1
|
Kaur S, Seem K, Duhan N, Kumar S, Kaundal R, Mohapatra T. Comparative miRNome and transcriptome analyses reveal the expression of novel miRNAs in the panicle of rice implicated in sustained agronomic performance under terminal drought stress. PLANTA 2024; 259:128. [PMID: 38639776 DOI: 10.1007/s00425-024-04399-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 03/27/2024] [Indexed: 04/20/2024]
Abstract
MAIN CONCLUSION Differential expression of 128 known and 111 novel miRNAs in the panicle of Nagina 22 under terminal drought stress targeting transcription factors, stress-associated genes, etc., enhances drought tolerance and helps sustain agronomic performance under terminal drought stress. Drought tolerance is a complex multigenic trait, wherein the genes are fine-tuned by coding and non-coding components in mitigating deleterious effects. MicroRNA (miRNA) controls gene expression at post-transcriptional level either by cleaving mRNA (transcript) or by suppressing its translation. miRNAs are known to control developmental processes and abiotic stress tolerance in plants. To identify terminal drought-responsive novel miRNA in contrasting rice cultivars, we constructed small RNA (sRNA) libraries from immature panicles of drought-tolerant rice [Nagina 22 (N 22)] and drought-sensitive (IR 64) cultivars grown under control and terminal drought stress. Our analysis of sRNA-seq data resulted in the identification of 169 known and 148 novel miRNAs in the rice cultivars. Among the novel miRNAs, 68 were up-regulated while 43 were down-regulated in the panicle of N 22 under stress. Interestingly, 31 novel miRNAs up-regulated in N 22 were down-regulated in IR 64, whereas 4 miRNAs down-regulated in N 22 were up-regulated in IR 64 under stress. To detect the effects of miRNA on mRNA expression level, transcriptome analysis was performed, while differential expression of miRNAs and their target genes was validated by RT-qPCR. Targets of the differentially expressed miRNAs include transcription factors and stress-associated genes involved in cellular/metabolic/developmental processes, response to abiotic stress, programmed cell death, photosynthesis, panicle/seed development, and grain yield. Differential expression of the miRNAs could be validated in an independent set of the samples. The findings might be useful in genetic improvement of drought-tolerant rice.
Collapse
Affiliation(s)
- Simardeep Kaur
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, USA
- ICAR-Research Complex for North Eastern Hill Region (NEH), Umiam, Meghalaya, 793103, India
| | - Karishma Seem
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Naveen Duhan
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, USA
| | - Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India.
| | - Rakesh Kaundal
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, USA.
- Bioinformatics Facility, Center for Integrated BioSystems, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, USA.
| | - Trilochan Mohapatra
- Protection of Plant Varieties and Farmers' Rights Authority, New Delhi, India
| |
Collapse
|
2
|
Zhao X, Xu H, Yang Y, Sun T, Ullah F, Zhu P, Lu Y, Huang J, Wang Z, Lu Z, Guo J. Defense Responses of Different Rice Varieties Affect Growth Performance and Food Utilization of Cnaphalocrocis medinalis Larvae. RICE (NEW YORK, N.Y.) 2024; 17:9. [PMID: 38244131 PMCID: PMC10799839 DOI: 10.1186/s12284-024-00683-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 01/03/2024] [Indexed: 01/22/2024]
Abstract
Rice leaf folder, Cnaphalocrocis medinalis (Guenée), is one of the most serious pests on rice. At present, chemical control is the main method for controlling this pest. However, the indiscriminate use of chemical insecticides has non-target effects and may cause environmental pollution. Besides, leaf curling behavior by C. medinalis may indirectly reduce the efficacy of chemical spray. Therefore, it is crucial to cultivate efficient rice varieties resistant to this pest. Previous studies have found that three different rice varieties, Zhongzao39 (ZZ39), Xiushui134 (XS134), and Yongyou1540 (YY1540), had varying degrees of infestation by C. medinalis. However, it is currently unclear whether the reason for this difference is related to the difference in defense ability of the three rice varieties against the infestation of C. medinalis. To explore this issue, the current study investigated the effects of three rice varieties on the growth performance and food utilization capability of the 4th instar C. medinalis. Further, it elucidated the differences in defense responses among different rice varieties based on the differences in leaf physiological and biochemical indicators and their impact on population occurrence. The results showed that the larval survival rate was the lowest, and the development period was significantly prolonged after feeding on YY1540. This was not related to the differences in leaf wax, pigments, and nutritional components among the three rice varieties nor to the feeding preferences of the larvae. The rate of superoxide anion production, hydrogen peroxide content, and the activity of three protective enzymes were negatively correlated with larval survival rate, and they all showed the highest in YY1540 leaves. Compared to other tested varieties, although the larvae feeding on YY1540 had higher conversion efficiency of ingested food and lower relative consumption rate, their relative growth was faster, indicating stronger food utilization capability. However, they had a lower accumulation of protein. This suggests that different rice varieties had different levels of oxidative stress after infestation by C. medinalis. The defense response of YY1540 was more intense, which was not conducive to the development of the larvae population. These results will provide new insights into the interaction mechanism between different rice varieties and C. medinalis and provide a theoretical basis for cultivating rice varieties resistant to this pest.
Collapse
Affiliation(s)
- Xiaoyu Zhao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro- Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
- College of Life Sciences, China Jiliang University, Hangzhou, 310018, China
| | - Hongxing Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro- Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Yajun Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro- Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Tianyi Sun
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro- Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Farman Ullah
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro- Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Pingyang Zhu
- College of Life Sciences, Zhejiang Normal University, Jinhua, 321004, China
| | - Yanhui Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro- Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Jianlei Huang
- College of Agriculture and Forestry, Hebei North University, Zhangjiakou, 075000, China
| | - Zhengliang Wang
- College of Life Sciences, China Jiliang University, Hangzhou, 310018, China
| | - Zhongxian Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro- Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
| | - Jiawen Guo
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro- Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
| |
Collapse
|
3
|
Dhingra Y, Lahiri M, Bhandari N, Kaur I, Gupta S, Agarwal M, Katiyar-Agarwal S. Genome-wide identification, characterization, and expression analysis unveil the roles of pseudouridine synthase (PUS) family proteins in rice development and stress response. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:1981-2004. [PMID: 38222285 PMCID: PMC10784261 DOI: 10.1007/s12298-023-01396-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/26/2023] [Accepted: 11/20/2023] [Indexed: 01/16/2024]
Abstract
Pseudouridylation, the conversion of uridine (U) to pseudouridine (Ѱ), is one of the most prevalent and evolutionary conserved RNA modifications, which is catalyzed by pseudouridine synthase (PUS) enzymes. Ѱs play a crucial epitranscriptomic role by regulating attributes of cellular RNAs across diverse organisms. However, the precise biological functions of PUSs in plants remain largely elusive. In this study, we identified and characterized 21 members in the rice PUS family which were categorized into six distinct subfamilies, with RluA and TruA emerging as the most extensive. A comprehensive analysis of domain structures, motifs, and homology modeling revealed that OsPUSs possess all canonical features of true PUS proteins, essential for substrate recognition and catalysis. The exploration of OsPUS promoters revealed presence of cis-acting regulatory elements associated with hormone and abiotic stress responses. Expression analysis of OsPUS genes showed differential expression at developmental stages and under stress conditions. Notably, OsTruB3 displayed high expression in salt, heat, and drought stresses. Several OsRluA members showed induction in heat stress, while a significant decline in expression was observed for various OsTruA members in drought and salinity. Furthermore, miRNAs predicted to target OsPUSs were themselves responsive to variable stresses, adding an additional layer of regulatory complexity of OsPUSs. Study of protein-protein interaction networks provided substantial support for the potential regulatory role of OsPUSs in numerous cellular and stress response pathways. Conclusively, our study provides functional insights into the OsPUS family, contributing to a better understanding of their crucial roles in shaping the development and stress adaptation in rice. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01396-4.
Collapse
Affiliation(s)
- Yashika Dhingra
- Department of Plant Molecular Biology, University of Delhi, South Campus, Benito Juarez Marg, Dhaula Kuan, New Delhi, 110021 India
| | - Milinda Lahiri
- Department of Plant Molecular Biology, University of Delhi, South Campus, Benito Juarez Marg, Dhaula Kuan, New Delhi, 110021 India
| | - Nikunj Bhandari
- Department of Plant Molecular Biology, University of Delhi, South Campus, Benito Juarez Marg, Dhaula Kuan, New Delhi, 110021 India
| | - Inderjit Kaur
- Department of Plant Molecular Biology, University of Delhi, South Campus, Benito Juarez Marg, Dhaula Kuan, New Delhi, 110021 India
| | - Shitij Gupta
- Department of Plant Molecular Biology, University of Delhi, South Campus, Benito Juarez Marg, Dhaula Kuan, New Delhi, 110021 India
- Present Address: Institute of Plant Sciences, Universität Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Manu Agarwal
- Department of Botany, University of Delhi, North Campus, Delhi, 110007 India
| | - Surekha Katiyar-Agarwal
- Department of Plant Molecular Biology, University of Delhi, South Campus, Benito Juarez Marg, Dhaula Kuan, New Delhi, 110021 India
| |
Collapse
|
4
|
Fu T, Wang C, Yang Y, Yang X, Wang J, Zhang L, Wang Z, Wang Y. Function identification of miR159a, a positive regulator during poplar resistance to drought stress. HORTICULTURE RESEARCH 2023; 10:uhad221. [PMID: 38077498 PMCID: PMC10709547 DOI: 10.1093/hr/uhad221] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 10/24/2023] [Indexed: 03/08/2024]
Abstract
Drought seriously affects the growth and development of plants. MiR159 is a highly conserved and abundant microRNA family that plays a crucial role in plant growth and stress responses. However, studies of its function in woody plants are still lacking. Here, the expression of miR159a was significantly upregulated after drought treatment in poplar, and the overexpression of miR159a (OX159a) significantly reduced the open area of the stomata and improved water-use efficiency in poplar. After drought treatment, OX159a lines had better scavenging ability of reactive oxygen species and damage of the membrane system was less than that in wild-type lines. MYB was the target gene of miR159a, as verified by psRNATarget prediction, RT-qPCR, degradome sequencing, and 5' rapid amplification of cDNA ends (5' RACE). Additionally, miR159a-short tandem target mimic suppression (STTM) poplar lines showed increased sensitivity to drought stress. Transcriptomic analysis comparing OX159a lines with wild-type lines revealed upregulation of a series of genes related to response to water deprivation and metabolite synthesis. Moreover, drought-responsive miR172d and miR398 were significantly upregulated and downregulated respectively in OX159a lines. This investigation demonstrated that miR159a played a key role in the tolerance of poplar to drought by reducing stomata open area, increasing the number and total area of xylem vessels, and enhancing water-use efficiency, and provided new insights into the role of plant miR159a and crucial candidate genes for the molecular breeding of trees with tolerance to drought stress.
Collapse
Affiliation(s)
- Tiantian Fu
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Chun Wang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Yuzhang Yang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Xiaoqian Yang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Jing Wang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Lichun Zhang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Zeqi Wang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Yanwei Wang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| |
Collapse
|
5
|
Kumar D, Ramkumar MK, Dutta B, Kumar A, Pandey R, Jain PK, Gaikwad K, Mishra DC, Chaturvedi KK, Rai A, Solanke AU, Sevanthi AM. Integration of miRNA dynamics and drought tolerant QTLs in rice reveals the role of miR2919 in drought stress response. BMC Genomics 2023; 24:526. [PMID: 37674140 PMCID: PMC10481553 DOI: 10.1186/s12864-023-09609-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 08/20/2023] [Indexed: 09/08/2023] Open
Abstract
To combat drought stress in rice, a major threat to global food security, three major quantitative trait loci for 'yield under drought stress' (qDTYs) were successfully exploited in the last decade. However, their molecular basis still remains unknown. To understand the role of secondary regulation by miRNA in drought stress response and their relation, if any, with the three qDTYs, the miRNA dynamics under drought stress was studied at booting stage in two drought tolerant (Sahbaghi Dhan and Vandana) and one drought sensitive (IR 20) cultivars. In total, 53 known and 40 novel differentially expressed (DE) miRNAs were identified. The primary drought responsive miRNAs were Osa-MIR2919, Osa-MIR3979, Osa-MIR159f, Osa-MIR156k, Osa-MIR528, Osa-MIR530, Osa-MIR2091, Osa-MIR531a, Osa-MIR531b as well as three novel ones. Sixty-one target genes that corresponded to 11 known and 4 novel DE miRNAs were found to be co-localized with the three qDTYs, out of the 1746 target genes identified. We could validate miRNA-mRNA expression under drought for nine known and three novel miRNAs in eight different rice genotypes showing varying degree of tolerance. From our study, Osa-MIR2919, Osa-MIR3979, Osa-MIR528, Osa-MIR2091-5p and Chr01_11911S14Astr and their target genes LOC_Os01g72000, LOC_Os01g66890, LOC_Os01g57990, LOC_Os01g56780, LOC_Os01g72834, LOC_Os01g61880 and LOC_Os01g72780 were identified as the most promising candidates for drought tolerance at booting stage. Of these, Osa-MIR2919 with 19 target genes in the qDTYs is being reported for the first time. It acts as a negative regulator of drought stress tolerance by modulating the cytokinin and brassinosteroid signalling pathway.
Collapse
Affiliation(s)
- Deepesh Kumar
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
- PG School, Indian Agricultural Research Institute, Pusa Campus New Delhi, New Delhi, 110012, India
| | - M K Ramkumar
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Bipratip Dutta
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
- PG School, Indian Agricultural Research Institute, Pusa Campus New Delhi, New Delhi, 110012, India
| | - Ajay Kumar
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Rakesh Pandey
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Pradeep Kumar Jain
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Dwijesh C Mishra
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - K K Chaturvedi
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Anil Rai
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | | | | |
Collapse
|
6
|
Riyazuddin R, Singh K, Iqbal N, Labhane N, Ramteke P, Singh VP, Gupta R. Unveiling the biosynthesis, mechanisms, and impacts of miRNAs in drought stress resilience in plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 202:107978. [PMID: 37660607 DOI: 10.1016/j.plaphy.2023.107978] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 08/13/2023] [Accepted: 08/17/2023] [Indexed: 09/05/2023]
Abstract
Drought stress is one of the most serious threats to sustainable agriculture and is predicted to be further intensified in the coming decades. Therefore, understanding the mechanism of drought stress tolerance and the development of drought-resilient crops are the major goals at present. In recent years, noncoding microRNAs (miRNAs) have emerged as key regulators of gene expressions under drought stress conditions and are turning out to be the potential candidates that can be targeted to develop drought-resilient crops in the future. miRNAs are known to target and decrease the expression of various genes to govern the drought stress response in plants. In addition, emerging evidence also suggests a regulatory role of long non-coding RNAs (lncRNAs) in the regulation of miRNAs and the expression of their target genes by a process referred as miRNA sponging. In this review, we present the regulatory roles of miRNAs in the modulation of drought-responsive genes along with discussing their biosynthesis and action mechanisms. Additionally, the interactive roles of miRNAs with phytohormone signaling components have also been highlighted to present the global view of miRNA functioning under drought-stress conditions.
Collapse
Affiliation(s)
- Riyazuddin Riyazuddin
- Institute of Plant Biology, Biological Research Centre, Temesvári krt. 62, H-6726, Szeged, Hungary.
| | - Kalpita Singh
- Doctoral School of Plant Sciences, Hungarian University of Agriculture and Life Sciences, 2100, Gödöllő, Hungary; Department of Biological Resources, Agricultural Institute, Centre for Agricultural Research, ELKH, Brunszvik u. 2, H-2462, Martonvásár, Hungary.
| | - Nadeem Iqbal
- Department of Plant Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, 6726, Szeged, Hungary; Doctoral School of Environmental Sciences, University of Szeged, Szeged, Hungary.
| | - Nitin Labhane
- Department of Botany, Bhavan's College Andheri West, Mumbai, 400058, India.
| | - Pramod Ramteke
- Department of Biotechnology, Dr. Ambedkar College, Nagpur, India.
| | - Vijay Pratap Singh
- Plant Physiology Laboratory, Department of Botany, C.M.P. Degree College, A Constituent Post Graduate College of University of Allahabad, Prayagraj, 211002, India
| | - Ravi Gupta
- College of General Education, Kookmin University, 02707, Seoul, Republic of Korea.
| |
Collapse
|
7
|
Raza A, Charagh S, Karikari B, Sharif R, Yadav V, Mubarik MS, Habib M, Zhuang Y, Zhang C, Chen H, Varshney RK, Zhuang W. miRNAs for crop improvement. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107857. [PMID: 37437345 DOI: 10.1016/j.plaphy.2023.107857] [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: 05/01/2023] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 07/14/2023]
Abstract
Climate change significantly impacts crop production by inducing several abiotic and biotic stresses. The increasing world population, and their food and industrial demands require focused efforts to improve crop plants to ensure sustainable food production. Among various modern biotechnological tools, microRNAs (miRNAs) are one of the fascinating tools available for crop improvement. miRNAs belong to a class of small non-coding RNAs playing crucial roles in numerous biological processes. miRNAs regulate gene expression by post-transcriptional target mRNA degradation or by translation repression. Plant miRNAs have essential roles in plant development and various biotic and abiotic stress tolerance. In this review, we provide propelling evidence from previous studies conducted around miRNAs and provide a one-stop review of progress made for breeding stress-smart future crop plants. Specifically, we provide a summary of reported miRNAs and their target genes for improvement of plant growth and development, and abiotic and biotic stress tolerance. We also highlight miRNA-mediated engineering for crop improvement and sequence-based technologies available for the identification of miRNAs associated with stress tolerance and plant developmental events.
Collapse
Affiliation(s)
- Ali Raza
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China
| | - Sidra Charagh
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Hangzhou, China
| | - Benjamin Karikari
- Department of Agricultural Biotechnology, Faculty of Agriculture, Food and Consumer Sciences, University for Development Studies, Tamale, Ghana
| | - Rahat Sharif
- Department of Horticulture, College of Horticulture and Landscape Architecture, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu 225009, China
| | - Vivek Yadav
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, Shanxi, 712100, China
| | | | - Madiha Habib
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Park Rd., Islamabad 45500, Pakistan
| | - Yuhui Zhuang
- College of Life Science, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Chong Zhang
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China
| | - Hua Chen
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China
| | - Rajeev K Varshney
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China; WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia.
| | - Weijian Zhuang
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China.
| |
Collapse
|
8
|
Kaur S, Seem K, Kumar S, Kaundal R, Mohapatra T. Comparative Genome-Wide Analysis of MicroRNAs and Their Target Genes in Roots of Contrasting Indica Rice Cultivars under Reproductive-Stage Drought. Genes (Basel) 2023; 14:1390. [PMID: 37510295 PMCID: PMC10379292 DOI: 10.3390/genes14071390] [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: 05/21/2023] [Revised: 06/26/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Recurrent occurrence of drought stress in varying intensity has become a common phenomenon in the present era of global climate change, which not only causes severe yield losses but also challenges the cultivation of rice. This raises serious concerns for sustainable food production and global food security. The root of a plant is primarily responsible to perceive drought stress and acquire sufficient water for the survival/optimal growth of the plant under extreme climatic conditions. Earlier studies reported the involvement/important roles of microRNAs (miRNAs) in plants' responses to environmental/abiotic stresses. A number (738) of miRNAs is known to be expressed in different tissues under varying environmental conditions in rice, but our understanding of the role, mode of action, and target genes of the miRNAs are still elusive. Using contrasting rice [IR-64 (reproductive-stage drought sensitive) and N-22 (drought-tolerant)] cultivars, imposed with terminal (reproductive-stage) drought stress, we demonstrate differential expression of 270 known and 91 novel miRNAs in roots of the contrasting rice cultivars in response to the stress. Among the known miRNAs, osamiR812, osamiR166, osamiR156, osamiR167, and osamiR396 were the most differentially expressed miRNAs between the rice cultivars. In the root of N-22, 18 known and 12 novel miRNAs were observed to be exclusively expressed, while only two known (zero novels) miRNAs were exclusively expressed in the roots of IR-64. The majority of the target gene(s) of the miRNAs were drought-responsive transcription factors playing important roles in flower, grain development, auxin signaling, root development, and phytohormone-crosstalk. The novel miRNAs identified in this study may serve as good candidates for the genetic improvement of rice for terminal drought stress towards developing climate-smart rice for sustainable food production.
Collapse
Affiliation(s)
- Simardeep Kaur
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA
- Bioinformatics Facility, Center for Integrated BioSystems, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA
| | - Karishma Seem
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Rakesh Kaundal
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA
- Bioinformatics Facility, Center for Integrated BioSystems, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA
| | | |
Collapse
|
9
|
Rawal HC, Ali S, Mondal TK. Role of non-coding RNAs against salinity stress in Oryza species: Strategies and challenges in analyzing miRNAs, tRFs and circRNAs. Int J Biol Macromol 2023; 242:125172. [PMID: 37268077 DOI: 10.1016/j.ijbiomac.2023.125172] [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: 03/29/2023] [Revised: 05/03/2023] [Accepted: 05/24/2023] [Indexed: 06/04/2023]
Abstract
Salinity is an imbalanced concentration of mineral salts in the soil or water that causes yield loss in salt-sensitive crops. Rice plant is vulnerable to soil salinity stress at seedling and reproductive stages. Different non-coding RNAs (ncRNAs) post-transcriptionally regulate different sets of genes during different developmental stages under varying salinity tolerance levels. While microRNAs (miRNAs) are well known small endogenous ncRNAs, tRNA-derived RNA fragments (tRFs) are an emerging class of small ncRNAs derived from tRNA genes with a demonstrated regulatory role, like miRNAs, in humans but unexplored in plants. Circular RNA (circRNA), another ncRNA produced by back-splicing events, acts as target mimics by preventing miRNAs from binding with their target mRNAs, thereby reducing the miRNA's action upon its target. Same may hold true between circRNAs and tRFs. Hence, the work done on these ncRNAs was reviewed and no reports were found for circRNAs and tRFs under salinity stress in rice, either at seedling or reproductive stages. Even the reports on miRNAs are restricted to seedling stage only, in spite of severe effects on rice crop production due to salt stress during reproductive stage. Moreover, this review sheds light on strategies to predict and analyze these ncRNAs in an effective manner.
Collapse
Affiliation(s)
- Hukam Chand Rawal
- ICAR-National Institute for Plant Biotechnology, LBS Centre, Pusa, New Delhi 110012, India; School of Interdisciplinary Sciences and Technology, Jamia Hamdard (Hamdard University), Hamdard Nagar, New Delhi 110062, India
| | - Shakir Ali
- School of Interdisciplinary Sciences and Technology, Jamia Hamdard (Hamdard University), Hamdard Nagar, New Delhi 110062, India; Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard (Hamdard University), Hamdard Nagar, New Delhi 110062, India
| | - Tapan Kumar Mondal
- ICAR-National Institute for Plant Biotechnology, LBS Centre, Pusa, New Delhi 110012, India.
| |
Collapse
|
10
|
Xu Y, Liu J, Ji X, Zhao G, Zhao T, Wang X, Wang L, Gao S, Hao Y, Gao Y, Gao Y, Weng X, Jia L, Chen Z. Integrative analysis of microRNAs and mRNAs reveals the regulatory networks of triterpenoid saponin metabolism in Soapberry ( Sapindus mukorossi Gaertn.). FRONTIERS IN PLANT SCIENCE 2023; 13:1037784. [PMID: 36699854 PMCID: PMC9869041 DOI: 10.3389/fpls.2022.1037784] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 12/19/2022] [Indexed: 06/13/2023]
Abstract
Triterpenoid saponin are important secondary metabolites and bioactive constituents of soapberry (Sapindus mukorossi Gaertn.) and are widely used in medicine and toiletry products. However, little is known about the roles of miRNAs in the regulation of triterpenoid saponin biosynthesis in soapberry. In this study, a total of 3036 miRNAs were identified, of which 1372 miRNAs were differentially expressed at different stages of pericarp development. Important KEGG pathways, such as terpenoid backbone biosynthesis, sesquiterpenoid and triterpenoid biosynthesis, and basal transcription factors were highlighted, as well the roles of some key miRNAs, such as ath-miR5021, han-miR3630-3p, and ppe-miR858, which may play important roles in regulating triterpenoid saponin biosynthesis. In addition, 58 miRNAs might participate in saponin biosynthesis pathways by predicting the targets of those miRNAs to 53 saponin biosynthesis structural genes. And 75 miRNAs were identified to potentially play vital role in saponin accumulation by targeting transcript factor genes, bHLH, bZIP, ERF, MYB, and WRKY, respectively, which are candidate regulatory genes in the pathway of saponin biosynthesis. The results of weighted gene coexpression network analysis (WGCNA) suggested that two saponin-specific miRNA modules and 10 hub miRNAs may participate in saponin biosynthesis. Furthermore, multiple miRNA-mRNA regulatory networks potentially involved in saponin biosynthesis were generated, e.g., ath-miR5021-SmIDI2/SmGPS5/SmbAS1/SmCYP71D-3/SmUGT74G-2, han-miR3630-3p-SmCYP71A-14/SmbHLH54/SmMYB135/SmWRKY32, and ppe-miR858-SmMYB5/SmMYB32. qRT-PCR analysis validated the expression patterns of nine miRNAs and 12 corresponding target genes. This study represents the first comprehensive analysis of miRNAs in soapberry and lays the foundation for further understanding of miRNA-based regulation in triterpenoid saponin biosynthesis.
Collapse
Affiliation(s)
- Yuanyuan Xu
- Key Laboratory of 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 Forestry University, Beijing, China
- National Innovation Alliance of Sapindus Industry, Beijing Forestry University, Beijing, China
| | - Jiming Liu
- Key Laboratory of 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 Forestry University, Beijing, China
- National Innovation Alliance of Sapindus Industry, Beijing Forestry University, Beijing, China
| | - Xiangqin Ji
- Bioinformatics Analysis Department, Hangzhou KaiTai Biotechnology Co., Ltd, Hangzhou, Zhejiang, China
| | - Guochun Zhao
- Key Laboratory of 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 Forestry University, Beijing, China
- National Innovation Alliance of Sapindus Industry, Beijing Forestry University, Beijing, China
| | - Tianyun Zhao
- Key Laboratory of 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 Forestry University, Beijing, China
- National Innovation Alliance of Sapindus Industry, Beijing Forestry University, Beijing, China
| | - Xin Wang
- Key Laboratory of 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 Forestry University, Beijing, China
- National Innovation Alliance of Sapindus Industry, Beijing Forestry University, Beijing, China
| | - Lixian Wang
- Key Laboratory of 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 Forestry University, Beijing, China
- National Innovation Alliance of Sapindus Industry, Beijing Forestry University, Beijing, China
| | - Shilun Gao
- Key Laboratory of 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 Forestry University, Beijing, China
- National Innovation Alliance of Sapindus Industry, Beijing Forestry University, Beijing, China
| | - Yingying Hao
- Key Laboratory of 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 Forestry University, Beijing, China
- National Innovation Alliance of Sapindus Industry, Beijing Forestry University, Beijing, China
| | - Yuhan Gao
- Key Laboratory of 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 Forestry University, Beijing, China
- National Innovation Alliance of Sapindus Industry, Beijing Forestry University, Beijing, China
| | - Yuan Gao
- Planning and Design Institute of Forest Products Industry, National Forestry and Grassland Administration, Beijing, China
| | - Xuehuang Weng
- Research and Development Department, Yuanhua Forestry Biological Technology Co., Ltd., Sanming, Fujian, China
| | - Liming Jia
- Key Laboratory of 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 Forestry University, Beijing, China
- National Innovation Alliance of Sapindus Industry, Beijing Forestry University, Beijing, China
| | - Zhong Chen
- Key Laboratory of 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 Forestry University, Beijing, China
- National Innovation Alliance of Sapindus Industry, Beijing Forestry University, Beijing, China
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| |
Collapse
|
11
|
Molecular Aspects of MicroRNAs and Phytohormonal Signaling in Response to Drought Stress: A Review. Curr Issues Mol Biol 2022; 44:3695-3710. [PMID: 36005149 PMCID: PMC9406886 DOI: 10.3390/cimb44080253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 07/29/2022] [Accepted: 08/10/2022] [Indexed: 11/16/2022] Open
Abstract
Phytohormones play an essential role in plant growth and development in response to environmental stresses. However, plant hormones require a complex signaling network combined with other signaling pathways to perform their proper functions. Thus, multiple phytohormonal signaling pathways are a prerequisite for understanding plant defense mechanism against stressful conditions. MicroRNAs (miRNAs) are master regulators of eukaryotic gene expression and are also influenced by a wide range of plant development events by suppressing their target genes. In recent decades, the mechanisms of phytohormone biosynthesis, signaling, pathways of miRNA biosynthesis and regulation were profoundly characterized. Recent findings have shown that miRNAs and plant hormones are integrated with the regulation of environmental stress. miRNAs target several components of phytohormone pathways, and plant hormones also regulate the expression of miRNAs or their target genes inversely. In this article, recent developments related to molecular linkages between miRNAs and phytohormones were reviewed, focusing on drought stress.
Collapse
|
12
|
Ansari MA, Bano N, Kumar A, Dubey AK, Asif MH, Sanyal I, Pande V, Pandey V. Comparative transcriptomic analysis and antioxidant defense mechanisms in clusterbean (Cyamopsis tetragonoloba (L.) Taub.) genotypes with contrasting drought tolerance. Funct Integr Genomics 2022; 22:625-642. [PMID: 35426545 DOI: 10.1007/s10142-022-00860-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/07/2022] [Accepted: 04/07/2022] [Indexed: 01/16/2023]
Abstract
To understand drought tolerance mechanism(s) in clusterbean (Cyamopsis tetragonoloba), we conducted physiological, biochemical, and de novo comparative transcriptome analysis of drought-tolerant (RGC-1002) and drought-sensitive (RGC-1066) genotypes subjected to 30 days of drought stress. Relative water content (RWC) was maintained in tolerant genotype but was reduced in sensitive genotype. Leaf pigment concentrations were higher in tolerant genotype. Net photosynthesis was significantly decreased in sensitive genotype but insignificant reduction was found in tolerant genotype. Enzymatic antioxidant (GR, APX, DHAR) activities were enhanced in tolerant genotype, while there were insignificant changes in these enzymes in sensitive genotype. The ratios of antioxidant molecules (ASC/DHA and GSH/GSSG) were higher in tolerant genotype as compared to sensitive genotype. In sensitive genotype, 6625 differentially expressed genes (DEGs) were upregulated and 5365 genes were downregulated. In tolerant genotype, 5206 genes were upregulated and 2793 genes were downregulated. In tolerant genotype, transketolase family protein, phosphoenolpyruvate carboxylase 3, temperature-induced lipocalin, and cytochrome oxidase were highly upregulated. Moreover, according to Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, the drought tolerance may be attributed to upregulated starch and sucrose metabolism-related genes in tolerant genotype. Finally, quantitative real-time PCR confirmed the reproducibility of the RNA-seq data.
Collapse
Affiliation(s)
- Mohd Akram Ansari
- Plant Ecology and Climate Change Science Division, CSIR-NBRI, Lucknow, India. .,Department of Biotechnology, Bhimtal Campus, Kumaun University, Nainital, India.
| | - Nasreen Bano
- Plant Molecular Biology and Biotechnology Division, CSIR-NBRI, Lucknow, India
| | - Anil Kumar
- Department of Biotechnology, Bhimtal Campus, Kumaun University, Nainital, India.,Plant Molecular Biology and Biotechnology Division, CSIR-NBRI, Lucknow, India
| | - Arvind Kumar Dubey
- Department of Biotechnology, Bhimtal Campus, Kumaun University, Nainital, India.,Plant Molecular Biology and Biotechnology Division, CSIR-NBRI, Lucknow, India
| | - Mehar Hasan Asif
- Plant Molecular Biology and Biotechnology Division, CSIR-NBRI, Lucknow, India
| | - Indraneel Sanyal
- Plant Molecular Biology and Biotechnology Division, CSIR-NBRI, Lucknow, India
| | - Veena Pande
- Department of Biotechnology, Bhimtal Campus, Kumaun University, Nainital, India
| | - Vivek Pandey
- Plant Ecology and Climate Change Science Division, CSIR-NBRI, Lucknow, India.
| |
Collapse
|
13
|
Luo Y, Xie Y, Li W, Wei M, Dai T, Li Z, Wang B. Physiological and Transcriptomic Analyses Reveal Exogenous Trehalose Is Involved in the Responses of Wheat Roots to High Temperature Stress. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10122644. [PMID: 34961115 PMCID: PMC8707964 DOI: 10.3390/plants10122644] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/18/2021] [Accepted: 11/29/2021] [Indexed: 05/05/2023]
Abstract
High temperature stress seriously limits the yield and quality of wheat. Trehalose, a non-reducing disaccharide, has been shown involved in regulating plant responses to a variety of environmental stresses. This study aimed to explore the molecular regulatory network of exogenous trehalose to improve wheat heat tolerance through RNA-sequencing technology and physiological determination. The physiological data and RNA-seq showed that trehalose reduced malondialdehyde content and relative conductivity in wheat roots, and affecting the phenylpropane biosynthesis, starch and sucrose metabolism, glutathione metabolism, and other pathways. Our results showed that exogenous trehalose alleviates the oxidative damage caused by high temperature, coordinating the effect of wheat on heat stress by re-encoding the overall gene expression, but two wheat varieties showed different responses to high temperature stress after trehalose pretreatment. This study preliminarily revealed the effect of trehalose on gene expression regulation of wheat roots under high temperature stress, which provided a reference for the study of trehalose.
Collapse
Affiliation(s)
- Yin Luo
- Instrument Sharing Platform of School of Life Sciences, East China Normal University, Shanghai 200241, China; (Y.X.); (M.W.); (T.D.); (Z.L.); (B.W.)
- Correspondence:
| | - Yanyang Xie
- Instrument Sharing Platform of School of Life Sciences, East China Normal University, Shanghai 200241, China; (Y.X.); (M.W.); (T.D.); (Z.L.); (B.W.)
| | - Weiqiang Li
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China;
| | - Maohuan Wei
- Instrument Sharing Platform of School of Life Sciences, East China Normal University, Shanghai 200241, China; (Y.X.); (M.W.); (T.D.); (Z.L.); (B.W.)
| | - Tian Dai
- Instrument Sharing Platform of School of Life Sciences, East China Normal University, Shanghai 200241, China; (Y.X.); (M.W.); (T.D.); (Z.L.); (B.W.)
| | - Zhen Li
- Instrument Sharing Platform of School of Life Sciences, East China Normal University, Shanghai 200241, China; (Y.X.); (M.W.); (T.D.); (Z.L.); (B.W.)
| | - Bozhi Wang
- Instrument Sharing Platform of School of Life Sciences, East China Normal University, Shanghai 200241, China; (Y.X.); (M.W.); (T.D.); (Z.L.); (B.W.)
| |
Collapse
|
14
|
Rawal HC, Ali S, Mondal TK. miRPreM and tiRPreM: Improved methodologies for the prediction of miRNAs and tRNA-induced small non-coding RNAs for model and non-model organisms. Brief Bioinform 2021; 23:6420093. [PMID: 34734232 DOI: 10.1093/bib/bbab448] [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: 08/20/2021] [Revised: 09/15/2021] [Accepted: 09/28/2021] [Indexed: 11/12/2022] Open
Abstract
In recent years, microRNAs (miRNAs) and tRNA-derived RNA fragments (tRFs) have been reported extensively following different approaches of identification and analysis. Comprehensively analyzing the present approaches to overcome the existing variations, we developed a benchmarking methodology each for the identification of miRNAs and tRFs, termed as miRNA Prediction Methodology (miRPreM) and tRNA-induced small non-coding RNA Prediction Methodology (tiRPreM), respectively. We emphasized the use of respective genome of organism under study for mapping reads, sample data with at least two biological replicates, normalized read count support and novel miRNA prediction by two standard tools with multiple runs. The performance of these methodologies was evaluated by using Oryza coarctata, a wild rice species as a case study for model and non-model organisms. With organism-specific reference genome approach, 98 miRNAs and 60 tRFs were exclusively found. We observed high accuracy (13 out of 15) when tested these genome-specific miRNAs in support of analyzing the data with respective organism. Such a strong impact of miRPreM, we have predicted more than double number of miRNAs (186) as compared with the traditional approaches (79) and with tiRPreM, we have predicted all known classes of tRFs within the same small RNA data. Moreover, the methodologies presented here are in standard form in order to extend its applicability to different organisms rather than restricting to plants. Hence, miRPreM and tiRPreM can fulfill the need of a comprehensive methodology for miRNA prediction and tRF identification, respectively, for model and non-model organisms.
Collapse
Affiliation(s)
- Hukam Chand Rawal
- ICAR-National Institute for Plant Biotechnology, LBS Centre, Pusa, New Delhi 110012, India.,School of Interdisciplinary Sciences and Technology, Jamia Hamdard (Hamdard University), Hamdard Nagar, New Delhi 110062, India
| | - Shakir Ali
- School of Interdisciplinary Sciences and Technology, Jamia Hamdard (Hamdard University), Hamdard Nagar, New Delhi 110062, India.,Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard (Hamdard University), Hamdard Nagar, New Delhi 110062, India
| | - Tapan Kumar Mondal
- ICAR-National Institute for Plant Biotechnology, LBS Centre, Pusa, New Delhi 110012, India
| |
Collapse
|
15
|
Zhu H, Yang X, Wang X, Li Q, Guo J, Ma T, Zhao C, Tang Y, Qiao L, Wang J, Sui J. The sweetpotato β-amylase gene IbBAM1.1 enhances drought and salt stress resistance by regulating ROS homeostasis and osmotic balance. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 168:167-176. [PMID: 34634642 DOI: 10.1016/j.plaphy.2021.09.034] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/23/2021] [Accepted: 09/27/2021] [Indexed: 06/13/2023]
Abstract
Abiotic stressors, such as drought and high salinity, seriously affect plant growth, productivity, and quality. Maintaining reactive oxygen species (ROS) homeostasis and osmotic balance plays a crucial role in abiotic stress tolerance. β-amylase (BAM) hydrolyzes α-1,4-glycosidic bonds by releasing maltose from starch in the regulation of soluble sugars. However, the function and mechanism of BAMs related to abiotic stress resistance remain unclear in sweetpotato (Ipomoea batatas (L.) Lam.). In this study, we isolated a novel β-amylase gene IbBAM1.1, which was strongly induced by PEG6000, NaCl, and maltose treatments in sweetpotato variety Yanshu25. Overexpression of IbBAM1.1 conferred enhanced tolerance to the drought and high salinity stressors in Arabidopsis thaliana. The activity of β-amylase and the degradation of starch were promoted under drought or salt stress. Accordingly, the contents of osmoprotectants, including maltose and proline were significantly higher in the transgenic lines than those in wild type (WT) plants. Less ROS, such as H2O2 and O2-, accumulated in the overexpressing lines than in WT plants. Superoxide dismutase activity was strongly enhanced and the level of malondialdehyde was lower under the drought or salt treatment in transgenic plants. Taken together, these results demonstrate that IbBAM1.1 acted as a positive regulator, at least in part, by regulating the level of osmoprotectants to balance the osmotic pressure and activate the scavenging system to maintain ROS homeostasis in the plants.
Collapse
Affiliation(s)
- Hong Zhu
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xue Yang
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xia Wang
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
| | - Qiyan Li
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
| | - Jiayu Guo
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
| | - Tao Ma
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
| | - Chunmei Zhao
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yanyan Tang
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
| | - Lixian Qiao
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
| | - Jingshan Wang
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
| | - Jiongming Sui
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China.
| |
Collapse
|
16
|
|
17
|
Singroha G, Sharma P, Sunkur R. Current status of microRNA-mediated regulation of drought stress responses in cereals. PHYSIOLOGIA PLANTARUM 2021; 172:1808-1821. [PMID: 33956991 DOI: 10.1111/ppl.13451] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 04/20/2021] [Accepted: 05/04/2021] [Indexed: 05/03/2023]
Abstract
Drought is one of the most important abiotic stress factors impeding crop productivity. With the uncovering of their role as potential regulators of gene expression, microRNAs (miRNAs) have been recognized as new targets for developing stress resistance. MicroRNAs are small noncoding RNAs whose abundance is significantly altered under stress conditions. Interestingly, plant miRNAs predominantly targets transcription factors (TFs), and some of which are also the most critical drought-responsive genes that in turn could regulate the expression of numerous loci with drought-adaptive potential. The phytohormone ABA plays important roles in regulating stomatal conductance and in initiating an adaptive response to drought stress. miRNAs are implicated in regulating ABA-(abscisic acid) and non-ABA-mediated drought resistance pathways. For instance, miR159-MYB module and miR169-NFYA module participates in an ABA-dependent pathway, whereas several other ABA-independent miRNA-target modules (miR156-SPL; miR393-TIR1; miR160-ARF10, ARF16, ARF17; miR167-ARF6 and ARF8; miR390/TAS3siRNA-ARF2, ARF3, ARF4) collectively regulate drought responses in plants. Overall, miRNA-mediated drought response manifests diverse molecular, biochemical and physiological processes. Because of their immense role in controlling gene expression, miRNA manipulation has significant potential to augment plant tolerance to drought stress. This review compiles the current understanding of drought-responsive miRNAs in major cereals. Also, potential miRNA manipulation strategies currently in use along with the challenges and future perspectives are discussed.
Collapse
Affiliation(s)
- Garima Singroha
- Crop Improvement Division, ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Pradeep Sharma
- Crop Improvement Division, ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Ramanjulu Sunkur
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma, USA
| |
Collapse
|
18
|
Selvi A, Devi K, Manimekalai R, Prathima PT, Valiyaparambth R, Lakshmi K. High-throughput miRNA deep sequencing in response to drought stress in sugarcane. 3 Biotech 2021; 11:312. [PMID: 34109097 DOI: 10.1007/s13205-021-02857-x] [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] [Received: 03/11/2021] [Accepted: 05/22/2021] [Indexed: 12/14/2022] Open
Abstract
Drought is a major factor which reduces cane growth and productivity. In the present study, we sequenced drought susceptible (V1) and drought tolerant (V2) sugarcane varieties using high-throughput miRNA deep sequencing method to study the regulation of gene expression by miRNAs during drought stress in sugarcane. A total of 1224 conserved miRNAs which belong to 89 miRNA families were identified and 38% of the differentially regulated miRNAs were common for both varieties. Additionally 435 novel miRNAs were also identified from four small RNA libraries. We identified 145 miRNAs that were differentially expressed in susceptible variety (V1-31) and 143 miRNAs differentially expressed in the tolerant variety (V2-31). Target prediction revealed that the genes mainly encoded transcription factors, proteins, phosphatase and kinases involved in signal transduction pathways, integral component of membrane and inorganic ion transport metabolism, enzymes involved in carbohydrate transport and metabolism and drought-stress-related proteins involved in defense mechanisms. Pathway analysis of targets revealed that "General function prediction only" was the most significant pathway observed in both tolerant and susceptible genotypes followed by "signal transduction mechanisms". Functional annotation of the transcripts revealed genes like calcium-dependent protein kinase, respiratory burst oxidase, caffeic acid 3-O-methyltransferase, peroxidase, calmodulin, glutathione S-transferase and transcription factors like MYB, WRKY that are involved in drought tolerant pathways. qRT-PCR was used to verify the expression levels of miRNAs and their potential targets obtained from RNA sequencing results. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-021-02857-x.
Collapse
Affiliation(s)
- Athiappan Selvi
- Biotechnology Section, Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641 007 India
| | - Kaliannan Devi
- Biotechnology Section, Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641 007 India
| | - Ramaswamy Manimekalai
- Biotechnology Section, Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641 007 India
| | | | - Rabisha Valiyaparambth
- Biotechnology Section, Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641 007 India
| | - Kasirajan Lakshmi
- Biotechnology Section, Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641 007 India
| |
Collapse
|
19
|
SA-Mediated Regulation and Control of Abiotic Stress Tolerance in Rice. Int J Mol Sci 2021; 22:ijms22115591. [PMID: 34070465 PMCID: PMC8197520 DOI: 10.3390/ijms22115591] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/07/2021] [Accepted: 05/14/2021] [Indexed: 12/18/2022] Open
Abstract
Environmental or abiotic stresses are a common threat that remains a constant and common challenge to all plants. These threats whether singular or in combination can have devastating effects on plants. As a semiaquatic plant, rice succumbs to the same threats. Here we systematically look into the involvement of salicylic acid (SA) in the regulation of abiotic stress in rice. Studies have shown that the level of endogenous salicylic acid (SA) is high in rice compared to any other plant species. The reason behind this elevated level and the contribution of this molecule towards abiotic stress management and other underlying mechanisms remains poorly understood in rice. In this review we will address various abiotic stresses that affect the biochemistry and physiology of rice and the role played by SA in its regulation. Further, this review will elucidate the potential mechanisms that control SA-mediated stress tolerance in rice, leading to future prospects and direction for investigation.
Collapse
|
20
|
Muslu T, Biyiklioglu-Kaya S, Akpinar BA, Yuce M, Budak H. Pan-Genome miRNomics in Brachypodium. PLANTS 2021; 10:plants10050991. [PMID: 34065739 PMCID: PMC8156279 DOI: 10.3390/plants10050991] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/17/2021] [Accepted: 05/12/2021] [Indexed: 01/14/2023]
Abstract
Pan-genomes are efficient tools for the identification of conserved and varying genomic sequences within lineages of a species. Investigating genetic variations might lead to the discovery of genes present in a subset of lineages, which might contribute into beneficial agronomic traits such as stress resistance or yield. The content of varying genomic regions in the pan-genome could include protein-coding genes as well as microRNA(miRNAs), small non-coding RNAs playing key roles in the regulation of gene expression. In this study, we performed in silico miRNA identification from the genomic sequences of 54 lineages of Brachypodium distachyon, aiming to explore varying miRNA contents and their functional interactions. A total of 115 miRNA families were identified in 54 lineages, 56 of which were found to be present in all lineages. The miRNA families were classified based on their conservation among lineages and potential mRNA targets were identified. Obtaining information about regulatory mechanisms stemming from these miRNAs offers strong potential to provide a better insight into the complex traits that were potentially present in some lineages. Future work could lead us to introduce these traits to different lineages or other economically important plant species in order to promote their survival in different environmental conditions.
Collapse
Affiliation(s)
- Tugdem Muslu
- Faculty of Engineering and Natural Sciences, Molecular Biology, Genetics and Bioengineering Program, Sabanci University, Istanbul 34956, Turkey; (T.M.); (S.B.-K.)
| | - Sezgi Biyiklioglu-Kaya
- Faculty of Engineering and Natural Sciences, Molecular Biology, Genetics and Bioengineering Program, Sabanci University, Istanbul 34956, Turkey; (T.M.); (S.B.-K.)
| | | | - Meral Yuce
- Sabanci University SUNUM Nanotechnology Research and Application Centre, Sabanci University, Istanbul 34956, Turkey;
| | - Hikmet Budak
- Montana BioAgriculture, Inc., Missoula, MT 59802, USA;
- Correspondence:
| |
Collapse
|
21
|
Waititu JK, Zhang C, Liu J, Wang H. Plant Non-Coding RNAs: Origin, Biogenesis, Mode of Action and Their Roles in Abiotic Stress. Int J Mol Sci 2020; 21:ijms21218401. [PMID: 33182372 PMCID: PMC7664903 DOI: 10.3390/ijms21218401] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 10/30/2020] [Accepted: 11/04/2020] [Indexed: 01/21/2023] Open
Abstract
As sessile species, plants have to deal with the rapidly changing environment. In response to these environmental conditions, plants employ a plethora of response mechanisms that provide broad phenotypic plasticity to allow the fine-tuning of the external cues related reactions. Molecular biology has been transformed by the major breakthroughs in high-throughput transcriptome sequencing and expression analysis using next-generation sequencing (NGS) technologies. These innovations have provided substantial progress in the identification of genomic regions as well as underlying basis influencing transcriptional and post-transcriptional regulation of abiotic stress response. Non-coding RNAs (ncRNAs), particularly microRNAs (miRNAs), short interfering RNAs (siRNAs), and long non-coding RNAs (lncRNAs), have emerged as essential regulators of plants abiotic stress response. However, shared traits in the biogenesis of ncRNAs and the coordinated cross-talk among ncRNAs mechanisms contribute to the complexity of these molecules and might play an essential part in regulating stress responses. Herein, we highlight the current knowledge of plant microRNAs, siRNAs, and lncRNAs, focusing on their origin, biogenesis, modes of action, and fundamental roles in plant response to abiotic stresses.
Collapse
Affiliation(s)
- Joram Kiriga Waititu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.K.W.); (C.Z.)
| | - Chunyi Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.K.W.); (C.Z.)
| | - Jun Liu
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Huan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.K.W.); (C.Z.)
- Correspondence:
| |
Collapse
|
22
|
Grabowska A, Smoczynska A, Bielewicz D, Pacak A, Jarmolowski A, Szweykowska-Kulinska Z. Barley microRNAs as metabolic sensors for soil nitrogen availability. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 299:110608. [PMID: 32900446 DOI: 10.1016/j.plantsci.2020.110608] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 07/06/2020] [Accepted: 07/16/2020] [Indexed: 06/11/2023]
Abstract
Barley (Hordeum vulgare) is one of the most important crops in the world, ranking 4th in the worldwide production. Crop breeders are facing increasing environmental obstacles in the field, such as drought, salinity but also toxic over fertilization which not only impacts quality of the grain but also an yield. One of the most prevalent mechanisms of gene expression regulation in plants is microRNA-mediated silencing of target genes. We identified 13 barley microRNAs and 2 microRNAs* that are nitrogen excess responsive. Four microRNAs respond only in root, eight microRNAs only in shoot and one displays broad response in roots and shoots. We demonstrate that 2 microRNAs* are induced in barley shoot by nitrogen excess. For all microRNAs we identified putative target genes and confirmed microRNA-guided cleavage sites for ten out of thirteen mRNAs. None of the identified microRNAs or their target genes is known as nitrogen excess responsive. Analysis of expression pattern of thirteen target mRNAs and their cognate microRNAs showed expected correlations of their levels. The plant microRNAs analyzed are also known to respond to nitrogen deprivation and exhibit the opposite expression pattern when nitrogen excess/deficiency conditions are compared. Thus, they can be regarded as metabolic sensors of the regulation of nitrogen homeostasis in plants.
Collapse
Affiliation(s)
- Aleksandra Grabowska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Aleksandra Smoczynska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Dawid Bielewicz
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Andrzej Pacak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland.
| |
Collapse
|
23
|
Buch DU, Sharma OA, Pable AA, Barvkar VT. Characterization of microRNA genes from Pigeonpea (Cajanus cajan L.) and understanding their involvement in drought stress. J Biotechnol 2020; 321:23-34. [PMID: 32610182 DOI: 10.1016/j.jbiotec.2020.06.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/22/2020] [Accepted: 06/23/2020] [Indexed: 12/20/2022]
Abstract
MicroRNAs (miRNA) are non-coding 20-24 nucleotide long RNAs regulating gene expression. In this study, we have characterized and analysed expression of miRNAs in Pigeonpea by using bioinformatics and experimental tools. We identified 116 miRNAs belonging to 32 phylogenetic families. Further, transcription start sites of miRNA genes revealed abundance and unique arrangement of adenine at +1 and thymine at -1 position. Promoter analysis exhibited presence of 19 most prevalent motifs which comprises majorly of TATA box and MYC domains. In total, 252 miRNA-targets were identified and found to be involved in various developmental processes and stress responses. Moreover, genome-wide localization studies demonstrated clustering of cca-miRNA 395 and 169 genes. The tandem and segmental duplication events were observed suggesting miRNA genes have been originated parallelly with protein coding genes. The expression analysis revealed induction of cca-miR169a, 398a and 408 miRNAs under drought stress highlighting their involvement. Conversely, down-regulation of their putative targets (NFYA, SOD, and UCLA, respectively) confirmed regulatory role of miRNAs in their expression emphasising the negative relationship between these miRNAs and targets in Pigeonpea. This study reports vast repertoire of miRNA genes which further can be experimentally characterized to elucidate their functions in various biological processes and can be recommended for Pigeonpea improvement programs.
Collapse
Affiliation(s)
- Drushtant U Buch
- Department of Botany, Savitribai Phule Pune University, Pune, 411007, India.
| | - Oshin A Sharma
- Department of Botany, Savitribai Phule Pune University, Pune, 411007, India.
| | - Anupama A Pable
- Department of Microbiology, Savitribai Phule Pune University, Pune, 411007, India.
| | - Vitthal T Barvkar
- Department of Botany, Savitribai Phule Pune University, Pune, 411007, India.
| |
Collapse
|
24
|
Nadarajah KK. ROS Homeostasis in Abiotic Stress Tolerance in Plants. Int J Mol Sci 2020; 21:E5208. [PMID: 32717820 PMCID: PMC7432042 DOI: 10.3390/ijms21155208] [Citation(s) in RCA: 193] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 06/23/2020] [Accepted: 06/26/2020] [Indexed: 12/21/2022] Open
Abstract
Climate change-induced abiotic stress results in crop yield and production losses. These stresses result in changes at the physiological and molecular level that affect the development and growth of the plant. Reactive oxygen species (ROS) is formed at high levels due to abiotic stress within different organelles, leading to cellular damage. Plants have evolved mechanisms to control the production and scavenging of ROS through enzymatic and non-enzymatic antioxidative processes. However, ROS has a dual function in abiotic stresses where, at high levels, they are toxic to cells while the same molecule can function as a signal transducer that activates a local and systemic plant defense response against stress. The effects, perception, signaling, and activation of ROS and their antioxidative responses are elaborated in this review. This review aims to provide a purview of processes involved in ROS homeostasis in plants and to identify genes that are triggered in response to abiotic-induced oxidative stress. This review articulates the importance of these genes and pathways in understanding the mechanism of resistance in plants and the importance of this information in breeding and genetically developing crops for resistance against abiotic stress in plants.
Collapse
Affiliation(s)
- Kalaivani K Nadarajah
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM BANGI, Malaysia
| |
Collapse
|
25
|
Xia H, Yu S, Kong D, Xiong J, Ma X, Chen L, Luo L. Temporal responses of conserved miRNAs to drought and their associations with drought tolerance and productivity in rice. BMC Genomics 2020; 21:232. [PMID: 32171232 PMCID: PMC7071783 DOI: 10.1186/s12864-020-6646-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 03/04/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Plant miRNAs play crucial roles in responses to drought and developmental processes. It is essential to understand the association of miRNAs with drought-tolerance (DT), as well as their impacts on growth, development, and reproduction (GDP). This will facilitate our utilization of rice miRNAs in breeding. RESULTS In this study, we investigated the time course of miRNA responses to a long-term drought among six rice genotypes by high-throughput sequencing. In total, 354 conserved miRNAs were drought responsive, representing obvious genotype- and stage-dependent patterns. The drought-responsive miRNAs (DRMs) formed complex regulatory network via their coexpression and direct/indirect impacts on the rice transcriptome. Based on correlation analyses, 211 DRMs were predicted to be associated with DT and/or GDP. Noticeably, 14.2% DRMs were inversely correlated with DT and GDP. In addition, 9 pairs of mature miRNAs, each derived from the same pre-miRNAs, were predicted to have opposite roles in regulating DT and GDP. This suggests a potential yield penalty if an inappropriate miRNA/pre-miRNA is utilized. miRNAs have profound impacts on the rice transcriptome reflected by great number of correlated drought-responsive genes. By regulating these genes, a miRNA could activate diverse biological processes and metabolic pathways to adapt to drought and have an influence on its GDP. CONCLUSION Based on the temporal pattern of miRNAs in response to drought, we have described the complex network between DRMs. Potential associations of DRMs with DT and/or GDP were disclosed. This knowledge provides valuable information for a better understanding in the roles of miRNAs play in rice DT and/or GDP, which can facilitate our utilization of miRNA in breeding.
Collapse
Affiliation(s)
- Hui Xia
- Shanghai Agrobiological Gene Center, Shanghai, China.
| | - Shunwu Yu
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Deyan Kong
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Jie Xiong
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Xiaosong Ma
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Liang Chen
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Lijun Luo
- Shanghai Agrobiological Gene Center, Shanghai, China.
| |
Collapse
|
26
|
Liu A, Zhou Z, Yi Y, Chen G. Transcriptome analysis reveals the roles of stem nodes in cadmium transport to rice grain. BMC Genomics 2020; 21:127. [PMID: 32028884 PMCID: PMC7003353 DOI: 10.1186/s12864-020-6474-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 01/09/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Node is the central organ of transferring nutrients and ions in plants. Cadmium (Cd) induced crop pollution threatens the food safety. Breeding of low Cd accumulation cultivar is a chance to resolve this universal problem. This study was performed to identify tissue specific genes involved in Cd accumulation in different rice stem nodes. Panicle node and the first node under panicle (node I) were sampled in two rice cultivars: Xiangwanxian No. 12 (low Cd accumulation cultivar) and Yuzhenxiang (high Cd accumulation cultivar). RNA-seq analysis was performed to identify differentially expressed genes (DEGs) and microRNAs. RESULTS Xiangwanxian No. 12 had lower Cd concentration in panicle node, node I and grain compared with Yuzhenxiang, and node I had the highest Cd concentration in the two cultivars. RNA seq analysis identified 4535 DEGs and 70 miRNAs between the two cultivars. Most genesrelated to the "transporter activity", such as OsIRT1, OsNramp5, OsVIT2, OsNRT1.5A, and OsABCC1, play roles in blocking the upward transport of Cd. Among the genes related to "response to stimulus", we identified OsHSP70 and OsHSFA2d/B2c in Xiangwanxian No. 12, but not in Yuzhenxiang, were all down-regulated by Cd stimulus. The up-regulation of miRNAs (osa-miR528 and osa-miR408) in Xiangwanxian No. 12 played a potent role in lowering Cd accumulation via down regulating the expression of candidate genes, such as bZIP, ERF, MYB, SnRK1 and HSPs. CONCLUSIONS Both panicle node and node I of Xiangwanxian No. 12 played a key role in blocking the upward transportation of Cd, while node I played a critical role in Yuzhenxiang. Distinct expression patterns of various transporter genes such as OsNRT1.5A, OsNramp5, OsIRT1, OsVIT2 and OsABCC1 resulted in differential Cd accumulation in different nodes. Likewise, distinct expression patterns of these transporter genes are likely responsible for the low Cd accumulation in Xiangwanxian No. 12 cultivar. MiRNAs drove multiple transcription factors, such as OsbZIPs, OsERFs, OsMYBs, to play a role in Cd stress response.
Collapse
Affiliation(s)
- Ailing Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan 410128 People’s Republic of China
| | - Zhibo Zhou
- College of Agronomy, Hunan Agricultural University, Changsha, Hunan 410128 People’s Republic of China
| | - Yake Yi
- College of Agronomy, Hunan Agricultural University, Changsha, Hunan 410128 People’s Republic of China
| | - Guanghui Chen
- College of Agronomy, Hunan Agricultural University, Changsha, Hunan 410128 People’s Republic of China
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops (CICGO), Hunan Agricultural University, Changsha, 410128 People’s Republic of China
| |
Collapse
|
27
|
Fan G, Liu Y, Du H, Kuang T, Zhang Y. Identification of drought-responsive miRNAs in Hippophae tibetana using high-throughput sequencing. 3 Biotech 2020; 10:53. [PMID: 32015949 DOI: 10.1007/s13205-019-2045-5] [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: 03/09/2019] [Accepted: 12/30/2019] [Indexed: 10/25/2022] Open
Abstract
MicroRNAs (miRNAs) play an important role in abiotic stress response in plants. However, the total miRNA profiles (miRNome) and drought-responsive miRNAs in H. tibetana have not been identified. In this study, we present the first report on the miRNome profiles of H. tibetana by high-throughput sequencing technology. 116 known and 4 predicted novel miRNAs were all identified in six H. tibetana samples. Moreover, to reveal the drought-responsive miRNAs in H. tibetana, we compared the miRNA profiles of H. tibetana grown under water sufficiency and drought stress. The results showed that 39 known miRNAs were up-regulated, while 34 miRNAs were downregulated under drought stress. Moreover, the expression of two novel miRNAs (novel_mir_24 and novel_mir_87) showed notable changes in response to drought stress. The target genes of these differentially expressed miRNAs were mainly enriched in cellular process, metabolic process, cell part, and response to stimulus. The identified drought-responsive miRNAs might be used for improving drought tolerance in H. tibetana and other plateau plants.
Collapse
|
28
|
Dong F, Wang C, Dong Y, Hao S, Wang L, Sun X, Liu S. Differential expression of microRNAs in tomato leaves treated with different light qualities. BMC Genomics 2020; 21:37. [PMID: 31931707 PMCID: PMC6958596 DOI: 10.1186/s12864-019-6440-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 12/29/2019] [Indexed: 11/12/2022] Open
Abstract
Background Light is the main source of energy and, as such, is one of the most important environmental factors for plant growth, morphogenesis, and other physiological responses. MicroRNAs (miRNAs) are endogenous non-coding RNAs that contain 21–24 nucleotides (nt) and play important roles in plant growth and development as well as stress responses. However, the role of miRNAs in the light response is less studied. We used tomato seedlings that were cultured in red light then transferred to blue light for 2 min to identify miRNAs related to light response by high-throughput sequencing. Results A total of 108 known miRNAs and 141 predicted novel miRNAs were identified in leaf samples from tomato leaves treated with the different light qualities. Among them, 15 known and 5 predicted novel miRNAs were differentially expressed after blue light treatment compared with the control (red light treatment). KEGG enrichment analysis showed that significantly enriched pathways included zeatin biosynthesis (ko00908), homologous recombination (ko03440), and plant hormone signal transduction (ko04075). Zeatin biosynthesis and plant hormone signal transduction are related to plant hormones, indicating that plant hormones play important roles in the light response. Conclusion Our results provide a theoretical basis for further understanding the role of miRNAs in the light response of plants.
Collapse
Affiliation(s)
- Fei Dong
- Vegetable and Flower Research Institute of Shandong Academy of Agricultural Sciences / Shandong Key Laboratory of Greenhouse Vegetable Biology / Shandong Branch of National Vegetable Improvement Center / Vegetable Science Observation and Experimental Station in Huang-Huai District of the Ministry of Agriculture, Jinan, 250100, China.,College of Horticulture Science and Engineering, Shandong Agricultural University, Tai An, 271018, China
| | - Chuanzeng Wang
- Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Yuhui Dong
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai An, 271018, China
| | - Shuqin Hao
- Shandong Agriculture and Engineering University, Jinan, 250100, China
| | - Lixia Wang
- Shenyang Agriculture University, Shenyang, 110866, China
| | - Xiudong Sun
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai An, 271018, China. .,State Key Laboratory of Crop Biology, Tai An, 271018, China. .,Ministry of Agriculture Key Laboratory of Biology and Genetic Improvement of Horticultural Crops in Huanghuai Region, Tai An, 271018, China.
| | - Shiqi Liu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai An, 271018, China. .,State Key Laboratory of Crop Biology, Tai An, 271018, China. .,Ministry of Agriculture Key Laboratory of Biology and Genetic Improvement of Horticultural Crops in Huanghuai Region, Tai An, 271018, China.
| |
Collapse
|
29
|
Ahsan MU, Hayward A, Alam M, Bandaralage JH, Topp B, Beveridge CA, Mitter N. Scion control of miRNA abundance and tree maturity in grafted avocado. BMC PLANT BIOLOGY 2019; 19:382. [PMID: 31481026 PMCID: PMC6724330 DOI: 10.1186/s12870-019-1994-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 08/27/2019] [Indexed: 05/24/2023]
Abstract
BACKGROUND Grafting is the common propagation method for avocado and primarily benefits orchard production by reducing the time to tree productivity. It also allows use of scions and rootstocks specifically selected for improved productivity and commercial acceptance. Rootstocks in avocado may be propagated from mature tree cuttings ('mature'), or from seed ('juvenile'). While the use of mature scion material hastens early bearing/maturity and economic return, the molecular factors involved in the role of the scion and/or rootstock in early bearing/reduced juvenility of the grafted tree are still unknown. RESULTS Here, we utilized juvenility and flowering associated miRNAs; miR156 and miR172 and their putative target genes to screen pre-graft and post-graft material in different combinations from avocado. The abundance of mature miR156, miR172 and the miR156 target gene SPL4, showed a strong correlation to the maturity of the scion and rootstock material in avocado. Graft transmissibility of miR156 and miR172 has been explored in annual plants. Here, we show that the scion may be responsible for grafted tree maturity involving these factors, while the rootstock maturity does not significantly influence miRNA abundance in the scion. We also demonstrate that the presence of leaves on cutting rootstocks supports graft success and contributes towards intergraft signalling involving the carbohydrate-marker TPS1. CONCLUSION Here, we suggest that the scion largely controls the molecular 'maturity' of grafted avocado trees, however, leaves on the rootstock not only promote graft success, but can influence miRNA and mRNA abundance in the scion. This constitutes the first study on scion and rootstock contribution towards grafted tree maturity using the miR156-SPL4-miR172 regulatory module as a marker for juvenility and reproductive competence.
Collapse
Affiliation(s)
- Muhammad Umair Ahsan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, Queensland 4072 Australia
| | - Alice Hayward
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, Queensland 4072 Australia
| | - Mobashwer Alam
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, Queensland 4072 Australia
| | - Jayeni Hiti Bandaralage
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, Queensland 4072 Australia
| | - Bruce Topp
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, Queensland 4072 Australia
| | - Christine Anne Beveridge
- School of Biological Sciences, The University of Queensland, St. Lucia, Brisbane, Queensland 4072 Australia
| | - Neena Mitter
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, Queensland 4072 Australia
| |
Collapse
|
30
|
Ahsan MU, Hayward A, Alam M, Bandaralage JH, Topp B, Beveridge CA, Mitter N. Scion control of miRNA abundance and tree maturity in grafted avocado. BMC PLANT BIOLOGY 2019; 19:382. [PMID: 31481026 DOI: 10.1186/s12870-019-1994-1995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 08/27/2019] [Indexed: 05/23/2023]
Abstract
BACKGROUND Grafting is the common propagation method for avocado and primarily benefits orchard production by reducing the time to tree productivity. It also allows use of scions and rootstocks specifically selected for improved productivity and commercial acceptance. Rootstocks in avocado may be propagated from mature tree cuttings ('mature'), or from seed ('juvenile'). While the use of mature scion material hastens early bearing/maturity and economic return, the molecular factors involved in the role of the scion and/or rootstock in early bearing/reduced juvenility of the grafted tree are still unknown. RESULTS Here, we utilized juvenility and flowering associated miRNAs; miR156 and miR172 and their putative target genes to screen pre-graft and post-graft material in different combinations from avocado. The abundance of mature miR156, miR172 and the miR156 target gene SPL4, showed a strong correlation to the maturity of the scion and rootstock material in avocado. Graft transmissibility of miR156 and miR172 has been explored in annual plants. Here, we show that the scion may be responsible for grafted tree maturity involving these factors, while the rootstock maturity does not significantly influence miRNA abundance in the scion. We also demonstrate that the presence of leaves on cutting rootstocks supports graft success and contributes towards intergraft signalling involving the carbohydrate-marker TPS1. CONCLUSION Here, we suggest that the scion largely controls the molecular 'maturity' of grafted avocado trees, however, leaves on the rootstock not only promote graft success, but can influence miRNA and mRNA abundance in the scion. This constitutes the first study on scion and rootstock contribution towards grafted tree maturity using the miR156-SPL4-miR172 regulatory module as a marker for juvenility and reproductive competence.
Collapse
Affiliation(s)
- Muhammad Umair Ahsan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, Queensland, 4072, Australia
| | - Alice Hayward
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, Queensland, 4072, Australia
| | - Mobashwer Alam
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, Queensland, 4072, Australia
| | - Jayeni Hiti Bandaralage
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, Queensland, 4072, Australia
| | - Bruce Topp
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, Queensland, 4072, Australia
| | - Christine Anne Beveridge
- School of Biological Sciences, The University of Queensland, St. Lucia, Brisbane, Queensland, 4072, Australia
| | - Neena Mitter
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, Queensland, 4072, Australia.
| |
Collapse
|
31
|
Nadarajah K, Kumar IS. Drought Response in Rice: The miRNA Story. Int J Mol Sci 2019; 20:ijms20153766. [PMID: 31374851 PMCID: PMC6696311 DOI: 10.3390/ijms20153766] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 07/17/2019] [Accepted: 07/22/2019] [Indexed: 01/07/2023] Open
Abstract
As a semi-aquatic plant, rice requires water for proper growth, development, and orientation of physiological processes. Stress is induced at the cellular and molecular level when rice is exposed to drought or periods of low water availability. Plants have existing defense mechanisms in planta that respond to stress. In this review we examine the role played by miRNAs in the regulation and control of drought stress in rice through a summary of molecular studies conducted on miRNAs with emphasis on their contribution to drought regulatory networks in comparison to other plant systems. The interaction between miRNAs, target genes, transcription factors and their respective roles in drought-induced stresses is elaborated. The cross talk involved in controlling drought stress responses through the up and down regulation of targets encoding regulatory and functional proteins is highlighted. The information contained herein can further be explored to identify targets for crop improvement in the future.
Collapse
Affiliation(s)
- Kalaivani Nadarajah
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Malaysia.
| | - Ilakiya Sharanee Kumar
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Malaysia
| |
Collapse
|
32
|
Fileccia V, Ingraffia R, Amato G, Giambalvo D, Martinelli F. Identification of microRNAS differentially regulated by water deficit in relation to mycorrhizal treatment in wheat. Mol Biol Rep 2019; 46:5163-5174. [PMID: 31327121 DOI: 10.1007/s11033-019-04974-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 07/09/2019] [Indexed: 11/29/2022]
Abstract
Arbuscular mycorrhizal fungi (AMF) are soil microrganisms that establish symbiosis with plants positively influencing their resistance to abiotic stresses. The aim of this work was to identify wheat miRNAs differentially regulated by water deficit conditions in presence or absence of AMF treatment. Small RNA libraries were constructed for both leaf and root tissues considering four conditions: control (irrigated) or water deficit in presence/absence of mycorrhizal (AMF) treatment. A total of 12 miRNAs were significantly regulated by water deficit in leaves: five in absence and seven in presence of AMF treatment. In roots, three miRNAs were water deficit-modulated in absence of mycorrhizal treatment while six were regulated in presence of it. The most represented miRNA family was miR167 that was regulated by water deficit in both leaf and root tissues. Interestingly, miR827-5p was differentially regulated in leaves in the absence of mycorrhizal treatment while it was water deficit-modulated in roots irrespective of AMF treatment. In roots, water deficit repressed miR827-5p, miR394, miR6187, miR167e-3p, and miR9666b-3p affecting transcription, RNA synthesis, protein synthesis, and protein modifications. In leaves, mycorrhizae modulated miR5384-3p and miR156e-3p affecting trafficking and cell redox homeostasis. DNA replication and transcription regulation should be targeted by the repression of miR1432-5p and miR166h-3p. This work provided interesting insights into the post-transcriptional mechanisms of wheat responses to water deficit in relation to mycorrhizal symbiosis.
Collapse
Affiliation(s)
- Veronica Fileccia
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | - Rosolino Ingraffia
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | - Gaetano Amato
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | - Dario Giambalvo
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | | |
Collapse
|
33
|
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.
Collapse
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
| |
Collapse
|
34
|
Tang W, Thompson WA. OsmiR528 Enhances Cold Stress Tolerance by Repressing Expression of Stress Response-related Transcription Factor Genes in Plant Cells. Curr Genomics 2019; 20:100-114. [PMID: 31555061 PMCID: PMC6728904 DOI: 10.2174/1389202920666190129145439] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 11/05/2018] [Accepted: 01/09/2019] [Indexed: 12/20/2022] Open
Abstract
Background: MicroRNAs participate in many molecular mechanisms and signaling trans-duction pathways that are associated with plant stress tolerance by repressing expression of their target genes. However, how microRNAs enhance tolerance to low temperature stress in plant cells remains elusive. Objective: In this investigation, we demonstrated that overexpression of the rice microRNA528 (Os-miR528) increases cell viability, growth rate, antioxidants content, ascorbate peroxidase (APOX) activi-ty, and superoxide dismutase (SOD) activity and decreases ion leakage rate and thiobarbituric acid reac-tive substances (TBARS) under low temperature stress in Arabidopsis (Arabidopsis thaliana), pine (Pi-nus elliottii), and rice (Oryza sativa). Methods: To investigate the potential mechanism of OsmiR528 in increasing cold stress tolerance, we examined expression of stress-associated MYB transcription factors OsGAMYB-like1, OsMYBS3, OsMYB4, OsMYB3R-2, OsMYB5, OsMYB59, OsMYB30, OsMYB1R, and OsMYB20 in rice cells by qRT-PCR. Results:
Our experiments demonstrated that OsmiR528 decreases expression of transcription factor OsMYB30 by targeting a F-box domain containing protein gene (Os06g06050), which is a positive regulator of OsMYB30. In OsmiR528 transgenic rice, reduced OsMYB30 expression results in in-creased expression of BMY genes OsBMY2, OsBMY6, and OsBMY10. The transcript levels of the OsBMY2, OsBMY6, and OsBMY10 were elevated by OsMYB30 knockdown, but decreased by Os-MYB30 overexpression in OsmiR528 transgenic cell lines, suggesting that OsmiR528 increases low temperature tolerance by modulating expression of stress response-related transcription factor. Conclusion: Our experiments provide novel information in increasing our understanding in molecular mechanisms of microRNAs-associated low temperature tolerance and are valuable in plant molecular breeding from monocotyledonous, dicotyledonous, and gymnosperm plants.
Collapse
Affiliation(s)
- Wei Tang
- 1College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei Province 434025, P.R. China; 2Program of Cellular and Molecular Biology, Duke University, Durham, NC27708, USA
| | - Wells A Thompson
- 1College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei Province 434025, P.R. China; 2Program of Cellular and Molecular Biology, Duke University, Durham, NC27708, USA
| |
Collapse
|
35
|
Fei Y, Luo C, Tang W. Differential Expression of MicroRNAs During Root Formation in Taxus Chinensis Var. mairei Cultivars. Open Life Sci 2019; 14:97-109. [PMID: 33817141 PMCID: PMC7874753 DOI: 10.1515/biol-2019-0011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 01/15/2019] [Indexed: 11/15/2022] Open
Abstract
MicroRNAs (miRNAs) have been shown to play key roles in the regulation of plant growth and development by modifying the expression of their target genes. However, the influence of miRNAs on root formation and development in woody plants, such as Taxus chinensis, remains largely unknown. In the current study, we explored the phytohormone-response and nutrition-response miRNA expression profiles during T. chinensis rooting by quantitative real-time PCR (qPCR). We identified six phytohormone-response miRNAs, namely, miR164a, miR165, miR167a, miR171b, miR319, and miR391, and eight nutrition-response miRNAs, namely, miR169b, miR395a, miR399c, miR408, miR826, miR827, miR857, and miR2111a, that were differentially expressed at different rooting phases of T. chinensis. Using northern blot analysis of the putative target genes of these miRNAs, we detected the relative gene expression changes of the target genes. Taken together, our results suggest that miRNAs are involved in root formation of T. chinensis and that miRNAs may play important regulatory roles in primary root, crown root, and root hair formation by targeting phytohormone and/or nutrition response genes in T. chinensis. For the first time, these results expand our understanding of the molecular mechanisms of plant root formation and development in a conifer species.
Collapse
Affiliation(s)
- Yongjun Fei
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei Province 434025, Jingzhou, People's Republic of China
| | - Caroline Luo
- Department of Microbiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, Chapel Hill, USA
| | - Wei Tang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei Province 434025, Jingzhou, People's Republic of China
| |
Collapse
|
36
|
Ahsan MU, Hayward A, Irihimovitch V, Fletcher S, Tanurdzic M, Pocock A, Beveridge CA, Mitter N. Juvenility and Vegetative Phase Transition in Tropical/Subtropical Tree Crops. FRONTIERS IN PLANT SCIENCE 2019; 10:729. [PMID: 31214234 PMCID: PMC6558100 DOI: 10.3389/fpls.2019.00729] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 05/16/2019] [Indexed: 05/16/2023]
Abstract
In plants, juvenile to adult phase transition is regulated by the sequential activity of two microRNAs: miR156 and miR172. A decline in miR156 and increase in miR172 abundance is associated with phase transition. There is very limited information on phase transition in economically important horticultural tree crops, which have a significantly long vegetative phase affecting fruit bearing. Here, we profiled various molecular cues known to be involved in phase transition and flowering, including the microRNAs miR156 and miR172, in three horticultural tree crops: avocado (Persea americana), mango (Mangifera indica), and macadamia (Macadamia integrifolia). We observed that miR156 expression decreases as these trees age and can potentially be used as a juvenility marker. Consistent with findings in annual plants, we also observed conserved regulation of the miR156-SPL3/4/5 regulatory module in these genetically distant tree crops, suggesting that this pathway may play a highly conserved role in vegetative identity. Meanwhile, the abundance of miR172 and its target AP2-like genes as well as the accumulation level of SPL9 transcripts were not related with plant age in these crops except in avocado where miR172 expression increased steadily. Finally, we demonstrate that various floral genes, including AP1 and SOC1 were upregulated in the reproductive phase and can be used as potential markers for the reproductive phase transition. Overall, this study provides an insight into the molecular associations of juvenility and phase transition in horticultural trees where crop breeding and improvement are encumbered by long juvenile phases.
Collapse
Affiliation(s)
- Muhammad Umair Ahsan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Alice Hayward
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Vered Irihimovitch
- The Volcani Center, Agricultural Research Organization, Institute of Plant Sciences, Rishon LeZion, Israel
| | - Stephen Fletcher
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Milos Tanurdzic
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Alexander Pocock
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, Australia
| | | | - Neena Mitter
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
- *Correspondence: Neena Mitter,
| |
Collapse
|
37
|
Niu C, Li H, Jiang L, Yan M, Li C, Geng D, Xie Y, Yan Y, Shen X, Chen P, Dong J, Ma F, Guan Q. Genome-wide identification of drought-responsive microRNAs in two sets of Malus from interspecific hybrid progenies. HORTICULTURE RESEARCH 2019; 6:75. [PMID: 31231533 PMCID: PMC6555824 DOI: 10.1038/s41438-019-0157-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 02/28/2019] [Accepted: 04/05/2019] [Indexed: 05/12/2023]
Abstract
Drought stress can negatively impact apple fruit quality and yield. Apple microRNAs (miRNAs) participate in apple tree and fruit development, as well as in biotic stress tolerance; however, it is largely unknown whether these molecules are involved in the drought response. To identify drought-responsive miRNAs in Malus, we first examined the drought stress tolerance of ten F1 progenies of R3 (M. × domestica) × M. sieversii. We performed Illumina sequencing on pooled total RNA from both drought-tolerant and drought-sensitive plants. The sequencing results identified a total of 206 known miRNAs and 253 candidate novel miRNAs from drought-tolerant plants and drought-sensitive plants under control or drought conditions. We identified 67 miRNAs that were differentially expressed in drought-tolerant plants compared with drought-sensitive plants under drought conditions. Under drought stress, 61 and 35 miRNAs were differentially expressed in drought-tolerant and drought-sensitive plants, respectively. We determined the expression levels of seven out of eight miRNAs by stem-loop qPCR analysis. We also predicted the target genes of all differentially expressed miRNAs and identified the expression of some genes. Gene Ontology analyses indicated that the target genes were mainly involved in stimulus response and cellular and metabolic processes. Finally, we confirmed roles of two miRNAs in apple response to mannitol. Our results reveal candidate miRNAs and their associated mRNAs that could be targeted for improving drought tolerance in Malus species, thus providing a foundation for understanding the molecular networks involved in the response of apple trees to drought stress.
Collapse
Affiliation(s)
- Chundong Niu
- 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
| | - Haiyan 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
| | - Lijuan Jiang
- 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
| | - Mingjia Yan
- 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
| | - Cuiying 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
| | - Yinpeng Xie
- 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
| | - Yan Yan
- 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
| | - 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
| | - 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
| | - Jun Dong
- 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
| |
Collapse
|
38
|
Xiong H, Yu J, Miao J, Li J, Zhang H, Wang X, Liu P, Zhao Y, Jiang C, Yin Z, Li Y, Guo Y, Fu B, Wang W, Li Z, Ali J, Li Z. Natural Variation in OsLG3 Increases Drought Tolerance in Rice by Inducing ROS Scavenging. PLANT PHYSIOLOGY 2018; 178:451-467. [PMID: 30068540 PMCID: PMC6130013 DOI: 10.1104/pp.17.01492] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 07/21/2018] [Indexed: 05/18/2023]
Abstract
Improving the performance of rice (Oryza sativa) under drought stress has the potential to significantly affect rice productivity. Here, we report that the ERF family transcription factor OsLG3 positively regulates drought tolerance in rice. In our previous work, we found that OsLG3 has a positive effect on rice grain length without affecting grain quality. In this study, we found that OsLG3 was more strongly expressed in upland rice than in lowland rice under drought stress conditions. By performing candidate gene association analysis, we found that natural variation in the promoter of OsLG3 is associated with tolerance to osmotic stress in germinating rice seeds. Overexpression of OsLG3 significantly improved the tolerance of rice plants to simulated drought, whereas suppression of OsLG3 resulted in greater susceptibility. Phylogenetic analysis indicated that the tolerant allele of OsLG3 may improve drought tolerance in cultivated japonica rice. Introgression lines and complementation transgenic lines containing the elite allele of OsLG3IRAT109 showed increased drought tolerance, demonstrating that natural variation in OsLG3 contributes to drought tolerance in rice. Further investigation suggested that OsLG3 plays a positive role in drought stress tolerance in rice by inducing reactive oxygen species scavenging. Collectively, our findings reveal that natural variation in OsLG3 contributes to rice drought tolerance and that the elite allele of OsLG3 is a promising genetic resource for the development of drought-tolerant rice varieties.
Collapse
Affiliation(s)
- Haiyan Xiong
- Key Laboratory of Crop Heterosis and Utilization of the Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Jianping Yu
- Key Laboratory of Crop Heterosis and Utilization of the Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Jinli Miao
- Key Laboratory of Crop Heterosis and Utilization of the Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Jinjie Li
- Key Laboratory of Crop Heterosis and Utilization of the Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Hongliang Zhang
- Key Laboratory of Crop Heterosis and Utilization of the Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Xin Wang
- Key Laboratory of Crop Heterosis and Utilization of the Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Pengli Liu
- Key Laboratory of Crop Heterosis and Utilization of the Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yan Zhao
- Key Laboratory of Crop Heterosis and Utilization of the Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Chonghui Jiang
- Key Laboratory of Crop Heterosis and Utilization of the Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhigang Yin
- Key Laboratory of Crop Heterosis and Utilization of the Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yang Li
- Key Laboratory of Crop Heterosis and Utilization of the Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yan Guo
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Binying Fu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wensheng Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhikang Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jauhar Ali
- International Rice Research Institute, Metro Manila 1301, Philippines
| | - Zichao Li
- Key Laboratory of Crop Heterosis and Utilization of the Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| |
Collapse
|
39
|
Martinelli F, Cannarozzi G, Balan B, Siegrist F, Weichert A, Blösch R, Tadele Z. Identification of miRNAs linked with the drought response of tef [Eragrostis tef (Zucc.) Trotter]. JOURNAL OF PLANT PHYSIOLOGY 2018; 224-225:163-172. [PMID: 29656008 DOI: 10.1016/j.jplph.2018.02.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 01/25/2018] [Accepted: 02/26/2018] [Indexed: 06/08/2023]
Abstract
Tef [Eragrostis tef (Zucc.) Trotter], a staple food crop in the Horn of Africa and particularly in Ethiopia, has several beneficial agronomical and nutritional properties, including waterlogging and drought tolerance. In this study, we performed microRNA profiling of tef using the Illumina HiSeq 2500 platform, analyzing both shoots and roots of two tef genotypes, one drought-tolerant (Tsedey) and one drought-susceptible (Alba). We obtained more than 10 million filtered reads for each of the 24 sequenced small cDNA libraries. Reads mapping to known miRNAs were more abundant in the root than shoot tissues. Thirteen and 35 miRNAs were significantly modulated in response to drought, in Alba and Tsedey roots, respectively. One miRNA was upregulated under drought conditions in both genotypes. In shoots, nine miRNAs were modulated in common between the two genotypes and all showed similar trends of expression. One-hundred and forty-seven new miRNA mature sequences were identified in silico, 22 of these were detected in all relevant samples and seven were differentially regulated when comparing drought with normal watering. Putative targets of the miRNA regulated under drought in root and shoot tissues were predicted. Among the targets were transcription factors such as CCAAT-HAP2, MADS and NAC. Verification with qRT-PCR revealed that five of six potential targets showed a pattern of expression that was consistent with the correspondent miRNA amount measured by RNA-Seq. In general, candidate miRNAs involved in the post-transcriptional regulation of the tef response to drought could be included in next-generation breeding programs.
Collapse
Affiliation(s)
- Federico Martinelli
- Dipartimento di Scienze Agrarie Alimentari Forestali, Università di Palermo, viale delle scienze Ed. 4., Palermo, Italy.
| | - Gina Cannarozzi
- Institute of Plant Sciences, Altenbergrain 21, University of Bern, Bern, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - Bipin Balan
- Dipartimento di Scienze Agrarie Alimentari Forestali, Università di Palermo, viale delle scienze Ed. 4., Palermo, Italy.
| | - Fredy Siegrist
- Institute of Plant Sciences, Altenbergrain 21, University of Bern, Bern, Switzerland.
| | - Annett Weichert
- Institute of Plant Sciences, Altenbergrain 21, University of Bern, Bern, Switzerland.
| | - Regula Blösch
- Institute of Plant Sciences, Altenbergrain 21, University of Bern, Bern, Switzerland.
| | - Zerihun Tadele
- Institute of Plant Sciences, Altenbergrain 21, University of Bern, Bern, Switzerland; Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia.
| |
Collapse
|
40
|
Identification of Blueberry miRNAs and Their Targets Based on High-Throughput Sequencing and Degradome Analyses. Int J Mol Sci 2018; 19:ijms19040983. [PMID: 29587414 PMCID: PMC5979386 DOI: 10.3390/ijms19040983] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 02/24/2018] [Accepted: 03/02/2018] [Indexed: 01/06/2023] Open
Abstract
miRNAs are important regulators of plant gene expression. To better characterize their functions, we applied high-throughput sequencing and degradome analyses to investigate three blueberry (Vaccinium ashei) tissues. A total of 127 known and 101 novel miRNAs were identified. Moreover, 141 targets for 42 known and 19 novel miRNAs were experimentally validated by degradome sequencing. A functional analysis of these miRNA targets revealed they were associated with diverse biological activities and several pathways, e.g., anthocyanin biosynthesis and cytokinin signal transduction. The data presented herein expand our understanding of the regulation of blueberry miRNAs during floral and fruit development stages. They may also provide new insights into the roles of miRNAs during anthocyanin biosynthesis in blueberry fruits.
Collapse
|
41
|
Xia K, Zeng X, Jiao Z, Li M, Xu W, Nong Q, Mo H, Cheng T, Zhang M. Formation of Protein Disulfide Bonds Catalyzed by OsPDIL1;1 is Mediated by MicroRNA5144-3p in Rice. PLANT & CELL PHYSIOLOGY 2018; 59:331-342. [PMID: 29194535 DOI: 10.1093/pcp/pcx189] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 11/23/2017] [Indexed: 05/20/2023]
Abstract
Correct folding of proteins in the endoplasmic reticulum is important for their stability and function under stress. The protein disulfide isomerase (PDI) OsPDIL1;1 is a key protein-folding catalyst in rice (Oryza sativa L.). Here, microRNA5144 (osa-miR5144-3p) is reported to mediate the formation of protein disulfide bonds via targeting OsPDIL1;1 mRNA in rice seeds and seedlings during development and under conditions of abiotic stress, respectively. Expression analysis of transgenic rice and identification of cleavage sites showed that OsPDIL1;1 mRNA is a target of osa-miR5144-3p. Expression of osa-miR5144-3p and OsPDIL1;1 was shown to be inversely regulated in developing organs and under abiotic stress. The down-regulation of osa-miR5144-3p or overexpression of OsPDIL1;1 in transgenic rice showed increased total protein-disulfide bond content, compared with the wild type. This indicates that protein-disulfide bond formation is enhanced by down-regulation of osa-miR5144-3p or overexpression of OsPDIL1;1. These transgenic rice plants also displayed strong resistance to salinity and mercury stress, in comparison with the wild type. In contrast, the transgenic rice plants overexpressing osa-miR5144-3p or down-regulating OsPDIL1;1 had a lower protein-disulfide bond content; they were susceptible to abiotic stress and produced abnormal grains with small and loosely packed starch granules. These results indicate that protein-disulfide bond formation catalyzed by OsPDIL1;1 is modulated by osa-miR5144-3p in rice during development and is involved in resistance to abiotic stress.
Collapse
Affiliation(s)
- Kuaifei Xia
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Xuan Zeng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Zhengli Jiao
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Maolin Li
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weijuan Xu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Quandong Nong
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui Mo
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Taihui Cheng
- Panyu District Guangzhou Agricultural Science Research Institute, Guangzhou 511400, China
| | - Mingyong Zhang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| |
Collapse
|
42
|
Srivastava S, Sharma A. Study of microRNA mediated gene regulation in Striga hermonthica through in-silico approach. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.aggene.2017.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
43
|
Balyan S, Kumar M, Mutum RD, Raghuvanshi U, Agarwal P, Mathur S, Raghuvanshi S. Identification of miRNA-mediated drought responsive multi-tiered regulatory network in drought tolerant rice, Nagina 22. Sci Rep 2017; 7:15446. [PMID: 29133823 PMCID: PMC5684420 DOI: 10.1038/s41598-017-15450-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 10/23/2017] [Indexed: 11/21/2022] Open
Abstract
Comparative characterization of microRNA-mediated stress regulatory networks in contrasting rice cultivars is critical to decipher plant stress response. Consequently, a multi-level comparative analysis, using sRNA sequencing, degradome analysis, enzymatic and metabolite assays and metal ion analysis, in drought tolerant and sensitive rice cultivars was conducted. The study identified a group of miRNAs "Cultivar-specific drought responsive" (CSDR)-miRNAs (osa-miR159f, osa-miR1871, osa-miR398b, osa-miR408-3p, osa-miR2878-5p, osa-miR528-5p and osa-miR397a) that were up-regulated in the flag-leaves of tolerant cultivar, Nagina 22 (N22) and Vandana, but down-regulated in the sensitive cultivar, Pusa Basmati 1 (PB1) and IR64, during drought. Interestingly, CSDR-miRNAs target several copper-protein coding transcripts like plantacyanins, laccases and Copper/Zinc superoxide dismutases (Cu/Zn SODs) and are themselves found to be similarly induced under simulated copper-starvation in both N22 and PB1. Transcription factor OsSPL9, implicated in Cu-homeostasis also interacted with osa-miR408-3p and osa-miR528-5p promoters. Further, N22 flag leaves showed lower SOD activity, accumulated ROS and had a higher stomata closure. Interestingly, compared to PB1, internal Cu levels significantly decreased in the N22 flag-leaves, during drought. Thus, the study identifies the unique drought mediated dynamism and interplay of Cu and ROS homeostasis, in the flag leaves of drought tolerant rice, wherein CSDR-miRNAs play a pivotal role.
Collapse
Affiliation(s)
- Sonia Balyan
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Mukesh Kumar
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Roseeta Devi Mutum
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Utkarsh Raghuvanshi
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Priyanka Agarwal
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Saloni Mathur
- National Institute of Plant Genome Research, Aruna Asaf Ali Road, New Delhi, 110067, India
| | - Saurabh Raghuvanshi
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India.
| |
Collapse
|
44
|
Identification of functionally important microRNAs from rice inflorescence at heading stage of a qDTY4.1-QTL bearing Near Isogenic Line under drought conditions. PLoS One 2017; 12:e0186382. [PMID: 29045473 PMCID: PMC5647096 DOI: 10.1371/journal.pone.0186382] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 09/30/2017] [Indexed: 12/13/2022] Open
Abstract
A cross between IR64 (high-yielding but drought-susceptible) and Aday Sel (drought-tolerant) rice cultivars yielded a stable line with enhanced grain yield under drought screening field trials at International Rice Research Institute. The major effect qDTY4.1 drought tolerance and yield QTL was detected in the IR77298-14-1-2-10 Backcrossed Inbred Line (BIL) and its IR87705-7-15-B Near Isogenic Line (NIL) with 93.9% genetic similarity to IR64. Although rice yield is extremely susceptible to water stress at reproductive stage, currently, there is only one report on the detection of drought-responsive microRNAs in inflorescence tissue of a Japonica rice line. In this study, more drought-responsive microRNAs were identified in the inflorescence tissues of IR64, IR77298-14-1-2-10 and IR87705-7-15-B via next-generation sequencing. Among the 32 families of inflorescence-specific non-conserved microRNAs that were identified, 22 families were up-regulated in IR87705-7-15-B. Overall 9 conserved and 34 non-conserved microRNA families were found as drought-responsive in rice inflorescence with 5 conserved and 30 non-conserved families induced in the IR87705-7-15-B. The observation of more drought-responsive non-conserved microRNAs may imply their prominence over conserved microRNAs in drought response mechanisms of rice inflorescence. Gene Ontology annotation analysis on the target genes of drought-responsive microRNAs identified in IR87705-7-15-B revealed over-representation of biological processes including development, signalling and response to stimulus. Particularly, four inflorescence-specific microRNAs viz. osa-miR5485, osa-miR5487, osa-miR5492 and osa-miR5517, and two non-inflorescence specific microRNAs viz. osa-miR169d and osa-miR169f.2 target genes that are involved in flower or embryonic development. Among them, osa-miR169d, osa-miR5492 and osa-miR5517 are related to flowering time control. It is also worth mentioning that osa-miR2118 and osa-miR2275, which are implicated in the biosynthesis of rice inflorescence-specific small interfering RNAs, were induced in IR87705-7-15-B but repressed in IR77298-14-1-2-10. Further, gene search within qDTY4.1 QTL region had identified multiple copies of NBS-LRR resistance genes (potential target of osa-miR2118), subtilisins and genes implicated in stomatal movement, ABA metabolism and cuticular wax biosynthesis.
Collapse
|
45
|
Liu M, Yu H, Zhao G, Huang Q, Lu Y, Ouyang B. Identification of drought-responsive microRNAs in tomato using high-throughput sequencing. Funct Integr Genomics 2017; 18:67-78. [PMID: 28956210 DOI: 10.1007/s10142-017-0575-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 09/12/2017] [Accepted: 09/19/2017] [Indexed: 11/29/2022]
Abstract
Drought is a major abiotic stress affecting crop productivity and quality. As a class of noncoding RNA, microRNA (miRNA) plays important roles in plant growth, development, and stress response. However, their response and roles in tomato drought stress is largely unknown. Here, by using high-throughput sequencing, we compared the miRNA profiles before and after drought treatment in two tomato genotypes: M82, a drought-sensitive cultivated tomato (Solanum lycopersicum), and IL2-5, a drought-tolerant introgression line derived from M82 and the tomato wild species S. pennellii (LA0716). A total of 108 conserved and 208 novel miRNAs were identified, among them, 32 and 68 were significantly changed in expression after stress. Further, 1936 putative target genes were predicted for those differentially-expressed miRNAs. Gene ontology and pathway analysis showed that many of the target genes were involved in stress resistance, such as genes in GO terms including response to stress, defense response, response to stimulus, phosphorylation, and signal transduction. Our results suggested that miRNAs play an essential role in the drought response of tomato. This work will help to further characterize specific miRNAs functioning in drought tolerance.
Collapse
Affiliation(s)
- Minmin Liu
- Key Laboratory of Horticultural Plant Biology (MOE), and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, 430070, China
| | - Huiyang Yu
- Key Laboratory of Horticultural Plant Biology (MOE), and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, 430070, China
| | - Gangjun Zhao
- Key Laboratory of Horticultural Plant Biology (MOE), and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qiufeng Huang
- Key Laboratory of Horticultural Plant Biology (MOE), and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yongen Lu
- Key Laboratory of Horticultural Plant Biology (MOE), and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, 430070, China
| | - Bo Ouyang
- Key Laboratory of Horticultural Plant Biology (MOE), and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, 430070, China.
| |
Collapse
|
46
|
Ganie SA, Debnath AB, Gumi AM, Mondal TK. Comprehensive survey and evolutionary analysis of genome-wide miRNA genes from ten diploid Oryza species. BMC Genomics 2017; 18:711. [PMID: 28893199 PMCID: PMC5594537 DOI: 10.1186/s12864-017-4089-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 08/25/2017] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are non-coding RNAs that play versatile roles in post-transcriptional gene regulation. Although much is known about their biogenesis, and gene regulation very little is known about their evolutionary relation among the closely related species. RESULT All the orthologous miRNA genes of Oryza sativa (japonica) from 10 different Oryza species were identified, and the evolutionary changes among these genes were analysed. Significant differences in the expansion of miRNA gene families were observed across the Oryza species. Analysis of the nucleotide substitution rates indicated that the mature sequences show the least substitution rates among the different regions of miRNA genes, and also show a very much less substitution rates as compared to that of all protein-coding genes across the Oryza species. Evolution of miRNA genes was also found to be contributed by transposons. A non-neutral selection was observed at 80 different miRNA loci across Oryza species which were estimated to have lost ~87% of the sequence diversity during the domestication. The phylogenetic analysis revealed that O. longistaminata diverged first among the AA-genomes, whereas O. brachyantha and O. punctata appeared as the eminent out-groups. The miR1861 family organised into nine distinct compact clusters in the studied Oryza species except O. brachyantha. Further, the expression analysis showed that 11 salt-responsive miRNAs were differentially regulated between O. coarctata and O. glaberrima. CONCLUSION Our study provides the evolutionary dynamics in the miRNA genes of 10 different Oryza species which will support more investigations about the structural and functional organization of miRNA genes of Oryza species.
Collapse
Affiliation(s)
- Showkat Ahmad Ganie
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, Pusa, IARI Campus, New Delhi, 110012, India
| | - Ananda Bhusan Debnath
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, Pusa, IARI Campus, New Delhi, 110012, India
| | - Abubakar Mohammad Gumi
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, Pusa, IARI Campus, New Delhi, 110012, India
| | - Tapan Kumar Mondal
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, Pusa, IARI Campus, New Delhi, 110012, India.
| |
Collapse
|
47
|
Liu M, Yu H, Zhao G, Huang Q, Lu Y, Ouyang B. Profiling of drought-responsive microRNA and mRNA in tomato using high-throughput sequencing. BMC Genomics 2017; 18:481. [PMID: 28651543 PMCID: PMC5485680 DOI: 10.1186/s12864-017-3869-1] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 06/19/2017] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Abiotic stresses cause severe loss of crop production. Among them, drought is one of the most frequent environmental stresses, which limits crop growth, development and productivity. Plant drought tolerance is fine-tuned by a complex gene regulatory network. Understanding the molecular regulation of this polygenic trait is crucial for the eventual success to improve plant yield and quality. Recent studies have demonstrated that microRNAs play critical roles in plant drought tolerance. However, little is known about the microRNA in drought response of the model plant tomato. Here, we described the profiling of drought-responsive microRNA and mRNA in tomato using high-throughput next-generation sequencing. RESULTS Drought stress was applied on the seedlings of M82, a drought-sensitive cultivated tomato genotype, and IL9-1, a drought-tolerant introgression line derived from the stress-resistant wild species Solanum pennellii LA0716 and M82. Under drought, IL9-1 performed superior than M82 regarding survival rate, H2O2 elimination and leaf turgor maintenance. A total of four small RNA and eight mRNA libraries were constructed and sequenced using Illumina sequencing technology. 105 conserved and 179 novel microRNAs were identified, among them, 54 and 98 were differentially expressed upon drought stress, respectively. The majority of the differentially-expressed conserved microRNAs was up-regulated in IL9-1 whereas down-regulated in M82. Under drought stress, 2714 and 1161 genes were found to be differentially expressed in M82 and IL9-1, respectively, and many of their homologues are involved in plant stress, such as genes encoding transcription factor and protein kinase. Various pathways involved in abiotic stress were revealed by Gene Ontology and pathway analysis. The mRNA sequencing results indicated that most of the target genes were regulated by their corresponding microRNAs, which suggested that microRNAs may play essential roles in the drought tolerance of tomato. CONCLUSION In this study, numerous microRNAs and mRNAs involved in the drought response of tomato were identified using high-throughput sequencing, which will provide new insights into the complex regulatory network of plant adaption to drought stress. This work will also help to exploit new players functioning in plant drought-stress tolerance.
Collapse
Affiliation(s)
- Minmin Liu
- Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan, 430070 China
| | - Huiyang Yu
- Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan, 430070 China
| | - Gangjun Zhao
- Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan, 430070 China
| | - Qiufeng Huang
- Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan, 430070 China
| | - Yongen Lu
- Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan, 430070 China
| | - Bo Ouyang
- Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan, 430070 China
| |
Collapse
|
48
|
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.
Collapse
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.
| |
Collapse
|
49
|
Identification and characterization of durum wheat microRNAs in leaf and root tissues. Funct Integr Genomics 2017; 17:583-598. [PMID: 28321518 DOI: 10.1007/s10142-017-0551-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 01/30/2017] [Accepted: 02/01/2017] [Indexed: 10/19/2022]
Abstract
MicroRNAs are a class of post-transcriptional regulators of plant developmental and physiological processes and responses to environmental stresses. Here, we present the study regarding the annotation and characterization of MIR genes conducted in durum wheat. We characterized the miRNAome of leaf and root tissues at tillering stage under two environmental conditions: irrigated with 100% (control) and 55% of evapotranspiration (early water stress). In total, 90 microRNAs were identified, of which 32 were classified as putative novel and species-specific miRNAs. In addition, seven microRNA homeologous groups were identified in each of the two genomes of the tetraploid durum wheat. Differential expression analysis highlighted a total of 45 microRNAs significantly differentially regulated in the pairwise comparisons leaf versus root. The miRNA families, miR530, miR395, miR393, miR5168, miR396 and miR166, miR171, miR319, and miR167, were the most expressed in leaves in comparison to roots. Putative microRNA targets were predicted for both five and three prime sequences derived from the stem-loop of the MIR gene. Gene ontology analysis showed significant overrepresented gene categories in microRNA targets belonging to transcription factors, phenylpropanoids, oxydases, and lipid binding-protein. This work represents one of the first genome wide characterization of MIR genes in durum wheat, identifying leaf and root tissue-specific microRNAs. This genomic identification of microRNAs together with the analysis of their expression profiles is a well-accepted starting point leading to a better comprehension of the role of MIR genes in the genus Triticum.
Collapse
|
50
|
Jin Q, Xu Y, Mattson N, Li X, Wang B, Zhang X, Jiang H, Liu X, Wang Y, Yao D. Identification of Submergence-Responsive MicroRNAs and Their Targets Reveals Complex MiRNA-Mediated Regulatory Networks in Lotus ( Nelumbo nucifera Gaertn). FRONTIERS IN PLANT SCIENCE 2017; 8:6. [PMID: 28149304 PMCID: PMC5241310 DOI: 10.3389/fpls.2017.00006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 01/03/2017] [Indexed: 05/25/2023]
Abstract
MicroRNAs (miRNAs) are endogenous non-coding RNAs with important regulatory functions in plant development and stress responses. However, their population abundance in lotus (Nelumbo nucifera Gaertn) has so far been poorly described, particularly in response to stresses. In this work, submergence-related miRNAs and their target genes were systematically identified, compared, and validated at the transcriptome-wide level using high-throughput sequencing data of small RNA, Mrna, and the degradome. A total of 128 known and 20 novel miRNAs were differentially expressed upon submergence. We identified 629 target transcripts for these submergence-responsive miRNAs. Based on the miRNA expression profiles and GO and KEGG annotation of miRNA target genes, we suggest possible molecular responses and physiological changes of lotus in response to submergence. Several metabolic, physiological and morphological adaptations-related miRNAs, i.e., NNU_far-miR159, NNU_gma-miR393h, and NNU_aly-miR319c-3p, were found to play important regulatory roles in lotus response to submergence. This work will contribute to a better understanding of miRNA-regulated adaption responses of lotus to submergence stress.
Collapse
Affiliation(s)
- Qijiang Jin
- College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Yingchun Xu
- College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Neil Mattson
- Horticulture Section, School of Integrative Plant Science, Cornell UniversityNew York, NY, USA
| | - Xin Li
- Institute of Agricultural Science of Taihu Lake DistrictSuzhou, China
| | - Bei Wang
- College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Xiao Zhang
- College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Hongwei Jiang
- Institute of Agricultural Science of Taihu Lake DistrictSuzhou, China
| | - Xiaojing Liu
- Institute of Botany, Jiangsu Province and Chinese Academy of SciencesNanjing, China
| | - Yanjie Wang
- College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Dongrui Yao
- Institute of Botany, Jiangsu Province and Chinese Academy of SciencesNanjing, China
| |
Collapse
|