs and their target transcripts. This network analysis serves as a reference for future studies on tobacco response stresses such as drought, cold and heavy metals.
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Affiliation(s)
- Fuqiang Yin
- School of Agricultural Sciences, Xichang College, Xichang 615000, China.
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China.
| | - Cheng Qin
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China.
- Zunyi Academy of Agricultural Sciences, Zunyi 563102, China.
| | - Jian Gao
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China.
| | - Ming Liu
- School of Agricultural Sciences, Xichang College, Xichang 615000, China.
| | - Xirong Luo
- Zunyi Academy of Agricultural Sciences, Zunyi 563102, China.
| | - Wenyou Zhang
- School of Agricultural Sciences, Xichang College, Xichang 615000, China.
| | - Hongjun Liu
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China.
| | - Xinhui Liao
- Beijing Genomics Institute-Shenzhen, Shenzhen 518083, China.
| | - Yaou Shen
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China.
| | - Likai Mao
- Beijing Genomics Institute-Shenzhen, Shenzhen 518083, China.
| | - Zhiming Zhang
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China.
| | - Haijian Lin
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China.
| | | | - Guangtang Pan
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China.
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22
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Budak H, Hussain B, Khan Z, Ozturk NZ, Ullah N. From Genetics to Functional Genomics: Improvement in Drought Signaling and Tolerance in Wheat. FRONTIERS IN PLANT SCIENCE 2015; 6:1012. [PMID: 26635838 PMCID: PMC4652017 DOI: 10.3389/fpls.2015.01012] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 11/02/2015] [Indexed: 05/18/2023]
Abstract
Drought being a yield limiting factor has become a major threat to international food security. It is a complex trait and drought tolerance response is carried out by various genes, transcription factors (TFs), microRNAs (miRNAs), hormones, proteins, co-factors, ions, and metabolites. This complexity has limited the development of wheat cultivars for drought tolerance by classical breeding. However, attempts have been made to fill the lost genetic diversity by crossing wheat with wild wheat relatives. In recent years, several molecular markers including single nucleotide polymorphisms (SNPs) and quantitative trait loci (QTLs) associated with genes for drought signaling pathways have been reported. Screening of large wheat collections by marker assisted selection (MAS) and transformation of wheat with different genes/TFs has improved drought signaling pathways and tolerance. Several miRNAs also provide drought tolerance to wheat by regulating various TFs/genes. Emergence of OMICS techniques including transcriptomics, proteomics, metabolomics, and ionomics has helped to identify and characterize the genes, proteins, metabolites, and ions involved in drought signaling pathways. Together, all these efforts helped in understanding the complex drought tolerance mechanism. Here, we have reviewed the advances in wide hybridization, MAS, QTL mapping, miRNAs, transgenic technique, genome editing system, and above mentioned functional genomics tools for identification and utility of signaling molecules for improvement in wheat drought tolerance.
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Affiliation(s)
- Hikmet Budak
- Plant Genomics Group, Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci UniversityIstanbul, Turkey
- *Correspondence: Hikmet Budak,
| | - Babar Hussain
- Plant Genomics Group, Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci UniversityIstanbul, Turkey
| | - Zaeema Khan
- Plant Genomics Group, Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci UniversityIstanbul, Turkey
| | - Neslihan Z. Ozturk
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Niǧde UniversityNiǧde, Turkey
| | - Naimat Ullah
- Plant Genomics Group, Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci UniversityIstanbul, Turkey
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