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Li G, Wu J, Kronzucker HJ, Li B, Shi W. Physiological and molecular mechanisms of plant-root responses to iron toxicity. JOURNAL OF PLANT PHYSIOLOGY 2024; 297:154257. [PMID: 38688043 DOI: 10.1016/j.jplph.2024.154257] [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: 03/29/2024] [Revised: 04/17/2024] [Accepted: 04/22/2024] [Indexed: 05/02/2024]
Abstract
The chemical form and physiological activity of iron (Fe) in soil are dependent on soil pH and redox potential (Eh), and Fe levels in soils are frequently elevated to the point of causing Fe toxicity in plants, with inhibition of normal physiological activities and of growth and development. In this review, we describe how iron toxicity triggers important physiological changes, including nitric-oxide (NO)-mediated potassium (K+) efflux at the tips of roots and accumulation of reactive oxygen species (ROS) and reactive nitrogen (RNS) in roots, resulting in physiological stress. We focus on the root system, as the first point of contact with Fe in soil, and describe the key processes engaged in Fe transport, distribution, binding, and other mechanisms that are drawn upon to defend against high-Fe stress. We describe the root-system regulation of key physiological processes and of morphological development through signaling substances such as ethylene, auxin, reactive oxygen species, and nitric oxide, and discuss gene-expression responses under high Fe. We especially focus on studies on the physiological and molecular mechanisms in rice and Arabidopsis under high Fe, hoping to provide a valuable theoretical basis for improving the ability of crop roots to adapt to soil Fe toxicity.
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Affiliation(s)
- Guangjie Li
- State Key Laboratory of Nutrient Use and Management, Institute of Agricultural Resources and Environment, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.
| | - Jinlin Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of the Chinese Academy of Sciences, No. 19(A) Yuquan Road, Shijingshan District, Beijing, 100049, China
| | - Herbert J Kronzucker
- School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Baohai Li
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China.
| | - Weiming Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, 528000, China; University of the Chinese Academy of Sciences, No. 19(A) Yuquan Road, Shijingshan District, Beijing, 100049, China.
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2
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Liu QQ, Xia JQ, Wu J, Han Y, Zhang GQ, Zhao PX, Xiang CB. Root-derived long-distance signals trigger ABA synthesis and enhance drought resistance in Arabidopsis. J Genet Genomics 2024:S1673-8527(24)00060-2. [PMID: 38554784 DOI: 10.1016/j.jgg.2024.03.007] [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: 03/21/2024] [Revised: 03/24/2024] [Accepted: 03/25/2024] [Indexed: 04/02/2024]
Abstract
Vascular plants have evolved intricate long-distance signaling mechanisms to cope with environmental stress, with reactive oxygen species (ROS) emerging as pivotal systemic signals in plant stress responses. However, the exact role of ROS as root-to-shoot signals in the drought response has not been determined. In this study, we reveal that compared with wild-type plants, ferric reductase defective 3 (frd3) mutants exhibit enhanced drought resistance concomitant with elevated NINE-CIS-EPOXYCAROTENOID DIOXYGENASE 3 (NCED3) transcript levels and abscisic acid (ABA) contents in leaves as well as increased hydrogen peroxide (H2O2) levels in roots and leaves. Grafting experiments distinctly illustrate that drought resistance can be conferred by the frd3 rootstock regardless of the scion genotype, indicating that long-distance signals originating from frd3 roots promote an increase in ABA levels in leaves. Intriguingly, the drought resistance conferred by the frd3 mutant rootstock is weakened by the CAT2-overexpressing scion, suggesting that H2O2 may be involved in long-distance signaling. Moreover, the results of comparative transcriptome and proteome analyses support the drought resistance phenotype of the frd3 mutant. Taken together, our findings substantiate the notion that frd3 root-derived long-distance signals trigger ABA synthesis in leaves and enhance drought resistance, providing new evidence for root-to-shoot long-distance signaling in the drought response of plants.
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Affiliation(s)
- Qian-Qian Liu
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui 230027, China
| | - Jin-Qiu Xia
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui 230027, China
| | - Jie Wu
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui 230027, China
| | - Yi Han
- College of Life Sciences, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Gui-Quan Zhang
- College of Agronomy, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Ping-Xia Zhao
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu 215123, China.
| | - Cheng-Bin Xiang
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui 230027, China.
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3
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Singh G, Kaur N, Khanna R, Kaur R, Gudi S, Kaur R, Sidhu N, Vikal Y, Mangat GS. 2Gs and plant architecture: breaking grain yield ceiling through breeding approaches for next wave of revolution in rice ( Oryza sativa L.). Crit Rev Biotechnol 2024; 44:139-162. [PMID: 36176065 DOI: 10.1080/07388551.2022.2112648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 07/10/2022] [Accepted: 07/27/2022] [Indexed: 11/03/2022]
Abstract
Rice is a principal food crop for more than half of the global population. Grain number and grain weight (2Gs) are the two complex traits controlled by several quantitative trait loci (QTLs) and are considered the most critical components for yield enhancement in rice. Novel molecular biology and QTL mapping strategies can be utilized in dissecting the complex genetic architecture of these traits. Discovering the valuable genes/QTLs associated with 2Gs traits hidden in the rice genome and utilizing them in breeding programs may bring a revolution in rice production. Furthermore, the positional cloning and functional characterization of identified genes and QTLs may aid in understanding the molecular mechanisms underlying the 2Gs traits. In addition, knowledge of modern genomic tools aids the understanding of the nature of plant and panicle architecture, which enhances their photosynthetic activity. Rice researchers continue to combine important yield component traits (including 2Gs for the yield ceiling) by utilizing modern breeding tools, such as marker-assisted selection (MAS), haplotype-based breeding, and allele mining. Physical co-localization of GW7 (for grain weight) and DEP2 (for grain number) genes present on chromosome 7 revealed the possibility of simultaneous introgression of these two genes, if desirable allelic variants were found in the single donor parent. This review article will reveal the genetic nature of 2Gs traits and use this knowledge to break the yield ceiling by using different breeding and biotechnological tools, which will sustain the world's food requirements.
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Affiliation(s)
- Gurjeet Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Navdeep Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Renu Khanna
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Rupinder Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Santosh Gudi
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Rajvir Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Navjot Sidhu
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Yogesh Vikal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - G S Mangat
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
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4
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Hassan AH, Mokhtar MM, El Allali A. Transposable elements: multifunctional players in the plant genome. FRONTIERS IN PLANT SCIENCE 2024; 14:1330127. [PMID: 38239225 PMCID: PMC10794571 DOI: 10.3389/fpls.2023.1330127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 12/06/2023] [Indexed: 01/22/2024]
Abstract
Transposable elements (TEs) are indispensable components of eukaryotic genomes that play diverse roles in gene regulation, recombination, and environmental adaptation. Their ability to mobilize within the genome leads to gene expression and DNA structure changes. TEs serve as valuable markers for genetic and evolutionary studies and facilitate genetic mapping and phylogenetic analysis. They also provide insight into how organisms adapt to a changing environment by promoting gene rearrangements that lead to new gene combinations. These repetitive sequences significantly impact genome structure, function and evolution. This review takes a comprehensive look at TEs and their applications in biotechnology, particularly in the context of plant biology, where they are now considered "genomic gold" due to their extensive functionalities. The article addresses various aspects of TEs in plant development, including their structure, epigenetic regulation, evolutionary patterns, and their use in gene editing and plant molecular markers. The goal is to systematically understand TEs and shed light on their diverse roles in plant biology.
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Affiliation(s)
- Asmaa H. Hassan
- Bioinformatics Laboratory, College of Computing, Mohammed VI Polytechnic University, Ben Guerir, Morocco
- Agricultural Genetic Engineering Research Institute, Agriculture Research Center, Giza, Egypt
| | - Morad M. Mokhtar
- Bioinformatics Laboratory, College of Computing, Mohammed VI Polytechnic University, Ben Guerir, Morocco
- Agricultural Genetic Engineering Research Institute, Agriculture Research Center, Giza, Egypt
| | - Achraf El Allali
- Bioinformatics Laboratory, College of Computing, Mohammed VI Polytechnic University, Ben Guerir, Morocco
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Shekhawat PK, Sardar S, Yadav B, Salvi P, Soni P, Ram H. Meta-analysis of transcriptomics studies identifies novel attributes and set of genes involved in iron homeostasis in rice. Funct Integr Genomics 2023; 23:336. [PMID: 37968542 DOI: 10.1007/s10142-023-01265-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/02/2023] [Accepted: 11/06/2023] [Indexed: 11/17/2023]
Abstract
Iron (Fe) is an important micronutrient for humans as well as for plant growth and development. Rice employs multiple mechanisms to counteract the negative effects of Fe deficiency and Fe toxicity. Previously, many transcriptomics studies have identified hundreds of genes affected by Fe deficiency and/or Fe toxicity. These studies are highly valuable to identify novel genes involved in Fe homeostasis. However, in the absence of their systematic integration, they remain underutilized. A systematic meta-analysis of transcriptomics data from such ten previous studies was performed here to identify various common attributes. From this meta-analysis, it is revealed that under Fe deficiency conditions, root transcriptome is more sensitive and exhibits greater similarity across multiple studies than the shoot transcriptome. Furthermore, under Fe toxicity conditions, upregulated genes are more reliable and consistent than downregulated genes in susceptible cultivars. The integration of data from Fe deficiency and Fe toxicity conditions helped to identify key marker genes for Fe stress. As a proof-of-concept of the analysis, among the genes consistently regulated in opposite directions under Fe deficiency and toxicity conditions, two genes were selected: a proton-dependent oligopeptide transporter (POT) family protein and Vacuolar Iron Transporter (VIT)-Like (VTL) gene, and validated their expression and sub-cellular localization. Since VIT genes are known to play an important role in Fe homeostasis in plants, the entire OsVTL gene family in rice was characterized. This meta-analysis has identified many novel candidate genes that exhibit consistent expression patterns across multiple tissues, conditions, and studies. This makes them potential targets for future research aimed at developing Fe-biofortified rice varieties, as well as varieties tolerant to sub-optimal Fe levels in soil.
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Affiliation(s)
- Pooja Kanwar Shekhawat
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, JNU Campus, New Delhi, 110067, India
- Department of Botany, University of Rajasthan, JLN Marg, Jaipur, 302004, India
| | - Shaswati Sardar
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, JNU Campus, New Delhi, 110067, India
| | - Banita Yadav
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, JNU Campus, New Delhi, 110067, India
| | - Prafull Salvi
- National Agri-Food Biotechnology Institute, Sector-81, SAS Nagar Mohali, India
| | - Praveen Soni
- Department of Botany, University of Rajasthan, JLN Marg, Jaipur, 302004, India.
| | - Hasthi Ram
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, JNU Campus, New Delhi, 110067, India.
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Kumar S, Seem K, Mohapatra T. Biochemical and Epigenetic Modulations under Drought: Remembering the Stress Tolerance Mechanism in Rice. Life (Basel) 2023; 13:life13051156. [PMID: 37240801 DOI: 10.3390/life13051156] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 05/07/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
A plant, being a sessile organism, needs to modulate biochemical, physiological, and molecular responses to the environment in a quick and efficient manner to be protected. Drought stress is a frequently occurring abiotic stress that severely affects plant growth, development, and productivity. Short- and long-term memories are well-known phenomena in animals; however, the existence of such remembrance in plants is still being discovered. In this investigation, different rice genotypes were imposed with drought stress just before flowering and the plants were re-watered for recovery from the stress. Seeds collected from the stress-treated (stress-primed) plants were used to raise plants for the subsequent two generations under a similar experimental setup. Modulations in physio-biochemical (chlorophyll, total phenolics and proline contents, antioxidant potential, lipid peroxidation) and epigenetic [5-methylcytosine (5-mC)] parameters were analyzed in the leaves of the plants grown under stress as well as after recovery. There was an increase in proline (>25%) and total phenolic (>19%) contents, antioxidant activity (>7%), and genome-wide 5-mC level (>56%), while a decrease (>9%) in chlorophyll content was recorded to be significant under the stress. Interestingly, a part of the increased proline content, total phenolics content, antioxidant activity, and 5-mC level was retained even after the withdrawal of the stress. Moreover, the increased levels of biochemical and epigenetic parameters were observed to be transmitted/inherited to the subsequent generations. These might help in developing stress-tolerant crops and improving crop productivity under the changing global climate for sustainable food production and global food security.
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Affiliation(s)
- Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Karishma Seem
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
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7
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Transcriptome and Physio-Biochemical Profiling Reveals Differential Responses of Rice Cultivars at Reproductive-Stage Drought Stress. Int J Mol Sci 2023; 24:ijms24021002. [PMID: 36674519 PMCID: PMC9863700 DOI: 10.3390/ijms24021002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/26/2022] [Accepted: 12/29/2022] [Indexed: 01/07/2023] Open
Abstract
Drought stress severely affects the growth and development of rice, especially at the reproductive stage, which results in disturbed metabolic processes, reduced seed-set/grain filling, deteriorated grain quality, declined productivity, and lower yield. Despite the recent advances in understanding the responses of rice to drought stress, there is a need to comprehensively integrate the morpho-physio-biochemical studies with the molecular responses/differential expression of genes and decipher the underlying pathways that regulate the adaptability of rice at various drought-sensitive growth stages. Our comparative analysis of immature panicle from a drought-tolerant (Nagina 22) and a drought-sensitive (IR 64) rice cultivar grown under control (well-watered) and water-deficit/drought stress (treatment, imposed at the reproductive stage) conditions unraveled some novel stress-responsive genes/pathways responsible for reproductive-stage drought stress tolerance. The results revealed a more important role of upregulated (6706) genes in the panicle of N 22 at reproductive-stage drought stress compared to that (5590) in IR 64. Functional enrichment and MapMan analyses revealed that majority of the DEGs were associated with the phytohormone, redox signalling/homeostasis, secondary metabolite, and transcription factor-mediated mitigation of the adverse effects of drought stress in N 22. The upregulated expression of the genes associated with starch/sucrose metabolism, secondary metabolites synthesis, transcription factors, glutathione, linoleic acid, and phenylalanine metabolism in N 22 was significantly more than that in the panicle of IR 64. Compared to IR 64, 2743 genes were upregulated in N 22 under control conditions, which further increased (4666) under drought stress in panicle of the tolerant cultivar. Interestingly, we observed 6706 genes to be upregulated in the panicle of N 22 over IR 64 under drought and 5814 genes get downregulated in the panicle of N 22 over IR 64 under the stress. In addition, RT-qPCR analysis confirmed differential expression patterns of the DEGs. These genes/pathways associated with the reproductive-stage drought tolerance might provide an important source of molecular markers for genetic manipulation of rice for enhanced drought tolerance.
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8
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Bernardt TM, Treviso EM, Cancian M, Silva MDM, da Rocha JBT, Loreto ELS. Chemotherapy Drugs Act Differently in the Expression and Somatic Mobilization of the mariner Transposable Element in Drosophila simulans. Genes (Basel) 2022; 13:genes13122374. [PMID: 36553641 PMCID: PMC9777735 DOI: 10.3390/genes13122374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/10/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Transposable elements (TEs) are abundant in genomes. Their mobilization can lead to genetic variability that is useful for evolution, but can also have deleterious biological effects. Somatic mobilization (SM) has been linked to degenerative diseases, such as Alzheimer's disease and cancer. We used a Drosophila simulans strain, in which SM can be measured by counting red spots in the eyes, to investigate how chemotherapeutic agents affect expression and SM of the mariner TE. Flies were treated with Cisplatin, Dacarbazine, and Daunorubicin. After acute exposure, relative expression of mariner was quantified by RT-qPCR and oxidative stress was measured by biochemical assays. Exposure to 50 and 100 µg/mL Cisplatin increased mariner expression and ROS levels; catalase activity increased at 100 µg/mL. With chronic exposure, the number of spots also increased, indicating higher mariner SM. Dacarbazine (50 and 100 µg/mL) did not significantly alter mariner expression or mobilization or ROS levels, but decreased catalase activity (100 µg/mL). Daunorubicin (25 and 50 µM) increased mariner expression, but decreased mariner SM. ROS and catalase activity were also reduced. Our data suggest that stress factors may differentially affect the expression and SM of TEs. The increase in mariner transposase gene expression is necessary, but not sufficient for mariner SM.
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Affiliation(s)
- Taís Maus Bernardt
- Biological Sciences, Federal University of Santa Maria (UFSM), Santa Maria 97105-000, RS, Brazil
| | - Estéfani Maria Treviso
- Biological Sciences, Federal University of Santa Maria (UFSM), Santa Maria 97105-000, RS, Brazil
| | - Mariana Cancian
- Genetic and Molecular Biology, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre 91501-970, RS, Brazil
| | - Monica de Medeiros Silva
- Department of Biochemistry and Molecular Biology, Federal University of Santa Maria (UFSM), Av. Roraima 1000, Camobi, Santa Maria 97105-900, RS, Brazil
| | - João Batista Teixeira da Rocha
- Department of Biochemistry and Molecular Biology, Federal University of Santa Maria (UFSM), Av. Roraima 1000, Camobi, Santa Maria 97105-900, RS, Brazil
| | - Elgion Lucio Silva Loreto
- Department of Biochemistry and Molecular Biology, Federal University of Santa Maria (UFSM), Av. Roraima 1000, Camobi, Santa Maria 97105-900, RS, Brazil
- Correspondence:
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Singh L, Coronejo S, Pruthi R, Chapagain S, Bhattarai U, Subudhi PK. Genetic Dissection of Alkalinity Tolerance at the Seedling Stage in Rice ( Oryza sativa) Using a High-Resolution Linkage Map. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11233347. [PMID: 36501386 PMCID: PMC9738157 DOI: 10.3390/plants11233347] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 06/12/2023]
Abstract
Although both salinity and alkalinity result from accumulation of soluble salts in soil, high pH and ionic imbalance make alkaline stress more harmful to plants. This study aimed to provide molecular insights into the alkalinity tolerance using a recombinant inbred line (RIL) population developed from a cross between Cocodrie and Dular with contrasting response to alkalinity stress. Forty-six additive QTLs for nine morpho-physiological traits were mapped on to a linkage map of 4679 SNPs under alkalinity stress at the seedling stage and seven major-effect QTLs were for alkalinity tolerance scoring, Na+ and K+ concentrations and Na+:K+ ratio. The candidate genes were identified based on the comparison of the impacts of variants of genes present in five QTL intervals using the whole genome sequences of both parents. Differential expression of no apical meristem protein, cysteine protease precursor, retrotransposon protein, OsWAK28, MYB transcription factor, protein kinase, ubiquitin-carboxyl protein, and NAD binding protein genes in parents indicated their role in response to alkali stress. Our study suggests that the genetic basis of tolerance to alkalinity stress is most likely different from that of salinity stress. Introgression and validation of the QTLs and genes can be useful for improving alkalinity tolerance in rice at the seedling stage and advancing understanding of the molecular genetic basis of alkalinity stress adaptation.
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10
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Nguyen NK, Wang J, Liu D, Hwang BK, Jwa NS. Rice iron storage protein ferritin 2 (OsFER2) positively regulates ferroptotic cell death and defense responses against Magnaporthe oryzae. FRONTIERS IN PLANT SCIENCE 2022; 13:1019669. [PMID: 36352872 PMCID: PMC9639352 DOI: 10.3389/fpls.2022.1019669] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
Ferritin is a ubiquitous iron storage protein that regulates iron homeostasis and oxidative stress in plants. Iron plays an important role in ferroptotic cell death response of rice (Oryza sativa) to Magnaporthe oryzae infection. Here, we report that rice ferritin 2, OsFER2, is required for iron- and reactive oxygen species (ROS)-dependent ferroptotic cell death and defense response against the avirulent M. oryzae INA168. The full-length ferritin OsFER2 and its transit peptide were localized to the chloroplast, the most Fe-rich organelle for photosynthesis. This suggests that the transit peptide acts as a signal peptide for the rice ferritin OsFER2 to move into chloroplasts. OsFER2 expression is involved in rice resistance to M. oryzae infection. OsFER2 knock-out in wild-type rice HY did not induce ROS and ferric ion (Fe3+) accumulation, lipid peroxidation and hypersensitive response (HR) cell death, and also downregulated the defense-related genes OsPAL1, OsPR1-b, OsRbohB, OsNADP-ME2-3, OsMEK2 and OsMPK1, and vacuolar membrane transporter OsVIT2 expression. OsFER2 complementation in ΔOsfer2 knock-out mutants restored ROS and iron accumulation and HR cell death phenotypes during infection. The iron chelator deferoxamine, the lipid-ROS scavenger ferrostatin-1, the actin microfilament polymerization inhibitor cytochalasin E and the redox inhibitor diphenyleneiodonium suppressed ROS and iron accumulation and HR cell death in rice leaf sheaths. However, the small-molecule inducer erastin did not trigger iron-dependent ROS accumulation and HR cell death induction in ΔOsfer2 mutants. These combined results suggest that OsFER2 expression positively regulates iron- and ROS-dependent ferroptotic cell death and defense response in rice-M. oryzae interactions.
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Affiliation(s)
- Nam Khoa Nguyen
- Division of Integrative Bioscience and Biotechnology, College of Life Sciences, Sejong University, Seoul, South Korea
| | - Juan Wang
- Division of Integrative Bioscience and Biotechnology, College of Life Sciences, Sejong University, Seoul, South Korea
| | - Dongping Liu
- Division of Integrative Bioscience and Biotechnology, College of Life Sciences, Sejong University, Seoul, South Korea
| | - Byung Kook Hwang
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea
| | - Nam-Soo Jwa
- Division of Integrative Bioscience and Biotechnology, College of Life Sciences, Sejong University, Seoul, South Korea
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11
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Viana VE, Maltzahn LE, Costa de Oliveira A, Pegoraro C. Genetic Approaches for Iron and Zinc Biofortification and Arsenic Decrease in Oryza sativa L. Grains. Biol Trace Elem Res 2022; 200:4505-4523. [PMID: 34773578 DOI: 10.1007/s12011-021-03018-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/04/2021] [Indexed: 12/29/2022]
Abstract
Rice is the staple diet to half of the world's population, being a major source of carbohydrates, vitamins, and some essential elements. However, rice naturally contains low amounts of essential minerals such as iron (Fe) and zinc (Zn), which are drastically decreased after milling. Thus, populations that consume mostly rice may have micronutrient deficiency, which is associated with different diseases. On the other hand, rice irrigated by flooding has a high ability to accumulate arsenic (As) in the grain. Therefore, when rice is grown in areas with contaminated soil or irrigation water, it represents a risk factor for consumers, since As is associated with cancer and other diseases. Different strategies have been used to mitigate micronutrient deficiencies such as Fe and Zn and to prevent As from entering the food chain. Each strategy has its positive and its negative sides. The development of genetically biofortified rice plants with Fe and Zn and with low As accumulation is one of the most promising strategies, since it does not represent an additional cost for farmers, and gives benefits to consumers as well. Considering the importance of genetic improvement (traditional or molecular) to decrease the impact of micronutrient deficiencies such as Fe and Zn and contamination with As, this review aimed to summarize the major efforts, advances, and challenges for genetic biofortification of Fe and Zn and decrease in As content in rice grains.
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Affiliation(s)
- Vívian Ebeling Viana
- Centro de Genômica E Fitomelhoramento, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Capão Do Leão, Brazil
| | - Latóia Eduarda Maltzahn
- Centro de Genômica E Fitomelhoramento, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Capão Do Leão, Brazil
| | - Antonio Costa de Oliveira
- Centro de Genômica E Fitomelhoramento, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Capão Do Leão, Brazil
| | - Camila Pegoraro
- Centro de Genômica E Fitomelhoramento, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Capão Do Leão, Brazil.
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12
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Prusty S, Sahoo RK, Nayak S, Poosapati S, Swain DM. Proteomic and Genomic Studies of Micronutrient Deficiency and Toxicity in Plants. PLANTS 2022; 11:plants11182424. [PMID: 36145825 PMCID: PMC9501179 DOI: 10.3390/plants11182424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 09/02/2022] [Accepted: 09/04/2022] [Indexed: 11/21/2022]
Abstract
Micronutrients are essential for plants. Their growth, productivity and reproduction are directly influenced by the supply of micronutrients. Currently, there are eight trace elements considered to be essential for higher plants: Fe, Zn, Mn, Cu, Ni, B, Mo, and Cl. Possibly, other essential elements could be discovered because of recent advances in nutrient solution culture techniques and in the commercial availability of highly sensitive analytical instrumentation for elemental analysis. Much remains to be learned about the physiology of micronutrient absorption, translocation and deposition in plants, and about the functions they perform in plant growth and development. With the recent advancements in the proteomic and molecular biology tools, researchers have attempted to explore and address some of these questions. In this review, we summarize the current knowledge of micronutrients in plants and the proteomic/genomic approaches used to study plant nutrient deficiency and toxicity.
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Affiliation(s)
- Suchismita Prusty
- Department of Biotechnology, Centurion University of Technology and Management, Bhubaneswar 752050, Odisha, India
| | - Ranjan Kumar Sahoo
- Department of Biotechnology, Centurion University of Technology and Management, Bhubaneswar 752050, Odisha, India
| | - Subhendu Nayak
- Division of Health Sciences, The Clorox Company, 210W Pettigrew Street, Durham, NC 27701, USA
| | - Sowmya Poosapati
- Division of Biological Sciences, Cell and Developmental Biology Section, University of California, San Diego, CA 92093, USA
- Correspondence: (S.P.); (D.M.S.)
| | - Durga Madhab Swain
- Division of Biological Sciences, Cell and Developmental Biology Section, University of California, San Diego, CA 92093, USA
- Correspondence: (S.P.); (D.M.S.)
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13
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Zhang X, Xue C, Wang R, Shen R, Lan P. Physiological and proteomic dissection of the rice roots in response to iron deficiency and excess. J Proteomics 2022; 267:104689. [PMID: 35914714 DOI: 10.1016/j.jprot.2022.104689] [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: 03/22/2022] [Revised: 07/14/2022] [Accepted: 07/17/2022] [Indexed: 10/16/2022]
Abstract
Iron (Fe) disorder is a pivotal factor that limits rice yields in many parts of the world. Extensive research has been devoted to studying how rice molecularly copes with the stresses of Fe deficiency or excess. However, a comprehensive dissection of the whole Fe-responsive atlas at the protein level is still lacking. Here, different concentrations of Fe (0, 40, 350, and 500 μM) were supplied to rice to demonstrate its response differences to Fe deficiency and excess via physiological and proteomic analysis. Results showed that compared with the normal condition, the seedling growth and contents of Fe and manganese were significantly disturbed under either Fe stress. Proteomic analysis revealed that differentially accumulated proteins under Fe deficiency and Fe excess were commonly enriched in localization, carbon metabolism, biosynthesis of amino acids, and antioxidant system. Notably, proteins with abundance retuned by Fe starvation were individually associated with phenylpropanoid biosynthesis, cysteine and methionine metabolism, while ribosome- and endocytosis-related proteins were specifically enriched in treatment of Fe overdose of 500 μM. Moreover, several novel proteins which may play potential roles in rice Fe homeostasis were predicted. These findings expand the understanding of rice Fe nutrition mechanisms, and provide efficient guidance for genetic breeding work. SIGNIFICANCE: Both iron (Fe) deficiency and excess significantly inhibited the growth of rice seedlings. Fe deficiency and excess disturbed processes of localization and cellular oxidant detoxification, metabolisms of carbohydrates and amino acids in different ways. The Fe-deficiency and Fe-excess-responsive proteins identified by the proteome were somewhat different from the reported transcriptional profiles, providing complementary information to the transcriptomic data.
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Affiliation(s)
- Xin Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Caiwen Xue
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Ruonan Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Renfang Shen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Ping Lan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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14
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Genetic dissection of grain iron and zinc, and thousand kernel weight in wheat (Triticum aestivum L.) using genome-wide association study. Sci Rep 2022; 12:12444. [PMID: 35858934 PMCID: PMC9300641 DOI: 10.1038/s41598-022-15992-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 07/04/2022] [Indexed: 01/13/2023] Open
Abstract
Genetic biofortification is recognized as a cost-effective and sustainable strategy to reduce micronutrient malnutrition. Genomic regions governing grain iron concentration (GFeC), grain zinc concentration (GZnC), and thousand kernel weight (TKW) were investigated in a set of 280 diverse bread wheat genotypes. The genome-wide association (GWAS) panel was genotyped using 35 K Axiom Array and phenotyped in five environments. The GWAS analysis showed a total of 17 Bonferroni-corrected marker-trait associations (MTAs) in nine chromosomes representing all the three wheat subgenomes. The TKW showed the highest MTAs (7), followed by GZnC (5) and GFeC (5). Furthermore, 14 MTAs were identified with more than 10% phenotypic variation. One stable MTA i.e. AX-95025823 was identified for TKW in both E4 and E5 environments along with pooled data, which is located at 68.9 Mb on 6A chromosome. In silico analysis revealed that the SNPs were located on important putative candidate genes such as Multi antimicrobial extrusion protein, F-box domain, Late embryogenesis abundant protein, LEA-18, Leucine-rich repeat domain superfamily, and C3H4 type zinc finger protein, involved in iron translocation, iron and zinc homeostasis, and grain size modifications. The identified novel MTAs will be validated to estimate their effects in different genetic backgrounds for subsequent use in marker-assisted selection. The identified SNPs will be valuable in the rapid development of biofortified wheat varieties to ameliorate the malnutrition problems.
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15
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Kirk GJD, Manwaring HR, Ueda Y, Semwal VK, Wissuwa M. Below-ground plant-soil interactions affecting adaptations of rice to iron toxicity. PLANT, CELL & ENVIRONMENT 2022; 45:705-718. [PMID: 34628670 DOI: 10.1111/pce.14199] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/11/2021] [Accepted: 08/13/2021] [Indexed: 06/13/2023]
Abstract
Iron toxicity is a major constraint to rice production, particularly in highly weathered soils of inland valleys in sub-Saharan Africa where the rice growing area is rapidly expanding. There is a wide variation in tolerance of iron toxicity in the rice germplasm. However, the introgression of tolerance traits into high-yielding germplasm has been slow owing to the complexity of the tolerance mechanisms and large genotype-by-environment effects. We review current understanding of tolerance mechanisms, particularly those involving below-ground plant-soil interactions. Until now these have been less studied than above-ground mechanisms. We cover processes in the rhizosphere linked to exclusion of toxic ferrous iron by oxidation, and resulting effects on the mobility of nutrient ions. We also cover the molecular physiology of below-ground processes controlling iron retention in roots and root-shoot transport, and also plant iron sensing. We conclude that future breeding programmes should be based on well-characterized molecular markers for iron toxicity tolerance traits. To successfully identify such markers, the complex tolerance response should be broken down into its components based on understanding of tolerance mechanisms, and tailored screening methods should be developed for individual mechanisms.
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Affiliation(s)
- Guy J D Kirk
- School of Water, Energy and Environment, Cranfield University, Cranfield, UK
| | - Hanna R Manwaring
- School of Water, Energy and Environment, Cranfield University, Cranfield, UK
| | - Yoshiaki Ueda
- Crop, Livestock and Environment Division, Japan International Research Center for Agricultural Sciences, Tsukuba, Japan
| | | | - Matthias Wissuwa
- Crop, Livestock and Environment Division, Japan International Research Center for Agricultural Sciences, Tsukuba, Japan
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16
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Regon P, Dey S, Rehman M, Pradhan AK, Chowra U, Tanti B, Talukdar AD, Panda SK. Transcriptomic Analysis Revealed Reactive Oxygen Species Scavenging Mechanisms Associated With Ferrous Iron Toxicity in Aromatic Keteki Joha Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:798580. [PMID: 35283928 PMCID: PMC8913046 DOI: 10.3389/fpls.2022.798580] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 01/21/2022] [Indexed: 06/14/2023]
Abstract
Lowland acidic soils with water-logged regions are often affected by ferrous iron (Fe2+) toxicity, a major yield-limiting factor of rice production. Under severe Fe2+ toxicity, reactive oxygen species (ROS) are crucial, although molecular mechanisms and associated ROS homeostasis genes are still unknown. In this study, a comparative RNA-Seq based transcriptome analysis was conducted to understand the Fe2+ toxicity tolerance mechanism in aromatic Keteki Joha. About 69 Fe homeostasis related genes and their homologs were identified, where most of the genes were downregulated. Under severe Fe2+ toxicity, the biosynthesis of amino acids, RNA degradation, and glutathione metabolism were induced, whereas phenylpropanoid biosynthesis, photosynthesis, and fatty acid elongation were inhibited. The mitochondrial iron transporter (OsMIT), vacuolar iron transporter 2 (OsVIT2), ferritin (OsFER), vacuolar mugineic acid transporter (OsVMT), phenolic efflux zero1 (OsPEZ1), root meander curling (OsRMC), and nicotianamine synthase (OsNAS3) were upregulated in different tissues, suggesting the importance of Fe retention and sequestration for detoxification. However, several antioxidants, ROS scavenging genes and abiotic stress-responsive transcription factors indicate ROS homeostasis as one of the most important defense mechanisms under severe Fe2+ toxicity. Catalase (CAT), glutathione (GSH), ascorbate peroxidase (APX), monodehydroascorbate reductase (MDHAR), dehydroascorbate reductase (DHAR), and glutathione reductase (GR) were upregulated. Moreover, abiotic stress-responsive transcription factors, no apical meristem (NAC), myeloblastosis (MYB), auxin response factor (ARF), basic helix-loop-helix (bZIP), WRKY, and C2H2-zinc finger protein (C2H2-ZFP) were also upregulated. Accordingly, ROS homeostasis has been proposed as an essential defense mechanism under such conditions. Thus, the current study may enrich the understanding of Fe-homeostasis in rice.
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Affiliation(s)
- Preetom Regon
- Department of Life Science and Bioinformatics, Assam University, Silchar, India
- Plant Molecular Biology Laboratory, Department of Botany, Gauhati University, Guwahati, India
| | - Sangita Dey
- Department of Life Science and Bioinformatics, Assam University, Silchar, India
| | - Mehzabin Rehman
- Plant Molecular Biology Laboratory, Department of Botany, Gauhati University, Guwahati, India
| | - Amit Kumar Pradhan
- Plant Molecular Biology Laboratory, Department of Botany, Gauhati University, Guwahati, India
- Department of Botany, Pragjyotish College, Guwahati, India
| | | | - Bhaben Tanti
- Plant Molecular Biology Laboratory, Department of Botany, Gauhati University, Guwahati, India
| | - Anupam Das Talukdar
- Department of Life Science and Bioinformatics, Assam University, Silchar, India
| | - Sanjib Kumar Panda
- Department of Biochemistry, Central University of Rajasthan, Ajmer, India
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17
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Papolu PK, Ramakrishnan M, Wei Q, Vinod KK, Zou LH, Yrjala K, Kalendar R, Zhou M. Long terminal repeats (LTR) and transcription factors regulate PHRE1 and PHRE2 activity in Moso bamboo under heat stress. BMC PLANT BIOLOGY 2021; 21:585. [PMID: 34886797 PMCID: PMC8656106 DOI: 10.1186/s12870-021-03339-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/12/2021] [Indexed: 05/28/2023]
Abstract
BACKGROUND LTR retrotransposons play a significant role in plant growth, genome evolution, and environmental stress response, but their regulatory response to heat stress remains unclear. We have investigated the activities of two LTR retrotransposons, PHRE1 and PHRE2, of moso bamboo (Phyllostachys edulis) in response to heat stress. RESULTS The differential overexpression of PHRE1 and PHRE2 with or without CaMV35s promoter showed enhanced expression under heat stress in transgenic plants. The transcriptional activity studies showed an increase in transposition activity and copy number among moso bamboo wild type and Arabidopsis transgenic plants under heat stress. Comparison of promoter activity in transgenic plants indicated that 5'LTR promoter activity was higher than CaMV35s promoter. Additionally, yeast one-hybrid (Y1H) system and in planta biomolecular fluorescence complementation (BiFC) assay revealed interactions of heat-dependent transcription factors (TFs) with 5'LTR sequence and direct interactions of TFs with pol and gag. CONCLUSIONS Our results conclude that the 5'LTR acts as a promoter and could regulate the LTR retrotransposons in moso bamboo under heat stress.
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Affiliation(s)
- Pradeep K Papolu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Muthusamy Ramakrishnan
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Qiang Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | | | - Long-Hai Zou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Kim Yrjala
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Ruslan Kalendar
- Helsinki Institute of Life Science HiLIFE, Biocenter 3, Viikinkaari 1, FI-00014 University of Helsinki, Helsinki, Finland
| | - Mingbing Zhou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China.
- Zhejiang Provincial Collaborative Innovation Centre for Bamboo Resources and High-efficiency Utilization, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China.
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18
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Introgression of Bacterial Blight Resistance Genes in the Rice Cultivar Ciherang: Response against Xanthomonas oryzae pv. oryzae in the F 6 Generation. PLANTS 2021; 10:plants10102048. [PMID: 34685858 PMCID: PMC8540907 DOI: 10.3390/plants10102048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/25/2021] [Accepted: 09/27/2021] [Indexed: 11/24/2022]
Abstract
Bacterial blight (BB) is caused by Xanthomonas oryzae pv. oryzae and is one of the most important diseases in rice. It results in significantly reduced productivity throughout all rice-growing regions of the world. Four BB resistance genes have been reported; however, introgression of a single gene into rice has not been able to sufficiently protect rice against BB infection. Pyramiding of effective BB resistance genes (i.e., Xa genes) into background varieties is a potential approach to controlling BB infection. In this study, combinations of four BB resistance genes, Xa4, xa5, xa13, and Xa21, were pyramided into populations. The populations were derived from crossing Ciherang (a widespread Indonesian rice variety) with IRBB60 (resistance to BB). Promising recombinants from the F6 generation were identified by scoring the phenotype against three virulent bacterial strains, C5, P6, and V, which cause widespread BB infection in most rice-growing countries. Pyramiding of genes for BB resistance in 265 recombinant introgressed lines (RILs) were confirmed through marker-assisted selection (MAS) of the F5 and F6 generations using gene-specific primers. Of these 265 RILs, 11, 34 and 45 lines had four, three, or two BB resistance genes, respectively. The RILs had pyramiding of two or three resistance genes, with the Xa4 resistance gene showing broad spectrum resistance against Xoo races with higher agronomic performance compared to their donor and recipients parents. The developed BB-resistant RILs have high yield potential to be further developed for cultivation or as sources of BB resistance donor material for varietal improvement in other rice lines.
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19
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Kar S, Mai HJ, Khalouf H, Ben Abdallah H, Flachbart S, Fink-Straube C, Bräutigam A, Xiong G, Shang L, Panda SK, Bauer P. Comparative Transcriptomics of Lowland Rice Varieties Uncovers Novel Candidate Genes for Adaptive Iron Excess Tolerance. PLANT & CELL PHYSIOLOGY 2021; 62:624-640. [PMID: 33561287 PMCID: PMC8462385 DOI: 10.1093/pcp/pcab018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 01/29/2021] [Indexed: 05/19/2023]
Abstract
Iron (Fe) toxicity is a major challenge for plant cultivation in acidic waterlogged soil environments, where lowland rice is a major staple food crop. Only few studies have addressed the molecular characterization of excess Fe tolerance in rice, and these highlight different mechanisms for Fe tolerance. Out of 16 lowland rice varieties, we identified a pair of contrasting lines, Fe-tolerant Lachit and -susceptible Hacha. The two lines differed in their physiological and morphological responses to excess Fe, including leaf growth, leaf rolling, reactive oxygen species generation and Fe and metal contents. These responses were likely due to genetic origin as they were mirrored by differential gene expression patterns, obtained through RNA sequencing, and corresponding gene ontology term enrichment in tolerant vs. susceptible lines. Thirty-five genes of the metal homeostasis category, mainly root expressed, showed differential transcriptomic profiles suggestive of an induced tolerance mechanism. Twenty-two out of these 35 metal homeostasis genes were present in selection sweep genomic regions, in breeding signatures, and/or differentiated during rice domestication. These findings suggest that Fe excess tolerance is an important trait in the domestication of lowland rice, and the identified genes may further serve to design the targeted Fe tolerance breeding of rice crops.
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Affiliation(s)
- Saradia Kar
- Institute of Botany, Heinrich Heine University, Universitätsstr. 1, Düsseldorf 40225, Germany
- Plant Molecular Biotechnology Laboratory, Department of Life Science and Bioinformatics, Assam University, Silchar, India
| | - Hans-Jörg Mai
- Institute of Botany, Heinrich Heine University, Universitätsstr. 1, Düsseldorf 40225, Germany
| | - Hadeel Khalouf
- Institute of Botany, Heinrich Heine University, Universitätsstr. 1, Düsseldorf 40225, Germany
| | - Heithem Ben Abdallah
- Institute of Botany, Heinrich Heine University, Universitätsstr. 1, Düsseldorf 40225, Germany
| | - Samantha Flachbart
- Institute of Plant Biochemistry, Heinrich Heine University, Universitätsstr. 1, Düsseldorf 40225, Germany
| | | | - Andrea Bräutigam
- Faculty of Biology, Bielefeld University, Universitätsstr. 27, Bielefeld 33615, Germany
| | - Guosheng Xiong
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Lianguang Shang
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Sanjib Kumar Panda
- Plant Molecular Biotechnology Laboratory, Department of Life Science and Bioinformatics, Assam University, Silchar, India
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan 305817, India
| | - Petra Bauer
- Institute of Botany, Heinrich Heine University, Universitätsstr. 1, Düsseldorf 40225, Germany
- Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, Düsseldorf, Germany
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20
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Kakei Y, Masuda H, Nishizawa NK, Hattori H, Aung MS. Elucidation of Novel cis-Regulatory Elements and Promoter Structures Involved in Iron Excess Response Mechanisms in Rice Using a Bioinformatics Approach. FRONTIERS IN PLANT SCIENCE 2021; 12:660303. [PMID: 34149757 PMCID: PMC8207140 DOI: 10.3389/fpls.2021.660303] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/06/2021] [Indexed: 05/24/2023]
Abstract
Iron (Fe) excess is a major constraint on crop production in flooded acidic soils, particularly in rice cultivation. Under Fe excess, plants activate a complex mechanism and network regulating Fe exclusion by roots and isolation in various tissues. In rice, the transcription factors and cis-regulatory elements (CREs) that regulate Fe excess response mechanisms remain largely elusive. We previously reported comprehensive microarray analyses of several rice tissues in response to various levels of Fe excess stress. In this study, we further explored novel CREs and promoter structures in rice using bioinformatics approaches with this microarray data. We first performed network analyses to predict Fe excess-related CREs through the categorization of the gene expression patterns of Fe excess-responsive transcriptional regulons, and found four major expression clusters: Fe storage type, Fe chelator type, Fe uptake type, and WRKY and other co-expression type. Next, we explored CREs within these four clusters of gene expression types using a machine-learning method called microarray-associated motif analyzer (MAMA), which we previously established. Through a comprehensive bioinformatics approach, we identified a total of 560 CRE candidates extracted by MAMA analyses and 42 important conserved sequences of CREs directly related to the Fe excess response in various rice tissues. We explored several novel cis-elements as candidate Fe excess CREs including GCWGCWGC, CGACACGC, and Myb binding-like motifs. Based on the presence or absence of candidate CREs using MAMA and known PLACE CREs, we found that the Boruta-XGBoost model explained expression patterns with high accuracy of about 83%. Enriched sequences of both novel MAMA CREs and known PLACE CREs led to high accuracy expression patterns. We also found new roles of known CREs in the Fe excess response, including the DCEp2 motif, IDEF1-, Zinc Finger-, WRKY-, Myb-, AP2/ERF-, MADS- box-, bZIP and bHLH- binding sequence-containing motifs among Fe excess-responsive genes. In addition, we built a molecular model and promoter structures regulating Fe excess-responsive genes based on new finding CREs. Together, our findings about Fe excess-related CREs and conserved sequences will provide a comprehensive resource for discovery of genes and transcription factors involved in Fe excess-responsive pathways, clarification of the Fe excess response mechanism in rice, and future application of the promoter sequences to produce genotypes tolerant of Fe excess.
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Affiliation(s)
- Yusuke Kakei
- Institute of Vegetable and Floriculture Science, Research Center for Agricultural Information Technology, National Agriculture and Food Research Organization, Ibaraki, Japan
| | - Hiroshi Masuda
- Faculty of Bioresource Sciences, Department of Biological Production, Akita Prefectural University, Akita, Japan
| | - Naoko K. Nishizawa
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Ishikawa, Japan
| | - Hiroyuki Hattori
- Faculty of Bioresource Sciences, Department of Biological Production, Akita Prefectural University, Akita, Japan
| | - May Sann Aung
- Faculty of Bioresource Sciences, Department of Biological Production, Akita Prefectural University, Akita, Japan
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Ishikawa, Japan
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21
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Chaâbene Z, Rorat A, Kriaa W, Rekik I, Mejdoub H, Vandenbulcke F, Elleuch A. In-site and Ex-site Date Palm Exposure to Heavy Metals Involved Infra-Individual Biomarkers Upregulation. PLANTS 2021; 10:plants10010137. [PMID: 33445405 PMCID: PMC7826821 DOI: 10.3390/plants10010137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/29/2020] [Accepted: 01/06/2021] [Indexed: 11/16/2022]
Abstract
As a tree of considerable importance in arid regions-date palm, Phoenix dactylifera L. survival in contaminated areas of Sfax city has drawn our attention. Leaf samples of the plants grown in the study area showed high levels of cadmium (Cd), copper (Cu), and chromium (Cr). On the basis of this finding, the cellular mechanisms that explain these metal accumulations were investigated in controlled conditions. After four months of exposure to Cd, Cr, or Cu, high bioconcentration and translocation factor (TF>1) have been shown for date palm plantlets exposed to Cd and low TF values were obtained for plantlets treated with Cr and Cu. Moreover, accumulation of oxidants and antioxidant enzyme activities occurred in exposed roots to Cu and Cd. Secondary metabolites, such as polyphenols and flavonoids, were enhanced in plants exposed at low metal concentrations and declined thereafter. Accumulation of flavonoids in cells may be correlated with the expression of the gene encoding Pdmate5, responsible for the transport of secondary metabolites, especially flavonoids. Other transporter genes responded positively to metal incorporation, especially Pdhma2, but also Pdabcc and Pdnramp6. The latter would be a new candidate gene sensitive to metallic stress in plants. Expressions of gene coding metal chelators were also investigated. Pdpcs1 and Pdmt3 exhibited a strong induction in plants exposed to Cr. These modifications of the expression of some biochemical and molecular based-markers in date palm helped to better understand the ability of the plant to tolerate metals. They could be useful in assessing heavy metal contaminations in polluted soils and may improve accumulation capacity of other plants.
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Affiliation(s)
- Zayneb Chaâbene
- Laboratory of Plant Biotechnology, Faculty of Sciences of Sfax, University of Sfax, Sfax 3000, Tunisia; (H.M.); (A.E.)
- Laboratoire de Génie Civil et géo-Environnement–Université de Lille 1, F-59655 Villeneuve d’Ascq, France; (A.R.); (F.V.)
- Correspondence:
| | - Agnieszka Rorat
- Laboratoire de Génie Civil et géo-Environnement–Université de Lille 1, F-59655 Villeneuve d’Ascq, France; (A.R.); (F.V.)
| | - Walid Kriaa
- Environmental Science Center, Qatar University, Doha P.O. Box 2713, Qatar;
| | - Imen Rekik
- High Institute of Applied Biology of Medenine, Medenine 4119, Tunisia;
| | - Hafedh Mejdoub
- Laboratory of Plant Biotechnology, Faculty of Sciences of Sfax, University of Sfax, Sfax 3000, Tunisia; (H.M.); (A.E.)
| | - Franck Vandenbulcke
- Laboratoire de Génie Civil et géo-Environnement–Université de Lille 1, F-59655 Villeneuve d’Ascq, France; (A.R.); (F.V.)
| | - Amine Elleuch
- Laboratory of Plant Biotechnology, Faculty of Sciences of Sfax, University of Sfax, Sfax 3000, Tunisia; (H.M.); (A.E.)
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22
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Androsiuk P, Chwedorzewska KJ, Dulska J, Milarska S, Giełwanowska I. Retrotransposon-based genetic diversity of Deschampsia antarctica Desv. from King George Island (Maritime Antarctic). Ecol Evol 2021; 11:648-663. [PMID: 33437458 PMCID: PMC7790655 DOI: 10.1002/ece3.7095] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 11/16/2020] [Accepted: 11/19/2020] [Indexed: 12/11/2022] Open
Abstract
Deschampsia antarctica Desv. can be found in diverse Antarctic habitats which may vary considerably in terms of environmental conditions and soil properties. As a result, the species is characterized by wide ecotypic variation in terms of both morphological and anatomical traits. The species is a unique example of an organism that can successfully colonize inhospitable regions due to its phenomenal ability to adapt to both the local mosaic of microhabitats and to general climatic fluctuations. For this reason, D. antarctica has been widely investigated in studies analyzing morphophysiological and biochemical responses to various abiotic stresses (frost, drought, salinity, increased UV radiation). However, there is little evidence to indicate whether the observed polymorphism is accompanied by the corresponding genetic variation. In the present study, retrotransposon-based iPBS markers were used to trace the genetic variation of D. antarctica collected in nine sites of the Arctowski oasis on King George Island (Western Antarctic). The genotyping of 165 individuals from nine populations with seven iPBS primers revealed 125 amplification products, 15 of which (12%) were polymorphic, with an average of 5.6% polymorphic fragments per population. Only one of the polymorphic fragments, observed in population 6, was represented as a private band. The analyzed specimens were characterized by low genetic diversity (uHe = 0.021, I = 0.030) and high population differentiation (F ST = 0.4874). An analysis of Fu's F S statistics and mismatch distribution in most populations (excluding population 2, 6 and 9) revealed demographic/spatial expansion, whereas significant traces of reduction in effective population size were found in three populations (1, 3 and 5). The iPBS markers revealed genetic polymorphism of D. antarctica, which could be attributed to the mobilization of random transposable elements, unique features of reproductive biology, and/or geographic location of the examined populations.
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Affiliation(s)
- Piotr Androsiuk
- Department of Plant Physiology, Genetics and BiotechnologyFaculty of Biology and BiotechnologyUniversity of Warmia and Mazury in OlsztynOlsztynPoland
| | | | - Justyna Dulska
- Department of Plant Physiology, Genetics and BiotechnologyFaculty of Biology and BiotechnologyUniversity of Warmia and Mazury in OlsztynOlsztynPoland
| | - Sylwia Milarska
- Department of Plant Physiology, Genetics and BiotechnologyFaculty of Biology and BiotechnologyUniversity of Warmia and Mazury in OlsztynOlsztynPoland
| | - Irena Giełwanowska
- Department of Plant Physiology, Genetics and BiotechnologyFaculty of Biology and BiotechnologyUniversity of Warmia and Mazury in OlsztynOlsztynPoland
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Marzec M, Situmorang A, Brewer PB, Brąszewska A. Diverse Roles of MAX1 Homologues in Rice. Genes (Basel) 2020; 11:E1348. [PMID: 33202900 PMCID: PMC7709044 DOI: 10.3390/genes11111348] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 10/30/2020] [Accepted: 11/10/2020] [Indexed: 02/07/2023] Open
Abstract
Cytochrome P450 enzymes encoded by MORE AXILLARY GROWTH1 (MAX1)-like genes produce most of the structural diversity of strigolactones during the final steps of strigolactone biosynthesis. The diverse copies of MAX1 in Oryza sativa provide a resource to investigate why plants produce such a wide range of strigolactones. Here we performed in silico analyses of transcription factors and microRNAs that may regulate each rice MAX1, and compared the results with available data about MAX1 expression profiles and genes co-expressed with MAX1 genes. Data suggest that distinct mechanisms regulate the expression of each MAX1. Moreover, there may be novel functions for MAX1 homologues, such as the regulation of flower development or responses to heavy metals. In addition, individual MAX1s could be involved in specific functions, such as the regulation of seed development or wax synthesis in rice. Our analysis reveals potential new avenues of strigolactone research that may otherwise not be obvious.
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Affiliation(s)
- Marek Marzec
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Jagiellonska 28, 40-032 Katowice, Poland;
| | - Apriadi Situmorang
- ARC Centre of Excellence in Plant Energy Biology, Waite Research Institute, School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA 5064, Australia; (A.S.); (P.B.B.)
| | - Philip B. Brewer
- ARC Centre of Excellence in Plant Energy Biology, Waite Research Institute, School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA 5064, Australia; (A.S.); (P.B.B.)
| | - Agnieszka Brąszewska
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Jagiellonska 28, 40-032 Katowice, Poland;
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Xiong Q, Zhong L, Du J, Zhu C, Peng X, He X, Fu J, Ouyang L, Bian J, Hu L, Sun X, Xu J, Zhou D, Cai Y, Fu H, He H, Chen X. Ribosome profiling reveals the effects of nitrogen application translational regulation of yield recovery after abrupt drought-flood alternation in rice. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 155:42-58. [PMID: 32738581 DOI: 10.1016/j.plaphy.2020.07.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 06/22/2020] [Accepted: 07/13/2020] [Indexed: 05/03/2023]
Abstract
Abrupt drought-flood alternation is a frequent meteorological disaster during the summer in Southern China. The study of physiological and translation mechanisms of rice yield recovery after abrupt drought-flood alternation has great potential benefits in field production. Our results showed that yield recovery upon nitrogen (N) application after abrupt drought-flood alternation was due to the increase in effective panicle numbers per plant. The N application resulted in the regulation of physiological and biochemical as well as growth development processes, which led to a rapid growth recovery effect after abrupt drought-flood alternation stress in rice. Using ribosome profiling combined with RNA sequencing (RNA-seq) technology, the interactions between transcription and translation for N application after abrupt drought-flood alternation were analyzed. It was found that a small proportion of response genes were shared at the transcriptional and translational levels, that is, 14% of the expressed genes were upregulated and 6.6% downregulated. Further analysis revealed that the translation efficiency (TE) of the genes was influenced by their sequence characteristics, including their GC content, coding sequence length and normalized minimal free energy. Compared with the number of untranslated upstream open reading frames (uORFs), the increased number of translated uORFs promoted the improvement of TE. The TE of the uORFs for N application was lower than the control without N application after abrupt drought-flood alternation. This study characterizes the translational regulatory pattern in response to N application after abrupt drought-flood alternation stress.
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Affiliation(s)
- Qiangqiang Xiong
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Lei Zhong
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Jie Du
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Changlan Zhu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xiaosong Peng
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xiaopeng He
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Junru Fu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Linjuan Ouyang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Jianmin Bian
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Lifang Hu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xiaotang Sun
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Jie Xu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Dahu Zhou
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Yicong Cai
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Haihui Fu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Haohua He
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Xiaorong Chen
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China.
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Aung MS, Masuda H. How Does Rice Defend Against Excess Iron?: Physiological and Molecular Mechanisms. FRONTIERS IN PLANT SCIENCE 2020; 11:1102. [PMID: 32849682 PMCID: PMC7426474 DOI: 10.3389/fpls.2020.01102,] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 07/03/2020] [Indexed: 05/29/2023]
Abstract
Iron (Fe) is an essential nutrient for all living organisms but can lead to cytotoxicity when present in excess. Fe toxicity often occurs in rice grown in submerged paddy fields with low pH, leading dramatical increases in ferrous ion concentration, disrupting cell homeostasis and impairing growth and yield. However, the underlying molecular mechanisms of Fe toxicity response and tolerance in plants are not well characterized yet. Microarray and genome-wide association analyses have shown that rice employs four defense systems to regulate Fe homeostasis under Fe excess. In defense 1, Fe excess tolerance is implemented by Fe exclusion as a result of suppression of genes involved in Fe uptake and translocation such as OsIRT1, OsYSL2, OsTOM1, OsYSL15, OsNRAMP1, OsNAS1, OsNAS2, OsNAAT1, OsDMAS1, and OsIRO2. The Fe-binding ubiquitin ligase, HRZ, is a key regulator that represses Fe uptake genes in response to Fe excess in rice. In defense 2, rice retains Fe in the root system rather than transporting it to shoots. In defense 3, rice compartmentalizes Fe in the shoot. In defense 2 and 3, the vacuolar Fe transporter OsVIT2, Fe storage protein ferritin, and the nicotinamine synthase OsNAS3 mediate the isolation or detoxification of excess Fe. In defense 4, rice detoxifies the ROS produced within the plant body in response to excess Fe. Some OsWRKY transcription factors, S-nitrosoglutathione-reductase variants, p450-family proteins, and OsNAC4, 5, and 6 are implicated in defense 4. These knowledge will facilitate the breeding of tolerant crops with increased productivity in low-pH, Fe-excess soils.
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Aung MS, Masuda H. How Does Rice Defend Against Excess Iron?: Physiological and Molecular Mechanisms. FRONTIERS IN PLANT SCIENCE 2020; 11:1102. [PMID: 32849682 PMCID: PMC7426474 DOI: 10.3389/fpls.2020.01102] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 07/03/2020] [Indexed: 05/25/2023]
Abstract
Iron (Fe) is an essential nutrient for all living organisms but can lead to cytotoxicity when present in excess. Fe toxicity often occurs in rice grown in submerged paddy fields with low pH, leading dramatical increases in ferrous ion concentration, disrupting cell homeostasis and impairing growth and yield. However, the underlying molecular mechanisms of Fe toxicity response and tolerance in plants are not well characterized yet. Microarray and genome-wide association analyses have shown that rice employs four defense systems to regulate Fe homeostasis under Fe excess. In defense 1, Fe excess tolerance is implemented by Fe exclusion as a result of suppression of genes involved in Fe uptake and translocation such as OsIRT1, OsYSL2, OsTOM1, OsYSL15, OsNRAMP1, OsNAS1, OsNAS2, OsNAAT1, OsDMAS1, and OsIRO2. The Fe-binding ubiquitin ligase, HRZ, is a key regulator that represses Fe uptake genes in response to Fe excess in rice. In defense 2, rice retains Fe in the root system rather than transporting it to shoots. In defense 3, rice compartmentalizes Fe in the shoot. In defense 2 and 3, the vacuolar Fe transporter OsVIT2, Fe storage protein ferritin, and the nicotinamine synthase OsNAS3 mediate the isolation or detoxification of excess Fe. In defense 4, rice detoxifies the ROS produced within the plant body in response to excess Fe. Some OsWRKY transcription factors, S-nitrosoglutathione-reductase variants, p450-family proteins, and OsNAC4, 5, and 6 are implicated in defense 4. These knowledge will facilitate the breeding of tolerant crops with increased productivity in low-pH, Fe-excess soils.
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27
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Overexpression of native Musa-miR397 enhances plant biomass without compromising abiotic stress tolerance in banana. Sci Rep 2019; 9:16434. [PMID: 31712582 PMCID: PMC6848093 DOI: 10.1038/s41598-019-52858-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 10/17/2019] [Indexed: 02/06/2023] Open
Abstract
Plant micro RNAs (miRNAs) control growth, development and stress tolerance but are comparatively unexplored in banana, whose cultivation is threatened by abiotic stress and nutrient deficiencies. In this study, a native Musa-miR397 precursor harboring 11 copper-responsive GTAC motifs in its promoter element was identified from banana genome. Musa-miR397 was significantly upregulated (8–10) fold in banana roots and leaves under copper deficiency, correlating with expression of root copper deficiency marker genes such as Musa-COPT and Musa-FRO2. Correspondingly, target laccases were significantly downregulated (>−2 fold), indicating miRNA-mediated silencing for Cu salvaging. No significant expression changes in the miR397-laccase module were observed under iron stress. Musa-miR397 was also significantly upregulated (>2 fold) under ABA, MV and heat treatments but downregulated under NaCl stress, indicating universal stress-responsiveness. Further, Musa-miR397 overexpression in banana significantly increased plant growth by 2–3 fold compared with wild-type but did not compromise tolerance towards Cu deficiency and NaCl stress. RNA-seq of transgenic and wild type plants revealed modulation in expression of 71 genes related to diverse aspects of growth and development, collectively promoting enhanced biomass. Summing up, our results not only portray Musa-miR397 as a candidate for enhancing plant biomass but also highlight it at the crossroads of growth-defense trade-offs.
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28
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Rekik I, Chaâbene Z, Kriaa W, Rorat A, Franck V, Hafedh M, Elleuch A. Transcriptome assembly and abiotic related gene expression analysis of date palm reveal candidate genes involved in response to cadmium stress. Comp Biochem Physiol C Toxicol Pharmacol 2019; 225:108569. [PMID: 31302231 DOI: 10.1016/j.cbpc.2019.108569] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 07/03/2019] [Accepted: 07/09/2019] [Indexed: 10/26/2022]
Abstract
Date palm in Tunisia is of major economic importance but are also factors of social, environmental and economic stability. An annotated assembly of the transcriptome of cultivar Deglet Nour was reported. RNA was isolated from plant Cd-contaminated leaves, and 37,049 unique Illumina RNA-seq reads were used in a transcriptome assembly. The draft transcriptome assembly consists of 6789 contigs and 17.285 singletons with a means length of 858 bp and 1.042 bp, respectively. The final assembly was functionally annotated using Blast2GO software, allowing the identification of putative genes controlling important agronomic traits. The annotated transcriptome data sets were used to query all known Kyoto Encyclopedia of Genes and Genomes pathways. The most represented molecular functions and biological processes were nucleotide binding and transcription, transport and response to stress and abiotic and biotic stimuli. A prediction of the genes interaction network was proposed by selecting corresponding functionally similar genes from Arabidopsis datasets, downloaded by GeneMANIA version 2.1. Several Cd-responsive genes expression was monitored in in vitro isolated explant of Cd stressed Deglet Nour. Some chelators encoding genes were upregulated confirming in silico findings. Genes encoding HMs transporters in date palm showed expression enhancement more pronounced after 20 days of exposure. P. dactylifera transcriptome provides a valuable resource for future functional analysis of candidate genes involved in metal stress response.
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Affiliation(s)
- Imen Rekik
- High Institute of Applied Biology of Medenine, Tunisia; Laboratory of Plant Biotechnology, Faculty of Sciences of Sfax, University of Sfax, Tunisia
| | - Zayneb Chaâbene
- Laboratory of Plant Biotechnology, Faculty of Sciences of Sfax, University of Sfax, Tunisia; Laboratoire de Génie Civil et géo-Environnement - Université de Lille 1, F-59655 Villeneuve d'Ascq, France
| | - Walid Kriaa
- Laboratory of Plant Biotechnology, Faculty of Sciences of Sfax, University of Sfax, Tunisia; Environmental Science Center, Qatar University, PO. Box 2713, Doha, Qatar
| | - Agnieszka Rorat
- Laboratoire de Génie Civil et géo-Environnement - Université de Lille 1, F-59655 Villeneuve d'Ascq, France
| | - Vandenbulcke Franck
- Laboratoire de Génie Civil et géo-Environnement - Université de Lille 1, F-59655 Villeneuve d'Ascq, France.
| | - Mejdoub Hafedh
- Laboratory of Plant Biotechnology, Faculty of Sciences of Sfax, University of Sfax, Tunisia
| | - Amine Elleuch
- Laboratory of Plant Biotechnology, Faculty of Sciences of Sfax, University of Sfax, Tunisia
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Turhadi T, Hamim H, Ghulamahdi M, Miftahudin M. Iron toxicity-induced physiological and metabolite profile variations among tolerant and sensitive rice varieties. PLANT SIGNALING & BEHAVIOR 2019; 14:1682829. [PMID: 31657655 PMCID: PMC6866706 DOI: 10.1080/15592324.2019.1682829] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 10/12/2019] [Accepted: 10/14/2019] [Indexed: 05/28/2023]
Abstract
Iron toxicity stress causes physiological and metabolic changes in rice and other plants. To date, there is little information about the metabolite profile of rice under Fe toxicity conditions. In fact, metabolite has a contribution to the physiological condition of plants. Plant metabolomics is a study of low-molecular weight metabolites in plants under certain conditions. The objective of the research was to investigate physiological and metabolic changes in rice under Fe toxicity stress. Two-week-old seedlings of four rice varieties with various Fe toxicity tolerance levels were stressed hydroponically with 400 ppm FeSO4.7H2O for 10 d. Numerous physiological characters were observed and untargeted metabolomic analysis was carried out using gas chromatography-mass spectrophotometry (GC-MS). The results showed Fe toxicity induced physiological and metabolite variation in rice. By comparing the metabolites synthesized in Fe toxicity-stressed plants with control plants, it showed that elaidic acid, linoleic acid, and linolenic acid could be as metabolite marker candidates for rice response to Fe toxicity stress. When plants exposed to Fe toxicity stress, elaidic acid increased, whereas linoleic- and linolenic acid decreased. The alteration of fatty acid composition in the root and shoot suggests the alteration of metabolites is one of the tolerance strategies of rice to Fe toxicity stress. This finding offers an insight about the tolerance strategies of rice under Fe toxicity stress related to the maintenance process of the cell membranes during this stress. The genes underlying biosynthesis of the fatty acid could be a target of future research on responsible genes for Fe toxicity tolerance in rice.
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Affiliation(s)
- Turhadi Turhadi
- Plant Biology Graduate Program, Department of Biology, Faculty of Mathematics and Natural Sciences-Bogor Agricultural University (IPB University), Kampus IPB Darmaga, Bogor, Indonesia
| | - Hamim Hamim
- Department of Biology, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University (IPB University), Kampus IPB Darmaga, Bogor, Indonesia
| | - Munif Ghulamahdi
- Department of Agronomy and Horticulture, Faculty of Agriculture, Bogor Agricultural University (IPB University), Kampus IPB Darmaga, Bogor, Indonesia
| | - Miftahudin Miftahudin
- Department of Biology, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University (IPB University), Kampus IPB Darmaga, Bogor, Indonesia
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Taie HAA, Seif El-Yazal MA, Ahmed SMA, Rady MM. Polyamines modulate growth, antioxidant activity, and genomic DNA in heavy metal-stressed wheat plant. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:22338-22350. [PMID: 31154641 DOI: 10.1007/s11356-019-05555-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 04/26/2019] [Accepted: 05/22/2019] [Indexed: 05/25/2023]
Abstract
A pot experiment was performed to assess the useful effects of seed soaking or seedling foliar spray using 0.25 mM spermine (Spm), 0.50 mM spermidine (Spd), or 1 mM putrescine (Put) on heavy metal tolerance in wheat plants irrigated with water contaminated by cadmium (2 mM Cd2+ in CdCl2) or lead (2 mM Pb2+ in PbCl2). Cd2+ or Pb2+ presence in the growth medium resulted in significant reductions in growth and yield characteristics and activities of leaf peroxidase (POD), glutathione reductase (GR), ascorbic acid oxidase (AAO), and polyphenol oxidase (PPO) of wheat plants. In contrast, significant increases were observed for Cd2+ content in roots, leaves and grains, superoxide dismutase (SOD) and catalase (CAT) activities, radical scavenging activity (DPPH), reducing power capacity, and fragmentation in DNA in comparison to controls (without Cd2+ or Pb2+ addition). However, treating the Cd2+- or Pb2+-stressed wheat plants with Spm, Spd, or Put, either by seed soaking or foliar spray, significantly improved growth and yield characteristics and activities of POD, GR, AAO, PPO, SOD, and CAT, DPPH, and reducing power capacity in wheat plants. In contrast, Cd2+ levels in roots, leaves, and yielded grains, and fragmentation in DNA were significantly reduced compared with the stressed (with Cd2+ or Pb2+) controls. Generally, seed soaking treatments were more effective than foliar spray treatments. More specifically, seed priming in Put was the best treatment under heavy metal stress. Results of this study recommend using polyamines, especially Put, as seed soaking to relieve the adverse effects of heavy metals in wheat plants.
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Affiliation(s)
- Hanan A A Taie
- Plant Biochemistry Department, National Research Centre, 33 Bohouth Street, Dokki, Cairo, Egypt
| | | | - Safia M A Ahmed
- Botany Department, Faculty of Agriculture, Fayoum University, Fayoum, 63514, Egypt
| | - Mostafa M Rady
- Botany Department, Faculty of Agriculture, Fayoum University, Fayoum, 63514, Egypt.
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31
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Mustafin RN, Khusnutdinova EK. The role of transposable elements in the ecological morphogenesis under the influence of stress. Vavilovskii Zhurnal Genet Selektsii 2019. [DOI: 10.18699/vj19.506] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In natural selection, insertional mutagenesis is an important source of genome variability. Transposons are sensors of environmental stress effects, which contribute to adaptation and speciation. These effects are due to changes in the mechanisms of morphogenesis, since transposons contain regulatory sequences that have cis and trans effects on specific protein-coding genes. In variability of genomes, the horizontal transfer of transposons plays an important role, because it contributes to changing the composition of transposons and the acquisition of new properties. Transposons are capable of site-specific transpositions, which lead to the activation of stress response genes. Transposons are sources of non-coding RNA, transcription factors binding sites and protein-coding genes due to domestication, exonization, and duplication. These genes contain nucleotide sequences that interact with non-coding RNAs processed from transposons transcripts, and therefore they are under the control of epigenetic regulatory networks involving transposons. Therefore, inherited features of the location and composition of transposons, along with a change in the phenotype, play an important role in the characteristics of responding to a variety of environmental stressors. This is the basis for the selection and survival of organisms with a specific composition and arrangement of transposons that contribute to adaptation under certain environmental conditions. In evolution, the capability to transpose into specific genome sites, regulate gene expression, and interact with transcription factors, along with the ability to respond to stressors, is the basis for rapid variability and speciation by altering the regulation of ontogenesis. The review presents evidence of tissue-specific and stage-specific features of transposon activation and their role in the regulation of cell differentiation to confirm their role in ecological morphogenesis.
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Affiliation(s)
| | - E. K. Khusnutdinova
- Bashkir State Medical University;
Institute of Biochemistry and Genetics – Subdivision of the Ufa Federal Research Centre of RAS
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32
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Bresolin APS, Dos Santos RS, Wolter RCD, de Sousa RO, da Maia LC, Costa de Oliveira A. Iron tolerance in rice: an efficient method for performing quick early genotype screening. BMC Res Notes 2019; 12:361. [PMID: 31238948 PMCID: PMC6593560 DOI: 10.1186/s13104-019-4362-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 06/05/2019] [Indexed: 11/25/2022] Open
Abstract
Objectives This study was conducted to establish a method for early, quick and cheap screening of iron excess tolerance in rice (Oryza sativa L.) cultivars. Results Based on the experiments, iron excess leads to reduction in shoot length (SL) and this can be a useful characteristic for adequate screening of tolerant genotypes. The sensitive genotypes Nipponbare and BR-IRGA 409 indicated higher accumulation of iron in their tissues while BRS-Agrisul and Epagri 108 also accumulated iron, but at lower concentrations. BR-IRGA 410 displayed an intermediate phenotype regarding iron accumulation. No changes in shoot Cu content can be observed when comparing treatments. On the other hand, an increase was seen for Zn and Mn when shoots are subjected to Fe2+ excess. Fe stress at a lower concentration than 7 mM increased Zn but decreased Mn contents in shoots of BR-IRGA 409. Strong positive correlations were found here for Fe × Zn (0.93); Fe × Mn (0.97) and Zn × Mn (0.92), probably due to the Fe-induced activation of bivalent cation transporters. Results show that genotypes scored as sensitive present higher concentration of Fe in shoots and this is an efficient method to characterize rice cultivars regarding iron response. Electronic supplementary material The online version of this article (10.1186/s13104-019-4362-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | - Luciano Carlos da Maia
- Plant Genomics and Breeding Center, Universidade Federal de Pelotas, Pelotas, RS, Brazil
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Ndjiondjop MN, Alachiotis N, Pavlidis P, Goungoulou A, Kpeki SB, Zhao D, Semagn K. Comparisons of molecular diversity indices, selective sweeps and population structure of African rice with its wild progenitor and Asian rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1145-1158. [PMID: 30578434 PMCID: PMC6449321 DOI: 10.1007/s00122-018-3268-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 12/11/2018] [Indexed: 05/20/2023]
Abstract
The extent of molecular diversity parameters across three rice species was compared using large germplasm collection genotyped with genomewide SNPs and SNPs that fell within selective sweep regions. Previous studies conducted on limited number of accessions have reported very low genetic variation in African rice (Oryza glaberrima Steud.) as compared to its wild progenitor (O. barthii A. Chev.) and to Asian rice (O. sativa L.). Here, we characterized a large collection of African rice and compared its molecular diversity indices and population structure with the two other species using genomewide single nucleotide polymorphisms (SNPs) and SNPs that mapped within selective sweeps. A total of 3245 samples representing African rice (2358), Asian rice (772) and O. barthii (115) were genotyped with 26,073 physically mapped SNPs. Using all SNPs, the level of marker polymorphism, average genetic distance and nucleotide diversity in African rice accounted for 59.1%, 63.2% and 37.1% of that of O. barthii, respectively. SNP polymorphism and overall nucleotide diversity of the African rice accounted for 20.1-32.1 and 16.3-37.3% of that of the Asian rice, respectively. We identified 780 SNPs that fell within 37 candidate selective sweeps in African rice, which were distributed across all 12 rice chromosomes. Nucleotide diversity of the African rice estimated from the 780 SNPs was 8.3 × 10-4, which is not only 20-fold smaller than the value estimated from all genomewide SNPs (π = 1.6 × 10-2), but also accounted for just 4.1%, 0.9% and 2.1% of that of O. barthii, lowland Asian rice and upland Asian rice, respectively. The genotype data generated for a large collection of rice accessions conserved at the AfricaRice genebank will be highly useful for the global rice community and promote germplasm use.
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Affiliation(s)
- Marie Noelle Ndjiondjop
- M'bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké 01, Côte d'Ivoire.
| | - Nikolaos Alachiotis
- Institute of Computer Science, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, 70013, Heraklion, Crete, Greece
| | - Pavlos Pavlidis
- Institute of Computer Science, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, 70013, Heraklion, Crete, Greece
| | - Alphonse Goungoulou
- M'bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké 01, Côte d'Ivoire
| | - Sèdjro Bienvenu Kpeki
- M'bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké 01, Côte d'Ivoire
| | - Dule Zhao
- M'bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké 01, Côte d'Ivoire
| | - Kassa Semagn
- M'bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké 01, Côte d'Ivoire.
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Nie Q, Qiao G, Peng L, Wen X. Transcriptional activation of long terminal repeat retrotransposon sequences in the genome of pitaya under abiotic stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 135:460-468. [PMID: 30497974 DOI: 10.1016/j.plaphy.2018.11.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/10/2018] [Accepted: 11/13/2018] [Indexed: 06/09/2023]
Abstract
Frequent somatic variations exist in pitaya (Hylocereus undatus) plants grown under abiotic stress conditions. Long terminal repeat (LTR) retrotransposons can be activated under stressful conditions and play key roles in plant genetic variation and evolution. However, whether LTR retrotransposons promotes pitaya somatic variations by regulating abiotic stress responses is still uncertain. In this study, transcriptionally active LTR retrotransposons were identified in pitaya after exposure to a number of stress factors, including in vitro culturing, osmotic changes, extreme temperatures and hormone treatments. In total, 26 LTR retrotransposon reverse transcriptase (RT) cDNA sequences were isolated and identified as belonging to 9 Ty1-copia and 4 Ty3-gypsy families. Several RT cDNA sequences had differing similarity levels with RTs from pitaya genomic DNA and other plant species, and were differentially expressed in pitaya under various stress conditions. LTR retrotransposons accounted for at least 13.07% of the pitaya genome. HuTy1P4 had a high copy number and low expression level in young stems of pitaya, and its expression level increased after exposure to hormones and abiotic stresses, including in vitro culturing, osmotic changes, cold and heat. HuTy1P4 may have been subjected to diverse transposon events in 13 pitaya plantlets successively subcultured for four cycles. Thus, the expression levels of these retrotransposons in pitaya were associated with stress responses and may be involved in the occurrence of the somaclonal variation in pitaya.
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Affiliation(s)
- Qiong Nie
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang, 550025, PR China; College of Agriculture, Guizhou University, Guiyang, 550025, Guizhou Province, PR China
| | - Guang Qiao
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang, 550025, PR China
| | - Lei Peng
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang, 550025, PR China
| | - Xiaopeng Wen
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang, 550025, PR China.
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Xiong Q, Cao C, Shen T, Zhong L, He H, Chen X. Comprehensive metabolomic and proteomic analysis in biochemical metabolic pathways of rice spikes under drought and submergence stress. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:237-247. [PMID: 30611782 DOI: 10.1016/j.bbapap.2019.01.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 12/12/2018] [Accepted: 01/02/2019] [Indexed: 12/11/2022]
Abstract
Drought and submergence are the main adverse factors affecting plant growth and yield formation in parts of China, especially in the Yangtze River region. In this study, T1 (drought duration: 10 d), T2 (submergence duration: 8 d) and CK (control) treatments were applied. This work aimed to study the changes in metabolic pathways of rice under drought and submergence stress during the panicle differentiation stage. The identification and analysis of differential metabolites and differentially expressed proteins functions indicate that drought and submergence mainly promoted the energy metabolism pathway, carbon fixation in photosynthetic organism pathway, carbohydrate metabolic process, and reactive oxygen species (ROS) metabolic process functions. Under drought stress, the inhibition of photosynthetic rate is mainly through stomatal conductance restriction, and flavonoid pathway regulates the metabolic process of ROS. Under submergence stress, the electron transfer chain was destroyed to inhibit the photosynthetic rate, and the antioxidant system was activated to regulate the metabolism of ROS. The changes in related enzymes or proteins in metabolic regulatory networks are analyzed, which will be conducive to understanding the response mechanism of rice drought and submergence more deeply and provide a scientific basis for rice drought and submergence prevention and mitigation, and the breeding of drought- and submergence-resistant varieties.
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Affiliation(s)
- Qiangqiang Xiong
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Jiangxi 330045, China
| | - Chaohao Cao
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Jiangxi 330045, China
| | - Tianhua Shen
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Jiangxi 330045, China
| | - Lei Zhong
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Jiangxi 330045, China
| | - HaoHua He
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Jiangxi 330045, China.
| | - Xiaorong Chen
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Jiangxi 330045, China.
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Stein RJ, Duarte GL, Scheunemann L, Spohr MG, de Araújo Júnior AT, Ricachenevsky FK, Rosa LMG, Zanchin NIT, dos Santos RP, Fett JP. Genotype Variation in Rice ( Oryza sativa L.) Tolerance to Fe Toxicity Might Be Linked to Root Cell Wall Lignification. FRONTIERS IN PLANT SCIENCE 2019; 10:746. [PMID: 31244872 PMCID: PMC6581717 DOI: 10.3389/fpls.2019.00746] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 05/21/2019] [Indexed: 05/09/2023]
Abstract
Iron (Fe) is an essential element to plants, but can be harmful if accumulated to toxic concentrations. Fe toxicity can be a major nutritional disorder in rice (Oryza sativa) when cultivated under waterlogged conditions, as a result of excessive Fe solubilization of in the soil. However, little is known about the basis of Fe toxicity and tolerance at both physiological and molecular level. To identify mechanisms and potential candidate genes for Fe tolerance in rice, we comparatively analyzed the effects of excess Fe on two cultivars with distinct tolerance to Fe toxicity, EPAGRI 108 (tolerant) and BR-IRGA 409 (susceptible). After excess Fe treatment, BR-IRGA 409 plants showed reduced biomass and photosynthetic parameters, compared to EPAGRI 108. EPAGRI 108 plants accumulated lower amounts of Fe in both shoots and roots compared to BR-IRGA 409. We conducted transcriptomic analyses of roots from susceptible and tolerant plants under control and excess Fe conditions. We found 423 up-regulated and 92 down-regulated genes in the susceptible cultivar, and 42 up-regulated and 305 down-regulated genes in the tolerant one. We observed striking differences in root gene expression profiles following exposure to excess Fe: the two cultivars showed no genes regulated in the same way (up or down in both), and 264 genes were oppositely regulated in both cultivars. Plants from the susceptible cultivar showed down-regulation of known Fe uptake-related genes, indicating that plants are actively decreasing Fe acquisition. On the other hand, plants from the tolerant cultivar showed up-regulation of genes involved in root cell wall biosynthesis and lignification. We confirmed that the tolerant cultivar has increased lignification in the outer layers of the cortex and in the vascular bundle compared to the susceptible cultivar, suggesting that the capacity to avoid excessive Fe uptake could rely in root cell wall remodeling. Moreover, we showed that increased lignin concentrations in roots might be linked to Fe tolerance in other rice cultivars, suggesting that a similar mechanism might operate in multiple genotypes. Our results indicate that changes in root cell wall and Fe permeability might be related to Fe toxicity tolerance in rice natural variation.
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Affiliation(s)
| | | | - Lívia Scheunemann
- Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Marta Gomes Spohr
- Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | | | - Luis Mauro Gonçalves Rosa
- Departamento de Plantas Forrageiras e Agrometeorologia, Faculdade de Agronomia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | | | - Janette Palma Fett
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- *Correspondence: Janette Palma Fett,
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Finatto T, Viana VE, Woyann LG, Busanello C, da Maia LC, de Oliveira AC. Can WRKY transcription factors help plants to overcome environmental challenges? Genet Mol Biol 2018; 41:533-544. [PMID: 30235398 PMCID: PMC6136380 DOI: 10.1590/1678-4685-gmb-2017-0232] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 01/22/2018] [Indexed: 12/13/2022] Open
Abstract
WRKY transcription factors (TFs) are responsible for the regulation of genes responsive to many plant growth and developmental cues, as well as to biotic and abiotic stresses. The modulation of gene expression by WRKY proteins primarily occurs by DNA binding at specific cis-regulatory elements, the W-box elements, which are short sequences located in the promoter region of certain genes. In addition, their action can occur through interaction with other TFs and the cellular transcription machinery. The current genome sequences available reveal a relatively large number of WRKY genes, reaching hundreds of copies. Recently, functional genomics studies in model plants have enabled the identification of function and mechanism of action of several WRKY TFs in plants. This review addresses the more recent studies in plants regarding the function of WRKY TFs in both model and crop plants for coping with environmental challenges, including a wide variety of abiotic and biotic stresses.
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Affiliation(s)
- Taciane Finatto
- Centro de Genômica e Fitomelhoramento, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Vívian Ebeling Viana
- Centro de Genômica e Fitomelhoramento, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Pelotas, RS, Brazil
- Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnologico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Leomar Guilherme Woyann
- Centro de Genômica e Fitomelhoramento, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Carlos Busanello
- Centro de Genômica e Fitomelhoramento, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Luciano Carlos da Maia
- Centro de Genômica e Fitomelhoramento, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Antonio Costa de Oliveira
- Centro de Genômica e Fitomelhoramento, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Pelotas, RS, Brazil
- Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnologico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
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Kumar J, Gunapati S, Kianian SF, Singh SP. Comparative analysis of transcriptome in two wheat genotypes with contrasting levels of drought tolerance. PROTOPLASMA 2018; 255:1487-1504. [PMID: 29651660 DOI: 10.1007/s00709-018-1237-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 03/05/2018] [Indexed: 05/19/2023]
Abstract
Drought tolerance is a complex trait that is governed by multiple genes. The study presents differential transcriptome analysis between drought-tolerant (Triticum aestivum Cv. C306) and drought-sensitive (Triticum aestivum Cv. WL711) genotypes, using Affymetrix GeneChip® Wheat Genome Array. Both genotypes exhibited diverse global transcriptional responses under control and drought conditions. Pathway analysis suggested significant induction or repression of genes involved in secondary metabolism, nucleic acid synthesis, protein synthesis, and transport in C306, as compared to WL711. Significant up- and downregulation of transcripts for enzymes, hormone metabolism, and stress response pathways were observed in C306 under drought. The elevated expression of plasma membrane intrinsic protein 1 and downregulation of late embryogenesis abundant in the leaf tissues could play an important role in delayed wilting in C306. The other regulatory genes such as MT, FT, AP2, SKP1, ABA2, ARF6, WRKY6, AOS, and LOX2 are involved in defense response in C306 genotype. Additionally, transcripts with unknown functions were identified as differentially expressed, which could participate in drought responses.
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Affiliation(s)
- Jitendra Kumar
- National Agri-Food Biotechnology Institute, Mohali, India
- USDA-ARS Cereal Disease Laboratory, St. Paul, MN, USA
| | - Samatha Gunapati
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA
| | | | - Sudhir P Singh
- National Agri-Food Biotechnology Institute, Mohali, India.
- Center of Innovative and Applied Bioprocessing, Mohali, India.
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Muhammad I, Jing XQ, Shalmani A, Ali M, Yi S, Gan PF, Li WQ, Liu WT, Chen KM. Comparative in Silico Analysis of Ferric Reduction Oxidase (FRO) Genes Expression Patterns in Response to Abiotic Stresses, Metal and Hormone Applications. Molecules 2018; 23:molecules23051163. [PMID: 29757203 PMCID: PMC6099960 DOI: 10.3390/molecules23051163] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 05/04/2018] [Accepted: 05/09/2018] [Indexed: 02/01/2023] Open
Abstract
The ferric reduction oxidase (FRO) gene family is involved in various biological processes widely found in plants and may play an essential role in metal homeostasis, tolerance and intricate signaling networks in response to a number of abiotic stresses. Our study describes the identification, characterization and evolutionary relationships of FRO genes families. Here, total 50 FRO genes in Plantae and 15 ‘FRO like’ genes in non-Plantae were retrieved from 16 different species. The entire FRO genes have been divided into seven clades according to close similarity in biological and functional behavior. Three conserved domains were common in FRO genes while in two FROs sub genome have an extra NADPH-Ox domain, separating the function of plant FROs. OsFRO1 and OsFRO7 genes were expressed constitutively in rice plant. Real-time RT-PCR analysis demonstrated that the expression of OsFRO1 was high in flag leaf, and OsFRO7 gene expression was maximum in leaf blade and flag leaf. Both genes showed vigorous expressions level in response to different abiotic and hormones treatments. Moreover, the expression of both genes was also substantial under heavy metal stresses. OsFRO1 gene expression was triggered following 6 h under Zn, Pb, Co and Ni treatments, whereas OsFRO7 gene expression under Fe, Pb and Ni after 12 h, Zn and Cr after 6 h, and Mn and Co after 3 h treatments. These findings suggest the possible involvement of both the genes under abiotic and metal stress and the regulation of phytohormones. Therefore, our current work may provide the foundation for further functional characterization of rice FRO genes family.
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Affiliation(s)
- Izhar Muhammad
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China.
| | - Xiu-Qing Jing
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China.
| | - Abdullah Shalmani
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China.
| | - Muhammad Ali
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Shi Yi
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China.
| | - Peng-Fei Gan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China.
| | - Wen-Qiang Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China.
| | - Wen-Ting Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China.
| | - Kun-Ming Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China.
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Yilmaz S, Marakli S, Yuzbasioglu G, Gozukirmizi N. Short-term mutagenicity test by using IRAP molecular marker in rice grown under herbicide treatment. BIOTECHNOL BIOTEC EQ 2018. [DOI: 10.1080/13102818.2018.1474137] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Affiliation(s)
- Sibel Yilmaz
- Department of Molecular Biology and Genetics, Faculty of Science, Istanbul University, Istanbul, Turkey
| | - Sevgi Marakli
- Department of Molecular Biology and Genetics, Faculty of Science, Istanbul University, Istanbul, Turkey
| | - Gozde Yuzbasioglu
- Department of Molecular Biology and Genetics, Faculty of Science, Istanbul University, Istanbul, Turkey
| | - Nermin Gozukirmizi
- Department of Molecular Biology and Genetics, Faculty of Science, Istanbul University, Istanbul, Turkey
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Mustafin RN, Khusnutdinova EK. The Role of Transposons in Epigenetic Regulation of Ontogenesis. Russ J Dev Biol 2018. [DOI: 10.1134/s1062360418020066] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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dos Santos FIDC, Marini N, dos Santos RS, Hoffman BSF, Alves-Ferreira M, de Oliveira AC. Selection and testing of reference genes for accurate RT-qPCR in rice seedlings under iron toxicity. PLoS One 2018; 13:e0193418. [PMID: 29494624 PMCID: PMC5832244 DOI: 10.1371/journal.pone.0193418] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 02/09/2018] [Indexed: 11/18/2022] Open
Abstract
Reverse Transcription quantitative PCR (RT-qPCR) is a technique for gene expression profiling with high sensibility and reproducibility. However, to obtain accurate results, it depends on data normalization by using endogenous reference genes whose expression is constitutive or invariable. Although the technique is widely used in plant stress analyzes, the stability of reference genes for iron toxicity in rice (Oryza sativa L.) has not been thoroughly investigated. Here, we tested a set of candidate reference genes for use in rice under this stressful condition. The test was performed using four distinct methods: NormFinder, BestKeeper, geNorm and the comparative ΔCt. To achieve reproducible and reliable results, Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines were followed. Valid reference genes were found for shoot (P2, OsGAPDH and OsNABP), root (OsEF-1a, P8 and OsGAPDH) and root+shoot (OsNABP, OsGAPDH and P8) enabling us to perform further reliable studies for iron toxicity in both indica and japonica subspecies. The importance of the study of other than the traditional endogenous genes for use as normalizers is also shown here.
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Proteomic and genomic responses of plants to nutritional stress. Biometals 2018; 31:161-187. [PMID: 29453655 DOI: 10.1007/s10534-018-0083-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Accepted: 02/10/2018] [Indexed: 12/17/2022]
Abstract
Minerals or trace elements in small amount are essential nutrients for every plant, but when the internal concentration exceeds the threshold, these essential elements do create phytotoxicity. Plant responses to elemental stresses are very common due to different anthropogenic activities; however it is a complex phenomenon with individual characteristics for various species. To cope up with the situation, a plant produces a group of strategies both in proteomic and genomic level to overcome it. Controlling the metal stress is known to activate a multigene response resulting in the changes in various proteins, which directly affects almost all biological processes in a living cell. Therefore, proteomic and genomic approaches can be useful for elucidating the molecular responses under metal stress. For this, it is tried to provide the latest knowledge and techniques used in proteomic and genomic study during nutritional stress and is represented here in review form.
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Das G, Rao GJN, Varier M, Prakash A, Prasad D. Improved Tapaswini having four BB resistance genes pyramided with six genes/QTLs, resistance/tolerance to biotic and abiotic stresses in rice. Sci Rep 2018; 8:2413. [PMID: 29402905 PMCID: PMC5799378 DOI: 10.1038/s41598-018-20495-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 01/19/2018] [Indexed: 12/31/2022] Open
Abstract
Rice, a major food crop, is grown in a wide range of ecological conditions and suffers significant yield losses as it is constantly exposed to a wide range of environmental and biotic stresses. The prevalence of different biotypes/strains has necessitated assembling of numerous resistance genes/QTLs into elite genotypes to confer a broader scale of resistance. The current study reports successful pyramiding of genes/QTLs that confer tolerance/resistance to submergence (Sub1), salinity (Saltol), blast (Pi2, Pi9) and gall midge (Gm1, Gm4) to supplement the four bacterial blight resistance genes (Xa 4, xa5, xa13, Xa21) present in Improved Tapaswini, an elite cultivar. The precise transfer of genes/QTLs was accomplished through effective foreground selection and suitable gene pyramids were identified. Background selection was practiced using morphological and grain quality traits to enhance the recovery of the recurrent parental genome. In the bioassays, the pyramids exhibited higher levels of resistance/ tolerance against the target stresses. The novel feature of the study was successful pyramidization and demonstration of the function of ten genes/QTLs in a new genotype. This success can stimulate several such studies to realize the full potential of molecular plant breeding as the foundation for rice improvement.
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Affiliation(s)
- Gitishree Das
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India.
- Research Institute of Biotechnology & Medical Converged Science, Dongguk University-Seoul, Ilsandong-gu, Gyeonggi-do, 10326, Republic of Korea.
| | - Gundimeda J N Rao
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India.
- Department of Bio Sciences and Bio Engineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India.
| | - M Varier
- NRRI-Central Rainfed Upland Rice Research Station, Hazaribagh, Jharkhand, 825301, India
| | - A Prakash
- Crop Protection Division, ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - Dokku Prasad
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
- Kaveri Seeds, Secunderabad, Telangana, 500003, India
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Sperotto RA, de Araújo Junior AT, Adamski JM, Cargnelutti D, Ricachenevsky FK, de Oliveira BHN, da Cruz RP, Dos Santos RP, da Silva LP, Fett JP. Deep RNAseq indicates protective mechanisms of cold-tolerant indica rice plants during early vegetative stage. PLANT CELL REPORTS 2018; 37:347-375. [PMID: 29151156 DOI: 10.1007/s00299-017-2234-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 11/08/2017] [Indexed: 05/13/2023]
Abstract
Cold-tolerance in rice may be related to increased cellulose deposition in the cell wall, membrane fatty acids unsaturation and differential expression of several newly identified genes. Low temperature exposure during early vegetative stages limits rice plant's growth and development. Most genes previously related to cold tolerance in rice are from the japonica subspecies. To help clarify the mechanisms that regulate cold tolerance in young indica rice plants, comparative transcriptome analysis of 6 h cold-treated (10 °C) leaves from two genotypes, cold-tolerant (CT) and cold-sensitive (CS), was performed. Differentially expressed genes were identified: 831 and 357 sequences more expressed in the tolerant and in the sensitive genotype, respectively. The genes with higher expression in the CT genotype were used in systems biology analyses to identify protein-protein interaction (PPI) networks and nodes (proteins) that are hubs and bottlenecks in the PPI. From the genes more expressed in the tolerant plants, 60% were reported as affected by cold in previous transcriptome experiments and 27% are located within QTLs related to cold tolerance during the vegetative stage. Novel cold-responsive genes were identified. Quantitative RT-PCR confirmed the high-quality of RNAseq libraries. Several genes related to cell wall assembly or reinforcement are cold-induced or constitutively highly expressed in the tolerant genotype. Cold-tolerant plants have increased cellulose deposition under cold. Genes related to lipid metabolism are more expressed in the tolerant genotype, which has higher membrane fatty acids unsaturation, with increasing levels of linoleic acid under cold. The CT genotype seems to have higher photosynthetic efficiency and antioxidant capacity, as well as more effective ethylene, Ca2+ and hormone signaling than the CS. These genes could be useful in future biotechnological approaches aiming to increase cold tolerance in rice.
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Affiliation(s)
- Raul Antonio Sperotto
- Centro de Ciências Biológicas e da Saúde (CCBS), Programa de Pós-Graduação em Biotecnologia (PPGBiotec), Universidade do Vale do Taquari-UNIVATES, Lajeado, RS, Brazil.
| | | | - Janete Mariza Adamski
- Departamento de Botânica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Denise Cargnelutti
- Departamento de Agronomia, Universidade Federal da Fronteira Sul (UFFS), Erechim, RS, Brazil
| | | | - Ben-Hur Neves de Oliveira
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Renata Pereira da Cruz
- Departamento de Plantas de Lavoura, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Rinaldo Pires Dos Santos
- Departamento de Botânica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Leila Picolli da Silva
- Departamento de Zootecnia, Universidade Federal de Santa Maria (UFSM), Santa Maria, RS, Brazil
| | - Janette Palma Fett
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.
- Departamento de Botânica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.
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dos Santos RS, de Araujo AT, Pegoraro C, de Oliveira AC. Dealing with iron metabolism in rice: from breeding for stress tolerance to biofortification. Genet Mol Biol 2017; 40:312-325. [PMID: 28304072 PMCID: PMC5452141 DOI: 10.1590/1678-4685-gmb-2016-0036] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 09/22/2016] [Indexed: 12/23/2022] Open
Abstract
Iron is a well-known metal. Used by humankind since ancient times in many different ways, this element is present in all living organisms, where, unfortunately, it represents a two-way problem. Being an essential block in the composition of different proteins and metabolic pathways, iron is a vital component for animals and plants. That is why iron deficiency has a severe impact on the lives of different organisms, including humans, becoming a major concern, especially in developing countries where access to adequate nutrition is still difficult. On the other hand, this metal is also capable of causing damage when present in excess, becoming toxic to cells and affecting the whole organism. Because of its importance, iron absorption, transport and storage mechanisms have been extensively investigated in order to design alternatives that may solve this problem. As the understanding of the strategies that plants use to control iron homeostasis is an important step in the generation of improved plants that meet both human agricultural and nutritional needs, here we discuss some of the most important points about this topic.
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Affiliation(s)
- Railson Schreinert dos Santos
- Plant Genomics and Breeding Center (CGF), Universidade Federal de
Pelotas, Pelotas, RS, Brazil
- Technology Development Center (CDTec), Universidade Federal de
Pelotas, Pelotas, RS, Brazil
| | | | - Camila Pegoraro
- Plant Genomics and Breeding Center (CGF), Universidade Federal de
Pelotas, Pelotas, RS, Brazil
| | - Antonio Costa de Oliveira
- Plant Genomics and Breeding Center (CGF), Universidade Federal de
Pelotas, Pelotas, RS, Brazil
- Technology Development Center (CDTec), Universidade Federal de
Pelotas, Pelotas, RS, Brazil
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Kabir AH, Khatun MA, Hossain MM, Haider SA, Alam MF, Paul NK. Regulation of Phytosiderophore Release and Antioxidant Defense in Roots Driven by Shoot-Based Auxin Signaling Confers Tolerance to Excess Iron in Wheat. FRONTIERS IN PLANT SCIENCE 2016; 7:1684. [PMID: 27891139 PMCID: PMC5103167 DOI: 10.3389/fpls.2016.01684] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 10/25/2016] [Indexed: 05/06/2023]
Abstract
Iron (Fe) is essential but harmful for plants at toxic level. However, how wheat plants tolerate excess Fe remains vague. This study aims at elucidating the mechanisms underlying tolerance to excess Fe in wheat. Higher Fe concentration caused morpho-physiological retardation in BR 26 (sensitive) but not in BR 27 (tolerant). Phytosiderophore and 2-deoxymugineic acid showed no changes in BR 27 but significantly increased in BR 26 due to excess Fe. Further, expression of TaSAMS. TaDMAS1, and TaYSL15 significantly downregulated in BR 27 roots, while these were upregulated in BR 26 under excess Fe. It confirms that inhibition of phytosiderophore directs less Fe accumulation in BR 27. However, phytochelatin and expression of TaPCS1 and TaMT1 showed no significant induction in response to excess Fe. Furthermore, excess Fe showed increased catalase, peroxidase, and glutathione reductase activities along with glutathione, cysteine, and proline accumulation in roots in BR 27. Interestingly, BR 27 self-grafts and plants having BR 26 rootstock attached to BR 27 scion had no Fe-toxicity induced adverse effect on morphology but showed BR 27 type expressions, confirming that shoot-derived signal triggering Fe-toxicity tolerance in roots. Finally, auxin inhibitor applied with higher Fe concentration caused a significant decline in morpho-physiological parameters along with increased TaSAMS and TaDMAS1 expression in roots of BR 27, revealing the involvement of auxin signaling in response to excess Fe. These findings propose that tolerance to excess Fe in wheat is attributed to the regulation of phytosiderophore limiting Fe acquisition along with increased antioxidant defense in roots driven by shoot-derived auxin signaling.
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Affiliation(s)
- Ahmad H. Kabir
- Plant and Crop Physiology Laboratory, Department of Botany, University of RajshahiRajshahi, Bangladesh
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Kabir AH, Begum MC, Haque A, Amin R, Swaraz AM, Haider SA, Paul NK, Hossain MM. Genetic variation in Fe toxicity tolerance is associated with the regulation of translocation and chelation of iron along with antioxidant defence in shoots of rice. FUNCTIONAL PLANT BIOLOGY : FPB 2016; 43:1070-1081. [PMID: 32480527 DOI: 10.1071/fp16068] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 06/15/2016] [Indexed: 06/11/2023]
Abstract
Excess iron (Fe) is phytotoxic and causes reduced growth and productivity in rice. In this study we elucidated the mechanisms conferring differential tolerance to Fe-toxicity in rice seedlings. Excess Fe caused retardation in roots of both Pokkali and BRRI 51, but it caused no significant changes on growth parameters, Fe accumulation and OsIRT1 expression in shoots of Pokkali only compared with control plants. These results suggest that the Pokkali genotype does have mechanisms in shoots to withstand Fe toxicity. Pokkali maintained membrane stability and total soluble protein in shoots due to Fe toxicity, further confirming its ability to tolerate excess Fe. Furthermore, a significant decrease of Fe-chelate reductase activity and OsFRO1 expression in shoots of Pokkali suggests that limiting Fe accumulation is possibly regulated by Fe-reductase activity. Our extensive expression analysis on the expression pattern of three chelators (OsDMAS1, OsYSL15, OsYSL2 and OsFRDL1) showed no significant changes in expression in shoots of Pokkali due to Fe toxicity, whereas these genes were significantly upregulated under Fe-toxicity in sensitive BRRI 51. These results imply that regulation of Fe chelation in shoots of Pokkali contributes to its tolerance to Fe toxicity. Finally, increased catalase (CAT), peroxidase (POD), glutathione reductase (GR) and superoxide dismutase (SOD), along with elevated ascorbic acid, glutathione, cysteine, methionine and proline in shoots of Pokkali caused by Fe toxicity suggests that strong antioxidant defence protects rice plants from oxidative injury under Fe toxicity. Taking these results together, we propose that genetic variation in Fe-toxicity tolerance in rice is shoot based, and is mainly associated with the regulation of translocation and chelation of Fe together with elevated antioxidant metabolites in shoots.
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Affiliation(s)
- Ahmad Humayan Kabir
- Plant and Crop Physiology Laboratory, Department of Botany, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Most Champa Begum
- Plant and Crop Physiology Laboratory, Department of Botany, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Ariful Haque
- Institute of Biological Sciences, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Ruhul Amin
- Bangladesh Council of Scientific and Industrial Research (BCSIR) Laboratories, Rajshahi 6206, Bangladesh
| | - A M Swaraz
- Department of Genetic Engineering and Biotechnology, Jessore University of Science and Technology, Jessore 7408, Bangladesh
| | - Syed Ali Haider
- Plant and Crop Physiology Laboratory, Department of Botany, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Nishit Kumar Paul
- Plant and Crop Physiology Laboratory, Department of Botany, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Mohammad Monzur Hossain
- Plant and Crop Physiology Laboratory, Department of Botany, University of Rajshahi, Rajshahi 6205, Bangladesh
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Negi P, Rai AN, Suprasanna P. Moving through the Stressed Genome: Emerging Regulatory Roles for Transposons in Plant Stress Response. FRONTIERS IN PLANT SCIENCE 2016; 7:1448. [PMID: 27777577 PMCID: PMC5056178 DOI: 10.3389/fpls.2016.01448] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Accepted: 09/12/2016] [Indexed: 05/02/2023]
Abstract
The recognition of a positive correlation between organism genome size with its transposable element (TE) content, represents a key discovery of the field of genome biology. Considerable evidence accumulated since then suggests the involvement of TEs in genome structure, evolution and function. The global genome reorganization brought about by transposon activity might play an adaptive/regulatory role in the host response to environmental challenges, reminiscent of McClintock's original 'Controlling Element' hypothesis. This regulatory aspect of TEs is also garnering support in light of the recent evidences, which project TEs as "distributed genomic control modules." According to this view, TEs are capable of actively reprogramming host genes circuits and ultimately fine-tuning the host response to specific environmental stimuli. Moreover, the stress-induced changes in epigenetic status of TE activity may allow TEs to propagate their stress responsive elements to host genes; the resulting genome fluidity can permit phenotypic plasticity and adaptation to stress. Given their predominating presence in the plant genomes, nested organization in the genic regions and potential regulatory role in stress response, TEs hold unexplored potential for crop improvement programs. This review intends to present the current information about the roles played by TEs in plant genome organization, evolution, and function and highlight the regulatory mechanisms in plant stress responses. We will also briefly discuss the connection between TE activity, host epigenetic response and phenotypic plasticity as a critical link for traversing the translational bridge from a purely basic study of TEs, to the applied field of stress adaptation and crop improvement.
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Affiliation(s)
| | | | - Penna Suprasanna
- Plant Stress Physiology and Biotechnology Section, Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research CentreTrombay, India
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