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Wairich A, Aung MS, Ricachenevsky FK, Masuda H. You can't always get as much iron as you want: how rice plants deal with excess of an essential nutrient. FRONTIERS IN PLANT SCIENCE 2024; 15:1381856. [PMID: 39100081 PMCID: PMC11294178 DOI: 10.3389/fpls.2024.1381856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 06/10/2024] [Indexed: 08/06/2024]
Abstract
Iron (Fe) is an essential nutrient for almost all organisms. However, free Fe within cells can lead to damage to macromolecules and oxidative stress, making Fe concentrations tightly controlled. In plants, Fe deficiency is a common problem, especially in well-aerated, calcareous soils. Rice (Oryza sativa L.) is commonly cultivated in waterlogged soils, which are hypoxic and can cause Fe reduction from Fe3+ to Fe2+, especially in low pH acidic soils, leading to high Fe availability and accumulation. Therefore, Fe excess decreases rice growth and productivity. Despite the widespread occurrence of Fe excess toxicity, we still know little about the genetic basis of how rice plants respond to Fe overload and what genes are involved in variation when comparing genotypes with different tolerance levels. Here, we review the current knowledge about physiological and molecular data on Fe excess in rice, providing a comprehensive summary of the field.
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Affiliation(s)
- Andriele Wairich
- Department of Agronomy and Crop Physiology, Justus Liebig University Giessen, Giessen, Germany
| | - May Sann Aung
- Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University, Akita, Japan
| | - Felipe Klein Ricachenevsky
- Botany Department, Institute of Biosciences, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
- Center of Biotechnology, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Hiroshi Masuda
- Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University, Akita, Japan
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Miao S, Lu J, Zhang G, Jiang J, Li P, Qian Y, Wang W, Xu J, Zhang F, Zhao X. Candidate Genes and Favorable Haplotypes Associated with Iron Toxicity Tolerance in Rice. Int J Mol Sci 2024; 25:6970. [PMID: 39000075 PMCID: PMC11241266 DOI: 10.3390/ijms25136970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 06/15/2024] [Accepted: 06/21/2024] [Indexed: 07/16/2024] Open
Abstract
Iron (Fe) toxicity is a major issue adversely affecting rice production worldwide. Unfortunately, the physiological and genetic mechanisms underlying Fe toxicity tolerance in rice remain relatively unknown. In this study, we conducted a genome-wide association study using a diverse panel consisting of 551 rice accessions to identify genetic mechanisms and candidate genes associated with Fe toxicity tolerance. Of the 29 quantitative trait loci (QTL) for Fe toxicity tolerance detected on chromosomes 1, 2, 5, and 12, five (qSH_Fe5, qSFW_Fe2.3, qRRL5.1, qRSFW1.1, and qRSFW12) were selected to identify candidate genes according to haplotype and bioinformatics analyses. The following five genes were revealed as promising candidates: LOC_Os05g40160, LOC_Os05g40180, LOC_Os12g36890, LOC_Os12g36900, and LOC_Os12g36940. The physiological characteristics of rice accessions with contrasting Fe toxicity tolerance reflected the importance of reactive oxygen species-scavenging antioxidant enzymes and Fe homeostasis for mitigating the negative effects of Fe toxicity on rice. Our findings have clarified the genetic and physiological mechanisms underlying Fe toxicity tolerance in rice. Furthermore, we identified valuable genetic resources for future functional analyses and the development of Fe toxicity-tolerant rice varieties via marker-assisted selection.
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Affiliation(s)
- Siyu Miao
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; (S.M.); (J.L.); (J.J.); (P.L.); (Y.Q.); (W.W.); (J.X.)
| | - Jingbing Lu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; (S.M.); (J.L.); (J.J.); (P.L.); (Y.Q.); (W.W.); (J.X.)
| | - Guogen Zhang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China;
| | - Jing Jiang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; (S.M.); (J.L.); (J.J.); (P.L.); (Y.Q.); (W.W.); (J.X.)
| | - Pingping Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; (S.M.); (J.L.); (J.J.); (P.L.); (Y.Q.); (W.W.); (J.X.)
| | - Yukang Qian
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; (S.M.); (J.L.); (J.J.); (P.L.); (Y.Q.); (W.W.); (J.X.)
| | - Wensheng Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; (S.M.); (J.L.); (J.J.); (P.L.); (Y.Q.); (W.W.); (J.X.)
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China;
| | - Jianlong Xu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; (S.M.); (J.L.); (J.J.); (P.L.); (Y.Q.); (W.W.); (J.X.)
| | - Fan Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; (S.M.); (J.L.); (J.J.); (P.L.); (Y.Q.); (W.W.); (J.X.)
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China;
| | - Xiuqin Zhao
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; (S.M.); (J.L.); (J.J.); (P.L.); (Y.Q.); (W.W.); (J.X.)
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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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Phosuwan S, Nounjan N, Theerakulpisut P, Siangliw M, Charoensawan V. Comparative quantitative trait loci analysis framework reveals relationships between salt stress responsive phenotypes and pathways. FRONTIERS IN PLANT SCIENCE 2024; 15:1264909. [PMID: 38463565 PMCID: PMC10920293 DOI: 10.3389/fpls.2024.1264909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 02/07/2024] [Indexed: 03/12/2024]
Abstract
Soil salinity is a complex abiotic stress that involves several biological pathways. Hence, focusing on a specific or a few salt-tolerant phenotypes is unlikely to provide comprehensive insights into the intricate and interwinding mechanisms that regulate salt responsiveness. In this study, we develop a heuristic framework for systematically integrating and comprehensively evaluating quantitative trait loci (QTL) analyses from multiple stress-related traits obtained by different studies. Making use of a combined set of 46 salinity-related traits from three independent studies that were based on the same chromosome segment substitution line (CSSL) population of rice (Oryza sativa), we demonstrate how our approach can address technical biases and limitations from different QTL studies and calling methods. This allows us to compile a comprehensive list of trait-specific and multi-trait QTLs, as well as salinity-related candidate genes. In doing so, we discover several novel relationships between traits that demonstrate similar trends of phenotype scores across the CSSLs, as well as the similarities between genomic locations that the traits were mapped to. Finally, we experimentally validate our findings by expression analyses and functional validations of several selected candidate genes from multiple pathways in rice and Arabidopsis orthologous genes, including OsKS7 (ENT-KAURENE SYNTHASE 7), OsNUC1 (NUCLEOLIN 1) and OsFRO1 (FERRIC REDUCTASE OXIDASE 1) to name a few. This work not only introduces a novel approach for conducting comparative analyses of multiple QTLs, but also provides a list of candidate genes and testable hypotheses for salinity-related mechanisms across several biological pathways.
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Affiliation(s)
- Sunadda Phosuwan
- Doctor of Philosophy Program in Biochemistry (International Program), Faculty of Science, Mahidol University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Noppawan Nounjan
- Biodiversity and Environmental Management Division, International College, Khon Kaen University, Khon Kaen, Thailand
| | - Piyada Theerakulpisut
- Salt-tolerant Rice Research Group, Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Meechai Siangliw
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Thailand
| | - Varodom Charoensawan
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
- Integrative Computational BioScience (ICBS) Center, Mahidol University, Nakhon Pathom, Thailand
- Division of Medical Bioinformatics, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, Thailand
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Müller B. Iron transport mechanisms and their evolution focusing on chloroplasts. JOURNAL OF PLANT PHYSIOLOGY 2023; 288:154059. [PMID: 37586271 DOI: 10.1016/j.jplph.2023.154059] [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: 01/23/2023] [Revised: 07/26/2023] [Accepted: 07/28/2023] [Indexed: 08/18/2023]
Abstract
Iron (Fe) is an essential element for photosynthetic organisms, required for several vital biological functions. Photosynthesis, which takes place in the chloroplasts of higher plants, is the major Fe consumer. Although the components of the root Fe uptake system in dicotyledonous and monocotyledonous plants have been extensively studied, the Fe transport mechanisms of chloroplasts in these two groups of plants have received little attention. This review focuses on the comparative analysis of Fe transport processes in the evolutionary ancestors of chloroplasts (cyanobacteria) with the processes in embryophytes and green algae (Viridiplantae). The aim is to summarize how chloroplasts are integrated into cellular Fe homeostasis and how Fe transporters and Fe transport mechanisms have been modified by evolution.
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Affiliation(s)
- Brigitta Müller
- Department of Plant Physiology and Molecular Biology, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, H-1117, Hungary.
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Kermeur N, Pédrot M, Cabello-Hurtado F. Iron Availability and Homeostasis in Plants: A Review of Responses, Adaptive Mechanisms, and Signaling. Methods Mol Biol 2023; 2642:49-81. [PMID: 36944872 DOI: 10.1007/978-1-0716-3044-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Iron is an essential element for all living organisms, playing a major role in plant biochemistry as a redox catalyst based on iron redox properties. Iron is the fourth most abundant element of the Earth's crust, but its uptake by plants is complex because it is often in insoluble forms that are not easily accessible for plants to use. The physical and chemical speciation of iron, as well as rhizosphere activity, are key factors controlling the bioavailability of Fe. Iron can be under reduced (Fe2+) or oxidized (Fe3+) ionic forms, adsorbed onto mineral surfaces, forming complexes with organic molecules, precipitated to form poorly crystalline hydroxides to highly crystalline iron oxides, or included in crystalline Fe-rich mineral phases. Plants must thus adapt to a complex and changing iron environment, and their response is finely regulated by multiple signaling pathways initiated by a diversity of stimulus perceptions. Higher plants possess two separate strategies to uptake iron from rhizosphere soil: the chelation strategy and the reduction strategy in grass and non-grass plants, respectively. Molecular actors involved in iron uptake and mobilization through the plant have been characterized for both strategies. All these processes that contribute to iron homeostasis in plants are highly regulated in response to iron availability by downstream signaling responses, some of which are characteristic signaling signatures of iron dynamics, while others are shared with other environmental stimuli. Recent research has thus revealed key transcription factors, cis-acting elements, post-translational regulators, and other molecular mechanisms controlling these genes or their encoded proteins in response to iron availability. In addition, the most recent research is increasingly highlighting the crosstalk between iron homeostasis and nutrient response regulation. These regulatory processes help to avoid plant iron concentrations building up to potential cell functioning disruptions that could adversely affect plant fitness. Indeed, when iron is in excess in the plant, it can lead to the production and accumulation of dangerous reactive oxygen species and free radicals (H2O2, HO•, O2•-, HO•2) that can cause considerable damages to most cellular components. To cope with iron oxidative stress, plants have developed defense systems involving the complementary action of antioxidant enzymes and molecular antioxidants, safe iron-storage mechanisms, and appropriate morphological adaptations.
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Affiliation(s)
- Nolenn Kermeur
- University of Rennes, CNRS, Ecobio, UMR 6553, Rennes, France
- University of Rennes, CNRS, Géosciences Rennes, UMR 6118, Rennes, France
| | - Mathieu Pédrot
- University of Rennes, CNRS, Géosciences Rennes, UMR 6118, Rennes, France
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Li J, Liu X, Xu L, Li W, Yao Q, Yin X, Wang Q, Tan W, Xing W, Liu D. Low nitrogen stress-induced transcriptome changes revealed the molecular response and tolerance characteristics in maintaining the C/N balance of sugar beet ( Beta vulgaris L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1164151. [PMID: 37152145 PMCID: PMC10160481 DOI: 10.3389/fpls.2023.1164151] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 03/31/2023] [Indexed: 05/09/2023]
Abstract
Nitrogen (N) is an essential macronutrient for plants, acting as a common limiting factor for crop yield. The application of nitrogen fertilizer is related to the sustainable development of both crops and the environment. To further explore the molecular response of sugar beet under low nitrogen (LN) supply, transcriptome analysis was performed on the LN-tolerant germplasm '780016B/12 superior'. In total, 580 differentially expressed genes (DEGs) were identified in leaves, and 1,075 DEGs were identified in roots (log2 |FC| ≥ 1; q value < 0.05). Gene Ontology (GO), protein-protein interaction (PPI), and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses clarified the role and relationship of DEGs under LN stress. Most of the downregulated DEGs were closely related to "photosynthesis" and the metabolism of "photosynthesis-antenna proteins", "carbon", "nitrogen", and "glutathione", while the upregulated DEGs were involved in flavonoid and phenylalanine biosynthesis. For example, GLUDB (glutamate dehydrogenase B) was identified as a key downregulated gene, linking carbon, nitrogen, and glutamate metabolism. Thus, low nitrogen-tolerant sugar beet reduced energy expenditure mainly by reducing the synthesis of energy-consuming amino acids, which in turn improved tolerance to low nitrogen stress. The glutathione metabolism biosynthesis pathway was promoted to quench reactive oxygen species (ROS) and protect cells from oxidative damage. The expression levels of nitrogen assimilation and amino acid transport genes, such as NRT2.5 (high-affinity nitrate transporter), NR (nitrate reductase [NADH]), NIR (ferredoxin-nitrite reductase), GS (glutamine synthetase leaf isozyme), GLUDB, GST (glutathione transferase) and GGT3 (glutathione hydrolase 3) at low nitrogen levels play a decisive role in nitrogen utilization and may affect the conversion of the carbon skeleton. DFRA (dihydroflavonol 4-reductase) in roots was negatively correlated with NIR in leaves (coefficient = -0.98, p < 0.05), suggesting that there may be corresponding remote regulation between "flavonoid biosynthesis" and "nitrogen metabolism" in roots and leaves. FBP (fructose 1,6-bisphosphatase) and PGK (phosphoglycerate kinase) were significantly positively correlated (p < 0.001) with Ci (intercellular CO2 concentration). The reliability and reproducibility of the RNA-seq data were further confirmed by real-time fluorescence quantitative PCR (qRT-PCR) validation of 22 genes (R2 = 0.98). This study reveals possible pivotal genes and metabolic pathways for sugar beet adaptation to nitrogen-deficient environments.
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Affiliation(s)
- Jiajia Li
- National Beet Medium-term Gene Bank, Heilongjiang University, Harbin, China
- Key Laboratory of Sugar Beet Genetics and Breeding, Heilongjiang Province Common College/College of Advanced agriculture and ecological environment, Heilongjiang University, Harbin, China
| | - Xinyu Liu
- National Beet Medium-term Gene Bank, Heilongjiang University, Harbin, China
- Key Laboratory of Sugar Beet Genetics and Breeding, Heilongjiang Province Common College/College of Advanced agriculture and ecological environment, Heilongjiang University, Harbin, China
- Key Laboratory of Molecular Biology, School of Life Sciences, Heilongjiang University, Harbin, China
| | - Lingqing Xu
- National Beet Medium-term Gene Bank, Heilongjiang University, Harbin, China
- Key Laboratory of Sugar Beet Genetics and Breeding, Heilongjiang Province Common College/College of Advanced agriculture and ecological environment, Heilongjiang University, Harbin, China
| | - Wangsheng Li
- National Beet Medium-term Gene Bank, Heilongjiang University, Harbin, China
- Key Laboratory of Sugar Beet Genetics and Breeding, Heilongjiang Province Common College/College of Advanced agriculture and ecological environment, Heilongjiang University, Harbin, China
| | - Qi Yao
- National Beet Medium-term Gene Bank, Heilongjiang University, Harbin, China
- Key Laboratory of Sugar Beet Genetics and Breeding, Heilongjiang Province Common College/College of Advanced agriculture and ecological environment, Heilongjiang University, Harbin, China
- Key Laboratory of Molecular Biology, School of Life Sciences, Heilongjiang University, Harbin, China
| | - Xilong Yin
- National Beet Medium-term Gene Bank, Heilongjiang University, Harbin, China
- Key Laboratory of Sugar Beet Genetics and Breeding, Heilongjiang Province Common College/College of Advanced agriculture and ecological environment, Heilongjiang University, Harbin, China
| | - Qiuhong Wang
- National Beet Medium-term Gene Bank, Heilongjiang University, Harbin, China
- Key Laboratory of Sugar Beet Genetics and Breeding, Heilongjiang Province Common College/College of Advanced agriculture and ecological environment, Heilongjiang University, Harbin, China
| | - Wenbo Tan
- National Beet Medium-term Gene Bank, Heilongjiang University, Harbin, China
- Key Laboratory of Sugar Beet Genetics and Breeding, Heilongjiang Province Common College/College of Advanced agriculture and ecological environment, Heilongjiang University, Harbin, China
| | - Wang Xing
- National Beet Medium-term Gene Bank, Heilongjiang University, Harbin, China
- Key Laboratory of Sugar Beet Genetics and Breeding, Heilongjiang Province Common College/College of Advanced agriculture and ecological environment, Heilongjiang University, Harbin, China
- *Correspondence: Dali Liu, ; Wang Xing,
| | - Dali Liu
- National Beet Medium-term Gene Bank, Heilongjiang University, Harbin, China
- Key Laboratory of Sugar Beet Genetics and Breeding, Heilongjiang Province Common College/College of Advanced agriculture and ecological environment, Heilongjiang University, Harbin, China
- *Correspondence: Dali Liu, ; Wang Xing,
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Panthri M, Gupta M. An insight into the act of iron to impede arsenic toxicity in paddy agro-system. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 316:115289. [PMID: 35598452 DOI: 10.1016/j.jenvman.2022.115289] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/13/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
Surplus research on the widespread arsenic (As) revealed its disturbing role in obstructing the metabolic function of plants. Also, the predilection of As towards rice has been an interesting topic. Contrary to As, iron (Fe) is an essential micronutrient for all life forms. Past findings propound about the enhanced As-resistance in rice plants during Fe supplementation. Thus, considering the severity of As contamination and resulting exposure through rice crops, as well as the studied cross-talks between As and Fe, we found this topic of relevance. Keeping these in view, we bring this review discussing the presence of As-Fe in the paddy environment, the criticality of Fe plaque in As sequestration, and the effectiveness of various Fe forms to overcome As toxicity in rice. This type of interactive analysis for As and Fe is also crucial in the context of the involvement of Fe in cellular redox activities such as oxidative stress. Also, this piece of work highlights Fe biofortification approaches for better rice varieties with optimum intrinsic Fe and limited As. Though elaborated by others, we lastly present the acquisition and transport mechanisms of both As and Fe in rice tissues. Altogether we suggest that Fe supply and Fe plaque might be a prospective agronomical tool against As poisoning and for phytostabilization, respectively.
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Affiliation(s)
- Medha Panthri
- Ecotoxicogenomics Lab, Department of Biotechnology, Jamia Millia Islamia, New Delhi, 110025, India
| | - Meetu Gupta
- Ecotoxicogenomics Lab, Department of Biotechnology, Jamia Millia Islamia, New Delhi, 110025, India.
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Iron Source and Medium pH Affect Nutrient Uptake and Pigment Content in Petunia hybrida ‘Madness Red’ Cultured In Vitro. Int J Mol Sci 2022; 23:ijms23168943. [PMID: 36012209 PMCID: PMC9409069 DOI: 10.3390/ijms23168943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/03/2022] [Accepted: 08/09/2022] [Indexed: 11/16/2022] Open
Abstract
Deficiency or excess of iron (Fe) and improper medium pH will inhibit the growth and development of plants, reduce the transfer and utilization of energy from the root to the leaf, and affect the utilization efficiency of inorganic nutrients. The most common symptom of Fe deficiency in plants is chlorosis of the young leaves. In this study, the effects of the iron source, in combination with the medium pH, on plant growth and development, plant pigment synthesis, and nutrient uptake in a model plant Petunia hybrida cultured in vitro were investigated. Iron sulfate (FeSO4·7H2O) or iron chelated with ethylenediaminetetraacetic acid (Fe-EDTA) were supplemented to the MNS (a multipurpose nutrient solution) medium at a concentration of 2.78 mg·L−1 Fe, and the treatment without any Fe was used as the control. The pH of the agar-solidified medium was adjusted to either 4.70, 5.70, or 6.70 before autoclaving. The experiment was carried out in an environmentally controlled culture room with a temperature of 24 °C with 100 µmol·m−2·s−1 photosynthetic photon flux density (PPFD) supplied by white light emitting diodes (LEDs) during a photoperiod of 16 h a day, 18 °C for 8 h a day in the dark, and 70% relative humidity. Regardless of the Fe source including the control, the greatest number of leaves was observed at pH 4.70. However, the greatest lengths of the leaf and root were observed in the treatment with Fe-EDTA combined with pH 5.70. The contents of the chlorophyll, carotenoid, and anthocyanin decreased with increasing medium pH, and contents of these plant pigments were positively correlated with the leaf color. The highest soluble protein content and activities of APX and CAT were observed in the Fe-EDTA under pH 5.70. However, the GPX activity was the highest in the control under pH 4.70. In addition, the highest contents of ammonium (NH4+) and nitrate (NO3−) were measured in the FeSO4-4.7 and EDTA-5.7, respectively. More than that, the treatment of Fe-EDTA combined with pH 5.70 (EDTA-5.7) enhanced nutrient absorption, as proven by the highest tissue contents of P, K, Ca, Mg, Fe, and Mn. The genes’ ferric reduction oxidase 1 and 8 (PhFRO1 and PhFRO8), iron-regulated transporter 1 (PhIRT1), nitrate transporter 2.5 (PhNRT2.5), and deoxyhypusine synthase (PhDHS) were expressed at the highest levels in this treatment as well. In the treatment of EDTA-5.7, the reduction and transport of chelated iron in P. hybrida leaves were enhanced, which also affected the transport of nitrate and catalyzed chlorophyll level in leaves. In conclusion, when the medium pH was adjusted to 5.70, supplementation of chelated Fe-EDTA was more conducive to promoting the growth and development of, and absorption of mineral nutrients by, the plant and the expression of related genes in the leaves.
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Gurr SJ, Trigg SA, Vadopalas B, Roberts SB, Putnam HM. Acclimatory gene expression of primed clams enhances robustness to elevated pCO 2. Mol Ecol 2022; 31:5005-5023. [PMID: 35947503 DOI: 10.1111/mec.16644] [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: 04/24/2022] [Revised: 08/02/2022] [Accepted: 08/02/2022] [Indexed: 11/30/2022]
Abstract
Sub-lethal exposure to environmental challenges may enhance ability to cope with chronic or repeated change, a process known as priming. In a previous study, pre-exposure to seawater enriched with pCO2 improved growth and reduced antioxidant capacity of juvenile Pacific geoduck Panopea generosa, suggesting that transcriptional shifts may drive phenotypic modifications post-priming. To this end, juvenile clams were sampled and TagSeq gene expression data analyzed after 1) a 110-day acclimation under ambient (921 μatm, naïve) and moderately-elevated pCO2 (2870 μatm, pre-exposed); then following 2) a second 7-day exposure to three pCO2 treatments (ambient: 754 μatm; moderately-elevated: 2750 μatm; severely-elevated: 4940 μatm), a 7-day return to ambient pCO2 , and a third 7-day exposure to two pCO2 treatments (ambient: 967 μatm; moderately-elevated: 3030 μatm). Pre-exposed geoducks frontloaded genes for stress and apoptosis/innate immune response, homeostatic processes, protein degradation, and transcriptional modifiers. Pre-exposed geoducks were also responsive to subsequent encounters, with gene sets enriched for mitochondrial recycling and immune defense under elevated pCO2 and energy metabolism and biosynthesis under ambient recovery. In contrast, gene sets with higher expression in naïve clams were enriched for fatty-acid degradation and glutathione components, suggesting naïve clams could be depleting endogenous fuels, with unsustainable energetic requirements if changes in carbonate chemistry persist. Collectively, our transcriptomic data indicates pCO2 priming during post-larval periods could, via gene expression regulation, enhance robustness in bivalves to environmental change. Such priming approaches may be beneficial for aquaculture, as seafood demand intensifies concurrent with increasing climate change in marine systems.
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Affiliation(s)
- Samuel J Gurr
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA
| | - Shelly A Trigg
- University of Washington, School of Aquatic and Fishery Sciences, Seattle, WA, USA
| | | | - Steven B Roberts
- University of Washington, School of Aquatic and Fishery Sciences, Seattle, WA, USA
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA
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11
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Sathee L, Jagadhesan B, Pandesha PH, Barman D, Adavi B S, Nagar S, Krishna GK, Tripathi S, Jha SK, Chinnusamy V. Genome Editing Targets for Improving Nutrient Use Efficiency and Nutrient Stress Adaptation. Front Genet 2022; 13:900897. [PMID: 35774509 PMCID: PMC9237392 DOI: 10.3389/fgene.2022.900897] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/17/2022] [Indexed: 11/22/2022] Open
Abstract
In recent years, the development of RNA-guided genome editing (CRISPR-Cas9 technology) has revolutionized plant genome editing. Under nutrient deficiency conditions, different transcription factors and regulatory gene networks work together to maintain nutrient homeostasis. Improvement in the use efficiency of nitrogen (N), phosphorus (P) and potassium (K) is essential to ensure sustainable yield with enhanced quality and tolerance to stresses. This review outlines potential targets suitable for genome editing for understanding and improving nutrient use (NtUE) efficiency and nutrient stress tolerance. The different genome editing strategies for employing crucial negative and positive regulators are also described. Negative regulators of nutrient signalling are the potential targets for genome editing, that may improve nutrient uptake and stress signalling under resource-poor conditions. The promoter engineering by CRISPR/dead (d) Cas9 (dCas9) cytosine and adenine base editing and prime editing is a successful strategy to generate precise changes. CRISPR/dCas9 system also offers the added advantage of exploiting transcriptional activators/repressors for overexpression of genes of interest in a targeted manner. CRISPR activation (CRISPRa) and CRISPR interference (CRISPRi) are variants of CRISPR in which a dCas9 dependent transcription activation or interference is achieved. dCas9-SunTag system can be employed to engineer targeted gene activation and DNA methylation in plants. The development of nutrient use efficient plants through CRISPR-Cas technology will enhance the pace of genetic improvement for nutrient stress tolerance of crops and improve the sustainability of agriculture.
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Affiliation(s)
- Lekshmy Sathee
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
- *Correspondence: Lekshmy Sathee, ; Viswanathan Chinnusamy,
| | - B. Jagadhesan
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Pratheek H. Pandesha
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
- Roy and Diana Vagelos Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO, United States
| | - Dipankar Barman
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Sandeep Adavi B
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Shivani Nagar
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - G. K. Krishna
- Department of Plant Physiology, College of Agriculture, KAU, Thrissur, India
| | - Shailesh Tripathi
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Shailendra K. Jha
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
- *Correspondence: Lekshmy Sathee, ; Viswanathan Chinnusamy,
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12
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Sági-Kazár M, Solymosi K, Solti Á. Iron in leaves: chemical forms, signalling, and in-cell distribution. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:1717-1734. [PMID: 35104334 PMCID: PMC9486929 DOI: 10.1093/jxb/erac030] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 01/26/2022] [Indexed: 05/26/2023]
Abstract
Iron (Fe) is an essential transition metal. Based on its redox-active nature under biological conditions, various Fe compounds serve as cofactors in redox enzymes. In plants, the photosynthetic machinery has the highest demand for Fe. In consequence, the delivery and incorporation of Fe into cofactors of the photosynthetic apparatus is the focus of Fe metabolism in leaves. Disturbance of foliar Fe homeostasis leads to impaired biosynthesis of chlorophylls and composition of the photosynthetic machinery. Nevertheless, mitochondrial function also has a significant demand for Fe. The proper incorporation of Fe into proteins and cofactors as well as a balanced intracellular Fe status in leaf cells require the ability to sense Fe, but may also rely on indirect signals that report on the physiological processes connected to Fe homeostasis. Although multiple pieces of information have been gained on Fe signalling in roots, the regulation of Fe status in leaves has not yet been clarified in detail. In this review, we give an overview on current knowledge of foliar Fe homeostasis, from the chemical forms to the allocation and sensing of Fe in leaves.
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Affiliation(s)
- Máté Sági-Kazár
- Department of Plant Physiology and Molecular Plant Biology, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, H-1117, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, H-1117, Hungary
| | - Katalin Solymosi
- Department of Plant Anatomy, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, H-1117, Hungary
| | - Ádám Solti
- Department of Plant Physiology and Molecular Plant Biology, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, H-1117, Hungary
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13
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Swamy BPM, Marathi B, Ribeiro-Barros AIF, Calayugan MIC, Ricachenevsky FK. Iron Biofortification in Rice: An Update on Quantitative Trait Loci and Candidate Genes. FRONTIERS IN PLANT SCIENCE 2021; 12:647341. [PMID: 34122472 PMCID: PMC8187908 DOI: 10.3389/fpls.2021.647341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/15/2021] [Indexed: 05/06/2023]
Abstract
Rice is the most versatile model for cereals and also an economically relevant food crop; as a result, it is the most suitable species for molecular characterization of Fe homeostasis and biofortification. Recently there have been significant efforts to dissect genes and quantitative trait loci (QTL) associated with Fe translocation into rice grains; such information is highly useful for Fe biofortification of cereals but very limited in other species, such as maize (Zea mays) and wheat (Triticum aestivum). Given rice's centrality as a model for Poaceae species, we review the current knowledge on genes playing important roles in Fe transport, accumulation, and distribution in rice grains and QTLs that might explain the variability in Fe concentrations observed in different genotypes. More than 90 Fe QTLs have been identified over the 12 rice chromosomes. From these, 17 were recorded as stable, and 25 harbored Fe-related genes nearby or within the QTL. Among the candidate genes associated with Fe uptake, translocation, and loading into rice grains, we highlight the function of transporters from the YSL and ZIP families; transporters from metal-binding molecules, such as nicotianamine and deoxymugineic acid; vacuolar iron transporters; citrate efflux transporters; and others that were shown to play a role in steps leading to Fe delivery to seeds. Finally, we discuss the application of these QTLs and genes in genomics assisted breeding for fast-tracking Fe biofortification in rice and other cereals in the near future.
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Affiliation(s)
| | - Balram Marathi
- Agricultural College, Warangal, Professor Jayashankar Telangana State Agricultural University, Hyderabad, India
| | - Ana I. F. Ribeiro-Barros
- Forest Research Centre (CEF), Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
| | - Mark Ian C. Calayugan
- Institute of Crop Science, University of the Philippines Los Baños, Laguna, Philippines
| | - Felipe Klein Ricachenevsky
- Departamento de Botânica, Instituto de Biociências, e Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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14
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Sági-Kazár M, Zelenyánszki H, Müller B, Cseh B, Gyuris B, Farkas SZ, Fodor F, Tóth B, Kovács B, Koncz A, Visnovitz T, Buzás EI, Bánkúti B, Bánáti F, Szenthe K, Solti Á. Supraoptimal Iron Nutrition of Brassica napus Plants Suppresses the Iron Uptake of Chloroplasts by Down-Regulating Chloroplast Ferric Chelate Reductase. FRONTIERS IN PLANT SCIENCE 2021; 12:658987. [PMID: 34093616 PMCID: PMC8172622 DOI: 10.3389/fpls.2021.658987] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/06/2021] [Indexed: 05/31/2023]
Abstract
Iron (Fe) is an essential micronutrient for plants. Due to the requirement for Fe of the photosynthetic apparatus, the majority of shoot Fe content is localised in the chloroplasts of mesophyll cells. The reduction-based mechanism has prime importance in the Fe uptake of chloroplasts operated by Ferric Reductase Oxidase 7 (FRO7) in the inner chloroplast envelope membrane. Orthologue of Arabidopsis thaliana FRO7 was identified in the Brassica napus genome. GFP-tagged construct of BnFRO7 showed integration to the chloroplast. The time-scale expression pattern of BnFRO7 was studied under three different conditions: deficient, optimal, and supraoptimal Fe nutrition in both leaves developed before and during the treatments. Although Fe deficiency has not increased BnFRO7 expression, the slight overload in the Fe nutrition of the plants induced significant alterations in both the pattern and extent of its expression leading to the transcript level suppression. The Fe uptake of isolated chloroplasts decreased under both Fe deficiency and supraoptimal Fe nutrition. Since the enzymatic characteristics of the ferric chelate reductase (FCR) activity of purified chloroplast inner envelope membranes showed a significant loss for the substrate affinity with an unchanged saturation rate, protein level regulation mechanisms are suggested to be also involved in the suppression of the reduction-based Fe uptake of chloroplasts together with the saturation of the requirement for Fe.
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Affiliation(s)
- Máté Sági-Kazár
- Department of Plant Physiology and Molecular Plant Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Helga Zelenyánszki
- Department of Plant Physiology and Molecular Plant Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Brigitta Müller
- Department of Plant Physiology and Molecular Plant Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Barnabás Cseh
- Department of Plant Physiology and Molecular Plant Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Balázs Gyuris
- Department of Plant Physiology and Molecular Plant Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Sophie Z. Farkas
- Department of Plant Physiology and Molecular Plant Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Ferenc Fodor
- Department of Plant Physiology and Molecular Plant Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Brigitta Tóth
- Institute of Food Science, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Debrecen, Hungary
| | - Béla Kovács
- Institute of Food Science, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Debrecen, Hungary
| | - Anna Koncz
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary
| | - Tamás Visnovitz
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary
| | - Edit I. Buzás
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary
- MTA-SE Immune-Proteogenomics Extracellular Vesicle Research Group, Budapest, Hungary
- HCEMM-SE Extracellular Vesicle Research Group, Budapest, Hungary
| | - Barbara Bánkúti
- RT-Europe Non-profit Research Ltd., Mosonmagyaróvár, Hungary
| | - Ferenc Bánáti
- RT-Europe Non-profit Research Ltd., Mosonmagyaróvár, Hungary
| | - Kálmán Szenthe
- Carlsbad Research Organization Center Ltd., Újrónafõ, Hungary
| | - Ádám Solti
- Department of Plant Physiology and Molecular Plant Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
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15
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Bandyopadhyay T, Prasad M. IRONing out stress problems in crops: a homeostatic perspective. PHYSIOLOGIA PLANTARUM 2021; 171:559-577. [PMID: 32770754 DOI: 10.1111/ppl.13184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 07/25/2020] [Indexed: 06/11/2023]
Abstract
Iron (Fe) is essential for plant growth and therefore plays a key role in influencing crop productivity worldwide. Apart from its central role in chlorophyll biosynthesis and oxidative phosphorylation (electron transfer), it is an important constituent of many enzymes involved in primary metabolism. Fe has different accessibilities to the roots in the rhizosphere depending upon whether it is ferrous (soluble) or ferric (insoluble) oxidation stages, which in turn, determine two kinds of Fe uptake strategies employed by the plants. The reduction strategy is exclusively found in non-graminaceous plants wherein the ferrous Fe2+ is absorbed and translocated from the soil through specialized transporters. In contrast, the chelation strategy (widespread in graminaceous plants) relies on the formation of Fe (III)-chelate complex as the necessary requirement of Fe uptake. Once inside the cell, Fe is translocated, compartmentalized and stored through a common set of physiological processes involving many transporters and enzymes whose functions are controlled by underlying genetic components, so that a fine balance of Fe homeostasis is maintained. Recently, molecular and mechanistic aspects of the process involving the role of transcription factors, signaling components, and cis-acting elements have been obtained, which has enabled a much better understanding of its ecophysiology. This mini-review summarizes recent developments in our understanding of Fe transport in higher plants with particular emphasis on crops in the context of major agronomically important abiotic stresses. It also highlights outstanding questions on the regulation of Fe homeostasis and lists potentially useful genes/regulatory pathways that may be useful for subsequent crop improvement under the stresses discussed through either conventional or transgenic approaches.
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Affiliation(s)
| | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
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16
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Bashir K, Ahmad Z, Kobayashi T, Seki M, Nishizawa NK. Roles of subcellular metal homeostasis in crop improvement. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2083-2098. [PMID: 33502492 DOI: 10.1093/jxb/erab018] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 01/25/2021] [Indexed: 06/12/2023]
Abstract
Improvement of crop production in response to rapidly changing environmental conditions is a serious challenge facing plant breeders and biotechnologists. Iron (Fe), zinc (Zn), manganese (Mn), and copper (Cu) are essential micronutrients for plant growth and reproduction. These minerals are critical to several cellular processes including metabolism, photosynthesis, and cellular respiration. Regulating the uptake and distribution of these minerals could significantly improve plant growth and development, ultimately leading to increased crop production. Plant growth is limited by mineral deficiency, but on the other hand, excess Fe, Mn, Cu, and Zn can be toxic to plants; therefore, their uptake and distribution must be strictly regulated. Moreover, the distribution of these metals among subcellular organelles is extremely important for maintaining optimal cellular metabolism. Understanding the mechanisms controlling subcellular metal distribution and availability would enable development of crop plants that are better adapted to challenging and rapidly changing environmental conditions. Here, we describe advances in understanding of subcellular metal homeostasis, with a particular emphasis on cellular Fe homeostasis in Arabidopsis and rice, and discuss strategies for regulating cellular metabolism to improve plant production.
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Affiliation(s)
- Khurram Bashir
- Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore, Pakistan
- Plant Genomics Network Research Team, Center for Sustainable Resource Science, Suehiro, Tsurumi Ku, Yokohama, Kanagawa, Japan
| | - Zarnab Ahmad
- Plant Genomics Network Research Team, Center for Sustainable Resource Science, Suehiro, Tsurumi Ku, Yokohama, Kanagawa, Japan
| | - Takanori Kobayashi
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
| | - Motoaki Seki
- Plant Genomics Network Research Team, Center for Sustainable Resource Science, Suehiro, Tsurumi Ku, Yokohama, Kanagawa, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
| | - Naoko K Nishizawa
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
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17
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Diop B, Wang DR, Drame KN, Gracen V, Tongoona P, Dzidzienyo D, Nartey E, Greenberg AJ, Djiba S, Danquah EY, McCouch SR. Bridging old and new: diversity and evaluation of high iron-associated stress response of rice cultivated in West Africa. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:4188-4200. [PMID: 32277700 DOI: 10.1093/jxb/eraa182] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 04/09/2020] [Indexed: 05/20/2023]
Abstract
Adoption of rice varieties that perform well under high iron-associated (HIA) stress environments can enhance rice production in West Africa. This study reports the genetic characterization of 323 rice accessions and breeding lines cultivated in West Africa using genotyping-by-sequencing and their phenotypic response to HIA treatments in hydroponic solution (1500 mg l-1 FeSO4·7H2O) and hot-spot fields. The germplasm consisted of four genetic subpopulations: Oryza glaberrima (14%), O. sativa-japonica (7%), O. sativa-indica Group 1 (45%), and O. sativa-indica Group 2 (25%). Severe versus mild stress in the field was associated with a reduced SPAD value (12%), biomass (56%), and grain yield (57%), with leaf bronzing explaining 30% and 21% of the variation for biomass and grain yield, respectively. Association mapping using 175 indica genotypes identified 23 significant single nucleotide polymorphism (SNP) markers that mapped to 14 genomic regions. Genome-wide association study (GWAS) signals associated with leaf bronzing, a routinely used indicator of HIA stress, differed in hydroponic compared with field conditions. Contrastingly, six significant SNPs on chromosomes 8 and 9 were associated with the SPAD value under HIA stress in both field and hydroponic experiments, and a candidate potassium transporter gene mapped under the peak on chromosome 8. This study helps define criteria for assessing rice performance under HIA environments.
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Affiliation(s)
- Bathe Diop
- Institut Sénégalais de Recherches Agricoles/Centre de Recherches Agricoles de Djibélor, Ziguinchor, Senegal
- West Africa Centre for Crop Improvement, University of Ghana, Legon, Ghana
| | - Diane R Wang
- Purdue University, Department of Agronomy, West Lafayette, IN, USA
- Plant Breeding & Genetics, School of Integrated Plant Sciences, Cornell University, Ithaca, NY, USA
| | - Khady N Drame
- Africa Rice Center (AfricaRice), Abidjan 01, Cote d'Ivoire
| | - Vernon Gracen
- West Africa Centre for Crop Improvement, University of Ghana, Legon, Ghana
- Plant Breeding & Genetics, School of Integrated Plant Sciences, Cornell University, Ithaca, NY, USA
| | - Pangirayi Tongoona
- West Africa Centre for Crop Improvement, University of Ghana, Legon, Ghana
| | - Daniel Dzidzienyo
- West Africa Centre for Crop Improvement, University of Ghana, Legon, Ghana
| | - Eric Nartey
- University of Ghana, Department of Soil Science, School of Agriculture, Legon, Ghana
| | | | - Saliou Djiba
- Institut Sénégalais de Recherches Agricoles/Centre de Recherches Agricoles de Djibélor, Ziguinchor, Senegal
| | - Eric Y Danquah
- West Africa Centre for Crop Improvement, University of Ghana, Legon, Ghana
| | - Susan R McCouch
- Plant Breeding & Genetics, School of Integrated Plant Sciences, Cornell University, Ithaca, NY, USA
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18
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Kawakami Y, Bhullar NK. Potential Implications of Interactions between Fe and S on Cereal Fe Biofortification. Int J Mol Sci 2020; 21:E2827. [PMID: 32325653 PMCID: PMC7216021 DOI: 10.3390/ijms21082827] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/08/2020] [Accepted: 04/14/2020] [Indexed: 01/17/2023] Open
Abstract
Iron (Fe) and sulfur (S) are two essential elements for plants, whose interrelation is indispensable for numerous physiological processes. In particular, Fe homeostasis in cereal species is profoundly connected to S nutrition because phytosiderophores, which are the metal chelators required for Fe uptake and translocation in cereals, are derived from a S-containing amino acid, methionine. To date, various biotechnological cereal Fe biofortification strategies involving modulation of genes underlying Fe homeostasis have been reported. Meanwhile, the resultant Fe-biofortified crops have been minimally characterized from the perspective of interaction between Fe and S, in spite of the significance of the crosstalk between the two elements in cereals. Here, we intend to highlight the relevance of Fe and S interrelation in cereal Fe homeostasis and illustrate the potential implications it has to offer for future cereal Fe biofortification studies.
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Affiliation(s)
| | - Navreet K. Bhullar
- Plant Biotechnology, Department of Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland;
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19
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Tiwari JK, Buckseth T, Zinta R, Saraswati A, Singh RK, Rawat S, Dua VK, Chakrabarti SK. Transcriptome analysis of potato shoots, roots and stolons under nitrogen stress. Sci Rep 2020; 10:1152. [PMID: 31980689 PMCID: PMC6981199 DOI: 10.1038/s41598-020-58167-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 01/13/2020] [Indexed: 12/19/2022] Open
Abstract
Potato crop requires high dose of nitrogen (N) to produce high tuber yield. Excessive application of N causes environmental pollution and increases cost of production. Hence, knowledge about genes and regulatory elements is essential to strengthen research on N metabolism in this crop. In this study, we analysed transcriptomes (RNA-seq) in potato tissues (shoot, root and stolon) collected from plants grown in aeroponic culture under controlled conditions with varied N supplies i.e. low N (0.2 milli molar N) and high N (4 milli molar N). High quality data ranging between 3.25 to 4.93 Gb per sample were generated using Illumina NextSeq500 that resulted in 83.60-86.50% mapping of the reads to the reference potato genome. Differentially expressed genes (DEGs) were observed in the tissues based on statistically significance (p ≤ 0.05) and up-regulation with ≥ 2 log2 fold change (FC) and down-regulation with ≤ -2 log2 FC values. In shoots, of total 19730 DEGs, 761 up-regulated and 280 down-regulated significant DEGs were identified. Of total 20736 DEGs in roots, 572 (up-regulated) and 292 (down-regulated) were significant DEGs. In stolons, of total 21494 DEG, 688 and 230 DEGs were significantly up-regulated and down-regulated, respectively. Venn diagram analysis showed tissue specific and common genes. The DEGs were functionally assigned with the GO terms, in which molecular function domain was predominant in all the tissues. Further, DEGs were classified into 24 KEGG pathways, in which 5385, 5572 and 5594 DEGs were annotated in shoots, roots and stolons, respectively. The RT-qPCR analysis validated gene expression of RNA-seq data for selected genes. We identified a few potential DEGs responsive to N deficiency in potato such as glutaredoxin, Myb-like DNA-binding protein, WRKY transcription factor 16 and FLOWERING LOCUS T in shoots; high-affinity nitrate transporter, protein phosphatase-2c, glutaredoxin family protein, malate synthase, CLE7, 2-oxoglutarate-dependent dioxygenase and transcription factor in roots; and glucose-6-phosphate/phosphate translocator 2, BTB/POZ domain-containing protein, F-box family protein and aquaporin TIP1;3 in stolons, and many genes of unknown function. Our study highlights that these potential genes play very crucial roles in N stress tolerance, which could be useful in augmenting research on N metabolism in potato.
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Affiliation(s)
- Jagesh Kumar Tiwari
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India.
| | - Tanuja Buckseth
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India
| | - Rasna Zinta
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India
| | - Aastha Saraswati
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India
| | - Rajesh Kumar Singh
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India
| | - Shashi Rawat
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India
| | - Vijay Kumar Dua
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India
| | - Swarup Kumar Chakrabarti
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India
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20
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Li Q, Chen L, Yang A. The Molecular Mechanisms Underlying Iron Deficiency Responses in Rice. Int J Mol Sci 2019; 21:E43. [PMID: 31861687 PMCID: PMC6981701 DOI: 10.3390/ijms21010043] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 12/15/2019] [Accepted: 12/17/2019] [Indexed: 01/27/2023] Open
Abstract
Iron (Fe) is an essential element required for plant growth and development. Under Fe-deficientconditions, plants have developed two distinct strategies (designated as strategy I and II) to acquire Fe from soil. As a graminaceous species, rice is not a typical strategy II plant, as it not only synthesizes DMA (2'-deoxymugineic acid) in roots to chelate Fe3+ but also acquires Fe2+ through transporters OsIRT1 and OsIRT2. During the synthesis of DMA in rice, there are three sequential enzymatic reactions catalyzed by enzymes NAS (nicotianamine synthase), NAAT (nicotianamine aminotransferase), and DMAS (deoxymugineic acid synthase). Many transporters required for Fe uptake from the rhizosphere and internal translocation have also been identified in rice. In addition, the signaling networks composed of various transcription factors (such as IDEF1, IDEF2, and members of the bHLH (basic helix-loop-helix) family), phytohormones, and signaling molecules are demonstrated to regulate Fe uptake and translocation. This knowledge greatly contributes to our understanding of the molecular mechanisms underlying iron deficiency responses in rice.
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Affiliation(s)
- Qian Li
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China;
| | - Lei Chen
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China;
| | - An Yang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China;
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Wang M, Kawakami Y, Bhullar NK. Molecular Analysis of Iron Deficiency Response in Hexaploid Wheat. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2019. [DOI: 10.3389/fsufs.2019.00067] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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