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Gill SS, Khan NA, Agarwala N, Singh K, Sunkar R, Tuteja N. ncRNAs in plant development and stress responses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 214:108950. [PMID: 39034172 DOI: 10.1016/j.plaphy.2024.108950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
Affiliation(s)
- Sarvajeet Singh Gill
- Stress Physiology and Molecular Biology Lab, Centre for Biotechnology, Maharshi Dayanand University, Rohtak, 124 001, Haryana, India.
| | - Nafees A Khan
- Plant Physiology and Biochemistry Laboratory, Department of Botany, Aligarh Muslim University, Aligarh, 202002, India.
| | - Niraj Agarwala
- Department of Botany, Gauhati University, Gopinath Bordoloi Nagar, Guwahati, Assam, 781014, India.
| | - Kashmir Singh
- Department of Biotechnology, Panjab University, Chandigarh, India.
| | - Ramanjulu Sunkar
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA.
| | - Narendra Tuteja
- Plant Molecular Biology Group, International Centre for Genetic Engineering & Biotechnology (ICGEB), New Delhi, India.
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Choudhary P, Pramitha L, Aggarwal PR, Rana S, Vetriventhan M, Muthamilarasan M. Biotechnological interventions for improving the seed longevity in cereal crops: progress and prospects. Crit Rev Biotechnol 2023; 43:309-325. [PMID: 35443842 DOI: 10.1080/07388551.2022.2027863] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Seed longevity is a measure of the viability of seeds during long-term storage and is crucial for germplasm conservation and crop improvement programs. Also, longevity is an important trait for ensuring food and nutritional security. Thus, a better understanding of various factors regulating seed longevity is requisite to improve this trait and to minimize the genetic drift during the regeneration of germplasm. In particular, seed deterioration of cereal crops during storage adversely affects agricultural productivity and food security. The irreversible process of seed deterioration involves a complex interplay between different genes and regulatory pathways leading to: loss of DNA integrity, membrane damage, inactivation of storage enzymes and mitochondrial dysfunction. Identifying the genetic determinants of seed longevity and manipulating them using biotechnological tools hold the key to ensuring prolonged seed storage. Genetics and genomics approaches had identified several genomic regions regulating the longevity trait in major cereals such as: rice, wheat, maize and barley. However, very few studies are available in other Poaceae members, including millets. Deploying omics tools, including genomics, proteomics, metabolomics, and phenomics, and integrating the datasets will pinpoint the precise molecular determinants affecting the survivability of seeds. Given this, the present review enumerates the genetic factors regulating longevity and demonstrates the importance of integrated omics strategies to dissect the molecular machinery underlying seed deterioration. Further, the review provides a roadmap for deploying biotechnological approaches to manipulate the genes and genomic regions to develop improved cultivars with prolonged storage potential.
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Affiliation(s)
- Pooja Choudhary
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Lydia Pramitha
- School of Agriculture and Biosciences, Karunya Institute of Technology and Sciences, Coimbatore, India
| | - Pooja Rani Aggarwal
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Sumi Rana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Mani Vetriventhan
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
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Xu P, Li Q, Liang W, Hu Y, Chen R, Lou K, Zhan L, Wu X, Pu J. A tissue-specific profile of miRNAs and their targets related to paeoniaflorin and monoterpenoids biosynthesis in Paeonia lactiflora Pall. by transcriptome, small RNAs and degradome sequencing. PLoS One 2023; 18:e0279992. [PMID: 36701382 PMCID: PMC9879538 DOI: 10.1371/journal.pone.0279992] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 12/19/2022] [Indexed: 01/27/2023] Open
Abstract
Paeonia lactiflora Pall. (Paeonia) has aroused many concerns due to its extensive medicinal value, in which monoterpene glucoside paeoniflorin and its derivatives are the active chemical components. However, little is known in the molecular mechanism of monoterpenoids biosynthesis, and the regulation network between small RNAs and mRNAs in monoterpenoids biosynthesis has not been investigated yet. Herein, we attempted to reveal the tissue-specific regulation network of miRNAs and their targets related to paeoniaflorin and monoterpenoids biosynthesis in Paeonia by combining mRNA and miRNA expression data with degradome analysis. In all, 289 miRNAs and 30177 unigenes were identified, of which nine miRNAs from seven miRNA families including miR396, miR393, miR835, miR1144, miR3638, miR5794 and miR9555 were verified as monoterpenoids biosynthesis-related miRNAs by degradome sequencing. Moreover, the co-expression network analysis showed that four monoterpenoids-regulating TFs, namely AP2, MYBC1, SPL12 and TCP2, were putatively regulated by five miRNAs including miR172, miR828, miR858, miR156 and miR319, respectively. The present study will improve our knowledge of the molecular mechanisms of the paeoniaflorin and monoterpenoids biosynthesis mediated by miRNA to a new level, and provide a valuable resource for further study on Paeonia.
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Affiliation(s)
- Pan Xu
- Center for Medicinal Resources Research, Zhejiang Academy of Traditional Chinese Medicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Research and Development of Chinese Medicine of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Quanqing Li
- Department of Pharmacy, Zhejiang Xiaoshan Hospital, Hangzhou, Zhejiang Province, China
| | - Weiqing Liang
- Center for Medicinal Resources Research, Zhejiang Academy of Traditional Chinese Medicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Research and Development of Chinese Medicine of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Yijuan Hu
- Center for Medicinal Resources Research, Zhejiang Academy of Traditional Chinese Medicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Research and Development of Chinese Medicine of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Rubing Chen
- Center for Medicinal Resources Research, Zhejiang Academy of Traditional Chinese Medicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Research and Development of Chinese Medicine of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Kelang Lou
- Center for Medicinal Resources Research, Zhejiang Academy of Traditional Chinese Medicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Research and Development of Chinese Medicine of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Lianghui Zhan
- Center for Medicinal Resources Research, Zhejiang Academy of Traditional Chinese Medicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Research and Development of Chinese Medicine of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Xiaojun Wu
- Center for Medicinal Resources Research, Zhejiang Academy of Traditional Chinese Medicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Research and Development of Chinese Medicine of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Jinbao Pu
- Center for Medicinal Resources Research, Zhejiang Academy of Traditional Chinese Medicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Research and Development of Chinese Medicine of Zhejiang Province, Hangzhou, Zhejiang Province, China
- * E-mail:
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Ahmad S, Chen Y, Shah AZ, Wang H, Xi C, Zhu H, Ge L. The Homeodomain-Leucine Zipper Genes Family Regulates the Jinggangmycin Mediated Immune Response of Oryza sativa to Nilaparvata lugens, and Laodelphax striatellus. Bioengineering (Basel) 2022; 9:bioengineering9080398. [PMID: 36004924 PMCID: PMC9405480 DOI: 10.3390/bioengineering9080398] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 12/16/2022] Open
Abstract
The homeodomain-leucine zipper (HDZIP) is an important transcription factor family, instrumental not only in growth but in finetuning plant responses to environmental adversaries. Despite the plethora of literature available, the role of HDZIP genes under chewing and sucking insects remains elusive. Herein, we identified 40 OsHDZIP genes from the rice genome database. The evolutionary relationship, gene structure, conserved motifs, and chemical properties highlight the key aspects of OsHDZIP genes in rice. The OsHDZIP family is divided into a further four subfamilies (i.e., HDZIP I, HDZIP II, HDZIP III, and HDZIP IV). Moreover, the protein–protein interaction and Gene Ontology (GO) analysis showed that OsHDZIP genes regulate plant growth and response to various environmental stimuli. Various microRNA (miRNA) families targeted HDZIP III subfamily genes. The microarray data analysis showed that OsHDZIP was expressed in almost all tested tissues. Additionally, the differential expression patterns of the OsHDZIP genes were found under salinity stress and hormonal treatments, whereas under brown planthopper (BPH), striped stem borer (SSB), and rice leaf folder (RLF), only OsHDZIP3, OsHDZIP4, OsHDZIP40, OsHDZIP10, and OsHDZIP20 displayed expression. The qRT-PCR analysis further validated the expression of OsHDZIP20, OsHDZIP40, and OsHDZIP10 under BPH, small brown planthopper (SBPH) infestations, and jinggangmycin (JGM) spraying applications. Our results provide detailed knowledge of the OsHDZIP gene family resistance in rice plants and will facilitate the development of stress-resilient cultivars, particularly against chewing and sucking insect pests.
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Chandra T, Mishra S, Panda BB, Sahu G, Dash SK, Shaw BP. Study of expressions of miRNAs in the spikelets based on their spatial location on panicle in rice cultivars provided insight into their influence on grain development. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 159:244-256. [PMID: 33388659 DOI: 10.1016/j.plaphy.2020.12.020] [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: 08/11/2020] [Accepted: 12/20/2020] [Indexed: 06/12/2023]
Abstract
Development of rice cultivars bearing numerous spikelets by breeding approach to increase the yearly production of rice to approximately 800 million metric tons to feed the ever increasing population of the world accompanies poor grain filling in the inferior spikelets preventing achievement of the yield potential. As the initial stages of caryopses development are of much importance for grain filling, spatio-temporal expressions of the miRNAs were studied during these periods in the spikelets of a compact-panicle rice cultivar, Oryza sativa cv. Mahalaxmi, bearing numerous spikelets per panicle to understand the reason of poor grain filling at the level of the initial biochemical events. Differential expression of several known miRNAs between the superior and inferior spikelets suggested great difference in metabolism related to grain filling in the spikelets based on their spatial location on compact panicle. Expressions of five known and four novel miRNAs were validated by Northern. Their targets included the enzymes directly involved in starch biosynthesis like sucrose synthase, starch synthase and pullulanase, besides others. Spatio-temporal expression studies of these miRNAs in the spikelets of Mahalaxmi revealed a pattern of mostly a greater expression in the inferior spikelets compared with the superior ones concomitant with an inverse expression of the target genes, which was not observed in the lax-panicle cultivar Upahar. The study thus revealed that the grain filling in rice is greatly regulated by miRNAs, and these miRNAs or their target genes could be considered for biotechnological interventions for improving grain filling in the rice cultivars of interest.
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Affiliation(s)
- Tilak Chandra
- Abiotic Stress and Agro-Biotechnology Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India.
| | - Sagarika Mishra
- Abiotic Stress and Agro-Biotechnology Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India.
| | - Binay Bhushan Panda
- Abiotic Stress and Agro-Biotechnology Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India.
| | - Gyanasri Sahu
- Abiotic Stress and Agro-Biotechnology Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India.
| | - Sushanta Kumar Dash
- Crop Improvement Division, ICAR-National Rice Research Institute (formerly Central Rice Research Institute), Cuttack, Odisha, India.
| | - Birendra Prasad Shaw
- Abiotic Stress and Agro-Biotechnology Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India.
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Krishnatreya DB, Agarwala N, Gill SS, Bandyopadhyay T. Understanding the role of miRNAs for improvement of tea quality and stress tolerance. J Biotechnol 2021; 328:34-46. [PMID: 33421509 DOI: 10.1016/j.jbiotec.2020.12.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 12/04/2020] [Accepted: 12/28/2020] [Indexed: 12/18/2022]
Abstract
MicroRNAs (miRNAs) are an emerging class of small non-coding RNAs that exhibit important role in regulation of gene expression, mostly through the mechanism of cleavage and/or inhibition of translation of target mRNAs during or after transcription. Although much has been unravelled about the role of miRNAs in diverse biological processes like maintenance of functional integrity of genes and genome, growth and development, metabolism, and adaptive responses towards biotic and abiotic stresses in plants, not much is known on their specific roles in majority of cash crops - an area of investigation with potentially significant and gainful economic implications. Tea (Camellia sinensis) is globally the second most consumed beverage after water and its cultivation has major agro-economic and social ramifications. In recent years, global tea production has been greatly challenged by many biotic and abiotic stress factors and a deeper understanding of molecular processes regulating stress adaptation in this largely under investigated crop stands to significantly facilitate potential crop improvement strategies towards durable stress tolerance. This review endeavours to highlight recent advances in our understanding of the role of miRNAs in regulating stress tolerance traits in tea plant with additional focus on their role in determining tea quality attributes.
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Affiliation(s)
| | - Niraj Agarwala
- Department of Botany, Gauhati University, Jalukbari, Guwahati, Assam, 781014, India.
| | - Sarvajeet Singh Gill
- Center for Biotechnology, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
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miRTil: An Extensive Repository for Nile Tilapia microRNA Next Generation Sequencing Data. Cells 2020; 9:cells9081752. [PMID: 32707870 PMCID: PMC7465656 DOI: 10.3390/cells9081752] [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: 06/25/2020] [Revised: 07/16/2020] [Accepted: 07/20/2020] [Indexed: 12/04/2022] Open
Abstract
Nile tilapia is the third most cultivated fish worldwide and a novel model species for evolutionary studies. Aiming to improve productivity and contribute to the selection of traits of economic impact, biotechnological approaches have been intensively applied to species enhancement. In this sense, recent studies have focused on the multiple roles played by microRNAs (miRNAs) in the post-transcriptional regulation of protein-coding genes involved in the emergence of phenotypes with relevance for aquaculture. However, there is still a growing demand for a reference resource dedicated to integrating Nile Tilapia miRNA information, obtained from both experimental and in silico approaches, and facilitating the analysis and interpretation of RNA sequencing data. Here, we present an open repository dedicated to Nile Tilapia miRNAs: the “miRTil database”. The database stores data on 734 mature miRNAs identified in 11 distinct tissues and five key developmental stages. The database provides detailed information about miRNA structure, genomic context, predicted targets, expression profiles, and relative 5p/3p arm usage. Additionally, miRTil also includes a comprehensive pre-computed miRNA-target interaction network containing 4936 targets and 19,580 interactions.
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Hrbáčková M, Dvořák P, Takáč T, Tichá M, Luptovčiak I, Šamajová O, Ovečka M, Šamaj J. Biotechnological Perspectives of Omics and Genetic Engineering Methods in Alfalfa. FRONTIERS IN PLANT SCIENCE 2020; 11:592. [PMID: 32508859 PMCID: PMC7253590 DOI: 10.3389/fpls.2020.00592] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 04/20/2020] [Indexed: 05/07/2023]
Abstract
For several decades, researchers are working to develop improved major crops with better adaptability and tolerance to environmental stresses. Forage legumes have been widely spread in the world due to their great ecological and economic values. Abiotic and biotic stresses are main factors limiting legume production, however, alfalfa (Medicago sativa L.) shows relatively high level of tolerance to drought and salt stress. Efforts focused on alfalfa improvements have led to the release of cultivars with new traits of agronomic importance such as high yield, better stress tolerance or forage quality. Alfalfa has very high nutritional value due to its efficient symbiotic association with nitrogen-fixing bacteria, while deep root system can help to prevent soil water loss in dry lands. The use of modern biotechnology tools is challenging in alfalfa since full genome, unlike to its close relative barrel medic (Medicago truncatula Gaertn.), was not released yet. Identification, isolation, and improvement of genes involved in abiotic or biotic stress response significantly contributed to the progress of our understanding how crop plants cope with these environmental challenges. In this review, we provide an overview of the progress that has been made in high-throughput sequencing, characterization of genes for abiotic or biotic stress tolerance, gene editing, as well as proteomic and metabolomics techniques bearing biotechnological potential for alfalfa improvement.
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Affiliation(s)
| | | | | | | | | | | | | | - Jozef Šamaj
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Olomouc, Czechia
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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.
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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
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Dubey S, Shri M, Gupta A, Rani V, Chakrabarty D. Toxicity and detoxification of heavy metals during plant growth and metabolism. ENVIRONMENTAL CHEMISTRY LETTERS 2018; 16:1169-1192. [DOI: 10.1007/s10311-018-0741-8] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 04/19/2018] [Indexed: 06/27/2023]
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Fang C, Zhang P, Jian X, Chen W, Lin H, Li Y, Lin W. Overexpression of Lsi1 in cold-sensitive rice mediates transcriptional regulatory networks and enhances resistance to chilling stress. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 262:115-126. [PMID: 28716407 DOI: 10.1016/j.plantsci.2017.06.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Revised: 05/21/2017] [Accepted: 06/02/2017] [Indexed: 05/21/2023]
Abstract
Frequent cold spells in late spring can damage early rice seedlings. However, overexpression of the silicon-uptake gene Lsi1 (Lsi1-OX) in cold-sensitive rice (Oryza sativa L., accession: Dular) notably enhances its chilling resistance. In this study, we found that continual chilling led to chlorophyll and RNA degradation in wild-type Dular leaves, whereas leaves from a Lsi1-OX line exhibited no obvious changes. A comparison of the global mRNA expression between the two rice lines showed that genes encoding photosynthesis-antenna proteins were downregulated and those encoding the proteasome were upregulated in the wild-type organism. Moreover, the differential responses of the two rice lines to chilling stress were found to correlate with the transcription factor OsWRKY53, which was predicted target of the respective microRNA (miRNA) novel-m0586-5p. In addition, miRNAs that targeted genes involved in the process of reactive oxygen species (ROS) metabolism were differentially expressed in the two rice lines after chilling stress, when comparative analysis of the outcomes of RNA sequencing on the two rice lines. Our results suggest that when overexpressed Lsi1 in cold-sensitive rice, it possibility regulates the transcription factor OsWRKY53 in addition to the genes involved in the ROS metabolism, thus mediating resistance to chilling stress.
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Affiliation(s)
- Changxun Fang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 35002, PR China; Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou 35002, PR China
| | - Pengli Zhang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 35002, PR China; Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou 35002, PR China
| | - Xin Jian
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 35002, PR China; Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou 35002, PR China
| | - Weisi Chen
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 35002, PR China; Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou 35002, PR China
| | - Hongmei Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 35002, PR China; Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou 35002, PR China
| | - Yingzhe Li
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 35002, PR China; Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou 35002, PR China
| | - Wenxiong Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 35002, PR China; Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, PR China; Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou 35002, PR China.
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Arshad M, Feyissa BA, Amyot L, Aung B, Hannoufa A. MicroRNA156 improves drought stress tolerance in alfalfa (Medicago sativa) by silencing SPL13. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 258:122-136. [PMID: 28330556 DOI: 10.1016/j.plantsci.2017.01.018] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 01/26/2017] [Accepted: 01/30/2017] [Indexed: 05/20/2023]
Abstract
Alfalfa (Medicago sativa) is an important forage crop that is often grown in areas that frequently experience drought and water shortage. MicroRNA156 (miR156) is an emerging tool for improving various traits in plants. We tested the role of miR156d in drought response of alfalfa, and observed a significant improvement in drought tolerance of miR156 overexpression (miR156OE) alfalfa genotypes compared to the wild type control (WT). In addition to higher survival and reduced water loss, miR156OE genotypes also maintained higher stomatal conductance compared to WT during drought stress. Furthermore, we observed an enhanced accumulation of compatible solute (proline) and increased levels of abscisic acid (ABA) and antioxidants in miR156OE genotypes. Similarly, alfalfa plants with reduced expression of miR156-targeted SPL13 showed reduced water loss and enhanced stomatal conductance, chlorophyll content and photosynthetic assimilation. Several genes known to be involved in drought tolerance were differentially expressed in leaf and root of miR156 overexpression plants. Taken together, our findings reveal that miR156 improves drought tolerance in alfalfa at least partially by silencing SPL13.
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Affiliation(s)
- Muhammad Arshad
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario N5 V 4T3, Canada.
| | - Biruk A Feyissa
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario N5 V 4T3, Canada; Biology Department, University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada.
| | - Lisa Amyot
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario N5 V 4T3, Canada.
| | - Banyar Aung
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario N5 V 4T3, Canada.
| | - Abdelali Hannoufa
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario N5 V 4T3, Canada; Biology Department, University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada.
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Noman A, Aqeel M. miRNA-based heavy metal homeostasis and plant growth. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:10068-10082. [PMID: 28229383 DOI: 10.1007/s11356-017-8593-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 02/07/2017] [Indexed: 05/27/2023]
Abstract
Plants have been naturally gifted with mechanisms to adjust under very high or low nutrient concentrations. Heavy metal toxicity is considered as a major growth and yield-limiting factor for plants. This stress includes essential as well as non-essential metals. MicroRNAs (miRNAs) are known for mediating post-transcriptional regulation by cleaving transcripts or translational inhibition. It is commonly agreed that an extensive understanding of plant miRNAs will significantly help in the induction of tolerance against environmental stresses. With the introduction of the latest technology like next generation sequencing (NGS), a growing figure of miRNAs has been productively recognized in several plants for their diverse roles. These miRNAs are well-known modulators of plant responses to heavy metal (HM) stress. Data regarding metal-responsive miRNAs point out the vital role of plant miRNAs in supplementing metal detoxification by means of transcription factors (TF) or gene regulation. Acting as systemic signals, miRNAs also synchronize different physiological processes for plant responses to metal toxicities. In contrast to practicing techniques, using miRNA is a greatly helpful, pragmatic, and feasible approach. The earlier findings point towards miRNAs as a prospective target to engineer heavy metal tolerance in plants. Therefore, there is a need to augment our knowledge about the orchestrated functions of miRNAs during HM stress. We reviewed the deterministic significance of plant miRNAs in heavy metal tolerance and their role in mediating plant responses to HM toxicities. This review also summarized the topical developments by identification and validation of different metal stress-responsive miRNAs.
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Affiliation(s)
- Ali Noman
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, People's Republic of China.
| | - Muhammad Aqeel
- School of Life Sciences, Lanzhou University, Lanzhou, People's Republic of China
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Khan MN, Mobin M, Abbas ZK, AlMutairi KA, Siddiqui ZH. Role of nanomaterials in plants under challenging environments. PLANT PHYSIOLOGY AND BIOCHEMISTRY 2017; 110:194-209. [PMID: 0 DOI: 10.1016/j.plaphy.2016.05.038] [Citation(s) in RCA: 155] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Revised: 05/22/2016] [Accepted: 05/26/2016] [Indexed: 05/21/2023]
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Wu X, Ning F, Hu X, Wang W. Genetic Modification for Improving Seed Vigor Is Transitioning from Model Plants to Crop Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:8. [PMID: 28149305 PMCID: PMC5241287 DOI: 10.3389/fpls.2017.00008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 01/03/2017] [Indexed: 05/09/2023]
Abstract
Although seed vigor is a complex physiological trait controlled by quantitative trait loci, technological advances in the laboratory are being translated into applications for enhancing seed vigor in crop plants. In this article, we summarize and discuss pioneering work in the genetic modification of seed vigor, especially through the over-expression of protein L-isoaspartyl methyltransferase (PIMT, EC 2.1.1.77) in seeds. The impressive success in improving rice seed vigor through the over-expression of PIMT provides a valuable reference for engineering high-vigor seeds for crop production. In recent decades, numerous genes/proteins associated with seed vigor have been identified. It is hoped that such potential candidates may be used in the development of genetically edited crops for a high and stable yield potential in crop production. This possibility is very valuable in the context of a changing climate and increasing world population.
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Wen M, Xie M, He L, Wang Y, Shi S, Tang T. Expression Variations of miRNAs and mRNAs in Rice (Oryza sativa). Genome Biol Evol 2016; 8:3529-3544. [PMID: 27797952 PMCID: PMC5203789 DOI: 10.1093/gbe/evw252] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Differences in expression levels are an important source of phenotypic variation within and between populations. MicroRNAs (miRNAs) are key players in post-transcriptional gene regulation that are important for plant development and stress responses. We surveyed expression variation of miRNAs and mRNAs of six accessions from two rice subspecies Oryza sativa L. ssp. indica and Oryza sativa L. ssp. japonica using deep sequencing. While more than half (53.7%) of the mature miRNAs exhibit differential expression between grains and seedlings of rice, only 11.0% show expression differences between subspecies, with an additional 2.2% differentiated for the development-by-subspecies interaction. Expression variation is greater for lowly conserved miRNAs than highly conserved miRNAs, whereas the latter show stronger negative correlation with their targets in expression changes between subspecies. Using a permutation test, we identified 51 miRNA–mRNA pairs that correlate negatively or positively in expression level among cultivated rice. Genes involved in various metabolic processes and stress responses are enriched in the differentially expressed genes between rice indica and japonica subspecies. Our results indicate that stabilizing selection is the major force governing miRNA expression in cultivated rice, albeit positive selection may be responsible for much of the between-subspecies expression divergence.
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Affiliation(s)
- Ming Wen
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Munan Xie
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | | | - Yushuai Wang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Suhua Shi
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Tian Tang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
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Yadav A, Khan Y, Prasad M. Dehydration-responsive miRNAs in foxtail millet: genome-wide identification, characterization and expression profiling. PLANTA 2016; 243:749-66. [PMID: 26676987 DOI: 10.1007/s00425-015-2437-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 11/20/2015] [Indexed: 05/27/2023]
Abstract
A set of novel and known dehydration-responsive miRNAs have been identified in foxtail millet. These findings provide new insights into understanding the functional role of miRNAs and their respective targets in regulating plant response to dehydration stress. MicroRNAs perform significant regulatory roles in growth, development and stress response of plants. Though the miRNA-mediated gene regulatory networks under dehydration stress remain largely unexplored in plant including foxtail millet (Setaria italica), which is a natural abiotic stress tolerant crop. To find out the dehydration-responsive miRNAs at the global level, four small RNA libraries were constructed from control and dehydration stress treated seedlings of two foxtail millet cultivars showing contrasting tolerance behavior towards dehydration stress. Using Illumina sequencing technology, 55 known and 136 novel miRNAs were identified, representing 22 and 48 miRNA families, respectively. Eighteen known and 33 novel miRNAs were differentially expressed during dehydration stress. After the stress treatment, 32 dehydration-responsive miRNAs were up-regulated in tolerant cultivar and 22 miRNAs were down-regulated in sensitive cultivar, suggesting that miRNA-mediated molecular regulation might play important roles in providing contrasting characteristics to these cultivars. Predicted targets of identified miRNAs were found to encode various transcription factors and functional enzymes, indicating their involvement in broad spectrum regulatory functions and biological processes. Further, differential expression patterns of seven known miRNAs were validated by northern blot and expression of ten novel dehydration-responsive miRNAs were confirmed by SL-qRT PCR. Differential expression behavior of five miRNA-target genes was verified under dehydration stress treatment and two of them also validated by RLM RACE. Overall, the present study highlights the importance of dehydration stress-associated post-transcriptional regulation governed by miRNAs and their targets in a naturally stress-tolerant model crop.
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Affiliation(s)
- Amita Yadav
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110 067, India
| | - Yusuf Khan
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110 067, India
| | - Manoj Prasad
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110 067, India.
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Aung B, Gruber MY, Hannoufa A. The MicroRNA156 system: A tool in plant biotechnology. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2015. [DOI: 10.1016/j.bcab.2015.08.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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19
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Aung B, Gruber MY, Amyot L, Omari K, Bertrand A, Hannoufa A. MicroRNA156 as a promising tool for alfalfa improvement. PLANT BIOTECHNOLOGY JOURNAL 2015; 13:779-90. [PMID: 25532560 DOI: 10.1111/pbi.12308] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 10/17/2014] [Accepted: 11/04/2014] [Indexed: 05/20/2023]
Abstract
A precursor of miR156 (MsmiR156d) was cloned and overexpressed in alfalfa (Medicago sativa L.) as a means to enhance alfalfa biomass yield. Of the five predicted SPL genes encoded by the alfalfa genome, three (SPL6, SPL12 and SPL13) contain miR156 cleavage sites and their expression was down-regulated in transgenic alfalfa plants overexpressing miR156. These transgenic plants had reduced internode length and stem thickness, enhanced shoot branching, increased trichome density, a delay in flowering time and elevated biomass production. Minor effects on sugar, starch, lignin and cellulose contents were also observed. Moreover, transgenic alfalfa plants had increased root length, while nodulation was maintained. The multitude of traits affected by miR156 may be due to the network of genes regulated by the three target SPLs. Our results show that the miR156/SPL system has strong potential as a tool to substantially improve quality and yield traits in alfalfa.
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Affiliation(s)
- Banyar Aung
- Agriculture and Agri-Food Canada, London, ON, Canada
- Biology Department, Western University, London, ON, Canada
| | | | - Lisa Amyot
- Agriculture and Agri-Food Canada, London, ON, Canada
| | - Khaled Omari
- Agriculture and Agri-Food Canada, London, ON, Canada
| | | | - Abdelali Hannoufa
- Agriculture and Agri-Food Canada, London, ON, Canada
- Biology Department, Western University, London, ON, Canada
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Landes Highlights. Bioengineered 2014. [PMCID: PMC3489702 DOI: 10.4161/bioe.22656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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21
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Li Z, Zhou X. Small RNA biology: from fundamental studies to applications. SCIENCE CHINA. LIFE SCIENCES 2013; 56:1059-1062. [PMID: 23943246 DOI: 10.1007/s11427-013-4535-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 07/22/2013] [Indexed: 06/02/2023]
Affiliation(s)
- Zhenghe Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
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