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Raimondi D, Passemiers A, Verplaetse N, Corso M, Ferrero-Serrano Á, Nazzicari N, Biscarini F, Fariselli P, Moreau Y. Biologically meaningful genome interpretation models to address data underdetermination for the leaf and seed ionome prediction in Arabidopsis thaliana. Sci Rep 2024; 14:13188. [PMID: 38851759 PMCID: PMC11162433 DOI: 10.1038/s41598-024-63855-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 06/03/2024] [Indexed: 06/10/2024] Open
Abstract
Genome interpretation (GI) encompasses the computational attempts to model the relationship between genotype and phenotype with the goal of understanding how the first leads to the second. While traditional approaches have focused on sub-problems such as predicting the effect of single nucleotide variants or finding genetic associations, recent advances in neural networks (NNs) have made it possible to develop end-to-end GI models that take genomic data as input and predict phenotypes as output. However, technical and modeling issues still need to be fixed for these models to be effective, including the widespread underdetermination of genomic datasets, making them unsuitable for training large, overfitting-prone, NNs. Here we propose novel GI models to address this issue, exploring the use of two types of transfer learning approaches and proposing a novel Biologically Meaningful Sparse NN layer specifically designed for end-to-end GI. Our models predict the leaf and seed ionome in A.thaliana, obtaining comparable results to our previous over-parameterized model while reducing the number of parameters by 8.8 folds. We also investigate how the effect of population stratification influences the evaluation of the performances, highlighting how it leads to (1) an instance of the Simpson's Paradox, and (2) model generalization limitations.
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Affiliation(s)
| | | | | | - Massimiliano Corso
- Université Paris-Saclay, INRAE, AgroParisTech, Institute Jean-Pierre Bourgin for Plant Sciences (IJPB), 78000, Versailles, France
| | - Ángel Ferrero-Serrano
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | | | | | - Piero Fariselli
- Department of Medical Sciences, University of Torino, 10123, Turin, Italy
| | - Yves Moreau
- ESAT-STADIUS, KU Leuven, 3001, Leuven, Belgium
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2
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Naqvi RZ, Mahmood MA, Mansoor S, Amin I, Asif M. Omics-driven exploration and mining of key functional genes for the improvement of food and fiber crops. FRONTIERS IN PLANT SCIENCE 2024; 14:1273859. [PMID: 38259913 PMCID: PMC10800452 DOI: 10.3389/fpls.2023.1273859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 12/08/2023] [Indexed: 01/24/2024]
Abstract
The deployment of omics technologies has obtained an incredible boost over the past few decades with the advances in next-generation sequencing (NGS) technologies, innovative bioinformatics tools, and the deluge of available biological information. The major omics technologies in the limelight are genomics, transcriptomics, proteomics, metabolomics, and phenomics. These biotechnological advances have modernized crop breeding and opened new horizons for developing crop varieties with improved traits. The genomes of several crop species are sequenced, and a huge number of genes associated with crucial economic traits have been identified. These identified genes not only provide insights into the understanding of regulatory mechanisms of crop traits but also decipher practical grounds to assist in the molecular breeding of crops. This review discusses the potential of omics technologies for the acquisition of biological information and mining of the genes associated with important agronomic traits in important food and fiber crops, such as wheat, rice, maize, potato, tomato, cassava, and cotton. Different functional genomics approaches for the validation of these important genes are also highlighted. Furthermore, a list of genes discovered by employing omics approaches is being represented as potential targets for genetic modifications by the latest genome engineering methods for the development of climate-resilient crops that would in turn provide great impetus to secure global food security.
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Affiliation(s)
- Rubab Zahra Naqvi
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Muhammad Arslan Mahmood
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
- International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Muhammad Asif
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
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3
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Janni M, Maestri E, Gullì M, Marmiroli M, Marmiroli N. Plant responses to climate change, how global warming may impact on food security: a critical review. FRONTIERS IN PLANT SCIENCE 2024; 14:1297569. [PMID: 38250438 PMCID: PMC10796516 DOI: 10.3389/fpls.2023.1297569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 12/14/2023] [Indexed: 01/23/2024]
Abstract
Global agricultural production must double by 2050 to meet the demands of an increasing world human population but this challenge is further exacerbated by climate change. Environmental stress, heat, and drought are key drivers in food security and strongly impacts on crop productivity. Moreover, global warming is threatening the survival of many species including those which we rely on for food production, forcing migration of cultivation areas with further impoverishing of the environment and of the genetic variability of crop species with fall out effects on food security. This review considers the relationship of climatic changes and their bearing on sustainability of natural and agricultural ecosystems, as well as the role of omics-technologies, genomics, proteomics, metabolomics, phenomics and ionomics. The use of resource saving technologies such as precision agriculture and new fertilization technologies are discussed with a focus on their use in breeding plants with higher tolerance and adaptability and as mitigation tools for global warming and climate changes. Nevertheless, plants are exposed to multiple stresses. This study lays the basis for the proposition of a novel research paradigm which is referred to a holistic approach and that went beyond the exclusive concept of crop yield, but that included sustainability, socio-economic impacts of production, commercialization, and agroecosystem management.
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Affiliation(s)
- Michela Janni
- Institute of Bioscience and Bioresources (IBBR), National Research Council (CNR), Bari, Italy
- Institute of Materials for Electronics and Magnetism (IMEM), National Research Council (CNR), Parma, Italy
| | - Elena Maestri
- Department of Chemistry, Life Sciences and Environmental Sustainability, Interdepartmental Centers SITEIA.PARMA and CIDEA, University of Parma, Parma, Italy
| | - Mariolina Gullì
- Department of Chemistry, Life Sciences and Environmental Sustainability, Interdepartmental Centers SITEIA.PARMA and CIDEA, University of Parma, Parma, Italy
| | - Marta Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, Interdepartmental Centers SITEIA.PARMA and CIDEA, University of Parma, Parma, Italy
| | - Nelson Marmiroli
- Consorzio Interuniversitario Nazionale per le Scienze Ambientali (CINSA) Interuniversity Consortium for Environmental Sciences, Parma/Venice, Italy
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4
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Ferrão LFV, Dhakal R, Dias R, Tieman D, Whitaker V, Gore MA, Messina C, Resende MFR. Machine learning applications to improve flavor and nutritional content of horticultural crops through breeding and genetics. Curr Opin Biotechnol 2023; 83:102968. [PMID: 37515935 DOI: 10.1016/j.copbio.2023.102968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/31/2023]
Abstract
Over the last decades, significant strides were made in understanding the biochemical factors influencing the nutritional content and flavor profile of fruits and vegetables. Product differentiation in the produce aisle is the natural consequence of increasing consumer power in the food industry. Cotton-candy grapes, specialty tomatoes, and pineapple-flavored white strawberries provide a few examples. Given the increased demand for flavorful varieties, and pressing need to reduce micronutrient malnutrition, we expect breeding to increase its prioritization toward these traits. Reaching this goal will, in part, necessitate knowledge of the genetic architecture controlling these traits, as well as the development of breeding methods that maximize their genetic gain. Can artificial intelligence (AI) help predict flavor preferences, and can such insights be leveraged by breeding programs? In this Perspective, we outline both the opportunities and challenges for the development of more flavorful and nutritious crops, and how AI can support these breeding initiatives.
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Affiliation(s)
- Luís Felipe V Ferrão
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Rakshya Dhakal
- Plant Breeding Graduate Program, University of Florida, Gainesville, FL, United States
| | - Raquel Dias
- Microbiology and Cell Science Department, University of Florida, Gainesville, FL, United States
| | - Denise Tieman
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Vance Whitaker
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States; Plant Breeding Graduate Program, University of Florida, Gainesville, FL, United States
| | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Carlos Messina
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States; Plant Breeding Graduate Program, University of Florida, Gainesville, FL, United States
| | - Márcio F R Resende
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States; Plant Breeding Graduate Program, University of Florida, Gainesville, FL, United States.
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Shekhawat PK, Goyal A, Akhatar J, Sharma S, Kaur N, Bharti B, Mittal M, Sardana VK, Chhuneja P, Banga SS, Atri C. Genetic analysis of the variation for mineral accumulation in the leaves and seeds of natural germplasm of Brassica rapa L. (AA) and the its derived forms extracted from an allotetraploid B.juncea L.(AABB). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108084. [PMID: 37832370 DOI: 10.1016/j.plaphy.2023.108084] [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: 06/18/2023] [Revised: 09/16/2023] [Accepted: 10/07/2023] [Indexed: 10/15/2023]
Abstract
Brassica rapa L. (2n = 20; AA) is a vegetable and oilseed crop that is grown all over the world. Its leaves, shoots, and seeds store significant amounts of minerals. We used inductively coupled plasma-optical emission spectroscopy (ICP-OES) to determine the concentrations of eleven minerals in the leaves and seeds of 195 advanced generation inbred lines, of which 92 represented natural (NR) B. rapa and the remaining 103 were derived (DR) from a set of mother genotypes originally extracted from an allotetraploid B. juncea (2n = 36; AABB). The inbred lines differed for the composition of leaf and seed minerals. Leaf concentrations of N, K, Zn, and Se were higher in the DR subpanel as compared to NR subpanel, along with high seed accumulations of K and Se. DArT genotyping and genome wide association mapping led to the identification of SNPs associated with leaf and seed mineral compositions. Chromosomes A03, A05, and A10 harboured the most associated loci. Annotations of the regions adjacent to respective GWAS peaks allowed prediction of genes known for acquisition, transport, and accumulation of minerals and heavy metal detoxification. Transcriptome analysis revealed differential expression patterns of the predicted candidates, with most genes either down-regulated in derived genotypes relative to natural forms or their expression being comparable between the two. General downregulation may be a consequence of extracting B. rapa from allotetraploid B. juncea through genome resection. Some of the identified SNPs may be used as DNA markers for breeding programmes designed to modify the leaf and seed mineral compositions.
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Affiliation(s)
- Pooja Kanwar Shekhawat
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Anna Goyal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Javed Akhatar
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Sanjula Sharma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Navneet Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Baudh Bharti
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Meenakshi Mittal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - V K Sardana
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Surinder S Banga
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Chhaya Atri
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India.
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6
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Vogels JJ, Van de Waal DB, WallisDeVries MF, Van den Burg AB, Nijssen M, Bobbink R, Berg MP, Olde Venterink H, Siepel H. Towards a mechanistic understanding of the impacts of nitrogen deposition on producer-consumer interactions. Biol Rev Camb Philos Soc 2023; 98:1712-1731. [PMID: 37265074 DOI: 10.1111/brv.12972] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 06/03/2023]
Abstract
Nitrogen (N) deposition has increased substantially since the second half of the 20th century due to human activities. This increase of reactive N into the biosphere has major implications for ecosystem functioning, including primary production, soil and water chemistry and producer community structure and diversity. Increased N deposition is also linked to the decline of insects observed over recent decades. However, we currently lack a mechanistic understanding of the effects of high N deposition on individual fitness, species richness and community structure of both invertebrate and vertebrate consumers. Here, we review the effects of N deposition on producer-consumer interactions, focusing on five existing ecological frameworks: C:N:P ecological stoichiometry, trace element ecological stoichiometry, nutritional geometry, essential micronutrients and allelochemicals. We link reported N deposition-mediated changes in producer quality to life-history strategies and traits of consumers, to gain a mechanistic understanding of the direction of response in consumers. We conclude that high N deposition influences producer quality via eutrophication and acidification pathways. This makes oligotrophic poorly buffered ecosystems most vulnerable to significant changes in producer quality. Changes in producer quality between the reviewed frameworks are often interlinked, complicating predictions of the effects of high N deposition on producer quality. The degree and direction of fitness responses of consumers to changes in producer quality varies among species but can be explained by differences in life-history traits and strategies, particularly those affecting species nutrient intake regulation, mobility, relative growth rate, host-plant specialisation, ontogeny and physiology. To increase our understanding of the effects of N deposition on these complex mechanisms, the inclusion of life-history traits of consumer species in future study designs is pivotal. Based on the reviewed literature, we formulate five hypotheses on the mechanisms underlying the effects of high N deposition on consumers, by linking effects of nutritional ecological frameworks to life-history strategies. Importantly, we expect that N-deposition-mediated changes in producer quality will result in a net decrease in consumer community as well as functional diversity. Moreover, we anticipate an increased risk of outbreak events of a small subset of generalist species, with concomitant declines in a multitude of specialist species. Overall, linking ecological frameworks with consumer life-history strategies provides a mechanistic understanding of the impacts of high N deposition on producer-consumer interactions, which can inform management towards more effective mitigation strategies.
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Affiliation(s)
- Joost J Vogels
- Bargerveen Foundation, Toernooiveld 1, 6525 ED, Nijmegen, The Netherlands
- Department of Animal Ecology and Physiology, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Dedmer B Van de Waal
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Sciencepark 904, 1098 XH, Amsterdam, The Netherlands
| | - Michiel F WallisDeVries
- De Vlinderstichting / Dutch Butterfly Conservation, P.O. Box 6700 AM, Wageningen, The Netherlands
| | | | - Marijn Nijssen
- Bargerveen Foundation, Toernooiveld 1, 6525 ED, Nijmegen, The Netherlands
- Department of Animal Ecology and Physiology, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Roland Bobbink
- B-WARE Research Centre, Radboud University Nijmegen, Toernooiveld 1, 6525 ED, Nijmegen, The Netherlands
| | - Matty P Berg
- A-LIFE, Section Ecology & Evolution, Vrije Universiteit, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
- GELIFES, Community and Conservation Ecology Group, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Harry Olde Venterink
- Department of Biology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Henk Siepel
- Department of Animal Ecology and Physiology, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
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7
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Esteves SM, Jadoul A, Iacono F, Schloesser M, Bosman B, Carnol M, Druet T, Cardol P, Hanikenne M. Natural variation of nutrient homeostasis among laboratory and field strains of Chlamydomonas reinhardtii. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5198-5217. [PMID: 37235689 DOI: 10.1093/jxb/erad194] [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: 12/02/2022] [Accepted: 05/24/2023] [Indexed: 05/28/2023]
Abstract
Natural variation among individuals and populations exists in all species, playing key roles in response to environmental stress and adaptation. Micro- and macronutrients have a wide range of functions in photosynthetic organisms, and mineral nutrition thus plays a sizable role in biomass production. To maintain nutrient concentrations inside the cell within physiological limits and prevent the detrimental effects of deficiency or excess, complex homeostatic networks have evolved in photosynthetic cells. The microalga Chlamydomonas reinhardtii (Chlamydomonas) is a unicellular eukaryotic model for studying such mechanisms. In this work, 24 Chlamydomonas strains, comprising field isolates and laboratory strains, were examined for intraspecific differences in nutrient homeostasis. Growth and mineral content were quantified in mixotrophy, as full nutrition control, and compared with autotrophy and nine deficiency conditions for macronutrients (-Ca, -Mg, -N, -P, and -S) and micronutrients (-Cu, -Fe, -Mn, and -Zn). Growth differences among strains were relatively limited. However, similar growth was accompanied by highly divergent mineral accumulation among strains. The expression of nutrient status marker genes and photosynthesis were scored in pairs of contrasting field strains, revealing distinct transcriptional regulation and nutrient requirements. Leveraging this natural variation should enable a better understanding of nutrient homeostasis in Chlamydomonas.
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Affiliation(s)
- Sara M Esteves
- InBioS-PhytoSystems, Translational Plant Biology, University of Liège, Belgium
| | - Alice Jadoul
- InBioS-PhytoSystems, Translational Plant Biology, University of Liège, Belgium
| | - Fabrizio Iacono
- InBioS-PhytoSystems, Genetics and Physiology of Microalgae, University of Liège, Belgium
| | - Marie Schloesser
- InBioS-PhytoSystems, Translational Plant Biology, University of Liège, Belgium
| | - Bernard Bosman
- InBioS-PhytoSystems, Laboratory of Plant and Microbial Ecology, University of Liège, Belgium
| | - Monique Carnol
- InBioS-PhytoSystems, Laboratory of Plant and Microbial Ecology, University of Liège, Belgium
| | - Tom Druet
- Unit of Animal Genomics (GIGA), University of Liège, Belgium
| | - Pierre Cardol
- InBioS-PhytoSystems, Genetics and Physiology of Microalgae, University of Liège, Belgium
| | - Marc Hanikenne
- InBioS-PhytoSystems, Translational Plant Biology, University of Liège, Belgium
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Kostic I, Nikolic N, Milanovic S, Milenkovic I, Pavlovic J, Paravinja A, Nikolic M. Silicon modifies leaf nutriome and improves growth of oak seedlings exposed to phosphorus deficiency and Phytophthora plurivora infection. FRONTIERS IN PLANT SCIENCE 2023; 14:1265782. [PMID: 37705706 PMCID: PMC10495579 DOI: 10.3389/fpls.2023.1265782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 08/10/2023] [Indexed: 09/15/2023]
Abstract
Beneficial effects of silicon (Si) on plants have primarily been studied in crop species under single stress. Moreover, nutrient acquisition-based responses to combination of biotic and abiotic stresses (a common situation in natural habitats) have rarely been reported, in particular in conjunction with soil amendments with Si. Pedunculate oak (Quercus robur L.), one of the ecologically and economically most important tree species in Europe, is facing a severe decline due to combined stresses, but also problems in assisted regeneration in nurseries. Here, we studied the effect of Si supply on the leaf nutriome, root traits and overall growth of 12-weeks-old oak seedlings exposed to abiotic stress [low phosphorus (P) supply], biotic stress (Phytophthora plurivora root infection), and their combination. The application of Si had the strongest ameliorative effect on growth, root health and root phenome under the most severe stress conditions (i.e., combination of P deficiency and P. plurivora root infection), where it differentially affected the uptake and leaf accumulation in 11 out of 13 analysed nutrients. Silicon supply tended to reverse the pattern of change of some, but not all, leaf nutrients affected by stresses: P, boron (B) and magnesium (Mg) under P deficiency, and P, B and sulphur (S) under pathogen attack, but also nickel (Ni) and molybdenum (Mo) under all three stresses. Surprisingly, Si affected some nutrients that were not changed by a particular stress itself and decreased leaf Mg levels under all the stresses. On the other hand, pathogen attack increased leaf accumulation of Si. This exploratory work presents the complexity of nutrient crosstalk under three stresses, and opens more questions about genetic networks that control plant physiological responses. Practically, we show a potential of Si application to improve P status and root health in oak seedlings, particularly in nurseries.
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Affiliation(s)
- Igor Kostic
- Laboratory of Plant Nutrition, Institute for Multidisciplinary Research, University of Belgrade, Belgrade, Serbia
| | - Nina Nikolic
- Laboratory of Plant Nutrition, Institute for Multidisciplinary Research, University of Belgrade, Belgrade, Serbia
| | - Slobodan Milanovic
- Faculty of Forestry, University of Belgrade, Belgrade, Serbia
- Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno, Czechia
| | - Ivan Milenkovic
- Faculty of Forestry, University of Belgrade, Belgrade, Serbia
- Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno, Czechia
| | - Jelena Pavlovic
- Laboratory of Plant Nutrition, Institute for Multidisciplinary Research, University of Belgrade, Belgrade, Serbia
| | - Ana Paravinja
- Laboratory of Plant Nutrition, Institute for Multidisciplinary Research, University of Belgrade, Belgrade, Serbia
| | - Miroslav Nikolic
- Laboratory of Plant Nutrition, Institute for Multidisciplinary Research, University of Belgrade, Belgrade, Serbia
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9
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Giehl RFH, Flis P, Fuchs J, Gao Y, Salt DE, von Wirén N. Cell type-specific mapping of ion distribution in Arabidopsis thaliana roots. Nat Commun 2023; 14:3351. [PMID: 37311779 DOI: 10.1038/s41467-023-38880-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 05/16/2023] [Indexed: 06/15/2023] Open
Abstract
Cell type-specific mapping of element distribution is critical to fully understand how roots partition nutrients and toxic elements with aboveground parts. In this study, we developed a method that combines fluorescence-activated cell sorting (FACS) with inductively coupled plasma mass spectrometry (ICP-MS) to assess the ionome of different cell populations within Arabidopsis thaliana roots. The method reveals that most elements exhibit a radial concentration gradient increasing from the rhizodermis to inner cell layers, and detected previously unknown ionomic changes resulting from perturbed xylem loading processes. With this approach, we also identify a strong accumulation of manganese in trichoblasts of iron-deficient roots. We demonstrate that confining manganese sequestration in trichoblasts but not in endodermal cells efficiently retains manganese in roots, therefore preventing toxicity in shoots. These results indicate the existence of cell type-specific constraints for efficient metal sequestration in roots. Thus, our approach opens an avenue to investigate element compartmentation and transport pathways in plants.
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Affiliation(s)
- Ricardo F H Giehl
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, 06466, Seeland, Germany.
| | - Paulina Flis
- Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Jörg Fuchs
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, 06466, Seeland, Germany
| | - Yiqun Gao
- Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - David E Salt
- Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Nicolaus von Wirén
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, 06466, Seeland, Germany.
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Ionome of Lithuanian Populations of Purple Loosestrife (Lythrum salicaria) and Its Relation to Genetic Diversity and Environmental Variables. DIVERSITY 2023. [DOI: 10.3390/d15030418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
Fifteen riparian populations of Lithuanian Lythrum salicaria were assessed for leaf macronutrient, micronutrient and non-essential element concentrations and compared to the former obtained molecular data at amplified fragment length polymorphism (PLP.AFLP) loci. Inductively coupled plasma mass spectrometry was used to profile the contents of 12 elements in the leaves. The leaf nutrient concentrations were within normal ranges for growth and development and heavy metal concentrations did not reach toxic levels. The concentrations of macroelements such as nitrogen, potassium, calcium and magnesium were in the range of 23,790–38,183; 7327–11,732; 7018–12,306; and 1377–3183 µg/g dry mass (d. m.), respectively; the concentrations of micronutrients such as sodium, iron, zinc and copper varied in the ranges of 536–6328; 24.7–167.1; 10.88–26.24; and 3.72–5.30 µg/g d. m., respectively, and the concentrations of non-essential elements such as lead, nickel, chromium, and cadmium were in the intervals of 0.136–0.940; 0.353–0.783; 0.207–0.467; and 0.012–0.028 µg/g d. m., respectively. When comparing the maximum and minimum values for site elements of L. salicaria, the concentration of N varied by 1.6, K—1.6, Ca—1.8, Mg—2.3, Na—6.1, Fe—6.8, Zn—2.4, Cu—1.5, Pb—6.9, Ni—2.2, Cr—2.2, and Cd—2.3 times. The coefficient of variation (CV) of element concentrations in sites was moderate to large: N—15.4%, K—14.3%, Ca—18.6%, Mg—24.8%, Na—50.7%, Fe—47.0%, Zn—24.9%, Cu—14.5%, Pb—57.1%, Ni—30.11%, Cr—26.0%, and Cd—38.6%. Lythrum salicaria populations growing near regulated riverbeds were characterized by significantly (p < 0.05) lower concentrations of Ca and Mg, and significantly (p < 0.05) higher concentrations of N, K, Fe, Na, Ni, Cr and Cd. The PLP.AFLP was negatively correlated with concentrations of N, Na, Fe, Ni, Cr, and Cd. The L. salicaria population with the lowest leaf N and Na concentration showed the highest genetic polymorphism (PLP.AFLP = 65.4%), while the least polymorphic population (PLP.AFLP = 35.0%) did not show extreme concentrations of either element. In conclusion, our elemental analysis of L. salicaria populations showed that ionomic parameters are related to genomic parameters, and some habitat differences are reflected in the ionomes of the populations.
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Kudapa H, Barmukh R, Vemuri H, Gorthy S, Pinnamaneni R, Vetriventhan M, Srivastava RK, Joshi P, Habyarimana E, Gupta SK, Govindaraj M. Genetic and genomic interventions in crop biofortification: Examples in millets. FRONTIERS IN PLANT SCIENCE 2023; 14:1123655. [PMID: 36950360 PMCID: PMC10025513 DOI: 10.3389/fpls.2023.1123655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Micronutrient malnutrition is a serious threat to the developing world's human population, which largely relies on a cereal-based diet that lacks diversity and micronutrients. Besides major cereals, millets represent the key sources of energy, protein, vitamins, and minerals for people residing in the dryland tropics and drought-prone areas of South Asia and sub-Saharan Africa. Millets serve as multi-purpose crops with several salient traits including tolerance to abiotic stresses, adaptation to diverse agro-ecologies, higher productivity in nutrient-poor soils, and rich nutritional characteristics. Considering the potential of millets in empowering smallholder farmers, adapting to changing climate, and transforming agrifood systems, the year 2023 has been declared by the United Nations as the International Year of Millets. In this review, we highlight recent genetic and genomic innovations that can be explored to enhance grain micronutrient density in millets. We summarize the advances made in high-throughput phenotyping to accurately measure grain micronutrient content in cereals. We shed light on genetic diversity in millet germplasm collections existing globally that can be exploited for developing nutrient-dense and high-yielding varieties to address food and nutritional security. Furthermore, we describe the progress made in the fields of genomics, proteomics, metabolomics, and phenomics with an emphasis on enhancing the grain nutritional content for designing competitive biofortified varieties for the future. Considering the close genetic-relatedness within cereals, upcoming research should focus on identifying the genetic and genomic basis of nutritional traits in millets and introgressing them into major cereals through integrated omics approaches. Recent breakthroughs in the genome editing toolbox would be crucial for mainstreaming biofortification in millets.
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Affiliation(s)
- Himabindu Kudapa
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - Rutwik Barmukh
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - Hindu Vemuri
- International Maize and Wheat Improvement Center (CIMMYT), Patancheru, Telangana, India
| | - Sunita Gorthy
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | | | - Mani Vetriventhan
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - Rakesh K. Srivastava
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - Priyanka Joshi
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - Ephrem Habyarimana
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - S. K. Gupta
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - Mahalingam Govindaraj
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
- HarvestPlus Program, Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali, Colombia
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12
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Silva JVDS, Baligar VC, Ahrnet D, de Almeida AAF. Transcriptomic, osmoregulatory and translocation changes modulates Ni toxicity in Theobroma cacao. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 196:624-633. [PMID: 36791534 DOI: 10.1016/j.plaphy.2023.01.053] [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: 08/09/2022] [Revised: 01/23/2023] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Nickel is one of the most released trace elements in the environment and in the case of bioaccumulation in foods and beverages derived from cocoa beans can cause risk to human health. It is very important to understand how plants respond to toxic metals and which are the defense strategies they adopt to mitigate their effects. In the present study we used young plants of T. cacao, submitted to increasing Ni doses (0, 100, 200, 300, 400 and 500 mg Ni kg-1 soil) and evaluated them for a period of 30 days. Doses of Ni, from 300 mg of Ni kg-1 onwards in the soil, promoted changes in photosynthetic, antioxidant, osmoregulatory, transcriptomic and translocation levels, evidenced by the increase in the activity of antioxidant enzymes, proline, glycine betaine, upregulation of the metallothionein 2B gene (Mt2b), and lipid peroxidation of the cell membranes. Foliar gas exchange was severely affected at higher doses of Ni. In addition, reduced levels of stomatal conductivity and transpiration rate were observed from 300 mg Ni kg-1 dose onwards in the soil, which consequently affected CO2 assimilation. Phytostabilization and exclusion mechanisms control the translocation of Ni from the root to the shoot and reduce harmful effects on plant metabolism. Our results highlighted the toxicity of Ni, a trace element often underestimated in T. cacao. In particular, it was noted that doses of 100 and 200 Ni kg-1 soil, although high, do not induce toxicity in T. cacao plants. But Ni toxicity is observed from 300 mg Ni kg-1 soil onwards. This study contributed to the understanding of the harmful effects of higher doses of Ni in cacao plants and the biochemical processes the plant uses to mitigate the effects of this metal.
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Affiliation(s)
- José Victor Dos Santos Silva
- Departamento de Sistemas Agrícolas, Forestales y Medio Ambiente, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Avda. Montañana 930, 50059, Zaragoza, Spain; State University of Santa Cruz, Department of Biological Sciences, Rodovia Jorge Amado, km 16, 45662-900, Ilhéus, BA, Brazil.
| | - Virupax C Baligar
- USDA-ARS-Beltsville Agricultural Research Center, Beltsville, MD, USA
| | - Dário Ahrnet
- State University of Santa Cruz, Department of Biological Sciences, Rodovia Jorge Amado, km 16, 45662-900, Ilhéus, BA, Brazil
| | - Alex-Alan Furtado de Almeida
- State University of Santa Cruz, Department of Biological Sciences, Rodovia Jorge Amado, km 16, 45662-900, Ilhéus, BA, Brazil
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13
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Abstract
Living systems are built from a small subset of the atomic elements, including the bulk macronutrients (C,H,N,O,P,S) and ions (Mg,K,Na,Ca) together with a small but variable set of trace elements (micronutrients). Here, we provide a global survey of how chemical elements contribute to life. We define five classes of elements: those that are (i) essential for all life, (ii) essential for many organisms in all three domains of life, (iii) essential or beneficial for many organisms in at least one domain, (iv) beneficial to at least some species, and (v) of no known beneficial use. The ability of cells to sustain life when individual elements are absent or limiting relies on complex physiological and evolutionary mechanisms (elemental economy). This survey of elemental use across the tree of life is encapsulated in a web-based, interactive periodic table that summarizes the roles chemical elements in biology and highlights corresponding mechanisms of elemental economy.
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Affiliation(s)
- Kaleigh A Remick
- Department of Microbiology, Cornell University, New York, NY, United States
| | - John D Helmann
- Department of Microbiology, Cornell University, New York, NY, United States.
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14
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Guo Y, Wang Y, Chen H, Du Q, Wang Z, Gong X, Sun Q, Li WX. Nitrogen supply affects ion homeostasis by modifying root Casparian strip formation through the miR528-LAC3 module in maize. PLANT COMMUNICATIONS 2023:100553. [PMID: 36681862 PMCID: PMC10363476 DOI: 10.1016/j.xplc.2023.100553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 12/02/2022] [Accepted: 01/18/2023] [Indexed: 06/17/2023]
Abstract
Although nitrogen (N) is known to affect mineral element homeostasis in plants, the molecular mechanisms of interactions between N and other nutrients remain largely unclear. We report here that N supply affects ion homeostasis in maize. Berberine hemisulfate staining and a propidium iodide penetration assay showed that N luxury significantly delayed Casparian strip (CS) formation in maize roots. We further demonstrated that N-mediated CS formation in maize was independent of RBOHF-activated H2O2 production. N luxury induced the expression of ZmmiR528 in whole roots and root tips. Knockdown and loss-of-function of ZmmiR528 promoted CS formation under both N-luxury and N-deficient conditions. Both ZmMIR528a and ZmMIR528b contribute to early CS formation under different N conditions. RNA-seq and real-time RT-PCR analysis demonstrated that ZmLAC3, but not ZmLAC5, responded to N treatments. Consistent with results obtained with ZmmiR528 TM transgenic maize and mir528a/b loss-of-function mutants, transgenic maize overexpressing ZmLAC3 displayed early CS formation under different N conditions. Under field conditions, K, Ca, Mn, Cu, Mg, and Zn concentrations were greater in the ear leaf of ZmLAC3-overexpressing transgenic maize than in the wild type. These results indicate that ZmmiR528 affects CS formation in maize by regulating the expression of ZmLAC3, and modification of CS formation has the potential to improve maize quality.
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Affiliation(s)
- Yu Guo
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yafei Wang
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huan Chen
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qingguo Du
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhonghua Wang
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaoping Gong
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qing Sun
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Qingdao Agricultural University, Qingdao 266109, China
| | - Wen-Xue Li
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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15
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Eckardt NA, Ainsworth EA, Bahuguna RN, Broadley MR, Busch W, Carpita NC, Castrillo G, Chory J, DeHaan LR, Duarte CM, Henry A, Jagadish SVK, Langdale JA, Leakey ADB, Liao JC, Lu KJ, McCann MC, McKay JK, Odeny DA, Jorge de Oliveira E, Platten JD, Rabbi I, Rim EY, Ronald PC, Salt DE, Shigenaga AM, Wang E, Wolfe M, Zhang X. Climate change challenges, plant science solutions. THE PLANT CELL 2023; 35:24-66. [PMID: 36222573 PMCID: PMC9806663 DOI: 10.1093/plcell/koac303] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Climate change is a defining challenge of the 21st century, and this decade is a critical time for action to mitigate the worst effects on human populations and ecosystems. Plant science can play an important role in developing crops with enhanced resilience to harsh conditions (e.g. heat, drought, salt stress, flooding, disease outbreaks) and engineering efficient carbon-capturing and carbon-sequestering plants. Here, we present examples of research being conducted in these areas and discuss challenges and open questions as a call to action for the plant science community.
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Affiliation(s)
| | - Elizabeth A Ainsworth
- USDA ARS Global Change and Photosynthesis Research Unit, Urbana, Illinois 61801, USA
| | - Rajeev N Bahuguna
- Centre for Advanced Studies on Climate Change, Dr Rajendra Prasad Central Agricultural University, Samastipur 848125, Bihar, India
| | - Martin R Broadley
- School of Biosciences, University of Nottingham, Nottingham, NG7 2RD, UK
- Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Wolfgang Busch
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Nicholas C Carpita
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
| | - Gabriel Castrillo
- School of Biosciences, University of Nottingham, Nottingham, NG7 2RD, UK
- Future Food Beacon of Excellence, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Joanne Chory
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | | | - Carlos M Duarte
- Red Sea Research Center (RSRC) and Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Amelia Henry
- International Rice Research Institute, Rice Breeding Innovations Platform, Los Baños, Laguna 4031, Philippines
| | - S V Krishna Jagadish
- Department of Plant and Soil Science, Texas Tech University, Lubbock, Texas 79410, USA
| | - Jane A Langdale
- Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Andrew D B Leakey
- Department of Plant Biology, Department of Crop Sciences, and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Illinois 61801, USA
| | - James C Liao
- Institute of Biological Chemistry, Academia Sinica, Taipei 11528, Taiwan
| | - Kuan-Jen Lu
- Institute of Biological Chemistry, Academia Sinica, Taipei 11528, Taiwan
| | - Maureen C McCann
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
| | - John K McKay
- Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Damaris A Odeny
- The International Crops Research Institute for the Semi-Arid Tropics–Eastern and Southern Africa, Gigiri 39063-00623, Nairobi, Kenya
| | | | - J Damien Platten
- International Rice Research Institute, Rice Breeding Innovations Platform, Los Baños, Laguna 4031, Philippines
| | - Ismail Rabbi
- International Institute of Tropical Agriculture (IITA), PMB 5320 Ibadan, Oyo, Nigeria
| | - Ellen Youngsoo Rim
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616, USA
| | - Pamela C Ronald
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616, USA
- Innovative Genomics Institute, Berkeley, California 94704, USA
| | - David E Salt
- School of Biosciences, University of Nottingham, Nottingham, NG7 2RD, UK
- Future Food Beacon of Excellence, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Alexandra M Shigenaga
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616, USA
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Marnin Wolfe
- Auburn University, Dept. of Crop Soil and Environmental Sciences, College of Agriculture, Auburn, Alabama 36849, USA
| | - Xiaowei Zhang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
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16
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Jeyasingh PD, Sherman RE, Prater C, Pulkkinen K, Ketola T. Adaptation to a limiting element involves mitigation of multiple elemental imbalances. J R Soc Interface 2023; 20:20220472. [PMID: 36596454 PMCID: PMC9810419 DOI: 10.1098/rsif.2022.0472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 12/05/2022] [Indexed: 01/05/2023] Open
Abstract
About 20 elements underlie biology and thus constrain biomass production. Recent systems-level observations indicate that altered supply of one element impacts the processing of most elements encompassing an organism (i.e. ionome). Little is known about the evolutionary tendencies of ionomes as populations adapt to distinct biogeochemical environments. We evolved the bacterium Serratia marcescens under five conditions (i.e. low carbon, nitrogen, phosphorus, iron or manganese) that limited the yield of the ancestor compared with replete medium, and measured the concentrations and use efficiency of these five, and five other elements. Both physiological responses of the ancestor, as well as evolutionary responses of descendants to experimental environments involved changes in the content and use efficiencies of the limiting element, and several others. Differences in coefficients of variation in elemental contents based on biological functions were evident, with those involved in biochemical building (C, N, P, S) varying least, followed by biochemical balance (Ca, K, Mg, Na), and biochemical catalysis (Fe, Mn). Finally, descendants evolved to mitigate elemental imbalances evident in the ancestor in response to limiting conditions. Understanding the tendencies of such ionomic responses will be useful to better forecast biological responses to geochemical changes.
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Affiliation(s)
- Punidan D. Jeyasingh
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, FI-40014, Finland
- Department of Integrative Biology, Oklahoma State University, 501 Life Sciences West, Stillwater, OK 74078, USA
| | - Ryan E. Sherman
- Department of Integrative Biology, Oklahoma State University, 501 Life Sciences West, Stillwater, OK 74078, USA
| | - Clay Prater
- Department of Integrative Biology, Oklahoma State University, 501 Life Sciences West, Stillwater, OK 74078, USA
| | - Katja Pulkkinen
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, FI-40014, Finland
| | - Tarmo Ketola
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, FI-40014, Finland
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17
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Study of the mineral contents of Matricaria pubescens and Brocchia cinerea from Algeria. ANNALES PHARMACEUTIQUES FRANÇAISES 2023; 81:107-114. [PMID: 35944698 DOI: 10.1016/j.pharma.2022.08.005] [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: 01/16/2022] [Revised: 07/05/2022] [Accepted: 08/01/2022] [Indexed: 01/07/2023]
Abstract
Two species of plants commonly used for mainly their therapeutic values and available in some herbalists shops, namely: Brocchia cinerea and Matricaria pubescens that both belong to asteraceae family, and encountered mainly in the Algerian desert, have drawn attention in the scope of assessing their mineral contents, in fact minerals play an important role in the plant homeostasis and metabolism, on the other hand they may influence the health conditions mainly due to toxicity, and also the benefits that the plant consumer could have, the current study aimed to assess the contents of Al, Cd, Cr, Cu, Fe, Hg, Ni, Pb, Zn, As, Na, K, Mg, P, S and SI, beside comparing the obtained results to other similar studies, the aerial parts of the plants are collected from several sites then mineralized and analyzed using ICP-AES and AAS, high levels of Na, K and Mg have been noted, on the other hands levels of metals were noted to be overall marginal, except for Al and Hg for the sample of Brocchia cinerea from El oued, the levels of As also seemed to be high in all the samples, inversely to the levels of S and P which seemed lower than those noted for other plants in paralleled studies, while that similar results were found for Zn, Fe, the chemical and geologic features of the soils may be the influencing factor. Additionally the current study may put first milestone for the establishment of national guidelines regarding the mineral contents of medicinal plants.
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18
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Nezamivand-Chegini M, Metzger S, Moghadam A, Tahmasebi A, Koprivova A, Eshghi S, Mohammadi-Dehchesmeh M, Kopriva S, Niazi A, Ebrahimie E. Integration of transcriptomic and metabolomic analyses provides insights into response mechanisms to nitrogen and phosphorus deficiencies in soybean. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 326:111498. [PMID: 36252857 DOI: 10.1016/j.plantsci.2022.111498] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 08/20/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Nitrogen (N) and phosphorus (P) are two essential plant macronutrients that can limit plant growth by different mechanisms. We aimed to shed light on how soybean respond to low nitrogen (LN), low phosphorus (LP) and their combined deficiency (LNP). Generally, these conditions triggered changes in gene expression of the same processes, including cell wall organization, defense response, response to oxidative stress, and photosynthesis, however, response was different in each condition. A typical primary response to LN and LP was detected also in soybean, i.e., the enhanced uptake of N and P, respectively, by upregulation of genes for the corresponding transporters. The regulation of genes involved in cell wall organization showed that in LP roots tended to produce more casparian strip, in LN more secondary wall biosynthesis occurred, and in LNP reduction in expression of genes involved in secondary wall production accompanied by cell wall loosening was observed. Flavonoid biosynthesis also showed distinct pattern of regulation in different conditions: more anthocyanin production in LP, and more isoflavonoid production in LN and LNP, which we confirmed also on the metabolite level. Interestingly, in soybean the nutrient deficiencies reduced defense response by lowering expression of genes involved in defense response, suggesting a role of N and P nutrition in plant disease resistance. In conclusion, we provide detailed information on how LN, LP, and LNP affect different processes in soybean roots on the molecular and physiological levels.
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Affiliation(s)
| | - Sabine Metzger
- MS Platform, Institute for Plant Sciences, Cluster of Excellence on Plant Sciences, University of Cologne, Cologne, Germany; Institute for Plant Sciences, Cluster of Excellence on Plant Sciences, University of Cologne, Cologne, Germany
| | - Ali Moghadam
- Institute of Biotechnology, Shiraz University, Shiraz, Iran
| | | | - Anna Koprivova
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences, University of Cologne, Cologne, Germany
| | - Saeid Eshghi
- Department of Horticultural Science, School of Agriculture, Shiraz University, Shiraz, Iran
| | | | - Stanislav Kopriva
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences, University of Cologne, Cologne, Germany
| | - Ali Niazi
- Institute of Biotechnology, Shiraz University, Shiraz, Iran.
| | - Esmaeil Ebrahimie
- Institute of Biotechnology, Shiraz University, Shiraz, Iran; School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide SA 5371, Australia; La Trobe Genomics Research Platform, School of Life Sciences, College of Science, Health and Engineering, La Trobe University, Melbourne, VIC 3086, Australia.
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19
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Zhou M, Zheng S. Multi-Omics Uncover the Mechanism of Wheat under Heavy Metal Stress. Int J Mol Sci 2022; 23:ijms232415968. [PMID: 36555610 PMCID: PMC9785819 DOI: 10.3390/ijms232415968] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/08/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Environmental pollution of heavy metals has received growing attention in recent years. Heavy metals such as cadmium, lead and mercury can cause physiological and morphological disturbances which adversely affect the growth and quality of crops. Wheat (Triticum aestivum L.) can accumulate high contents of heavy metals in its edible parts. Understanding wheat response to heavy metal stress and its management in decreasing heavy metal uptake and accumulation may help to improve its growth and grain quality. Very recently, emerging advances in heavy metal toxicity and phytoremediation methods to reduce heavy metal pollution have been made in wheat. Especially, the molecular mechanisms of wheat under heavy metal stress are increasingly being recognized. In this review, we focus on the recently described epigenomics, transcriptomics, proteomics, metabolomics, ionomics and multi-omics combination, as well as functional genes uncovering heavy metal stress in wheat. The findings in this review provide some insights into challenges and future recommendations for wheat under heavy metal stress.
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Affiliation(s)
- Min Zhou
- School of Life Sciences, Chongqing University, Chongqing 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing 401331, China
| | - Shigang Zheng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
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20
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Metal ion availability and homeostasis as drivers of metabolic evolution and enzyme function. Curr Opin Genet Dev 2022; 77:101987. [PMID: 36183585 DOI: 10.1016/j.gde.2022.101987] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/25/2022] [Accepted: 08/29/2022] [Indexed: 01/27/2023]
Abstract
Metal ions are potent catalysts and have been available for cellular biochemistry at all stages of evolution. Growing evidence suggests that metal catalysis was critical for the origin of the very first metabolic reactions. With approximately 80% of modern metabolic pathways being dependent on metal ions, metallocatalysis and homeostasis continue to be essential for intracellular metabolic networks and physiology. However, the genetic network that controls metal ion homeostasis and the impact of metal availability on metabolism is poorly understood. Here, we review recent work on gene and protein evolution relevant for better understanding metal ion biology and its role in metabolism. We highlight the importance of analysing the origin and evolution of enzyme catalysis in the context of catalytically relevant metal ions, summarise unanswered questions essential for developing a comprehensive understanding of metal ion homeostasis and advocate for the consideration of metal ion properties and availability in the design and directed evolution of novel enzymes and pathways.
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21
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Yin H, Yan Y, Hu W, Liu G, Zeng H, Wei Y, Shi H. Genome-wide association studies reveal genetic basis of ionomic variation in cassava. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:1212-1223. [PMID: 36239073 DOI: 10.1111/tpj.16006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/09/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
As one of the most important food crops, cassava (Manihot esculenta) is the main dietary source of micronutrients for about 1 billion people. However, the ionomic variation in cassava and the underlying genetic mechanisms remain unclear so far. Herein, genome-wide association studies were performed to reveal the specific single nucleotide polymorphisms (SNPs) that affect the ionomic variation in cassava. We identified 164 SNPs with P-values lower than the threshold located in 88 loci associated with divergent ionomic variations. Among them, 13 SNPs are related to both calcium (Ca) and magnesium (Mg), and many loci for different ionomic traits seem to be clustered on specific chromosome regions. Moreover, we identified the peak SNPs in the promoter regions of Sc10g003170 (encoding methionyl-tRNA synthetase [MetRS]) and Sc18g015190 (encoding the transcriptional regulatory protein AlgP) for nitrogen (N) and phosphorus (P) accumulation, respectively. Notably, these two SNPs (chr10_32807962 and chr18_31343738) were directly correlated with the transcript levels of Sc10g003170 (MetRS) and Sc18g015190 (AlgP), which positively modulated N accumulation and P concentration in cassava, respectively. Taken together, this study provides important insight into the genetic basis of cassava natural ionomic variation, which will promote genetic breeding to improve nutrient use and accumulation of elements in cassava.
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Affiliation(s)
- Hongyan Yin
- Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources (Provincial Ministry Building State Key Laboratory Breeding Base), Sanya Nanfan Research Institute, College of Tropical Crops, Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, Hainan University, Hainan Province, Sanya and Haikou, China
| | - Yu Yan
- Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources (Provincial Ministry Building State Key Laboratory Breeding Base), Sanya Nanfan Research Institute, College of Tropical Crops, Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, Hainan University, Hainan Province, Sanya and Haikou, China
- Hainan Yazhou Bay Seed Laboratory, Hainan Province, Sanya, China
| | - Wei Hu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 571101, Hainan Province, Haikou, Xueyuan Road 4, China
| | - Guoyin Liu
- Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources (Provincial Ministry Building State Key Laboratory Breeding Base), Sanya Nanfan Research Institute, College of Tropical Crops, Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, Hainan University, Hainan Province, Sanya and Haikou, China
- Hainan Yazhou Bay Seed Laboratory, Hainan Province, Sanya, China
| | - Hongqiu Zeng
- Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources (Provincial Ministry Building State Key Laboratory Breeding Base), Sanya Nanfan Research Institute, College of Tropical Crops, Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, Hainan University, Hainan Province, Sanya and Haikou, China
- Hainan Yazhou Bay Seed Laboratory, Hainan Province, Sanya, China
| | - Yunxie Wei
- Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources (Provincial Ministry Building State Key Laboratory Breeding Base), Sanya Nanfan Research Institute, College of Tropical Crops, Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, Hainan University, Hainan Province, Sanya and Haikou, China
- Hainan Yazhou Bay Seed Laboratory, Hainan Province, Sanya, China
| | - Haitao Shi
- Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources (Provincial Ministry Building State Key Laboratory Breeding Base), Sanya Nanfan Research Institute, College of Tropical Crops, Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, Hainan University, Hainan Province, Sanya and Haikou, China
- Hainan Yazhou Bay Seed Laboratory, Hainan Province, Sanya, China
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22
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Assunção AGL. The F-bZIP-regulated Zn deficiency response in land plants. PLANTA 2022; 256:108. [PMID: 36348172 PMCID: PMC9643250 DOI: 10.1007/s00425-022-04019-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 10/22/2022] [Indexed: 06/16/2023]
Abstract
This review describes zinc sensing and transcriptional regulation of the zinc deficiency response in Arabidopsis, and discusses how their evolutionary conservation in land plants facilitates translational approaches for improving the Zn nutritional value of crop species. Zinc is an essential micronutrient for all living organisms due to its presence in a large number of proteins, as a structural or catalytic cofactor. In plants, zinc homeostasis mechanisms comprise uptake from soil, transport and distribution throughout the plant to provide adequate cellular zinc availability. Here, I discuss the transcriptional regulation of the response to zinc deficiency and the zinc sensing mechanisms in Arabidopsis, and their evolutionary conservation in land plants. The Arabidopsis F-group basic region leucine-zipper (F-bZIP) transcription factors bZIP19 and bZIP23 function simultaneously as sensors of intracellular zinc status, by direct binding of zinc ions, and as the central regulators of the zinc deficiency response, with their target genes including zinc transporters from the ZRT/IRT-like Protein (ZIP) family and nicotianamine synthase enzymes that produce the zinc ligand nicotianamine. I note that this relatively simple mechanism of zinc sensing and regulation, together with the evolutionary conservation of F-bZIP transcription factors across land plants, offer important research opportunities. One of them is to use the F-bZIP-regulated zinc deficiency response as a tractable module for evolutionary and comparative functional studies. Another research opportunity is translational research in crop plants, modulating F-bZIP activity as a molecular switch to enhance zinc accumulation. This should become a useful plant-based solution to alleviate effects of zinc deficiency in soils, which impact crop production and crop zinc content, with consequences for human nutrition globally.
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Affiliation(s)
- Ana G L Assunção
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871, Frederiksberg, Denmark.
- CIBIO-InBIO, Research Centre in Biodiversity and Genetic Resources, University of Porto, 4485-661, Vairão, Portugal.
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23
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Filipiak M, Shields MW, Cairns SM, Grainger MNC, Wratten SD. The conserved and high K-to-Na ratio in sunflower pollen: Possible implications for bee health and plant-bee interactions. FRONTIERS IN PLANT SCIENCE 2022; 13:1042348. [PMID: 36388528 PMCID: PMC9664163 DOI: 10.3389/fpls.2022.1042348] [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: 09/12/2022] [Accepted: 10/13/2022] [Indexed: 06/16/2023]
Abstract
Sodium (Na) concentrations are low in plant tissues, and its metabolic function in plants is minor; however, Na is a key nutrient for plant consumers. Previous studies have thus far focused on Na concentration. Nevertheless, a balanced potassium (K) to Na ratio (K:Na) is more important than Na concentration alone since food with high K:Na has detrimental effects on consumers irrespective of Na concentration. Therefore, plants may actively regulate K:Na in their tissues and products, shaping plant-insect interactions. Studies considering nutritional aspects of plant-insect interactions have focused on nonreproductive tissues and nectar. In this study, we consider pollen as serving a primary reproductive function for plants as well as a food of pollinivores. Plants might regulate K:Na in pollen to affect their interactions with pollinivorous pollinators. To investigate whether such a mechanism exists, we manipulated Na concentrations in soil and measured the proportion of K, Na, and 13 other nutrient elements in the pollen of two sunflower (Helianthus annuus) cultivars. This approach allowed us to account for the overall nutritional quality of pollen by investigating the proportions of many elements that could correlate with the concentrations of K and Na. Of the elements studied, only the concentrations of Na and K were highly correlated. Pollen K:Na was high in both cultivars irrespective of Na fertilization, and it remained high regardless of pollen Na concentration. Interestingly, pollen K:Na did not decrease as pollen increased the Na concentration. We hypothesize that high K:Na in pollen might benefit plant fertilization and embryonic development; therefore, a tradeoff might occur between producing low K:Na pollen as a reward for pollinators and high K:Na pollen to optimize the plant fertilization process. This is the first study to provide data on pollen K:Na regulation by plants. Our findings broaden the understanding of plant-bee interactions and provide a foundation for a better understanding of the role of the soil-plant-pollen-pollinator pathway in nutrient cycling in ecosystems. Specifically, unexplored costs and tradeoffs related to balancing the K:Na by plants and pollinivores might play a role in past and current shaping of pollination ecology.
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Affiliation(s)
- Michał Filipiak
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Morgan W. Shields
- Bio-Protection Research Centre, Lincoln University, Lincoln, New Zealand
| | - Sarah M. Cairns
- Bio-Protection Research Centre, Lincoln University, Lincoln, New Zealand
| | | | - Stephen D. Wratten
- Bio-Protection Research Centre, Lincoln University, Lincoln, New Zealand
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24
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Mondaca P, Valenzuela P, Quiroz W, Valdenegro M, Abades S, Celis-Diez JL. Environmental conditions and plant physiology modulate Cu phytotoxicity in field-contaminated soils. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 246:114179. [PMID: 36244170 DOI: 10.1016/j.ecoenv.2022.114179] [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: 02/19/2022] [Revised: 09/30/2022] [Accepted: 10/09/2022] [Indexed: 06/16/2023]
Abstract
Foliar Cu concentration has been widely used as a biomarker of plant growth in phytotoxicity bioassays. This relation has helped find plant processes altered by Cu in dose-response experiments (a bivariate approach). However, when plants are grown in field conditions, their responses can vary in function of multiple variables, such as the environment, plant physiology, and other elements in plant (plant ionome). These sources of variability are commonly unreported, which could limit bioassays' utility. Thus, the present study aimed to assess and integrate the mentioned sources of variability on Cu phytotoxicity. Lettuce was used as plant model. Lettuces were grown in growth chambers with contrasting light and air humidity conditions and on two different field-contaminated soils (sandy and loamy soils). Results showed that environmental conditions significantly affected foliar Cu and plant growth, but this effect differed in the two studied soils. Foliar Cu was not a good biomarker of plant growth. In contrast, integrating the potential phytotoxicity effect with the plant's nutritional status allowed a better understanding of plant growth. We remarked on using a structural equation modeling approach (SEM) to integrate plant physiology and plant ionome as moderators of plant growth. Results showed that plant growth was primarily related to plant nutritional status rather than Cu phytotoxicity. Also, the foliar Cu concentration would affect plant nutritional status due to photosynthesis-related plant processes and cation balance. Finally, this research invites to state and include sources of variability when assessing phytotoxicity. This way, it is possible to advance toward understanding complex linked processes occurring in field conditions.
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Affiliation(s)
- Pedro Mondaca
- Escuela de Agronomía, Pontificia Universidad Católica de Valparaíso, Chile
| | - Patricio Valenzuela
- Departamento de Sistemas y Recursos Naturales, Universidad Politécnica de Madrid, Madrid, Spain
| | - Waldo Quiroz
- Instituto de Química, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Monika Valdenegro
- Escuela de Agronomía, Pontificia Universidad Católica de Valparaíso, Chile
| | - Sebastián Abades
- GEMA Center for Genomics, Ecology & Environment, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
| | - Juan L Celis-Diez
- Escuela de Agronomía, Pontificia Universidad Católica de Valparaíso, Chile; Instituto de Ecología y Biodiversidad, Chile.
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25
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Houdegbe AC, Achigan-Dako EG, Sogbohossou EOD, Schranz ME, Odindo AO, Sibiya J. Leaf elemental composition analysis in spider plant [ Gynandropsis gynandra L. (Briq.)] differentiates three nutritional groups. FRONTIERS IN PLANT SCIENCE 2022; 13:841226. [PMID: 36119621 PMCID: PMC9478508 DOI: 10.3389/fpls.2022.841226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 08/04/2022] [Indexed: 06/15/2023]
Abstract
Understanding the genetic variability within a plant species is paramount in implementing a successful breeding program. Spider plant (Gynandropsis gynandra) is an orphan leafy vegetable and an extraordinary source of vitamins, secondary metabolites and minerals, representing an important resource for combatting malnutrition. However, an evaluation of the leaf elemental composition, using a worldwide germplasm collection to inform breeding programs and the species valorization in human nutrition is still lacking. The present study aimed to profile the leaf elemental composition of G. gynandra and depict any potential geographical signature using a collection of 70 advanced lines derived from accessions originating from Asia and Eastern, Southern and West Africa. The collection was grown in a greenhouse using a 9 × 8 alpha lattice design with two replications in 2020 and 2021. Inductively coupled plasma-optical emission spectrometry was used to profile nine minerals contents. A significant difference (p < 0.05) was observed among the lines for all nine minerals. Microelements such as iron, zinc, copper and manganese contents ranged from 12.59-430.72, 16.98-166.58, 19.04-955.71, 5.39-25.10 mg kg-1 dry weight, respectively, while the concentrations of macroelements such as potassium, calcium, phosphorus and magnesium varied in the ranges of 9992.27-49854.23, 8252.80-33681.21, 3633.55-14216.16, 2068.03-12475.60 mg kg-1 dry weight, respectively. Significant and positive correlations were observed between iron and zinc and calcium and magnesium. Zinc, calcium, phosphorus, copper, magnesium, and manganese represented landmark elements in the genotypes. Eastern and Southern African genotypes were clustered together in group 1 with higher phosphorus, copper and zinc contents than Asian and West African lines, which clustered in group 2 and were characterized by higher calcium, magnesium and manganese contents. An additional outstanding group 3 of six genotypes was identified with high iron, zinc, magnesium, manganese and calcium contents and potential candidates for cultivar release. The genotype × year interaction variance was greater than the genotypic variance, which might translate to phenotypic plasticity in the species. Broad-sense heritability ranged from low to high and was element-specific. The present results reveal the leaf minerals diversity in spider plant and represent a baseline for implementing a minerals-based breeding program for human nutrition.
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Affiliation(s)
- Aristide Carlos Houdegbe
- Discipline of Plant Breeding, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
- Laboratory of Genetics, Biotechnology and Seed Science, Faculty of Agronomic Sciences, University of Abomey-Calavi, Abomey-Calavi, Benin
| | - Enoch G. Achigan-Dako
- Laboratory of Genetics, Biotechnology and Seed Science, Faculty of Agronomic Sciences, University of Abomey-Calavi, Abomey-Calavi, Benin
| | - E. O. Dêêdi Sogbohossou
- Laboratory of Genetics, Biotechnology and Seed Science, Faculty of Agronomic Sciences, University of Abomey-Calavi, Abomey-Calavi, Benin
| | - M. Eric Schranz
- Biosystematics Group, Wageningen University, Wageningen, Netherlands
| | - Alfred O. Odindo
- Discipline of Crop Science, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Julia Sibiya
- Discipline of Plant Breeding, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
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26
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Palacio S, Cera A, Escudero A, Luzuriaga AL, Sánchez AM, Mota JF, Pérez‐Serrano Serrano M, Merlo ME, Martínez‐Hernández F, Salmerón‐Sánchez E, Mendoza‐Fernández AJ, Pérez‐García FJ, Montserrat‐Martí G, Tejero P. Recent and ancient evolutionary events shaped plant elemental composition of edaphic endemics: a phylogeny-wide analysis of Iberian gypsum plants. THE NEW PHYTOLOGIST 2022; 235:2406-2423. [PMID: 35704043 PMCID: PMC9545410 DOI: 10.1111/nph.18309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 05/24/2022] [Indexed: 05/19/2023]
Abstract
The analysis of plant elemental composition and the underlying factors affecting its variation are a current hot topic in ecology. Ecological adaptation to atypical soils may shift plant elemental composition. However, no previous studies have evaluated its relevance against other factors such as phylogeny, climate or individual soil conditions. We evaluated the effect of the phylogeny, environment (climate, soil), and affinity to gypsum soils on the elemental composition of 83 taxa typical of Iberian gypsum ecosystems. We used a new statistical procedure (multiple phylogenetic variance decomposition, MPVD) to decompose total explained variance by different factors across all nodes in the phylogenetic tree of target species (covering 120 million years of Angiosperm evolution). Our results highlight the relevance of phylogeny on the elemental composition of plants both at early (with the development of key preadaptive traits) and recent divergence times (diversification of the Iberian gypsum flora concurrent with Iberian gypsum deposit accumulation). Despite the predominant phylogenetic effect, plant adaptation to gypsum soils had a strong impact on the elemental composition of plants, particularly on sulphur concentrations, while climate and soil effects were smaller. Accordingly, we detected a convergent evolution of gypsum specialists from different lineages on increased sulphur and magnesium foliar concentrations.
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Affiliation(s)
- Sara Palacio
- Instituto Pirenaico de Ecología (IPE‐CSIC)Av. Nuestra Señora de la Victoria 1622700JacaHuescaSpain
| | - Andreu Cera
- Instituto Pirenaico de Ecología (IPE‐CSIC)Av. Nuestra Señora de la Victoria 1622700JacaHuescaSpain
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals (BEECA), Secció de Botànica i Micologia, Facultat de BiologiaUniversitat de BarcelonaDiagonal 64308028BarcelonaSpain
| | - Adrián Escudero
- Área de Biodiversidad y Conservación, Departamento de Biología y Geología, Física y Química InorgánicaUniversidad Rey Juan Carlos28933Móstoles, MadridSpain
| | - Arantzazu L. Luzuriaga
- Área de Biodiversidad y Conservación, Departamento de Biología y Geología, Física y Química InorgánicaUniversidad Rey Juan Carlos28933Móstoles, MadridSpain
| | - Ana M. Sánchez
- Área de Biodiversidad y Conservación, Departamento de Biología y Geología, Física y Química InorgánicaUniversidad Rey Juan Carlos28933Móstoles, MadridSpain
| | - Juan Francisco Mota
- Departamento de Biología y Geología, CEI·MAR and CECOUALUniversidad de Almería04120AlmeríaSpain
| | | | - M. Encarnación Merlo
- Departamento de Biología y Geología, CEI·MAR and CECOUALUniversidad de Almería04120AlmeríaSpain
| | | | | | - Antonio Jesús Mendoza‐Fernández
- Departamento de Biología y Geología, CEI·MAR and CECOUALUniversidad de Almería04120AlmeríaSpain
- Departamento de Botánica, Unidad de Conservación VegetalUniversidad de Granada18071GranadaSpain
| | | | | | - Pablo Tejero
- Instituto Pirenaico de Ecología (IPE‐CSIC)Av. Nuestra Señora de la Victoria 1622700JacaHuescaSpain
- Botanika Saila, Sociedad de Ciencias AranzadiZorroagagaina 1120014Donostia‐San SebastianGipuzkoaSpain
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27
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Babele PK, Kudapa H, Singh Y, Varshney RK, Kumar A. Mainstreaming orphan millets for advancing climate smart agriculture to secure nutrition and health. FRONTIERS IN PLANT SCIENCE 2022; 13:902536. [PMID: 36035707 PMCID: PMC9412166 DOI: 10.3389/fpls.2022.902536] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 07/18/2022] [Indexed: 05/29/2023]
Abstract
The ever-changing climate and the current COVID-19 pandemic compound the problems and seriously impact agriculture production, resulting in socio-economic insecurities and imposing health implications globally. Most of the poor and malnourished population in the developing countries depends on agriculture for food, income, and employment. Impact of climate change together with the COVID-19 outbreak revealed immense problems highlighting the importance of mainstreaming climate-resilient and low input crops with more contemporary agriculture practices. Orphan millets play a vital role in the poor and malnourished population's livelihood, food and nutrition security. Recognizing their unique potential, the United Nations-Food and Agriculture Organization has announced the year 2023 as the "International Year of Millets". However, despite the unique properties for present and future agriculture of orphan millets, their cultivation is declining in many countries. As a result, millets have gained attention from researchers which eventually decelerated "multi-omics" resource generation. This review summarizes the benefits of millets and major barriers/ bottlenecks in their improvement. We also discuss the pre- and post-harvest technologies; policies required to introduce and establish millets in mainstream agriculture. To improve and ensure the livelihood of the poor/malnourished population, intensive efforts are urgently needed in advancing the research and development, implementing pre- and post-harvest technological intervention strategies, and making favorable policies for orphan crops to accomplish food and nutrition security. National and international collaborations are also indispensable to address the uncertain effects of climate change and COVID-19.
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Affiliation(s)
- Piyoosh K. Babele
- College of Agriculture, Rani Lakshmi Bai Central Agricultural University, Jhansi, Uttar Pradesh, India
| | - Himabindu Kudapa
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Yogeshwar Singh
- College of Agriculture, Rani Lakshmi Bai Central Agricultural University, Jhansi, Uttar Pradesh, India
| | - Rajeev K. Varshney
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
- Murdoch's Centre for Crop Research & Food Innovation, State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, Australia
| | - Anil Kumar
- College of Agriculture, Rani Lakshmi Bai Central Agricultural University, Jhansi, Uttar Pradesh, India
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28
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Lee SB, Kim GJ, Shin JD, Chung W, Park SK, Choi GH, Park SW, Park YJ. Genome-Scale Profiling and High-Throughput Analyses Unravel the Genetic Basis of Arsenic Content Variation in Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:905842. [PMID: 35958208 PMCID: PMC9361212 DOI: 10.3389/fpls.2022.905842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
Abstract
Ionomics, the study of the composition of mineral nutrients and trace elements in organisms that represent the inorganic component of cells and tissues, has been widely studied to explore to unravel the molecular mechanism regulating the elemental composition of plants. However, the genetic factors of rice subspecies in the interaction between arsenic and functional ions have not yet been explained. Here, the correlation between As and eight essential ions in a rice core collection was analyzed, taking into account growing condition and genetic factors. The results demonstrated that the correlation between As and essential ions was affected by genetic factors and growing condition, but it was confirmed that the genetic factor was slightly larger with the heritability for arsenic content at 53%. In particular, the cluster coefficient of japonica (0.428) was larger than that of indica (0.414) in the co-expression network analysis for 23 arsenic genes, and it was confirmed that the distance between genes involved in As induction and detoxification of japonica was far than that of indica. These findings provide evidence that japonica populations could accumulate more As than indica populations. In addition, the cis-eQTLs of AIR2 (arsenic-induced RING finger protein) were isolated through transcriptome-wide association studies, and it was confirmed that AIR2 expression levels of indica were lower than those of japonica. This was consistent with the functional haplotype results for the genome sequence of AIR2, and finally, eight rice varieties with low AIR2 expression and arsenic content were selected. In addition, As-related QTLs were identified on chromosomes 5 and 6 under flooded and intermittently flooded conditions through genome-scale profiling. Taken together, these results might assist in developing markers and breeding plans to reduce toxic element content and breeding high-quality rice varieties in future.
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Affiliation(s)
- Sang-Beom Lee
- Crop Foundation Research Division, National Institute of Crop Science, Wanju, South Korea
| | - Gyeong-Jin Kim
- Residual Agrochemical Assessment Division, National Institute of Agriculture Science, Wanju, South Korea
| | - Jung-Du Shin
- Bio-Technology of Multidisciplinary Sciences Co., Wanju, South Korea
| | - Woojin Chung
- Department of Environmental Energy Engineering, Kyonggi University, Suwon, South Korea
| | - Soo-Kwon Park
- Crop Foundation Research Division, National Institute of Crop Science, Wanju, South Korea
| | - Geun-Hyoung Choi
- Residual Agrochemical Assessment Division, National Institute of Agriculture Science, Wanju, South Korea
| | - Sang-Won Park
- Reserch Policy Bureau, Rural Development Administration, Wanju, South Korea
| | - Yong-Jin Park
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, South Korea
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29
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Zhang Y, He J, Jin J, Ren C. Recent advances in the application of metallomics in diagnosis and prognosis of human cancer. Metallomics 2022; 14:6596881. [PMID: 35648480 DOI: 10.1093/mtomcs/mfac037] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 05/12/2022] [Indexed: 11/13/2022]
Abstract
Metals play a critical role in human health and diseases. In recent years, metallomics has been introduced and extensively applied to investigate the distribution, regulation, function, and crosstalk of metal(loid) ions in various physiological and pathological processes. Based on high-throughput multielemental analytical techniques and bioinformatics methods, it is possible to elucidate the correlation between the metabolism and homeostasis of diverse metals and complex diseases, in particular for cancer. This review aims to provide an overview of recent progress made in the application of metallomics in cancer research. We mainly focuses on the studies about metallomic profiling of different human biological samples for several major types of cancer, which reveal distinct and dynamic patterns of metal ion contents and the potential benefits of using such information in the detection and prognosis of these malignancies. Elevated levels of copper appear to be a significant risk factor for various cancers, and each type of cancer has a unique distribution of metals in biofluids, hair/nails, and tumor-affected tissues. Furthermore, associations between genetic variations in representative metalloprotein genes and cancer susceptibility have also been demonstrated. Overall, metallomics not only offers a better understanding of the relationship between metal dyshomeostasis and the development of cancer but also facilitates the discovery of new diagnostic and prognostic markers for cancer translational medicine.
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Affiliation(s)
- Yan Zhang
- Shenzhen Key Laboratory of Marine Bioresources and Ecology, Brain Disease and Big Data Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518055, Guangdong Province, P. R. China.,Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, 518055, Guangdong Province, P. R. China
| | - Jie He
- Shenzhen Key Laboratory of Marine Bioresources and Ecology, Brain Disease and Big Data Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518055, Guangdong Province, P. R. China
| | - Jiao Jin
- Shenzhen Key Laboratory of Marine Bioresources and Ecology, Brain Disease and Big Data Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518055, Guangdong Province, P. R. China
| | - Cihan Ren
- Experimental High School Attached to Beijing Normal University, Beijing 100052, P. R. China
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30
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Huang XY, Hu DW, Zhao FJ. Molybdenum: More than an essential element. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:1766-1774. [PMID: 34864981 DOI: 10.1093/jxb/erab534] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 12/03/2021] [Indexed: 06/13/2023]
Abstract
Molybdenum (Mo) is an essential element for almost all living organisms. After being taken up into the cells as molybdate, it is incorporated into the molybdenum cofactor, which functions as the active site of several molybdenum-requiring enzymes and thus plays crucial roles in multiple biological processes. The uptake and transport of molybdate is mainly mediated by two types of molybdate transporters. The homeostasis of Mo in plant cells is tightly controlled, and such homeostasis likely plays vital roles in plant adaptation to local environments. Recent evidence suggests that Mo is more than an essential element required for plant growth and development; it is also involved in local adaptation to coastal salinity. In this review, we summarize recent research progress on molybdate uptake and transport, molybdenum homeostasis network in plants, and discuss the potential roles of the molybdate transporter in plant adaptation to their local environment.
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Affiliation(s)
- Xin-Yuan Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Da-Wei Hu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Fang-Jie Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
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31
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Assunção AGL, Cakmak I, Clemens S, González-Guerrero M, Nawrocki A, Thomine S. Micronutrient homeostasis in plants for more sustainable agriculture and healthier human nutrition. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:1789-1799. [PMID: 35134869 PMCID: PMC8921004 DOI: 10.1093/jxb/erac014] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 01/28/2022] [Indexed: 05/03/2023]
Abstract
The provision of sustainable, sufficient, and nutritious food to the growing population is a major challenge for agriculture and the plant research community. In this respect, the mineral micronutrient content of food crops deserves particular attention. Micronutrient deficiencies in cultivated soils and plants are a global problem that adversely affects crop production and plant nutritional value, as well as human health and well-being. In this review, we call for awareness of the importance and relevance of micronutrients in crop production and quality. We stress the need for better micronutrient nutrition in human populations, not only in developing but also in developed nations, and describe strategies to identify and characterize new varieties with high micronutrient content. Furthermore, we explain how adequate nutrition of plants with micronutrients impacts metabolic functions and the capacity of plants to express tolerance mechanisms against abiotic and biotic constraints. Finally, we provide a brief overview and a critical discussion on current knowledge, future challenges, and specific technological needs for research on plant micronutrient homeostasis. Research in this area is expected to foster the sustainable development of nutritious and healthy food crops for human consumption.
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Affiliation(s)
- Ana G L Assunção
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark
- CIBIO-InBIO, Research Centre in Biodiversity and Genetic Resources, University of Porto, 4485-661 Vairão, Portugal
| | - Ismail Cakmak
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey
| | - Stephan Clemens
- Department of Plant Physiology and Faculty of Life Sciences: Food, Nutrition and Health, University of Bayreuth, 95440 Bayreuth, Germany
| | - Manuel González-Guerrero
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcón (Madrid), Spain
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Jin X, Zou Z, Wu Z, Liu C, Yan S, Peng Y, Lei Z, Zhou Z. Genome-Wide Association Study Reveals Genomic Regions Associated With Molybdenum Accumulation in Wheat Grains. FRONTIERS IN PLANT SCIENCE 2022; 13:854966. [PMID: 35310638 PMCID: PMC8924584 DOI: 10.3389/fpls.2022.854966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
Molybdenum (Mo) is an essential micronutrient for almost all organisms. Wheat, a major staple crop worldwide, is one of the main dietary sources of Mo. However, the genetic basis for the variation of Mo content in wheat grains remains largely unknown. Here, a genome-wide association study (GWAS) was performed on the Mo concentration in the grains of 207 wheat accessions to dissect the genetic basis of Mo accumulation in wheat grains. As a result, 77 SNPs were found to be significantly associated with Mo concentration in wheat grains, among which 52 were detected in at least two sets of data and distributed on chromosome 2A, 7B, and 7D. Moreover, 48 out of the 52 common SNPs were distributed in the 726,761,412-728,132,521 bp genomic region of chromosome 2A. Three putative candidate genes, including molybdate transporter 1;2 (TraesCS2A02G496200), molybdate transporter 1;1 (TraesCS2A02G496700), and molybdopterin biosynthesis protein CNX1 (TraesCS2A02G497200), were identified in this region. These findings provide new insights into the genetic basis for Mo accumulation in wheat grains and important information for further functional characterization and breeding to improve wheat grain quality.
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Affiliation(s)
- Xiaojie Jin
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan, China
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Zhaojun Zou
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhengqing Wu
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Congcong Liu
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Songxian Yan
- Department of Resources and Environment, Moutai Institute, Renhuai, China
| | - Yanchun Peng
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Zhensheng Lei
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Zhengfu Zhou
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
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Zeng H, Hu W, Liu G, Xu H, Wei Y, Zhang J, Shi H. Microbiome-wide association studies between phyllosphere microbiota and ionome highlight the beneficial symbiosis of Lactococcus lactis in alleviating aluminium in cassava. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 171:66-74. [PMID: 34971956 DOI: 10.1016/j.plaphy.2021.12.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/23/2021] [Accepted: 12/25/2021] [Indexed: 06/14/2023]
Abstract
The phyllosphere is one of the most abundant habitats for global microbiota. The ionome is the composition of mineral elements in plants. The correlation between phyllosphere microbiota and the ionome remains elusive in plants, especially in the most important tropical crop cassava. In this study, microbiome-wide association studies (MWASs) of thirty varieties were performed to reveal the association between phyllosphere microbiota and ionomic variations in cassava. Annotation of metagenomic species identified some species that were significantly correlated with ionomic variations in cassava. Among them, Lactococcus lactis abundance was negatively associated with leaf aluminium (Al) levels but positively related to leaf potassium (K) levels. Notably, both the reference and isolated L. lactis showed strong binding capacity to Al. Further bacterial transplantation of isolated L. lactis could significantly decrease endogenous Al levels but increase K levels in cassava, and it can also lead to increased citric acid and lactic acid levels as well as higher transcript levels of K uptake-related genes. Taken together, this study reveals the involvement of phyllosphere microbiota in ionomic variation in cassava, and the correlation between L. lactis abundance and Al and K levels provides novel insights into alleviating Al accumulation and promoting K uptake simultaneously.
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Affiliation(s)
- Hongqiu Zeng
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, Hainan province, 570228, China
| | - Wei Hu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, Hainan province, 571101, China
| | - Guoyin Liu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, Hainan province, 570228, China
| | - Haoran Xu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, Hainan province, 570228, China
| | - Yunxie Wei
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, Hainan province, 570228, China
| | - Jiachao Zhang
- College of Food Science and Engineering, Hainan University, Haikou, Hainan province, 570228, China.
| | - Haitao Shi
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, Hainan province, 570228, China.
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Soil Salinity, a Serious Environmental Issue and Plant Responses: A Metabolomics Perspective. Metabolites 2021; 11:metabo11110724. [PMID: 34822381 PMCID: PMC8620211 DOI: 10.3390/metabo11110724] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/16/2021] [Accepted: 10/18/2021] [Indexed: 12/12/2022] Open
Abstract
The effects of global warming have increasingly led to devastating environmental stresses, such as heat, salinity, and drought. Soil salinization is a serious environmental issue and results in detrimental abiotic stress, affecting 7% of land area and 33% of irrigated lands worldwide. The proportion of arable land facing salinity is expected to rise due to increasing climate change fuelled by anthropogenic activities, exacerbating the threat to global food security for the exponentially growing populace. As sessile organisms, plants have evolutionarily developed mechanisms that allow ad hoc responses to salinity stress. The orchestrated mechanisms include signalling cascades involving phytohormones, kinases, reactive oxygen species (ROS), and calcium regulatory networks. As a pillar in a systems biology approach, metabolomics allows for comprehensive interrogation of the biochemistry and a deconvolution of molecular mechanisms involved in plant responses to salinity. Thus, this review highlights soil salinization as a serious environmental issue and points to the negative impacts of salinity on plants. Furthermore, the review summarises mechanisms regulating salinity tolerance on molecular, cellular, and biochemical levels with a focus on metabolomics perspectives. This critical synthesis of current literature is an opportunity to revisit the current models regarding plant responses to salinity, with an invitation to further fundamental research for novel and actionable insights.
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Busoms S, Terés J, Yant L, Poschenrieder C, Salt DE. Adaptation to coastal soils through pleiotropic boosting of ion and stress hormone concentrations in wild Arabidopsis thaliana. THE NEW PHYTOLOGIST 2021; 232:208-220. [PMID: 34153129 PMCID: PMC8429122 DOI: 10.1111/nph.17569] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 06/16/2021] [Indexed: 05/05/2023]
Abstract
Local adaptation in coastal areas is driven chiefly by tolerance to salinity stress. To survive high salinity, plants have evolved mechanisms to specifically tolerate sodium. However, the pathways that mediate adaptive changes in these conditions reach well beyond Na+ . Here we perform a high-resolution genetic, ionomic, and functional study of the natural variation in Molybdenum transporter 1 (MOT1) associated with coastal Arabidopsis thaliana accessions. We quantify the fitness benefits of a specific deletion-harbouring allele (MOT1DEL ) present in coastal habitats that is associated with lower transcript expression and molybdenum accumulation. Analysis of the leaf ionome revealed that MOT1DEL plants accumulate more copper (Cu) and less sodium (Na+ ) than plants with the noncoastal MOT1 allele, revealing a complex interdependence in homeostasis of these three elements. Our results indicate that under salinity stress, reduced MOT1 function limits leaf Na+ accumulation through abscisic acid (ABA) signalling. Enhanced ABA biosynthesis requires Cu. This demand is met in Cu deficient coastal soils through MOT1DEL increasing the expression of SPL7 and the copper transport protein COPT6. MOT1DEL is able to deliver a pleiotropic suite of phenotypes that enhance salinity tolerance in coastal soils deficient in Cu. This is achieved by inducing ABA biosynthesis and promoting reduced uptake or better compartmentalization of Na+ , leading to coastal adaptation.
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Affiliation(s)
- Silvia Busoms
- Plant Physiology Laboratory, Bioscience Faculty, Universitat Autònoma de Barcelona. Carrer de la Vall Moronta s/n, E-08193 Bellaterra, Barcelona (Spain)
- Future Food Beacon and School of Biosciences, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Joana Terés
- Plant Physiology Laboratory, Bioscience Faculty, Universitat Autònoma de Barcelona. Carrer de la Vall Moronta s/n, E-08193 Bellaterra, Barcelona (Spain)
| | - Levi Yant
- Future Food Beacon and School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Charlotte Poschenrieder
- Plant Physiology Laboratory, Bioscience Faculty, Universitat Autònoma de Barcelona. Carrer de la Vall Moronta s/n, E-08193 Bellaterra, Barcelona (Spain)
| | - David E Salt
- Future Food Beacon and School of Biosciences, University of Nottingham, Nottingham NG7 2RD, United Kingdom
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Singh D, Chaudhary P, Taunk J, Singh CK, Singh D, Tomar RSS, Aski M, Konjengbam NS, Raje RS, Singh S, Sengar RS, Yadav RK, Pal M. Fab Advances in Fabaceae for Abiotic Stress Resilience: From 'Omics' to Artificial Intelligence. Int J Mol Sci 2021; 22:10535. [PMID: 34638885 PMCID: PMC8509049 DOI: 10.3390/ijms221910535] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/17/2021] [Accepted: 09/23/2021] [Indexed: 11/16/2022] Open
Abstract
Legumes are a better source of proteins and are richer in diverse micronutrients over the nutritional profile of widely consumed cereals. However, when exposed to a diverse range of abiotic stresses, their overall productivity and quality are hugely impacted. Our limited understanding of genetic determinants and novel variants associated with the abiotic stress response in food legume crops restricts its amelioration. Therefore, it is imperative to understand different molecular approaches in food legume crops that can be utilized in crop improvement programs to minimize the economic loss. 'Omics'-based molecular breeding provides better opportunities over conventional breeding for diversifying the natural germplasm together with improving yield and quality parameters. Due to molecular advancements, the technique is now equipped with novel 'omics' approaches such as ionomics, epigenomics, fluxomics, RNomics, glycomics, glycoproteomics, phosphoproteomics, lipidomics, regulomics, and secretomics. Pan-omics-which utilizes the molecular bases of the stress response to identify genes (genomics), mRNAs (transcriptomics), proteins (proteomics), and biomolecules (metabolomics) associated with stress regulation-has been widely used for abiotic stress amelioration in food legume crops. Integration of pan-omics with novel omics approaches will fast-track legume breeding programs. Moreover, artificial intelligence (AI)-based algorithms can be utilized for simulating crop yield under changing environments, which can help in predicting the genetic gain beforehand. Application of machine learning (ML) in quantitative trait loci (QTL) mining will further help in determining the genetic determinants of abiotic stress tolerance in pulses.
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Affiliation(s)
- Dharmendra Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Priya Chaudhary
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Jyoti Taunk
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Chandan Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Deepti Singh
- Department of Botany, Meerut College, Meerut 250001, India
| | - Ram Sewak Singh Tomar
- College of Horticulture and Forestry, Rani Lakshmi Bai Central Agricultural University, Jhansi 284003, India
| | - Muraleedhar Aski
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Noren Singh Konjengbam
- College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University, Imphal 793103, India
| | - Ranjeet Sharan Raje
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Sanjay Singh
- ICAR- National Institute of Plant Biotechnology, LBS Centre, Pusa Campus, New Delhi 110012, India
| | - Rakesh Singh Sengar
- College of Biotechnology, Sardar Vallabh Bhai Patel Agricultural University, Meerut 250001, India
| | - Rajendra Kumar Yadav
- Department of Genetics and Plant Breeding, Chandra Shekhar Azad University of Agriculture and Technology, Kanpur 208002, India
| | - Madan Pal
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
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Singhal RK, Saha D, Skalicky M, Mishra UN, Chauhan J, Behera LP, Lenka D, Chand S, Kumar V, Dey P, Indu, Pandey S, Vachova P, Gupta A, Brestic M, El Sabagh A. Crucial Cell Signaling Compounds Crosstalk and Integrative Multi-Omics Techniques for Salinity Stress Tolerance in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:670369. [PMID: 34484254 PMCID: PMC8414894 DOI: 10.3389/fpls.2021.670369] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 05/28/2021] [Indexed: 10/29/2023]
Abstract
In the era of rapid climate change, abiotic stresses are the primary cause for yield gap in major agricultural crops. Among them, salinity is considered a calamitous stress due to its global distribution and consequences. Salinity affects plant processes and growth by imposing osmotic stress and destroys ionic and redox signaling. It also affects phytohormone homeostasis, which leads to oxidative stress and eventually imbalances metabolic activity. In this situation, signaling compound crosstalk such as gasotransmitters [nitric oxide (NO), hydrogen sulfide (H2S), hydrogen peroxide (H2O2), calcium (Ca), reactive oxygen species (ROS)] and plant growth regulators (auxin, ethylene, abscisic acid, and salicylic acid) have a decisive role in regulating plant stress signaling and administer unfavorable circumstances including salinity stress. Moreover, recent significant progress in omics techniques (transcriptomics, genomics, proteomics, and metabolomics) have helped to reinforce the deep understanding of molecular insight in multiple stress tolerance. Currently, there is very little information on gasotransmitters and plant growth regulator crosstalk and inadequacy of information regarding the integration of multi-omics technology during salinity stress. Therefore, there is an urgent need to understand the crucial cell signaling crosstalk mechanisms and integrative multi-omics techniques to provide a more direct approach for salinity stress tolerance. To address the above-mentioned words, this review covers the common mechanisms of signaling compounds and role of different signaling crosstalk under salinity stress tolerance. Thereafter, we mention the integration of different omics technology and compile recent information with respect to salinity stress tolerance.
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Affiliation(s)
| | - Debanjana Saha
- Department of Biotechnology, Centurion University of Technology and Management, Bhubaneswar, India
| | - Milan Skalicky
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Prague, Czechia
| | - Udit N. Mishra
- Faculty of Agriculture, Sri Sri University, Cuttack, India
| | - Jyoti Chauhan
- Narayan Institute of Agricultural Sciences, Gopal Narayan Singh University, Jamuhar, India
| | - Laxmi P. Behera
- Department of Agriculture Biotechnology, Orissa University of Agriculture and Technology, Bhubaneswar, India
| | - Devidutta Lenka
- Department of Plant Breeding and Genetics, Orissa University of Agriculture and Technology, Bhubaneswar, India
| | - Subhash Chand
- ICAR-Indian Grassland and Fodder Research Institute, Jhansi, India
| | - Vivek Kumar
- Institute of Agriculture Sciences, Banaras Hindu University, Varanasi, India
| | - Prajjal Dey
- Faculty of Agriculture, Sri Sri University, Cuttack, India
| | - Indu
- ICAR-Indian Grassland and Fodder Research Institute, Jhansi, India
| | - Saurabh Pandey
- Department of Agriculture, Guru Nanak Dev University, Amritsar, India
| | - Pavla Vachova
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Prague, Czechia
| | - Aayushi Gupta
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Prague, Czechia
| | - Marian Brestic
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Prague, Czechia
- Department of Plant Physiology, Slovak University of Agriculture in Nitra, Nitra, Slovakia
| | - Ayman El Sabagh
- Department of Agronomy, Faculty of Agriculture, University of Kafrelsheikh, Kafr El Sheikh, Egypt
- Department of Field Crops, Faculty of Agriculture, Siirt University, Siirt, Turkey
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Baseggio M, Murray M, Wu D, Ziegler G, Kaczmar N, Chamness J, Hamilton JP, Buell CR, Vatamaniuk OK, Buckler ES, Smith ME, Baxter I, Tracy WF, Gore MA. Genome-wide association study suggests an independent genetic basis of zinc and cadmium concentrations in fresh sweet corn kernels. G3 (BETHESDA, MD.) 2021; 11:6287658. [PMID: 34849806 PMCID: PMC8496296 DOI: 10.1093/g3journal/jkab186] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 05/25/2021] [Indexed: 01/05/2023]
Abstract
Despite being one of the most consumed vegetables in the United States, the elemental profile of sweet corn (Zea mays L.) is limited in its dietary contributions. To address this through genetic improvement, a genome-wide association study was conducted for the concentrations of 15 elements in fresh kernels of a sweet corn association panel. In concordance with mapping results from mature maize kernels, we detected a probable pleiotropic association of zinc and iron concentrations with nicotianamine synthase5 (nas5), which purportedly encodes an enzyme involved in synthesis of the metal chelator nicotianamine. In addition, a pervasive association signal was identified for cadmium concentration within a recombination suppressed region on chromosome 2. The likely causal gene underlying this signal was heavy metal ATPase3 (hma3), whose counterpart in rice, OsHMA3, mediates vacuolar sequestration of cadmium and zinc in roots, whereby regulating zinc homeostasis and cadmium accumulation in grains. In our association panel, hma3 associated with cadmium but not zinc accumulation in fresh kernels. This finding implies that selection for low cadmium will not affect zinc levels in fresh kernels. Although less resolved association signals were detected for boron, nickel, and calcium, all 15 elements were shown to have moderate predictive abilities via whole-genome prediction. Collectively, these results help enhance our genomics-assisted breeding efforts centered on improving the elemental profile of fresh sweet corn kernels.
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Affiliation(s)
- Matheus Baseggio
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Matthew Murray
- Department of Agronomy, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Di Wu
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Gregory Ziegler
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Nicholas Kaczmar
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - James Chamness
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - John P Hamilton
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Olena K Vatamaniuk
- Soil and Crop Sciences Section, Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Edward S Buckler
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.,Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA.,US Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, NY 14853, USA
| | - Margaret E Smith
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Ivan Baxter
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - William F Tracy
- Department of Agronomy, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
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Kumar A, Anju T, Kumar S, Chhapekar SS, Sreedharan S, Singh S, Choi SR, Ramchiary N, Lim YP. Integrating Omics and Gene Editing Tools for Rapid Improvement of Traditional Food Plants for Diversified and Sustainable Food Security. Int J Mol Sci 2021; 22:8093. [PMID: 34360856 PMCID: PMC8348985 DOI: 10.3390/ijms22158093] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 12/20/2022] Open
Abstract
Indigenous communities across the globe, especially in rural areas, consume locally available plants known as Traditional Food Plants (TFPs) for their nutritional and health-related needs. Recent research shows that many TFPs are highly nutritious as they contain health beneficial metabolites, vitamins, mineral elements and other nutrients. Excessive reliance on the mainstream staple crops has its own disadvantages. Traditional food plants are nowadays considered important crops of the future and can act as supplementary foods for the burgeoning global population. They can also act as emergency foods in situations such as COVID-19 and in times of other pandemics. The current situation necessitates locally available alternative nutritious TFPs for sustainable food production. To increase the cultivation or improve the traits in TFPs, it is essential to understand the molecular basis of the genes that regulate some important traits such as nutritional components and resilience to biotic and abiotic stresses. The integrated use of modern omics and gene editing technologies provide great opportunities to better understand the genetic and molecular basis of superior nutrient content, climate-resilient traits and adaptation to local agroclimatic zones. Recently, realizing the importance and benefits of TFPs, scientists have shown interest in the prospection and sequencing of TFPs for their improvements, cultivation and mainstreaming. Integrated omics such as genomics, transcriptomics, proteomics, metabolomics and ionomics are successfully used in plants and have provided a comprehensive understanding of gene-protein-metabolite networks. Combined use of omics and editing tools has led to successful editing of beneficial traits in several TFPs. This suggests that there is ample scope for improvement of TFPs for sustainable food production. In this article, we highlight the importance, scope and progress towards improvement of TFPs for valuable traits by integrated use of omics and gene editing techniques.
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Affiliation(s)
- Ajay Kumar
- Department of Plant Science, Central University of Kerala, Kasaragod 671316, Kerala, India; (T.A.); (S.S.)
| | - Thattantavide Anju
- Department of Plant Science, Central University of Kerala, Kasaragod 671316, Kerala, India; (T.A.); (S.S.)
| | - Sushil Kumar
- Department of Botany, Govt. Degree College, Kishtwar 182204, Jammu and Kashmir, India;
| | - Sushil Satish Chhapekar
- Molecular Genetics & Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon 34134, Korea; (S.S.C.); (S.S.); (S.R.C.)
| | - Sajana Sreedharan
- Department of Plant Science, Central University of Kerala, Kasaragod 671316, Kerala, India; (T.A.); (S.S.)
| | - Sonam Singh
- Molecular Genetics & Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon 34134, Korea; (S.S.C.); (S.S.); (S.R.C.)
| | - Su Ryun Choi
- Molecular Genetics & Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon 34134, Korea; (S.S.C.); (S.S.); (S.R.C.)
| | - Nirala Ramchiary
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, Delhi, India
| | - Yong Pyo Lim
- Molecular Genetics & Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon 34134, Korea; (S.S.C.); (S.S.); (S.R.C.)
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Wu D, Tanaka R, Li X, Ramstein GP, Cu S, Hamilton JP, Buell CR, Stangoulis J, Rocheford T, Gore MA. High-resolution genome-wide association study pinpoints metal transporter and chelator genes involved in the genetic control of element levels in maize grain. G3-GENES GENOMES GENETICS 2021; 11:6156830. [PMID: 33677522 PMCID: PMC8759812 DOI: 10.1093/g3journal/jkab059] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 02/21/2021] [Indexed: 12/18/2022]
Abstract
Despite its importance to plant function and human health, the genetics underpinning element levels in maize grain remain largely unknown. Through a genome-wide association study in the maize Ames panel of nearly 2,000 inbred lines that was imputed with ∼7.7 million SNP markers, we investigated the genetic basis of natural variation for the concentration of 11 elements in grain. Novel associations were detected for the metal transporter genes rte2 (rotten ear2) and irt1 (iron-regulated transporter1) with boron and nickel, respectively. We also further resolved loci that were previously found to be associated with one or more of five elements (copper, iron, manganese, molybdenum, and/or zinc), with two metal chelator and five metal transporter candidate causal genes identified. The nas5 (nicotianamine synthase5) gene involved in the synthesis of nicotianamine, a metal chelator, was found associated with both zinc and iron and suggests a common genetic basis controlling the accumulation of these two metals in the grain. Furthermore, moderate predictive abilities were obtained for the 11 elemental grain phenotypes with two whole-genome prediction models: Bayesian Ridge Regression (0.33–0.51) and BayesB (0.33–0.53). Of the two models, BayesB, with its greater emphasis on large-effect loci, showed ∼4–10% higher predictive abilities for nickel, molybdenum, and copper. Altogether, our findings contribute to an improved genotype-phenotype map for grain element accumulation in maize.
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Affiliation(s)
- Di Wu
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Ryokei Tanaka
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Xiaowei Li
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | | | - Suong Cu
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
| | - John P Hamilton
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - James Stangoulis
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
| | - Torbert Rocheford
- Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
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41
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Alcock TD, Thomas CL, Ó Lochlainn S, Pongrac P, Wilson M, Moore C, Reyt G, Vogel-Mikuš K, Kelemen M, Hayden R, Wilson L, Stephenson P, Østergaard L, Irwin JA, Hammond JP, King GJ, Salt DE, Graham NS, White PJ, Broadley MR. Magnesium and calcium overaccumulate in the leaves of a schengen3 mutant of Brassica rapa. PLANT PHYSIOLOGY 2021; 186:1616-1631. [PMID: 33831190 PMCID: PMC8260142 DOI: 10.1093/plphys/kiab150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 03/12/2021] [Indexed: 05/04/2023]
Abstract
Magnesium (Mg) and calcium (Ca) are essential mineral nutrients poorly supplied in many human food systems. In grazing livestock, Mg and Ca deficiencies are costly welfare issues. Here, we report a Brassica rapa loss-of-function schengen3 (sgn3) mutant, braA.sgn3.a-1, which accumulates twice as much Mg and a third more Ca in its leaves. We mapped braA.sgn3.a to a single recessive locus using a forward ionomic screen of chemically mutagenized lines with subsequent backcrossing and linked-read sequencing of second back-crossed, second filial generation (BC2F2) segregants. Confocal imaging revealed a disrupted root endodermal diffusion barrier, consistent with SGN3 encoding a receptor-like kinase required for normal formation of Casparian strips, as reported in thale cress (Arabidopsis thaliana). Analysis of the spatial distribution of elements showed elevated extracellular Mg concentrations in leaves of braA.sgn3.a-1, hypothesized to result from preferential export of excessive Mg from cells to ensure suitable cellular concentrations. This work confirms a conserved role of SGN3 in controlling nutrient homeostasis in B. rapa, and reveals mechanisms by which plants are able to deal with perturbed shoot element concentrations resulting from a "leaky" root endodermal barrier. Characterization of variation in leaf Mg and Ca accumulation across a mutagenized population of B. rapa shows promise for using such populations in breeding programs to increase edible concentrations of essential human and animal nutrients.
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Affiliation(s)
- Thomas D Alcock
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
- Future Food Beacon of Excellence, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
- School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Catherine L Thomas
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
- Department of Sustainable Agriculture Sciences, Rothamsted Research, West Common, Hertfordshire AL5 2JQ, UK
| | - Seosamh Ó Lochlainn
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Paula Pongrac
- Jožef Stefan Institute, 1000 Ljubljana, Slovenia
- Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Michael Wilson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
- Future Food Beacon of Excellence, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Christopher Moore
- Future Food Beacon of Excellence, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
- School of Life Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham NG7 2UH, UK
| | - Guilhem Reyt
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
- Future Food Beacon of Excellence, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Katarina Vogel-Mikuš
- Jožef Stefan Institute, 1000 Ljubljana, Slovenia
- Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | | | - Rory Hayden
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Lolita Wilson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Pauline Stephenson
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Lars Østergaard
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Judith A Irwin
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - John P Hammond
- School of Agriculture, Policy and Development and the Centre for Food Security, University of Reading, Whiteknights, P.O. Box 237, Reading RG6 6AR, UK
- Southern Cross Plant Science, Southern Cross University, Lismore, New South Wales 2480, Australia
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, New South Wales 2480, Australia
| | - David E Salt
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
- Future Food Beacon of Excellence, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Neil S Graham
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Philip J White
- Ecological Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
- Distinguished Scientist Fellowship Program, King Saud University, Riyadh 11451, Saudi Arabia
| | - Martin R Broadley
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
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42
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Ali S, Tyagi A, Bae H. Ionomic Approaches for Discovery of Novel Stress-Resilient Genes in Plants. Int J Mol Sci 2021; 22:7182. [PMID: 34281232 PMCID: PMC8267685 DOI: 10.3390/ijms22137182] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 01/03/2023] Open
Abstract
Plants, being sessile, face an array of biotic and abiotic stresses in their lifespan that endanger their survival. Hence, optimized uptake of mineral nutrients creates potential new routes for enhancing plant health and stress resilience. Recently, minerals (both essential and non-essential) have been identified as key players in plant stress biology, owing to their multifaceted functions. However, a realistic understanding of the relationship between different ions and stresses is lacking. In this context, ionomics will provide new platforms for not only understanding the function of the plant ionome during stresses but also identifying the genes and regulatory pathways related to mineral accumulation, transportation, and involvement in different molecular mechanisms under normal or stress conditions. This article provides a general overview of ionomics and the integration of high-throughput ionomic approaches with other "omics" tools. Integrated omics analysis is highly suitable for identification of the genes for various traits that confer biotic and abiotic stress tolerance. Moreover, ionomics advances being used to identify loci using qualitative trait loci and genome-wide association analysis of element uptake and transport within plant tissues, as well as genetic variation within species, are discussed. Furthermore, recent developments in ionomics for the discovery of stress-tolerant genes in plants have also been addressed; these can be used to produce more robust crops with a high nutritional value for sustainable agriculture.
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Affiliation(s)
- Sajad Ali
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Korea;
| | - Anshika Tyagi
- National Institute for Plant Biotechnology, New Delhi 110012, India;
| | - Hanhong Bae
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Korea;
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43
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Marzorati F, Wang C, Pavesi G, Mizzi L, Morandini P. Cleaning the Medicago Microarray Database to Improve Gene Function Analysis. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10061240. [PMID: 34207216 PMCID: PMC8234645 DOI: 10.3390/plants10061240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/30/2021] [Accepted: 05/11/2021] [Indexed: 06/13/2023]
Abstract
Transcriptomics studies have been facilitated by the development of microarray and RNA-Seq technologies, with thousands of expression datasets available for many species. However, the quality of data can be highly variable, making the combined analysis of different datasets difficult and unreliable. Most of the microarray data for Medicago truncatula, the barrel medic, have been stored and made publicly accessible on the web database Medicago truncatula Gene Expression atlas (MtGEA). The aim of this work is to ameliorate the quality of the MtGEA database through a general method based on logical and statistical relationships among parameters and conditions. The initial 716 columns available in the dataset were reduced to 607 by evaluating the quality of data through the sum of the expression levels over the entire transcriptome probes and Pearson correlation among hybridizations. The reduced dataset shows great improvements in the consistency of the data, with a reduction in both false positives and false negatives resulting from Pearson correlation and GO enrichment analysis among genes. The approach we used is of general validity and our intent is to extend the analysis to other plant microarray databases.
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Affiliation(s)
- Francesca Marzorati
- Department of Environmental Science and Policy, University of Milan, Via Celoria 10, 20133 Milano, Italy;
| | - Chu Wang
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milano, Italy; (C.W.); (G.P.); (L.M.)
| | - Giulio Pavesi
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milano, Italy; (C.W.); (G.P.); (L.M.)
| | - Luca Mizzi
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milano, Italy; (C.W.); (G.P.); (L.M.)
| | - Piero Morandini
- Department of Environmental Science and Policy, University of Milan, Via Celoria 10, 20133 Milano, Italy;
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44
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Wang Y, Xu Y, Liang X, Wang L, Sun Y, Huang Q, Qin X, Zhao L. Soil application of manganese sulfate could reduce wheat Cd accumulation in Cd contaminated soil by the modulation of the key tissues and ionomic of wheat. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 770:145328. [PMID: 33736398 DOI: 10.1016/j.scitotenv.2021.145328] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 01/12/2021] [Accepted: 01/17/2021] [Indexed: 06/12/2023]
Abstract
Wheat is one of the main sources of dietary Cd in northern China, and the reduction of Cd accumulation in wheat is of great significance for human health. This study explored and highlighted the effects of soil application of manganese sulfate (MnSO4) on the distribution and transport of Cd in two wheat cultivars, and identified the key tissues and elements during the Cd translocation in wheat by measuring the concentrations of eight elements in 17 parts of wheat under MnSO4 treatment. The bioaccumulation factor of Cd in the roots and the translocation factor of Cd in node1 (connected to the panicle) of the high-Cd wheat cultivar were found to be higher than that of the low-Cd wheat cultivar. Soil application of MnSO4 (0.05-0.2%) significantly reduced the Cd concentration in high- and low-Cd wheat grains by 24.16-57.52% and 25.90-63.44%, respectively, and decreased the Cd concentrations in all wheat tissues. MnSO4 application had no effect on wheat growth, and the inhibition effects on wheat Cd accumulation were more pronounced at wheat-seeding stage. MnSO4 application inhibited Cd uptake by the ion antagonism between Mn/Zn/Fe and Cd in the wheat roots and reduced Cd upward transport by reducing the Cd transport from node1 to internode1 and from panicle to wheat grain. Nodes 2-4 can restrict the transport of both Cd and Mn, whereas node1 and the panicle can inhibit Cd transport but have no effect on Mn transport. The ionomic results show that the overall spatial distribution of different tissues is consistent with the growth morphology of wheat plants. MnSO4 application significantly changed the ionomes of the roots, nodes, glumes, and wheat grains; meanwhile, the differences in the ionomic responses among the roots are the most remarkable. The results of this study show that soil application of MnSO4 is efficient for reducing the Cd accumulation in wheat grown in Cd-contaminated soil, demonstrating wide application potential.
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Affiliation(s)
- Yale Wang
- Innovation Team of Remediation for Heavy Metal Contaminated Farmlands, Agro-Environmental Protection Institute, Ministry of Agriculture, Tianjin 300191, People's Republic of China; Key Laboratory of Original Environmental Pollution Control, Ministry of Agriculture, Agro-Environmental Protection Institute, Ministry of Agriculture, Tianjin 300191, People's Republic of China
| | - Yingming Xu
- Innovation Team of Remediation for Heavy Metal Contaminated Farmlands, Agro-Environmental Protection Institute, Ministry of Agriculture, Tianjin 300191, People's Republic of China; Key Laboratory of Original Environmental Pollution Control, Ministry of Agriculture, Agro-Environmental Protection Institute, Ministry of Agriculture, Tianjin 300191, People's Republic of China.
| | - Xuefeng Liang
- Innovation Team of Remediation for Heavy Metal Contaminated Farmlands, Agro-Environmental Protection Institute, Ministry of Agriculture, Tianjin 300191, People's Republic of China; Key Laboratory of Original Environmental Pollution Control, Ministry of Agriculture, Agro-Environmental Protection Institute, Ministry of Agriculture, Tianjin 300191, People's Republic of China
| | - Lin Wang
- Innovation Team of Remediation for Heavy Metal Contaminated Farmlands, Agro-Environmental Protection Institute, Ministry of Agriculture, Tianjin 300191, People's Republic of China; Key Laboratory of Original Environmental Pollution Control, Ministry of Agriculture, Agro-Environmental Protection Institute, Ministry of Agriculture, Tianjin 300191, People's Republic of China
| | - Yuebing Sun
- Innovation Team of Remediation for Heavy Metal Contaminated Farmlands, Agro-Environmental Protection Institute, Ministry of Agriculture, Tianjin 300191, People's Republic of China; Key Laboratory of Original Environmental Pollution Control, Ministry of Agriculture, Agro-Environmental Protection Institute, Ministry of Agriculture, Tianjin 300191, People's Republic of China
| | - Qingqing Huang
- Innovation Team of Remediation for Heavy Metal Contaminated Farmlands, Agro-Environmental Protection Institute, Ministry of Agriculture, Tianjin 300191, People's Republic of China; Key Laboratory of Original Environmental Pollution Control, Ministry of Agriculture, Agro-Environmental Protection Institute, Ministry of Agriculture, Tianjin 300191, People's Republic of China
| | - Xu Qin
- Innovation Team of Remediation for Heavy Metal Contaminated Farmlands, Agro-Environmental Protection Institute, Ministry of Agriculture, Tianjin 300191, People's Republic of China; Key Laboratory of Original Environmental Pollution Control, Ministry of Agriculture, Agro-Environmental Protection Institute, Ministry of Agriculture, Tianjin 300191, People's Republic of China
| | - Lijie Zhao
- Innovation Team of Remediation for Heavy Metal Contaminated Farmlands, Agro-Environmental Protection Institute, Ministry of Agriculture, Tianjin 300191, People's Republic of China; Key Laboratory of Original Environmental Pollution Control, Ministry of Agriculture, Agro-Environmental Protection Institute, Ministry of Agriculture, Tianjin 300191, People's Republic of China
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45
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Zhang L, MacQueen A, Bonnette J, Fritschi FB, Lowry DB, Juenger TE. QTL x environment interactions underlie ionome divergence in switchgrass. G3-GENES GENOMES GENETICS 2021; 11:6259145. [PMID: 33914881 PMCID: PMC8495926 DOI: 10.1093/g3journal/jkab144] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/23/2021] [Indexed: 01/02/2023]
Abstract
Ionomics measures elemental concentrations in biological organisms and provides a snapshot of physiology under different conditions. In this study, we evaluate genetic variation of the ionome in outbred, perennial switchgrass in three environments across the species' native range, and explore patterns of genotype-by-environment interactions. We grew 725 clonally replicated genotypes of a large full sib family from a four-way linkage mapping population, created from deeply diverged upland and lowland switchgrass ecotypes, at three common gardens. Concentrations of 18 mineral elements were determined in whole post-anthesis tillers using ion coupled plasma mass spectrometry (ICP-MS). These measurements were used to identify quantitative trait loci (QTL) with and without QTL-by-environment interactions (QTLxE) using a multi-environment QTL mapping approach. We found that element concentrations varied significantly both within and between switchgrass ecotypes, and GxE was present at both the trait and QTL level. Concentrations of 14 of the 18 elements were under some genetic control, and 77 QTL were detected for these elements. 74% of QTL colocalized multiple elements, half of QTL exhibited significant QTLxE, and roughly equal numbers of QTL had significant differences in magnitude and sign of their effects across environments. The switchgrass ionome is under moderate genetic control and by loci with highly variable effects across environments.
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Affiliation(s)
- Li Zhang
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712
| | - Alice MacQueen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712
| | - Jason Bonnette
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712
| | - Felix B Fritschi
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211
| | - David B Lowry
- Department of Plant Biology and DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712
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46
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Campos ACAL, van Dijk WFA, Ramakrishna P, Giles T, Korte P, Douglas A, Smith P, Salt DE. 1,135 ionomes reveal the global pattern of leaf and seed mineral nutrient and trace element diversity in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:536-554. [PMID: 33506585 DOI: 10.1111/tpj.15177] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 01/07/2021] [Accepted: 01/20/2021] [Indexed: 05/06/2023]
Abstract
Soil is a heterogeneous reservoir of essential elements needed for plant growth and development. Plants have evolved mechanisms to balance their nutritional needs based on availability of nutrients. This has led to genetically based variation in the elemental composition, the 'ionome', of plants, both within and between species. We explore this natural variation using a panel of wild-collected, geographically widespread Arabidopsis thaliana accessions from the 1001 Genomes Project including over 1,135 accessions, and the 19 parental accessions of the Multi-parent Advanced Generation Inter-Cross (MAGIC) panel, all with full-genome sequences available. We present an experimental design pipeline for high-throughput ionomic screenings and analyses with improved normalisation procedures to account for errors and variability in conditions often encountered in large-scale, high-throughput data collection. We report quantification of the complete leaf and seed ionome of the entire collection using this pipeline and a digital tool, Ion Explorer, to interact with the dataset. We describe the pattern of natural ionomic variation across the A. thaliana species and identify several accessions with extreme ionomic profiles. It forms a valuable resource for exploratory genetic mapping studies to identify genes underlying natural variation in leaf and seed ionome and genetic adaptation of plants to soil conditions.
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Affiliation(s)
- Ana Carolina A L Campos
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, United Kingdom
| | - William F A van Dijk
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, United Kingdom
| | - Priya Ramakrishna
- Future Food Beacon of Excellence and School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, United Kingdom
| | - Tom Giles
- Digital Research Service and Advanced Data Analysis Centre, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, United Kingdom
| | - Pamela Korte
- Gregor Mendel Institute of Molecular Plant Biology, Vienna, Austria
| | - Alex Douglas
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, United Kingdom
| | - Pete Smith
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, United Kingdom
| | - David E Salt
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, United Kingdom
- Future Food Beacon of Excellence and School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, United Kingdom
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47
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Zhang C, Hiradate S, Kusumoto Y, Morita S, Koyanagi TF, Chu Q, Watanabe T. Ionomic Responses of Local Plant Species to Natural Edaphic Mineral Variations. FRONTIERS IN PLANT SCIENCE 2021; 12:614613. [PMID: 33854517 PMCID: PMC8039527 DOI: 10.3389/fpls.2021.614613] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 03/09/2021] [Indexed: 05/13/2023]
Abstract
Leaf ionome indicates plant phylogenetic evolution and responses to environmental stress, which is a critical influential factor to the structure of species populations in local edaphic sites. However, little is known about leaf ionomic responses of local plant species to natural edaphic mineral variations. In the present study, all plant species and soil samples from a total of 80 soil sites in Shiozuka Highland were collected for multi-elemental analysis. Ioniomic data of species were used for statistical analysis, representing 24 species and 10 families. Specific preferences to ionomic accumulation in plants were obviously affected by the phylogeny, whereas edaphic impacts were also strong but limited within the phylogenetic preset. Correlations among elements resulted from not only elemental synergy and competition but also the adaptive evolution to withstand environmental stresses. Furthermore, ionomic differences of plant families were mainly derived from non-essential elements. The majority of variations in leaf ionome is undoubtedly regulated by evolutionary factors, but externalities, especially environmental stresses also have an important regulating function for landscape formation, determining that the contributions of each factor to ionomic variations of plant species for adaptation to environmental stress provides a new insight for further research on ionomic responses of ecological speciation to environmental perturbations and their corresponding adaptive evolutions.
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Affiliation(s)
- Chengming Zhang
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Syuntaro Hiradate
- National Institute for Agro-Environmental Sciences (NIAES), Tsukuba, Japan
| | - Yoshinobu Kusumoto
- National Institute for Agro-Environmental Sciences (NIAES), Tsukuba, Japan
| | - Sayaka Morita
- National Institute for Agro-Environmental Sciences (NIAES), Tsukuba, Japan
| | - Tomoyo F. Koyanagi
- National Institute for Agro-Environmental Sciences (NIAES), Tsukuba, Japan
| | - Qingnan Chu
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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48
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Ricachenevsky FK, Punshon T, Salt DE, Fett JP, Guerinot ML. Arabidopsis thaliana zinc accumulation in leaf trichomes is correlated with zinc concentration in leaves. Sci Rep 2021; 11:5278. [PMID: 33674630 PMCID: PMC7935932 DOI: 10.1038/s41598-021-84508-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 02/17/2021] [Indexed: 11/21/2022] Open
Abstract
Zinc (Zn) is a key micronutrient for plants and animals, and understanding Zn homeostasis in plants can improve both agriculture and human health. While root Zn transporters in plant model species have been characterized in detail, comparatively little is known about shoot processes controlling Zn concentrations and spatial distribution. Previous work showed that Zn hyperaccumulator species such as Arabidopsis halleri accumulate Zn and other metals in leaf trichomes. To date there is no systematic study regarding Zn accumulation in the trichomes of the non-accumulating, genetic model species A. thaliana. Here, we used Synchrotron X-Ray Fluorescence mapping to show that Zn accumulates at the base of trichomes of A. thaliana. Using transgenic and natural accessions of A thaliana that vary in bulk leaf Zn concentration, we demonstrate that higher leaf Zn increases total Zn found at the base of trichome cells. Our data indicates that Zn accumulation in trichomes is a function of the Zn status of the plant, and provides the basis for future studies on a genetically tractable plant species to understand the molecular steps involved in Zn spatial distribution in leaves.
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Affiliation(s)
- Felipe K Ricachenevsky
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande Do Sul, Porto Alegre, Brazil. .,Departamento de Botânica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, Porto Alegre, RS, 9500, Brazil. .,Department of Biological Sciences, Life Sciences Center, Dartmouth College, 78 College St, Hanover, NH, 03755, USA.
| | - Tracy Punshon
- Department of Biological Sciences, Life Sciences Center, Dartmouth College, 78 College St, Hanover, NH, 03755, USA
| | - David E Salt
- Future Food Beacon of Excellence and the School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Janette P Fett
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande Do Sul, Porto Alegre, Brazil.,Departamento de Botânica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, Porto Alegre, RS, 9500, Brazil
| | - Mary Lou Guerinot
- Department of Biological Sciences, Life Sciences Center, Dartmouth College, 78 College St, Hanover, NH, 03755, USA.
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49
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Navrátilová A, Kovár M, Požgajová M. Ascorbic acid mitigates cadmium-induced stress, and contributes to ionome stabilization in fission yeast. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:15380-15393. [PMID: 33236313 DOI: 10.1007/s11356-020-11480-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 10/29/2020] [Indexed: 06/11/2023]
Abstract
Cadmium is a highly toxic environmental pollutant which through enhancement of reactive oxygen species (ROS) production triggers oxidative stress to the cell. Cell growth, a fundamental feature of all living organisms is closely connected to the cell shape and homeostasis. As these processes largely depend on cell fitness status and environmental conditions we have analyzed, the impact of different cadmium concentrations and the effect of ascorbic acid (ascorbate, AsA) supplementation on cell growth parameters, cell morphology, and ionome balance maintenance in Schizosaccharomyces pombe. We show that cadmium causes membrane lipid peroxidation resulting in cell shape alterations leading to growth impairment and through mineral elements disequilibrium affects ionome homeostasis in a dose- and time-dependent manner. AsA recognized as one of the most prominent antioxidants, when overdosed, displays considerable pro-oxidant activity, though precise dosing of its supplementation is desired. We present here that AsA under efficacious concentration largely improves cell condition affected by cadmium. Although, we clearly demonstrate the beneficial feature of AsA, further studies are required to fully understand its protective nature on cell homeostasis maintenance under conditions of the broken environment.
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Affiliation(s)
- Alica Navrátilová
- Department of Genetics and Breeding Biology, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76, Nitra, Slovakia
| | - Marek Kovár
- Department of Plant Physiology, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76, Nitra, Slovakia
| | - Miroslava Požgajová
- AgroBioTech Research Centre, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76, Nitra, Slovakia.
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Fischer S, Sánchez-Bermejo E, Xu X, Flis P, Ramakrishna P, Guerinot ML, Zhao FJ, Salt DE. Targeted expression of the arsenate reductase HAC1 identifies cell type specificity of arsenic metabolism and transport in plant roots. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:415-425. [PMID: 33038235 PMCID: PMC7853597 DOI: 10.1093/jxb/eraa465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 10/05/2020] [Indexed: 05/14/2023]
Abstract
High Arsenic Concentration 1 (HAC1), an Arabidopsis thaliana arsenate reductase, plays a key role in arsenate [As(V)] tolerance. Through conversion of As(V) to arsenite [As(III)], HAC1 enables As(III) export from roots, and restricts translocation of As(V) to shoots. To probe the ability of different root tissues to detoxify As(III) produced by HAC1, we generated A. thaliana lines expressing HAC1 in different cell types. We investigated the As(V) tolerance phenotypes: root growth, As(III) efflux, As translocation, and As chemical speciation. We showed that HAC1 can function in the outer tissues of the root (epidermis, cortex, and endodermis) to confer As(V) tolerance, As(III) efflux, and limit As accumulation in shoots. HAC1 is less effective in the stele at conferring As(V) tolerance phenotypes. The exception is HAC1 activity in the protoxylem, which we found to be sufficient to restrict As translocation, but not to confer As(V) tolerance. In conclusion, we describe cell type-specific functions of HAC1 that spatially separate the control of As(V) tolerance and As translocation. Further, we identify a key function of protoxylem cells in As(V) translocation, consistent with the model where endodermal passage cells, above protoxylem pericycle cells, form a 'funnel' loading nutrients and potentially toxic elements into the vasculature.
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Affiliation(s)
- Sina Fischer
- Future Food Beacon of Excellence and the School of Biosciences, University of Nottingham, Nottingham, UK
| | - Eduardo Sánchez-Bermejo
- Future Food Beacon of Excellence and the School of Biosciences, University of Nottingham, Nottingham, UK
| | - Xuejie Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Paulina Flis
- Future Food Beacon of Excellence and the School of Biosciences, University of Nottingham, Nottingham, UK
| | - Priya Ramakrishna
- Future Food Beacon of Excellence and the School of Biosciences, University of Nottingham, Nottingham, UK
| | - Mary Lou Guerinot
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
| | - Fang-Jie Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - David E Salt
- Future Food Beacon of Excellence and the School of Biosciences, University of Nottingham, Nottingham, UK
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