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Gaude AA, Siqueira RH, Botelho SB, Jalmi SK. Epigenetic arsenal for stress mitigation in plants. Biochim Biophys Acta Gen Subj 2024; 1868:130620. [PMID: 38636616 DOI: 10.1016/j.bbagen.2024.130620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 02/23/2024] [Accepted: 04/15/2024] [Indexed: 04/20/2024]
Abstract
Plant's ability to perceive, respond to, and ultimately adapt to various stressors is a testament to their remarkable resilience. In response to stresses, plants activate a complex array of molecular and physiological mechanisms. These include the rapid activation of stress-responsive genes, the manufacturing of protective compounds, modulation of cellular processes and alterations in their growth and development patterns to enhance their chances of survival. Epigenetic mechanisms play a pivotal role in shaping the responses of plants to environmental stressors. This review explores the intricate interplay between epigenetic regulation and plant stress mitigation. We delve into the dynamic landscape of epigenetic modifications, highlighting their influence on gene expression and ultimately stress tolerance. This review assembles current research, shedding light on the promising strategies within plants' epigenetic arsenal to thrive amidst adverse conditions.
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Affiliation(s)
- Aishwarya Ashok Gaude
- Discipline of Botany, School of Biological Sciences and Biotechnology, Goa University, Goa 403206, India.
| | - Roxiette Heromina Siqueira
- Discipline of Botany, School of Biological Sciences and Biotechnology, Goa University, Goa 403206, India.
| | - Savia Bernadette Botelho
- Discipline of Botany, School of Biological Sciences and Biotechnology, Goa University, Goa 403206, India.
| | - Siddhi Kashinath Jalmi
- Discipline of Botany, School of Biological Sciences and Biotechnology, Goa University, Goa 403206, India.
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2
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Imaduwage I, Hewadikaram M. Predicted roles of long non-coding RNAs in abiotic stress tolerance responses of plants. MOLECULAR HORTICULTURE 2024; 4:20. [PMID: 38745264 PMCID: PMC11094901 DOI: 10.1186/s43897-024-00094-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 04/06/2024] [Indexed: 05/16/2024]
Abstract
The plant genome exhibits a significant amount of transcriptional activity, with most of the resulting transcripts lacking protein-coding potential. Non-coding RNAs play a pivotal role in the development and regulatory processes in plants. Long non-coding RNAs (lncRNAs), which exceed 200 nucleotides, may play a significant role in enhancing plant resilience to various abiotic stresses, such as excessive heat, drought, cold, and salinity. In addition, the exogenous application of chemicals, such as abscisic acid and salicylic acid, can augment plant defense responses against abiotic stress. While how lncRNAs play a role in abiotic stress tolerance is relatively well-studied in model plants, this review provides a comprehensive overview of the current understanding of this function in horticultural crop plants. It also delves into the potential role of lncRNAs in chemical priming of plants in order to acquire abiotic stress tolerance, although many limitations exist in proving lncRNA functionality under such conditions.
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Affiliation(s)
- Iuh Imaduwage
- Department of Biomedical Sciences, Faculty of Science, NSBM Green University, Pitipana, Homagama, Sri Lanka
| | - Madhavi Hewadikaram
- Department of Biomedical Sciences, Faculty of Science, NSBM Green University, Pitipana, Homagama, Sri Lanka.
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3
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Sharma M, Tisarum R, Kohli RK, Batish DR, Cha-Um S, Singh HP. Inroads into saline-alkaline stress response in plants: unravelling morphological, physiological, biochemical, and molecular mechanisms. PLANTA 2024; 259:130. [PMID: 38647733 DOI: 10.1007/s00425-024-04368-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 02/22/2024] [Indexed: 04/25/2024]
Abstract
MAIN CONCLUSION This article discusses the complex network of ion transporters, genes, microRNAs, and transcription factors that regulate crop tolerance to saline-alkaline stress. The framework aids scientists produce stress-tolerant crops for smart agriculture. Salinity and alkalinity are frequently coexisting abiotic limitations that have emerged as archetypal mediators of low yield in many semi-arid and arid regions throughout the world. Saline-alkaline stress, which occurs in an environment with high concentrations of salts and a high pH, negatively impacts plant metabolism to a greater extent than either stress alone. Of late, saline stress has been the focus of the majority of investigations, and saline-alkaline mixed studies are largely lacking. Therefore, a thorough understanding and integration of how plants and crops rewire metabolic pathways to repair damage caused by saline-alkaline stress is of particular interest. This review discusses the multitude of resistance mechanisms that plants develop to cope with saline-alkaline stress, including morphological and physiological adaptations as well as molecular regulation. We examine the role of various ion transporters, transcription factors (TFs), differentially expressed genes (DEGs), microRNAs (miRNAs), or quantitative trait loci (QTLs) activated under saline-alkaline stress in achieving opportunistic modes of growth, development, and survival. The review provides a background for understanding the transport of micronutrients, specifically iron (Fe), in conditions of iron deficiency produced by high pH. Additionally, it discusses the role of calcium in enhancing stress tolerance. The review highlights that to encourage biomolecular architects to reconsider molecular responses as auxiliary for developing tolerant crops and raising crop production, it is essential to (a) close the major gaps in our understanding of saline-alkaline resistance genes, (b) identify and take into account crop-specific responses, and (c) target stress-tolerant genes to specific crops.
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Affiliation(s)
- Mansi Sharma
- Department of Environment Studies, Panjab University, Chandigarh, 160 014, India
- Department of Environmental Sciences, Sharda School of Basic Sciences and Research, Sharda University, Greater Noida, 201310, Uttar Pradesh, India
| | - Rujira Tisarum
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Ravinder Kumar Kohli
- Department of Botany, Panjab University, Chandigarh, 160014, India
- Amity University, Mohali Campus, Sector 82A, Mohali, 140306, Punjab, India
| | - Daizy R Batish
- Department of Botany, Panjab University, Chandigarh, 160014, India
| | - Suriyan Cha-Um
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Harminder Pal Singh
- Department of Environment Studies, Panjab University, Chandigarh, 160 014, India.
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Hu Z, Chen J, Olatoye MO, Zhang H, Lin Z. Transcriptome-wide expression landscape and starch synthesis pathway co-expression network in sorghum. THE PLANT GENOME 2024:e20448. [PMID: 38602082 DOI: 10.1002/tpg2.20448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
The gene expression landscape across different tissues and developmental stages reflects their biological functions and evolutionary patterns. Integrative and comprehensive analyses of all transcriptomic data in an organism are instrumental to obtaining a comprehensive picture of gene expression landscape. Such studies are still very limited in sorghum, which limits the discovery of the genetic basis underlying complex agricultural traits in sorghum. We characterized the genome-wide expression landscape for sorghum using 873 RNA-sequencing (RNA-seq) datasets representing 19 tissues. Our integrative analysis of these RNA-seq data provides the most comprehensive transcriptomic atlas for sorghum, which will be valuable for the sorghum research community for functional characterizations of sorghum genes. Based on the transcriptome atlas, we identified 595 housekeeping genes (HKGs) and 2080 tissue-specific expression genes (TEGs) for the 19 tissues. We identified different gene features between HKGs and TEGs, and we found that HKGs have experienced stronger selective constraints than TEGs. Furthermore, we built a transcriptome-wide co-expression network (TW-CEN) comprising 35 modules with each module enriched in specific Gene Ontology terms. High-connectivity genes in TW-CEN tend to express at high levels while undergoing intensive selective pressure. We also built global and seed-preferential co-expression networks of starch synthesis pathways, which indicated that photosynthesis and microtubule-based movement play important roles in starch synthesis. The global transcriptome atlas of sorghum generated by this study provides an important functional genomics resource for trait discovery and insight into starch synthesis regulation in sorghum.
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Affiliation(s)
- Zhenbin Hu
- Department of Biology, Saint Louis University, Saint Louis, Missouri, USA
| | - Junhao Chen
- Department of Biology, Saint Louis University, Saint Louis, Missouri, USA
| | - Marcus O Olatoye
- USDA-ARS, Forage Seed and Cereal Research Unit, Prosser, Washington, USA
| | - Hengyou Zhang
- State Key Laboratory of Black Soils Conservation and Utilization, Key Laboratory of Soybean Molecular Design and Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Zhenguo Lin
- Department of Biology, Saint Louis University, Saint Louis, Missouri, USA
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5
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Gonzales LR, Blom S, Henriques R, Bachem CWB, Immink RGH. LncRNAs: the art of being influential without protein. TRENDS IN PLANT SCIENCE 2024:S1360-1385(24)00021-9. [PMID: 38368122 DOI: 10.1016/j.tplants.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 01/15/2024] [Accepted: 01/23/2024] [Indexed: 02/19/2024]
Abstract
The plant long noncoding (lnc)RNA field is on the brink of transitioning from large-scale identification of lncRNAs to their functional characterization. Due to the cross-kingdom conservation of interaction types and molecular functions, there is much to be learned from mammalian lncRNA research. Here, we discuss the different molecular processes involving lncRNAs from the regulation of chromatin to splicing. Furthermore, we discuss the lncRNA interactome, which includes proteins, other RNAs, and DNA. We explore and discuss how mammalian lncRNA functionalities could be reflected in similar pathways in plants and hypothesize that several breakthroughs in mammalian research could lead to the discovery of novel plant lncRNA molecular functions. Expanding our knowledge of the biological role of lncRNAs and their multiple applications paves the way for future agricultural applications.
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Affiliation(s)
| | - Suze Blom
- Laboratory of Molecular Biology, Wageningen University and Research, Wageningen, The Netherlands; Bioscience, Wageningen University and Research, Wageningen, The Netherlands
| | - Rossana Henriques
- School of Biological, Earth, and Environmental Sciences, University College Cork, Cork, Ireland; Environmental Research Institute, University College Cork, Cork, Ireland
| | - Christian W B Bachem
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands.
| | - Richard G H Immink
- Laboratory of Molecular Biology, Wageningen University and Research, Wageningen, The Netherlands; Bioscience, Wageningen University and Research, Wageningen, The Netherlands.
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6
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Magar ND, Shah P, Barbadikar KM, Bosamia TC, Madhav MS, Mangrauthia SK, Pandey MK, Sharma S, Shanker AK, Neeraja CN, Sundaram RM. Long non-coding RNA-mediated epigenetic response for abiotic stress tolerance in plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108165. [PMID: 38064899 DOI: 10.1016/j.plaphy.2023.108165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 10/30/2023] [Accepted: 11/02/2023] [Indexed: 02/15/2024]
Abstract
Plants perceive environmental fluctuations as stress and confront several stresses throughout their life cycle individually or in combination. Plants have evolved their sensing and signaling mechanisms to perceive and respond to a variety of stresses. Epigenetic regulation plays a critical role in the regulation of genes, spatiotemporal expression of genes under stress conditions and imparts a stress memory to encounter future stress responses. It is quintessential to integrate our understanding of genetics and epigenetics to maintain plant fitness, achieve desired genetic gains with no trade-offs, and durable long-term stress tolerance. The long non-coding RNA >200 nts having no coding potential (or very low) play several roles in epigenetic memory, contributing to the regulation of gene expression and the maintenance of cellular identity which include chromatin remodeling, imprinting (dosage compensation), stable silencing, facilitating nuclear organization, regulation of enhancer-promoter interactions, response to environmental signals and epigenetic switching. The lncRNAs are involved in a myriad of stress responses by activation or repression of target genes and hence are potential candidates for deploying in climate-resilient breeding programs. This review puts forward the significant roles of long non-coding RNA as an epigenetic response during abiotic stresses in plants and the prospects of deploying lncRNAs for designing climate-resilient plants.
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Affiliation(s)
- Nakul D Magar
- Biotechnology Section, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India; Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250004, India
| | - Priya Shah
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, 502324, India
| | - Kalyani M Barbadikar
- Biotechnology Section, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India.
| | - Tejas C Bosamia
- Plant Omics Division, CSIR-Central Salt and Marine Chemicals Research Institute, Gujarat, 364002, India
| | - M Sheshu Madhav
- Biotechnology Section, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India
| | | | - Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, 502324, India
| | - Shailendra Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250004, India
| | - Arun K Shanker
- Plant Physiology, ICAR-Central Research Institute for Dryland Agriculture, Hyderabad, 500059, India
| | - C N Neeraja
- Biotechnology Section, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India
| | - R M Sundaram
- Biotechnology Section, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India
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Zheng H, Dang Y, Sui N. Sorghum: A Multipurpose Crop. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:17570-17583. [PMID: 37933850 DOI: 10.1021/acs.jafc.3c04942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Sorghum (Sorghum bicolor L.) is one of the top five cereal crops in the world in terms of production and planting area and is widely grown in areas with severe abiotic stresses such as drought and saline-alkali land due to its excellent stress resistance. Moreover, sorghum is a rare multipurpose crop that can be classified into grain sorghum, energy sorghum, and silage sorghum according to its domestication direction and utilization traits, endowing it with broad breeding and economic value. In this review, we mainly discuss the latest research progress and regulatory genes of agronomic traits of sorghum as a grain, energy, and silage crop, as well as the future improvement direction of multipurpose sorghum. We also emphasize the feasibility of cultivating multipurpose sorghum through genetic engineering methods by exploring potential targets using wild sorghum germplasm and genetic resources, as well as genomic resources.
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Affiliation(s)
- Hongxiang Zheng
- Shandong Provincial Key Laboratory of Plant Stress, College of life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Yingying Dang
- Shandong Provincial Key Laboratory of Plant Stress, College of life Sciences, Shandong Normal University, Jinan, 250014, China
- Dongying Institute, Shandong Normal University, Dongying, 257000, China
| | - Na Sui
- Shandong Provincial Key Laboratory of Plant Stress, College of life Sciences, Shandong Normal University, Jinan, 250014, China
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8
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Rehman OU, Uzair M, Farooq MS, Saleem B, Attacha S, Attia KA, Farooq U, Fiaz S, El-Kallawy WH, Kimiko I, Khan MR. Comprehensive insights into the regulatory mechanisms of lncRNA in alkaline-salt stress tolerance in rice. Mol Biol Rep 2023; 50:7381-7392. [PMID: 37450076 DOI: 10.1007/s11033-023-08648-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 06/27/2023] [Indexed: 07/18/2023]
Abstract
BACKGROUND Alkaline-salt is one of the abiotic stresses that slows plant growth and developmental processes and threatens crop yield. Long non-coding RNAs (lncRNAs) are endogenous RNA found in plants that engage in a variety of cellular functions and stress responses. METHOD lncRNAs act as competing endogenous RNAs (ceRNA) and constitute a new set of gene control. The precise regulatory mechanism by which lncRNAs function as ceRNAs in response to alkaline-salt stress remains unclear. We identified alkaline-salt responsive lncRNAs using transcriptome-wide analysis of two varieties including alkaline-salt tolerant [WD20342 (WD)] and alkaline-salt sensitive [Caidao (CD)] rice cultivar under control and alkaline-salt stress treated [WD20342 (WDT, and Caidao (CDT)] conditions. RESULTS Investigating the competitive relationships between mRNAs and lncRNAs, we next built a ceRNA network involving lncRNAs based on the ceRNA hypothesis. Expression profiles revealed that a total of 65, 34, and 1549 differentially expressed (DE) lncRNAs, miRNAs, and mRNAs were identified in alkaline-salt tolerant WD (Control) vs. WDT (Treated). Similarly, 75 DE-lncRNAs, 34 DE-miRNAs, and 1725 DE-mRNAs (including up-regulated and down-regulated) were identified in alkaline-salt sensitive CD (Control) vs. CDT (Treated), respectively. An alkaline-salt stress ceRNA network discovered 321 lncRNA-miRNA-mRNA triplets in CD and CDT, with 32 lncRNAs, 121 miRNAs, and 111 mRNAs. Likewise, 217 lncRNA-miRNA-mRNA triplets in WD and WDT revealed the NONOSAT000455-osa_miR5809b-LOC_Os11g01210 triplet with the highest degree as a hub node with the most significant positive correlation in alkaline-salt stress response. CONCLUSION The results of our investigation indicate that osa-miR5809b is dysregulated and plays a part in regulating the defense response of rice against alkaline-salt stress. Our study highlights the regulatory functions of lncRNAs acting as ceRNAs in the mechanisms underlying alkaline-salt resistance in rice.
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Affiliation(s)
- Obaid Ur Rehman
- Food Science and Biological Engineering, Jiangsu University, Zhenjiang, Jiangsu, China
- National Institute for Genomics and Advanced Biotechnology, Park Road, Islamabad, 45500, Pakistan
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology, Park Road, Islamabad, 45500, Pakistan.
| | - Muhammad Shahbaz Farooq
- Food Science and Biological Engineering, Jiangsu University, Zhenjiang, Jiangsu, China
- National Institute for Genomics and Advanced Biotechnology, Park Road, Islamabad, 45500, Pakistan
| | - Bilal Saleem
- National Institute for Genomics and Advanced Biotechnology, Park Road, Islamabad, 45500, Pakistan
| | - Safira Attacha
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture, Peshawar, Pakistan
| | - Kotb A Attia
- Department of Biochemistry, Science College, King Saud University, POX, Riyadh, 2455-11451, Saudi Arabia.
| | - Umer Farooq
- National Institute for Genomics and Advanced Biotechnology, Park Road, Islamabad, 45500, Pakistan
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, 22620, Pakistan
| | - Wael H El-Kallawy
- Agriculture Research Center, (ARC), Rice Research and Training Center, (RRTC) Sakha, Field Crop Research Institute, Sakha, Egypt
| | - Itoh Kimiko
- Institute of Science and Technology, Niigata University, Ikarashi-2, Nishi-ku, Niigata, 950-2181, Japan
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology, Park Road, Islamabad, 45500, Pakistan.
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Tu M, Du C, Yu B, Wang G, Deng Y, Wang Y, Chen M, Chang J, Yang G, He G, Xiong Z, Li Y. Current advances in the molecular regulation of abiotic stress tolerance in sorghum via transcriptomic, proteomic, and metabolomic approaches. FRONTIERS IN PLANT SCIENCE 2023; 14:1147328. [PMID: 37235010 PMCID: PMC10206308 DOI: 10.3389/fpls.2023.1147328] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023]
Abstract
Sorghum (Sorghum bicolor L. Moench), a monocot C4 crop, is an important staple crop for many countries in arid and semi-arid regions worldwide. Because sorghum has outstanding tolerance and adaptability to a variety of abiotic stresses, including drought, salt, and alkaline, and heavy metal stressors, it is valuable research material for better understanding the molecular mechanisms of stress tolerance in crops and for mining new genes for their genetic improvement of abiotic stress tolerance. Here, we compile recent progress achieved using physiological, transcriptome, proteome, and metabolome approaches; discuss the similarities and differences in how sorghum responds to differing stresses; and summarize the candidate genes involved in the process of responding to and regulating abiotic stresses. More importantly, we exemplify the differences between combined stresses and a single stress, emphasizing the necessity to strengthen future studies regarding the molecular responses and mechanisms of combined abiotic stresses, which has greater practical significance for food security. Our review lays a foundation for future functional studies of stress-tolerance-related genes and provides new insights into the molecular breeding of stress-tolerant sorghum genotypes, as well as listing a catalog of candidate genes for improving the stress tolerance for other key monocot crops, such as maize, rice, and sugarcane.
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Affiliation(s)
- Min Tu
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Canghao Du
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Boju Yu
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Guoli Wang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yanbin Deng
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yuesheng Wang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Mingjie Chen
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Junli Chang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Guangxiao Yang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Guangyuan He
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Zhiyong Xiong
- Laboratory of Forage and Endemic Crop Biology (Inner Mongolia University), Ministry of Education, School of Life Sciences, Hohhot, China
| | - Yin Li
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
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Li L, Zhou B, Liu D, Wu H, Shi Q, Lin S, Yao W. Transcriptomic Complexity of Culm Growth and Development in Different Types of Moso Bamboo. Int J Mol Sci 2023; 24:ijms24087425. [PMID: 37108588 PMCID: PMC10138756 DOI: 10.3390/ijms24087425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/03/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Moso bamboo is capable of both sexual and asexual reproduction during natural growth, resulting in four distinct types of culms: the bamboo shoot-culm, the seedling stem, the leptomorph rhizome, and a long-ignored culm-the outward-rhizome. Sometimes, when the outward rhizomes break through the soil, they continue to grow longitudinally and develop into a new individual. However, the roles of alternative transcription start sites (aTSS) or termination sites (aTTS) as well as alternative splicing (AS) have not been comprehensively studied for their development. To re-annotate the moso bamboo genome and identify genome-wide aTSS, aTTS, and AS in growing culms, we utilized single-molecule long-read sequencing technology. In total, 169,433 non-redundant isoforms and 14,840 new gene loci were identified. Among 1311 lncRNAs, most of which showed a positive correlation with their target mRNAs, one-third of these IncRNAs were preferentially expressed in winter bamboo shoots. In addition, the predominant AS type observed in moso bamboo was intron retention, while aTSS and aTTS events occurred more frequently than AS. Notably, most genes with AS events were also accompanied by aTSS and aTTS events. Outward rhizome growth in moso bamboo was associated with a significant increase in intron retention, possibly due to changes in the growth environment. As different types of moso bamboo culms grow and develop, a significant number of isoforms undergo changes in their conserved domains due to the regulation of aTSS, aTTS, and AS. As a result, these isoforms may play different roles than their original functions. These isoforms then performed different functions from their original roles, contributing to the transcriptomic complexity of moso bamboo. Overall, this study provided a comprehensive overview of the transcriptomic changes underlying different types of moso bamboo culm growth and development.
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Affiliation(s)
- Long Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
| | - Binao Zhou
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
| | - Dong Liu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
| | - Hongyu Wu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
| | - Qianqian Shi
- College of Landscape Architecture and Art, Northwest A&F University, Xianyang 712100, China
| | - Shuyan Lin
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
| | - Wenjing Yao
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
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11
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Liu J, Wu Y, Dong G, Zhu G, Zhou G. Progress of Research on the Physiology and Molecular Regulation of Sorghum Growth under Salt Stress by Gibberellin. Int J Mol Sci 2023; 24:ijms24076777. [PMID: 37047750 PMCID: PMC10094886 DOI: 10.3390/ijms24076777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 03/30/2023] [Accepted: 04/02/2023] [Indexed: 04/14/2023] Open
Abstract
Plant growth often encounters diverse abiotic stresses. As a global resource-based ecological problem, salinity is widely distributed and one of the major abiotic stresses affecting crop yields worldwide. Sorghum, a cereal crop with medium salt tolerance and great value for the development and utilization of salted soils, is an important source of food, brewing, energy, and forage production. However, in soils with high salt concentrations, sorghum experiences low emergence and suppressed metabolism. It has been demonstrated that the effects of salt stress on germination and seedling growth can be effectively mitigated to a certain extent by the exogenous amendment of hormonal gibberellin (GA). At present, most of the studies on sorghum salt tolerance at home and abroad focus on morphological and physiological levels, including the transcriptome analysis of the exogenous hormone on sorghum salt stress tolerance, the salt tolerance metabolism pathway, and the mining of key salt tolerance regulation genes. The high-throughput sequencing technology is increasingly widely used in the study of crop resistance, which is of great significance to the study of plant resistance gene excavation and mechanism. In this study, we aimed to review the effects of the exogenous hormone GA on leaf morphological traits of sorghum seedlings and further analyze the physiological response of sorghum seedling leaves and the regulation of sorghum growth and development. This review not only focuses on the role of GA but also explores the signal transduction pathways of GA and the performance of their responsive genes under salt stress, thus helping to further clarify the mechanism of regulating growth and production under salt stress. This will serve as a reference for the molecular discovery of key genes related to salt stress and the development of new sorghum varieties.
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Affiliation(s)
- Jiao Liu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Yanqing Wu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Guichun Dong
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Guanglong Zhu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Guisheng Zhou
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
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12
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Cui J, Ren G, Bai Y, Gao Y, Yang P, Chang J. Genome-wide identification and expression analysis of the U-box E3 ubiquitin ligase gene family related to salt tolerance in sorghum ( Sorghum bicolor L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1141617. [PMID: 37008506 PMCID: PMC10063820 DOI: 10.3389/fpls.2023.1141617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 03/01/2023] [Indexed: 06/19/2023]
Abstract
Plant U-box (PUB) E3 ubiquitin ligases play essential roles in many biological processes and stress responses, but little is known about their functions in sorghum (Sorghum bicolor L.). In the present study, 59 SbPUB genes were identified in the sorghum genome. Based on the phylogenetic analysis, the 59 SbPUB genes were clustered into five groups, which were also supported by the conserved motifs and structures of these genes. SbPUB genes were found to be unevenly distributed on the 10 chromosomes of sorghum. Most PUB genes (16) were found on chromosome 4, but there were no PUB genes on chromosome 5. Analysis of cis-acting elements showed that SbPUB genes were involved in many important biological processes, particularly in response to salt stress. From proteomic and transcriptomic data, we found that several SbPUB genes had diverse expressions under different salt treatments. To verify the expression of SbPUBs, qRT-PCR analyses also were conducted under salt stress, and the result was consistent with the expression analysis. Furthermore, 12 SbPUB genes were found to contain MYB-related elements, which are important regulators of flavonoid biosynthesis. These results, which were consistent with our previous multi-omics analysis of sorghum salt stress, laid a solid foundation for further mechanistic study of salt tolerance in sorghum. Our study showed that PUB genes play a crucial role in regulating salt stress, and might serve as promising targets for the breeding of salt-tolerant sorghum in the future.
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Affiliation(s)
- Jianghui Cui
- College of Agronomy, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Germplasm Resources of Education Ministry, Baoding, China
| | - Genzeng Ren
- College of Agronomy, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Germplasm Resources of Education Ministry, Baoding, China
| | - Yuzhe Bai
- College of Agronomy, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Germplasm Resources of Education Ministry, Baoding, China
| | - Yukun Gao
- College of Agronomy, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Germplasm Resources of Education Ministry, Baoding, China
| | - Puyuan Yang
- College of Agronomy, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Germplasm Resources of Education Ministry, Baoding, China
| | - Jinhua Chang
- College of Agronomy, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Germplasm Resources of Education Ministry, Baoding, China
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13
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Long Non-Coding RNAs of Plants in Response to Abiotic Stresses and Their Regulating Roles in Promoting Environmental Adaption. Cells 2023; 12:cells12050729. [PMID: 36899864 PMCID: PMC10001313 DOI: 10.3390/cells12050729] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/10/2023] [Accepted: 02/21/2023] [Indexed: 03/03/2023] Open
Abstract
Abiotic stresses triggered by climate change and human activity cause substantial agricultural and environmental problems which hamper plant growth. Plants have evolved sophisticated mechanisms in response to abiotic stresses, such as stress perception, epigenetic modification, and regulation of transcription and translation. Over the past decade, a large body of literature has revealed the various regulatory roles of long non-coding RNAs (lncRNAs) in the plant response to abiotic stresses and their irreplaceable functions in environmental adaptation. LncRNAs are recognized as a class of ncRNAs that are longer than 200 nucleotides, influencing a variety of biological processes. In this review, we mainly focused on the recent progress of plant lncRNAs, outlining their features, evolution, and functions of plant lncRNAs in response to drought, low or high temperature, salt, and heavy metal stress. The approaches to characterize the function of lncRNAs and the mechanisms of how they regulate plant responses to abiotic stresses were further reviewed. Moreover, we discuss the accumulating discoveries regarding the biological functions of lncRNAs on plant stress memory as well. The present review provides updated information and directions for us to characterize the potential functions of lncRNAs in abiotic stresses in the future.
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14
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Patra GK, Gupta D, Rout GR, Panda SK. Role of long non coding RNA in plants under abiotic and biotic stresses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 194:96-110. [PMID: 36399914 DOI: 10.1016/j.plaphy.2022.10.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 10/28/2022] [Accepted: 10/31/2022] [Indexed: 06/16/2023]
Abstract
Evolutionary processes have evolved plants to cope with several different natural stresses. Basic physiological activities of crop plants are significantly harmed by these stresses, reducing productivity and eventually leading to death. The recent advancements in high-throughput sequencing of transcriptome and expression profiling with NGS techniques lead to the innovation of various RNAs which do not code for proteins, more specifically long non-coding RNAs (lncRNAs), undergirding regulate growth, development, and the plant defence mechanism transcriptionally under stress situations. LncRNAs are a diverse set of RNAs that play key roles in various biological processes at the level of transcription, post-transcription, and epigenetics. These are thought to serve crucial functions in plant immunity and response to changes in the environment. In plants, however, just a few lncRNAs have been functionally identified. In this review, we will address recent advancements in comprehending lncRNA regulatory functions, focusing on the expanding involvement of lncRNAs in modulating environmental stress responsiveness in plants.
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Affiliation(s)
- Gyanendra K Patra
- Department of Agriculture Biotechnology, Orissa University of Agriculture and Technology, Bhubaneswar, 751 003, Odisha, India
| | - Divya Gupta
- School of Life Sciences, Central University of Rajasthan, NH 8, Bandarsindri, Ajmer, 305817, Rajasthan, India
| | - Gyana Ranjan Rout
- Department of Agriculture Biotechnology, Orissa University of Agriculture and Technology, Bhubaneswar, 751 003, Odisha, India
| | - Sanjib Kumar Panda
- School of Life Sciences, Central University of Rajasthan, NH 8, Bandarsindri, Ajmer, 305817, Rajasthan, India.
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Wu Y, Liu J, Zhou G. Whole-transcriptome analyses of Sorghum leaves identify key mRNAs and ncRNAs associated with GA 3-mediated alleviation of salt stress. FRONTIERS IN PLANT SCIENCE 2022; 13:1071657. [PMID: 36531388 PMCID: PMC9754216 DOI: 10.3389/fpls.2022.1071657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 11/16/2022] [Indexed: 06/17/2023]
Abstract
Sorghum has recently attracted much attention for its tolerance in high salt environment. However, the effect and regulatory mechanism of the gibberellic acid (GA3)-mediated alleviation of salt stress in sorghum remains unclear. Herein, we reported that a GA3 concentration of 50 mg/L is optimal for sorghum ("Jitian 3") development under salt stress. We conducted a whole-transcriptome analysis between GA3-treated and control sorghum leaves under salt stress, and we identified 1002 differentially expressed (DE)-messenger RNAs (mRNAs), 81 DE-long non-coding RNAs (lncRNAs), 7 DE-circular RNAs (circRNAs), and 26 DE-microRNA (miRNAs) in sorghum following GA3 treatment. We also identified a majority of DE-mRNAs and non-coding RNAs (ncRNAs) targets that serve essential roles in phenylpropanoid biosynthesis and plant hormone networks. In addition, we generated a competitive endogenous RNA (ceRNA)-miRNA-target gene network, and 3 circRNAs (circRNA_2746, circRNA_6515, circRNA_5622), 4 lncRNAs (XR_002450182.1, XR_002452422.1, XR_002448510.1, XR_002448296.1) and 4 genes (LOC8056546, LOC8062245, LOC8061469, LOC8071960) probably act as valuable candidates for the regulation of the GA3-mediated alleviation of salt stress in sorghum. Our findings uncovered potential mRNA and non-coding RNAs that contribute to GA3 regulation, thus offering a basis for the future investigation of underlying mechanisms of salt stress in sorghum.
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Affiliation(s)
- Yanqing Wu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Jiao Liu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Guisheng Zhou
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, Jiangsu, China
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16
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Zhao Z, Zang S, Zou W, Pan YB, Yao W, You C, Que Y. Long Non-Coding RNAs: New Players in Plants. Int J Mol Sci 2022; 23:ijms23169301. [PMID: 36012566 PMCID: PMC9409372 DOI: 10.3390/ijms23169301] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/14/2022] [Accepted: 08/15/2022] [Indexed: 11/16/2022] Open
Abstract
During the process of growth and development, plants are prone to various biotic and abiotic stresses. They have evolved a variety of strategies to resist the adverse effects of these stresses. lncRNAs (long non-coding RNAs) are a type of less conserved RNA molecules of more than 200 nt (nucleotides) in length. lncRNAs do not code for any protein, but interact with DNA, RNA, and protein to affect transcriptional, posttranscriptional, and epigenetic modulation events. As a new regulatory element, lncRNAs play a critical role in coping with environmental pressure during plant growth and development. This article presents a comprehensive review on the types of plant lncRNAs, the role and mechanism of lncRNAs at different molecular levels, the coordination between lncRNA and miRNA (microRNA) in plant immune responses, the latest research progress of lncRNAs in plant growth and development, and their response to biotic and abiotic stresses. We conclude with a discussion on future direction for the elaboration of the function and mechanism of lncRNAs.
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Affiliation(s)
- Zhennan Zhao
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shoujian Zang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wenhui Zou
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yong-Bao Pan
- Sugarcane Research Unit, USDA-ARS, Houma, LA 70360, USA
| | - Wei Yao
- Guangxi Key Laboratory for Sugarcane Biology & State Key Laboratory for Conservation and Utilization of Agro Bioresources, Guangxi University, Nanning 530005, China
| | - Cuihuai You
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (C.Y.); (Y.Q.); Tel.: +86-591-8385-2547 (C.Y. & Y.Q.)
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (C.Y.); (Y.Q.); Tel.: +86-591-8385-2547 (C.Y. & Y.Q.)
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17
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Li N, Wang Z, Wang B, Wang J, Xu R, Yang T, Huang S, Wang H, Yu Q. Identification and Characterization of Long Non-coding RNA in Tomato Roots Under Salt Stress. FRONTIERS IN PLANT SCIENCE 2022; 13:834027. [PMID: 35865296 PMCID: PMC9295719 DOI: 10.3389/fpls.2022.834027] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
As one of the most important vegetable crops in the world, the production of tomatoes was restricted by salt stress. Therefore, it is of great interest to analyze the salt stress tolerance genes. As the non-coding RNAs (ncRNAs) with a length of more than 200 nucleotides, long non-coding RNAs (lncRNAs) lack the ability of protein-coding, but they can play crucial roles in plant development and response to abiotic stresses by regulating gene expression. Nevertheless, there are few studies on the roles of salt-induced lncRNAs in tomatoes. Therefore, we selected wild tomato Solanum pennellii (S. pennellii) and cultivated tomato M82 to be materials. By high-throughput sequencing, 1,044 putative lncRNAs were identified here. Among them, 154 and 137 lncRNAs were differentially expressed in M82 and S. pennellii, respectively. Through functional analysis of target genes of differentially expressed lncRNAs (DE-lncRNAs), some genes were found to respond positively to salt stress by participating in abscisic acid (ABA) signaling pathway, brassinosteroid (BR) signaling pathway, ethylene (ETH) signaling pathway, and anti-oxidation process. We also construct a salt-induced lncRNA-mRNA co-expression network to dissect the putative mechanisms of high salt tolerance in S. pennellii. We analyze the function of salt-induced lncRNAs in tomato roots at the genome-wide levels for the first time. These results will contribute to understanding the molecular mechanisms of salt tolerance in tomatoes from the perspective of lncRNAs.
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Affiliation(s)
- Ning Li
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
- Key Laboratory of Horticulture Crop Genomics and Genetic Improvement in Xinjiang, Urumqi, China
| | - Zhongyu Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Baike Wang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
- Key Laboratory of Horticulture Crop Genomics and Genetic Improvement in Xinjiang, Urumqi, China
| | - Juan Wang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
- Key Laboratory of Horticulture Crop Genomics and Genetic Improvement in Xinjiang, Urumqi, China
| | - Ruiqiang Xu
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
- Key Laboratory of Horticulture Crop Genomics and Genetic Improvement in Xinjiang, Urumqi, China
| | - Tao Yang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
- Key Laboratory of Horticulture Crop Genomics and Genetic Improvement in Xinjiang, Urumqi, China
| | - Shaoyong Huang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
- Key Laboratory of Horticulture Crop Genomics and Genetic Improvement in Xinjiang, Urumqi, China
| | - Huan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qinghui Yu
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
- Key Laboratory of Horticulture Crop Genomics and Genetic Improvement in Xinjiang, Urumqi, China
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18
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Xiao Q, Lin Y, Li H, Chen Y, Wei W, Li P, Chen L. Transcriptome sequencing reveals the differentially expressed lncRNAs and mRNAs in response to cold acclimation and cold stress in Pomacea canaliculata. BMC Genomics 2022; 23:382. [PMID: 35590244 PMCID: PMC9121591 DOI: 10.1186/s12864-022-08622-5] [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: 12/02/2021] [Accepted: 05/10/2022] [Indexed: 11/17/2022] Open
Abstract
Background Tolerance of low temperature has a significant impact on survival and expansion of invasive snail Pomacea canalicuata. Cold acclimation can enhance cold tolerance of Pomacea canalicuata. To elucidate the molecular mechanism of P. canaliculata’s responses to cold acclimation and cold stress, a high-throughput transcriptome analysis of P. canaliculata was performed, and gene expression following artificial cold acclimation and then cold stress at 0 °C for 24 h was compared using RNA sequencing. Results Using the Illumina platform, we obtained 151.59 G subreads. A total of 5,416 novel lncRNAs were identified, and 3166 differentially expressed mRNAs and 211 differentially expressed lncRNAs were screened with stringent thresholds. The potential antisense, cis and trans targets of lncRNAs were predicted. Kyoto Encyclopedia of Genes and Genomes enrichment analysis showed that many target genes were involved in proteasome, linoleic acid metabolism and retinol metabolism under cold acclimation. The lncRNA of P. canaliculata could participate in cold acclimation by regulating the expression of E3 ubiquitin protein ligase, 26S proteasome non-ATPase dependent regulation subunit, glutathione S-transferase, sodium/glucose cotransporter and cytochrome P450. Conclusions These results broaden our understanding of cold acclimation and cold stress associated lncRNAs and mRNAs, and provide new insights into lncRNA mediated regulation of P. canaliculata cold acclimation and cold stress response. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08622-5.
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Affiliation(s)
- Qi Xiao
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China.,Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Youfu Lin
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Hong Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Yu Chen
- College of Life Sciences, Chemistry and Chemical Engineering, Jiangsu Second Normal University, Nanjing, 210013, China
| | - Wei Wei
- College of Life Sciences, Chemistry and Chemical Engineering, Jiangsu Second Normal University, Nanjing, 210013, China
| | - Peng Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
| | - Lian Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China.
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19
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Sotta N, Chiba Y, Aoyama H, Takamatsu S, Suzuki T, Miwa K, Yamashita Y, Naito S, Fujiwara T. Translational Landscape of a C4 Plant, Sorghum bicolor, Under Normal and Sulfur-Deficient Conditions. PLANT & CELL PHYSIOLOGY 2022; 63:592-604. [PMID: 35166349 DOI: 10.1093/pcp/pcac023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/01/2022] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
Recent accumulation of genomic and transcriptomic information has facilitated genetic studies. Increasing evidence has demonstrated that translation is an important regulatory step, and the transcriptome does not necessarily reflect the profile of functional protein production. Deep sequencing of ribosome-protected mRNA fragments (ribosome profiling or Ribo-seq) has enabled genome-wide analysis of translation. Sorghum is a C4 cereal important not only as food but also as forage and a bioenergy resource. Its resistance to harsh environments has made it an agriculturally important research subject. Yet genome-wide translational profiles in sorghum are still missing. In this study, we took advantage of Ribo-seq and identified actively translated reading frames throughout the genome. We detected translation of 4,843 main open reading frames (ORFs) annotated in the sorghum reference genome version 3.1 and revealed a number of unannotated translational events. A comparison of the transcriptome and translatome between sorghums grown under normal and sulfur-deficient conditions revealed that gene expression is modulated independently at transcript and translation levels. Our study revealed the translational landscape of sorghum's response to sulfur and provides datasets that could serve as a fundamental resource to extend genetic research on sorghum, including studies on translational regulation.
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Affiliation(s)
- Naoyuki Sotta
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657 Japan
| | - Yukako Chiba
- Faculty of Science, Hokkaido University, Sapporo, 060-0810 Japan
- Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810 Japan
| | - Haruka Aoyama
- Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810 Japan
| | - Seidai Takamatsu
- Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810 Japan
| | - Takamasa Suzuki
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, Kasugai, 487-8501 Japan
| | - Kyoko Miwa
- Graduate School of Environmental Science, Hokkaido University, Sapporo, 060-0810 Japan
| | - Yui Yamashita
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589 Japan
| | - Satoshi Naito
- Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810 Japan
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589 Japan
| | - Toru Fujiwara
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657 Japan
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20
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Wu F, Chen Z, Zhang F, Zheng H, Li S, Gao Y, Yang J, Sui N. Identification and Transcriptome Analysis of Genes Related to Membrane Lipid Regulation in Sweet Sorghum under Salt Stress. Int J Mol Sci 2022; 23:ijms23105465. [PMID: 35628281 PMCID: PMC9141458 DOI: 10.3390/ijms23105465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/07/2022] [Accepted: 05/10/2022] [Indexed: 12/04/2022] Open
Abstract
Sweet sorghum has strong stress resistance and is considered a promising energy crop. In the present study, the effects of salt on the membrane lipid metabolism of two sweet sorghum inbred lines (salt-tolerant M-81E and salt-sensitive Roma) were analyzed. After treatment with 150 mM NaCl, higher levels of fresh weight and chlorophyll fluorescence, as well as lower levels of malondialdehyde (MDA) were found in salt-tolerant M-81E. Concomitantly, 702 and 1339 differentially expression genes (DEGs) in M-81E and Roma were identified in response to salt stress. We determined that most DEGs were related to glycerophospholipid metabolism, glycerolipid metabolism, and other membrane lipid metabolisms. Under NaCl treatment, the expression of the membrane-associated phospholipase A1 was down-regulated at the transcriptional level, along with an increased content of phosphatidylcholine (PC) in both cultivars. The inhibition of triacylglycerol (TAG) mobilization in M-81E delayed salt-induced leaf senescence. Furthermore, enhanced levels of glycerol-3-phosphate acyltransferase (GPAT) expression contributed to improved salt resistance in M-81E. The results of this study demonstrate membrane the role of lipid regulation in mediating salt-defensive responses in sweet sorghum and expand our understanding of the relationship between changes in membrane lipid content and salt resistance.
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21
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Singroha G, Kumar S, Gupta OP, Singh GP, Sharma P. Uncovering the Epigenetic Marks Involved in Mediating Salt Stress Tolerance in Plants. Front Genet 2022; 13:811732. [PMID: 35495170 PMCID: PMC9053670 DOI: 10.3389/fgene.2022.811732] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 03/15/2022] [Indexed: 12/29/2022] Open
Abstract
The toxic effects of salinity on agricultural productivity necessitate development of salt stress tolerance in food crops in order to meet the escalating demands. Plants use sophisticated epigenetic systems to fine-tune their responses to environmental cues. Epigenetics is the study of heritable, covalent modifications of DNA and histone proteins that regulate gene expression without altering the underlying nucleotide sequence and consequently modify the phenotype. Epigenetic processes such as covalent changes in DNA, histone modification, histone variants, and certain non-coding RNAs (ncRNA) influence chromatin architecture to regulate its accessibility to the transcriptional machinery. Under salt stress conditions, there is a high frequency of hypermethylation at promoter located CpG sites. Salt stress results in the accumulation of active histones marks like H3K9K14Ac and H3K4me3 and the downfall of repressive histone marks such as H3K9me2 and H3K27me3 on salt-tolerance genes. Similarly, the H2A.Z variant of H2A histone is reported to be down regulated under salt stress conditions. A thorough understanding of the plasticity provided by epigenetic regulation enables a modern approach to genetic modification of salt-resistant cultivars. In this review, we summarize recent developments in understanding the epigenetic mechanisms, particularly those that may play a governing role in the designing of climate smart crops in response to salt stress.
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Comparative Transcriptome Analysis of Two Sweet Sorghum Genotypes with Different Salt Tolerance Abilities to Reveal the Mechanism of Salt Tolerance. Int J Mol Sci 2022; 23:ijms23042272. [PMID: 35216389 PMCID: PMC8877675 DOI: 10.3390/ijms23042272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/09/2022] [Accepted: 02/12/2022] [Indexed: 12/13/2022] Open
Abstract
Sweet sorghum is a C4 crop that can be grown for silage forage, fiber, syrup and fuel production. It is generally considered a salt-tolerant plant. However, the salt tolerance ability varies among genotypes, and the mechanism is not well known. To further uncover the salt tolerance mechanism, we performed comparative transcriptome analysis with RNA samples in two sweet sorghum genotypes showing different salt tolerance abilities (salt-tolerant line RIO and salt-sensitive line SN005) upon salt treatment. These response processes mainly focused on secondary metabolism, hormone signaling and stress response. The expression pattern cluster analysis showed that RIO-specific response genes were significantly enriched in the categories related to secondary metabolic pathways. GO enrichment analysis indicated that RIO responded earlier than SN005 in the 2 h after treatment. In addition, we identified more transcription factors (TFs) in RIO than SN005 that were specifically expressed differently in the first 2 h of salt treatment, and the pattern of TF change was obviously different. These results indicate that an early response in secondary metabolism might be essential for salt tolerance in sweet sorghum. In conclusion, we found that an early response, especially in secondary metabolism and hormone signaling, might be essential for salt tolerance in sweet sorghum.
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Liu P, Zhang Y, Zou C, Yang C, Pan G, Ma L, Shen Y. Integrated analysis of long non-coding RNAs and mRNAs reveals the regulatory network of maize seedling root responding to salt stress. BMC Genomics 2022; 23:50. [PMID: 35026983 PMCID: PMC8756644 DOI: 10.1186/s12864-021-08286-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 12/29/2021] [Indexed: 01/10/2023] Open
Abstract
Background Long non-coding RNAs (lncRNAs) play important roles in response to abiotic stresses in plants, by acting as cis- or trans-acting regulators of protein-coding genes. As a widely cultivated crop worldwide, maize is sensitive to salt stress particularly at the seedling stage. However, it is unclear how the expressions of protein-coding genes are affected by non-coding RNAs in maize responding to salt tolerance. Results The whole transcriptome sequencing was employed to investigate the differential lncRNAs and target transcripts responding to salt stress between two maize inbred lines with contrasting salt tolerance. We developed a flexible, user-friendly, and modular RNA analysis workflow, which facilitated the identification of lncRNAs and novel mRNAs from whole transcriptome data. Using the workflow, 12,817 lncRNAs and 8,320 novel mRNAs in maize seedling roots were identified and characterized. A total of 742 lncRNAs and 7,835 mRNAs were identified as salt stress-responsive transcripts. Moreover, we obtained 41 cis- and 81 trans-target mRNA for 88 of the lncRNAs. Among these target transcripts, 11 belonged to 7 transcription factor (TF) families including bHLH, C2H2, Hap3/NF-YB, HAS, MYB, WD40, and WRKY. The above 8,577 salt stress-responsive transcripts were further classified into 28 modules by weighted gene co-expression network analysis. In the salt-tolerant module, we constructed an interaction network containing 79 nodes and 3081 edges, which included 5 lncRNAs, 18 TFs and 56 functional transcripts (FTs). As a trans-acting regulator, the lncRNA MSTRG.8888.1 affected the expressions of some salt tolerance-relative FTs, including protein-serine/threonine phosphatase 2C and galactinol synthase 1, by regulating the expression of the bHLH TF. Conclusions The contrasting genetic backgrounds of the two inbred lines generated considerable variations in the expression abundance of lncRNAs and protein-coding transcripts. In the co-expression networks responding to salt stress, some TFs were targeted by the lncRNAs, which further regulated the salt tolerance-related functional transcripts. We constructed a regulatory pathway of maize seedlings to salt stress, which was mediated by the hub lncRNA MSTRG.8888.1 and participated by the bHLH TF and its downstream target transcripts. Future work will be focused on the functional revelation of the regulatory pathway. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08286-7.
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Long Non-Coding RNAs as Emerging Regulators of Pathogen Response in Plants. Noncoding RNA 2022; 8:ncrna8010004. [PMID: 35076574 PMCID: PMC8788567 DOI: 10.3390/ncrna8010004] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/07/2022] [Accepted: 01/08/2022] [Indexed: 12/14/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are transcripts without protein-coding potential that contain more than 200 nucleotides that play important roles in plant survival in response to different stresses. They interact with molecules such as DNA, RNA, and protein, and play roles in the regulation of chromatin remodeling, RNA metabolism, and protein modification activities. These lncRNAs regulate the expression of their downstream targets through epigenetic changes, at the level of transcription and post-transcription. Emerging information from computational biology and functional characterization of some of them has revealed their diverse mechanisms of action and possible roles in biological processes such as flowering time, reproductive organ development, as well as biotic and abiotic stress responses. In this review, we have mainly focused on the role of lncRNAs in biotic stress response due to the limited availability of knowledge in this domain. We have discussed the available molecular mechanisms of certain known lncRNAs against specific pathogens. Further, considering that fungal, viral, and bacterial diseases are major factors in the global food crisis, we have highlighted the importance of lncRNAs against pathogen responses and the progress in plant research to develop a better understanding of their functions and molecular mechanisms.
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Ren G, Yang P, Cui J, Gao Y, Yin C, Bai Y, Zhao D, Chang J. Multiomics Analyses of Two Sorghum Cultivars Reveal the Molecular Mechanism of Salt Tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:886805. [PMID: 35677242 PMCID: PMC9168679 DOI: 10.3389/fpls.2022.886805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/29/2022] [Indexed: 05/14/2023]
Abstract
Sorghum [Sorghum bicolor (L.) Moench] is one of the most important cereal crops and contains many health-promoting substances. Sorghum has high tolerance to abiotic stress and contains a variety of flavonoids compounds. Flavonoids are produced by the phenylpropanoid pathway and performed a wide range of functions in plants resistance to biotic and abiotic stress. A multiomics analysis of two sorghum cultivars (HN and GZ) under different salt treatments time (0, 24, 48, and 72) was performed. A total of 45 genes, 58 secondary metabolites, and 246 proteins were recognized with significant differential abundances in different comparison models. The common differentially expressed genes (DEGs) were allocated to the "flavonoid biosynthesis" and "phenylpropanoid biosynthesis" pathways. The most enriched pathways of the common differentially accumulating metabolites (DAMs) were "flavonoid biosynthesis," followed by "phenylpropanoid biosynthesis" and "arginine and proline metabolism." The common differentially expressed proteins (DEPs) were mainly distributed in "phenylpropanoid biosynthesis," "biosynthesis of cofactors," and "RNA transport." Furthermore, considerable differences were observed in the accumulation of low molecular weight nonenzymatic antioxidants and the activity of antioxidant enzymes. Collectively, the results of our study support the idea that flavonoid biological pathways may play an important physiological role in the ability of sorghum to withstand salt stress.
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Affiliation(s)
- Genzeng Ren
- College of Agronomy, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, China
| | - Puyuan Yang
- College of Agronomy, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, China
| | - Jianghui Cui
- College of Agronomy, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, China
| | - Yukun Gao
- College of Agronomy, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, China
| | - Congpei Yin
- College of Agronomy, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, China
| | - Yuzhe Bai
- College of Agronomy, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, China
| | - Dongting Zhao
- College of Agronomy, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, China
| | - Jinhua Chang
- College of Agronomy, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, China
- *Correspondence: Jinhua Chang,
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26
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Regulatory long non-coding RNAs in root growth and development. Biochem Soc Trans 2021; 50:403-412. [PMID: 34940811 DOI: 10.1042/bst20210743] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 12/06/2021] [Accepted: 12/08/2021] [Indexed: 12/26/2022]
Abstract
As sessile organisms, plants have evolved sophisticated mechanisms of gene regulation to cope with changing environments. Among them, long non-coding RNAs (lncRNAs) are a class of RNAs regulating gene expression at both transcriptional and post-transcriptional levels. They are highly responsive to environmental cues or developmental processes and are generally involved in fine-tuning plant responses to these signals. Roots, in addition to anchoring the plant to the soil, allow it to absorb the major part of its mineral nutrients and water. Furthermore, roots directly sense environmental constraints such as mineral nutrient availability and abiotic or biotic stresses and dynamically adapt their growth and architecture. Here, we review the role of lncRNAs in the control of root growth and development. In particular, we highlight their action in fine-tuning primary root growth and the development of root lateral organs, such as lateral roots and symbiotic nodules. Lastly, we report their involvement in plant response to stresses and the regulation of nutrient assimilation and homeostasis, two processes leading to the modification of root architecture. LncRNAs could become interesting targets in plant breeding programs to subtly acclimate crops to coming environmental changes.
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Negi P, Mishra S, Ganapathi TR, Srivastava AK. Regulatory short RNAs: A decade's tale for manipulating salt tolerance in plants. PHYSIOLOGIA PLANTARUM 2021; 173:1535-1555. [PMID: 34227692 DOI: 10.1111/ppl.13492] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/25/2021] [Accepted: 06/29/2021] [Indexed: 06/13/2023]
Abstract
Salt stress is a globally increasing environmental detriment to crop growth and productivity. Exposure to salt stress evokes a complex medley of cellular signals, which rapidly reprogram transcriptional and metabolic networks to shape plant phenotype. To date, genetic engineering approaches were used with success to enhance salt tolerance; however, their performance is yet to be evaluated under realistic field conditions. Regulatory short non-coding RNAs (rsRNAs) are emerging as next-generation candidates for engineering salt tolerance in crops. In view of this, the present review provides a comprehensive analysis of a decade's worth of functional studies on non-coding RNAs involved in salt tolerance. Further, we have integrated this knowledge of rsRNA-mediated regulation with the current paradigm of salt tolerance to highlight two regulatory complexes (RCs) for regulating salt tolerance in plants. Finally, a knowledge-driven roadmap is proposed to judiciously utilize RC component(s) for enhancing salt tolerance in crops.
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Affiliation(s)
- Pooja Negi
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Shefali Mishra
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Thumballi Ramabhatta Ganapathi
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Ashish Kumar Srivastava
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
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Punia H, Tokas J, Mor VS, Bhuker A, Malik A, Singh N, Satpal, Alsahli AA, Hefft DI. Deciphering Reserve Mobilization, Antioxidant Potential, and Expression Analysis of Starch Synthesis in Sorghum Seedlings under Salt Stress. PLANTS (BASEL, SWITZERLAND) 2021; 10:2463. [PMID: 34834826 PMCID: PMC8623787 DOI: 10.3390/plants10112463] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 10/31/2021] [Accepted: 11/03/2021] [Indexed: 02/07/2023]
Abstract
Salt stress is one of the major constraints affecting plant growth and agricultural productivity worldwide. Sorghum is a valuable food source and a potential model for studying and better understanding the salt stress mechanics in the cereals and obtaining a more comprehensive knowledge of their cellular responses. Herein, we examined the effects of salinity on reserve mobilization, antioxidant potential, and expression analysis of starch synthesis genes. Our findings show that germination percentage is adversely affected by all salinity levels, more remarkably at 120 mM (36% reduction) and 140 mM NaCl (46% reduction) than in the control. Lipid peroxidation increased in salt-susceptible genotypes (PC-5: 2.88 and CSV 44F: 2.93 nmloe/g.FW), but not in tolerant genotypes. SSG 59-3 increased activities of α-amylase, and protease enzymes corroborated decreased starch and protein content, respectively. SSG 59-3 alleviated adverse effects of salinity by suppressing oxidative stress (H2O2) and stimulating enzymatic and non-enzymatic antioxidant activities (SOD, APX, CAT, POD, GR, and GPX), as well as protecting cell membrane integrity (MDA, electrolyte leakage). A significant increase (p ≤ 0.05) was also observed in SSG 59-3 with proline, ascorbic acid, and total carbohydrates. Among inorganic cations and anions, Na+, Cl-, and SO42- increased, whereas K+, Mg2+, and Ca2+ decreased significantly. SSG 59-3 had a less pronounced effect of excess Na+ ions on the gene expression of starch synthesis. Salinity also influenced Na+ ion efflux and maintained a lower cytosolic Na+/K+ ratio via concomitant upregulation of SbNHX-1 and SbVPPase-I ion transporter genes. Thus, we have highlighted that salinity physiologically and biochemically affect sorghum seedling growth. Based on these findings, we highlighted that SSG 59-3 performed better by retaining higher plant water status, antioxidant potential, and upregulation of ion transporter genes and starch synthesis, thereby alleviating stress, which may be augmented as genetic resources to establish sorghum cultivars with improved quality in saline soils.
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Affiliation(s)
- Himani Punia
- Department of Biochemistry, College of Basic Sciences & Humanities, CCS Haryana Agricultural University, Hisar 125 004, Haryana, India;
| | - Jayanti Tokas
- Department of Biochemistry, College of Basic Sciences & Humanities, CCS Haryana Agricultural University, Hisar 125 004, Haryana, India;
| | - Virender Singh Mor
- Department of Seed Science & Technology, College of Agriculture, CCS Haryana Agricultural University, Hisar 125 004, Haryana, India; (V.S.M.); (A.B.); (N.S.)
| | - Axay Bhuker
- Department of Seed Science & Technology, College of Agriculture, CCS Haryana Agricultural University, Hisar 125 004, Haryana, India; (V.S.M.); (A.B.); (N.S.)
| | - Anurag Malik
- Department of Seed Science & Technology, College of Agriculture, CCS Haryana Agricultural University, Hisar 125 004, Haryana, India; (V.S.M.); (A.B.); (N.S.)
| | - Nirmal Singh
- Department of Seed Science & Technology, College of Agriculture, CCS Haryana Agricultural University, Hisar 125 004, Haryana, India; (V.S.M.); (A.B.); (N.S.)
| | - Satpal
- Forage Section, Department of Genetics & Plant Breeding, College of Agriculture, CCS Haryana Agricultural University, Hisar 125 004, Haryana, India;
| | - Abdulaziz Abdullah Alsahli
- Botany and Microbiology Department, Faculty of Science, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Daniel Ingo Hefft
- Department of Food Sciences, University Centre Reaseheath, Reaseheath College, Nantwich CW5 6DF, UK;
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Kumar N, Bharadwaj C, Sahu S, Shiv A, Shrivastava AK, Reddy SPP, Soren KR, Patil BS, Pal M, Soni A, Roorkiwal M, Varshney RK. Genome-wide identification and functional prediction of salt- stress related long non-coding RNAs (lncRNAs) in chickpea ( Cicer arietinum L.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2605-2619. [PMID: 34916736 PMCID: PMC8639897 DOI: 10.1007/s12298-021-01093-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 10/06/2021] [Accepted: 10/19/2021] [Indexed: 05/14/2023]
Abstract
LncRNAs (long noncoding RNAs) are 200 bp length crucial RNA molecules, lacking coding potential and having important roles in regulating gene expression, particularly in response to abiotic stresses. In this study, we identified salt stress-induced lncRNAs in chickpea roots and predicted their intricate regulatory roles. A total of 3452 novel lncRNAs were identified to be distributed across all 08 chickpea chromosomes. On comparing salt-tolerant (ICCV 10, JG 11) and salt-sensitive cultivars (DCP 92-3, Pusa 256), 4446 differentially expressed lncRNAs were detected under various salt treatments. We predicted 3373 lncRNAs to be regulating their target genes in cis regulating manner and 80 unique lncRNAs were observed as interacting with 136 different miRNAs, as eTMs (endogenous target mimic) targets of miRNAs and implicated them in the regulatory network of salt stress response. Functional analysis of these lncRNA revealed their association in targeting salt stress response-related genes like potassium transporter, transporter family genes, serine/threonine-protein kinase, aquaporins like TIP1-2, PIP2-5 and transcription factors like, AP2, NAC, bZIP, ERF, MYB and WRKY. Furthermore, about 614 lncRNA-SSRs (simple sequence repeats) were identified as a new generation of molecular markers with higher efficiency and specificity in chickpea. Overall, these findings will pave the understanding of comprehensive functional role of potential lncRNAs, which can help in providing insight into the molecular mechanism of salt tolerance in chickpea. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01093-0.
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Affiliation(s)
- Neeraj Kumar
- Division of Genetics, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi 110012 India
| | - Chellapilla Bharadwaj
- Division of Genetics, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi 110012 India
| | - Sarika Sahu
- ICAR-Indian Agricultural Statistics Research Institute, Pusa, New Delhi 110012 India
| | - Aalok Shiv
- Division of Genetics, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi 110012 India
- Present Address: ICAR-Indian Institute of Sugarcane Research, Lucknow, 226002 India
| | | | | | - Khela Ram Soren
- ICAR-Indian Institute of Pulses Research, Kanpur, 282 004 India
| | | | - Madan Pal
- Division of Genetics, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi 110012 India
| | - Anjali Soni
- Division of Genetics, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi 110012 India
| | - Manish Roorkiwal
- Centre of Excellence in Genomics, ICRISAT, Hyderabad, 502324 India
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Fang X, Li W, Yuan H, Chen H, Bo C, Ma Q, Cai R. Mutation of ZmWRKY86 confers enhanced salt stress tolerance in maize. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 167:840-850. [PMID: 34534799 DOI: 10.1016/j.plaphy.2021.09.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 09/08/2021] [Accepted: 09/08/2021] [Indexed: 05/24/2023]
Abstract
As one of the largest families of transcription factors in plants, the WRKY proteins play crucial roles in plant growth and development, defense regulation and stress responses. In this research, ZmWRKY86 encoding a WRKY transcription factor was cloned from maize (Zea mays L.). ZmWRKY86 expression was up-regulated by salt stress. ZmWRKY86 is a nuclear protein and has no transcriptional activation ability in yeast. ZmWRKY86 can specifically bind to W-box (TTGACC), which was confirmed by electrophoretic mobility shift assay (EMSA) and dual-LUC experiments. As compared with control, the wrky86 mutants showed enhanced plant tolerance to salt stress with higher survival rate, catalase activity and K+ content, but lower malondialdehyde accumulation, relative electrical leakage level and Na+ content under salt-stress condition. Transcriptome and quantitative real-time PCR analyses indicated that the mutation of ZmWRKY86 led to significant changes in the expression of stress-related genes in maize. Further assays showed that ZmWRKY86 directly interacted with the promoter of two salt stress-related genes Zm00001d020840 and Zm00001d046813. In summary, we identified a WRKY transcription factor ZmWRKY86 that participates in salt stress regulation through controlling the expression of stress-related genes.
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Affiliation(s)
- Xiu Fang
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Wei Li
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Haotian Yuan
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Haowei Chen
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Chen Bo
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Qing Ma
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China; Engineering Research Center for Maize of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China.
| | - Ronghao Cai
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China; Engineering Research Center for Maize of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China.
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Kaur B, Sandhu KS, Kamal R, Kaur K, Singh J, Röder MS, Muqaddasi QH. Omics for the Improvement of Abiotic, Biotic, and Agronomic Traits in Major Cereal Crops: Applications, Challenges, and Prospects. PLANTS 2021; 10:plants10101989. [PMID: 34685799 PMCID: PMC8541486 DOI: 10.3390/plants10101989] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 12/22/2022]
Abstract
Omics technologies, namely genomics, transcriptomics, proteomics, metabolomics, and phenomics, are becoming an integral part of virtually every commercial cereal crop breeding program, as they provide substantial dividends per unit time in both pre-breeding and breeding phases. Continuous advances in omics assure time efficiency and cost benefits to improve cereal crops. This review provides a comprehensive overview of the established omics methods in five major cereals, namely rice, sorghum, maize, barley, and bread wheat. We cover the evolution of technologies in each omics section independently and concentrate on their use to improve economically important agronomic as well as biotic and abiotic stress-related traits. Advancements in the (1) identification, mapping, and sequencing of molecular/structural variants; (2) high-density transcriptomics data to study gene expression patterns; (3) global and targeted proteome profiling to study protein structure and interaction; (4) metabolomic profiling to quantify organ-level, small-density metabolites, and their composition; and (5) high-resolution, high-throughput, image-based phenomics approaches are surveyed in this review.
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Affiliation(s)
- Balwinder Kaur
- Everglades Research and Education Center, University of Florida, 3200 E. Palm Beach Rd., Belle Glade, FL 33430, USA;
| | - Karansher S. Sandhu
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99163, USA;
| | - Roop Kamal
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466 Stadt Seeland, Germany; (R.K.); or (M.S.R.)
| | - Kawalpreet Kaur
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada;
| | - Jagmohan Singh
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India;
| | - Marion S. Röder
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466 Stadt Seeland, Germany; (R.K.); or (M.S.R.)
| | - Quddoos H. Muqaddasi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466 Stadt Seeland, Germany; (R.K.); or (M.S.R.)
- Correspondence: or
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Zhang H, Jin J, Xu G, Li Z, Zhai N, Zheng Q, Lv H, Liu P, Jin L, Chen Q, Cao P, Zhou H. Reconstruction of the full-length transcriptome of cigar tobacco without a reference genome and characterization of anion channel/transporter transcripts. BMC PLANT BIOLOGY 2021; 21:299. [PMID: 34187357 PMCID: PMC8240255 DOI: 10.1186/s12870-021-03091-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 06/10/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Cigar wrapper leaves are the most important raw material of cigars. Studying the genomic information of cigar tobacco is conducive to improving cigar quality from the perspective of genetic breeding. However, no reference genome or full-length transcripts at the genome-wide scale have been reported for cigar tobacco. In particular, anion channels/transporters are of high interest for their potential application in regulating the chloride content of cigar tobacco growing on coastal lands, which usually results in relatively high Cl- accumulation, which is unfavorable. Here, the PacBio platform and NGS technology were combined to generate a full-length transcriptome of cigar tobacco used for cigar wrappers. RESULTS High-quality RNA isolated from the roots, leaves and stems of cigar tobacco were subjected to both the PacBio platform and NGS. From PacBio, a total of 11,652,432 subreads (19-Gb) were generated, with an average read length of 1,608 bp. After corrections were performed in conjunction with the NGS reads, we ultimately identified 1,695,064 open reading frames including 21,486 full-length ORFs and 7,342 genes encoding transcription factors from 55 TF families, together with 2,230 genes encoding long non-coding RNAs. Members of gene families related to anion channels/transporters, including members of the SLAC and CLC families, were identified and characterized. CONCLUSIONS The full-length transcriptome of cigar tobacco was obtained, annotated, and analyzed, providing a valuable genetic resource for future studies in cigar tobacco.
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Affiliation(s)
- Hui Zhang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, 450000 Zhengzhou, China
| | - Jingjing Jin
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, 450000 Zhengzhou, China
| | - Guoyun Xu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, 450000 Zhengzhou, China
| | - Zefeng Li
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, 450000 Zhengzhou, China
| | - Niu Zhai
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, 450000 Zhengzhou, China
| | - Qingxia Zheng
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, 450000 Zhengzhou, China
| | - Hongkun Lv
- Haikou Cigar Research Institute of China National Tobacco Corporation, Hainan Province 570000 Haikou, China
| | - Pingping Liu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, 450000 Zhengzhou, China
| | - Lifeng Jin
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, 450000 Zhengzhou, China
| | - Qiansi Chen
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, 450000 Zhengzhou, China
| | - Peijian Cao
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, 450000 Zhengzhou, China
| | - Huina Zhou
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, 450000 Zhengzhou, China
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Nath VS, Mishra AK, Awasthi P, Shrestha A, Matoušek J, Jakse J, Kocábek T, Khan A. Identification and characterization of long non-coding RNA and their response against citrus bark cracking viroid infection in Humulus lupulus. Genomics 2021; 113:2350-2364. [PMID: 34051324 DOI: 10.1016/j.ygeno.2021.05.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 04/22/2021] [Accepted: 05/25/2021] [Indexed: 02/06/2023]
Abstract
Long non-coding RNAs (lncRNAs) are a highly heterogeneous class of non-protein-encoding transcripts that play an essential regulatory role in diverse biological processes, including stress responses. The severe stunting disease caused by Citrus bark cracking viroid (CBCVd) poses a major threat to the production of Humulus lupulus (hop) plants. In this study, we systematically investigate the characteristics of the lncRNAs in hop and their role in CBCVd-infection using RNA-sequencing data. Following a stringent filtration criterion, a total of 3598 putative lncRNAs were identified with a high degree of certainty, of which 19% (684) of the lncRNAs were significantly differentially expressed (DE) in CBCVd-infected hop, which were predicted to be mainly involved in plant-pathogen interactions, kinase cascades, secondary metabolism and phytohormone signal transduction. Besides, several lncRNAs and CBCVd-responsive lncRNAs were identified as the precursor of microRNAs and predicted as endogenous target mimics (eTMs) for hop microRNAs involved in CBCVd-infection.
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Affiliation(s)
- Vishnu Sukumari Nath
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Ajay Kumar Mishra
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic.
| | - Praveen Awasthi
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Ankita Shrestha
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Jaroslav Matoušek
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Jernej Jakse
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Tomáš Kocábek
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Ahamed Khan
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic
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Meng X, Li A, Yu B, Li S. Interplay between miRNAs and lncRNAs: Mode of action and biological roles in plant development and stress adaptation. Comput Struct Biotechnol J 2021; 19:2567-2574. [PMID: 34025943 PMCID: PMC8114054 DOI: 10.1016/j.csbj.2021.04.062] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 04/24/2021] [Accepted: 04/24/2021] [Indexed: 11/28/2022] Open
Abstract
Plants employ sophisticated mechanisms to control developmental processes and to cope with environmental changes at transcriptional and post-transcriptional levels. MicroRNAs (miRNAs) and long noncoding RNAs (lncRNAs), two classes of endogenous noncoding RNAs, are key regulators of gene expression in plants. Recent studies have identified the interplay between miRNAs and lncRNAs as a novel regulatory layer of gene expression in plants. On one hand, miRNAs target lncRNAs for the production of phased small interfering RNAs (phasiRNAs). On the other hand, lncRNAs serve as origin of miRNAs or regulate the accumulation or activity of miRNAs at transcription and post-transcriptional levels. Theses lncRNA-miRNA interplays are crucial for plant development, physiology and responses to biotic and abiotic stresses. In this review, we summarize recent advances in the biological roles, interaction mechanisms and computational predication methods of the interplay between miRNAs and lncRNAs in plants.
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Affiliation(s)
- Xiangxiang Meng
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Aixia Li
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Bin Yu
- School of Biological Sciences & Center for Plant Science Innovation University of Nebraska-Lincoln, Lincoln, Nebraska 68588–0666, USA
| | - Shengjun Li
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
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Urquiaga MCDO, Thiebaut F, Hemerly AS, Ferreira PCG. From Trash to Luxury: The Potential Role of Plant LncRNA in DNA Methylation During Abiotic Stress. FRONTIERS IN PLANT SCIENCE 2021; 11:603246. [PMID: 33488652 PMCID: PMC7815527 DOI: 10.3389/fpls.2020.603246] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 12/07/2020] [Indexed: 05/27/2023]
Abstract
Remarkable progress has been made in elucidating important roles of plant non-coding RNAs. Among these RNAs, long noncoding RNAs (lncRNAs) have gained widespread attention, especially their role in plant environmental stress responses. LncRNAs act at different levels of gene expression regulation, and one of these mechanisms is by recruitment of DNA methyltransferases or demethylases to regulate the target gene transcription. In this mini-review, we highlight the function of lncRNAs, including their potential role in RNA-directed DNA Methylation (RdDM) silencing pathway and their potential function under abiotic stresses conditions. Moreover, we also present and discuss studies of lncRNAs in crops. Finally, we propose a path outlook for future research that may be important for plant breeding.
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Affiliation(s)
| | - Flávia Thiebaut
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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Long Non-Coding RNAs, the Dark Matter: An Emerging Regulatory Component in Plants. Int J Mol Sci 2020; 22:ijms22010086. [PMID: 33374835 PMCID: PMC7795044 DOI: 10.3390/ijms22010086] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/18/2020] [Accepted: 12/19/2020] [Indexed: 02/07/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are pervasive transcripts of longer than 200 nucleotides and indiscernible coding potential. lncRNAs are implicated as key regulatory molecules in various fundamental biological processes at transcriptional, post-transcriptional, and epigenetic levels. Advances in computational and experimental approaches have identified numerous lncRNAs in plants. lncRNAs have been found to act as prime mediators in plant growth, development, and tolerance to stresses. This review summarizes the current research status of lncRNAs in planta, their classification based on genomic context, their mechanism of action, and specific bioinformatics tools and resources for their identification and characterization. Our overarching goal is to summarize recent progress on understanding the regulatory role of lncRNAs in plant developmental processes such as flowering time, reproductive growth, and abiotic stresses. We also review the role of lncRNA in nutrient stress and the ability to improve biotic stress tolerance in plants. Given the pivotal role of lncRNAs in various biological processes, their functional characterization in agriculturally essential crop plants is crucial for bridging the gap between phenotype and genotype.
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Tu M, Li Y. Profiling Alternative 3' Untranslated Regions in Sorghum using RNA-seq Data. Front Genet 2020; 11:556749. [PMID: 33193635 PMCID: PMC7649775 DOI: 10.3389/fgene.2020.556749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 09/30/2020] [Indexed: 12/18/2022] Open
Abstract
Sorghum is an important crop widely used for food, feed, and fuel. Transcriptome-wide studies of 3′ untranslated regions (3′UTR) using regular RNA-seq remain scarce in sorghum, while transcriptomes have been characterized extensively using Illumina short-read sequencing platforms for many sorghum varieties under various conditions or developmental contexts. 3′UTR is a critical regulatory component of genes, controlling the translation, transport, and stability of messenger RNAs. In the present study, we profiled the alternative 3′UTRs at the transcriptome level in three genetically related but phenotypically contrasting lines of sorghum: Rio, BTx406, and R9188. A total of 1,197 transcripts with alternative 3′UTRs were detected using RNA-seq data. Their categorization identified 612 high-confidence alternative 3′UTRs. Importantly, the high-confidence alternative 3′UTR genes significantly overlapped with the genesets that are associated with RNA N6-methyladenosine (m6A) modification, suggesting a clear indication between alternative 3′UTR and m6A methylation in sorghum. Moreover, taking advantage of sorghum genetics, we provided evidence of genotype specificity of alternative 3′UTR usage. In summary, our work exemplifies a transcriptome-wide profiling of alternative 3′UTRs using regular RNA-seq data in non-model crops and gains insights into alternative 3′UTRs and their genotype specificity.
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Affiliation(s)
- Min Tu
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, United States
| | - Yin Li
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, United States
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