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Mumithrakamatchi AK, Alagarswamy S, Anitha K, Djanaguiraman M, Kalarani MK, Swarnapriya R, Marimuthu S, Vellaikumar S, Kanagarajan S. Melatonin imparts tolerance to combined drought and high-temperature stresses in tomato through osmotic adjustment and ABA accumulation. FRONTIERS IN PLANT SCIENCE 2024; 15:1382914. [PMID: 38606062 PMCID: PMC11007154 DOI: 10.3389/fpls.2024.1382914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 03/05/2024] [Indexed: 04/13/2024]
Abstract
In recent years, environmental stresses viz., drought and high-temperature negatively impacts the tomato growth, yield and quality. The effects of combined drought and high-temperature (HT) stresses during the flowering stage were investigated. The main objective was to assess the effects of foliar spray of melatonin under both individual and combined drought and HT stresses at the flowering stage. Drought stress was imposed by withholding irrigation, whereas HT stress was imposed by exposing the plants to an ambient temperature (AT)+5°C temperature. The drought+HT stress was imposed by exposing the plants to drought first, followed by exposure to AT+5°C temperature. The duration of individual and combined drought or HT stress was 10 days. The results showed that drought+HT stress had a significant negative effect compared with individual drought or HT stress alone. However, spraying 100 µM melatonin on the plants challenged with individual or combined drought and HT stress showed a significant increase in total chlorophyll content [drought: 16%, HT: 14%, and drought+HT: 11%], Fv/Fm [drought: 16%, HT: 15%, and drought+HT: 13%], relative water content [drought: 10%, HT: 2%, and drought+HT: 8%], and proline [drought: 26%, HT: 17%, and drought+HT: 14%] compared with their respective stress control. Additionally, melatonin positively influenced the stomatal and trichome characteristics compared with stress control plants. Also, the osmotic adjustment was found to be significantly increased in the melatonin-sprayed plants, which, in turn, resulted in an increased number of fruits, fruit set percentage, and fruit yield. Moreover, melatonin spray also enhanced the quality of fruits through increased lycopene content, carotenoid content, titratable acidity, and ascorbic acid content, compared with the stress control. Overall, this study highlights the usefulness of melatonin in effectively mitigating the negative effects of drought, HT, and drought+HT stress, thus leading to an increased drought and HT stress tolerance in tomato.
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Affiliation(s)
| | - Senthil Alagarswamy
- Department of Crop Physiology, Tamil Nadu Agricultural University (TNAU), Coimbatore, India
| | - Kuppusamy Anitha
- Department of Crop Physiology, Tamil Nadu Agricultural University (TNAU), Coimbatore, India
| | | | | | | | - Subramanian Marimuthu
- Department of Agronomy, Agricultural College and Research Institute (AC&RI), Eachangkottai, Thanjavur, India
| | - Sampathrajan Vellaikumar
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
| | - Selvaraju Kanagarajan
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
- School of Science and Technology, The Life Science Centre, Örebro University, Örebro, Sweden
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Saini S, Sharma P, Sharma J, Pooja P, Sharma A. Drought stress in Lens culinaris: effects, tolerance mechanism, and its smart reprogramming by using modern biotechnological approaches. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:227-247. [PMID: 38623164 PMCID: PMC11016033 DOI: 10.1007/s12298-024-01417-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 01/20/2024] [Accepted: 02/12/2024] [Indexed: 04/17/2024]
Abstract
Among legumes, lentil serves as an imperative source of dietary proteins and are considered an important pillar of global food and nutritional security. The crop is majorly cultivated in arid and semi-arid regions and exposed to different abiotic stresses. Drought stress is a polygenic stress that poses a major threat to the crop productivity of lentils. It negatively influenced the seed emergence, water relations traits, photosynthetic machinery, metabolites, seed development, quality, and yield in lentil. Plants develop several complex physiological and molecular protective mechanisms for tolerance against drought stress. These complicated networks are enabled to enhance the cellular potential to survive under extreme water-scarce conditions. As a result, proper drought stress-mitigating novel and modern approaches are required to improve lentil productivity. The currently existing biotechnological techniques such as transcriptomics, genomics, proteomics, metabolomics, CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/cas9), and detection of QTLs (quantitative trait loci), proteins, and genes responsible for drought tolerance have gained appreciation among plant breeders for developing climate-resilient lentil varieties. In this review, we critically elaborate the impact of drought on lentil, mechanisms employed by plants to tolerate drought, and the contribution of omics approaches in lentils for dealing with drought, providing deep insights to enhance lentil productivity and improve resistance against abiotic stresses. We hope this updated review will directly help the lentil breeders to develop resistance against drought stress. Graphical Abstract
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Affiliation(s)
- Sakshi Saini
- Department of Botany, Maharshi Dayanand University, Rohtak, Haryana 124001 India
| | - Priyanka Sharma
- Department of Botany, Maharshi Dayanand University, Rohtak, Haryana 124001 India
| | - Jyoti Sharma
- Department of Botany, Maharshi Dayanand University, Rohtak, Haryana 124001 India
| | - Pooja Pooja
- Department of Botany and Physiology, Haryana Agricultural University, Hisar, Haryana 125004 India
| | - Asha Sharma
- Department of Botany, Maharshi Dayanand University, Rohtak, Haryana 124001 India
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El Haddad N, En-nahli Y, Choukri H, Aloui K, Mentag R, El-Baouchi A, Hejjaoui K, Rajendran K, Smouni A, Maalouf F, Kumar S. Metabolic Mechanisms Underlying Heat and Drought Tolerance in Lentil Accessions: Implications for Stress Tolerance Breeding. PLANTS (BASEL, SWITZERLAND) 2023; 12:3962. [PMID: 38068599 PMCID: PMC10708188 DOI: 10.3390/plants12233962] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 08/17/2023] [Accepted: 08/22/2023] [Indexed: 04/12/2024]
Abstract
Climate change has significantly exacerbated the effects of abiotic stresses, particularly high temperatures and drought stresses. This study aims to uncover the mechanisms underlying heat and drought tolerance in lentil accessions. To achieve this objective, twelve accessions were subjected to high-temperature stress (32/20 °C), while seven accessions underwent assessment under drought stress conditions (50% of field capacity) during the reproductive stage. Our findings revealed a significant increase in catalase activity across all accessions under both stress conditions, with ILL7814 and ILL7835 recording the highest accumulations of 10.18 and 9.33 under drought stress, respectively, and 14 µmol H2O2 mg protein-1 min-1 under high temperature. Similarly, ascorbate peroxidase significantly increased in all tolerant accessions due to high temperatures, with ILL6359, ILL7835, and ILL8029 accumulating the highest values with up 50 µmol ascorbate mg protein-1 min-1. In contrast, no significant increase was obtained for all accessions subjected to water stress, although the drought-tolerant accessions accumulated more APX activity (16.59 t to 25.08 µmol ascorbate mg protein-1 min-1) than the sensitive accessions. The accessions ILL6075, ILL7814, and ILL8029 significantly had the highest superoxide dismutase activity under high temperature, while ILL6363, ILL7814, and ILL7835 accumulated the highest values under drought stress, each with 22 to 25 units mg protein-1. Under both stress conditions, ILL7814 and ILL7835 recorded the highest contents in proline (38 to 45 µmol proline/g FW), total flavonoids (0.22 to 0.77 mg QE g-1 FW), total phenolics (7.50 to 8.79 mg GAE g-1 FW), total tannins (5.07 to 20 µg CE g-1 FW), and total antioxidant activity (60 to 70%). Further, ILL7814 and ILL6338 significantly recorded the highest total soluble sugar content under high temperature (71.57 and 74.24 mg g-1, respectively), while ILL7835 achieved the maximum concentration (125 mg g-1) under drought stress. The accessions ILL8029, ILL6104, and ILL7814 had the highest values of reducing sugar under high temperature with 0.62 to 0.79 mg g-1, whereas ILL6075, ILL6363, and ILL6362 accumulated the highest levels of this component under drought stress with 0.54 to 0.66 mg g-1. Overall, our findings contribute to a deeper understanding of the metabolomic responses of lentil to drought and heat stresses, serving as a valuable reference for lentil stress tolerance breeding.
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Affiliation(s)
- Noureddine El Haddad
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat 10112, Morocco; (Y.E.-n.); (H.C.); (K.A.)
- Laboratoire de Biotechnologie et de Physiologie Végétales, Centre de Recherche BioBio, Faculté des Sciences, Mohammed V University Rabat, Rabat 10112, Morocco;
| | - Youness En-nahli
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat 10112, Morocco; (Y.E.-n.); (H.C.); (K.A.)
- Materials Science Center, Ecole Normale Supérieure, LPCMIO, Mohammed V University of Rabat, Rabat 10100, Morocco
- AgroBioSciences Program (AgBS), College of Sustainable Agriculture and Environmental Science (CSAES), University Mohammed VI Polytechnic (UM6P), Ben Guerir 43150, Morocco; (A.E.-B.); (K.H.)
| | - Hasnae Choukri
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat 10112, Morocco; (Y.E.-n.); (H.C.); (K.A.)
- Laboratoire de Biotechnologie et de Physiologie Végétales, Centre de Recherche BioBio, Faculté des Sciences, Mohammed V University Rabat, Rabat 10112, Morocco;
| | - Khawla Aloui
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat 10112, Morocco; (Y.E.-n.); (H.C.); (K.A.)
- Laboratory of Ecology and Environment, Ben M’Sick Faculty of Sciences, University Hassan II, Casablanca 20800, Morocco
| | - Rachid Mentag
- Biotechnology Research Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research (INRA), Rabat 10090, Morocco;
| | - Adil El-Baouchi
- AgroBioSciences Program (AgBS), College of Sustainable Agriculture and Environmental Science (CSAES), University Mohammed VI Polytechnic (UM6P), Ben Guerir 43150, Morocco; (A.E.-B.); (K.H.)
| | - Kamal Hejjaoui
- AgroBioSciences Program (AgBS), College of Sustainable Agriculture and Environmental Science (CSAES), University Mohammed VI Polytechnic (UM6P), Ben Guerir 43150, Morocco; (A.E.-B.); (K.H.)
| | - Karthika Rajendran
- Vellore Institute of Technology (VIT), VIT School of Agricultural Innovations and Advanced Learning (VAIAL), Vellore 632014, India;
| | - Abdelaziz Smouni
- Laboratoire de Biotechnologie et de Physiologie Végétales, Centre de Recherche BioBio, Faculté des Sciences, Mohammed V University Rabat, Rabat 10112, Morocco;
| | - Fouad Maalouf
- International Center for Agricultural Research in the Dry Areas (ICARDA), Beirut 1108 2010, Lebanon;
| | - Shiv Kumar
- International Center for Agricultural Research in the Dry Areas (ICARDA), New Delhi 110012, India;
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Nawaz M, Sun J, Shabbir S, Khattak WA, Ren G, Nie X, Bo Y, Javed Q, Du D, Sonne C. A review of plants strategies to resist biotic and abiotic environmental stressors. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 900:165832. [PMID: 37524179 DOI: 10.1016/j.scitotenv.2023.165832] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 08/02/2023]
Abstract
Plants exposed to a variety of abiotic and biotic stressors including environmental pollution and global warming pose significant threats to biodiversity and ecosystem services. Despite substantial literature documenting how plants adapt to distinct stressors, there still is a lack of knowledge regarding responses to multiple stressors and how these affects growth and development. Exposure of plants to concurrent biotic and abiotic stressors such as cadmium and drought, leads to pronounced inhibition in above ground biomass, imbalance in oxidative homeostasis, nutrient assimilation and stunted root growth, elucidating the synergistic interactions of multiple stressors culminating in adverse physiological outcomes. Impact of elevated heavy metal and water deficit exposure extends beyond growth and development, influencing the biodiversity of the microenvironment including the rhizosphere nutrient profile and microbiome. These findings have significant implications for plant-stress interactions and ecosystem functioning that prompt immediate action in order to eliminate effect of pollution and address global environmental issues to promote sustainable tolerance for multiple stress combinations in plants. Here, we review plant tolerance against stress combinations, highlighting the need for interdisciplinary approaches and advanced technologies, such as omics and molecular tools, to achieve a comprehensive understanding of underlying stress tolerance mechanisms. To accelerate progress towards developing stress-tolerance in plants against multiple environmental stressors, future research in plant stress tolerance should adopt a collaborative approach, involving researchers from multiple disciplines with diverse expertise and resources.
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Affiliation(s)
- Mohsin Nawaz
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Jianfan Sun
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China.
| | - Samina Shabbir
- Department of Chemistry, The Women University Multan, Pakistan
| | - Wajid Ali Khattak
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Guangqian Ren
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yanwen Bo
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Qaiser Javed
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Daolin Du
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Christian Sonne
- Aarhus University, Faculty of Technological Sciences, Department of Ecoscience, Frederiksborgvej 399, 358, DK-4000 Roskilde, Denmark; Sustainability Cluster, School of Engineering, University of Petroleum & Energy Studies, Dehradun, Uttarakhand 248007, India.
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Xu X, Fonseca de Lima CF, Vu LD, De Smet I. When drought meets heat - a plant omics perspective. FRONTIERS IN PLANT SCIENCE 2023; 14:1250878. [PMID: 37674736 PMCID: PMC10478009 DOI: 10.3389/fpls.2023.1250878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 08/07/2023] [Indexed: 09/08/2023]
Abstract
Changes in weather patterns with emerging drought risks and rising global temperature are widespread and negatively affect crop growth and productivity. In nature, plants are simultaneously exposed to multiple biotic and abiotic stresses, but most studies focus on individual stress conditions. However, the simultaneous occurrence of different stresses impacts plant growth and development differently than a single stress. Plants sense the different stress combinations in the same or in different tissues, which could induce specific systemic signalling and acclimation responses; impacting different stress-responsive transcripts, protein abundance and modifications, and metabolites. This mini-review focuses on the combination of drought and heat, two abiotic stress conditions that often occur together. Recent omics studies indicate common or independent regulators involved in heat or drought stress responses. Here, we summarize the current research results, highlight gaps in our knowledge, and flag potential future focus areas.
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Affiliation(s)
- Xiangyu Xu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Cassio Flavio Fonseca de Lima
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Lam Dai Vu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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Raza A, Mubarik MS, Sharif R, Habib M, Jabeen W, Zhang C, Chen H, Chen ZH, Siddique KHM, Zhuang W, Varshney RK. Developing drought-smart, ready-to-grow future crops. THE PLANT GENOME 2023; 16:e20279. [PMID: 36366733 DOI: 10.1002/tpg2.20279] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 08/02/2022] [Indexed: 05/10/2023]
Abstract
Breeding crop plants with increased yield potential and improved tolerance to stressful environments is critical for global food security. Drought stress (DS) adversely affects agricultural productivity worldwide and is expected to rise in the coming years. Therefore, it is vital to understand the physiological, biochemical, molecular, and ecological mechanisms associated with DS. This review examines recent advances in plant responses to DS to expand our understanding of DS-associated mechanisms. Suboptimal water sources adversely affect crop growth and yields through physical impairments, physiological disturbances, biochemical modifications, and molecular adjustments. To control the devastating effect of DS in crop plants, it is important to understand its consequences, mechanisms, and the agronomic and genetic basis of DS for sustainable production. In addition to plant responses, we highlight several mitigation options such as omics approaches, transgenics breeding, genome editing, and biochemical to mechanical methods (foliar treatments, seed priming, and conventional agronomic practices). Further, we have also presented the scope of conventional and speed breeding platforms in helping to develop the drought-smart future crops. In short, we recommend incorporating several approaches, such as multi-omics, genome editing, speed breeding, and traditional mechanical strategies, to develop drought-smart cultivars to achieve the 'zero hunger' goal.
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Affiliation(s)
- Ali Raza
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry Univ., Fuzhou, 350002, China
| | | | - Rahat Sharif
- Dep. of Horticulture, College of Horticulture and Plant Protection, Yangzhou Univ., Yangzhou, Jiangsu, 225009, China
| | - Madiha Habib
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Park Rd., Islamabad, 45500, Pakistan
| | - Warda Jabeen
- Institute of Environmental Sciences and Engineering, School of Civil and Environmental Engineering, National Univ. of Sciences and Technology, Islamabad, 44000, Pakistan
| | - Chong Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry Univ., Fuzhou, 350002, China
| | - Hua Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry Univ., Fuzhou, 350002, China
| | - Zhong-Hua Chen
- School of Science, Hawkesbury Institute for the Environment, Western Sydney Univ., Penrith, NSW, 2751, Australia
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The Univ. of Western Australia, Crawley, Perth, 6009, Australia
| | - Weijian Zhuang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry Univ., Fuzhou, 350002, China
| | - Rajeev K Varshney
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry Univ., Fuzhou, 350002, China
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch Univ., Murdoch, WA, 6150, Australia
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Joudaki F, Ismaili A, Sohrabi SS, Hosseini SZ, Kahrizi D, Ahmadi H. Transcriptome analysis of gall oak (Quercus infectoria): De novo assembly, functional annotation and metabolic pathways analysis. Genomics 2023; 115:110588. [PMID: 36841311 DOI: 10.1016/j.ygeno.2023.110588] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 02/16/2023] [Accepted: 02/21/2023] [Indexed: 02/27/2023]
Abstract
Gall oak (Quercus infectoria) is a native tree of Iran, whose gall extract is used to treat many diseases. The presence of abundant secondary metabolites with various bioactivities in this plant has made it medically important. Despite its medicinal value, due to the lack of genomic information, the biosynthetic pathways of these compounds in this species are still unknown. The current research was aimed at observing, characterizing, and investigating the biosynthetic pathways of these compounds in Q.infectoria. De novo transcriptome assembly was conducted using the RNA sequencing technique. A total of 89,335 unigenes were generated, of which 6928 unigenes showed differential expression in leaves compared to root tissue. Gene ontology examination of DEGs revealed GO-term enrichment was related to cellular processes and enzyme activity. KEGG enrichment analysis for DEGs showed that most unigenes were related to metabolic pathways and biosynthesis of secondary metabolites. Moreover, 39 families of transcription factors were identified, of which the C2H2, bZIP, bHLH, and ERF TFs had the highest frequency. In the absence of a reference genome, the overall study of transcriptome will provide a reference for future functional and comparative studies. Moreover, the data obtained from sequencing and de novo assembly can be a valuable scientific resource for Q.infectoria.
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Affiliation(s)
- Forough Joudaki
- Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran
| | - Ahmad Ismaili
- Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran.
| | - Seyed Sajad Sohrabi
- Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran.
| | - Seyedeh Zahra Hosseini
- Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran.
| | - Danial Kahrizi
- Agricultural Biotechnology Department, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.
| | - Hadi Ahmadi
- Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran.
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Transcriptome Analysis of Persian Oak (Quercus brantii L.) Decline Using RNA-seq Technology. Biochem Genet 2022; 61:879-900. [PMID: 36214954 DOI: 10.1007/s10528-022-10283-8] [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: 12/13/2021] [Accepted: 09/01/2022] [Indexed: 11/02/2022]
Abstract
Since the late 1980s, the oak decline has affected the Zagros oak forests in western Iran. Persian oak (Quercus brantii L.) the most important tree species of these forests has been damaged more than any other plant species. In the present study, the RNA sequencing technique was used for the first time to identify key genes and molecular mechanisms involved in Persian oak decline. The RNA was extracted from the leaves of healthy and declined oak trees, and sequenced using the Illumina HiSeq 2500 platform (2 × 150 bp paired-end reads). De novo transcriptome assembly of Persian oak revealed 56,743 unigenes and 6049 differentially expressed genes (DEGs) between declined and control samples. The results of gene ontology analysis showed that most of the DEGs involved in oak decline belong to the group of stress-responsive genes. In general, oak decline samples showed significant reductions in gene expression associated with "photosynthesis and storage of sugar" and "protein synthesis and related processes." Additionally, DEGs related to the starch degradation pathway were up-regulated, whereas DEGs associated with acetate-mevalonate (MVA), biosynthesis of lignin, and lignases pathways were down-regulated. The present study's findings can be an effective step in identifying the genes involved in oak decline and deciphering the relationship between this phenomenon and biotic and abiotic stresses.
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9
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Huang LZ, Zhou M, Ding YF, Zhu C. Gene Networks Involved in Plant Heat Stress Response and Tolerance. Int J Mol Sci 2022; 23:ijms231911970. [PMID: 36233272 PMCID: PMC9569452 DOI: 10.3390/ijms231911970] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/28/2022] [Accepted: 10/03/2022] [Indexed: 12/03/2022] Open
Abstract
Global warming is an environmental problem that cannot be ignored. High temperatures seriously affect the normal growth and development of plants, and threaten the development of agriculture and the distribution and survival of species at risk. Plants have evolved complex but efficient mechanisms for sensing and responding to high temperatures, which involve the activation of numerous functional proteins, regulatory proteins, and non-coding RNAs. These mechanisms consist of large regulatory networks that regulate protein and RNA structure and stability, induce Ca2+ and hormone signal transduction, mediate sucrose and water transport, activate antioxidant defense, and maintain other normal metabolic pathways. This article reviews recent research results on the molecular mechanisms of plant response to high temperatures, highlighting future directions or strategies for promoting plant heat tolerance, thereby helping to identify the regulatory mechanisms of heat stress responses in plants.
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Affiliation(s)
| | | | - Yan-Fei Ding
- Correspondence: (Y.-F.D.); (C.Z.); Tel.: +86-571-8683-6090 (C.Z.)
| | - Cheng Zhu
- Correspondence: (Y.-F.D.); (C.Z.); Tel.: +86-571-8683-6090 (C.Z.)
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10
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Dutta H, Mishra GP, Aski MS, Bosamia TC, Mishra DC, Bhati J, Sinha SK, Vijay D, C. T. MP, Das S, Pawar PAM, Kumar A, Tripathi K, Kumar RR, Yadava DK, Kumar S, Dikshit HK. Comparative transcriptome analysis, unfolding the pathways regulating the seed-size trait in cultivated lentil (Lens culinaris Medik.). Front Genet 2022; 13:942079. [PMID: 36035144 PMCID: PMC9399355 DOI: 10.3389/fgene.2022.942079] [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: 05/12/2022] [Accepted: 07/11/2022] [Indexed: 11/16/2022] Open
Abstract
Market class, cooking time, quality, and milled grain yield are largely influenced by the seed size and shape of the lentil (Lens culinaris Medik.); thus, they are considered to be important quality traits. To unfold the pathways regulating seed size in lentils, a transcriptomic approach was performed using large-seeded (L4602) and small-seeded (L830) genotypes. The study has generated nearly 375 million high-quality reads, of which 98.70% were properly aligned to the reference genome. Among biological replicates, very high similarity in fragments per kilobase of exon per million mapped fragments values (R > 0.9) showed the consistency of RNA-seq results. Various differentially expressed genes associated mainly with the hormone signaling and cell division pathways, transcription factors, kinases, etc. were identified as having a role in cell expansion and seed growth. A total of 106,996 unigenes were used for differential expression (DE) analysis. String analysis identified various modules having certain key proteins like Ser/Thr protein kinase, seed storage protein, DNA-binding protein, microtubule-associated protein, etc. In addition, some growth and cell division–related micro-RNAs like miR3457 (cell wall formation), miR1440 (cell proliferation and cell cycles), and miR1533 (biosynthesis of plant hormones) were identified as having a role in seed size determination. Using RNA-seq data, 5254 EST-SSR primers were generated as a source for future studies aiming for the identification of linked markers. In silico validation using Genevestigator® was done for the Ser/Thr protein kinase, ethylene response factor, and Myb transcription factor genes. It is of interest that the xyloglucan endotransglucosylase gene was found differentially regulated, suggesting their role during seed development; however, at maturity, no significant differences were recorded for various cell wall parameters including cellulose, lignin, and xylose content. This is the first report on lentils that has unfolded the key seed size regulating pathways and unveiled a theoretical way for the development of lentil genotypes having customized seed sizes.
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Affiliation(s)
- Haragopal Dutta
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, India
| | - Gyan P. Mishra
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, India
- *Correspondence: Gyan P. Mishra, ; Shiv Kumar, ; Harsh Kumar Dikshit,
| | - Muraleedhar S. Aski
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, India
| | - Tejas C. Bosamia
- Plant Omics Division, Central Salt and Marine Chemicals Research Institute, Bhavnagar, India
| | - Dwijesh C. Mishra
- Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Jyotika Bhati
- Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, New Delhi, India
| | | | - Dunna Vijay
- Division of Seed Science and Technology, Indian Agricultural Research Institute, New Delhi, India
| | - Manjunath Prasad C. T.
- Division of Seed Science and Technology, Indian Agricultural Research Institute, New Delhi, India
| | - Shouvik Das
- Laboratory of Plant Cell Wall Biology, Regional Centre for Biotechnology, Faridabad, India
| | | | - Atul Kumar
- Division of Seed Science and Technology, Indian Agricultural Research Institute, New Delhi, India
| | - Kuldeep Tripathi
- Germplasm Evaluation Division, National Bureau of Plant Genetic Resources, New Delhi, India
| | - Ranjeet Ranjan Kumar
- Division of Biochemistry, Indian Agricultural Research Institute, New Delhi, India
| | | | - Shiv Kumar
- South Asia and China Program, International Center for Agricultural Research in the Dry Areas, NASC Complex, New Delhi, India
- *Correspondence: Gyan P. Mishra, ; Shiv Kumar, ; Harsh Kumar Dikshit,
| | - Harsh Kumar Dikshit
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, India
- *Correspondence: Gyan P. Mishra, ; Shiv Kumar, ; Harsh Kumar Dikshit,
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11
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Can Nanofertilizers Mitigate Multiple Environmental Stresses for Higher Crop Productivity? SUSTAINABILITY 2022. [DOI: 10.3390/su14063480] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The global food production for the worldwide population mainly depends on the huge contributions of the agricultural sector. The cultivated crops of foods need various elements or nutrients to complete their growth, and these are indirectly consumed by humans. During this production, several environmental constraints or stresses may cause losses in the global agricultural production. These obstacles may include abiotic and biotic stresses, which have already been studied in both individual and combined cases. However, there are very few studies on multiple stresses. On the basis of the myriad benefits of nanotechnology in agriculture, nanofertilizers (or nanonutrients) have become promising tools for agricultural sustainability. Nanofertilizers are also the proper solution to overcoming the environmental and health problems that can result from conventional fertilizers. The role of nanofertilizers has increased, especially under different environmental stresses, which can include individual, combined, and multiple stresses. The stresses are most commonly the result of nature; however, studies are still needed on the different stress levels. Nanofertilizers can play a crucial role in supporting cultivated plants under stress and in improving the plant yield, both quantitatively and qualitatively. Similar to other biological issues, many open-ended questions still require further investigation: Is the right time and era for nanofertilizers in agriculture? Will the nanofertilizers be the dominant source of nutrients in modern agriculture? Are nanofertilizers, and particularly biological synthesized ones, the magic solution for sustainable agriculture? What are the expected damages of multiple stresses on plants?
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12
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Sohrabi SS, Ismaili A, Nazarian-Firouzabadi F, Fallahi H, Hosseini SZ. Identification of key genes and molecular mechanisms associated with temperature stress in lentil. Gene 2022; 807:145952. [PMID: 34500049 DOI: 10.1016/j.gene.2021.145952] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/24/2021] [Accepted: 09/03/2021] [Indexed: 02/03/2023]
Abstract
Extreme temperature is one of the serious threats to crop production in present and future scenarios of global climate changes. Lentil (Lens culinaris) is an important crop, and there is a serious lack of genetic information regarding environmental and temperature stresses responses. This study is the first report of evaluation of key genes and molecular mechanisms related to temperature stresses in lentil using the RNA sequencing technique. De novo transcriptome assembly created 44,673 contigs and differential gene expression analysis revealed 7494 differentially expressed genes between the temperature stresses and control group. Basic annotation of generated transcriptome assembly in our study led to the identification of 2765 novel transcripts that have not been identified yet in lentil genome draft v1.2. In addition, several unigenes involved in mechanisms of temperature sensing, calcium and hormone signaling and DNA-binding transcription factor activity were identified. Also, common mechanisms in response to temperature stresses, including the proline biosynthesis, the photosynthetic light reactions balancing, chaperone activity and circadian rhythms, are determined by the hub genes through the protein-protein interaction networks analysis. Deciphering the mechanisms of extreme temperature tolerance would be a new way for developing crops with enhanced plasticity against climate change. In general, this study has identified set of mechanisms and various genes related to cold and heat stresses which will be useful in better understanding of the lentil's reaction to temperature stresses.
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Affiliation(s)
- Seyed Sajad Sohrabi
- Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran.
| | - Ahmad Ismaili
- Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran.
| | - Farhad Nazarian-Firouzabadi
- Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran.
| | - Hossein Fallahi
- Department of Biology, School of Sciences, Razi University, Kermanshah, Iran.
| | - Seyedeh Zahra Hosseini
- Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran.
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13
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Arab MM, Brown PJ, Abdollahi-Arpanahi R, Sohrabi SS, Askari H, Aliniaeifard S, Mokhtassi-Bidgoli A, Mesgaran MB, Leslie CA, Marrano A, Neale DB, Vahdati K. Genome-wide association analysis and pathway enrichment provide insights into the genetic basis of photosynthetic responses to drought stress in Persian walnut. HORTICULTURE RESEARCH 2022; 9:uhac124. [PMID: 35928405 PMCID: PMC9343916 DOI: 10.1093/hr/uhac124] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 05/17/2022] [Indexed: 05/17/2023]
Abstract
Uncovering the genetic basis of photosynthetic trait variation under drought stress is essential for breeding climate-resilient walnut cultivars. To this end, we examined photosynthetic capacity in a diverse panel of 150 walnut families (1500 seedlings) from various agro-climatic zones in their habitats and grown in a common garden experiment. Photosynthetic traits were measured under well-watered (WW), water-stressed (WS) and recovery (WR) conditions. We performed genome-wide association studies (GWAS) using three genomic datasets: genotyping by sequencing data (∼43 K SNPs) on both mother trees (MGBS) and progeny (PGBS) and the Axiom™ Juglans regia 700 K SNP array data (∼295 K SNPs) on mother trees (MArray). We identified 578 unique genomic regions linked with at least one trait in a specific treatment, 874 predicted genes that fell within 20 kb of a significant or suggestive SNP in at least two of the three GWAS datasets (MArray, MGBS, and PGBS), and 67 genes that fell within 20 kb of a significant SNP in all three GWAS datasets. Functional annotation identified several candidate pathways and genes that play crucial roles in photosynthesis, amino acid and carbohydrate metabolism, and signal transduction. Further network analysis identified 15 hub genes under WW, WS and WR conditions including GAPB, PSAN, CRR1, NTRC, DGD1, CYP38, and PETC which are involved in the photosynthetic responses. These findings shed light on possible strategies for improving walnut productivity under drought stress.
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Affiliation(s)
- Mohammad M Arab
- Department of Horticulture, College of Aburaihan, University of Tehran, Tehran, Iran
| | - Patrick J Brown
- Department of Plant Sciences, University of California, Davis, CA 95616
| | | | - Seyed Sajad Sohrabi
- Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran
| | - Hossein Askari
- Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Sasan Aliniaeifard
- Photosynthesis laboratory, Department of Horticulture, College of Aburaihan, University of Tehran, Tehran, Iran
| | - Ali Mokhtassi-Bidgoli
- Department of Agronomy, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Mohsen B Mesgaran
- Department of Plant Sciences, University of California, Davis, CA 95616
| | - Charles A Leslie
- Department of Plant Sciences, University of California, Davis, CA 95616
| | - Annarita Marrano
- Department of Plant Sciences, University of California, Davis, CA 95616
| | - David B Neale
- Department of Plant Sciences, University of California, Davis, CA 95616
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14
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Mishra S, Sahu G, Shaw BP. Integrative small RNA and transcriptome analysis provides insight into key role of miR408 towards drought tolerance response in cowpea. PLANT CELL REPORTS 2022; 41:75-94. [PMID: 34570259 DOI: 10.1007/s00299-021-02783-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 09/07/2021] [Indexed: 06/13/2023]
Abstract
Drought stress response studies and overexpression of vun-miR408 proved it to be essential for abiotic stress tolerance in cowpea. Small RNA and transcriptome sequencing of an elite high-yielding drought-tolerant Indian cowpea cultivar, Pusa Komal revealed a differential expression of 198 highly conserved, 21 legume-specific, 14 less-conserved, and 10 novel drought-responsive microRNAs (miRNAs) along with 3391 (up-regulated) and 3799 (down-regulated) genes, respectively, in the leaf and root libraries. Among the differentially expressed miRNAs, vun-miR408-3p, showed an up-regulation of 3.53-log2-fold change under drought stress. Furthermore, laccase 12 (LAC 12) was identified as the potential target of vun-miR408-3p using 5' RNA ligase-mediated rapid amplification of cDNA ends. The stable transgenic cowpea lines overexpressing artificial vun-miR408-3p (OX-amiR408) displayed enhanced drought and salinity tolerance as compared to the wild-type plants. An average increase of 30.17% in chlorophyll, 26.57% in proline, and 27.62% in relative water content along with lesser cellular H2O2 level was observed in the transgenic lines in comparison with the wild-type plants under drought stress. Additionally, the scanning electron microscopic study revealed a decrease in the stomatal aperture and an increase in the trichome density in the transgenic lines. The expression levels of laccase 3 and laccase 12, the potential targets of miR408, related to lipid catabolic processes showed a significant reduction in the wild-type plants under drought stress and the transgenic lines, indicating the regulation of lignin content as a plausibly essential trait related to the drought tolerance in cowpea. Taken together, this study primarily focused on identification of drought-responsive miRNAs and genes in cowpea, and functional validation of role of miR408 towards drought stress response in cowpea.
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Affiliation(s)
- Sagarika Mishra
- Abiotic Stress and Agro-Biotechnology Lab, Institute of Life Sciences, Bhubaneswar, India.
| | - Gyanasri Sahu
- Abiotic Stress and Agro-Biotechnology Lab, Institute of Life Sciences, Bhubaneswar, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Birendra Prasad Shaw
- Abiotic Stress and Agro-Biotechnology Lab, Institute of Life Sciences, Bhubaneswar, India
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15
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Mishra GP, Aski MS, Bosamia T, Chaurasia S, Mishra DC, Bhati J, Kumar A, Javeria S, Tripathi K, Kohli M, Kumar RR, Singh AK, Devi J, Kumar S, Dikshit HK. Insights into the Host-Pathogen Interaction Pathways through RNA-Seq Analysis of Lens culinaris Medik. in Response to Rhizoctonia bataticola Infection. Genes (Basel) 2021; 13:genes13010090. [PMID: 35052429 PMCID: PMC8774501 DOI: 10.3390/genes13010090] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/20/2021] [Accepted: 12/23/2021] [Indexed: 12/13/2022] Open
Abstract
Dry root rot (Rhizoctonia bataticola) is an important disease of lentils (Lens culinaris Medik.).To gain an insight into the molecular aspects of host-pathogen interactions, the RNA-seq approach was used in lentils following inoculation with R.bataticola. The RNA-Seq has generated >450 million high-quality reads (HQRs) and nearly 96.97% were properly aligned to the reference genome. Very high similarity in FPKM (fragments per kilobase of exon per million mapped fragments) values (R > 0.9) among biological replicates showed the consistency of the RNA-Seq results. The study revealed various DEGs (differentially expressed genes) that were associated with changes in phenolic compounds, transcription factors (TFs), antioxidants, receptor kinases, hormone signals which corresponded to the cell wall modification enzymes, defense-related metabolites, and jasmonic acid (JA)/ethylene (ET) pathways. Gene ontology (GO) categorization also showed similar kinds of significantly enriched similar GO terms. Interestingly, of the total unigenes (42,606), 12,648 got assembled and showed significant hit with Rhizoctonia species. String analysis also revealed the role of various disease responsive proteins viz., LRR family proteins, LRR-RLKs, protein kinases, etc. in the host-pathogen interaction. Insilico validation analysis was performed using Genevestigator® and DEGs belonging to six major defense-response groups viz., defense-related enzymes, disease responsive genes, hormones, kinases, PR (pathogenesis related) proteins, and TFs were validated. For the first time some key miRNA targets viz. miR156, miR159, miR167, miR169, and miR482 were identified from the studied transcriptome, which may have some vital role in Rhizoctonia-based responses in lentils. The study has revealed the molecular mechanisms of the lentil/R.bataticola interactions and also provided a theoretical approach for the development of lentil genotypes resistant to R.bataticola.
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Affiliation(s)
- Gyan P. Mishra
- Division of Genetics, Indian Agricultural Research Institute, New Delhi 110012, India; (G.P.M.); (M.S.A.); (S.C.); (M.K.)
| | - Muraleedhar S. Aski
- Division of Genetics, Indian Agricultural Research Institute, New Delhi 110012, India; (G.P.M.); (M.S.A.); (S.C.); (M.K.)
| | - Tejas Bosamia
- Plant Omics Division, Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, India;
| | - Shiksha Chaurasia
- Division of Genetics, Indian Agricultural Research Institute, New Delhi 110012, India; (G.P.M.); (M.S.A.); (S.C.); (M.K.)
| | - Dwijesh Chandra Mishra
- Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, New Delhi 110012, India; (D.C.M.); (J.B.)
| | - Jyotika Bhati
- Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, New Delhi 110012, India; (D.C.M.); (J.B.)
| | - Atul Kumar
- Division of Seed Science and Technology, Indian Agricultural Research Institute, New Delhi 110012, India; (A.K.); (S.J.)
| | - Shaily Javeria
- Division of Seed Science and Technology, Indian Agricultural Research Institute, New Delhi 110012, India; (A.K.); (S.J.)
| | - Kuldeep Tripathi
- Germplasm Evaluation Division, National Bureau of Plant Genetic Resources, New Delhi 110012, India;
| | - Manju Kohli
- Division of Genetics, Indian Agricultural Research Institute, New Delhi 110012, India; (G.P.M.); (M.S.A.); (S.C.); (M.K.)
| | - Ranjeet Ranjan Kumar
- Division of Biochemistry, Indian Agricultural Research Institute, New Delhi 110012, India;
| | - Amit Kumar Singh
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, New Delhi 110012, India;
| | - Jyoti Devi
- Division of Crop Improvement, Indian Institute of Vegetable Research, Varanasi 221305, India;
| | - Shiv Kumar
- Biodiversity and Integrated Gene Management Program, International Center for Agricultural Research in the Dry Areas, Avenue HafianeCherkaoui, Rabat 10112, Morocco
- Correspondence: (S.K.); (H.K.D.)
| | - Harsh Kumar Dikshit
- Division of Genetics, Indian Agricultural Research Institute, New Delhi 110012, India; (G.P.M.); (M.S.A.); (S.C.); (M.K.)
- Correspondence: (S.K.); (H.K.D.)
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