1
|
Aycan M, Nahar L, Baslam M, Mitsui T. Transgenerational plasticity in salinity tolerance of rice: unraveling non-genetic phenotypic modifications and environmental influences. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:5037-5053. [PMID: 38727615 DOI: 10.1093/jxb/erae211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 05/08/2024] [Indexed: 08/29/2024]
Abstract
Transgenerational plasticity in plants enables rapid adaptation to environmental changes, allowing organisms and their offspring to adapt to the environment without altering their underlying DNA. In this study, we investigated the transgenerational plasticity in salinity tolerance of rice plants using a reciprocal transplant experimental strategy. Our aim was to assess whether non-genetic environment-induced phenotypic modifications and transgenerational salinity affect the salinity tolerance of progeny while excluding nuclear genomic factors for two generations. Using salt-tolerant and salt-sensitive rice genotypes, we observed that the parentally salt-stressed salt-sensitive genotype displayed greater growth performance, photosynthetic activity, yield performance, and transcriptional responses than the parentally non-stressed salt-sensitive plants under salt stress conditions. Surprisingly, salt stress-exposed salt-tolerant progeny did not exhibit as much salinity tolerance as salt stress-exposed salt-sensitive progeny under salt stress. Our findings indicate that the phenotypes of offspring plants differed based on the environment experienced by their ancestors, resulting in heritable transgenerational phenotypic modifications in salt-sensitive genotypes via maternal effects. These results elucidated the mechanisms underlying transgenerational plasticity in salinity tolerance, providing valuable insights into how plants respond to changing environmental conditions.
Collapse
Affiliation(s)
- Murat Aycan
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan
| | - Lutfun Nahar
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan
- Department of Agricultural Botany, Sher-e-Bangla Agricultural University, Dhaka 1207, Bangladesh
| | - Marouane Baslam
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan
- GrowSmart, Seoul 03129, Republic of Korea
- Centre d'Agrobiotechnologie et Bioingénierie, Unité de Recherche labellisée CNRST (Centre AgroBio-tech-URL-CNRST-05), Université Cadi Ayyad, Marrakech, 40000, Morocco
- Laboratory of Agro-Food, Biotechnologies and Valorization of Plant Bioresources (AGROBIOVAL), Department of Biology, Faculty of Science Semlalia, Université Cadi Ayyad, Marrakech, 40000, Morocco
| | - Toshiaki Mitsui
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan
| |
Collapse
|
2
|
Aufiero G, Fruggiero C, D’Angelo D, D’Agostino N. Homoeologs in Allopolyploids: Navigating Redundancy as Both an Evolutionary Opportunity and a Technical Challenge-A Transcriptomics Perspective. Genes (Basel) 2024; 15:977. [PMID: 39202338 PMCID: PMC11353593 DOI: 10.3390/genes15080977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 07/22/2024] [Accepted: 07/23/2024] [Indexed: 09/03/2024] Open
Abstract
Allopolyploidy in plants involves the merging of two or more distinct parental genomes into a single nucleus, a significant evolutionary process in the plant kingdom. Transcriptomic analysis provides invaluable insights into allopolyploid plants by elucidating the fate of duplicated genes, revealing evolutionary novelties and uncovering their environmental adaptations. By examining gene expression profiles, scientists can discern how duplicated genes have evolved to acquire new functions or regulatory roles. This process often leads to the development of novel traits and adaptive strategies that allopolyploid plants leverage to thrive in diverse ecological niches. Understanding these molecular mechanisms not only enhances our appreciation of the genetic complexity underlying allopolyploidy but also underscores their importance in agriculture and ecosystem resilience. However, transcriptome profiling is challenging due to genomic redundancy, which is further complicated by the presence of multiple chromosomes sets and the variations among homoeologs and allelic genes. Prior to transcriptome analysis, sub-genome phasing and homoeology inference are essential for obtaining a comprehensive view of gene expression. This review aims to clarify the terminology in this field, identify the most challenging aspects of transcriptome analysis, explain their inherent difficulties, and suggest reliable analytic strategies. Furthermore, bulk RNA-seq is highlighted as a primary method for studying allopolyploid gene expression, focusing on critical steps like read mapping and normalization in differential gene expression analysis. This approach effectively captures gene expression from both parental genomes, facilitating a comprehensive analysis of their combined profiles. Its sensitivity in detecting low-abundance transcripts allows for subtle differences between parental genomes to be identified, crucial for understanding regulatory dynamics and gene expression balance in allopolyploids.
Collapse
Affiliation(s)
| | | | | | - Nunzio D’Agostino
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy; (G.A.); (C.F.); (D.D.)
| |
Collapse
|
3
|
Zhou L, Yang S, Chen C, Li M, Du Q, Wang J, Yin Y, Xiao H. CaCP15 Gene Negatively Regulates Salt and Osmotic Stress Responses in Capsicum annuum L. Genes (Basel) 2023; 14:1409. [PMID: 37510313 PMCID: PMC10379065 DOI: 10.3390/genes14071409] [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: 05/29/2023] [Revised: 07/02/2023] [Accepted: 07/05/2023] [Indexed: 07/30/2023] Open
Abstract
Salt and osmotic stress seriously restrict the growth, development, and productivity of horticultural crops in the greenhouse. The papain-like cysteine proteases (PLCPs) participate in multi-stress responses in plants. We previously demonstrated that salt and osmotic stress affect cysteine protease 15 of pepper (Capsicum annuum L.) (CaCP15); however, the role of CaCP15 in salt and osmotic stress responses is unknown. Here, the function of CaCP15 in regulating pepper salt and osmotic stress resistance was explored. Pepper plants were subjected to abiotic (sodium chloride, mannitol, salicylic acid, ethrel, methyl jasmonate, etc.) and biotic stress (Phytophthora capsici inoculation). The CaCP15 was silenced through the virus-induced gene silencing (VIGS) and transiently overexpressed in pepper plants. The full-length CaCP15 fragment is 1568 bp, with an open reading frame of 1032 bp, encoding a 343 amino acid protein. CaCP15 is a senescence-associated gene 12 (SAG12) subfamily member containing two highly conserved domains, Inhibitor 129 and Peptidase_C1. CaCP15 expression was the highest in the stems of pepper plants. The expression was induced by salicylic acid, ethrel, methyl jasmonate, and was infected by Phytophthora capsici inoculation. Furthermore, CaCP15 was upregulated under salt and osmotic stress, and CaCP15 silencing in pepper enhanced salt and mannitol stress resistance. Conversely, transient overexpression of CaCP15 increased the sensitivity to salt and osmotic stress by reducing the antioxidant enzyme activities and negatively regulating the stress-related genes. This study indicates that CaCP15 negatively regulates salt and osmotic stress resistance in pepper via the ROS-scavenging.
Collapse
Affiliation(s)
- Luyao Zhou
- Department of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
- Cash Crops Research Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Sizhen Yang
- Department of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Chunlin Chen
- Department of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Meng Li
- Department of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Qingjie Du
- Department of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Jiqing Wang
- Department of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Yanxu Yin
- Cash Crops Research Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Huaijuan Xiao
- Department of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| |
Collapse
|
4
|
Song Y, Zheng C, Li S, Chen J, Jiang M. Chitosan-Magnesium Oxide Nanoparticles Improve Salinity Tolerance in Rice ( Oryza sativa L.). ACS APPLIED MATERIALS & INTERFACES 2023; 15:20649-20660. [PMID: 37078774 DOI: 10.1021/acsami.3c00043] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
High-salinity (HS) stress is a global element restricting agricultural productivity. Rice is a significant food crop, but soil salinity has a detrimental impact on its yield and product quality. Nanoparticles (NPs) have been found as a mitigation method against different abiotic stresses, even HS stress. In this study, chitosan-magnesium oxide NPs (CMgO NPs) were used as a new method for rice plants to alleviate salt stress (200 mM NaCl). The results showed that 100 mg/L CMgO NPs greatly ameliorated salt stress by enhancing the root length by 37.47%, dry biomass by 32.86%, plant height by 35.20%, and tetrapyrrole biosynthesis in hydroponically cultured rice seedlings. The application of 100 mg/L CMgO NPs greatly alleviated salt-generated oxidative stress with induced activities of antioxidative enzymes, catalase by 67.21%, peroxidase by 88.01%, and superoxide dismutase by 81.19%, and decreased contents of malondialdehyde by 47.36% and H2O2 by 39.07% in rice leaves. The investigation of ion content in rice leaves revealed that rice treated with 100 mg/L CMgO NPs maintained a noticeably higher K+ level by 91.41% and a lower Na+ level by 64.49% and consequently a higher ratio of K+/Na+ than the control under HS stress. Moreover, the CMgO NPs supplement greatly enhanced the contents of free amino acids under salt stress in rice leaves. Therefore, our findings propose that CMgO NPs supplementation could mitigate the salt stress in rice seedlings.
Collapse
Affiliation(s)
- Yue Song
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya 572025, P. R. China
- National Key Laboratory of Rice Biology, The Advanced Seed Institute, Zhejiang University, Hangzhou 310058, P. R. China
| | - Chenfan Zheng
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya 572025, P. R. China
- National Key Laboratory of Rice Biology, The Advanced Seed Institute, Zhejiang University, Hangzhou 310058, P. R. China
| | - Shan Li
- National Key Laboratory of Rice Biology, The Advanced Seed Institute, Zhejiang University, Hangzhou 310058, P. R. China
| | - Jinhong Chen
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya 572025, P. R. China
- National Key Laboratory of Rice Biology, The Advanced Seed Institute, Zhejiang University, Hangzhou 310058, P. R. China
| | - Meng Jiang
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya 572025, P. R. China
- National Key Laboratory of Rice Biology, The Advanced Seed Institute, Zhejiang University, Hangzhou 310058, P. R. China
| |
Collapse
|
5
|
Wei J, Luo B, Kong S, Liu W, Zhang C, Wei Z, Min X. Screening and identification of multiple abiotic stress responsive candidate genes based on hybrid-sequencing in Vicia sativa. Heliyon 2023; 9:e13536. [PMID: 36816321 PMCID: PMC9929474 DOI: 10.1016/j.heliyon.2023.e13536] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 01/27/2023] [Accepted: 02/01/2023] [Indexed: 02/07/2023] Open
Abstract
Common vetch is an important leguminous forage for both livestock fodder and green manure and has a tremendous latent capacity in a sustainable agroecosystem. In the present study, a comprehensive transcriptome analysis of the aboveground leaves and underground roots of common vetch under multiple abiotic stress treatments, including NaCl, drought, cold, and cold drought, was performed using hybrid-sequencing technology, i. e. single-molecule real-time sequencing technology (SMRT) and supplemented by next-generation sequencing (NGS) technology. A total of 485,038 reads of insert (ROIs) with a mean length of 2606 bp and 228,261 full-length nonchimeric (FLNC) reads were generated. After deduplication, 39,709 transcripts were generated. Of these transcripts, we identified 1059 alternative splicing (AS) events, 17,227 simple sequence repeats (SSRs), and 1647 putative transcription factors (TFs). Furthermore, 640 candidates long noncoding RNAs (lncRNAs) and 28,256 complete coding sequences (CDSs) were identified. In gene annotation analyses, a total of 38,826 transcripts (97.78%) were annotated in eight public databases. Finally, seven multiple abiotic stress-responsive candidate genes were obtained through gene expression, annotation information, and protein-protein interaction (PPI) networks. Our research not only enriched the structural information of FL transcripts in common vetch, but also provided useful information for exploring the molecular mechanism of multiple abiotic stress tolerance between aboveground and underground tissues in common vetch and related legumes.
Collapse
Affiliation(s)
- Jia Wei
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, People’s Republic of China
| | - Bo Luo
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, People’s Republic of China
| | - Shiyi Kong
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, People’s Republic of China
| | - Wenxian Liu
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, People’s Republic of China
| | - Chuanjie Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, People’s Republic of China
| | - Zhenwu Wei
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, People’s Republic of China
- Corresponding author.
| | - Xueyang Min
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, People’s Republic of China
- Corresponding author.
| |
Collapse
|
6
|
Tian T, Wang J, Wang H, Cui J, Shi X, Song J, Li W, Zhong M, Qiu Y, Xu T. Nitrogen application alleviates salt stress by enhancing osmotic balance, ROS scavenging, and photosynthesis of rapeseed seedlings ( Brassica napus). PLANT SIGNALING & BEHAVIOR 2022; 17:2081419. [PMID: 35621189 PMCID: PMC9154800 DOI: 10.1080/15592324.2022.2081419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 05/18/2022] [Accepted: 05/20/2022] [Indexed: 06/02/2023]
Abstract
Nitrogen application could alleviate salt stress on crops, but the specific physiological mechanism is still unclear. Therefore, in this study, a pot experiment was conducted to explore the effects of different application rates of nitrogen (0, 0.15, 0.30, and 0.45 g·kg-1) on the growth parameters, osmotic adjustment, reactive oxygen species scavenging, and photosynthesis of rapeseed seedlings planted in the soils with different concentrations of sodium chloride (1.5, 3.5, 5.5, and 7.5 g·kg-1). The results showed that nitrogen could alleviate the inhibition of salt on rapeseed growth, and improve the antioxidant enzyme activities and the contents of non-enzymatic substances, K+, soluble protein (SP), soluble sugar (SS), and proline. Besides, there was a significant correlation between the indexes of active oxygen scavenging system, osmoregulation system, and photosynthesis. Therefore, applying appropriate amount of nitrogen can promote the growth and development of rapeseed seedlings under salt stress, accelerate the scavenging of reactive oxygen species, maintain osmotic balance, and promote photosynthesis. This study will improve our understanding on the mechanism by which nitrogen application alleviates salt stress to crops.
Collapse
Affiliation(s)
- Tian Tian
- College of Agriculture, Shihezi University, Xinjiang, China
- The Key Laboratory of Oasis Ecological Agriculture of Xinjiang Production and Construction Group, Shihezi University, Xinjiang, China
| | - Jingang Wang
- College of Agriculture, Shihezi University, Xinjiang, China
- The Key Laboratory of Oasis Ecological Agriculture of Xinjiang Production and Construction Group, Shihezi University, Xinjiang, China
| | - Haijiang Wang
- College of Agriculture, Shihezi University, Xinjiang, China
- The Key Laboratory of Oasis Ecological Agriculture of Xinjiang Production and Construction Group, Shihezi University, Xinjiang, China
| | - Jing Cui
- College of Agriculture, Shihezi University, Xinjiang, China
- The Key Laboratory of Oasis Ecological Agriculture of Xinjiang Production and Construction Group, Shihezi University, Xinjiang, China
| | - Xiaoyan Shi
- College of Agriculture, Shihezi University, Xinjiang, China
- The Key Laboratory of Oasis Ecological Agriculture of Xinjiang Production and Construction Group, Shihezi University, Xinjiang, China
| | - Jianghui Song
- College of Agriculture, Shihezi University, Xinjiang, China
- The Key Laboratory of Oasis Ecological Agriculture of Xinjiang Production and Construction Group, Shihezi University, Xinjiang, China
| | - Weidi Li
- College of Agriculture, Shihezi University, Xinjiang, China
- The Key Laboratory of Oasis Ecological Agriculture of Xinjiang Production and Construction Group, Shihezi University, Xinjiang, China
| | - Mingtao Zhong
- College of Agriculture, Shihezi University, Xinjiang, China
- The Key Laboratory of Oasis Ecological Agriculture of Xinjiang Production and Construction Group, Shihezi University, Xinjiang, China
| | - Yue Qiu
- College of Agriculture, Shihezi University, Xinjiang, China
- The Key Laboratory of Oasis Ecological Agriculture of Xinjiang Production and Construction Group, Shihezi University, Xinjiang, China
| | - Ting Xu
- College of Agriculture, Shihezi University, Xinjiang, China
- The Key Laboratory of Oasis Ecological Agriculture of Xinjiang Production and Construction Group, Shihezi University, Xinjiang, China
| |
Collapse
|
7
|
Wang Q, Peng X, Lang D, Ma X, Zhang X. Physio-biochemical and transcriptomic analysis reveals that the mechanism of Bacillus cereus G2 alleviated oxidative stress of salt-stressed Glycyrrhiza uralensis Fisch. seedlings. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 247:114264. [PMID: 36334340 DOI: 10.1016/j.ecoenv.2022.114264] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 10/28/2022] [Accepted: 10/30/2022] [Indexed: 06/16/2023]
Abstract
Salt stress severely affects the growth and productivity of Glycyrrhiza uralensis. Our previous research found that the endophyte Bacillus cereus G2 alleviated the osmotic and oxidative stress in G. uralensis exposed to salinity. However, the mechanism is still unclear. Here, a pot experiment was conducted to analyse the change in parameters related to osmotic adjustment and antioxidant metabolism by G2 in salt-stressed G. uralensis at the physio-biochemistry and transcriptome levels. The results showed that G2 significantly increased proline content by 48 %, glycine betaine content by 75 % due to activated expression of BADH1, and soluble sugar content by 77 % due to upregulated expression of α-glucosidase and SS, which might help to decrease the cell osmotic potential, enable the cell to absorb water, and stabilize the cell's protein and membrane structure, thereby alleviating osmotic stress. Regarding antioxidant metabolism, G2 significantly decreased malondialdehyde (MDA) content by 27 %, which might be ascribed to the increase in superoxide dismutase (SOD) activity that facilitated the decrease in the superoxide radical (O2‾) production rate; it also increased the activities of catalase (CAT), ascorbate peroxidase (APX) and glutathione peroxidase (GPX), which helped stabilize the normal level of hydrogen peroxide (H2O2). G2 also increased glutathione (GSH) content by 65 % due to increased glutathione reductase (GR) activity and GSH/GSSG ratio, but G2 decreased oxidized glutathione (GSSG) content by 13 % due to decreased activity of dehydroascorbate reductase (DHAR), which could provide sufficient substrates for the ascorbate-glutathione (AsA-GSH) cycle to eliminate excess H2O2 that was not cleared in a timely manner by the antioxidant enzyme system. Taken together, G2 alleviated osmotic stress by increasing proline, soluble sugar, and glycine betaine contents and alleviated oxidative stress by the synergistic effect of antioxidant enzymes and the AsA-GSH cycle. Therefore, the results may be useful for explaining the mechanism by which endophyte inoculation regulates the salt tolerance of crops.
Collapse
Affiliation(s)
- Qiuli Wang
- College of Pharmacy, Ningxia Medical University, Yinchuan 750004, China
| | - Xueying Peng
- College of Pharmacy, Ningxia Medical University, Yinchuan 750004, China
| | - Duoyong Lang
- Laboratory Animal Center, Ningxia Medical University, Yinchuan 750004, China
| | - Xin Ma
- College of Pharmacy, Ningxia Medical University, Yinchuan 750004, China
| | - Xinhui Zhang
- College of Pharmacy, Ningxia Medical University, Yinchuan 750004, China; Ningxia Engineering and Technology Research Center of Regional Characterizistic Traditional Chinese Medicine, Ningxia Collaborative Innovation Center of Regional Characterizistic Traditional Chinese Medicine, Key Laboratory of Ningxia Minority Medicine Modernization, Ministry of Education, Yinchuan 750004, China.
| |
Collapse
|
8
|
Yang X, Patil S, Joshi S, Jamla M, Kumar V. Exploring epitranscriptomics for crop improvement and environmental stress tolerance. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 183:56-71. [PMID: 35567875 DOI: 10.1016/j.plaphy.2022.04.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/27/2022] [Accepted: 04/30/2022] [Indexed: 06/15/2023]
Abstract
Climate change and stressful environmental conditions severely hamper crop growth, development and yield. Plants respond to environmental perturbations, through their plasticity provided by key-genes, governed at post-/transcriptional levels. Gene-regulation in plants is a multilevel process controlled by diverse cellular entities that includes transcription factors (TF), epigenetic regulators and non-coding RNAs beside others. There are successful studies confirming the role of epigenetic modifications (DNA-methylation/histone-modifications) in gene expression. Recent years have witnessed emergence of a highly specialized field the "Epitranscriptomics". Epitranscriptomics deals with investigating post-transcriptional RNA chemical-modifications present across the life forms that change structural, functional and biological characters of RNA. However, deeper insights on of epitranscriptomic modifications, with >140 types known so far, are to be understood fully. Researchers have identified epitranscriptome marks (writers, erasers and readers) and mapped the site-specific RNA modifications (m6A, m5C, 3' uridylation, etc.) responsible for fine-tuning gene expression in plants. Simultaneous advancement in sequencing platforms, upgraded bioinformatic tools and pipelines along with conventional labelled techniques have further given a statistical picture of these epitranscriptomic modifications leading to their potential applicability in crop improvement and developing climate-smart crops. We present herein the insights on epitranscriptomic machinery in plants and how epitranscriptome and epitranscriptomic modifications underlying plant growth, development and environmental stress responses/adaptations. Third-generation sequencing technology, advanced bioinformatics tools and databases being used in plant epitranscriptomics are also discussed. Emphasis is given on potential exploration of epitranscriptome engineering for crop-improvement and developing environmental stress tolerant plants covering current status, challenges and future directions.
Collapse
Affiliation(s)
- Xiangbo Yang
- College of Agriculture, Jilin Agricultural Science and Technology University, Jilin, 132101, PR China.
| | - Suraj Patil
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Ganeshkhind, Pune, 411016, India
| | - Shrushti Joshi
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Ganeshkhind, Pune, 411016, India
| | - Monica Jamla
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Ganeshkhind, Pune, 411016, India
| | - Vinay Kumar
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Ganeshkhind, Pune, 411016, India.
| |
Collapse
|
9
|
Díaz-Silva M, Maldonado J, Veloso P, Delgado N, Silva H, Gallardo JA. RNA-Seq analysis and transcriptome assembly of Salicornia neei reveals a powerful system for ammonium detoxification. ELECTRON J BIOTECHN 2022. [DOI: 10.1016/j.ejbt.2022.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
|
10
|
Feng G, Xiao P, Wang X, Huang L, Nie G, Li Z, Peng Y, Li D, Zhang X. Comprehensive Transcriptome Analysis Uncovers Distinct Expression Patterns Associated with Early Salinity Stress in Annual Ryegrass ( Lolium Multiflorum L.). Int J Mol Sci 2022; 23:3279. [PMID: 35328700 PMCID: PMC8948850 DOI: 10.3390/ijms23063279] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/15/2022] [Indexed: 02/07/2023] Open
Abstract
Soil salination is likely to reduce crop production worldwide. Annual ryegrass (Lolium multiflorum L.) is one of the most important forages cultivated in temperate and subtropical regions. We performed a time-course comparative transcriptome for salinity-sensitive (SS) and salinity-insensitive (SI) genotypes of the annual ryegrass at six intervals post-stress to describe the transcriptional changes and identify the core genes involved in the early responses to salt stress. Our study generated 215.18 Gb of clean data and identified 7642 DEGs in six pairwise comparisons between the SS and SI genotypes of annual ryegrass. Function enrichment of the DEGs indicated that the differences in lipid, vitamins, and carbohydrate metabolism are responsible for variation in salt tolerance of the SS and SI genotypes. Stage-specific profiles revealed novel regulation mechanisms in salinity stress sensing, phytohormones signaling transduction, and transcriptional regulation of the early salinity responses. High-affinity K+ (HAKs) and high-affinity K1 transporter (HKT1) play different roles in the ionic homeostasis of the two genotypes. Moreover, our results also revealed that transcription factors (TFs), such as WRKYs, ERFs, and MYBs, may have different functions during the early signaling sensing of salt stress, such as WRKYs, ERFs, and MYBs. Generally, our study provides insights into the mechanisms of the early salinity response in the annual ryegrass and accelerates the breeding of salt-tolerant forage.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Xinquan Zhang
- Department of Forage Science, College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (G.F.); (P.X.); (X.W.); (L.H.); (G.N.); (Z.L.); (Y.P.); (D.L.)
| |
Collapse
|
11
|
Yao H, Wang F, Bi Q, Liu H, Liu L, Xiao G, Zhu J, Shen H, Li H. Combined Analysis of Pharmaceutical Active Ingredients and Transcriptomes of Glycyrrhiza uralensis Under PEG6000-Induced Drought Stress Revealed Glycyrrhizic Acid and Flavonoids Accumulation via JA-Mediated Signaling. FRONTIERS IN PLANT SCIENCE 2022; 13:920172. [PMID: 35769299 PMCID: PMC9234494 DOI: 10.3389/fpls.2022.920172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 05/19/2022] [Indexed: 05/16/2023]
Abstract
Glycyrrhiza uralensis contains many secondary metabolites with a wide range of pharmacological activities. Drought stress acts as a positive regulator to stimulate the production of medicinal active component in G. uralensis, however, the underlying mechanism remains unclear. The aim of this work is to investigate the accumulation and regulatory mechanism of pharmaceutical active ingredients in G. uralensis under drought stress. The materials of the aerial and underground parts of G. uralensis seedlings treated by 10% PEG6000 for 0, 2, 6, 12, and 24 h were used for RNA sequencing and determination of phytohormones and pharmaceutical active ingredients. PEG6000, ibuprofen (IBU), and jasmonic acid (JA) were utilized to treat G. uralensis seedlings for content detection and gene expression analysis. The results showed that, the contents of glycyrrhizic acid, glycyrrhetinic acid, and flavonoids (licochalcone A, glabridin, liquiritigenin, isoliquiritigenin, and liquiritin) were significantly accumulated in G. uralensis underground parts under drought stress. Kyoto Encyclopedia of Genes and Genomes analysis of the transcriptome data of drought-treated G. uralensis indicated that up-regulated differentially expressed genes (UDEGs) involved in glycyrrhizic acid synthesis in the underground parts and flavonoids synthesis in both aerial and underground parts were significantly enriched. Interestingly, the UDEGs participating in jasmonic acid (JA) signal transduction in both aerial and underground parts were discovered. In addition, JA content in both aerial and underground parts under drought stress showed the most significantly accumulated. And drought stress stimulated the contents of JA, glycyrrhizic acid, and flavonoids, coupled with the induced expressions of genes regulating the synthesis and transduction pathway. Moreover, In PEG6000- and JA-treated G. uralensis, significant accumulations of glycyrrhizic acid and flavonoids, and induced expressions of corresponding genes in these pathways, were observed, while, these increases were significantly blocked by JA signaling inhibitor IBU. JA content and expression levels of genes related to JA biosynthesis and signal transduction were also significantly increased by PEG treatment. Our study concludes that drought stress might promote the accumulation of pharmaceutical active ingredients via JA-mediated signaling pathway, and lay a foundation for improving the medicinal component of G. uralensis through genetic engineering technology.
Collapse
Affiliation(s)
- Hua Yao
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, China
- Department of Pharmacology, Institute of Materia Medica of Xinjiang, Urumqi, China
| | - Fei Wang
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, China
| | - Quan Bi
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, China
| | - Hailiang Liu
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, China
- Institute for Regenerative Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Li Liu
- Cotton Institute, Xingjiang Academy of Agricultural and Reclamation Science/Northwest Inland Region Key Laboratory of Cotton Biology and Genetic Breeding, Shihezi, China
| | - Guanghui Xiao
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Jianbo Zhu
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, China
- *Correspondence: Jianbo Zhu,
| | - Haitao Shen
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, China
- Haitao Shen,
| | - Hongbin Li
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, China
- Hongbin Li,
| |
Collapse
|
12
|
The First De Novo Transcriptome Assembly and Transcriptomic Dynamics of the Mangrove Tree Rhizophora stylosa Griff. (Rhizophoraceae). Int J Mol Sci 2021; 22:ijms222111964. [PMID: 34769393 PMCID: PMC8584393 DOI: 10.3390/ijms222111964] [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: 10/10/2021] [Revised: 10/30/2021] [Accepted: 11/02/2021] [Indexed: 12/13/2022] Open
Abstract
Mangroves are salt-tolerant plant species that grow in coastal saline water and are adapted to harsh environmental conditions. In this study, we de novo assembled and functionally annotated the transcriptome of Rhizophora stylosa, the widely distributed mangrove from the largest mangrove family (Rhizophoraceae). The final transcriptome consists of 200,491 unigenes with an average length, and N50 of 912.7 and 1334 base pair, respectively. We then compared the genome-wide expression profiles between the two morphologically distinct natural populations of this species growing under different levels of salinity depending on their distance from the ocean. Among the 200,491 unigenes, 40,253 were identified as differentially expressed between the two populations, while 15,741 and 24,512 were up- and down-regulated, respectively. Functional annotation assigned thousands of upregulated genes in saline environment to the categories related to abiotic stresses such as response to salt-, osmotic-, and oxidative-stress. Validation of those genes may contribute to a better understanding of adaptation in mangroves species. This study reported, for the first time, the transcriptome of R. stylosa, and the dynamic of it in response to salt stress and provided a valuable resource for elucidation of the molecular mechanism underlying the salt stress response in mangroves and other plants that live under stress.
Collapse
|
13
|
De Novo Transcriptome Assembly, Functional Annotation, and Transcriptome Dynamics Analyses Reveal Stress Tolerance Genes in Mangrove Tree ( Bruguiera gymnorhiza). Int J Mol Sci 2021; 22:ijms22189874. [PMID: 34576037 PMCID: PMC8467813 DOI: 10.3390/ijms22189874] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/09/2021] [Accepted: 09/11/2021] [Indexed: 12/13/2022] Open
Abstract
Their high adaptability to difficult coastal conditions makes mangrove trees a valuable resource and an interesting model system for understanding the molecular mechanisms underlying stress tolerance and adaptation of plants to the stressful environmental conditions. In this study, we used RNA sequencing (RNA-Seq) for de novo assembling and characterizing the Bruguiera gymnorhiza (L.) Lamk leaf transcriptome. B. gymnorhiza is one of the most widely distributed mangrove species from the biggest family of mangroves; Rhizophoraceae. The de novo assembly was followed by functional annotations and identification of individual transcripts and gene families that are involved in abiotic stress response. We then compared the genome-wide expression profiles between two populations of B. gymnorhiza, growing under different levels of stress, in their natural habitats. One population living in high salinity environment, in the shore of the Pacific Ocean- Japan, and the other population living about one kilometre farther from the ocean, and next to the estuary of a river; in less saline and more brackish condition. Many genes involved in response to salt and osmotic stress, showed elevated expression levels in trees growing next to the ocean in high salinity condition. Validation of these genes may contribute to future salt-resistance research in mangroves and other woody plants. Furthermore, the sequences and transcriptome data provided in this study are valuable scientific resources for future comparative transcriptome research in plants growing under stressful conditions.
Collapse
|
14
|
Liu J, Li G, Chen L, Gu J, Wu H, Li Z. Cerium oxide nanoparticles improve cotton salt tolerance by enabling better ability to maintain cytosolic K +/Na + ratio. J Nanobiotechnology 2021; 19:153. [PMID: 34034767 PMCID: PMC8146236 DOI: 10.1186/s12951-021-00892-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 05/11/2021] [Indexed: 12/18/2022] Open
Abstract
Background Salinity is a worldwide factor limiting the agricultural production. Cotton is an important cash crop; however, its yield and product quality are negatively affected by soil salinity. Use of nanomaterials such as cerium oxide nanoparticles (nanoceria) to improve plant tolerance to stress conditions, e.g. salinity, is an emerged approach in agricultural production. Nevertheless, to date, our knowledge about the role of nanoceria in cotton salt response and the behind mechanisms is still rare. Results We found that PNC (poly acrylic acid coated nanoceria) helped to improve cotton tolerance to salinity, showing better phenotypic performance, higher chlorophyll content (up to 68% increase) and biomass (up to 38% increase), and better photosynthetic performance such as carbon assimilation rate (up to 144% increase) in PNC treated cotton plants than the NNP (non-nanoparticle control) group. Under salinity stress, in consistent to the results of the enhanced activities of antioxidant enzymes, PNC treated cotton plants showed significant lower MDA (malondialdehyde, up to 44% decrease) content and reactive oxygen species (ROS) level such as hydrogen peroxide (H2O2, up to 79% decrease) than the NNP control group, both in the first and second true leaves. Further experiments showed that under salinity stress, PNC treated cotton plants had significant higher cytosolic K+ (up to 84% increase) and lower cytosolic Na+ (up to 77% decrease) fluorescent intensity in both the first and second true leaves than the NNP control group. This is further confirmed by the leaf ion content analysis, showed that PNC treated cotton plants maintained significant higher leaf K+ (up to 84% increase) and lower leaf Na+ content (up to 63% decrease), and thus the higher K+/Na+ ratio than the NNP control plants under salinity stress. Whereas no significant increase of mesophyll cell vacuolar Na+ intensity was observed in PNC treated plants than the NNP control under salinity stress, suggesting that the enhanced leaf K+ retention and leaf Na+ exclusion, but not leaf vacuolar Na+ sequestration are the main mechanisms behind PNC improved cotton salt tolerance. qPCR results showed that under salinity stress, the modulation of HKT1 but not SOS1 refers more to the PNC improved cotton leaf Na+ exclusion than the NNP control. Conclusions PNC enhanced leaf K+ retention and Na+ exclusion, but not vacuolar Na+ sequestration to enable better maintained cytosolic K+/Na+ homeostasis and thus to improve cotton salt tolerance. Our results add more knowledge for better understanding the complexity of plant-nanoceria interaction in terms of nano-enabled plant stress tolerance. Graphic abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12951-021-00892-7.
Collapse
Affiliation(s)
- Jiahao Liu
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guangjing Li
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Linlin Chen
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jiangjiang Gu
- College of Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Honghong Wu
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Zhaohu Li
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China.,College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100083, China
| |
Collapse
|