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Ruang-Areerate P, Travis AJ, Pinson SRM, Tarpley L, Eizenga GC, Guerinot ML, Salt DE, Douglas A, Price AH, Norton GJ. Genome-wide association mapping for grain manganese in rice (Oryza sativa L.) using a multi-experiment approach. Heredity (Edinb) 2021; 126:505-520. [PMID: 33235293 PMCID: PMC8026592 DOI: 10.1038/s41437-020-00390-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 11/06/2020] [Accepted: 11/06/2020] [Indexed: 11/09/2022] Open
Abstract
Manganese (Mn) is an essential trace element for plants and commonly contributes to human health; however, the understanding of the genes controlling natural variation in Mn in crop plants is limited. Here, the integration of two of genome-wide association study approaches was used to increase the identification of valuable quantitative trait loci (QTL) and candidate genes responsible for the concentration of grain Mn across 389 diverse rice cultivars grown in Arkansas and Texas, USA, in multiple years. Single-trait analysis was initially performed using three different SNP datasets. As a result, significant loci could be detected using the high-density SNP dataset. Based on the 5.2 M SNP dataset, major QTLs were located on chromosomes 3 and 7 for Mn containing six candidate genes. In addition, the phenotypic data of grain Mn concentration were combined from three flooded-field experiments from the two sites and 3 years using multi-experiment analysis based on the 5.2 M SNP dataset. Two previous QTLs on chromosome 3 were identified across experiments, whereas new Mn QTLs were identified that were not found in individual experiments, on chromosomes 3, 4, 9 and 11. OsMTP8.1 was identified in both approaches and is a good candidate gene that could be controlling grain Mn concentration. This work demonstrates the utilisation of multi-experiment analysis to identify constitutive QTLs and candidate genes associated with the grain Mn concentration. Hence, the approach should be advantageous to facilitate genomic breeding programmes in rice and other crops considering QTLs and genes associated with complex traits in natural populations.
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Affiliation(s)
- Panthita Ruang-Areerate
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK.
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand.
| | - Anthony J Travis
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK
| | - Shannon R M Pinson
- USDA-ARS Dale Bumpers National Rice Research Center, Stuttgart, AR, 72160, USA
| | - Lee Tarpley
- Texas A&M System AgriLife Research Center, Beaumont, TX, 77713, USA
| | - Georgia C Eizenga
- USDA-ARS Dale Bumpers National Rice Research Center, Stuttgart, AR, 72160, USA
| | - Mary Lou Guerinot
- Department of Biological Sciences, Dartmouth College, Hanover, NH, 03755, USA
| | - David E Salt
- Future Food Beacon of Excellence and the School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Alex Douglas
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK
| | - Adam H Price
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK
| | - Gareth J Norton
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK
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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: 10] [Impact Index Per Article: 3.3] [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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Yang Y, Saand MA, Huang L, Abdelaal WB, Zhang J, Wu Y, Li J, Sirohi MH, Wang F. Applications of Multi-Omics Technologies for Crop Improvement. FRONTIERS IN PLANT SCIENCE 2021; 12:563953. [PMID: 34539683 PMCID: PMC8446515 DOI: 10.3389/fpls.2021.563953] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/06/2021] [Indexed: 05/19/2023]
Abstract
Multiple "omics" approaches have emerged as successful technologies for plant systems over the last few decades. Advances in next-generation sequencing (NGS) have paved a way for a new generation of different omics, such as genomics, transcriptomics, and proteomics. However, metabolomics, ionomics, and phenomics have also been well-documented in crop science. Multi-omics approaches with high throughput techniques have played an important role in elucidating growth, senescence, yield, and the responses to biotic and abiotic stress in numerous crops. These omics approaches have been implemented in some important crops including wheat (Triticum aestivum L.), soybean (Glycine max), tomato (Solanum lycopersicum), barley (Hordeum vulgare L.), maize (Zea mays L.), millet (Setaria italica L.), cotton (Gossypium hirsutum L.), Medicago truncatula, and rice (Oryza sativa L.). The integration of functional genomics with other omics highlights the relationships between crop genomes and phenotypes under specific physiological and environmental conditions. The purpose of this review is to dissect the role and integration of multi-omics technologies for crop breeding science. We highlight the applications of various omics approaches, such as genomics, transcriptomics, proteomics, metabolomics, phenomics, and ionomics, and the implementation of robust methods to improve crop genetics and breeding science. Potential challenges that confront the integration of multi-omics with regard to the functional analysis of genes and their networks as well as the development of potential traits for crop improvement are discussed. The panomics platform allows for the integration of complex omics to construct models that can be used to predict complex traits. Systems biology integration with multi-omics datasets can enhance our understanding of molecular regulator networks for crop improvement. In this context, we suggest the integration of entire omics by employing the "phenotype to genotype" and "genotype to phenotype" concept. Hence, top-down (phenotype to genotype) and bottom-up (genotype to phenotype) model through integration of multi-omics with systems biology may be beneficial for crop breeding improvement under conditions of environmental stresses.
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Affiliation(s)
- Yaodong Yang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
- *Correspondence: Yaodong Yang
| | - Mumtaz Ali Saand
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
- Department of Botany, Shah Abdul Latif University, Khairpur, Pakistan
| | - Liyun Huang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Walid Badawy Abdelaal
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Jun Zhang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Yi Wu
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Jing Li
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | | | - Fuyou Wang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
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Roorkiwal M, Pandey S, Thavarajah D, Hemalatha R, Varshney RK. Molecular Mechanisms and Biochemical Pathways for Micronutrient Acquisition and Storage in Legumes to Support Biofortification for Nutritional Security. FRONTIERS IN PLANT SCIENCE 2021; 12:682842. [PMID: 34163513 PMCID: PMC8215609 DOI: 10.3389/fpls.2021.682842] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/06/2021] [Indexed: 05/10/2023]
Abstract
The world faces a grave situation of nutrient deficiency as a consequence of increased uptake of calorie-rich food that threaten nutritional security. More than half the world's population is affected by different forms of malnutrition. Unhealthy diets associated with poor nutrition carry a significant risk of developing non-communicable diseases, leading to a high mortality rate. Although considerable efforts have been made in agriculture to increase nutrient content in cereals, the successes are insufficient. The number of people affected by different forms of malnutrition has not decreased much in the recent past. While legumes are an integral part of the food system and widely grown in sub-Saharan Africa and South Asia, only limited efforts have been made to increase their nutrient content in these regions. Genetic variation for a majority of nutritional traits that ensure nutritional security in adverse conditions exists in the germplasm pool of legume crops. This diversity can be utilized by selective breeding for increased nutrients in seeds. The targeted identification of precise factors related to nutritional traits and their utilization in a breeding program can help mitigate malnutrition. The principal objective of this review is to present the molecular mechanisms of nutrient acquisition, transport and metabolism to support a biofortification strategy in legume crops to contribute to addressing malnutrition.
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Affiliation(s)
- Manish Roorkiwal
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - Sarita Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Dil Thavarajah
- Plant and Environmental Sciences, Poole Agricultural Center, Clemson University, Clemson, SC, United States
| | - R. Hemalatha
- ICMR-National Institute of Nutrition (NIN), Hyderabad, India
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch University, Murdoch, WA, Australia
- *Correspondence: Rajeev K. Varshney, ;
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56
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Konečná V, Yant L, Kolář F. The Evolutionary Genomics of Serpentine Adaptation. FRONTIERS IN PLANT SCIENCE 2020; 11:574616. [PMID: 33391295 PMCID: PMC7772150 DOI: 10.3389/fpls.2020.574616] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 11/23/2020] [Indexed: 06/12/2023]
Abstract
Serpentine barrens are among the most challenging settings for plant life. Representing a perfect storm of hazards, serpentines consist of broadly skewed elemental profiles, including abundant toxic metals and low nutrient contents on drought-prone, patchily distributed substrates. Accordingly, plants that can tolerate the challenges of serpentine have fascinated biologists for decades, yielding important insights into adaptation to novel ecologies through physiological change. Here we highlight recent progress from studies which demonstrate the power of serpentine as a model for the genomics of adaptation. Given the moderate - but still tractable - complexity presented by the mix of hazards on serpentine, these venues are well-suited for the experimental inquiry of adaptation both in natural and manipulated conditions. Moreover, the island-like distribution of serpentines across landscapes provides abundant natural replicates, offering power to evolutionary genomic inference. Exciting recent insights into the genomic basis of serpentine adaptation point to a partly shared basis that involves sampling from common allele pools available from retained ancestral polymorphism or via gene flow. However, a lack of integrated studies deconstructing complex adaptations and linking candidate alleles with fitness consequences leaves room for much deeper exploration. Thus, we still seek the crucial direct link between the phenotypic effect of candidate alleles and their measured adaptive value - a prize that is exceedingly rare to achieve in any study of adaptation. We expect that closing this gap is not far off using the promising model systems described here.
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Affiliation(s)
- Veronika Konečná
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
- Institute of Botany, The Czech Academy of Sciences, Pru˚honice, Czechia
| | - Levi Yant
- Future Food Beacon and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Filip Kolář
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
- Institute of Botany, The Czech Academy of Sciences, Pru˚honice, Czechia
- Natural History Museum, University of Oslo, Oslo, Norway
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57
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Disease Ionomics: Understanding the Role of Ions in Complex Disease. Int J Mol Sci 2020; 21:ijms21228646. [PMID: 33212764 PMCID: PMC7697569 DOI: 10.3390/ijms21228646] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 12/12/2022] Open
Abstract
Ionomics is a novel multidisciplinary field that uses advanced techniques to investigate the composition and distribution of all minerals and trace elements in a living organism and their variations under diverse physiological and pathological conditions. It involves both high-throughput elemental profiling technologies and bioinformatic methods, providing opportunities to study the molecular mechanism underlying the metabolism, homeostasis, and cross-talk of these elements. While much effort has been made in exploring the ionomic traits relating to plant physiology and nutrition, the use of ionomics in the research of serious diseases is still in progress. In recent years, a number of ionomic studies have been carried out for a variety of complex diseases, which offer theoretical and practical insights into the etiology, early diagnosis, prognosis, and therapy of them. This review aims to give an overview of recent applications of ionomics in the study of complex diseases and discuss the latest advances and future trends in this area. Overall, disease ionomics may provide substantial information for systematic understanding of the properties of the elements and the dynamic network of elements involved in the onset and development of diseases.
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Stich B, Benke A, Schmidt M, Urbany C, Shi R, von Wirén N. The maize shoot ionome: Its interaction partners, predictive power, and genetic determinants. PLANT, CELL & ENVIRONMENT 2020; 43:2095-2111. [PMID: 32529648 DOI: 10.1111/pce.13823] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 04/05/2020] [Accepted: 04/18/2020] [Indexed: 05/28/2023]
Abstract
An improved understanding of how to manipulate the accumulation and enrichment of mineral elements in aboveground plant tissues holds promise for future resource efficient and sustainable crop production. The objectives of this study were to (a) evaluate the influence of Fe regimes on mineral element concentrations and contents in the maize shoot as well as their correlations, (b) examine the predictive ability of physiological and morphological traits of individual genotypes of the IBM population from the concentration of mineral elements, and (c) identify genetic factors influencing the mineral element composition within and across Fe regimes. We evaluated the concentration and content of 12 mineral elements in shoots of the IBM population grown in sufficient and deficient Fe regimes and found for almost all mineral elements a significant (α = 0.05) genotypic variance. Across all mineral elements, the variance of genotype*Fe regime interactions was on average even more pronounced. High prediction abilities indicated that mineral elements are powerful predictors of morphological and physiological traits. Furthermore, our results suggest that ZmHMA2/3 and ZmMOT1 are major players in the natural genetic variation of Cd and Mo concentrations and contents of maize shoots, respectively.
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Affiliation(s)
- Benjamin Stich
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences, Düsseldorf, Germany
- Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Andreas Benke
- Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Maria Schmidt
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, Düsseldorf, Germany
| | - Claude Urbany
- Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Rongli Shi
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Nicolaus von Wirén
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
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Mochida K, Nishii R, Hirayama T. Decoding Plant-Environment Interactions That Influence Crop Agronomic Traits. PLANT & CELL PHYSIOLOGY 2020; 61:1408-1418. [PMID: 32392328 PMCID: PMC7434589 DOI: 10.1093/pcp/pcaa064] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/26/2020] [Indexed: 05/16/2023]
Abstract
To ensure food security in the face of increasing global demand due to population growth and progressive urbanization, it will be crucial to integrate emerging technologies in multiple disciplines to accelerate overall throughput of gene discovery and crop breeding. Plant agronomic traits often appear during the plants' later growth stages due to the cumulative effects of their lifetime interactions with the environment. Therefore, decoding plant-environment interactions by elucidating plants' temporal physiological responses to environmental changes throughout their lifespans will facilitate the identification of genetic and environmental factors, timing and pathways that influence complex end-point agronomic traits, such as yield. Here, we discuss the expected role of the life-course approach to monitoring plant and crop health status in improving crop productivity by enhancing the understanding of plant-environment interactions. We review recent advances in analytical technologies for monitoring health status in plants based on multi-omics analyses and strategies for integrating heterogeneous datasets from multiple omics areas to identify informative factors associated with traits of interest. In addition, we showcase emerging phenomics techniques that enable the noninvasive and continuous monitoring of plant growth by various means, including three-dimensional phenotyping, plant root phenotyping, implantable/injectable sensors and affordable phenotyping devices. Finally, we present an integrated review of analytical technologies and applications for monitoring plant growth, developed across disciplines, such as plant science, data science and sensors and Internet-of-things technologies, to improve plant productivity.
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Affiliation(s)
- Keiichi Mochida
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Japan
- Kihara Institute for Biological Research, Yokohama City University, Totsuka-ku, Yokohama, Japan
- Graduate School of Nanobioscience, Yokohama City University, Kanazawa-ku, Yokohama, Japan
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
- Corresponding author: E-mail, ; Fax, +81-45-503-9609
| | - Ryuei Nishii
- School of Information and Data Sciences, Nagasaki University, Nagasaki, Japan
| | - Takashi Hirayama
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
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Guarino F, Improta G, Triassi M, Cicatelli A, Castiglione S. Effects of Zinc Pollution and Compost Amendment on the Root Microbiome of a Metal Tolerant Poplar Clone. Front Microbiol 2020; 11:1677. [PMID: 32760392 PMCID: PMC7373765 DOI: 10.3389/fmicb.2020.01677] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 06/26/2020] [Indexed: 02/02/2023] Open
Abstract
Until recently, many phytoremediation studies were focused solely on a plants ability to reclaim heavy metal (HM) polluted soil through a range of different processes, such as phytoextraction and phytostabilization. However, the interaction between plants and their own rhizosphere microbiome represents a new research frontier for phytoremediation. Our hypothesis is that rhizomicrobiome might play a key role in plant wellness and in the response to external stimuli; therefore, this study aimed to shed light the rhizomicrobiome dynamics after an organic amendment (e.g., compost) and/or HM pollution (e.g., Zn), and its relation with plant reclamation ability. To reach this goal we set up a greenhouse experiment cultivating in pot an elite black poplar clone (N12) selected in the past for its excellent ability to reclaim heavy metals. N12 saplings were grown on a soil amended with compost and/or spiked with high Zn doses. At the end of the experiment, we observed that the compost amendment strongly increased the foliar size but did not affect significantly the Zn accumulation in plant. Furthermore, the rhizomicrobiome communities (bacteria and fungi), investigated through NGS, highlighted how α diversity increased in all treatments compared to the untreated N12 saplings. Soil compost amendment, as well as Zn pollution, strongly modified the bacterial rhizomicrobiome structure. Conversely, the variation of the fungal rhizomicrobiome was only marginally affected by soil Zn addition, and only partially impaired by compost. Nevertheless, substantial alterations of the fungal community were due to both compost and Zn. Together, our experimental results revealed that organic amendment increased the bacterial resistance to external stimuli whilst, in the case of fungi, the amendment made the fungi microbiome more susceptible. Finally, the greater microbiome biodiversity does not imply, in this case, a better plant wellness or phytoremediation ability, although the microbiome plays a role in the external stimuli response supporting plant life.
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Affiliation(s)
- Francesco Guarino
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, Salerno, Italy
| | - Giovanni Improta
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Maria Triassi
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Angela Cicatelli
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, Salerno, Italy
| | - Stefano Castiglione
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, Salerno, Italy
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61
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Wang W, Ding G, White PJ, Wang M, Zou J, Xu F, Hammond JP, Shi L. Genetic dissection of the shoot and root ionomes of Brassica napus grown with contrasting phosphate supplies. ANNALS OF BOTANY 2020; 126:119-140. [PMID: 32221530 PMCID: PMC7304470 DOI: 10.1093/aob/mcaa055] [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: 09/22/2019] [Accepted: 03/26/2020] [Indexed: 05/09/2023]
Abstract
BACKGROUND AND AIMS Mineral elements have many essential and beneficial functions in plants. Phosphorus (P) deficiency can result in changes in the ionomes of plant organs. The aims of this study were to characterize the effects of P supply on the ionomes of shoots and roots, and to identify chromosomal quantitative trait loci (QTLs) for shoot and root ionomic traits, as well as those affecting the partitioning of mineral elements between shoot and root in Brassica napus grown with contrasting P supplies. METHODS Shoot and root concentrations of 11 mineral elements (B, Ca, Cu, Fe, K, Mg, Mn, Na, P, S and Zn) were investigated by inductively coupled plasma optical emission spectrometry (ICP-OES) in a Brassica napus double haploid population grown at an optimal (OP) and a low phosphorus supply (LP) in an agar system. Shoot, root and plant contents, and the partitioning of mineral elements between shoot and root were calculated. KEY RESULTS The tissue concentrations of B, Ca, Cu, K, Mg, Mn, Na, P and Zn were reduced by P starvation, while the concentration of Fe was increased by P starvation in the BnaTNDH population. A total of 133 and 123 QTLs for shoot and root ionomic traits were identified at OP and LP, respectively. A major QTL cluster on chromosome C07 had a significant effect on shoot Mg and S concentrations at LP and was narrowed down to a 2.1 Mb region using an advanced backcross population. CONCLUSIONS The tissue concentration and partitioning of each mineral element was affected differently by P starvation. There was a significant difference in mineral element composition between shoots and roots. Identification of the genes underlying these QTLs will enhance our understanding of processes affecting the uptake and partitioning of mineral elements in Brassica napus.
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Affiliation(s)
- Wei Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Microelement Research Centre, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Guangda Ding
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Microelement Research Centre, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Philip J White
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Microelement Research Centre, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- The James Hutton Institute, Invergowrie, Dundee, UK
| | - Meng Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Microelement Research Centre, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - John P Hammond
- School of Agriculture, Policy and Development, University of Reading, Reading, UK
- Southern Cross Plant Science, Southern Cross University, Lismore, Australia
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Microelement Research Centre, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
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McKeating DR, Fisher JJ, Zhang P, Bennett WW, Perkins AV. Elemental metabolomics in human cord blood: Method validation and trace element quantification. J Trace Elem Med Biol 2020; 59:126419. [PMID: 31711786 DOI: 10.1016/j.jtemb.2019.126419] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/26/2019] [Accepted: 10/18/2019] [Indexed: 01/15/2023]
Abstract
BACKGROUND Trace elements are an essential requirement for human health and development and changes in trace element status have been associated with pregnancy complications such as gestational diabetes mellitus (GDM), pre-eclampsia (PE), fetal growth restriction (FGR), and preterm birth. Elemental metabolomics, which involves the simultaneous quantification and characterisation of multiple elements, could provide important insights into these gestational disorders. METHODS This study used an Agilent 7900 inductively coupled plasma mass spectrometer (ICP-MS) to simultaneously measure 68 elements, in 166 placental cord blood samples collected from women with various pregnancy complications (control, hypertensive, PE, GDM, FGR, pre-term, and post-term birth). RESULTS There were single element differences across gestational outcomes for elements Mg, P, Cr, Ni, Sr, Mo, I, Au, Pb, and U. Hypertensive and post-term pregnancies were significantly higher in Ni concentrations when compared to controls (control = 2.74 μg/L, hypertensive = 6.72 μg/L, post-term = 7.93 μg/L, p < 0.05), iodine concentration was significantly higher in post-term pregnancies (p < 0.05), and Pb concentrations were the lowest in pre-term pregnancies (pre-term = 2.79 μg/L, control = 4.68 μg/L, PE = 5.32 μg/L, GDM = 8.27 μg/L, p < 0.01). Further analysis was conducted using receiver operating characteristic (ROC) curves for differentiating pregnancy groups. The ratio of Sn/Pb showed the best diagnostic power in discriminating between control and pre-term birth with area under the curve (AUC) 0.86. When comparing control and post-term birth, Mg/Cr (AUC = 0.84), and Cr (AUC = 0.83) had the best diagnostic powers. In pre-term and post-term comparisons Ba was the best single element (81.5%), and P/Cu provided the best ratio (91.7%). CONCLUSIONS This study has shown that analysis of multiple elements can enable differentiation between fetal cord blood samples from control, hypertensive, PE, GDM, FGR, pre and post-term pregnancies. This data highlights the power of elemental metabolomics and provides a basis for future gestational studies.
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Affiliation(s)
- Daniel R McKeating
- School of Medical Science, Griffith University, Gold Coast Campus, Southport, 9726, Queensland, Australia
| | - Joshua J Fisher
- School of Medical Science, Griffith University, Gold Coast Campus, Southport, 9726, Queensland, Australia
| | - Ping Zhang
- School of Medical Science, Griffith University, Gold Coast Campus, Southport, 9726, Queensland, Australia
| | - William W Bennett
- School of Environmental Science, Griffith University, Gold Coast Campus, Southport, 9726, Queensland, Australia
| | - Anthony V Perkins
- School of Medical Science, Griffith University, Gold Coast Campus, Southport, 9726, Queensland, Australia.
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Jeyasingh PD, Goos JM, Lind PR, Roy Chowdhury P, Sherman RE. Phosphorus supply shifts the quotas of multiple elements in algae and
Daphnia
: ionomic basis of stoichiometric constraints. Ecol Lett 2020; 23:1064-1072. [DOI: 10.1111/ele.13505] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/20/2020] [Accepted: 03/11/2020] [Indexed: 12/22/2022]
Affiliation(s)
| | - Jared M. Goos
- Department of Integrative Biology Oklahoma State University Stillwater OK USA
- BioFire Diagnostics Salt Lake City UT USA
| | - Patrick R. Lind
- Department of Integrative Biology Oklahoma State University Stillwater OK USA
- Department of Biological Sciences University of Arkansas Fayetteville AR USA
| | - Priyanka Roy Chowdhury
- Department of Integrative Biology Oklahoma State University Stillwater OK USA
- Department of Biology Keene State College Keene NH USA
| | - Ryan E. Sherman
- Department of Integrative Biology Oklahoma State University Stillwater OK USA
- Biology Program MacMurray College Jacksonville IL USA
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64
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Coulibali Z, Cambouris AN, Parent SÉ. Cultivar-specific nutritional status of potato (Solanum tuberosum L.) crops. PLoS One 2020; 15:e0230458. [PMID: 32168339 PMCID: PMC7069643 DOI: 10.1371/journal.pone.0230458] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 03/01/2020] [Indexed: 11/28/2022] Open
Abstract
Gradients in the elemental composition of a potato leaf tissue (i.e. its ionome) can be linked to crop potential. Because the ionome is a function of genetics and environmental conditions, practitioners aim at fine-tuning fertilization to obtain an optimal ionome based on the needs of potato cultivars. Our objective was to assess the validity of cultivar grouping and predict potato tuber yields using foliar ionomes. The dataset comprised 3382 observations in Québec (Canada) from 1970 to 2017. The first mature leaves from top were sampled at the beginning of flowering for total N, P, K, Ca, and Mg analysis. We preprocessed nutrient concentrations (ionomes) by centering each nutrient to the geometric mean of all nutrients and to a filling value, a transformation known as row-centered log ratios (clr). A density-based clustering algorithm (dbscan) on these preprocessed ionomes failed to delineate groups of high-yield cultivars. We also used the preprocessed ionomes to assess their effects on tuber yield classes (high- and low-yields) on a cultivar basis using k-nearest neighbors, random forest and support vector machines classification algorithms. Our machine learning models returned an average accuracy of 70%, a fair diagnostic potential to detect in-season nutrient imbalance of potato cultivars using clr variables considering potential confounding factors. Optimal ionomic regions of new cultivars could be assigned to the one of the closest documented cultivar.
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Affiliation(s)
- Zonlehoua Coulibali
- Department of Soils and Agrifood Engineering, Université Laval, Québec City, Québec, Canada
| | - Athyna Nancy Cambouris
- Quebec Research and Development Centre, Agriculture and Agri-Food Canada, Québec City, Québec, Canada
| | - Serge-Étienne Parent
- Department of Soils and Agrifood Engineering, Université Laval, Québec City, Québec, Canada
- * E-mail:
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65
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Chen A, Hansen TH, Olsen LI, Palmgren M, Husted S, Schjoerring JK, Persson DP. Towards single-cell ionomics: a novel micro-scaled method for multi-element analysis of nanogram-sized biological samples. PLANT METHODS 2020; 16:31. [PMID: 32165911 PMCID: PMC7059671 DOI: 10.1186/s13007-020-00566-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 02/07/2020] [Indexed: 05/24/2023]
Abstract
BACKGROUND To understand processes regulating nutrient homeostasis at the single-cell level there is a need for new methods that allow multi-element profiling of biological samples ultimately only available as isolated tissues or cells, typically in nanogram-sized samples. Apart from tissue isolation, the main challenges for such analyses are to obtain a complete and homogeneous digestion of each sample, to keep sample dilution at a minimum and to produce accurate and reproducible results. In particular, determining the weight of small samples becomes increasingly challenging when the sample amount decreases. RESULTS We developed a novel method for sampling, digestion and multi-element analysis of nanogram-sized plant tissue, along with strategies to quantify element concentrations in samples too small to be weighed. The method is based on tissue isolation by laser capture microdissection (LCM), followed by pressurized micro-digestion and ICP-MS analysis, the latter utilizing a stable µL min-1 sample aspiration system. The method allowed for isolation, digestion and analysis of micro-dissected tissues from barley roots with an estimated sample weight of only ~ 400 ng. In the collection and analysis steps, a number of contamination sources were identified. Following elimination of these sources, several elements, including magnesium (Mg), phosphorus (P), potassium (K) and manganese (Mn), could be quantified. By measuring the exact area and thickness of each of the micro-dissected tissues, their volume was calculated. Combined with an estimated sample density, the sample weights could subsequently be calculated and the fact that these samples were too small to be weighed could thereby be circumvented. The method was further documented by analysis of Arabidopsis seeds (~ 20 µg) as well as tissue fractions of such seeds (~ 10 µg). CONCLUSIONS The presented method enables collection and multi-element analysis of small-sized biological samples, ranging down to the nanogram level. As such, the method paves the road for single cell and tissue-specific quantitative ionomics, which allow for future transcriptional, proteomic and metabolomic data to be correlated with ionomic profiles. Such analyses will deepen our understanding of how the elemental composition of plants is regulated, e.g. by transporter proteins and physical barriers (i.e. the Casparian strip and suberin lamellae in the root endodermis).
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Affiliation(s)
- Anle Chen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Thomas H. Hansen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Lene I. Olsen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Michael Palmgren
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Søren Husted
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Jan K. Schjoerring
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Daniel Pergament Persson
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
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66
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Shelden MC, Gilbert SE, Tyerman SD. A laser ablation technique maps differences in elemental composition in roots of two barley cultivars subjected to salinity stress. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:1462-1473. [PMID: 31686423 DOI: 10.1111/tpj.14599] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 10/29/2019] [Indexed: 05/06/2023]
Abstract
In saline soils, high levels of sodium (Na+ ) and chloride (Cl- ) ions reduce root growth by inhibiting cell division and elongation, thereby impacting on crop yield. Soil salinity can lead to Na+ toxicity of plant cells, influencing the uptake and retention of other important ions [i.e. potassium (K+ )] required for growth. However, measuring and quantifying soluble ions in their native, cellular environment is inherently difficult. Technologies that allow in situ profiling of plant tissues are fundamental for our understanding of abiotic stress responses and the development of tolerant crops. Here, we employ laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) to quantify Na, K and other elements [calcium (Ca), magnesium (Mg), sulphur (S), phosphorus (P), iron (Fe)] at high spatial resolution in the root growth zone of two genotypes of barley (Hordeum vulgare) that differ in salt-tolerance, cv. Clipper (tolerant) and Sahara (sensitive). The data show that Na+ was excluded from the meristem and cell division zone, indicating that Na+ toxicity is not directly reducing cell division in the salt-sensitive genotype, Sahara. Interestingly, in both genotypes, K+ was strongly correlated with Na+ concentration, in response to salt stress. In addition, we also show important genetic differences and salt-specific changes in elemental composition in the root growth zone. These results show that LA-ICP-MS can be used for fine mapping of soluble ions (i.e. Na+ and K+ ) in plant tissues, providing insight into the link between Na+ toxicity and root growth responses to salt stress.
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Affiliation(s)
- Megan C Shelden
- ARC Centre of Excellence in Plant Energy Biology, School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA, 5064, Australia
| | - Sarah E Gilbert
- Adelaide Microscopy, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Stephen D Tyerman
- ARC Centre of Excellence in Plant Energy Biology, School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA, 5064, Australia
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Fatiukha A, Klymiuk V, Peleg Z, Saranga Y, Cakmak I, Krugman T, Korol AB, Fahima T. Variation in phosphorus and sulfur content shapes the genetic architecture and phenotypic associations within the wheat grain ionome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:555-572. [PMID: 31571297 DOI: 10.1111/tpj.14554] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 09/10/2019] [Accepted: 09/23/2019] [Indexed: 05/04/2023]
Abstract
Dissection of the genetic basis of wheat ionome is crucial for understanding the physiological and biochemical processes underlying mineral accumulation in seeds, as well as for efficient crop breeding. Most of the elements essential for plants are metals stored in seeds as chelate complexes with phytic acid or sulfur-containing compounds. We assume that the involvement of phosphorus and sulfur in metal chelation is the reason for strong phenotypic correlations within ionome. Adjustment of element concentrations for the effect of variation in phosphorus and sulfur seed content resulted in drastic change of phenotypic correlations between the elements. The genetic architecture of wheat grain ionome was characterized by quantitative trait loci (QTL) analysis using a cross between durum and wild emmer wheat. QTL analysis of the adjusted traits and two-trait analysis of the initial traits paired with either P or S considerably improved QTL detection power and accuracy, resulting in the identification of 105 QTLs and 617 QTL effects for 11 elements. Candidate gene search revealed some potential functional associations between QTLs and corresponding genes within their intervals. Thus, we have shown that accounting for variation in P and S is crucial for understanding of the physiological and genetic regulation of mineral composition of wheat grain ionome and can be implemented for other plants.
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Affiliation(s)
- Andrii Fatiukha
- Institute of Evolution, University of Haifa, Haifa, 3498838, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, 199 Abba-Khoushy Ave, Mt. Carmel, Haifa, 3498838, Israel
| | - Valentyna Klymiuk
- Institute of Evolution, University of Haifa, Haifa, 3498838, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, 199 Abba-Khoushy Ave, Mt. Carmel, Haifa, 3498838, Israel
| | - Zvi Peleg
- R. H. Smith Institute of Plant Science & Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Yehoshua Saranga
- R. H. Smith Institute of Plant Science & Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Ismail Cakmak
- Faculty of Engineering & Natural Sciences, Sabanci University, Tuzla İstanbul, 34956, Turkey
| | - Tamar Krugman
- Institute of Evolution, University of Haifa, Haifa, 3498838, Israel
| | - Abraham B Korol
- Institute of Evolution, University of Haifa, Haifa, 3498838, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, 199 Abba-Khoushy Ave, Mt. Carmel, Haifa, 3498838, Israel
| | - Tzion Fahima
- Institute of Evolution, University of Haifa, Haifa, 3498838, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, 199 Abba-Khoushy Ave, Mt. Carmel, Haifa, 3498838, Israel
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Tan Y, Sun L, Song Q, Mao D, Zhou J, Jiang Y, Wang J, Fan T, Zhu Q, Huang D, Xiao H, Chen C. Genetic architecture of subspecies divergence in trace mineral accumulation and elemental correlations in the rice grain. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:529-545. [PMID: 31734869 DOI: 10.1007/s00122-019-03485-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 11/11/2019] [Indexed: 05/12/2023]
Abstract
Genome differentiation has shaped the divergence in element concentration between rice subspecies and contributed to the correlation among trace minerals in the rice grain. The balance between trace minerals in rice, a staple food for more than half of the world's population, is crucial for human health. However, the genetic basis underlying the correlation between trace minerals has not been fully elucidated. To address this issue, we first quantified the concentrations of 11 trace minerals in the grains of a diversity panel of 575 rice cultivars. We found that eight elements were accumulated at significantly different levels between the indica and japonica subspecies, and we also observed significant correlation patterns among a number of elements. Further, using a genome-wide association study, we identified a total of 96 significant association loci (SALs). The differentiation of the major-effect SALs along with the different number of high-concentration alleles present in the two subspecies shaped the different element performance in indica and japonica varieties. Only a few SALs located in clusters and the majority of SALs showed subspecies/subgroup differentiation, indicating that the correlations between elements in the diversity panel were mainly caused by genome differentiation instead of shared genetic basis. The genetic architecture unveiled in this study will facilitate improvement in breeding for trace mineral content.
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Affiliation(s)
- Yongjun Tan
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Innovation Academy for Seed Design, Chinese Academy of Sciences, Changsha, 410125, Hunan, China
- University of Chinese Academy of Science, Beijing, 100049, China
| | - Liang Sun
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Innovation Academy for Seed Design, Chinese Academy of Sciences, Changsha, 410125, Hunan, China
| | - Qingnan Song
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Science, Beijing, 100049, China
| | - Donghai Mao
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Innovation Academy for Seed Design, Chinese Academy of Sciences, Changsha, 410125, Hunan, China
| | - Jieqiang Zhou
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Innovation Academy for Seed Design, Chinese Academy of Sciences, Changsha, 410125, Hunan, China
| | - Youru Jiang
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Innovation Academy for Seed Design, Chinese Academy of Sciences, Changsha, 410125, Hunan, China
| | - Jiurong Wang
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Innovation Academy for Seed Design, Chinese Academy of Sciences, Changsha, 410125, Hunan, China
| | - Tony Fan
- University of Toronto, Toronto, M5S2E5, Canada
| | - Qihong Zhu
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Innovation Academy for Seed Design, Chinese Academy of Sciences, Changsha, 410125, Hunan, China
| | - Daoyou Huang
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Innovation Academy for Seed Design, Chinese Academy of Sciences, Changsha, 410125, Hunan, China
| | - Han Xiao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Caiyan Chen
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Innovation Academy for Seed Design, Chinese Academy of Sciences, Changsha, 410125, Hunan, China.
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69
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Streich J, Romero J, Gazolla JGFM, Kainer D, Cliff A, Prates ET, Brown JB, Khoury S, Tuskan GA, Garvin M, Jacobson D, Harfouche AL. Can exascale computing and explainable artificial intelligence applied to plant biology deliver on the United Nations sustainable development goals? Curr Opin Biotechnol 2020; 61:217-225. [DOI: 10.1016/j.copbio.2020.01.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 01/27/2020] [Accepted: 01/28/2020] [Indexed: 01/26/2023]
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70
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Pita-Barbosa A, Ricachenevsky FK, Wilson M, Dottorini T, Salt DE. Transcriptional plasticity buffers genetic variation in zinc homeostasis. Sci Rep 2019; 9:19482. [PMID: 31862901 PMCID: PMC6925235 DOI: 10.1038/s41598-019-55736-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 12/02/2019] [Indexed: 11/08/2022] Open
Abstract
In roots of Arabidopsis thaliana, Zn can be either loaded into the xylem for translocation to the shoot or stored in vacuoles. Vacuolar storage is achieved through the action of the Zn/Cd transporter HMA3 (Heavy Metal Atpase 3). The Col-0 accession has an HMA3 loss-of-function allele resulting in high shoot Cd, when compared to accession CSHL-5 which has a functional allele and low shoot Cd. Interestingly, both Col-0 and CSHL-5 have similar shoot Zn concentrations. We hypothesize that plants sense changes in cytosolic Zn that are due to variation in HMA3 function, and respond by altering expression of genes related to Zn uptake, transport and compartmentalisation, in order to maintain Zn homeostasis. The expression level of genes known to be involved in Zn homeostasis were quantified in both wild-type Col-0 and Col-0::HMA3CSHL-5 plants transformed with the functional CSHL-5 allele of HMA3. We observed significant positive correlations between expression of HMA3 and of genes known to be involved in Zn homeostasis, including ZIP3, ZIP4, MTP1, and bZIP19. The results support our hypothesis that alteration in the level of function of HMA3 is counterbalanced by the fine regulation of the Zn homeostasis gene network in roots of A. thaliana.
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Affiliation(s)
- Alice Pita-Barbosa
- Center for Coastal, Limnology and Marine Studies, Federal University of Rio Grande do Sul, Litoral Norte Campus, Imbé, RS, 95625-000, Brazil
- Future Food Beacon of Excellence and the School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Felipe K Ricachenevsky
- Biology Department, Center of Natural and Exact Sciences, Federal University of Santa Maria, Santa Maria, Brazil
| | - Michael Wilson
- Future Food Beacon of Excellence and the School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Tania Dottorini
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, LE12 5RD, UK
| | - David E Salt
- Future Food Beacon of Excellence and the School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK.
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71
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Wang Z, Shi M, Wei Q, Chen Z, Huang J, Xia J. OsCASP1 forms complexes with itself and OsCASP2 in rice. PLANT SIGNALING & BEHAVIOR 2019; 15:1706025. [PMID: 31851568 PMCID: PMC7012095 DOI: 10.1080/15592324.2019.1706025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/29/2019] [Accepted: 11/30/2019] [Indexed: 05/27/2023]
Abstract
OsCASP1 (Casparian strip domain protein 1) was recently identified to function in Casparian strip (CS) formation at the endodermal cells in rice roots, which was required for selective mineral uptake in rice. Here, we further investigate the functional form of OsCASP1 in vivo. Expression analysis shows that OsCASP1, OsCASP2, OsCASP3, and OsCASP5 were expressed in roots apart from OsCASP4. A yeast two-hybrid (Y2H) assay revealed that OsCASP1 can interact with itself and OsCASP2, but not with OsCASP3 and OsCASP5. These interactions of OsCASP1 with itself and OsCASP2 at the plasma membrane were confirmed using bimolecular fluorescence complementation (BiFC) in rice protoplasts. These results indicated that OsCASP1 can form complexes with itself and OsCASP2 in rice roots.
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Affiliation(s)
- Zhigang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning China
| | - Mingxing Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning China
| | - Qiuxing Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning China
| | - Zhiwei Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning China
| | - Jingjing Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning China
| | - Jixing Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning China
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72
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Wang C, Tang Z, Zhuang JY, Tang Z, Huang XY, Zhao FJ. Genetic mapping of ionomic quantitative trait loci in rice grain and straw reveals OsMOT1;1 as the putative causal gene for a molybdenum QTL qMo8. Mol Genet Genomics 2019; 295:391-407. [PMID: 31797032 DOI: 10.1007/s00438-019-01632-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 11/25/2019] [Indexed: 10/25/2022]
Abstract
Rice is a major dietary source of essential mineral nutrients and toxic elements (aka ionome) for humans. However, the genetic basis underlying the variation in ionome is still largely unknown. Here, we mapped 51 and 61 quantitative trait loci (QTLs) controlling the concentrations of 13 and 15 elements in rice (Oryza sativa L.) grain and straw, respectively, using a recombinant inbred lines (RILs) that were grown at three different field sites in 3 years. Several QTLs were repeatedly detected in both grain and straw or in multiple years; the resulting 87 unique QTLs with 17 of them (20%) were co-localized with previously reported corresponding QTLs and 70 were novel ionomic QTLs. At least, 14 genomic clusters that controlled the concentrations of multiple elements were identified. Furthermore, we identified a molybdate transporter gene OsMOT1;1 as the putative causal gene for a QTL controlling molybdenum concentration in both straw and grain. QTL analyses based on the concentrations of multiple elements in both grain and straw of RIL population grown in three field sites in 3 years allow us to identify tissue common QTLs and reproducible QTLs that were validated in multiple years. The identification of ionomic QTLs will be useful in revealing the molecular mechanisms underlying the accumulation of elements in rice and providing the opportunity to reduce the accumulation of toxic elements and enrich the accumulation of beneficial elements in rice grain.
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Affiliation(s)
- Chengcheng Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhong Tang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jie-Yun Zhuang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, National Rice Research Institute China, Hangzhou, 310006, China
| | - Zhu Tang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xin-Yuan Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Fang-Jie Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
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Rana N, Rahim MS, Kaur G, Bansal R, Kumawat S, Roy J, Deshmukh R, Sonah H, Sharma TR. Applications and challenges for efficient exploration of omics interventions for the enhancement of nutritional quality in rice (Oryza sativa L.). Crit Rev Food Sci Nutr 2019; 60:3304-3320. [DOI: 10.1080/10408398.2019.1685454] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Nitika Rana
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | | | - Gazaldeep Kaur
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Ruchi Bansal
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Surbhi Kumawat
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Joy Roy
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Humira Sonah
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Tilak Raj Sharma
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
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Abstract
Selenium is an essential trace element for maintenance of overall health, whose deficiency and dyshomeostasis have been linked to a variety of diseases and disorders. The majority of previous researches focused on characterization of genes encoding selenoproteins or proteins involved in selenium metabolism as well as their functions. Many studies in humans also investigated the relationship between selenium and complex diseases, but their results have been inconsistent. In recent years, systems biology and "-omics" approaches have been widely used to study complex and global variations of selenium metabolism and function in physiological and different pathological conditions. The present paper reviews recent progress in large-scale and systematic analyses of the relationship between selenium status or selenoproteins and several complex diseases, mainly including population-based cohort studies and meta-analyses, genetic association studies, and some other omics-based studies. Advances in ionomics and its application in studying the interaction between selenium and other trace elements in human health and diseases are also discussed.
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Affiliation(s)
- Huimin Ying
- Department of Endocrinology, Xixi Hospital of Hangzhou, Hangzhou, 310023, Zhejiang, People's Republic of China
- 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, People's Republic of China
| | - 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, People's Republic of China.
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Orłowski G, Karg J, Kamiński P, Baszyński J, Szady-Grad M, Ziomek K, Klawe JJ. Edge effect imprint on elemental traits of plant-invertebrate food web components of oilseed rape fields. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 687:1285-1294. [PMID: 31412462 DOI: 10.1016/j.scitotenv.2019.06.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 05/31/2019] [Accepted: 06/02/2019] [Indexed: 06/10/2023]
Abstract
Of fundamental importance for the functioning of a community is the flow of energy and elements through its components. However, the question of how (if at all) the edge effect of habitats can drive elemental traits of organisms has hitherto been largely neglected issue in ecosystem ecology at the community level. We quantified the abundance of invertebrates and measured the elemental composition (K, Na, Ca, Mg, Cu, Zn, Fe, Mn, As, Cd, Co and Pb) of 15 different organisms within the plant-invertebrate food web (plant - oilseed rape pests/herbivores - pollinators = wild bees - saprovores - predators - parasitoids) sampled in 34 fields of a key bioenergy crop that is an exceptionally strong biodiversity driver, the oilseed rape. Then these were related to the individual field edge habitat features (including typically anthropogenic ones like dirt and tarred roads) measured within a 100 m radius around the invertebrate sampling sites. Our study showed that elemental traits of the plant-invertebrate food web components in oilseed rape crops varied owing to the habitat specificity determined at the relatively small spatial scale of an individual field, and that the elemental traits of these organisms differed from both an inter- and an intra-guild perspective. The major mechanistic explanation for most of these relationships seems to derive from the secondary gut content effect. Determining one single state for the homeostatic/stoichiometric regulation of chemical elements in invertebrates based on the application of whole-body metal concentrations is in principle impossible, because of the unknown noise caused by the inclusion of extracellular portions of metals in the analysis. It is thus imperative to develop consistent principles for assessing elemental traits of organisms that are based on highly sensitive and high-throughput analytical methods for the ionomic profiling of microsamples at the organ, tissue, cellular or even sub-cellular levels.
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Affiliation(s)
- Grzegorz Orłowski
- Institute of Agricultural and Forest Environment, Polish Academy of Sciences, Bukowska 19, 60-809 Poznań, Poland.
| | - Jerzy Karg
- Department of Nature Conservation, Faculty of Biological Sciences, University of Zielona Góra, Prof. Z. Szafrana 1, 65-516 Zielona Góra, Poland
| | - Piotr Kamiński
- Department of Medical Biology and Biochemistry, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, M. Skłodowska-Curie 9, 85-094 Bydgoszcz, Poland; Department of Biotechnology, Faculty of Biological Sciences, University of Zielona Góra, Prof. Z. Szafran St. 1, 65-516 Zielona Góra, Poland
| | - Jędrzej Baszyński
- Department of Medical Biology and Biochemistry, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, M. Skłodowska-Curie 9, 85-094 Bydgoszcz, Poland
| | - Małgorzata Szady-Grad
- Department of Biotechnology, Faculty of Biological Sciences, University of Zielona Góra, Prof. Z. Szafran St. 1, 65-516 Zielona Góra, Poland
| | - Krzysztof Ziomek
- Institute of Agricultural and Forest Environment, Polish Academy of Sciences, Bukowska 19, 60-809 Poznań, Poland
| | - Jacek J Klawe
- Department of Hygiene, Epidemiology and Ergonomics, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, M. Skłodowska-Curie 9, 85-094 Bydgoszcz, Poland
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76
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Courbet G, Gallardo K, Vigani G, Brunel-Muguet S, Trouverie J, Salon C, Ourry A. Disentangling the complexity and diversity of crosstalk between sulfur and other mineral nutrients in cultivated plants. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:4183-4196. [PMID: 31055598 DOI: 10.1093/jxb/erz214] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 04/29/2019] [Indexed: 05/02/2023]
Abstract
A complete understanding of ionome homeostasis requires a thorough investigation of the dynamics of the nutrient networks in plants. This review focuses on the complexity of interactions occurring between S and other nutrients, and these are addressed at the level of the whole plant, the individual tissues, and the cellular compartments. With regards to macronutrients, S deficiency mainly acts by reducing plant growth, which in turn restricts the root uptake of, for example, N, K, and Mg. Conversely, deficiencies in N, K, or Mg reduce uptake of S. TOR (target of rapamycin) protein kinase, whose involvement in the co-regulation of C/N and S metabolism has recently been unravelled, provides a clue to understanding the links between S and plant growth. In legumes, the original crosstalk between N and S can be found at the level of nodules, which show high requirements for S, and hence specifically express a number of sulfate transporters. With regards to micronutrients, except for Fe, their uptake can be increased under S deficiency through various mechanisms. One of these results from the broad specificity of root sulfate transporters that are up-regulated during S deficiency, which can also take up some molybdate and selenate. A second mechanism is linked to the large accumulation of sulfate in the leaf vacuoles, with its reduced osmotic contribution under S deficiency being compensated for by an increase in Cl uptake and accumulation. A third group of broader mechanisms that can explain at least some of the interactions between S and micronutrients concerns metabolic networks where several nutrients are essential, such as the synthesis of the Mo co-factor needed by some essential enzymes, which requires S, Fe, Zn and Cu for its synthesis, and the synthesis and regulation of Fe-S clusters. Finally, we briefly review recent developments in the modelling of S responses in crops (allocation amongst plant parts and distribution of mineral versus organic forms) in order to provide perspectives on prediction-based approaches that take into account the interactions with other minerals such as N.
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Affiliation(s)
- Galatéa Courbet
- Normandie Université, UNICAEN, INRA, UMR 950 Ecophysiologie Végétale, Agronomie et Nutritions N, C, S, Esplanade de la Paix, Caen Cedex, France
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne, Franche-Comté, Dijon, France
| | - Karine Gallardo
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne, Franche-Comté, Dijon, France
| | - Gianpiero Vigani
- Plant Physiology Unit, Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Sophie Brunel-Muguet
- Normandie Université, UNICAEN, INRA, UMR 950 Ecophysiologie Végétale, Agronomie et Nutritions N, C, S, Esplanade de la Paix, Caen Cedex, France
| | - Jacques Trouverie
- Normandie Université, UNICAEN, INRA, UMR 950 Ecophysiologie Végétale, Agronomie et Nutritions N, C, S, Esplanade de la Paix, Caen Cedex, France
| | - Christophe Salon
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne, Franche-Comté, Dijon, France
| | - Alain Ourry
- Normandie Université, UNICAEN, INRA, UMR 950 Ecophysiologie Végétale, Agronomie et Nutritions N, C, S, Esplanade de la Paix, Caen Cedex, France
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77
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Li Q, Hu C, Lin J, Yang Z, Zhou Q, Yang R, Yuan H, Zhu X, Lv Y, Liang Q, Lv Z, Sun L, Zhang Y. Urinary ionomic analysis reveals new relationship between minerals and longevity in a Han Chinese population. J Trace Elem Med Biol 2019; 53:69-75. [PMID: 30910209 DOI: 10.1016/j.jtemb.2019.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 01/18/2019] [Accepted: 02/11/2019] [Indexed: 12/14/2022]
Abstract
Human longevity involves genetic, nutritional, environmental and many other factors playing a key role in healthy aging. Previous studies have shown that mineral metabolism and homeostasis are associated with lifespan extension. However, the majority of them have focused on a limited number of elements and ignored the complex relationship between them. In this study, we carried out a network-based approach to investigate the urinary ionome of nonagenarians and centenarians (longevity group) when compared with their biologically unrelated and younger family members (control group) from a Han Chinese population. Several differentially changed elements were identified, almost all of which showed an elevated level in the longevity group. Correlation analysis of the ionome revealed significant element-element interactions in each group. We then divided each group into distinct subgroups according to age ranges, and built the elemental correlation network for each of them. Significant elemental correlations and correlation changes involving all examined elements were identified within or between different subgroups, implying a highly dynamic and complex crosstalk among the elements during human life. Finally, more similar elemental patterns were observed between extremely old and middle-aged people. Overall, our data reveal new relationship between urinary minerals and human longevity, which may extend our understanding of the mechanism of healthy aging.
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Affiliation(s)
- Qingxiu Li
- Shenzhen Key Laboratory of Marine Bioresources and Ecology, Brain Disease and Big Data Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, Guangdong, PR China; The MOH Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing 100730, PR China
| | - Caiyou Hu
- Department of Neurology, Jiangbin Hospital, Nanning 530021, Guangxi, PR China
| | - Jie Lin
- Shenzhen Key Laboratory of Marine Bioresources and Ecology, Brain Disease and Big Data Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, Guangdong, PR China
| | - Ze Yang
- The MOH Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing 100730, PR China
| | - Qi Zhou
- The MOH Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing 100730, PR China
| | - Ruiyue Yang
- The MOH Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing 100730, PR China
| | - Huiping Yuan
- The MOH Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing 100730, PR China
| | - Xiaoquan Zhu
- The MOH Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing 100730, PR China
| | - Yuan Lv
- Department of Neurology, Jiangbin Hospital, Nanning 530021, Guangxi, PR China
| | - Qinghua Liang
- Department of Neurology, Jiangbin Hospital, Nanning 530021, Guangxi, PR China
| | - Zeping Lv
- Department of Neurology, Jiangbin Hospital, Nanning 530021, Guangxi, PR China
| | - Liang Sun
- The MOH Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing 100730, PR China.
| | - 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, 518060, Guangdong, PR China.
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Peñuelas J, Fernández‐Martínez M, Ciais P, Jou D, Piao S, Obersteiner M, Vicca S, Janssens IA, Sardans J. The bioelements, the elementome, and the biogeochemical niche. Ecology 2019; 100:e02652. [DOI: 10.1002/ecy.2652] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 12/26/2018] [Accepted: 01/16/2019] [Indexed: 01/30/2023]
Affiliation(s)
- Josep Peñuelas
- CSIC Global Ecology Unit CREAF‐CSIC‐UAB Bellaterra 08193 Spain
- CREAF Cerdanyola del Valles 08193 Spain
| | - Marcos Fernández‐Martínez
- CREAF Cerdanyola del Valles 08193 Spain
- Research Group Plants and Ecosystems (PLECO) Department of Biology University of Antwerp Wilrijk B‐2610 Belgium
| | - Philippe Ciais
- Laboratoire des Sciences du Climat et de l'Environnement IPSL Gif‐sur‐Yvette 91191 France
| | - David Jou
- Department of Physics Universitat Autònoma de Barcelona Bellaterra 08193 Spain
| | - Shilong Piao
- Sino‐French Institute for Earth System Science College of Urban and Environmental Sciences Peking University Beijing 100871 China
| | - Michael Obersteiner
- International Institute for Applied Systems Analysis (IIASA), Ecosystems Services and Management Schlossplatz 1 Laxenburg A‐2361 Austria
| | - Sara Vicca
- Research Group Plants and Ecosystems (PLECO) Department of Biology University of Antwerp Wilrijk B‐2610 Belgium
| | - Ivan A. Janssens
- Research Group Plants and Ecosystems (PLECO) Department of Biology University of Antwerp Wilrijk B‐2610 Belgium
| | - Jordi Sardans
- CSIC Global Ecology Unit CREAF‐CSIC‐UAB Bellaterra 08193 Spain
- CREAF Cerdanyola del Valles 08193 Spain
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79
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Nicolas O, Charles MT, Jenni S, Toussaint V, Parent SÉ, Beaulieu C. The Ionomics of Lettuce Infected by Xanthomonas campestris pv. vitians. FRONTIERS IN PLANT SCIENCE 2019; 10:351. [PMID: 30984219 PMCID: PMC6448033 DOI: 10.3389/fpls.2019.00351] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 03/07/2019] [Indexed: 05/31/2023]
Abstract
Bacterial leaf spot (BLS) caused by Xanthomonas campestris pv. vitians (Xcv) places a major constraint on lettuce production worldwide. The most sustainable strategy known to date for controlling BLS is the use of resistant cultivars. The nutrient elemental signature (ionome) of ten lettuce cultivars with three levels of resistance was analyzed by inductively coupled plasma optical emission spectroscopy (ICP-OES) to determine which nutrient balances are linked to resistance to BLS, and to assess the effect of Xcv infection on the ionome. The elemental concentrations were preprocessed with isometric log-ratios to define nutrient balances. Using this approach, 4 out of 11 univariate nutrient balances were found to significantly influence the resistance of lettuce cultivars to BLS (P < 0.05). These significant balances were the overall nutritional status balancing all measured nutrients with their complementary in the dry mass, as well as balances [Mn | Zn,Cu], [Zn | Cu], and [S,N | P]. Moreover, the infection of lettuce cultivars mostly affected the lettuce ionome on the [N,S | P] balance, where infection tended to lean the balance toward the N,S part relatively to P. This study shows that nutrient uptake in lettuce can be affected by BLS infection and that nutrient status influences resistance to BLS infection.
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Affiliation(s)
- Olbert Nicolas
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada
- Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu Research and Development Centre, Saint-Jean-sur-Richelieu, QC, Canada
| | - Marie Thérèse Charles
- Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu Research and Development Centre, Saint-Jean-sur-Richelieu, QC, Canada
| | - Sylvie Jenni
- Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu Research and Development Centre, Saint-Jean-sur-Richelieu, QC, Canada
| | - Vicky Toussaint
- Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu Research and Development Centre, Saint-Jean-sur-Richelieu, QC, Canada
| | - Serge-Étienne Parent
- Department of Soils and Agri-Food Engineering, Université Laval, Quebec City, QC, Canada
| | - Carole Beaulieu
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada
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80
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Rudman SM, Goos JM, Burant JB, Brix KV, Gibbons TC, Brauner CJ, Jeyasingh PD. Ionome and elemental transport kinetics shaped by parallel evolution in threespine stickleback. Ecol Lett 2019; 22:645-653. [DOI: 10.1111/ele.13225] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 12/22/2018] [Accepted: 01/05/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Seth M. Rudman
- Department of Biology University of Pennsylvania Philadelphia PA USA
| | - Jared M. Goos
- Department of Integrative Biology Oklahoma State University Stillwater OK USA
| | - Joseph B. Burant
- Department of Integrative Biology University of Guelph Guelph ON Canada
| | - Kevin V. Brix
- Department of Marine Biology and Ecology University of Miami RSMAS Miami FL USA
| | - Taylor C. Gibbons
- Department of Zoology University of British Columbia Vancouver BC Canada
| | - Colin J. Brauner
- Department of Zoology University of British Columbia Vancouver BC Canada
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81
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McKeating DR, Fisher JJ, Perkins AV. Elemental Metabolomics and Pregnancy Outcomes. Nutrients 2019; 11:E73. [PMID: 30609706 PMCID: PMC6356574 DOI: 10.3390/nu11010073] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 12/26/2018] [Accepted: 01/01/2019] [Indexed: 01/22/2023] Open
Abstract
Trace elements are important for human health and development. The body requires specific micronutrients to function, with aberrant changes associated with a variety of negative health outcomes. Despite this evidence, the status and function of micronutrients during pregnancy are relatively unknown and more information is required to ensure that women receive optimal intakes for foetal development. Changes in trace element status have been associated with pregnancy complications such as gestational diabetes mellitus (GDM), pre-eclampsia (PE), intrauterine growth restriction (IUGR), and preterm birth. Measuring micronutrients with methodologies such as elemental metabolomics, which involves the simultaneous quantification and characterisation of multiple elements, could provide insight into gestational disorders. Identifying unique and subtle micronutrient changes may highlight associated proteins that are affected underpinning the pathophysiology of these complications, leading to new means of disease diagnosis. This review will provide a comprehensive summary of micronutrient status during pregnancy, and their associations with gestational disorders. Furthermore, it will also comment on the potential use of elemental metabolomics as a technique for disease characterisation and prediction.
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Affiliation(s)
- Daniel R McKeating
- School of Medical Science, Menzies Health Institute Queensland, Griffith University, Southport 9726, Queensland, Australia.
| | - Joshua J Fisher
- School of Medical Science, Menzies Health Institute Queensland, Griffith University, Southport 9726, Queensland, Australia.
| | - Anthony V Perkins
- School of Medical Science, Menzies Health Institute Queensland, Griffith University, Southport 9726, Queensland, Australia.
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82
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Misra BB, Reichman SM, Chen S. The guard cell ionome: Understanding the role of ions in guard cell functions. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 146:50-62. [PMID: 30458181 DOI: 10.1016/j.pbiomolbio.2018.11.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 11/01/2018] [Accepted: 11/16/2018] [Indexed: 12/20/2022]
Abstract
The ionome is critical for plant growth, productivity, defense, and it eventually affects human food quantity and quality. Located on the leaf surface, stomatal guard cells are critical gatekeepers for water, gas, and pathogens. Insights form ionomics (metallomics) is imperative as we enter an omics-driven systems biology era where an understanding of guard cell function and physiology is advanced through efforts in genomics, transcriptomics, proteomics, and metabolomics. While the roles of major cations (K, Ca) and anions (Cl) are well known in guard cell function, the related physiology, movement and regulation of trace elements, metal ions, and heavy metals are poorly understood. The majority of the information on the role of trace elements in guard cells emanates from classical feeding experiments, field or in vitro fortification, micropropagation, and microscopy studies, while novel insights are available from limited metal ion transporter and ion channel studies. Given the rejuvenated and recent interest in the constantly changing ionome in plant mineral balance and eventually in human nutrition and health, we looked into the far from established guard cell ionome in lieu of the modern omics era of high throughput research endeavors. Newer technologies and tools i.e., high resolution mass spectrometry, advanced imaging, and phenomics are now available to delve into the guard cell ionomes. In this review, research efforts on guard cell ionomes were collated and categorized, and we highlight the underlying role of the largely unknown ionome in guard cell function towards a systems physiology understanding of plant health and productivity.
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Affiliation(s)
- Biswapriya B Misra
- Center for Precision Medicine, Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston Salem, 27157, NC, USA; Department of Biology, Genetics Institute, Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, 32610, USA.
| | - Suzie M Reichman
- School of Engineering, RMIT University, GPO Box 2476, Melbourne, 3001, Australia; Centre for Environmental Sustainability and Remediation, RMIT University, GPO Box 2476, Melbourne, 3001, Australia
| | - Sixue Chen
- Department of Biology, Genetics Institute, Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, 32610, USA; Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, 32610, USA
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83
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Yang M, Lu K, Zhao FJ, Xie W, Ramakrishna P, Wang G, Du Q, Liang L, Sun C, Zhao H, Zhang Z, Liu Z, Tian J, Huang XY, Wang W, Dong H, Hu J, Ming L, Xing Y, Wang G, Xiao J, Salt DE, Lian X. Genome-Wide Association Studies Reveal the Genetic Basis of Ionomic Variation in Rice. THE PLANT CELL 2018; 30:2720-2740. [PMID: 30373760 PMCID: PMC6305983 DOI: 10.1105/tpc.18.00375] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 09/28/2018] [Accepted: 10/24/2018] [Indexed: 05/18/2023]
Abstract
Rice (Oryza sativa) is an important dietary source of both essential micronutrients and toxic trace elements for humans. The genetic basis underlying the variations in the mineral composition, the ionome, in rice remains largely unknown. Here, we describe a comprehensive study of the genetic architecture of the variation in the rice ionome performed using genome-wide association studies (GWAS) of the concentrations of 17 mineral elements in rice grain from a diverse panel of 529 accessions, each genotyped at ∼6.4 million single nucleotide polymorphism loci. We identified 72 loci associated with natural ionomic variations, 32 that are common across locations and 40 that are common within a single location. We identified candidate genes for 42 loci and provide evidence for the causal nature of three genes, the sodium transporter gene Os-HKT1;5 for sodium, Os-MOLYBDATE TRANSPORTER1;1 for molybdenum, and Grain number, plant height, and heading date7 for nitrogen. Comparison of GWAS data from rice versus Arabidopsis (Arabidopsis thaliana) also identified well-known as well as new candidates with potential for further characterization. Our study provides crucial insights into the genetic basis of ionomic variations in rice and serves as an important foundation for further studies on the genetic and molecular mechanisms controlling the rice ionome.
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Affiliation(s)
- Meng Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Kai Lu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Center of Applied Biotechnology, Wuhan Institute of Bioengineering, Wuhan 430415, China
| | - Fang-Jie Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Weibo Xie
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Priya Ramakrishna
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, United Kingdom
| | - Guangyuan Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Qingqing Du
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Limin Liang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Cuiju Sun
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Hu Zhao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Zhanyi Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Zonghao Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Jingjing Tian
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Xin-Yuan Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Wensheng Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Huaxia Dong
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Jintao Hu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Luchang Ming
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Gongwei Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Jinhua Xiao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - David E Salt
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, United Kingdom
| | - Xingming Lian
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
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Trace Elements and Healthcare: A Bioinformatics Perspective. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1005:63-98. [PMID: 28916929 DOI: 10.1007/978-981-10-5717-5_4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Biological trace elements are essential for human health. Imbalance in trace element metabolism and homeostasis may play an important role in a variety of diseases and disorders. While the majority of previous researches focused on experimental verification of genes involved in trace element metabolism and those encoding trace element-dependent proteins, bioinformatics study on trace elements is relatively rare and still at the starting stage. This chapter offers an overview of recent progress in bioinformatics analyses of trace element utilization, metabolism, and function, especially comparative genomics of several important metals. The relationship between individual elements and several diseases based on recent large-scale systematic studies such as genome-wide association studies and case-control studies is discussed. Lastly, developments of ionomics and its recent application in human health are also introduced.
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85
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Ricachenevsky FK, de Araújo Junior AT, Fett JP, Sperotto RA. You Shall Not Pass: Root Vacuoles as a Symplastic Checkpoint for Metal Translocation to Shoots and Possible Application to Grain Nutritional Quality. FRONTIERS IN PLANT SCIENCE 2018; 9:412. [PMID: 29666628 PMCID: PMC5891630 DOI: 10.3389/fpls.2018.00412] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 03/14/2018] [Indexed: 05/10/2023]
Abstract
Plant nutrient uptake is performed mostly by roots, which have to acquire nutrients while avoiding excessive amounts of essential and toxic elements. Apoplastic barriers such as the casparian strip and suberin deposition block free diffusion from the rhizosphere into the xylem, making selective plasma membrane transporters able to control elemental influx into the root symplast, efflux into the xylem and therefore shoot translocation. Additionally, transporters localized to the tonoplast of root cells have been demonstrated to regulate the shoot ionome, and may be important for seed elemental translocation. Here we review the role of vacuolar transporters in the detoxification of elements such as zinc (Zn), manganese (Mn), cadmium (Cd), cobalt (Co) and nickel (Ni) that are co-transported with iron (Fe) during the Fe deficiency response in Arabidopsis thaliana, and the possible conservation of this mechanism in rice (Oryza sativa). We also discuss the evidence that vacuolar transporters are linked to natural variation in shoot ionome in Arabidopsis and rice, indicating that vacuolar storage might be amenable to genetic engineering without strong phenotypical changes. Finally, we discuss the possible use of root's vacuolar transporters to increase the nutritional quality of crop grains.
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Affiliation(s)
- Felipe K. Ricachenevsky
- Departamento de Biologia, Programa de Pós-Graduação em Agrobiologia, Universidade Federal de Santa Maria, Santa Maria, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- *Correspondence: Felipe K. Ricachenevsky,
| | - Artur T. de Araújo Junior
- Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Janette P. Fett
- Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Departamento de Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Raul A. Sperotto
- Centro de Ciências Biológicas e da Saúde, Programa de Pós-Graduação em Biotecnologia, Universidade do Vale do Taquari – UNIVATES, Lajeado, Brazil
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86
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Stevanato P, Broccanello C, Moliterni VMC, Mandolino G, Barone V, Lucini L, Bertoldo G, Bertaggia M, Cagnin M, Pizzeghello D, Baglieri A, Squartini A, Concheri G, Nardi S. Innovative Approaches to Evaluate Sugar Beet Responses to Changes in Sulfate Availability. FRONTIERS IN PLANT SCIENCE 2018; 9:14. [PMID: 29445382 PMCID: PMC5797807 DOI: 10.3389/fpls.2018.00014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 01/04/2018] [Indexed: 05/23/2023]
Abstract
In this study, a system based on omics profiling was set-up for sugar beet (Beta vulgaris L. subsp. vulgaris) evaluation after changes in sulfate availability. Seedlings were grown on sulfate-deprived Hoagland solution. Six days after germination, 100 μM MgSO4 was added to the solution. Root samples were collected 36 h after treatments. WinRHIZO root-scanning approach was used for the automated image analysis of plant root morphology. Inductively Coupled Plasma Spectrometry (ICP-OES) and quadrupole-time-of-flight mass spectrometry (Q-TOF) were used for ionomic and metabolic analysis, respectively. Nanofluidic real-time PCR (OpenArray system) was used for molecular profiling. OpenArray chips were designed with TaqMan probes for 53 sugar beet genes putatively involved in sulfate nutrition. At morphological level treated seedlings showed significantly higher values (P < 0.01) than untreated plants for root traits related to soil exploration and nutrient uptake, such as total root length, fine roots length and root tips number. ICP-OES, Q-TOF and transcriptomic data revealed changes due to sulfate availability in sugar beet samples. Two key results are highlighted in sulfate-supplied roots and leaves. Firstly, high expression levels of auxin efflux carrier component 1 (PIN) and 5-phosphoribosyl-anthranilate, precursor of tryptophan and auxin synthesis, were observed in roots. Secondly, high levels of 2-Cys peroxiredoxin BAS1, chloroplastic, thioredoxin reductase (NADPH) and cysteine synthase, chloroplastic/chromoplastic, O-acetylserine sulfhydrylase, involved in protection against oxidative stress and cysteine synthase activity, respectively, were observed in leaves. Based on our findings, the combination of evaluated omics approaches could become a key system for the evaluation of the nutritional status of sugar beet under different nutrient availability conditions.
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Affiliation(s)
- Piergiorgio Stevanato
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Padova, Italy
- *Correspondence: Piergiorgio Stevanato,
| | - Chiara Broccanello
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Padova, Italy
| | - Vita M. C. Moliterni
- Council for Agricultural Research and Economics, Genomics Research Centre, Fiorenzuola d’Arda, Italy
| | - Giuseppe Mandolino
- Council for Agricultural Research and Economics, Research Centre for Industrial Crops, Bologna, Italy
| | - Valeria Barone
- Department of Agriculture, Food and Environment, University of Catania, Catania, Italy
| | - Luigi Lucini
- Institute of Agricultural and Environmental Chemistry, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Giovanni Bertoldo
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Padova, Italy
| | - Marco Bertaggia
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Padova, Italy
| | - Massimo Cagnin
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Padova, Italy
| | - Diego Pizzeghello
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Padova, Italy
| | - Andrea Baglieri
- Department of Agriculture, Food and Environment, University of Catania, Catania, Italy
| | - Andrea Squartini
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Padova, Italy
| | - Giuseppe Concheri
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Padova, Italy
| | - Serenella Nardi
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Padova, Italy
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87
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Montes A, Bisson MA, Gardella JA, Aga DS. Uptake and transformations of engineered nanomaterials: Critical responses observed in terrestrial plants and the model plant Arabidopsis thaliana. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 607-608:1497-1516. [PMID: 28793406 DOI: 10.1016/j.scitotenv.2017.06.190] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 06/22/2017] [Accepted: 06/23/2017] [Indexed: 05/12/2023]
Abstract
With the applications of engineered nanomaterials (ENMs) continually expanding and production quickly growing, residues of ENMs will end up in the environment at levels that may be harmful to non-target organisms. Many of the tunable properties that have made them desirable, such as type, size, charge, or coating, also contribute to the current difficulties in understanding the fate of ENMs in the environment. This review article focuses on studies that investigate plant-ENM interactions, including techniques used to study these interactions and documented plant responses due to the phytotoxic effects of ENMs. The many variables which can be altered for an experiment, such as type, size, and concentration of ENMs, make it difficult to formulate generalizations about the uptake mechanism involved, or to make an inference on the subcellular localization and distribution of the internalized ENMs in plant tissue. In order to avoid these challenges, studies can utilize a model organism such as Arabidopsis thaliana, and a combination of analytical techniques that can reveal complementary information in order to assess how the different experimental conditions influence the uptake and phytotoxicity of ENMs. This review presents recent studies regarding plant-ENM interactions employing Arabidopsis to demonstrate how the use of this model plant can advance our understanding of plant-ENM interactions and guide additional studies using other plant species. Overarching results suggest that more sensitive tests and consistency in experimental designs are needed to fully assess and understand the phytotoxic effects of ENMs in the environment.
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Affiliation(s)
- Angelina Montes
- Department of Chemistry, University at Buffalo, The State University of New York at Buffalo, Buffalo, NY, United States
| | - Mary A Bisson
- Department of Biological Sciences, University at Buffalo, The State University of New York at Buffalo, Buffalo, NY, United States
| | - Joseph A Gardella
- Department of Chemistry, University at Buffalo, The State University of New York at Buffalo, Buffalo, NY, United States
| | - Diana S Aga
- Department of Chemistry, University at Buffalo, The State University of New York at Buffalo, Buffalo, NY, United States.
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88
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Gao YQ, Chen JG, Chen ZR, An D, Lv QY, Han ML, Wang YL, Salt DE, Chao DY. A new vesicle trafficking regulator CTL1 plays a crucial role in ion homeostasis. PLoS Biol 2017; 15:e2002978. [PMID: 29284002 PMCID: PMC5746208 DOI: 10.1371/journal.pbio.2002978] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 11/21/2017] [Indexed: 11/18/2022] Open
Abstract
Ion homeostasis is essential for plant growth and environmental adaptation, and maintaining ion homeostasis requires the precise regulation of various ion transporters, as well as correct root patterning. However, the mechanisms underlying these processes remain largely elusive. Here, we reported that a choline transporter gene, CTL1, controls ionome homeostasis by regulating the secretory trafficking of proteins required for plasmodesmata (PD) development, as well as the transport of some ion transporters. Map-based cloning studies revealed that CTL1 mutations alter the ion profile of Arabidopsis thaliana. We found that the phenotypes associated with these mutations are caused by a combination of PD defects and ion transporter misregulation. We also established that CTL1 is involved in regulating vesicle trafficking and is thus required for the trafficking of proteins essential for ion transport and PD development. Characterizing choline transporter-like 1 (CTL1) as a new regulator of protein sorting may enable researchers to understand not only ion homeostasis in plants but also vesicle trafficking in general.
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Affiliation(s)
- Yi-Qun Gao
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jiu-Geng Chen
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zi-Ru Chen
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dong An
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Qiao-Yan Lv
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mei-Ling Han
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ya-Ling Wang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - David E. Salt
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Dai-Yin Chao
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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89
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Abstract
Most biological mechanisms involve more than one type of biomolecule, and hence operate not solely at the level of either genome, transcriptome, proteome, metabolome or ionome. Datasets resulting from single-omic analysis are rapidly increasing in throughput and quality, rendering multi-omic studies feasible. These should offer a comprehensive, structured and interactive overview of a biological mechanism. However, combining single-omic datasets in a meaningful manner has so far proved challenging, and the discovery of new biological information lags behind expectation. One reason is that experiments conducted in different laboratories can typically not to be combined without restriction. Second, the interpretation of multi-omic datasets represents a significant challenge by nature, as the biological datasets are heterogeneous not only for technical, but also for biological, chemical, and physical reasons. Here, multi-layer network theory and methods of artificial intelligence might contribute to solve these problems. For the efficient application of machine learning however, biological datasets need to become more systematic, more precise - and much larger. We conclude our review with basic guidelines for the successful set-up of a multi-omic experiment.
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90
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Natural variation in Arabidopsis thaliana Cd responses and the detection of quantitative trait loci affecting Cd tolerance. Sci Rep 2017. [PMID: 28623252 PMCID: PMC5473843 DOI: 10.1038/s41598-017-03540-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Metal tolerance is often a result of metal storage or distribution. Thus, with the goal of advancing the molecular understanding of such metal homeostatic mechanisms, natural variation of metal tolerance in Arabidopsis thaliana was investigated. Substantial variation exists in tolerance of excess copper (Cu), zinc (Zn) and cadmium (Cd). Two accessions, Col-0 and Bur-0, and a recombinant inbred line (RIL) population derived from these parents were chosen for further analysis of Cd and Zn tolerance variation, which is evident at different plant ages in various experimental systems and appears to be genetically linked. Three QTLs, explaining in total nearly 50% of the variation in Cd tolerance, were mapped. The one obvious candidate gene in the mapped intervals, HMA3, is unlikely to contribute to the variation. In order to identify additional candidate genes the Cd responses of Col-0 and Bur-0 were compared at the transcriptome level. The sustained common Cd response of the two accessions was dominated by processes implicated in plant pathogen defense. Accession-specific differences suggested a more efficient activation of acclimative responses as underlying the higher Cd tolerance of Bur-0. The second hypothesis derived from the physiological characterization of the accessions is a reduced Cd accumulation in Bur-0.
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91
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Campos ACAL, Kruijer W, Alexander R, Akkers RC, Danku J, Salt DE, Aarts MGM. Natural variation in Arabidopsis thaliana reveals shoot ionome, biomass, and gene expression changes as biomarkers for zinc deficiency tolerance. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:3643-3656. [PMID: 28859376 DOI: 10.1093/jxb/erx191] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 05/20/2017] [Indexed: 05/12/2023]
Abstract
Zinc (Zn) is an essential nutrient for plants, with a crucial role as a cofactor for many enzymes. Approximately one-third of the global arable land area is Zn deficient, leading to reduced crop yield and quality. To improve crop tolerance to Zn deficiency, it is important to understand the mechanisms plants have adopted to tolerate suboptimal Zn supply. In this study, physiological and molecular aspects of traits related to Zn deficiency tolerance were examined in a panel of 19 Arabidopsis thaliana accessions. Accessions showed a larger variation for shoot biomass than for Zn concentration, indicating that they have different requirements for their minimal Zn concentration required for growth. Accessions with a higher tolerance to Zn deficiency showed an increased expression of the Zn deficiency-responsive genes ZIP4 and IRT3 in comparison with Zn deficiency-sensitive accessions. Changes in the shoot ionome, as a result of the Zn treatment of the plants, were used to build a multinomial logistic regression model able to distinguish plants regarding their Zn nutritional status. This set of biomarkers, reflecting the A. thaliana response to Zn deficiency and Zn deficiency tolerance, can be useful for future studies aiming to improve the performance and Zn status of crop plants grown under suboptimal Zn concentrations.
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Affiliation(s)
- Ana Carolina A L Campos
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen AB24 3UU, UK
| | - Willem Kruijer
- Biometris, Wageningen University and Research, PO Box 100, 6700AC Wageningen, The Netherlands
| | - Ross Alexander
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- School of Life Sciences, John Muir Building, Heriot Watt University, Edinburgh EH14 4AS, UK
| | - Robert C Akkers
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - John Danku
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen AB24 3UU, UK
| | - David E Salt
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen AB24 3UU, UK
| | - Mark G M Aarts
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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92
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Jeyasingh PD, Goos JM, Thompson SK, Godwin CM, Cotner JB. Ecological Stoichiometry beyond Redfield: An Ionomic Perspective on Elemental Homeostasis. Front Microbiol 2017; 8:722. [PMID: 28487686 PMCID: PMC5403914 DOI: 10.3389/fmicb.2017.00722] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 04/07/2017] [Indexed: 11/13/2022] Open
Abstract
Elemental homeostasis has been largely characterized using three important elements that were part of the Redfield ratio (i.e., carbon: nitrogen: phosphorus). These efforts have revealed substantial diversity in homeostasis among taxonomic groups and even within populations. Understanding the evolutionary basis, and ecological consequences of such diversity is a central challenge. Here, we propose that a more complete understanding of homeostasis necessitates the consideration of other elements beyond C, N, and P. Specifically, we posit that physiological complexity underlying maintenance of elemental homeostasis along a single elemental axis impacts processing of other elements, thus altering elemental homeostasis along other axes. Indeed, transcriptomic studies in a wide variety of organisms have found that individuals differentially express significant proportions of the genome in response to variability in supply stoichiometry in order to maintain varying levels of homeostasis. We review the literature from the emergent field of ionomics that has established the consequences of such physiological trade-offs on the content of the entire suite of elements in an individual. Further, we present experimental data on bacteria exhibiting divergent phosphorus homeostasis phenotypes demonstrating the fundamental interconnectedness among elemental quotas. These observations suggest that physiological adjustments can lead to unexpected patterns in biomass stoichiometry, such as correlated changes among suites of non-limiting microelements in response to limitation by macroelements. Including the entire suite of elements that comprise biomass will foster improved quantitative understanding of the links between chemical cycles and the physiology of organisms.
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Affiliation(s)
- Punidan D Jeyasingh
- Department of Integrative Biology, Oklahoma State UniversityStillwater, OK, USA
| | - Jared M Goos
- Department of Biology, University of Texas at ArlingtonArlington, TX, USA
| | - Seth K Thompson
- Water Resources Science Program, University of MinnesotaSt. Paul, MN, USA
| | - Casey M Godwin
- School of Natural Resources and Environment, University of MichiganAnn Arbor, MI, USA
| | - James B Cotner
- Department of Ecology, Evolution, and Behavior, University of MinnesotaSt. Paul, MN, USA
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93
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Huang XY, Chao DY, Koprivova A, Danku J, Wirtz M, Müller S, Sandoval FJ, Bauwe H, Roje S, Dilkes B, Hell R, Kopriva S, Salt DE. Nuclear Localised MORE SULPHUR ACCUMULATION1 Epigenetically Regulates Sulphur Homeostasis in Arabidopsis thaliana. PLoS Genet 2016; 12:e1006298. [PMID: 27622452 PMCID: PMC5021336 DOI: 10.1371/journal.pgen.1006298] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 08/12/2016] [Indexed: 12/25/2022] Open
Abstract
Sulphur (S) is an essential element for all living organisms. The uptake, assimilation and metabolism of S in plants are well studied. However, the regulation of S homeostasis remains largely unknown. Here, we report on the identification and characterisation of the more sulphur accumulation1 (msa1-1) mutant. The MSA1 protein is localized to the nucleus and is required for both S-adenosylmethionine (SAM) production and DNA methylation. Loss of function of the nuclear localised MSA1 leads to a reduction in SAM in roots and a strong S-deficiency response even at ample S supply, causing an over-accumulation of sulphate, sulphite, cysteine and glutathione. Supplementation with SAM suppresses this high S phenotype. Furthermore, mutation of MSA1 affects genome-wide DNA methylation, including the methylation of S-deficiency responsive genes. Elevated S accumulation in msa1-1 requires the increased expression of the sulphate transporter genes SULTR1;1 and SULTR1;2 which are also differentially methylated in msa1-1. Our results suggest a novel function for MSA1 in the nucleus in regulating SAM biosynthesis and maintaining S homeostasis epigenetically via DNA methylation. Sulphur is an essential element for all living organisms including plants. Plants take up sulphur from the soil mainly in the form of inorganic sulphate. The uptake of sulphate and assimilation of sulphur have been well studied. However, the regulation of sulphur accumulation in plants remains largely unknown. In this study, we characterize the high leaf sulphur mutant more sulphur accumulation1 (msa1-1) and demonstrate the function of MSA1 in controlling sulphur accumulation in Arabidopsis thaliana. The MSA1 protein is localized to the nucleus and is required for the biosynthesis of S-adenosylmethionine (SAM) which is a universal methyl donor for many methylation reactions, including DNA methylation. Loss of function of MSA1 reduces the SAM level in roots and affects genome-wide DNA methylation, including the methylation of sulphate transporter genes. We show that the high sulphur phenotype of msa1-1 requires elevated expression of the sulphate transporter genes which are differentially methylated in msa1-1. Our results suggest a connection between sulphur homeostasis and DNA methylation that is mediated by MSA1.
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Affiliation(s)
- Xin-Yuan Huang
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Dai-Yin Chao
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Anna Koprivova
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - John Danku
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Markus Wirtz
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Steffen Müller
- Department of Plant Physiology, University of Rostock, Rostock, Germany
| | - Francisco J. Sandoval
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, United States of America
| | - Hermann Bauwe
- Department of Plant Physiology, University of Rostock, Rostock, Germany
| | - Sanja Roje
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, United States of America
| | - Brian Dilkes
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, United States of America
| | - Rüdiger Hell
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Stanislav Kopriva
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - David E Salt
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
- * E-mail:
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94
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Ricachenevsky FK, Sperotto RA. Into the Wild: Oryza Species as Sources for Enhanced Nutrient Accumulation and Metal Tolerance in Rice. FRONTIERS IN PLANT SCIENCE 2016; 7:974. [PMID: 27446193 PMCID: PMC4925693 DOI: 10.3389/fpls.2016.00974] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 06/20/2016] [Indexed: 05/07/2023]
Affiliation(s)
- Felipe K. Ricachenevsky
- Departamento de Biologia, Programa de Pós-Graduação em Agrobiologia, Universidade Federal de Santa MariaSanta Maria, Brazil
- *Correspondence: Felipe K. Ricachenevsky
| | - Raul A. Sperotto
- Setor de Genética e Biologia Molecular do Museu de Ciências Naturais, Programa de Pós-Graduação em Biotecnologia, Centro de Ciências Biológicas e da Saúde, Centro Universitário UNIVATESLajeado, Brazil
- Raul A. Sperotto
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