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Song Z, Li S, Li Y, Zhou X, Liu X, Yang W, Chen R. Identification and characterization of yellow stripe-like genes in maize suggest their roles in the uptake and transport of zinc and iron. BMC PLANT BIOLOGY 2024; 24:3. [PMID: 38163880 PMCID: PMC10759363 DOI: 10.1186/s12870-023-04691-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 12/14/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND Yellow Stripe-Like (YSL) proteins are involved in the uptake and transport of metal ions. They play important roles in maintaining the zinc and iron homeostasis in Arabidopsis, rice (Oryza sativa), and barley (Hordeum vulgare). However, proteins in this family have not been fully identified and comprehensively analyzed in maize (Zea mays L.). RESULTS In this study, we identified 19 ZmYSLs in the maize genome and analyzed their structural features. The results of a phylogenetic analysis showed that ZmYSLs are homologous to YSLs of Arabidopsis and rice, and these proteins are divided into four independent branches. Although their exons and introns have structural differences, the motif structure is relatively conserved. Analysis of the cis-regulatory elements in the promoters indicated that ZmYSLs might play a role in response to hypoxia and light. The results of RNA sequencing and quantitative real-time PCR analysis revealed that ZmYSLs are expressed in various tissues and respond differently to zinc and iron deficiency. The subcellular localization of ZmYSLs in the protoplast of maize mesophyll cells showed that they may function in the membrane system. CONCLUSIONS This study provided important information for the further functional analysis of ZmYSL, especially in the spatio-temporal expression and adaptation to nutrient deficiency stress. Our findings provided important genes resources for the maize biofortification.
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Affiliation(s)
- Zizhao Song
- Crop Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- CAS Center for Excellence in Biotic Interactions, College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Suzhen Li
- Crop Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yu Li
- College of Food Science and Technology, Hebei Agricultural University, Baoding, 071000, China
| | - Xiaojin Zhou
- Crop Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaoqing Liu
- Crop Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wenzhu Yang
- Crop Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Rumei Chen
- Crop Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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2
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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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Printarakul N, Meeinkuirt W. The bryophyte community as bioindicator of heavy metals in a waterfall outflow. Sci Rep 2022; 12:6942. [PMID: 35484326 PMCID: PMC9050711 DOI: 10.1038/s41598-022-10980-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 04/15/2022] [Indexed: 11/19/2022] Open
Abstract
The species diversity and heavy metal accumulation in bryophytes were determined in Huay Pah Lahd stream in Doi Suthep-Pui National Park, Thailand. Eight bryophytes from two major taxonomic groupings (epilithic mosses and liverworts) were investigated. Of these, Fissidens crispulus var. crispulus was the most dominant taxon with an importance value (IV) of 28.98%, while Ectropothecium zollingeri, Claopodium prionophyllum, and Hyophila involuta were also dominant taxa with IV ≥ 10%. Scopelophila cataractae, a rare moss species with the lowest IV (0.91%) had the greatest capacity to accumulate metals in tissue, particularly Fe, Zn, Cd and Cu in protonemata (8026.7, 1187.2, 16.9 and 530.1 mg kg−1, respectively). The highest enrichment factors (EFs) of Zn, Cd and Cu (5.3, 2.4 and 0.9, respectively) were also found in S. cataractae, while the highest EFMn (1.1) was found in H. involuta. Enrichment factors of most heavy metals were < 5 from the study bryophytes, which suggests that natural processes were the key source of heavy metals. Dilution effects caused by increased water volume during the rainy season may be responsible for low pollutant loads and the maintenance of good water quality in this waterfall stream, which is favorable for biota and general environmental health.
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Affiliation(s)
- Narin Printarakul
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand.,Research Center in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Weeradej Meeinkuirt
- Water and Soil Environmental Research Unit, Nakhonsawan Campus, Mahidol University, Nakhonsawan, 60130, Thailand.
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Singh P, Khan A, Kumar R, Ojha KK, Singh VK, Srivastava A. In silico analysis of comparative affinity of phytosiderophore and bacillibactin for iron uptake by YSL15 and YSL18 receptors of Oryza sativa. J Biomol Struct Dyn 2022; 41:2733-2746. [PMID: 35139756 DOI: 10.1080/07391102.2022.2037464] [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: 10/19/2022]
Abstract
Iron is an important micronutrient for plant growth and development. In the case of Oryza sativa, iron is made available primarily with the help of iron chelators called phytosiderophores i.e. variants of deoxymugineic acid (DMA). They bind with ferric ions and get internalized through Yellow Stripe Like transporters viz. YSL15 and YSL18. However, due to low amount of secretion of phytosiderophores, rice suffers from iron deficiency. Alternatively, siderophores of plant growth promoting rhizobacteria may support iron uptake and make it available to plants via transporting ferric ions possibly through the same transporters. Present study aims to assess comparative binding of DMA and a xenosiderophore (siderophores used by organisms other than the ones producing them) of rhizobacteria i.e. bacillibactin with Fe3+ ion and subsequent transporters of rice. Protein-protein interaction and gene expression analysis predicts uptake of Fe3+ by YSL15 from the rhizosphere region and further distribution through YSL18 with the help of various predicted functional partners. Docking studies confirm the thermodynamically more favourable structure of bacillibactin-Fe3+ complex than DMA-Fe3+ complex. Molecular modelling of YSL15 and YSL18 was done through ab initio method and their evaluation by Ramachandran plot, ProSA, ERRAT value and verify 3 D score revealed a good quality models. Comparative binding assessment through docking and molecular dynamics simulation suggests better binding energies of YSL transporters with bacillibactin-Fe3+ complex as compared to DMA-Fe3+ complex. The current study suggests possible application of xenosiderophores of PGPR origin in supporting plant growth via iron uptake and distribution in rice.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Pratika Singh
- Department of Life Science, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, Bihar, India
| | - Azmi Khan
- Department of Life Science, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, Bihar, India
| | - Rakesh Kumar
- Department of Bioinformatics, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, Bihar, India
| | - Krishna Kumar Ojha
- Department of Bioinformatics, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, Bihar, India
| | - Vijay Kumar Singh
- Department of Bioinformatics, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, Bihar, India
| | - Amrita Srivastava
- Department of Life Science, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, Bihar, India
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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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6
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Tadaiesky LBA, da Silva BRS, Batista BL, Lobato AKDS. Brassinosteroids trigger tolerance to iron toxicity in rice. PHYSIOLOGIA PLANTARUM 2021; 171:371-387. [PMID: 33090462 DOI: 10.1111/ppl.13230] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 10/05/2020] [Accepted: 10/06/2020] [Indexed: 06/11/2023]
Abstract
Iron (Fe) toxicity is one of the most frequent abiotic stresses in rice, as it affects from 15% to 30% of the total production. Brassinosteroids (BRs), including 24-epibrassinolide (EBR), regulate ion homeostasis and improve the antioxidant system. The aim of this research was to determine whether EBR can contribute to the tolerance of rice plants exposed to Fe toxicity and to evaluate the possible effect on anatomical characteristics, nutrient concentrations, the antioxidant system, and gas exchange. The experiment was randomized with four treatments, two with different concentrations of Fe (250 and 6250 μM, control and toxicity, respectively) and these were either supplied with EBR or not (0 and 10 nM EBR, described as -EBR and +EBR, respectively). Treating plants grown under Fe toxic conditions with EBR caused an 70% increase in root aerenchyma area, compared to plants without steroid treatment. Our results revealed that EBR treatment could mitigate the deleterious effects of Fe toxicity in rice plants, by modulating the aerenchyma area, which contributes to the formation of an oxidative barrier and reduce the Fe mobilization at the root surface. Plants that were exposed to Fe toxic concentrations and treated with EBR showed (1) an increase in the enzyme activities of superoxide dismutase, catalase, ascorbate peroxidase and peroxidase, (2) mitigation of oxidative damage and (3) increased scavenging of reactive oxygen species. Finally, EBR alleviated the negative impacts induced by excess Fe on the net photosynthetic rate and the instantaneous carboxylation efficiency. These benefits were directly related to higher electron transport and stomatal density and indirectly linked to the protection mechanism exercised by the antioxidant enzymes on photosynthetic machinery. We conclude that EBR is able to confer tolerance to Fe toxicity in rice plants.
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Affiliation(s)
- Lorene B A Tadaiesky
- Núcleo de Pesquisa Vegetal Básica e Aplicada, Universidade Federal Rural da Amazônia, Paragominas, Brazil
| | - Breno R S da Silva
- Núcleo de Pesquisa Vegetal Básica e Aplicada, Universidade Federal Rural da Amazônia, Paragominas, Brazil
| | - Bruno Lemos Batista
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, São Paulo, Brazil
| | - Allan K da S Lobato
- Núcleo de Pesquisa Vegetal Básica e Aplicada, Universidade Federal Rural da Amazônia, Paragominas, Brazil
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Chandra AK, Pandey D, Tiwari A, Sharma D, Agarwal A, Sood S, Kumar A. An Omics Study of Iron and Zinc Homeostasis in Finger Millet: Biofortified Foods for Micronutrient Deficiency in an Era of Climate Change? ACTA ACUST UNITED AC 2020; 24:688-705. [DOI: 10.1089/omi.2020.0095] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Ajay Kumar Chandra
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G.B. Pant University of Agriculture and Technology, Pantnagar, India
| | - Dinesh Pandey
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G.B. Pant University of Agriculture and Technology, Pantnagar, India
| | - Apoorv Tiwari
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G.B. Pant University of Agriculture and Technology, Pantnagar, India
- Department of Computational Biology and Bioinformatics, Sam Higginbottom University of Agriculture, Technology and Sciences (SHUATS), Allahabad, India
| | - Divya Sharma
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G.B. Pant University of Agriculture and Technology, Pantnagar, India
- Department of Botany, Delhi University, Delhi, India
| | - Aparna Agarwal
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G.B. Pant University of Agriculture and Technology, Pantnagar, India
- Department of Microbiology, College of Basic Sciences and Humanities, G.B. Pant University of Agriculture and Technology, Pantnagar, India
| | - Salej Sood
- Department of Crop Improvement, Central Potato Research Institute, Shimla, India
| | - Anil Kumar
- Director of Education, Rani Lakshmi Bai Central Agricultural University, Jhansi, India
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Roda FA, Marques I, Batista-Santos P, Esquível MG, Ndayiragije A, Lidon FC, Swamy BPM, Ramalho JC, Ribeiro-Barros AI. Rice Biofortification With Zinc and Selenium: A Transcriptomic Approach to Understand Mineral Accumulation in Flag Leaves. Front Genet 2020; 11:543. [PMID: 32733530 PMCID: PMC7359728 DOI: 10.3389/fgene.2020.00543] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 05/05/2020] [Indexed: 11/13/2022] Open
Abstract
Human malnutrition due to micronutrient deficiencies, particularly with regards to Zinc (Zn) and Selenium (Se), affects millions of people around the world, and the enrichment of staple foods through biofortification has been successfully used to fight hidden hunger. Rice (Oryza sativa L.) is one of the staple foods most consumed in countries with high levels of malnutrition. However, it is poor in micronutrients, which are often removed during grain processing. In this study, we have analyzed the transcriptome of rice flag leaves biofortified with Zn (900 g ha-1), Se (500 g ha-1), and Zn-Se. Flag leaves play an important role in plant photosynthesis and provide sources of metal remobilization for developing grains. A total of 3170 differentially expressed genes (DEGs) were identified. The expression patterns and gene ontology of DEGs varied among the three sets of biofortified plants and were limited to specific metabolic pathways related to micronutrient mobilization and to the specific functions of Zn (i.e., its enzymatic co-factor/coenzyme function in the biosynthesis of nitrogenous compounds, carboxylic acids, organic acids, and amino acids) and Se (vitamin biosynthesis and ion homeostasis). The success of this approach should be followed in future studies to understand how landraces and other cultivars respond to biofortification.
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Affiliation(s)
- Faustino Adriano Roda
- Ministério de Agricultura e Segurança Alimentar, Instituto de Investigação Agrária de Moçambique, Centro Zonal Noroeste, Lichinga, Mozambique
- Universidade Eduardo Mondlane-Centro de Biotechnologia, Maputo, Mozambique
- PlantStress&Biodiversity Lab, Forest Research Center (IM, JCR, AIRB) and Linking, Landscape, Environment, Agriculture and Food (PBS, MGE), Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
| | - Isabel Marques
- PlantStress&Biodiversity Lab, Forest Research Center (IM, JCR, AIRB) and Linking, Landscape, Environment, Agriculture and Food (PBS, MGE), Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
| | - Paula Batista-Santos
- PlantStress&Biodiversity Lab, Forest Research Center (IM, JCR, AIRB) and Linking, Landscape, Environment, Agriculture and Food (PBS, MGE), Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
| | - Maria Glória Esquível
- PlantStress&Biodiversity Lab, Forest Research Center (IM, JCR, AIRB) and Linking, Landscape, Environment, Agriculture and Food (PBS, MGE), Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
| | - Alexis Ndayiragije
- International Rice Research Institute, Maputo, Mozambique
- International Rice Research Institute, Laguna, Philippines
| | - Fernando Cebola Lidon
- Unidade de Geobiociências, Geoengenharias e Geotecnologias, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
| | - B. P. Mallikarjuna Swamy
- International Rice Research Institute, Maputo, Mozambique
- International Rice Research Institute, Laguna, Philippines
| | - José Cochicho Ramalho
- PlantStress&Biodiversity Lab, Forest Research Center (IM, JCR, AIRB) and Linking, Landscape, Environment, Agriculture and Food (PBS, MGE), Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
- Unidade de Geobiociências, Geoengenharias e Geotecnologias, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Ana I. Ribeiro-Barros
- PlantStress&Biodiversity Lab, Forest Research Center (IM, JCR, AIRB) and Linking, Landscape, Environment, Agriculture and Food (PBS, MGE), Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
- Unidade de Geobiociências, Geoengenharias e Geotecnologias, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
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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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10
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Mahender A, Swamy BPM, Anandan A, Ali J. Tolerance of Iron-Deficient and -Toxic Soil Conditions in Rice. PLANTS (BASEL, SWITZERLAND) 2019; 8:E31. [PMID: 30696039 PMCID: PMC6409647 DOI: 10.3390/plants8020031] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/21/2019] [Accepted: 01/23/2019] [Indexed: 01/04/2023]
Abstract
Iron (Fe) deficiency and toxicity are the most widely prevalent soil-related micronutrient disorders in rice (Oryza sativa L.). Progress in rice cultivars with improved tolerance has been hampered by a poor understanding of Fe availability in the soil, the transportation mechanism, and associated genetic factors for the tolerance of Fe toxicity soil (FTS) or Fe deficiency soil (FDS) conditions. In the past, through conventional breeding approaches, rice varieties were developed especially suitable for low- and high-pH soils, which indirectly helped the varieties to tolerate FTS and FDS conditions. Rice-Fe interactions in the external environment of soil, internal homeostasis, and transportation have been studied extensively in the past few decades. However, the molecular and physiological mechanisms of Fe uptake and transport need to be characterized in response to the tolerance of morpho-physiological traits under Fe-toxic and -deficient soil conditions, and these traits need to be well integrated into breeding programs. A deeper understanding of the several factors that influence Fe absorption, uptake, and transport from soil to root and above-ground organs under FDS and FTS is needed to develop tolerant rice cultivars with improved grain yield. Therefore, the objective of this review paper is to congregate the different phenotypic screening methodologies for prospecting tolerant rice varieties and their responsible genetic traits, and Fe homeostasis related to all the known quantitative trait loci (QTLs), genes, and transporters, which could offer enormous information to rice breeders and biotechnologists to develop rice cultivars tolerant of Fe toxicity or deficiency. The mechanism of Fe regulation and transport from soil to grain needs to be understood in a systematic manner along with the cascade of metabolomics steps that are involved in the development of rice varieties tolerant of FTS and FDS. Therefore, the integration of breeding with advanced genome sequencing and omics technologies allows for the fine-tuning of tolerant genotypes on the basis of molecular genetics, and the further identification of novel genes and transporters that are related to Fe regulation from FTS and FDS conditions is incredibly important to achieve further success in this aspect.
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Affiliation(s)
- Anumalla Mahender
- Rice Breeding Platform, International Rice Research Institute (IRRI), Los Baños, Laguna 4031, Philippines.
| | - B P Mallikarjuna Swamy
- Rice Breeding Platform, International Rice Research Institute (IRRI), Los Baños, Laguna 4031, Philippines.
| | - Annamalai Anandan
- ICAR-National Rice Research Institute, Cuttack, Odisha 753006, India.
| | - Jauhar Ali
- Rice Breeding Platform, International Rice Research Institute (IRRI), Los Baños, Laguna 4031, Philippines.
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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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