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Hekmati Z, Solouki M, Emamjomeh A, Zahiri J, Mirzaie-Asl A. Transcriptomic Analysis of Cyclamen persicum to Identify Invovled Genes in Triterpene Secondary Metabolites Pathway. Biochem Genet 2024:10.1007/s10528-024-10745-1. [PMID: 38578589 DOI: 10.1007/s10528-024-10745-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 02/16/2024] [Indexed: 04/06/2024]
Abstract
Saponins are considered as a diverse group of natural active compounds, which are widely found in crops. Mevalonate pathway (MVA) is regarded as the main pathway for synthesis of saponins in crops. This study aims to compare transcriptome of the leaf with tuber of crop including tubers and roots. First, more than 166 million reads were generated. The existence of 36,678 unigenes in the two samples out of 48,936 assembled ones showed a significant difference in expression. Finally, 310 and 290 highly up-regulated genes in leaf and tuber were selected for the next analysis. In addition, the expression profiles of 13 key genes in the MVA pathway were compared in RNA sequencing and reverse transcription-quantitative polymerase chain reaction analysis. The results indicated that cyclamen tuber has a higher level of expression of MVA pathway genes. The topological analysis for gene co-expression network involved in triterpenoid synthesis represented that the genes at the beginning of such pathway play a critical role so that the reduction of their expression challenges triterpenoid synthesis severely. The tuber of the cyclamen appears to be the major site of triterpene synthesis, and transfer of excess Isopentenyl pyrophosphate (IPP) from tuber to leaf activates downstream genes in leaf of crop.
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Affiliation(s)
- Zahra Hekmati
- Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Daneshgah Blvd., Zabol, Iran
| | - Mahmood Solouki
- Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Daneshgah Blvd., Zabol, Iran.
| | - Abbasali Emamjomeh
- Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Daneshgah Blvd., Zabol, Iran.
- Laboratory of Computational Biotechnology and Bioinformatics (CBB Lab), Department of Bioinformatics, University of Zabol, Zabol, Iran.
| | - Javad Zahiri
- Department of Neuroscience, University of California, San Diego, San Diego, CA, USA
| | - Asghar Mirzaie-Asl
- Department of Agricultural Biotechnology, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran
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Shaban AS, Safhi FA, Fakhr MA, Pruthi R, Abozahra MS, El-Tahan AM, Subudhi PK. Comparison of the Morpho-Physiological and Molecular Responses to Salinity and Alkalinity Stresses in Rice. PLANTS (BASEL, SWITZERLAND) 2023; 13:60. [PMID: 38202367 PMCID: PMC10780433 DOI: 10.3390/plants13010060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 12/10/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024]
Abstract
Rice is a major food crop that has a critical role in ensuring food security for the global population. However, major abiotic stresses such as salinity and alkalinity pose a major threat to rice farming worldwide. Compared with salinity stress, there is limited progress in elucidating the molecular mechanisms associated with alkalinity tolerance in rice. Since both stresses coexist in coastal and arid regions, unraveling of the underlying molecular mechanisms will help the breeding of high-yielding stress-tolerant rice varieties for these areas. This study examined the morpho-physiological and molecular response of four rice genotypes to both salinity and alkalinity stresses. Geumgangbyeo was highly tolerant and Mermentau was the least tolerant to both stresses, while Pokkali and Bengal were tolerant to only salinity and alkalinity stress, respectively. A set of salinity and alkalinity stress-responsive genes showed differential expression in the above rice genotypes under both stress conditions. The expression patterns were consistent with the observed morphological responses in these rice genotypes, suggesting the potential role of these genes in regulating tolerance to these abiotic stresses. Overall, this study suggested that divergence in response to alkalinity and salinity stresses among rice genotypes could be due to different molecular mechanisms conferring tolerance to each stress. In addition to providing a basis for further investigations into differentiating the molecular bases underlying tolerance, this study also emphasizes the possibilities of developing climate-resilient rice varieties using donors that are tolerant to both abiotic stresses.
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Affiliation(s)
- Abdelghany S. Shaban
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA;
- Botany and Microbiology Department, Faculty of Science (Boys), Al-Azhar University, Cairo 11884, Egypt;
| | - Fatmah Ahmed Safhi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia;
| | - Marwa A. Fakhr
- Botany Department, Faculty of Science, Fayoum University, Fayoum 63514, Egypt;
- Green materials Technology Department, Environment and Natural Materials Research Institute, City of Scientific Research and Technological Applications (SRTA-City), Borg El-Arab, Alexandria 21934, Egypt
| | - Rajat Pruthi
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA;
| | - Mahmoud S. Abozahra
- Botany and Microbiology Department, Faculty of Science (Boys), Al-Azhar University, Cairo 11884, Egypt;
| | - Amira M. El-Tahan
- Plant Production Department, Arid Lands Cultivation Research Institute, City of Scientific Research and Technological Applications (SRTA-City), Borg El-Arab, Alexandria 21934, Egypt;
| | - Prasanta K. Subudhi
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA;
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Rajkumari N, Chowrasia S, Nishad J, Ganie SA, Mondal TK. Metabolomics-mediated elucidation of rice responses to salt stress. PLANTA 2023; 258:111. [PMID: 37919614 DOI: 10.1007/s00425-023-04258-1] [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: 07/03/2023] [Accepted: 10/01/2023] [Indexed: 11/04/2023]
Abstract
MAIN CONCLUSION Role of salinity responsive metabolites of rice and its wild species has been discussed. Salinity stress is one of the important environmental stresses that severely affects rice productivity. Although, several vital physio-biochemical and molecular responses have been activated in rice under salinity stress which were well described in literatures, the mechanistic role of salt stress and microbes-induced metabolites to overcome salt stress in rice are less studied. Nevertheless, over the years, metabolomic studies have allowed a comprehensive analyses of rice salt stress responses. Hence, we review the salt stress-triggered alterations of various metabolites in rice and discuss their significant roles toward salinity tolerance. Some of the metabolites such as serotonin, salicylic acid, ferulic acid and gentisic acid may act as signaling molecules to activate different downstream salt-tolerance mechanisms; whereas, the other compounds such as amino acids, sugars and organic acids directly act as protective agents to maintain osmotic balance and scavenger of reactive oxygen species during the salinity stress. The quantity, type, tissues specificity and time of accumulation of metabolites induced by salinity stress vary between salt-sensitive and tolerant rice genotypes and thus, contribute to their different degrees of salt tolerance. Moreover, few tolerance metabolites such as allantoin, serotonin and melatonin induce unique pathways for activation of defence mechanisms in salt-tolerant varieties of rice, suggesting their potential roles as the universal biomarkers for salt tolerance. Therefore, these metabolites can be applied exogenously to the sensitive genotypes of rice to enhance their performance under salt stress. Furthermore, the microbes of rhizosphere also participated in rice salt tolerance either directly or indirectly by regulating their metabolic pathways. Thus, this review for the first time offers valuable and comprehensive insights into salt-induced spatio-temporal and genotype-specific metabolites in different genotypes of rice which provide a reference point to analyze stress-gene-metabolite relationships for the biomarker designing in rice. Further, it can also help to decipher several metabolic systems associated with salt tolerance in rice which will be useful in developing salt-tolerance cultivars by conventional breeding/genetic engineering/exogenous application of metabolites.
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Affiliation(s)
- Nitasana Rajkumari
- ICAR-National Institute for Plant Biotechnology, LBS Centre, New Delhi, 110012, India
- ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, 110012, India
| | - Soni Chowrasia
- ICAR-National Institute for Plant Biotechnology, LBS Centre, New Delhi, 110012, India
- Department of Bioscience and Biotechnology, Banastahli Vidyapith, Tonk, Rajasthan, 304022, India
| | - Jyoti Nishad
- ICAR-National Institute for Plant Biotechnology, LBS Centre, New Delhi, 110012, India
| | - Showkat Ahmad Ganie
- Plant Molecular Sciences and Centre of Systems and Synthetic Biology, Department of Biological Sciences, Royal Holloway University of London, Egham, TW20 0EX, Surrey, UK
- School of Life Sciences, University of Essex, Colchester, CO4 3SQ, UK
| | - Tapan Kumar Mondal
- ICAR-National Institute for Plant Biotechnology, LBS Centre, New Delhi, 110012, India.
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Shahid M, Khan MS, Singh UB. Pesticide-tolerant microbial consortia: Potential candidates for remediation/clean-up of pesticide-contaminated agricultural soil. ENVIRONMENTAL RESEARCH 2023; 236:116724. [PMID: 37500042 DOI: 10.1016/j.envres.2023.116724] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 07/16/2023] [Accepted: 07/21/2023] [Indexed: 07/29/2023]
Abstract
Reclamation of pesticide-polluted lands has long been a difficult endeavour. The use of synthetic pesticides could not be restricted due to rising agricultural demand. Pesticide toxicity has become a pressing agronomic problem due to its adverse impact on agroecosystems, agricultural output, and consequently food security and safety. Among different techniques used for the reclamation of pesticide-polluted sites, microbial bioremediation is an eco-friendly approach, which focuses on the application of resilient plant growth promoting rhizobacteria (PGPR) that may transform or degrade chemical pesticides to innocuous forms. Such pesticide-resilient PGPR has demonstrated favourable effects on soil-plant systems, even in pesticide-contaminated environments, by degrading pesticides, providing macro-and micronutrients, and secreting active but variable secondary metabolites like-phytohormones, siderophores, ACC deaminase, etc. This review critically aims to advance mechanistic understanding related to the reduction of phytotoxicity of pesticides via the use of microbe-mediated remediation techniques leading to crop optimization in pesticide-stressed soils. The literature surveyed and data presented herein are extremely useful, offering agronomists-and crop protectionists microbes-assisted remedial strategies for affordably enhancing crop productivity in pesticide-stressed soils.
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Affiliation(s)
- Mohammad Shahid
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Kushmaur, Mau Nath Bhanjan, 275103, UP, India; Department of Agricultural Microbiology, Faculty of Agriculture Science, Aligarh Muslim University (A.M.U.), Aligarh, 202001, UP, India.
| | - Mohammad Saghir Khan
- Department of Agricultural Microbiology, Faculty of Agriculture Science, Aligarh Muslim University (A.M.U.), Aligarh, 202001, UP, India
| | - Udai B Singh
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Kushmaur, Mau Nath Bhanjan, 275103, UP, India
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Degon Z, Dixon S, Rahmatallah Y, Galloway M, Gulutzo S, Price H, Cook J, Glazko G, Mukherjee A. Azospirillum brasilense improves rice growth under salt stress by regulating the expression of key genes involved in salt stress response, abscisic acid signaling, and nutrient transport, among others. FRONTIERS IN AGRONOMY 2023; 5:1216503. [PMID: 38223701 PMCID: PMC10785826 DOI: 10.3389/fagro.2023.1216503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Major food crops, such as rice and maize, display severe yield losses (30-50%) under salt stress. Furthermore, problems associated with soil salinity are anticipated to worsen due to climate change. Therefore, it is necessary to implement sustainable agricultural strategies, such as exploiting beneficial plant-microbe associations, for increased crop yields. Plants can develop associations with beneficial microbes, including arbuscular mycorrhiza and plant growth-promoting bacteria (PGPB). PGPB improve plant growth via multiple mechanisms, including protection against biotic and abiotic stresses. Azospirillum brasilense, one of the most studied PGPB, can mitigate salt stress in different crops. However, little is known about the molecular mechanisms by which A. brasilense mitigates salt stress. This study shows that total and root plant mass is improved in A. brasilense-inoculated rice plants compared to the uninoculated plants grown under high salt concentrations (100 mM and 200 mM NaCl). We observed this growth improvement at seven- and fourteen days post-treatment (dpt). Next, we used transcriptomic approaches and identified differentially expressed genes (DEGs) in rice roots when exposed to three treatments: 1) A. brasilense, 2) salt (200 mM NaCl), and 3) A. brasilense and salt (200 mM NaCl), at seven dpt. We identified 786 DEGs in the A. brasilense-treated plants, 4061 DEGs in the salt-stressed plants, and 1387 DEGs in the salt-stressed A. brasilense-treated plants. In the A. brasilense-treated plants, we identified DEGs involved in defense, hormone, and nutrient transport, among others. In the salt-stressed plants, we identified DEGs involved in abscisic acid and jasmonic acid signaling, antioxidant enzymes, sodium and potassium transport, and calcium signaling, among others. In the salt-stressed A. brasilense-treated plants, we identified some genes involved in salt stress response and tolerance (e.g., abscisic acid and jasmonic acid signaling, antioxidant enzymes, calcium signaling), and sodium and potassium transport differentially expressed, among others. We also identified some A. brasilense-specific plant DEGs, such as nitrate transporters and defense genes. Furthermore, our results suggest genes involved in auxin and ethylene signaling are likely to play an important role during these interactions. Overall, our transcriptomic data indicate that A. brasilense improves rice growth under salt stress by regulating the expression of key genes involved in defense and stress response, abscisic acid and jasmonic acid signaling, and ion and nutrient transport, among others. Our findings will provide essential insights into salt stress mitigation in rice by A. brasilense.
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Affiliation(s)
- Zachariah Degon
- Department of Biology, University of Central Arkansas, Conway, AR, United States
| | - Seth Dixon
- Department of Biology, University of Central Arkansas, Conway, AR, United States
| | - Yasir Rahmatallah
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Mary Galloway
- Department of Biology, University of Central Arkansas, Conway, AR, United States
| | - Sophia Gulutzo
- Department of Biology, University of Central Arkansas, Conway, AR, United States
| | - Hunter Price
- Department of Biology, University of Central Arkansas, Conway, AR, United States
| | - John Cook
- Department of Biology, University of Central Arkansas, Conway, AR, United States
| | - Galina Glazko
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Arijit Mukherjee
- Department of Biology, University of Central Arkansas, Conway, AR, United States
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Kitavi M, Gemenet DC, Wood JC, Hamilton JP, Wu S, Fei Z, Khan A, Buell CR. Identification of genes associated with abiotic stress tolerance in sweetpotato using weighted gene co-expression network analysis. PLANT DIRECT 2023; 7:e532. [PMID: 37794882 PMCID: PMC10546384 DOI: 10.1002/pld3.532] [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: 01/28/2023] [Revised: 04/22/2023] [Accepted: 08/31/2023] [Indexed: 10/06/2023]
Abstract
Sweetpotato, Ipomoea batatas (L.), a key food security crop, is negatively impacted by heat, drought, and salinity stress. The orange-fleshed sweetpotato cultivar "Beauregard" was exposed to heat, salt, and drought treatments for 24 and 48 h to identify genes responding to each stress condition in leaves. Analysis revealed both common (35 up regulated, 259 down regulated genes in the three stress conditions) and unique sets of up regulated (1337 genes by drought, 516 genes by heat, and 97 genes by salt stress) and down regulated (2445 genes by drought, 678 genes by heat, and 204 genes by salt stress) differentially expressed genes (DEGs) suggesting common, yet stress-specific transcriptional responses to these three abiotic stressors. Gene Ontology analysis of down regulated DEGs common to both heat and salt stress revealed enrichment of terms associated with "cell population proliferation" suggestive of an impact on the cell cycle by the two stress conditions. To identify shared and unique gene co-expression networks under multiple abiotic stress conditions, weighted gene co-expression network analysis was performed using gene expression profiles from heat, salt, and drought stress treated 'Beauregard' leaves yielding 18 co-expression modules. One module was enriched for "response to water deprivation," "response to abscisic acid," and "nitrate transport" indicating synergetic crosstalk between nitrogen, water, and phytohormones with genes encoding osmotin, cell expansion, and cell wall modification proteins present as key hub genes in this drought-associated module. This research lays the groundwork for exploring to a further degree, mechanisms for abiotic stress tolerance in sweetpotato.
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Affiliation(s)
- Mercy Kitavi
- Research Technology Support Facility (RTSF)Michigan State UniversityEast LansingMichiganUSA
- Center for Applied Genetic TechnologiesUniversity of GeorgiaAthensGeorgiaUSA
| | - Dorcus C. Gemenet
- International Potato CenterLimaPeru
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF HouseNairobiKenya
| | - Joshua C. Wood
- Center for Applied Genetic TechnologiesUniversity of GeorgiaAthensGeorgiaUSA
| | - John P. Hamilton
- Center for Applied Genetic TechnologiesUniversity of GeorgiaAthensGeorgiaUSA
- Department of Crop & Soil SciencesUniversity of GeorgiaAthensGeorgiaUSA
| | - Shan Wu
- Boyce Thompson InstituteCornell UniversityIthacaNew YorkUSA
| | - Zhangjun Fei
- Boyce Thompson InstituteCornell UniversityIthacaNew YorkUSA
| | - Awais Khan
- International Potato CenterLimaPeru
- Present address:
Plant Pathology and Plant‐Microbe Biology Section, School of Integrative Plant ScienceCornell UniversityGenevaNew YorkUSA
| | - C. Robin Buell
- Center for Applied Genetic TechnologiesUniversity of GeorgiaAthensGeorgiaUSA
- Department of Crop & Soil SciencesUniversity of GeorgiaAthensGeorgiaUSA
- Institute of Plant Breeding, Genetics, & GenomicsUniversity of GeorgiaAthensGeorgiaUSA
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7
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Tasnim A, Jahan I, Azim T, Karmoker D, Seraj ZI. Paired growth of cultivated and halophytic wild rice under salt stress induces bacterial endophytes and gene expression responses. FRONTIERS IN PLANT SCIENCE 2023; 14:1244743. [PMID: 37746015 PMCID: PMC10516563 DOI: 10.3389/fpls.2023.1244743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 08/17/2023] [Indexed: 09/26/2023]
Abstract
Introduction Utilizing salt-affected marginal lands in coastal regions can help meet the growing demand for rice. We explored a nature-based solution involving wild halophytic rice (O. coarctata, Oc) and commercial rice BRRI Dhan 67 (O. sativa, Os) grown in close proximity to each other under salt stress. Methods This was to investigate whether a paired planting strategy could help complement rice growth and yield under stress. We also investigated the gene expression and endophytic bacterial profiles of both Os and Oc in unpaired and paired conditions without and with salt. Results Paired plants exhibited lower salt damage indicators such as smaller reduction in plant height, electrolyte leakage and chlorophyll loss, as well as higher K+/Na+ ratio under saline stress. Some of the 39 endophytic bacteria in the mutualism experiment were unique to Oc and transferred to Os when paired. Differentially expressed genes in leaves of paired Os versus unpaired Os were 1097 (994 up-regulated, 101 down-regulated) without salt and 893 (763 up-regulated, 130 down-regulated) under salt stress. The presence of Oc plants under salt stress influenced major biological processes in Os, including oxidative stress; chitinase activity; phenylalanine catabolic process and response to ABA. Protein binding and serine/threonine kinase activity were primarily affected in molecular function. The downregulated WRKY transcription factor 22 in paired conditions under salt stress played a role in the MAPK signaling pathway, reducing respiratory cell death. The upregulated auxin-responsive protein IAA18 gene, involved in hormone signaling and cell enlargement, was present only in paired plants. Discussion Our findings therefore, offer insights into developing more effective cultivation strategies for sustainable rice production.
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Mangena P. Cell Mutagenic Autopolyploidy Enhances Salinity Stress Tolerance in Leguminous Crops. Cells 2023; 12:2082. [PMID: 37626892 PMCID: PMC10453822 DOI: 10.3390/cells12162082] [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: 06/20/2023] [Revised: 07/30/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
Salinity stress affects plant growth and development by causing osmotic stress and nutrient imbalances through excess Na+, K+, and Cl- ion accumulations that induce toxic effects during germination, seedling development, vegetative growth, flowering, and fruit set. However, the effects of salt stress on growth and development processes, especially in polyploidized leguminous plants, remain unexplored and scantly reported compared to their diploid counterparts. This paper discusses the physiological and molecular response of legumes towards salinity stress-based osmotic and ionic imbalances in plant cells. A multigenic response involving various compatible solutes, osmolytes, ROS, polyamines, and antioxidant activity, together with genes encoding proteins involved in the signal transduction, regulation, and response mechanisms to this stress, were identified and discussed. This discussion reaffirms polyploidization as the driving force in plant evolution and adaptation to environmental stress constraints such as drought, feverish temperatures, and, in particular, salt stress. As a result, thorough physiological and molecular elucidation of the role of gene duplication through induced autopolyploidization and possible mechanisms regulating salinity stress tolerance in grain legumes must be further studied.
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Affiliation(s)
- Phetole Mangena
- Department of Biodiversity, School of Molecular and Life Sciences, Faculty of Science and Agriculture, University of Limpopo, Private Bag X1106, Sovenga 0727, South Africa
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Purwestri YA, Nurbaiti S, Putri SPM, Wahyuni IM, Yulyani SR, Sebastian A, Nuringtyas TR, Yamaguchi N. Seed Halopriming: A Promising Strategy to Induce Salt Tolerance in Indonesian Pigmented Rice. PLANTS (BASEL, SWITZERLAND) 2023; 12:2879. [PMID: 37571030 PMCID: PMC10420915 DOI: 10.3390/plants12152879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/28/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023]
Abstract
Unfavorable environmental conditions and climate change impose stress on plants, causing yield losses worldwide. The Indonesian pigmented rice (Oryza sativa L.) cultivars Cempo Ireng Pendek (black rice) and Merah Kalimantan Selatan (red rice) are becoming popular functional foods due to their high anthocyanin contents and have great potential for widespread cultivation. However, their ability to grow on marginal, high-salinity lands is limited. In this study, we investigated whether seed halopriming enhances salt tolerance in the two pigmented rice cultivars. The non-pigmented cultivars IR64, a salt-stress-sensitive cultivar, and INPARI 35, a salt tolerant, were used as control. We pre-treated seeds with a halopriming solution before germination and then exposed the plants to a salt stress of 150 mM NaCl at 21 days after germination using a hydroponic system in a greenhouse. Halopriming was able to mitigate the negative effects of salinity on plant growth, including suppressing reactive oxygen species accumulation, increasing the membrane stability index (up to two-fold), and maintaining photosynthetic pigment contents. Halopriming had different effects on the accumulation of proline, in different rice varieties: the proline content increased in IR64 and Cempo Ireng Pendek but decreased in INPARI 35 and Merah Kalimantan Selatan. Halopriming also had disparate effects in the expression of stress-related genes: OsMYB91 expression was positively correlated with salt treatment, whereas OsWRKY42 and OsWRKY70 expression was negatively correlated with this treatment. These findings highlighted the potential benefits of halopriming in salt-affected agro-ecosystems.
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Affiliation(s)
- Yekti Asih Purwestri
- Department of Tropical Biology, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia; (S.N.); (T.R.N.)
- Research Center for Biotechnology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Siti Nurbaiti
- Department of Tropical Biology, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia; (S.N.); (T.R.N.)
- Research Center for Biotechnology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Sekar Pelangi Manik Putri
- Biotechnology Master Program, The Graduate School, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia; (S.P.M.P.); (I.M.W.); (S.R.Y.)
| | - Ignasia Margi Wahyuni
- Biotechnology Master Program, The Graduate School, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia; (S.P.M.P.); (I.M.W.); (S.R.Y.)
| | - Siti Roswiyah Yulyani
- Biotechnology Master Program, The Graduate School, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia; (S.P.M.P.); (I.M.W.); (S.R.Y.)
| | - Alfino Sebastian
- Institute of Plant Science and Resources, Okayama University, Okayama 710-0046, Japan;
| | - Tri Rini Nuringtyas
- Department of Tropical Biology, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia; (S.N.); (T.R.N.)
- Research Center for Biotechnology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Nobutoshi Yamaguchi
- Plant Stem Cell Regulation and Floral Patterning Laboratory, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma 630-0101, Japan;
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Karumanchi AR, Sivan P, Kummari D, Rajasheker G, Kumar SA, Reddy PS, Suravajhala P, Podha S, Kishor PBK. Root and Leaf Anatomy, Ion Accumulation, and Transcriptome Pattern under Salt Stress Conditions in Contrasting Genotypes of Sorghum bicolor. PLANTS (BASEL, SWITZERLAND) 2023; 12:2400. [PMID: 37446963 DOI: 10.3390/plants12132400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/11/2023] [Accepted: 06/15/2023] [Indexed: 07/15/2023]
Abstract
Roots from salt-susceptible ICSR-56 (SS) sorghum plants display metaxylem elements with thin cell walls and large diameter. On the other hand, roots with thick, lignified cell walls in the hypodermis and endodermis were noticed in salt-tolerant CSV-15 (ST) sorghum plants. The secondary wall thickness and number of lignified cells in the hypodermis have increased with the treatment of sodium chloride stress to the plants (STN). Lignin distribution in the secondary cell wall of sclerenchymatous cells beneath the lower epidermis was higher in ST leaves compared to the SS genotype. Casparian thickenings with homogenous lignin distribution were observed in STN roots, but inhomogeneous distribution was evident in SS seedlings treated with sodium chloride (SSN). Higher accumulation of K+ and lower Na+ levels were noticed in ST compared to the SS genotype. To identify the differentially expressed genes among SS and ST genotypes, transcriptomic analysis was carried out. Both the genotypes were exposed to 200 mM sodium chloride stress for 24 h and used for analysis. We obtained 70 and 162 differentially expressed genes (DEGs) exclusive to SS and SSN and 112 and 26 DEGs exclusive to ST and STN, respectively. Kyoto Encyclopaedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analysis unlocked the changes in metabolic pathways in response to salt stress. qRT-PCR was performed to validate 20 DEGs in each SSN and STN sample, which confirms the transcriptomic results. These results surmise that anatomical changes and higher K+/Na+ ratios are essential for mitigating salt stress in sorghum apart from the genes that are differentially up- and downregulated in contrasting genotypes.
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Affiliation(s)
- Appa Rao Karumanchi
- Department of Biotechnology, Acharya Nagarjuna University, Nagarjuna Nagar, Guntur 522 209, India
| | - Pramod Sivan
- Department of Chemistry, Division of Glycoscience, KTH Royal Institute of Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, Albanova University Center, SE-10691 Stockholm, Sweden
| | - Divya Kummari
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad 502 324, India
| | - G Rajasheker
- Department of Genetics, Osmania University, Hyderabad 500 007, India
| | - S Anil Kumar
- Department of Biotechnology, Vignan's Foundation for Science, Technology & Research (Deemed to Be University), Guntur 522 213, India
| | - Palakolanu Sudhakar Reddy
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad 502 324, India
| | | | - Sudhakar Podha
- Department of Biotechnology, Acharya Nagarjuna University, Nagarjuna Nagar, Guntur 522 209, India
| | - P B Kavi Kishor
- Department of Genetics, Osmania University, Hyderabad 500 007, India
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11
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Singh L, Pruthi R, Chapagain S, Subudhi PK. Genome-Wide Association Study Identified Candidate Genes for Alkalinity Tolerance in Rice. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12112206. [PMID: 37299185 DOI: 10.3390/plants12112206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/01/2023] [Accepted: 06/01/2023] [Indexed: 06/12/2023]
Abstract
Alkalinity stress is a major hindrance to enhancing rice production globally due to its damaging effect on plants' growth and development compared with salinity stress. However, understanding of the physiological and molecular mechanisms of alkalinity tolerance is limited. Therefore, a panel of indica and japonica rice genotypes was evaluated for alkalinity tolerance at the seedling stage in a genome-wide association study to identify tolerant genotypes and candidate genes. Principal component analysis revealed that traits such as alkalinity tolerance score, shoot dry weight, and shoot fresh weight had the highest contribution to variations in tolerance, while shoot Na+ concentration, shoot Na+:K+ ratio, and root-to-shoot ratio had moderate contributions. Phenotypic clustering and population structure analysis grouped the genotypes into five subgroups. Several salt-susceptible genotypes such as IR29, Cocodrie, and Cheniere placed in the highly tolerant cluster suggesting different underlying tolerance mechanisms for salinity and alkalinity tolerance. Twenty-nine significant SNPs associated with alkalinity tolerance were identified. In addition to three alkalinity tolerance QTLs, qSNK4, qSNC9, and qSKC10, which co-localized with the earlier reported QTLs, a novel QTL, qSNC7, was identified. Six candidate genes that were differentially expressed between tolerant and susceptible genotypes were selected: LOC_Os04g50090 (Helix-loop-helix DNA-binding protein), LOC_Os08g23440 (amino acid permease family protein), LOC_Os09g32972 (MYB protein), LOC_Os08g25480 (Cytochrome P450), LOC_Os08g25390 (Bifunctional homoserine dehydrogenase), and LOC_Os09g38340 (C2H2 zinc finger protein). The genomic and genetic resources such as tolerant genotypes and candidate genes would be valuable for investigating the alkalinity tolerance mechanisms and for marker-assisted pyramiding of the favorable alleles for improving alkalinity tolerance at the seedling stage in rice.
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Affiliation(s)
- Lovepreet Singh
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
| | - Rajat Pruthi
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
| | - Sandeep Chapagain
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
| | - Prasanta K Subudhi
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
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12
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Moghaddam A, Larijani HR, Oveysi M, Moghaddam HRT, Nasri M. Alleviating the adverse effects of salinity stress on Salicornia persica using sodium nitroprusside and potassium nitrate. BMC PLANT BIOLOGY 2023; 23:166. [PMID: 36977975 PMCID: PMC10052858 DOI: 10.1186/s12870-023-04179-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 03/20/2023] [Indexed: 06/12/2023]
Abstract
BACKGROUND Glasswort (Salicornia persica) is identified as a halophyte plant, which is one of the most tolerant plants to salt conditions. The seed oil of the plant contains about 33% oil. In the present study, the effects of sodium nitroprusside (SNP; 0, 0.1, 0.2, and 0.4 mM) and potassium nitrate (KNO3; 0, 0.5, and 1%) were evaluated on several characteristics of glasswort under salinity stress (0, 10, 20, and 40 dS/m). RESULTS morphological features, phenological traits, and yield parameters such as plant height, number of days to flowering, seed oil, biological yield, and seed yield significantly decreased in response to severe salt stress. However, the plants needed an optimal salinity concentration (20 dS/m NaCl) to obtain high amounts of seed oil and seed yield. The results also showed that a high level of salinity (40 dS/m NaCl) caused a decrease in plant oil and yield. In addition, by increasing the exogenous application of SNP and KNO3, the seed oil and seed yield increased. CONCLUSIONS The application of SNP and KNO3 were effective in protecting S. persica plants from the deleterious effects of severe salt stress (40 dS/m NaCl), thereby restoring the activity of antioxidant enzymes, increasing the proline content, and maintaining cell membrane stability. It seems that both factors, i.e. SNP and KNO3, can be applied as mitigators of salt stress in plants.
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Affiliation(s)
- Abbasali Moghaddam
- Department of Agronomy, Varamin-Pishva Branch, Islamic Azad University, Varamin, Iran
| | - Hamid Reza Larijani
- Department of Agronomy, Varamin-Pishva Branch, Islamic Azad University, Varamin, Iran.
| | - Meysam Oveysi
- Department of Agronomy, Varamin-Pishva Branch, Islamic Azad University, Varamin, Iran
| | | | - Mohammad Nasri
- Department of Agronomy, Varamin-Pishva Branch, Islamic Azad University, Varamin, Iran
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Fang S, Cong B, Zhao L, Liu C, Zhang Z, Liu S. Genome-Wide Analysis of Long Non-Coding RNAs Related to UV-B Radiation in the Antarctic Moss Pohlia nutans. Int J Mol Sci 2023; 24:ijms24065757. [PMID: 36982830 PMCID: PMC10051584 DOI: 10.3390/ijms24065757] [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: 12/21/2022] [Revised: 02/22/2023] [Accepted: 02/22/2023] [Indexed: 03/30/2023] Open
Abstract
Antarctic organisms are consistently suffering from multiple environmental pressures, especially the strong UV radiation caused by the loss of the ozone layer. The mosses and lichens dominate the vegetation of the Antarctic continent, which grow and propagate in these harsh environments. However, the molecular mechanisms and related regulatory networks of these Antarctic plants against UV-B radiation are largely unknown. Here, we used an integrated multi-omics approach to study the regulatory mechanism of long non-coding RNAs (lncRNAs) of an Antarctic moss (Pohlia nutans) in response to UV-B radiation. We identified a total of 5729 lncRNA sequences by transcriptome sequencing, including 1459 differentially expressed lncRNAs (DELs). Through functional annotation, we found that the target genes of DELs were significantly enriched in plant-pathogen interaction and the flavonoid synthesis pathway. In addition, a total of 451 metabolites were detected by metabonomic analysis, and 97 differentially change metabolites (DCMs) were found. Flavonoids account for 20% of the total significantly up-regulated metabolites. In addition, the comprehensive transcriptome and metabolome analyses revealed the co-expression pattern of DELs and DCMs of flavonoids. Our results provide insights into the regulatory network of lncRNA under UV-B radiation and the adaptation of Antarctic moss to the polar environments.
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Affiliation(s)
- Shuo Fang
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
| | - Bailin Cong
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
| | - Linlin Zhao
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
- Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266061, China
| | - Chenlin Liu
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
| | - Zhaohui Zhang
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
- Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266061, China
| | - Shenghao Liu
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
- Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266061, China
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Haque US, Elias SM, Jahan I, Seraj ZI. Functional genomic analysis of K + related salt-responsive transporters in tolerant and sensitive genotypes of rice. FRONTIERS IN PLANT SCIENCE 2023; 13:1089109. [PMID: 36743539 PMCID: PMC9893783 DOI: 10.3389/fpls.2022.1089109] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 12/19/2022] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Salinity is a complex environmental stress that affects the growth and production of rice worldwide. But there are some rice landraces in coastal regions that can survive in presence of highly saline conditions. An understanding of the molecular attributes contributing to the salinity tolerance of these genotypes is important for developing salt-tolerant high yielding modern genotypes to ensure food security. Therefore, we investigated the role and functional differences of two K+ salt-responsive transporters. These are OsTPKa or Vacuolar two-pore potassium channel and OsHAK_like or a hypothetical protein of the HAK family. These transporters were selected from previously identified QTLs from the tolerant rice landrace genotype (Horkuch) and sensitive genotype (IR29). METHODS In silico comparative sequence analysis of the promoter sequences of two these genes between Horkuch and IR29 was done. Real-Time expression of the selected genes in leaves and roots of IR29 (salt-sensitive), I-14 and I-71 (Recombinant Inbred Lines of IR29(♀)× Horkuch), Horkuch and Pokkali (salt-tolerant) under salt-stress at different time points was analyzed. For further insight, OsTPKa and OsHAK_like were chosen for loss-of-function genomic analysis in Horkuch using the CRISPR/Cas9 tool. Furthermore, OsTPKa was chosen for cloning into a sensitive variety by Gateway technology to observe the effect of gain-of-function. RESULTS The promoter sequences of the OsTPKa and OsHAK_like genes showed some significant differences in promoter sequences which may give a survival advantage to Horkuch under salt-stress. These two genes were also found to be overexpressed in tolerant varieties (Horkuch and Pokkali). Moreover, a coordinated expression pattern between these two genes was observed in tolerant Horkuch under salt-stress. Independently transformed plants where the expression of these genes was significantly lowered, performed poorly in physiological tests for salinity tolerance. On the other hand, positively transformed T0 plants with the OsTPKa gene from Horkuch consistently showed growth advantage under both control and salt stress. DISCUSSION The poor performance of the transgenic plants with the down-regulated genes OsTPKa and OsHAK_like under salt stress supports the assumption that OsTPKa and OsHAK_like play important roles in defending the rice landrace Horkuch against salt stress, minimizing salt injury, and maintaining plant growth. Moreover, the growth advantage provided by overexpression of the vacuolar OsTPKa K+ transporter, particularly under salt stress reconfirms its important role in providing salt tolerance. The QTL locus from Horkuch containing these two transporters maybe bred into commercial rice to produce high-yielding salt tolerant rice.
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Affiliation(s)
- Umme Sabrina Haque
- Plant Biotechnology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Sabrina M. Elias
- Department of Life Sciences, Independent University Bangladesh, Dhaka, Bangladesh
| | - Israt Jahan
- Plant Biotechnology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Zeba I. Seraj
- Plant Biotechnology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
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15
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Alkaloid production and response to natural adverse conditions in Peganum harmala: in silico transcriptome analyses. BIOTECHNOLOGIA 2022; 103:355-384. [PMID: 36685700 PMCID: PMC9837557 DOI: 10.5114/bta.2022.120706] [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: 08/22/2021] [Revised: 07/25/2022] [Accepted: 09/16/2022] [Indexed: 01/06/2023] Open
Abstract
Peganum harmala is a valuable wild plant that grows and survives under adverse conditions and produces pharmaceutical alkaloid metabolites. Using different assemblers to develop a transcriptome improves the quality of assembled transcriptome. In this study, a concrete and accurate method for detecting stress-responsive transcripts by comparing stress-related gene ontology (GO) terms and public domains was designed. An integrated transcriptome for P. harmala including 42 656 coding sequences was created by merging de novo assembled transcriptomes. Around 35 000 transcripts were annotated with more than 90% resemblance to three closely related species of Citrus, which confirmed the robustness of the assembled transcriptome; 4853 stress-responsive transcripts were identified. CYP82 involved in alkaloid biosynthesis showed a higher number of transcripts in P. harmala than in other plants, indicating its diverse alkaloid biosynthesis attributes. Transcription factors (TFs) and regulatory elements with 3887 transcripts comprised 9% of the transcriptome. Among the TFs of the integrated transcriptome, cystein2/histidine2 (C2H2) and WD40 repeat families were the most abundant. The Kyoto Encyclopedia of Genes and Genomes (KEGG) MAPK (mitogen-activated protein kinase) signaling map and the plant hormone signal transduction map showed the highest assigned genes to these pathways, suggesting their potential stress resistance. The P. harmala whole-transcriptome survey provides important resources and paves the way for functional and comparative genomic studies on this plant to discover stress-tolerance-related markers and response mechanisms in stress physiology, phytochemistry, ecology, biodiversity, and evolution. P. harmala can be a potential model for studying adverse environmental cues and metabolite biosynthesis and a major source for the production of various alkaloids.
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16
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Mirdar Mansuri R, Azizi AH, Sadri AH, Shobbar ZS. Long non-coding RNAs as the regulatory hubs in rice response to salt stress. Sci Rep 2022; 12:21696. [PMID: 36522395 PMCID: PMC9755261 DOI: 10.1038/s41598-022-26133-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
Salinity seriously constrains growth and fertility of rice worldwide. Long non-coding RNAs (lncRNAs) play crucial roles in plant abiotic stress response. However, salt responsive lncRNAs are poorly understood in rice. Herein, salt responsive lncRNAs (DE-lncRNAs) were identified in FL478 (salt tolerant) compared to its susceptible parent (IR29) using RNA-seq in root tissues at seedling stage. In FL478 and IR29, 8724 and 9235 transcripts with length of > 200 bp were nominated as potential lncRNAs, respectively. Rigorous filtering left four (in FL478) and nine (in IR29) DE-lncRNAs with only 2 DE-lncRNAs in common. ATAC-seq data showed that the genomic regions of all four lncRNAs in FL478 and 6/9 in IR29 are significantly accessible for transcription. Weighted correlation network analysis (WGCNA) revealed that lncRNA.2-FL was highly correlated with 173 mRNAs as trans-targets and a gene encoding pentatricopeptide repeat (PPR) protein was predicted as cis-target of lncRNA.2-FL. In silico mutagenesis analysis proposed the same transcription factor binding sites (TFBSs) in vicinity of the trans- and cis-regulatory target genes of lncRNA.2-FL, which significantly affect their transcription start site (TSS). This study provides new insights into involvement of the DE-lncRNAs in rice response to salt stress. Among them, lncRNA.2-FL may play a significant regulatory role in the salt stress tolerance of FL478.
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Affiliation(s)
- Raheleh Mirdar Mansuri
- grid.417749.80000 0004 0611 632XDepartment of Systems Biology, Agricultural Research, Education and Extension Organization (AREEO), Agricultural Biotechnology Research Institute of Iran (ABRII), PO Box 31535-1897, Karaj, Iran
| | - Amir-Hossein Azizi
- grid.417749.80000 0004 0611 632XDepartment of Systems Biology, Agricultural Research, Education and Extension Organization (AREEO), Agricultural Biotechnology Research Institute of Iran (ABRII), PO Box 31535-1897, Karaj, Iran
| | - Amir-Hossein Sadri
- grid.417749.80000 0004 0611 632XDepartment of Systems Biology, Agricultural Research, Education and Extension Organization (AREEO), Agricultural Biotechnology Research Institute of Iran (ABRII), PO Box 31535-1897, Karaj, Iran
| | - Zahra-Sadat Shobbar
- grid.417749.80000 0004 0611 632XDepartment of Systems Biology, Agricultural Research, Education and Extension Organization (AREEO), Agricultural Biotechnology Research Institute of Iran (ABRII), PO Box 31535-1897, Karaj, Iran
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Jian G, Mo Y, Hu Y, Huang Y, Ren L, Zhang Y, Hu H, Zhou S, Liu G, Guo J, Ling Y. Variety-Specific Transcriptional and Alternative Splicing Regulations Modulate Salt Tolerance in Rice from Early Stage of Stress. RICE (NEW YORK, N.Y.) 2022; 15:56. [PMID: 36326968 PMCID: PMC9633917 DOI: 10.1186/s12284-022-00599-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Salt stress poses physiological drought, ionic toxicity and oxidative stress to plants, which causes premature senescence and death of the leaves if the stress sustained. Salt tolerance varied between different rice varieties, but how different rice varieties respond at the early stage of salt stress has been seldom studied comprehensively. By employing third generation sequencing technology, we compared gene expressional changes in leaves of three rice varieties that varied in their level of tolerance after salt stress treatment for 6 h. Commonly up-regulated genes in all rice varieties were related to water shortage response and carbon and amino acids metabolism at the early stage of salt stress, while reactive oxygen species cleavage genes were induced more in salt-tolerant rice. Unexpectedly, genes involved in chloroplast development and photosynthesis were more significantly down-regulated in the two salt tolerant rice varieties 'C34' and 'Nona Bokra'. At the same time, genes coding ribosomal protein were suppressed to a more severe extent in the salt-sensitive rice variety 'IR29'. Interestingly, not only variety-specific gene transcriptional regulation, but also variety-specific mRNA alternative splicing, on both coding and long-noncoding genes, were found at the early stage of salt stress. In summary, differential regulation in gene expression at both transcriptional and post-transcriptional levels, determine and fine-tune the observed response in level of damage in leaves of specific rice genotypes at early stage of salt stress.
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Affiliation(s)
- Guihua Jian
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Yujian Mo
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Yan Hu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Yongxiang Huang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, People's Republic of China
| | - Lei Ren
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, People's Republic of China
| | - Yueqin Zhang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, People's Republic of China
| | - Hanqiao Hu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, People's Republic of China
| | - Shuangxi Zhou
- Department of Biological Sciences, Macquarie University, North Ryde, NSW, 2019, Australia
| | - Gang Liu
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430064, People's Republic of China
| | - Jianfu Guo
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China.
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, People's Republic of China.
| | - Yu Ling
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China.
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, People's Republic of China.
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18
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Salt tolerance QTLs of an endemic rice landrace, Horkuch at seedling and reproductive stages. Sci Rep 2022; 12:17306. [PMID: 36243755 PMCID: PMC9569374 DOI: 10.1038/s41598-022-21737-9] [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: 05/17/2022] [Accepted: 09/30/2022] [Indexed: 01/10/2023] Open
Abstract
Salinity has a significant negative impact on production of rice. To cope with the increased soil salinity due to climate change, we need to develop salt tolerant rice varieties that can maintain their high yield. Rice landraces indigenous to coastal Bangladesh can be a great resource to study the genetic basis of salt adaptation. In this study, we implemented a QTL analysis framework with a reciprocal mapping population developed from a salt tolerant landrace Horkuch and a high yielding rice variety IR29. Our aim was to detect genetic loci that contributes to the salt adaptive responses of the two different developmental stages of rice which are very sensitive to salinity stress. We identified 14 QTLs for 9 traits and found that most are unique to specific developmental stages. In addition, we detected a significant effect of the cytoplasmic genome on the QTL model for some traits such as leaf total potassium and filled grain weight. This underscores the importance of considering cytoplasm-nuclear interaction for breeding programs. Finally, we identified QTLs co-localization for multiple traits that highlights the possible constraint of multiple QTL selection for breeding programs due to different contributions of a donor allele for different traits.
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Hidayah A, Nisak RR, Susanto FA, Nuringtyas TR, Yamaguchi N, Purwestri YA. Seed Halopriming Improves Salinity Tolerance of Some Rice Cultivars During Seedling Stage. BOTANICAL STUDIES 2022; 63:24. [PMID: 35877013 PMCID: PMC9314496 DOI: 10.1186/s40529-022-00354-9] [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: 12/14/2021] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Saline land in coastal areas has great potential for crop cultivation. Improving salt tolerance in rice is a key to expanding the available area for its growth and thus improving global food security. Seed priming with salt (halopriming) can enhance plant growth and decrease saline intolerance under salt stress conditions during the subsequent seedling stage. However, there is little known about rice defense mechanisms against salinity at seedling stages after seed halopriming treatment. This study focused on the effect of seed halopriming treatment on salinity tolerance in a susceptible cultivar, IR 64, a resistant cultivar, Pokkali, and two pigmented rice cultivars, Merah Kalimantan Selatan (Merah Kalsel) and Cempo Ireng Pendek (CI Pendek). We grew these cultivars in hydroponic culture, with and without halopriming at the seed stage, under either non-salt or salt stress conditions during the seedling stage. RESULTS The SES scoring assessment showed that the level of salinity tolerance in susceptible cultivar, IR 64, and moderate cultivar, Merah Kalsel, improved after seed halopriming treatment. Furthermore, seed halopriming improved the growth performance of IR 64 and Merah Kalsel rice seedlings. Quantitative PCR revealed that seed halopriming induced expression of the OsNHX1 and OsHKT1 genes in susceptible rice cultivar, IR 64 and Merah Kalsel thereby increasing the level of resistance to salinity. The expression levels of OsSOS1 and OsHKT1 genes in resistant cultivar, Pokkali, also increased but there was no affect on the level of salinity tolerance. On the contrary, seed halopriming decreased the expression level of OsSOS1 genes in pigmented rice cultivar, CI Pendek, but did not affect the level of salinity tolerance. The transporter gene expression induction significantly improved salinity tolerance in salinity-susceptible rice, IR 64, and moderately tolerant rice cultivar, Merah Kalsel. Induction of expression of the OsNHX1 and OsHKT1 genes in susceptible rice, IR 64, after halopriming seed treatment balances the osmotic pressure and prevents the accumulation of toxic concentrations of Na+, resulting in tolerance to salinity stress. CONCLUSION These results suggest that seed halopriming can improve salinity tolerance of salinity-susceptible and moderately tolerant rice cultivars.
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Affiliation(s)
- Anik Hidayah
- Biotechnology Study Program, The Graduate School, Universitas Gadjah Mada, Jl. Teknika Utara, Sleman, Yogyakarta, 55281, Indonesia
- Agricultural Environmental Division, Indonesian Agency For Agricultural Research and Development, Jl. Raya Jakenan-Jaken Km. 5, Central Java, 59182, Pati, Indonesia
| | - Rizka Rohmatin Nisak
- Biochemistry Laboratory, Department of Tropical Biology, Faculty of Biology, Universitas Gadjah Mada, Jl. Teknika Selatan, Sekip Utara, Yogyakarta, 55281, Indonesia
| | - Febri Adi Susanto
- Research Center for Biotechnology, Universitas Gadjah Mada, Jl. Teknika Utara, Sleman, Yogyakarta, 55281, Indonesia
| | - Tri Rini Nuringtyas
- Biochemistry Laboratory, Department of Tropical Biology, Faculty of Biology, Universitas Gadjah Mada, Jl. Teknika Selatan, Sekip Utara, Yogyakarta, 55281, Indonesia
- Research Center for Biotechnology, Universitas Gadjah Mada, Jl. Teknika Utara, Sleman, Yogyakarta, 55281, Indonesia
| | - Nobutoshi Yamaguchi
- Plant Stem Cell Regulation and Floral Patterning Laboratory, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Japan
| | - Yekti Asih Purwestri
- Biochemistry Laboratory, Department of Tropical Biology, Faculty of Biology, Universitas Gadjah Mada, Jl. Teknika Selatan, Sekip Utara, Yogyakarta, 55281, Indonesia.
- Research Center for Biotechnology, Universitas Gadjah Mada, Jl. Teknika Utara, Sleman, Yogyakarta, 55281, Indonesia.
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20
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Muthuramalingam P, Jeyasri R, Rakkammal K, Satish L, Shamili S, Karthikeyan A, Valliammai A, Priya A, Selvaraj A, Gowri P, Wu QS, Karutha Pandian S, Shin H, Chen JT, Baskar V, Thiruvengadam M, Akilan M, Ramesh M. Multi-Omics and Integrative Approach towards Understanding Salinity Tolerance in Rice: A Review. BIOLOGY 2022; 11:biology11071022. [PMID: 36101403 PMCID: PMC9312129 DOI: 10.3390/biology11071022] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/04/2022] [Accepted: 07/04/2022] [Indexed: 11/16/2022]
Abstract
Rice (Oryza sativa L.) plants are simultaneously encountered by environmental stressors, most importantly salinity stress. Salinity is the major hurdle that can negatively impact growth and crop yield. Understanding the salt stress and its associated complex trait mechanisms for enhancing salt tolerance in rice plants would ensure future food security. The main aim of this review is to provide insights and impacts of molecular-physiological responses, biochemical alterations, and plant hormonal signal transduction pathways in rice under saline stress. Furthermore, the review highlights the emerging breakthrough in multi-omics and computational biology in identifying the saline stress-responsive candidate genes and transcription factors (TFs). In addition, the review also summarizes the biotechnological tools, genetic engineering, breeding, and agricultural practicing factors that can be implemented to realize the bottlenecks and opportunities to enhance salt tolerance and develop salinity tolerant rice varieties. Future studies pinpointed the augmentation of powerful tools to dissect the salinity stress-related novel players, reveal in-depth mechanisms and ways to incorporate the available literature, and recent advancements to throw more light on salinity responsive transduction pathways in plants. Particularly, this review unravels the whole picture of salinity stress tolerance in rice by expanding knowledge that focuses on molecular aspects.
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Affiliation(s)
- Pandiyan Muthuramalingam
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630 003, India; (P.M.); (R.J.); (K.R.); (A.V.); (A.P.); (A.S.); (S.K.P.)
- Department of Horticultural Science, Gyeongsang National University, Jinju 52725, Korea
- Department of GreenBio Science, Gyeongsang National University, Jinju 52725, Korea
| | - Rajendran Jeyasri
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630 003, India; (P.M.); (R.J.); (K.R.); (A.V.); (A.P.); (A.S.); (S.K.P.)
| | - Kasinathan Rakkammal
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630 003, India; (P.M.); (R.J.); (K.R.); (A.V.); (A.P.); (A.S.); (S.K.P.)
| | - Lakkakula Satish
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel;
- The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel;
| | - Sasanala Shamili
- The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel;
| | - Adhimoolam Karthikeyan
- Subtropical Horticulture Research Institute, Jeju National University, Jeju 63243, Korea;
| | - Alaguvel Valliammai
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630 003, India; (P.M.); (R.J.); (K.R.); (A.V.); (A.P.); (A.S.); (S.K.P.)
| | - Arumugam Priya
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630 003, India; (P.M.); (R.J.); (K.R.); (A.V.); (A.P.); (A.S.); (S.K.P.)
| | - Anthonymuthu Selvaraj
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630 003, India; (P.M.); (R.J.); (K.R.); (A.V.); (A.P.); (A.S.); (S.K.P.)
| | - Pandiyan Gowri
- Department of Botany, Science Campus, Alagappa University, Karaikudi 630 003, India;
| | - Qiang-Sheng Wu
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, China;
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, 50003 Hradec Kralove, Czech Republic
| | - Shunmugiah Karutha Pandian
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630 003, India; (P.M.); (R.J.); (K.R.); (A.V.); (A.P.); (A.S.); (S.K.P.)
| | - Hyunsuk Shin
- Department of Horticultural Science, Gyeongsang National University, Jinju 52725, Korea
- Department of GreenBio Science, Gyeongsang National University, Jinju 52725, Korea
- Correspondence: (H.S.); (M.T.); (M.R.)
| | - Jen-Tsung Chen
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung 811, Taiwan;
| | - Venkidasamy Baskar
- Department of Oral and Maxillofaciel Surgery, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Chennai 602 105, India;
| | - Muthu Thiruvengadam
- Department of Crop Science, College of Sanghuh Life Science, Konkuk University, Seoul 05029, Korea
- Correspondence: (H.S.); (M.T.); (M.R.)
| | - Manoharan Akilan
- Department of Plant Breeding and Genetics, Anbil Dharmalingam Agricultural College and Research Institute, Tamil Nadu Agricultural University, Trichy 620 027, India;
| | - Manikandan Ramesh
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630 003, India; (P.M.); (R.J.); (K.R.); (A.V.); (A.P.); (A.S.); (S.K.P.)
- Correspondence: (H.S.); (M.T.); (M.R.)
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Habila S, Khunpolwattana N, Chantarachot T, Buaboocha T, Comai L, Chadchawan S, Pongpanich M. Salt stress responses and SNP-based phylogenetic analysis of Thai rice cultivars. THE PLANT GENOME 2022; 15:e20189. [PMID: 34994516 DOI: 10.1002/tpg2.20189] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 11/30/2021] [Indexed: 05/24/2023]
Abstract
Genetic diversity is important for developing salt-tolerant rice (Oryza sativa L.) cultivars. Certain Thai rice accessions display salt tolerance at the adult or reproductive stage, but their response to salinity at the seedling stage is unknown. In this study, a total of 10 rice cultivars/line, including eight Thai cultivars and standard salt-tolerant cultivar and susceptible line, were screened using a hydroponic system to identify salt-tolerant genotypes at the seedling stage. Different morphophysiological indicators were used to classify tolerant and susceptible genotypes. Phylogenetic analyses were performed to determine the evolutionary relationships between the cultivars. Results showed that 'Lai Mahk', 'Jao Khao', 'Luang Pratahn', and 'Ma Gawk' exhibited salt stress tolerance comparable with the standard salt-tolerance check 'Pokkali'. Whole-exome single-nucleotide polymorphism (SNP)-based phylogenetic analysis showed that the Thai rice cultivars were monophyletic and distantly related to Pokkali and IR29. Lai Mahk and Luang Pratahn were found closely related when using the whole-exome SNPs for the analysis. This is also the case for the analysis of SNPs from 164 salt-tolerance genes and transcription regulatory genes. The tolerant cultivars shared the same haplotype for 16 genes. Overall, the findings of this study identified four salt-stress-tolerant Thai rice cultivars, which could be used in rice breeding programs for salinity tolerance.
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Affiliation(s)
- Susinya Habila
- Center of Excellence in Environment and Plant Physiology, Dep. of Botany, Faculty of Science, Chulalongkorn Univ., Pathum Wan District, Bangkok, 10330, Thailand
- Dep. of Plant Science and Biotechnology, Faculty of Natural Science, Univ. of Jos, Jos Plateau State, Nigeria
| | - Nopphakhun Khunpolwattana
- Center of Excellence in Environment and Plant Physiology, Dep. of Botany, Faculty of Science, Chulalongkorn Univ., Pathum Wan District, Bangkok, 10330, Thailand
| | - Thanin Chantarachot
- Center of Excellence in Environment and Plant Physiology, Dep. of Botany, Faculty of Science, Chulalongkorn Univ., Pathum Wan District, Bangkok, 10330, Thailand
| | - Teerapong Buaboocha
- Molecular Crop Research Unit, Dep. of Biochemistry, Faculty of Science, Chulalongkorn Univ., Pathum Wan District, Bangkok, 10330, Thailand
- Omics Sciences Center, Faculty of Science, Chulalongkorn Univ., Pathum Wan District, Bangkok, 10330, Thailand
| | - Luca Comai
- Genome Center and Dep. of Plant Biology, UC Davis Genome Center, Univ. of California-Davis, Davis, CA, 95616, USA
| | - Supachitra Chadchawan
- Center of Excellence in Environment and Plant Physiology, Dep. of Botany, Faculty of Science, Chulalongkorn Univ., Pathum Wan District, Bangkok, 10330, Thailand
- Omics Sciences Center, Faculty of Science, Chulalongkorn Univ., Pathum Wan District, Bangkok, 10330, Thailand
| | - Monnat Pongpanich
- Omics Sciences Center, Faculty of Science, Chulalongkorn Univ., Pathum Wan District, Bangkok, 10330, Thailand
- Dep. of Mathematics and Computer Science, Faculty Science, Chulalongkorn Univ., Pathum Wan District, Bangkok, 10330, Thailand
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Chennakesavulu K, Singh H, Trivedi PK, Jain M, Yadav SR. State-of-the-Art in CRISPR Technology and Engineering Drought, Salinity, and Thermo-tolerant crop plants. PLANT CELL REPORTS 2022; 41:815-831. [PMID: 33742256 DOI: 10.1007/s00299-021-02681-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/04/2021] [Indexed: 05/28/2023]
Abstract
Our review has described principles and functional importance of CRISPR-Cas9 with emphasis on the recent advancements, such as CRISPR-Cpf1, base editing (BE), prime editing (PE), epigenome editing, tissue-specific (CRISPR-TSKO), and inducible genome editing and their potential applications in generating stress-tolerant plants. Improved agricultural practices and enhanced food crop production using innovative crop breeding technology is essential for increasing access to nutritious foods across the planet. The crop plants play a pivotal role in energy and nutrient supply to humans. The abiotic stress factors, such as drought, heat, and salinity cause a substantial yield loss in crop plants and threaten food security. The most sustainable and eco-friendly way to overcome these challenges are the breeding of crop cultivars with improved tolerance against abiotic stress factors. The conventional plant breeding methods have been highly successful in developing abiotic stress-tolerant crop varieties, but usually cumbersome and time-consuming. Alternatively, the CRISPR/Cas genome editing has emerged as a revolutionary tool for making efficient and precise genetic manipulations in plant genomes. Here, we provide a comprehensive review of the CRISPR/Cas genome editing (GE) technology with an emphasis on recent advances in the plant genome editing, including base editing (BE), prime editing (PE), epigenome editing, tissue-specific (CRISPR-TSKO), and inducible genome editing (CRISPR-IGE), which can be used for obtaining cultivars with enhanced tolerance to various abiotic stress factors. We also describe tissue culture-free, DNA-free GE technology, and some of the CRISPR-based tools that can be modified for their use in crop plants.
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Affiliation(s)
- Kunchapu Chennakesavulu
- Department of Biotechnology, Indian Institute of Technology, Roorkee, Uttarakhand, 247667, India
| | - Harshita Singh
- Department of Biotechnology, Indian Institute of Technology, Roorkee, Uttarakhand, 247667, India
| | - Prabodh Kumar Trivedi
- CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Near Kukrail Picnic Spot, Lucknow, 226015, India
| | - Mukesh Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Shri Ram Yadav
- Department of Biotechnology, Indian Institute of Technology, Roorkee, Uttarakhand, 247667, India.
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Roy S, Mishra M, Kaur G, Singh S, Rawat N, Singh P, Singla-Pareek SL, Pareek A. OsCyp2-P, an auxin-responsive cyclophilin, regulates Ca 2+ calmodulin interaction for an ion-mediated stress response in rice. PHYSIOLOGIA PLANTARUM 2022; 174:e13631. [PMID: 35049071 DOI: 10.1111/ppl.13631] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/23/2021] [Accepted: 01/14/2022] [Indexed: 05/24/2023]
Abstract
OsCYP2-P is an active cyclophilin (having peptidyl-prolyl cis/trans-isomerase activity, PPIase) isolated from the wild rice Pokkali having a natural capacity to grow and yield seeds in coastal saline regions of India. Transcript abundance analysis in rice seedlings showed the gene is inducible by multiple stresses, including salinity, drought, high temperature, and heavy metals. To dissect the role of OsCYP2-P gene in stress response, we raised overexpression (OE) and knockdown (KD) transgenic rice plants with >2-3 folds higher and approximately 2-fold lower PPIase activity, respectively. Plants overexpressing this gene had more favorable physiological and biochemical parameters (K+ /Na+ ratio, electrolytic leakage, membrane damage, antioxidant enzymes) than wild type, and the reverse was observed in plants that were knocked down for this gene. We propose that OsCYP2-P contributes to stress tolerance via maintenance of ion homeostasis and thus prevents toxic cellular ion buildup and membrane damage. OE plants were found to have a higher harvest index and higher number of filled grains under salinity and drought stress than wild type. OsCYP2-P interacts with calmodulin, indicating it functions via the Ca-CaM pathway. Compared to the WT, the germinating OE seeds exhibited a substantially higher auxin level, and this hormone was below the detection limits in the WT and KD lines. These observations strongly indicate that OsCyp2-P affects the signaling and transport of auxin in rice.
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Affiliation(s)
- Suchismita Roy
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Manjari Mishra
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Gundeep Kaur
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, India
| | - Supreet Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, India
| | - Nishtha Rawat
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Prabhjeet Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, India
| | - Sneh L Singla-Pareek
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Ashwani Pareek
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
- National Agri-Food Biotechnology Institute (NABI), Mohali, India
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24
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Ravelombola W, Shi A, Huynh BL, Qin J, Xiong H, Manley A, Dong L, Olaoye D, Bhattarai G, Zia B, Alshaya H, Alatawi I. Genetic architecture of salt tolerance in a Multi-Parent Advanced Generation Inter-Cross (MAGIC) cowpea population. BMC Genomics 2022; 23:100. [PMID: 35123403 PMCID: PMC8817504 DOI: 10.1186/s12864-022-08332-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 01/21/2022] [Indexed: 11/22/2022] Open
Abstract
Background Previous reports have shown that soil salinity is a growing threat to cowpea production, and thus the need for breeding salt-tolerant cowpea cultivars. A total of 234 Multi-Parent Advanced Generation Inter-Cross (MAGIC) lines along with their 8 founders were evaluated for salt tolerance under greenhouse conditions. The objectives of this study were to evaluate salt tolerance in a multi-parent advanced generation inter-cross (MAGIC) cowpea population, to identify single nucleotide polymorphism (SNP) markers associated with salt tolerance, and to assess the accuracy of genomic selection (GS) in predicting salt tolerance, and to explore possible epistatic interactions affecting salt tolerance in cowpea. Phenotyping was validated through the use of salt-tolerant and salt-susceptible controls that were previously reported. Genome-wide association study (GWAS) was conducted using a total of 32,047 filtered SNPs. The epistatic interaction analysis was conducted using the PLINK platform. Results Results indicated that: (1) large variation in traits evaluated for salt tolerance was identified among the MAGIC lines, (2) a total of 7, 2, 18, 18, 3, 2, 5, 1, and 23 were associated with number of dead plants, salt injury score, leaf SPAD chlorophyll under salt treatment, relative tolerance index for leaf SPAD chlorophyll, fresh leaf biomass under salt treatment, relative tolerance index for fresh leaf biomass, relative tolerance index for fresh stem biomass, relative tolerance index for the total above-ground fresh biomass, and relative tolerance index for plant height, respectively, with overlapping SNP markers between traits, (3) candidate genes encoding for proteins involved in ion transport such as Na+/Ca2+ K+ independent exchanger and H+/oligopeptide symporter were identified, and (4) epistatic interactions were identified. Conclusions These results will have direct applications in breeding programs aiming at improving salt tolerance in cowpea through marker-assisted selection. To the best of our knowledge, this study was one of the earliest reports using a MAGIC population to investigate the genetic architecture of salt tolerance in cowpea. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08332-y.
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Bansal J, Gupta K, Rajkumar MS, Garg R, Jain M. Draft genome and transcriptome analyses of halophyte rice Oryza coarctata provide resources for salinity and submergence stress response factors. PHYSIOLOGIA PLANTARUM 2021; 173:1309-1322. [PMID: 33215706 DOI: 10.1111/ppl.13284] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 11/05/2020] [Accepted: 11/17/2020] [Indexed: 05/24/2023]
Abstract
Oryza coarctata is a wild relative of rice that has adapted to diverse ecological environments, including high salinity and submergence. Thus, it can provide an important resource for discovering candidate genes/factors involved in tolerance to these stresses. Here, we report a draft genome assembly of 573 Mb comprised of 8877 scaffolds with N50 length of 205 kb. We predicted a total of 50,562 protein-coding genes, of which a significant fraction was found to be involved in secondary metabolite biosynthesis and hormone signal transduction pathways. Several salinity and submergence stress-responsive protein-coding and long noncoding RNAs involved in diverse biological processes were identified using RNA-sequencing data. Based on small RNA sequencing, we identified 168 unique miRNAs and 3219 target transcripts (coding and noncoding) involved in several biological processes, including abiotic stress responses. Further, whole genome bisulphite sequencing data analysis revealed at least 19%-48% methylcytosines in different sequence contexts and the influence of methylation status on gene expression. The genome assembly along with other datasets have been made publicly available at http://ccbb.jnu.ac.in/ory-coar. Altogether, we provide a comprehensive genomic resource for understanding the regulation of salinity and submergence stress responses and identification of candidate genes/factors involved for functional genomics studies.
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Affiliation(s)
- Juhi Bansal
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Khushboo Gupta
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Noida, India
| | - Mohan Singh Rajkumar
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Rohini Garg
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Noida, India
| | - Mukesh Jain
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
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26
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Saradadevi GP, Das D, Mangrauthia SK, Mohapatra S, Chikkaputtaiah C, Roorkiwal M, Solanki M, Sundaram RM, Chirravuri NN, Sakhare AS, Kota S, Varshney RK, Mohannath G. Genetic, Epigenetic, Genomic and Microbial Approaches to Enhance Salt Tolerance of Plants: A Comprehensive Review. BIOLOGY 2021; 10:biology10121255. [PMID: 34943170 PMCID: PMC8698797 DOI: 10.3390/biology10121255] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 12/17/2022]
Abstract
Simple Summary Globally, soil salinity, which refers to salt-affected soils, is increasing due to various environmental factors and human activities. Soil salinity poses one of the most serious challenges in the field of agriculture as it significantly reduces the growth and yield of crop plants, both quantitatively and qualitatively. Over the last few decades, several studies have been carried out to understand plant biology in response to soil salinity stress with a major emphasis on genetic and other hereditary components. Based on the outcome of these studies, several approaches are being followed to enhance plants’ ability to tolerate salt stress while still maintaining reasonable levels of crop yields. In this manuscript, we comprehensively list and discuss various biological approaches being followed and, based on the recent advances in the field of molecular biology, we propose some new approaches to improve salinity tolerance of crop plants. The global scientific community can make use of this information for the betterment of crop plants. This review also highlights the importance of maintaining global soil health to prevent several crop plant losses. Abstract Globally, soil salinity has been on the rise owing to various factors that are both human and environmental. The abiotic stress caused by soil salinity has become one of the most damaging abiotic stresses faced by crop plants, resulting in significant yield losses. Salt stress induces physiological and morphological modifications in plants as a result of significant changes in gene expression patterns and signal transduction cascades. In this comprehensive review, with a major focus on recent advances in the field of plant molecular biology, we discuss several approaches to enhance salinity tolerance in plants comprising various classical and advanced genetic and genetic engineering approaches, genomics and genome editing technologies, and plant growth-promoting rhizobacteria (PGPR)-based approaches. Furthermore, based on recent advances in the field of epigenetics, we propose novel approaches to create and exploit heritable genome-wide epigenetic variation in crop plants to enhance salinity tolerance. Specifically, we describe the concepts and the underlying principles of epigenetic recombinant inbred lines (epiRILs) and other epigenetic variants and methods to generate them. The proposed epigenetic approaches also have the potential to create additional genetic variation by modulating meiotic crossover frequency.
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Affiliation(s)
- Gargi Prasad Saradadevi
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Hyderabad Campus, Hyderabad 500078, India; (G.P.S.); (S.M.)
| | - Debajit Das
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat 785006, India; (D.D.); (C.C.)
| | - Satendra K. Mangrauthia
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (S.K.M.); (M.S.); (R.M.S.); (N.N.C.); (A.S.S.)
| | - Sridev Mohapatra
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Hyderabad Campus, Hyderabad 500078, India; (G.P.S.); (S.M.)
| | - Channakeshavaiah Chikkaputtaiah
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat 785006, India; (D.D.); (C.C.)
| | - Manish Roorkiwal
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India;
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia
| | - Manish Solanki
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (S.K.M.); (M.S.); (R.M.S.); (N.N.C.); (A.S.S.)
| | - Raman Meenakshi Sundaram
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (S.K.M.); (M.S.); (R.M.S.); (N.N.C.); (A.S.S.)
| | - Neeraja N. Chirravuri
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (S.K.M.); (M.S.); (R.M.S.); (N.N.C.); (A.S.S.)
| | - Akshay S. Sakhare
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (S.K.M.); (M.S.); (R.M.S.); (N.N.C.); (A.S.S.)
| | - Suneetha Kota
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (S.K.M.); (M.S.); (R.M.S.); (N.N.C.); (A.S.S.)
- Correspondence: (S.K.); (R.K.V.); (G.M.); Tel.: +91-40-245-91268 (S.K.); +91-84-556-83305 (R.K.V.); +91-40-66303697 (G.M.)
| | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India;
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA 6150, Australia
- Correspondence: (S.K.); (R.K.V.); (G.M.); Tel.: +91-40-245-91268 (S.K.); +91-84-556-83305 (R.K.V.); +91-40-66303697 (G.M.)
| | - Gireesha Mohannath
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Hyderabad Campus, Hyderabad 500078, India; (G.P.S.); (S.M.)
- Correspondence: (S.K.); (R.K.V.); (G.M.); Tel.: +91-40-245-91268 (S.K.); +91-84-556-83305 (R.K.V.); +91-40-66303697 (G.M.)
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Riccio-Rengifo C, Finke J, Rocha C. Identifying stress responsive genes using overlapping communities in co-expression networks. BMC Bioinformatics 2021; 22:541. [PMID: 34743699 PMCID: PMC8574028 DOI: 10.1186/s12859-021-04462-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 10/26/2021] [Indexed: 11/17/2022] Open
Abstract
Background This paper proposes a workflow to identify genes that respond to specific treatments in plants. The workflow takes as input the RNA sequencing read counts and phenotypical data of different genotypes, measured under control and treatment conditions. It outputs a reduced group of genes marked as relevant for treatment response. Technically, the proposed approach is both a generalization and an extension of WGCNA. It aims to identify specific modules of overlapping communities underlying the co-expression network of genes. Module detection is achieved by using Hierarchical Link Clustering. The overlapping nature of the systems’ regulatory domains that generate co-expression can be identified by such modules. LASSO regression is employed to analyze phenotypic responses of modules to treatment. Results The workflow is applied to rice (Oryza sativa), a major food source known to be highly sensitive to salt stress. The workflow identifies 19 rice genes that seem relevant in the response to salt stress. They are distributed across 6 modules: 3 modules, each grouping together 3 genes, are associated to shoot K content; 2 modules of 3 genes are associated to shoot biomass; and 1 module of 4 genes is associated to root biomass. These genes represent target genes for the improvement of salinity tolerance in rice. Conclusions A more effective framework to reduce the search-space for target genes that respond to a specific treatment is introduced. It facilitates experimental validation by restraining efforts to a smaller subset of genes of high potential relevance.
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Affiliation(s)
- Camila Riccio-Rengifo
- Department of Natural Sciences and Mathematics, Pontificia Universidad Javeriana, Cali, Colombia.
| | - Jorge Finke
- Department of Electronics and Computer Science, Pontificia Universidad Javeriana, Cali, Colombia
| | - Camilo Rocha
- Department of Electronics and Computer Science, Pontificia Universidad Javeriana, Cali, Colombia
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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.
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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.
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Abstract
Lysine is the first limiting essential amino acid in rice because it is present in the lowest quantity compared to all the other amino acids. Amino acids are the building block of proteins and play an essential role in maintaining the human body’s healthy functioning. Rice is a staple food for more than half of the global population; thus, increasing the lysine content in rice will help improve global health. In this paper, we studied the lysine biosynthesis pathway in rice (Oryza sativa) to identify the regulators of the lysine reporter gene LYSA (LOC_Os02g24354). Genetically intervening at the regulators has the potential to increase the overall lysine content in rice. We modeled the lysine biosynthesis pathway in rice seedlings under normal and saline (NaCl) stress conditions using Bayesian networks. We estimated the model parameters using experimental data and identified the gene DAPF(LOC_Os12g37960) as a positive regulator of the lysine reporter gene LYSA under both normal and saline stress conditions. Based on this analysis, we conclude that the gene DAPF is a potent candidate for genetic intervention. Upregulating DAPF using methods such as CRISPR-Cas9 gene editing strategy has the potential to upregulate the lysine reporter gene LYSA and increase the overall lysine content in rice.
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Giorio P, Sellami MH. Polyphasic OKJIP Chlorophyll a Fluorescence Transient in a Landrace and a Commercial Cultivar of Sweet Pepper ( Capsicum annuum, L.) under Long-Term Salt Stress. PLANTS 2021; 10:plants10050887. [PMID: 33924904 PMCID: PMC8145502 DOI: 10.3390/plants10050887] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 04/22/2021] [Accepted: 04/25/2021] [Indexed: 11/16/2022]
Abstract
In a soilless long-term salt-stress experiment, we tested the differences between the commercial sweet pepper cultivar “Quadrato d’Asti” and the landrace “Cazzone Giallo” in the structure and function of PSII through the JIP test analysis of the fast chlorophyll fluorescence transients (OKJIP). Salt stress inactivated the oxygen-evolving complex. Performance index detected the stress earlier than the maximum quantum yield of PSII, which remarkably decreased in the long term. The detrimental effects of salinity on the oxygen evolving-complex, the trapping of light energy in PSII, and delivering in the electron transport chain occurred earlier and more in the landrace than the cultivar. Performance indexes decreased earlier than the maximum quantum yield of PSII. Stress-induced inactivation of PSII reaction centers reached 22% in the cultivar and 45% in the landrace. The resulted heat dissipation had the trade-off of a correspondent reduced energy flow per sample leaf area, thus an impaired potential carbon fixation. These results corroborate the reported higher tolerance to salt stress of the commercial cultivar than the landrace in terms of yield. PSII was more affected than PSI, which functionality recovered in the late of trial, especially in the cultivar, possibly due to heat dissipation mechanisms. This study gives valuable information for breeding programs aiming to improve tolerance in salt stress sensitive sweet pepper genotypes.
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Wuxal amino (Bio stimulant) improved growth and physiological performance of tomato plants under salinity stress through adaptive mechanisms and antioxidant potential. Saudi J Biol Sci 2021; 28:3204-3213. [PMID: 34121857 PMCID: PMC8176060 DOI: 10.1016/j.sjbs.2021.04.040] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/15/2021] [Accepted: 04/17/2021] [Indexed: 12/28/2022] Open
Abstract
In the present study, ameliorative capabilities of wuxal amino (bio stimulant) under salt stress has been investigated through adaptive mechanisms and antioxidant potential in tomato plants. In the experiment, two different concentrations (2 cm L-1 and 3 cm L-1) of wuxal amino through foliar application and soil irrigation were applied to the salt (150 mM) treated tomato plants and then morphological traits, photosynthetic pigments, osmolytes, secondary metabolites, oxidative stress and antioxidant enzymes activity were assessed at 60 days after planting. The results revealed that salt stress decreased the growth parameters, photosynthetic pigments, soluble sugars and soluble protein whereas, content of proline, ascorbic acid, total phenols, malondialdehyde, hydrogen peroxide and the activity of antioxidant enzymes activity increased under salt stress. Moreover, Wuxal amino application through foliar or soil to salt stressed plants improved morphological traits, photosynthetic pigments, osmolytes, total phenol and antioxidant enzymes activity. Interestingly, the deleterious impact of salinity on tomato plants were significantly reduced and it can be evident from reduced MDA and H2O2 levels. These responses varied with the mode (foliar or soil) of application of Wuxal amino under different concentrations (2 cm L-1 and 3 cm L-1). It was concluded that application of Wuxal amino (2 cm L-1, foliar) and (3 cm L-1; soil) proved best and could be commercially used as eco-friendly tool for the protection of tomato plants grown under salinity stress.
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Ganie SA, Reddy ASN. Stress-Induced Changes in Alternative Splicing Landscape in Rice: Functional Significance of Splice Isoforms in Stress Tolerance. BIOLOGY 2021; 10:309. [PMID: 33917813 PMCID: PMC8068108 DOI: 10.3390/biology10040309] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 04/01/2021] [Accepted: 04/06/2021] [Indexed: 12/20/2022]
Abstract
Improvements in yield and quality of rice are crucial for global food security. However, global rice production is substantially hindered by various biotic and abiotic stresses. Making further improvements in rice yield is a major challenge to the rice research community, which can be accomplished through developing abiotic stress-resilient rice varieties and engineering durable agrochemical-independent pathogen resistance in high-yielding elite rice varieties. This, in turn, needs increased understanding of the mechanisms by which stresses affect rice growth and development. Alternative splicing (AS), a post-transcriptional gene regulatory mechanism, allows rapid changes in the transcriptome and can generate novel regulatory mechanisms to confer plasticity to plant growth and development. Mounting evidence indicates that AS has a prominent role in regulating rice growth and development under stress conditions. Several regulatory and structural genes and splicing factors of rice undergo different types of stress-induced AS events, and the functional significance of some of them in stress tolerance has been defined. Both rice and its pathogens use this complex regulatory mechanism to devise strategies against each other. This review covers the current understanding and evidence for the involvement of AS in biotic and abiotic stress-responsive genes, and its relevance to rice growth and development. Furthermore, we discuss implications of AS for the virulence of different rice pathogens and highlight the areas of further research and potential future avenues to develop climate-smart and disease-resistant rice varieties.
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Affiliation(s)
| | - Anireddy S. N. Reddy
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
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Ganie SA, Wani SH, Henry R, Hensel G. Improving rice salt tolerance by precision breeding in a new era. CURRENT OPINION IN PLANT BIOLOGY 2021; 60:101996. [PMID: 33444976 DOI: 10.1016/j.pbi.2020.101996] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/16/2020] [Accepted: 12/19/2020] [Indexed: 05/03/2023]
Abstract
Rice is a premier staple food that constitutes the bulk of the daily diet of the majority of people in Asia. Agricultural productivity must be boosted to support this huge demand for rice. However, production is jeopardized by soil salinity. Advances in whole-genome sequencing, marker-assisted breeding strategies, and targeted mutagenesis have substantially improved the toolbox of today's breeders. Given that salinity has a major influence on rice at both the seedling and reproductive stages, understanding and manipulating this trait will have an enormous impact on sustainable production. This article summarizes recent developments in the understanding of the mechanisms of salt tolerance and how state-of-the-art tools such as RNA guided CRISPR endonuclease technology including targeted mutagenesis or base and prime editing can help in gene discovery and functional analysis as well as in transferring favorable alleles into elite breeding material to speed the breeding of salt-tolerant rice cultivars.
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Affiliation(s)
- Showkat Ahmad Ganie
- Department of Biotechnology, Visva-Bharati, Santiniketan 731235, West Bengal, India.
| | - Shabir Hussain Wani
- Mountain Research Centre for Field Crops, Khudwani - 192101, Sher-e-Kashmir University of Agricultural Sciences and Technology, Kashmir, J&K, India
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Goetz Hensel
- Centre for Plant Genome Engineering, Institute of Plant Biochemistry, Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany; Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstraße 3, OT Gatersleben, 06466 Seeland, Germany; Division of Molecular Biology, Centre of Region Haná for Biotechnological and Agriculture Research, Czech Advanced Technology and Research Institute, Palacký University, Olomouc, Czech Republic.
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Marx HE, Scheidt S, Barker MS, Dlugosch KM. TagSeq for gene expression in non-model plants: A pilot study at the Santa Rita Experimental Range NEON core site. APPLICATIONS IN PLANT SCIENCES 2020; 8:e11398. [PMID: 33304661 PMCID: PMC7705334 DOI: 10.1002/aps3.11398] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 08/20/2020] [Indexed: 05/12/2023]
Abstract
PREMISE TagSeq is a cost-effective approach for gene expression studies requiring a large number of samples. To date, TagSeq studies in plants have been limited to those with a high-quality reference genome. We tested the suitability of reference transcriptomes for TagSeq in non-model plants, as part of a study of natural gene expression variation at the Santa Rita Experimental Range National Ecological Observatory Network (NEON) core site. METHODS Tissue for TagSeq was sampled from multiple individuals of four species (Bouteloua aristidoides and Eragrostis lehmanniana [Poaceae], Tidestromia lanuginosa [Amaranthaceae], and Parkinsonia florida [Fabaceae]) at two locations on three dates (56 samples total). One sample per species was used to create a reference transcriptome via standard RNA-seq. TagSeq performance was assessed by recovery of reference loci, specificity of tag alignments, and variation among samples. RESULTS A high fraction of tags aligned to each reference and mapped uniquely. Expression patterns were quantifiable for tens of thousands of loci, which revealed consistent spatial differentiation in expression for all species. DISCUSSION TagSeq using de novo reference transcriptomes was an effective approach to quantifying gene expression in this study. Tags were highly locus specific and generated biologically informative profiles for four non-model plant species.
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Affiliation(s)
- Hannah E. Marx
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonArizona85721USA
- Department of Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborMichigan48109‐1048USA
| | - Stephen Scheidt
- Howard University2400 6th Street NWWashingtonD.C.20059USA
- Solar System Exploration DivisionNASA Goddard Space Flight CenterGreenbeltMaryland20771USA
- Center for Research and Exploration in Space Science and TechnologyNASA Goddard Space Flight CenterGreenbeltMaryland20771USA
| | - Michael S. Barker
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonArizona85721USA
| | - Katrina M. Dlugosch
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonArizona85721USA
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Giorio P, Cirillo V, Caramante M, Oliva M, Guida G, Venezia A, Grillo S, Maggio A, Albrizio R. Physiological Basis of Salt Stress Tolerance in a Landrace and a Commercial Variety of Sweet Pepper ( Capsicum annuum L.). PLANTS 2020; 9:plants9060795. [PMID: 32630481 PMCID: PMC7356216 DOI: 10.3390/plants9060795] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 06/17/2020] [Accepted: 06/22/2020] [Indexed: 01/09/2023]
Abstract
Salt stress is one of the most impactful abiotic stresses that plants must cope with. Plants’ ability to tolerate salt stress relies on multiple mechanisms, which are associated with biomass and yield reductions. Sweet pepper is a salt-sensitive crop that in Mediterranean regions can be exposed to salt build-up in the root zone due to irrigation. Understanding the physiological mechanisms that plants activate to adapt to soil salinization is essential to develop breeding programs and agricultural practices that counteract this phenomenon and ultimately minimize yield reductions. With this aim, the physiological and productive performances of Quadrato D’Asti, a common commercial sweet pepper cultivar in Italy, and Cazzone Giallo, a landrace of the Campania region (Italy), were compared under different salt stress treatments. Quadrato D’Asti had higher tolerance to salt stress when compared to Cazzone Giallo in terms of yield, which was associated with higher leaf biomass vs. fruit ratio in the former. Ion accumulation and profiling between the two genoptypes revealed that Quadrato D’Asti was more efficient at excluding chloride from green tissues, allowing the maintenance of photosystem functionality under stress. In contrast, Cazzone Giallo seemed to compartmentalize most sodium in the stem. While sodium accumulation in the stems has been shown to protect shoots from sodium toxicity, in pepper and/or in the specific experimental conditions imposed, this strategy was less efficient than chloride exclusion for salt stress tolerance.
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Affiliation(s)
- Pasquale Giorio
- National Research Council of Italy, Institute for Mediterranean Agricultural and Forestry Systems (CNR-ISAFOM), Ercolano, 80056 Naples, Italy; (P.G.); (M.O.); (G.G.); (R.A.)
| | - Valerio Cirillo
- Department of Agricultural Science, University of Napoli Federico II, Portici, 80055 Naples, Italy;
- Correspondence:
| | - Martina Caramante
- Council for Agricultural Research and Economics, Research Centre for Vegetable and Ornamental Crops (CREA-OF), Pontecagnano, 84098 Salerno, Italy; (M.C.); (A.V.)
| | - Marco Oliva
- National Research Council of Italy, Institute for Mediterranean Agricultural and Forestry Systems (CNR-ISAFOM), Ercolano, 80056 Naples, Italy; (P.G.); (M.O.); (G.G.); (R.A.)
| | - Gianpiero Guida
- National Research Council of Italy, Institute for Mediterranean Agricultural and Forestry Systems (CNR-ISAFOM), Ercolano, 80056 Naples, Italy; (P.G.); (M.O.); (G.G.); (R.A.)
| | - Accursio Venezia
- Council for Agricultural Research and Economics, Research Centre for Vegetable and Ornamental Crops (CREA-OF), Pontecagnano, 84098 Salerno, Italy; (M.C.); (A.V.)
| | - Stefania Grillo
- National Research Council of Italy, Institute of Biosciences and Bioresources (CNR-IBBR), Research Division Portici, 80055 Naples, Italy;
| | - Albino Maggio
- Department of Agricultural Science, University of Napoli Federico II, Portici, 80055 Naples, Italy;
| | - Rossella Albrizio
- National Research Council of Italy, Institute for Mediterranean Agricultural and Forestry Systems (CNR-ISAFOM), Ercolano, 80056 Naples, Italy; (P.G.); (M.O.); (G.G.); (R.A.)
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Guarino F, Ruiz KB, Castiglione S, Cicatelli A, Biondi S. The combined effect of Cr(III) and NaCl determines changes in metal uptake, nutrient content, and gene expression in quinoa (Chenopodium quinoa Willd.). ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 193:110345. [PMID: 32092578 DOI: 10.1016/j.ecoenv.2020.110345] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 02/05/2020] [Accepted: 02/14/2020] [Indexed: 06/10/2023]
Abstract
Many areas of the world are affected simultaneously by salinity and heavy metal pollution. Halophytes are considered as useful candidates in remediation of such soils due to their ability to withstand both osmotic stress and ion toxicity deriving from high salt concentrations. Quinoa (Chenopodium quinoa Willd) is a halophyte with a high resistance to abiotic stresses (drought, salinity, frost), but its capacity to cope with heavy metals has not yet been fully investigated. In this pot experiment, we investigated phytoextraction capacity, effects on nutrient levels (P and Fe), and changes in gene expression in response to application of Cr(III) in quinoa plants grown on saline or non-saline soil. Plants were exposed for three weeks to 500 mg kg-1 soil of Cr(NO3)3·9H2O either in the presence or absence of 150 mM NaCl. Results show that plants were able tolerate this soil concentration of Cr(III); the metal was mainly accumulated in roots where it reached the highest concentration (ca. 2.6 mg g-1 DW) in the presence of NaCl. On saline soil, foliar Na concentration was significantly reduced by Cr(III). Phosphorus translocation to leaves was reduced in the presence of Cr(III), while Fe accumulation was enhanced by treatment with NaCl alone. A real-time RT-qPCR analysis was conducted on genes encoding for sulfate, iron, and phosphate transporters, a phytochelatin, a metallothionein, glutathione synthetase, a dehydrin, Hsp70, and enzymes responsible for the biosynthesis of proline (P5CS), glycine betaine (BADH), tocopherols (TAT), and phenolic compounds (PAL). Cr(III), and especially Cr(III)+NaCl, affected transcript levels of most of the investigated genes, indicating that tolerance to Cr is associated with changes in phosphorus and sulfur allocation, and activation of stress-protective molecules. Moderately saline conditions, in most cases, enhanced this response, suggesting that the halophytism of quinoa could contribute to prime the plants to respond to chromium stress.
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Affiliation(s)
- Francesco Guarino
- Dipartimento di Chimica e Biologia "A. Zambelli", Università di Salerno, Fisciano, Salerno, Italy
| | - Karina B Ruiz
- Departamento Agricultura del Desierto, Universidad Arturo Prat (UNAP), Iquique, Chile; Dipartimento di Science Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
| | - Stefano Castiglione
- Dipartimento di Chimica e Biologia "A. Zambelli", Università di Salerno, Fisciano, Salerno, Italy
| | - Angela Cicatelli
- Dipartimento di Chimica e Biologia "A. Zambelli", Università di Salerno, Fisciano, Salerno, Italy.
| | - Stefania Biondi
- Dipartimento di Science Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
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Hu Y, Huang Y, Zhou S, Zhang Y, Cheng R, Guo J, Ling Y. Traditional rice landraces in Lei-Qiong area of South China tolerate salt stress with strong antioxidant activity. PLANT SIGNALING & BEHAVIOR 2020; 15:1740466. [PMID: 32180487 PMCID: PMC7194380 DOI: 10.1080/15592324.2020.1740466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Salt stress, causing serious loss on crop productions, is one of the most important environmental stresses throughout the world. The aim of this study is to select salt-tolerant traditional rice resources collected from Lei-Qiong area of South China and investigate their physiological performances and biochemical regulations during salt stress response, together with two well-known international varieties, Nona Bokra (salt-tolerant sample) and IR29 (salt-sensitive sample). After comprehensive analyses, we discovered that two Lei-Qiong traditional salt-tolerant rice samples showed less growth inhibition by salt stress during both germination and seedling stage, in comparison with other rice samples. Moreover, there were less chlorosis symptoms in these two kinds of salt tolerant rice under salt stress, corresponding to their better water-holding capacity. We measured malondialdehyde and proline contents, and activities of CAT and POD of seedlings treated with 100 mM NaCl for 5 dand 10 d, respectively. Interestingly, less cellular membrane damage and stronger antioxidant enzyme system were found in the two Lei-Qiong rice samples. Our study suggests that traditional rice landrace growing onshore of Lei-Qiong area in China possesses good salt-tolerant capacity, which could be attributed to their efficient antioxidant enzyme system.
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Affiliation(s)
- Yan Hu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, PR China
| | - Yongxiang Huang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, PR China
| | - Shuangxi Zhou
- New Zealand Institute for Plant and Food Research Limited, Hawkes Bay, New Zealand
| | - Yueqin Zhang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, PR China
| | - Risheng Cheng
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, PR China
| | - Jianfu Guo
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, PR China
- CONTACT Jianfu Guo
| | - Yu Ling
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, PR China
- Yu Ling College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088 PR China
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