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Claussen J, Wittenberg T, Uhlmann N, Gerth S. "Chamber #8" - a holistic approach of high-throughput non-destructive assessment of plant roots. Front Plant Sci 2024; 14:1269005. [PMID: 38239230 PMCID: PMC10794641 DOI: 10.3389/fpls.2023.1269005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 11/01/2023] [Indexed: 01/22/2024]
Abstract
Introduction In the past years, it has been observed that the breeding of plants has become more challenging, as the visible difference in phenotypic data is much smaller than decades ago. With the ongoing climate change, it is necessary to breed crops that can cope with shifting climatic conditions. To select good breeding candidates for the future, phenotypic experiments can be conducted under climate-controlled conditions. Above-ground traits can be assessed with different optical sensors, but for the root growth, access to non-destructively measured traits is much more challenging. Even though MRI or CT imaging techniques have been established in the past years, they rely on an adequate infrastructure for the automatic handling of the pots as well as the controlled climate. Methods To address both challenges simultaneously, the non-destructive imaging of plant roots combined with a highly automated and standardized mid-throughput approach, we developed a workflow and an integrated scanning facility to study root growth. Our "chamber #8" contains a climate chamber, a material flow control, an irrigation system, an X-ray system, a database for automatic data collection, and post-processing. The goals of this approach are to reduce the human interaction with the various components of the facility to a minimum on one hand, and to automate and standardize the complete process from plant care via measurements to root trait calculation on the other. The user receives standardized phenotypic traits and properties that were collected objectively. Results The proposed holistic approach allows us to study root growth of plants in a field-like substrate non-destructively over a defined period and to calculate phenotypic traits of root architecture. For different crops, genotypic differences can be observed in response to climatic conditions which have already been applied to a wide variety of root structures, such as potatoes, cassava, or corn. Discussion It enables breeders and scientists non-destructive access to root traits. Additionally, due to the non-destructive nature of X-ray computed tomography, the analysis of time series for root growing experiments is possible and enables the observation of kinetic traits. Furthermore, using this automation scheme for simultaneously controlled plant breeding and non-destructive testing reduces the involvement of human resources.
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Affiliation(s)
- Joelle Claussen
- Fraunhofer Institute for Integrated Circuits (IIS), Department Development Center X-ray Technology, Fuerth, Germany
| | - Thomas Wittenberg
- Fraunhofer Institute for Integrated Circuits (IIS), Department Development Center X-ray Technology, Fuerth, Germany
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Department for Visual Computing, Erlangen, Germany
| | - Norman Uhlmann
- Fraunhofer Institute for Integrated Circuits (IIS), Department Development Center X-ray Technology, Fuerth, Germany
| | - Stefan Gerth
- Fraunhofer Institute for Integrated Circuits (IIS), Department Development Center X-ray Technology, Fuerth, Germany
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Julkowska MM. Data insights: Descriptive data papers with high information impact are a new gold mine for readers of plant, cell and environment. Plant Cell Environ 2024. [PMID: 38173307 DOI: 10.1111/pce.14804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024]
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3
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Dumschott K, Dörpholz H, Laporte MA, Brilhaus D, Schrader A, Usadel B, Neumann S, Arnaud E, Kranz A. Ontologies for increasing the FAIRness of plant research data. Front Plant Sci 2023; 14:1279694. [PMID: 38098789 PMCID: PMC10720748 DOI: 10.3389/fpls.2023.1279694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 11/15/2023] [Indexed: 12/17/2023]
Abstract
The importance of improving the FAIRness (findability, accessibility, interoperability, reusability) of research data is undeniable, especially in the face of large, complex datasets currently being produced by omics technologies. Facilitating the integration of a dataset with other types of data increases the likelihood of reuse, and the potential of answering novel research questions. Ontologies are a useful tool for semantically tagging datasets as adding relevant metadata increases the understanding of how data was produced and increases its interoperability. Ontologies provide concepts for a particular domain as well as the relationships between concepts. By tagging data with ontology terms, data becomes both human- and machine- interpretable, allowing for increased reuse and interoperability. However, the task of identifying ontologies relevant to a particular research domain or technology is challenging, especially within the diverse realm of fundamental plant research. In this review, we outline the ontologies most relevant to the fundamental plant sciences and how they can be used to annotate data related to plant-specific experiments within metadata frameworks, such as Investigation-Study-Assay (ISA). We also outline repositories and platforms most useful for identifying applicable ontologies or finding ontology terms.
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Affiliation(s)
- Kathryn Dumschott
- Institute of Bio- and Geosciences (IBG-4: Bioinformatics) & Bioeconomy Science Center (BioSC), CEPLAS, Forschungszentrum Jülich, Jülich, Germany
| | - Hannah Dörpholz
- Institute of Bio- and Geosciences (IBG-4: Bioinformatics) & Bioeconomy Science Center (BioSC), CEPLAS, Forschungszentrum Jülich, Jülich, Germany
| | - Marie-Angélique Laporte
- Digital Solutions Team, Digital Inclusion Lever, Bioversity International, Montpellier Office, Montpellier, France
| | - Dominik Brilhaus
- Data Science and Management & Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Andrea Schrader
- Data Science and Management & Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Björn Usadel
- Institute of Bio- and Geosciences (IBG-4: Bioinformatics) & Bioeconomy Science Center (BioSC), CEPLAS, Forschungszentrum Jülich, Jülich, Germany
- Institute for Biological Data Science & Cluster of Excellence on Plant Sciences (CEPLAS), Faculty of Mathematics and Life Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Steffen Neumann
- Program Center MetaCom, Leibniz Institute of Plant Biochemistry, Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Germany
| | - Elizabeth Arnaud
- Digital Solutions Team, Digital Inclusion Lever, Bioversity International, Montpellier Office, Montpellier, France
| | - Angela Kranz
- Institute of Bio- and Geosciences (IBG-4: Bioinformatics) & Bioeconomy Science Center (BioSC), CEPLAS, Forschungszentrum Jülich, Jülich, Germany
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Papoutsoglou EA, Athanasiadis IN, Visser RGF, Finkers R. The benefits and struggles of FAIR data: the case of reusing plant phenotyping data. Sci Data 2023; 10:457. [PMID: 37443110 PMCID: PMC10345100 DOI: 10.1038/s41597-023-02364-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
Plant phenotyping experiments are conducted under a variety of experimental parameters and settings for diverse purposes. The data they produce is heterogeneous, complicated, often poorly documented and, as a result, difficult to reuse. Meeting societal needs (nutrition, crop adaptation and stability) requires more efficient methods toward data integration and reuse. In this work, we examine what "making data FAIR" entails, and investigate the benefits and the struggles not only of reusing FAIR data, but also making data FAIR using genotype by environment and QTL by environment interactions for developmental traits in potato as a case study. We assume the role of a scientist discovering a phenotypic dataset on a FAIR data point, verifying the existence of related datasets with environmental data, acquiring both and integrating them. We report and discuss the challenges and the potential for reusability and reproducibility of FAIRifying existing datasets, using metadata standards such as MIAPPE, that were encountered in this process.
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Affiliation(s)
- Evangelia A Papoutsoglou
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
- Taxonic B.V., De Meern, The Netherlands
| | - Ioannis N Athanasiadis
- Wageningen Data Competence Center and Geo-Information Science & Remote Sensing Lab, Wageningen University and Research, Wageningen, The Netherlands
| | - Richard G F Visser
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Richard Finkers
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands.
- GenNovation B.V., Wageningen, The Netherlands.
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5
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Karabulut E, Erkoç K, Acı M, Aydın M, Barriball S, Braley J, Cassetta E, Craine EB, Diaz-Garcia L, Hershberger J, Meyering B, Miller AJ, Rubin MJ, Tesdell O, Schlautman B, Şakiroğlu M. Sainfoin ( Onobrychis spp.) crop ontology: supporting germplasm characterization and international research collaborations. Front Plant Sci 2023; 14:1177406. [PMID: 37255566 PMCID: PMC10225502 DOI: 10.3389/fpls.2023.1177406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 04/18/2023] [Indexed: 06/01/2023]
Abstract
Sainfoin (Onobrychis spp.) is a perennial forage legume that is also attracting attention as a perennial pulse with potential for human consumption. The dual use of sainfoin underpins diverse research and breeding programs focused on improving sainfoin lines for forage and pulses, which is driving the generation of complex datasets describing high dimensional phenotypes in the post-omics era. To ensure that multiple user groups, for example, breeders selecting for forage and those selecting for edible seed, can utilize these rich datasets, it is necessary to develop common ontologies and accessible ontology platforms. One such platform, Crop Ontology, was created in 2008 by the Consortium of International Agricultural Research Centers (CGIAR) to host crop-specific trait ontologies that support standardized plant breeding databases. In the present study, we describe the sainfoin crop ontology (CO). An in-depth literature review was performed to develop a comprehensive list of traits measured and reported in sainfoin. Because the same traits can be measured in different ways, ultimately, a set of 98 variables (variable = plant trait + method of measurement + scale of measurement) used to describe variation in sainfoin were identified. Variables were formatted and standardized based on guidelines provided here for inclusion in the sainfoin CO. The 98 variables contained a total of 82 traits from four trait classes of which 24 were agronomic, 31 were morphological, 19 were seed and forage quality related, and 8 were phenological. In addition to the developed variables, we have provided a roadmap for developing and submission of new traits to the sainfoin CO.
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Affiliation(s)
- Ebrar Karabulut
- Bioengineering Department, Adana Alparslan Türkeş Science and Technology University, Adana, Türkiye
| | - Kübra Erkoç
- Bioengineering Department, Adana Alparslan Türkeş Science and Technology University, Adana, Türkiye
| | - Murat Acı
- Bioengineering Department, Adana Alparslan Türkeş Science and Technology University, Adana, Türkiye
- The Land Institute, Salina, KS, United States
| | - Mahmut Aydın
- Department of Computer Engineering, Kafkas University, Kars, Türkiye
| | | | - Jackson Braley
- Donald Danforth Plant Science Center, St. Louis, MO, United States
| | | | | | - Luis Diaz-Garcia
- Department of Viticulture and Enology, University of California Davis, Davis, CA, United States
| | - Jenna Hershberger
- Plant and Environmental Sciences Department, Clemson University, Clemson, SC, United States
| | - Bo Meyering
- The Land Institute, Salina, KS, United States
| | - Allison J. Miller
- Donald Danforth Plant Science Center, St. Louis, MO, United States
- Department. of Biology, Saint Louis University, St. Louis, MO, United States
| | - Matthew J. Rubin
- Donald Danforth Plant Science Center, St. Louis, MO, United States
| | - Omar Tesdell
- Department of Geography, Birzeit University, Birzeit, West Bank, Palestine
| | | | - Muhammet Şakiroğlu
- Bioengineering Department, Adana Alparslan Türkeş Science and Technology University, Adana, Türkiye
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6
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Harfouche AL, Nakhle F, Harfouche AH, Sardella OG, Dart E, Jacobson D. A primer on artificial intelligence in plant digital phenomics: embarking on the data to insights journey. Trends Plant Sci 2023; 28:154-184. [PMID: 36167648 DOI: 10.1016/j.tplants.2022.08.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 08/22/2022] [Accepted: 08/25/2022] [Indexed: 06/16/2023]
Abstract
Artificial intelligence (AI) has emerged as a fundamental component of global agricultural research that is poised to impact on many aspects of plant science. In digital phenomics, AI is capable of learning intricate structure and patterns in large datasets. We provide a perspective and primer on AI applications to phenome research. We propose a novel human-centric explainable AI (X-AI) system architecture consisting of data architecture, technology infrastructure, and AI architecture design. We clarify the difference between post hoc models and 'interpretable by design' models. We include guidance for effectively using an interpretable by design model in phenomic analysis. We also provide directions to sources of tools and resources for making data analytics increasingly accessible. This primer is accompanied by an interactive online tutorial.
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Affiliation(s)
- Antoine L Harfouche
- Department for Innovation in Biological, Agro-Food, and Forest Systems, University of Tuscia, Viterbo, VT 01100, Italy.
| | - Farid Nakhle
- Department for Innovation in Biological, Agro-Food, and Forest Systems, University of Tuscia, Viterbo, VT 01100, Italy
| | - Antoine H Harfouche
- Unité de Formation et de Recherche en Sciences Économiques, Gestion, Mathématiques, et Informatique, Université Paris Nanterre, 92001 Nanterre, France
| | - Orlando G Sardella
- Department for Innovation in Biological, Agro-Food, and Forest Systems, University of Tuscia, Viterbo, VT 01100, Italy
| | - Eli Dart
- Energy Sciences Network (ESnet), Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Daniel Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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7
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Yang F, Liu Z, Wang Y, Wang X, Zhang Q, Han Y, Zhao X, Pan S, Yang S, Wang S, Zhang Q, Qiu J, Wang K. A variety test platform for the standardization and data quality improvement of crop variety tests. Front Plant Sci 2023; 14:1077196. [PMID: 36760650 PMCID: PMC9902355 DOI: 10.3389/fpls.2023.1077196] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 01/09/2023] [Indexed: 06/18/2023]
Abstract
Variety testing is an indispensable and essential step in the process of creating new improved varieties from breeding to adoption. The performance of the varieties can be compared and evaluated based on multi-trait data from multi-location variety tests in multiple years. Although high-throughput phenotypic platforms have been used for observing some specific traits, manual phenotyping is still widely used. The efficient management of large amounts of data is still a significant problem for crop variety testing. This study reports a variety test platform (VTP) that was created to manage the whole workflow for the standardization and data quality improvement of crop variety testing. Through the VTP, the phenotype data of varieties can be integrated and reused based on standardized data elements and datasets. Moreover, the information support and automated functions for the whole testing workflow help users conduct tests efficiently through a series of functions such as test design, data acquisition and processing, and statistical analyses. The VTP has been applied to regional variety tests covering more than seven thousand locations across the whole country, and then a standardized and authoritative phenotypic database covering five crops has been generated. In addition, the VTP can be deployed on either privately or publicly available high-performance computing nodes so that test management and data analysis can be conveniently done using a web-based interface or mobile application. In this way, the system can provide variety test management services to more small and medium-sized breeding organizations, and ensures the mutual independence and security of test data. The application of VTP shows that the platform can make variety testing more efficient and can be used to generate a reliable database suitable for meta-analysis in multi-omics breeding and variety development projects.
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Affiliation(s)
- Feng Yang
- Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Zhongqiang Liu
- Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yuxi Wang
- National Agro-Tech Extension and Service Center, Beijing, China
| | - Xiaofeng Wang
- Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Agri-informatics, Ministry of Agriculture, Beijing, China
| | - Qiusi Zhang
- Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Agri-informatics, Ministry of Agriculture, Beijing, China
| | - Yanyun Han
- Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Agri-informatics, Ministry of Agriculture, Beijing, China
| | - Xiangyu Zhao
- Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- National Engineering Research Center for Information Technology in Agriculture, Beijing, China
| | - Shouhui Pan
- Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- National Engineering Research Center for Information Technology in Agriculture, Beijing, China
| | - Shuo Yang
- AgChip Science and Technology (Beijing) Co., Ltd., Beijing, China
| | - Shufeng Wang
- Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Agri-informatics, Ministry of Agriculture, Beijing, China
| | - Qi Zhang
- Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Agri-informatics, Ministry of Agriculture, Beijing, China
| | - Jun Qiu
- National Agro-Tech Extension and Service Center, Beijing, China
| | - Kaiyi Wang
- Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- National Engineering Research Center for Information Technology in Agriculture, Beijing, China
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8
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Senger E, Osorio S, Olbricht K, Shaw P, Denoyes B, Davik J, Predieri S, Karhu S, Raubach S, Lippi N, Höfer M, Cockerton H, Pradal C, Kafkas E, Litthauer S, Amaya I, Usadel B, Mezzetti B. Towards smart and sustainable development of modern berry cultivars in Europe. Plant J 2022; 111:1238-1251. [PMID: 35751152 DOI: 10.1111/tpj.15876] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/15/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
Fresh berries are a popular and important component of the human diet. The demand for high-quality berries and sustainable production methods is increasing globally, challenging breeders to develop modern berry cultivars that fulfill all desired characteristics. Since 1994, research projects have characterized genetic resources, developed modern tools for high-throughput screening, and published data in publicly available repositories. However, the key findings of different disciplines are rarely linked together, and only a limited range of traits and genotypes has been investigated. The Horizon2020 project BreedingValue will address these challenges by studying a broader panel of strawberry, raspberry and blueberry genotypes in detail, in order to recover the lost genetic diversity that has limited the aroma and flavor intensity of recent cultivars. We will combine metabolic analysis with sensory panel tests and surveys to identify the key components of taste, flavor and aroma in berries across Europe, leading to a high-resolution map of quality requirements for future berry cultivars. Traits linked to berry yields and the effect of environmental stress will be investigated using modern image analysis methods and modeling. We will also use genetic analysis to determine the genetic basis of complex traits for the development and optimization of modern breeding technologies, such as molecular marker arrays, genomic selection and genome-wide association studies. Finally, the results, raw data and metadata will be made publicly available on the open platform Germinate in order to meet FAIR data principles and provide the basis for sustainable research in the future.
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Affiliation(s)
- Elisa Senger
- Institute of Bio- and Geosciences, IBG-4 Bioinformatics, BioSC, CEPLAS, Forschungszentrum Jülich, Jülich, Germany
| | - Sonia Osorio
- Departamento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Campus de Teatinos, Málaga, Spain
| | | | - Paul Shaw
- Department of Information and Computational Sciences, The James Hutton Institute, Invergowrie, Scotland, UK
| | - Béatrice Denoyes
- Université de Bordeaux, UMR BFP, INRAE, Villenave d'Ornon, France
| | - Jahn Davik
- Department of Molecular Plant Biology, Norwegian Institute of Bioeconomy Research (NIBIO), Ås, Norway
| | - Stefano Predieri
- Bio-Agrofood Department, Institute for Bioeconomy, IBE-CNR, Italian National Research Council, Bologna, Italy
| | - Saila Karhu
- Natural Resources Institute Finland (Luke), Turku, Finland
| | - Sebastian Raubach
- Department of Information and Computational Sciences, The James Hutton Institute, Invergowrie, Scotland, UK
| | - Nico Lippi
- Bio-Agrofood Department, Institute for Bioeconomy, IBE-CNR, Italian National Research Council, Bologna, Italy
| | - Monika Höfer
- Institute of Breeding Research on Fruit Crops, Federal Research Centre for Cultivated Plants (JKI), Dresden, Germany
| | - Helen Cockerton
- Genetics, Genomics and Breeding Department, NIAB, East Malling, UK
| | - Christophe Pradal
- CIRAD and UMR AGAP Institute, Montpellier, France
- INRIA and LIRMM, University Montpellier, CNRS, Montpellier, France
| | - Ebru Kafkas
- Department of Horticulture, Faculty of Agriculture, Çukurova University, Balcalı, Adana, Turkey
| | | | - Iraida Amaya
- Unidad Asociada deI + D + i IFAPA-CSIC Biotecnología y Mejora en Fresa, Málaga, Spain
- Laboratorio de Genómica y Biotecnología, Centro IFAPA de Málaga, Instituto Andaluz de Investigación y Formación Agraria y Pesquera, Málaga, Spain
| | - Björn Usadel
- Institute of Bio- and Geosciences, IBG-4 Bioinformatics, BioSC, CEPLAS, Forschungszentrum Jülich, Jülich, Germany
- Institute for Biological Data Science, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Bruno Mezzetti
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy
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Possamai T, Wiedemann-Merdinoglu S. Phenotyping for QTL identification: A case study of resistance to Plasmopara viticola and Erysiphe necator in grapevine. Front Plant Sci 2022; 13:930954. [PMID: 36035702 PMCID: PMC9403010 DOI: 10.3389/fpls.2022.930954] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/27/2022] [Indexed: 06/01/2023]
Abstract
Vitis vinifera is the most widely cultivated grapevine species. It is highly susceptible to Plasmopara viticola and Erysiphe necator, the causal agents of downy mildew (DM) and powdery mildew (PM), respectively. Current strategies to control DM and PM mainly rely on agrochemical applications that are potentially harmful to humans and the environment. Breeding for resistance to DM and PM in wine grape cultivars by introgressing resistance loci from wild Vitis spp. is a complementary and more sustainable solution to manage these two diseases. During the last two decades, 33 loci of resistance to P. viticola (Rpv) and 15 loci of resistance to E. necator (Ren and Run) have been identified. Phenotyping is salient for QTL characterization and understanding the genetic basis of resistant traits. However, phenotyping remains a major bottleneck for research on Rpv and Ren/Run loci and disease resistance evaluation. A thorough analysis of the literature on phenotyping methods used for DM and PM resistance evaluation highlighted phenotyping performed in the vineyard, greenhouse or laboratory with major sources of variation, such as environmental conditions, plant material (organ physiology and age), pathogen inoculum (genetic and origin), pathogen inoculation (natural or controlled), and disease assessment method (date, frequency, and method of scoring). All these factors affect resistance assessment and the quality of phenotyping data. We argue that the use of new technologies for disease symptom assessment, and the production and adoption of standardized experimental guidelines should enhance the accuracy and reliability of phenotyping data. This should contribute to a better replicability of resistance evaluation outputs, facilitate QTL identification, and contribute to streamline disease resistance breeding programs.
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Affiliation(s)
- Tyrone Possamai
- CREA—Research Centre for Viticulture and Enology, Conegliano, Italy
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10
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Abstract
In contrast to the rapid advances made in plant genotyping, plant phenotyping is considered a bottleneck in plant science. This has promoted high-throughput plant phenotyping (HTP) studies, resulting in an exponential increase in phenotyping-related publications. The development of HTP was originally intended for use as indoor HTP technologies for model plant species under controlled environments. However, this subsequently shifted to HTP for use in crops in fields. Although HTP in fields is much more difficult to conduct due to unstable environmental conditions compared to HTP in controlled environments, recent advances in HTP technology have allowed these difficulties to be overcome, allowing for rapid, efficient, non-destructive, non-invasive, quantitative, repeatable, and objective phenotyping. Recent HTP developments have been accelerated by the advances in data analysis, sensors, and robot technologies, including machine learning, image analysis, three dimensional (3D) reconstruction, image sensors, laser sensors, environmental sensors, and drones, along with high-speed computational resources. This article provides an overview of recent HTP technologies, focusing mainly on canopy-based phenotypes of major crops, such as canopy height, canopy coverage, canopy biomass, and canopy stressed appearance, in addition to crop organ detection and counting in the fields. Current topics in field HTP are also presented, followed by a discussion on the low rates of adoption of HTP in practical breeding programs.
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Affiliation(s)
- Seishi Ninomiya
- Graduate School of Agriculture and Life Sciences, The University of Tokyo, Nishitokyo, Tokyo 188-0002, Japan
- Plant Phenomics Research Center, Nanjing Agricultural University, Nanjing, China
- Corresponding author (e-mail: )
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11
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Pandey P, Young S. Design Considerations for In-Field Measurement of Plant Architecture Traits Using Ground-Based Platforms. Methods Mol Biol 2022; 2539:171-190. [PMID: 35895204 DOI: 10.1007/978-1-0716-2537-8_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
This work provides a high-level overview of system design considerations for measuring plant architecture traits in row crops using ground-based, mobile platforms. High-throughput phenotyping technologies are commonly deployed in isolated growth chambers or greenhouses; however, there is a need for field-based systems to measure large quantities of plants exposed to natural climates throughout a growing season. High-throughput methods using ground-based mobile systems collect valuable phenotypic information at higher temporal resolutions compared to manual methods (e.g., handheld calipers and measuring sticks). Additionally, the close proximity to plants when using ground-based systems compared to aerial platforms enables plant phenotyping at the organ level. While there is no single best platform for obtaining ground-based plant measurements across crop varieties with different planting configurations, there are a wide range of off-the-shelf systems and sensors that can be integrated to accommodate varying row widths, plant spacing, plant heights, and plot sizes, in addition to emerging commercially available platforms. This chapter will provide an overview of sensor types suitable for phenotyping plant size and shape, as well as provide guidance for deployment with ground-based systems, including push carts or buggies, modified tractors, and robotic platforms.
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Affiliation(s)
- Piyush Pandey
- Department of Biological and Agricultural Engineering, North Carolina State University, Raleigh, NC, USA
| | - Sierra Young
- Department of Civil and Environmental Engineering, Utah State University, Logan, UT, USA.
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Xiao Q, Bai X, Zhang C, He Y. Advanced high-throughput plant phenotyping techniques for genome-wide association studies: A review. J Adv Res 2022; 35:215-230. [PMID: 35003802 PMCID: PMC8721248 DOI: 10.1016/j.jare.2021.05.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 05/05/2021] [Accepted: 05/09/2021] [Indexed: 01/22/2023] Open
Abstract
Linking phenotypes and genotypes to identify genetic architectures that regulate important traits is crucial for plant breeding and the development of plant genomics. In recent years, genome-wide association studies (GWASs) have been applied extensively to interpret relationships between genes and traits. Successful GWAS application requires comprehensive genomic and phenotypic data from large populations. Although multiple high-throughput DNA sequencing approaches are available for the generation of genomics data, the capacity to generate high-quality phenotypic data is lagging far behind. Traditional methods for plant phenotyping mostly rely on manual measurements, which are laborious, inaccurate, and time-consuming, greatly impairing the acquisition of phenotypic data from large populations. In contrast, high-throughput phenotyping has unique advantages, facilitating rapid, non-destructive, and high-throughput detection, and, in turn, addressing the shortcomings of traditional methods. Aim of Review: This review summarizes the current status with regard to the integration of high-throughput phenotyping and GWAS in plants, in addition to discussing the inherent challenges and future prospects. Key Scientific Concepts of Review: High-throughput phenotyping, which facilitates non-contact and dynamic measurements, has the potential to offer high-quality trait data for GWAS and, in turn, to enhance the unraveling of genetic structures of complex plant traits. In conclusion, high-throughput phenotyping integration with GWAS could facilitate the revealing of coding information in plant genomes.
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Affiliation(s)
- Qinlin Xiao
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Spectroscopy Sensing, Ministry of Agriculture and Rural Affairs, Hangzhou 310058, China
| | - Xiulin Bai
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Spectroscopy Sensing, Ministry of Agriculture and Rural Affairs, Hangzhou 310058, China
| | - Chu Zhang
- School of Information Engineering, Huzhou University, Huzhou 313000, China
| | - Yong He
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Spectroscopy Sensing, Ministry of Agriculture and Rural Affairs, Hangzhou 310058, China
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13
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Langstroff A, Heuermann MC, Stahl A, Junker A. Opportunities and limits of controlled-environment plant phenotyping for climate response traits. Theor Appl Genet 2022; 135:1-16. [PMID: 34302493 PMCID: PMC8741719 DOI: 10.1007/s00122-021-03892-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 06/17/2021] [Indexed: 05/19/2023]
Abstract
Rising temperatures and changing precipitation patterns will affect agricultural production substantially, exposing crops to extended and more intense periods of stress. Therefore, breeding of varieties adapted to the constantly changing conditions is pivotal to enable a quantitatively and qualitatively adequate crop production despite the negative effects of climate change. As it is not yet possible to select for adaptation to future climate scenarios in the field, simulations of future conditions in controlled-environment (CE) phenotyping facilities contribute to the understanding of the plant response to special stress conditions and help breeders to select ideal genotypes which cope with future conditions. CE phenotyping facilities enable the collection of traits that are not easy to measure under field conditions and the assessment of a plant's phenotype under repeatable, clearly defined environmental conditions using automated, non-invasive, high-throughput methods. However, extrapolation and translation of results obtained under controlled environments to field environments is ambiguous. This review outlines the opportunities and challenges of phenotyping approaches under controlled environments complementary to conventional field trials. It gives an overview on general principles and introduces existing phenotyping facilities that take up the challenge of obtaining reliable and robust phenotypic data on climate response traits to support breeding of climate-adapted crops.
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Affiliation(s)
- Anna Langstroff
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Heinrich Buff-Ring 26, 35392, Giessen, Germany
| | - Marc C Heuermann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, OT Gatersleben, 06466, Seeland, Germany
| | - Andreas Stahl
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Heinrich Buff-Ring 26, 35392, Giessen, Germany
- Institute for Resistance Research and Stress Tolerance, Federal Research Centre for Cultivated Plants, Julius Kühn-Institut (JKI), Erwin-Baur-Strasse 27, 06484, Quedlinburg, Germany
| | - Astrid Junker
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, OT Gatersleben, 06466, Seeland, Germany.
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14
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Johnson D, Batista D, Cochrane K, Davey RP, Etuk A, Gonzalez-Beltran A, Haug K, Izzo M, Larralde M, Lawson TN, Minotto A, Moreno P, Nainala VC, O'Donovan C, Pireddu L, Roger P, Shaw F, Steinbeck C, Weber RJM, Sansone SA, Rocca-Serra P. ISA API: An open platform for interoperable life science experimental metadata. Gigascience 2021; 10:giab060. [PMID: 34528664 PMCID: PMC8444265 DOI: 10.1093/gigascience/giab060] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 03/19/2021] [Accepted: 08/23/2021] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND The Investigation/Study/Assay (ISA) Metadata Framework is an established and widely used set of open source community specifications and software tools for enabling discovery, exchange, and publication of metadata from experiments in the life sciences. The original ISA software suite provided a set of user-facing Java tools for creating and manipulating the information structured in ISA-Tab-a now widely used tabular format. To make the ISA framework more accessible to machines and enable programmatic manipulation of experiment metadata, the JSON serialization ISA-JSON was developed. RESULTS In this work, we present the ISA API, a Python library for the creation, editing, parsing, and validating of ISA-Tab and ISA-JSON formats by using a common data model engineered as Python object classes. We describe the ISA API feature set, early adopters, and its growing user community. CONCLUSIONS The ISA API provides users with rich programmatic metadata-handling functionality to support automation, a common interface, and an interoperable medium between the 2 ISA formats, as well as with other life science data formats required for depositing data in public databases.
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Affiliation(s)
- David Johnson
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, Oxford, OX1 3QG, UK
- Department of Informatics and Media, Uppsala University, Box 513, 75120 Uppsala, Sweden
| | - Dominique Batista
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, Oxford, OX1 3QG, UK
| | - Keeva Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Robert P Davey
- Earlham Institute, Data infrastructure and algorithms, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Anthony Etuk
- Earlham Institute, Data infrastructure and algorithms, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Alejandra Gonzalez-Beltran
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, Oxford, OX1 3QG, UK
- Science and Technology Facilities Council, Scientific Computing Department, Rutherford Appleton Laboratory, Harwell Campus, Didcot, OX11 0QX, UK
| | - Kenneth Haug
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
- Genome Research Limited, Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Saffron Walden, CB10 1RQ, UK
| | - Massimiliano Izzo
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, Oxford, OX1 3QG, UK
| | - Martin Larralde
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Thomas N Lawson
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Alice Minotto
- Earlham Institute, Data infrastructure and algorithms, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Pablo Moreno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Venkata Chandrasekhar Nainala
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Claire O'Donovan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Luca Pireddu
- Distributed Computing Group, CRS4: Center for Advanced Studies, Research & Development in Sardinia, Pula 09050, Italy
| | - Pierrick Roger
- CEA, LIST, Laboratory for Data Analysis and Systems’ Intelligence, MetaboHUB, Gif-Sur-Yvette F-91191, France
| | - Felix Shaw
- Earlham Institute, Data infrastructure and algorithms, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Christoph Steinbeck
- Cheminformatics and Computational Metabolomics, Institute for Analytical Chemistry, Lessingstr. 8, 07743 Jena, Germany
| | - Ralf J M Weber
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Susanna-Assunta Sansone
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, Oxford, OX1 3QG, UK
| | - Philippe Rocca-Serra
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, Oxford, OX1 3QG, UK
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15
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Engels JMM, Ebert AW. A Critical Review of the Current Global Ex Situ Conservation System for Plant Agrobiodiversity. II. Strengths and Weaknesses of the Current System and Recommendations for Its Improvement. Plants (Basel) 2021; 10:1904. [PMID: 34579439 PMCID: PMC8472064 DOI: 10.3390/plants10091904] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 09/05/2021] [Accepted: 09/09/2021] [Indexed: 02/08/2023]
Abstract
In this paper, we review gene bank operations that have an influence on the global conservation system, with the intention to identify critical aspects that should be improved for optimum performance. We describe the role of active and base collections and the importance of linking germplasm conservation and use, also in view of new developments in genomics and phenomics that facilitate more effective and efficient conservation and use of plant agrobiodiversity. Strengths, limitations, and opportunities of the existing global ex situ conservation system are discussed, and measures are proposed to achieve a rational, more effective, and efficient global system for germplasm conservation and sustainable use. The proposed measures include filling genetic and geographic gaps in current ex situ collections; determining unique accessions at the global level for long-term conservation in virtual base collections; intensifying existing international collaborations among gene banks and forging collaborations with the botanic gardens community; increasing investment in conservation research and user-oriented supportive research; improved accession-level description of the genetic diversity of crop collections; improvements of the legal and policy framework; and oversight of the proposed network of global base collections.
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16
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Ćwiek-Kupczyńska H, Krajewski P. Polish network of research infrastructure for plant phenotyping. RIO 2021. [DOI: 10.3897/rio.7.e73858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
This document is an edited version of the original application for inclusion of a strategic research infrastructure project in the Polish Roadmap for Research Infrastructures. The application entitled "Polish network of research infrastructure for plant phenotyping" was submitted to the Polish Ministry of Science and Higher Education in June 2018; the project was not included in the Roadmap published in January 2020. The original document did not contain this abstract.
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17
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Mayer G, Müller W, Schork K, Uszkoreit J, Weidemann A, Wittig U, Rey M, Quast C, Felden J, Glöckner FO, Lange M, Arend D, Beier S, Junker A, Scholz U, Schüler D, Kestler HA, Wibberg D, Pühler A, Twardziok S, Eils J, Eils R, Hoffmann S, Eisenacher M, Turewicz M. Implementing FAIR data management within the German Network for Bioinformatics Infrastructure (de.NBI) exemplified by selected use cases. Brief Bioinform 2021; 22:bbab010. [PMID: 33589928 PMCID: PMC8425304 DOI: 10.1093/bib/bbab010] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 12/21/2020] [Accepted: 01/06/2021] [Indexed: 12/21/2022] Open
Abstract
This article describes some use case studies and self-assessments of FAIR status of de.NBI services to illustrate the challenges and requirements for the definition of the needs of adhering to the FAIR (findable, accessible, interoperable and reusable) data principles in a large distributed bioinformatics infrastructure. We address the challenge of heterogeneity of wet lab technologies, data, metadata, software, computational workflows and the levels of implementation and monitoring of FAIR principles within the different bioinformatics sub-disciplines joint in de.NBI. On the one hand, this broad service landscape and the excellent network of experts are a strong basis for the development of useful research data management plans. On the other hand, the large number of tools and techniques maintained by distributed teams renders FAIR compliance challenging.
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Affiliation(s)
- Gerhard Mayer
- Ruhr University Bochum, Faculty of Medicine, Medizinisches Proteom-Center, Bochum, Germany
- Ruhr University Bochum, Center for Protein Diagnostics (ProDi), Medical Proteome Analysis, Bochum, Germany
- Ulm University, Institute of Medical Systems Biology, Ulm, Germany
| | - Wolfgang Müller
- Heidelberg Institute for Theoretical Studies (HITS gGmbH), Scientific Databases and Visualization Group, Heidelberg, Germany
| | - Karin Schork
- Ruhr University Bochum, Faculty of Medicine, Medizinisches Proteom-Center, Bochum, Germany
- Ruhr University Bochum, Center for Protein Diagnostics (ProDi), Medical Proteome Analysis, Bochum, Germany
| | - Julian Uszkoreit
- Ruhr University Bochum, Faculty of Medicine, Medizinisches Proteom-Center, Bochum, Germany
- Ruhr University Bochum, Center for Protein Diagnostics (ProDi), Medical Proteome Analysis, Bochum, Germany
| | - Andreas Weidemann
- Heidelberg Institute for Theoretical Studies (HITS gGmbH), Scientific Databases and Visualization Group, Heidelberg, Germany
| | - Ulrike Wittig
- Heidelberg Institute for Theoretical Studies (HITS gGmbH), Scientific Databases and Visualization Group, Heidelberg, Germany
| | - Maja Rey
- Heidelberg Institute for Theoretical Studies (HITS gGmbH), Scientific Databases and Visualization Group, Heidelberg, Germany
| | | | - Janine Felden
- Jacobs University Bremen gGmbH, Bremen, Germany
- University of Bremen, MARUM - Center for Marine Environmental Sciences, Bremen, Germany
| | - Frank Oliver Glöckner
- Jacobs University Bremen gGmbH, Bremen, Germany
- University of Bremen, MARUM - Center for Marine Environmental Sciences, Bremen, Germany
- Alfred Wegener Institute - Helmholtz Center for Polar- and Marine Research, Bremerhaven, Germany
| | - Matthias Lange
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Daniel Arend
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Sebastian Beier
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Astrid Junker
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Danuta Schüler
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Hans A Kestler
- Ulm University, Institute of Medical Systems Biology, Ulm, Germany
- Leibniz Institute on Ageing - Fritz Lipmann Institute, Jena
| | - Daniel Wibberg
- Bielefeld University, Center for Biotechnology (CeBiTec), Bielefeld, Germany
| | - Alfred Pühler
- Bielefeld University, Center for Biotechnology (CeBiTec), Bielefeld, Germany
| | - Sven Twardziok
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Center for Digital Health, Berlin, Germany
| | - Jürgen Eils
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Center for Digital Health, Berlin, Germany
| | - Roland Eils
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Center for Digital Health, Berlin, Germany
- Heidelberg University Hospital and BioQuant, Health Data Science Unit, Heidelberg, Germany
| | - Steve Hoffmann
- Leibniz Institute on Ageing - Fritz Lipmann Institute, Jena
| | - Martin Eisenacher
- Ruhr University Bochum, Faculty of Medicine, Medizinisches Proteom-Center, Bochum, Germany
- Ruhr University Bochum, Center for Protein Diagnostics (ProDi), Medical Proteome Analysis, Bochum, Germany
| | - Michael Turewicz
- Ruhr University Bochum, Faculty of Medicine, Medizinisches Proteom-Center, Bochum, Germany
- Ruhr University Bochum, Center for Protein Diagnostics (ProDi), Medical Proteome Analysis, Bochum, Germany
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18
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Shook JM, Zhang J, Jones SE, Singh A, Diers BW, Singh AK. Meta-GWAS for quantitative trait loci identification in soybean. G3 (Bethesda) 2021; 11:jkab117. [PMID: 33856425 PMCID: PMC8495947 DOI: 10.1093/g3journal/jkab117] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 04/02/2021] [Indexed: 01/03/2023]
Abstract
We report a meta-Genome Wide Association Study involving 73 published studies in soybean [Glycine max L. (Merr.)] covering 17,556 unique accessions, with improved statistical power for robust detection of loci associated with a broad range of traits. De novo GWAS and meta-analysis were conducted for composition traits including fatty acid and amino acid composition traits, disease resistance traits, and agronomic traits including seed yield, plant height, stem lodging, seed weight, seed mottling, seed quality, flowering timing, and pod shattering. To examine differences in detectability and test statistical power between single- and multi-environment GWAS, comparison of meta-GWAS results to those from the constituent experiments were performed. Using meta-GWAS analysis and the analysis of individual studies, we report 483 peaks at 393 unique loci. Using stringent criteria to detect significant marker-trait associations, 59 candidate genes were identified, including 17 agronomic traits loci, 19 for seed-related traits, and 33 for disease reaction traits. This study identified potentially valuable candidate genes that affect multiple traits. The success in narrowing down the genomic region for some loci through overlapping mapping results of multiple studies is a promising avenue for community-based studies and plant breeding applications.
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Affiliation(s)
| | - Jiaoping Zhang
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - Sarah E Jones
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - Arti Singh
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - Brian W Diers
- Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA
| | - Asheesh K Singh
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
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19
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Andrés-Hernández L, Halimi RA, Mauleon R, Mayes S, Baten A, King GJ. Challenges for FAIR-compliant description and comparison of crop phenotype data with standardized controlled vocabularies. Database (Oxford) 2021; 2021:baab028. [PMID: 33991093 PMCID: PMC8122365 DOI: 10.1093/database/baab028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 04/14/2021] [Accepted: 04/30/2021] [Indexed: 12/04/2022]
Abstract
Crop phenotypic data underpin many pre-breeding efforts to characterize variation within germplasm collections. Although there has been an increase in the global capacity for accumulating and comparing such data, a lack of consistency in the systematic description of metadata often limits integration and sharing. We therefore aimed to understand some of the challenges facing findable, accesible, interoperable and reusable (FAIR) curation and annotation of phenotypic data from minor and underutilized crops. We used bambara groundnut (Vigna subterranea) as an exemplar underutilized crop to assess the ability of the Crop Ontology system to facilitate curation of trait datasets, so that they are accessible for comparative analysis. This involved generating a controlled vocabulary Trait Dictionary of 134 terms. Systematic quantification of syntactic and semantic cohesiveness of the full set of 28 crop-specific COs identified inconsistencies between trait descriptor names, a relative lack of cross-referencing to other ontologies and a flat ontological structure for classifying traits. We also evaluated the Minimal Information About a Phenotyping Experiment and FAIR compliance of bambara trait datasets curated within the CropStoreDB schema. We discuss specifications for a more systematic and generic approach to trait controlled vocabularies, which would benefit from representation of terms that adhere to Open Biological and Biomedical Ontologies principles. In particular, we focus on the benefits of reuse of existing definitions within pre- and post-composed axioms from other domains in order to facilitate the curation and comparison of datasets from a wider range of crops. Database URL: https://www.cropstoredb.org/cs_bambara.html.
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Affiliation(s)
- Liliana Andrés-Hernández
- Southern Cross Plant Science, Southern Cross University, PO Box 157, Lismore, NSW 2480, Australia
| | - Razlin Azman Halimi
- Southern Cross Plant Science, Southern Cross University, PO Box 157, Lismore, NSW 2480, Australia
| | - Ramil Mauleon
- Southern Cross Plant Science, Southern Cross University, PO Box 157, Lismore, NSW 2480, Australia
| | - Sean Mayes
- School of Biosciences, University of Nottingham, Sutton Bonington, Leicestershire, LE12 5RD,Nottingham, Nottingham, UK
| | - Abdul Baten
- Institute of Precision Medicine & Bioinformatics, Sydney Local Health District, Royal Prince Alfred Hospital, Missenden Road, Camperdown, NSW 2050, Australia
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, PO Box 157, Lismore, NSW 2480, Australia
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20
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Rajesh A, Chang Y, Abedalthagafi MS, Wong-Beringer A, Love MI, Mangul S. Improving the completeness of public metadata accompanying omics studies. Genome Biol 2021; 22:106. [PMID: 33858487 PMCID: PMC8048353 DOI: 10.1186/s13059-021-02332-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 03/29/2021] [Indexed: 12/17/2022] Open
Affiliation(s)
- Anushka Rajesh
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089 USA
| | - Yutong Chang
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089 USA
| | - Malak S. Abedalthagafi
- Genomics Research Department, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Annie Wong-Beringer
- Department of Clinical Pharmacy, University of Southern California, Los Angeles, CA 90089 USA
| | - Michael I. Love
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516 USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514 USA
| | - Serghei Mangul
- Department of Clinical Pharmacy, University of Southern California, Los Angeles, CA 90089 USA
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21
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Tian Z, Wang JW, Li J, Han B. Designing future crops: challenges and strategies for sustainable agriculture. Plant J 2021; 105:1165-1178. [PMID: 33258137 DOI: 10.1111/tpj.15107] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/22/2020] [Accepted: 11/26/2020] [Indexed: 05/26/2023]
Abstract
Crop production is facing unprecedented challenges. Despite the fact that the food supply has significantly increased over the past half-century, ~8.9 and 14.3% people are still suffering from hunger and malnutrition, respectively. Agricultural environments are continuously threatened by a booming world population, a shortage of arable land, and rapid changes in climate. To ensure food and ecosystem security, there is a need to design future crops for sustainable agriculture development by maximizing net production and minimalizing undesirable effects on the environment. The future crops design projects, recently launched by the National Natural Science Foundation of China and Chinese Academy of Sciences (CAS), aim to develop a roadmap for rapid design of customized future crops using cutting-edge technologies in the Breeding 4.0 era. In this perspective, we first introduce the background and missions of these projects. We then outline strategies to design future crops, such as improvement of current well-cultivated crops, de novo domestication of wild species and redomestication of current cultivated crops. We further discuss how these ambitious goals can be achieved by the recent development of new integrative omics tools, advanced genome-editing tools and synthetic biology approaches. Finally, we summarize related opportunities and challenges in these projects.
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Affiliation(s)
- Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Innovation Academy for Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jia-Wei Wang
- 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
- ShanghaiTech University, Shanghai, 200031, China
| | - Jiayang Li
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research (Beijing), Innovation Academy for Seed Design, Institute of Genetics and Developmental Biology Chinese Academy of Sciences, Beijing, 100101, China
| | - Bin Han
- 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
- ShanghaiTech University, Shanghai, 200031, China
- National Center for Gene Research, Shanghai, 200233, China
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22
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Rodrigues AM, Miguel C, Chaves I, António C. Mass spectrometry-based forest tree metabolomics. Mass Spectrom Rev 2021; 40:126-157. [PMID: 31498921 DOI: 10.1002/mas.21603] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 08/05/2019] [Indexed: 05/24/2023]
Abstract
Research in forest tree species has advanced slowly when compared with other agricultural crops and model organisms, mainly due to the long-life cycles, large genome sizes, and lack of genomic tools. Additionally, trees are complex matrices, and the presence of interferents (e.g., oleoresins and cellulose) challenges the analysis of tree tissues with mass spectrometry (MS)-based analytical platforms. In this review, advances in MS-based forest tree metabolomics are discussed. Given their economic and ecological significance, particular focus is given to Pinus, Quercus, and Eucalyptus forest tree species to better understand their metabolite responses to abiotic and biotic stresses in the current climate change scenario. Furthermore, MS-based metabolomics technologies produce large and complex datasets that require expertize to adequately manage, process, analyze, and store the data in dedicated repositories. To ensure that the full potential of forest tree metabolomics data are translated into new knowledge, these data should comply with the FAIR principles (i.e., Findable, Accessible, Interoperable, and Re-usable). It is essential that adequate standards are implemented to annotate metadata from forest tree metabolomics studies as is already required by many science and governmental agencies and some major scientific publishers. © 2019 John Wiley & Sons Ltd. Mass Spec Rev 40:126-157, 2021.
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Affiliation(s)
- Ana Margarida Rodrigues
- Plant Metabolomics Laboratory, GreenIT-Bioresources for Sustainability, Instituto de Tecnologia Química e Biológica António Xavie, Universidade Nova de Lisboa (ITQB NOVA) Avenida da República, Oeiras, 2780-157, Portugal
| | - Célia Miguel
- Forest Genomics & Molecular Genetics Lab, BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016, Lisboa, Portugal
- Instituto de Biologia Experimental e Tecnológica (iBET), 2780-157, Oeiras, Portugal
| | - Inês Chaves
- Forest Genomics & Molecular Genetics Lab, BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016, Lisboa, Portugal
- Instituto de Biologia Experimental e Tecnológica (iBET), 2780-157, Oeiras, Portugal
| | - Carla António
- Plant Metabolomics Laboratory, GreenIT-Bioresources for Sustainability, Instituto de Tecnologia Química e Biológica António Xavie, Universidade Nova de Lisboa (ITQB NOVA) Avenida da República, Oeiras, 2780-157, Portugal
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23
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Bowles AMC, Paps J, Bechtold U. Evolutionary Origins of Drought Tolerance in Spermatophytes. Front Plant Sci 2021; 12:655924. [PMID: 34239520 PMCID: PMC8258419 DOI: 10.3389/fpls.2021.655924] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 05/11/2021] [Indexed: 05/19/2023]
Abstract
It is commonly known that drought stress is a major constraint limiting crop production. Drought stress and associated drought tolerance mechanisms are therefore under intense investigation with the view to future production of drought tolerant crops. With an ever-growing population and variable climate, novel approaches need to be considered to sustainably feed future generations. In this context, definitions of drought tolerance are highly variable, which poses a major challenge for the systematic assessment of this trait across the plant kingdom. Furthermore, drought tolerance is a polygenic trait and understanding the evolution of this complex trait may inform us about patterns of gene gain and loss in relation to diverse drought adaptations. We look at the transition of plants from water to land, and the role of drought tolerance in enabling this transition, before discussing the first drought tolerant plant and common drought responses amongst vascular plants. We reviewed the distribution of a combined "drought tolerance" trait in very broad terms to encompass different experimental systems and definitions used in the current literature and assigned a binary trait "tolerance vs. sensitivity" in 178 extant plant species. By simplifying drought responses of plants into this "binary" trait we were able to explore the evolution of drought tolerance across the wider plant kingdom, compared to previous studies. We show how this binary "drought tolerance/sensitivity" trait has evolved and discuss how incorporating this information into an evolutionary genomics framework could provide insights into the molecular mechanisms underlying extreme drought adaptations.
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Affiliation(s)
| | - Jordi Paps
- School of Life Sciences, University of Essex, Colchester, United Kingdom
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Ulrike Bechtold
- School of Life Sciences, University of Essex, Colchester, United Kingdom
- *Correspondence: Ulrike Bechtold,
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24
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Li M, Hensel G, Melzer M, Junker A, Tschiersch H, Ruwe H, Arend D, Kumlehn J, Börner T, Stein N. Mutation of the ALBOSTRIANS Ohnologous Gene HvCMF3 Impairs Chloroplast Development and Thylakoid Architecture in Barley. Front Plant Sci 2021; 12:732608. [PMID: 34659298 PMCID: PMC8517540 DOI: 10.3389/fpls.2021.732608] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/10/2021] [Indexed: 05/12/2023]
Abstract
Gene pairs resulting from whole genome duplication (WGD), so-called ohnologous genes, are retained if at least one member of the pair undergoes neo- or sub-functionalization. Phylogenetic analyses of the ohnologous genes ALBOSTRIANS (HvAST/HvCMF7) and ALBOSTRIANS-LIKE (HvASL/HvCMF3) of barley (Hordeum vulgare) revealed them as members of a subfamily of genes coding for CCT motif (CONSTANS, CONSTANS-LIKE and TIMING OF CAB1) proteins characterized by a single CCT domain and a putative N-terminal chloroplast transit peptide. Recently, we showed that HvCMF7 is needed for chloroplast ribosome biogenesis. Here we demonstrate that mutations in HvCMF3 lead to seedlings delayed in development. They exhibit a yellowish/light green - xantha - phenotype and successively develop pale green leaves. Compared to wild type, plastids of mutant seedlings show a decreased PSII efficiency, impaired processing and reduced amounts of ribosomal RNAs; they contain less thylakoids and grana with a higher number of more loosely stacked thylakoid membranes. Site-directed mutagenesis of HvCMF3 identified a previously unknown functional domain, which is highly conserved within this subfamily of CCT domain containing proteins. HvCMF3:GFP fusion constructs were localized to plastids and nucleus. Hvcmf3Hvcmf7 double mutants exhibited a xantha-albino or albino phenotype depending on the strength of molecular lesion of the HvCMF7 allele. The chloroplast ribosome deficiency is discussed as the primary observed defect of the Hvcmf3 mutants. Based on our observations, the genes HvCMF3 and HvCMF7 have similar but not identical functions in chloroplast development of barley supporting our hypothesis of neo-/sub-functionalization between both ohnologous genes.
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Affiliation(s)
- Mingjiu Li
- Genomics of Genetic Resources, Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
| | - Goetz Hensel
- Plant Reproductive Biology, Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
| | - Michael Melzer
- Structural Cell Biology, Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
| | - Astrid Junker
- Acclimation Dynamics and Phenotyping, Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
| | - Henning Tschiersch
- Heterosis Research Group, Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
| | - Hannes Ruwe
- Molecular Genetics, Institute of Biology, Humboldt University, Berlin, Germany
| | - Daniel Arend
- Research Group Bioinformatics and Information Technology, Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
| | - Jochen Kumlehn
- Plant Reproductive Biology, Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
| | - Thomas Börner
- Molecular Genetics, Institute of Biology, Humboldt University, Berlin, Germany
- *Correspondence: Thomas Börner,
| | - Nils Stein
- Genomics of Genetic Resources, Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
- Department of Crop Sciences, Center for Integrated Breeding Research, Georg-August-University, Göttingen, Germany
- Nils Stein,
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25
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Arnaud E, Laporte MA, Kim S, Aubert C, Leonelli S, Miro B, Cooper L, Jaiswal P, Kruseman G, Shrestha R, Buttigieg PL, Mungall CJ, Pietragalla J, Agbona A, Muliro J, Detras J, Hualla V, Rathore A, Das RR, Dieng I, Bauchet G, Menda N, Pommier C, Shaw F, Lyon D, Mwanzia L, Juarez H, Bonaiuti E, Chiputwa B, Obileye O, Auzoux S, Yeumo ED, Mueller LA, Silverstein K, Lafargue A, Antezana E, Devare M, King B. The Ontologies Community of Practice: A CGIAR Initiative for Big Data in Agrifood Systems. Patterns (N Y) 2020; 1:100105. [PMID: 33205138 PMCID: PMC7660444 DOI: 10.1016/j.patter.2020.100105] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/28/2020] [Accepted: 08/24/2020] [Indexed: 12/15/2022]
Abstract
Heterogeneous and multidisciplinary data generated by research on sustainable global agriculture and agrifood systems requires quality data labeling or annotation in order to be interoperable. As recommended by the FAIR principles, data, labels, and metadata must use controlled vocabularies and ontologies that are popular in the knowledge domain and commonly used by the community. Despite the existence of robust ontologies in the Life Sciences, there is currently no comprehensive full set of ontologies recommended for data annotation across agricultural research disciplines. In this paper, we discuss the added value of the Ontologies Community of Practice (CoP) of the CGIAR Platform for Big Data in Agriculture for harnessing relevant expertise in ontology development and identifying innovative solutions that support quality data annotation. The Ontologies CoP stimulates knowledge sharing among stakeholders, such as researchers, data managers, domain experts, experts in ontology design, and platform development teams.
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Affiliation(s)
- Elizabeth Arnaud
- Digital Solutions Team, Digital Inclusion Lever, Bioversity International, Montpellier Office, Montpellier, France
| | - Marie-Angélique Laporte
- Digital Solutions Team, Digital Inclusion Lever, Bioversity International, Montpellier Office, Montpellier, France
| | - Soonho Kim
- Markets, Trade and Institutions Division (MTID), International Food Policy Research Institute (IFPRI), Washington, DC, USA
| | - Céline Aubert
- Environment and Production Technology Division (EPTD), International Food Policy Research Institute (IFPRI), Washington, DC, USA
| | - Sabina Leonelli
- Department of Sociology, Philosophy and Anthropology & Exeter Centre for the Study of the Life Sciences (Egenis), University of Exeter, Exeter, UK
| | - Berta Miro
- Agrifood Policy Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Laurel Cooper
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Gideon Kruseman
- Socio-Economics Program, International Maize and Wheat Improvement Center (CIMMYT), Texcoco, State of México, Mexico
| | - Rosemary Shrestha
- Genetic Resources Program, International Maize and Wheat Improvement Center (CIMMYT), Texcoco, State of México, México
| | - Pier Luigi Buttigieg
- Helmholtz Metadata Collaboration, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Christopher J. Mungall
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Afolabi Agbona
- Cassava Breeding Program, International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | | | - Jeffrey Detras
- Bioinformatics Cluster, Strategic Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Vilma Hualla
- Research Informatics Unit (RIU), International Potato Center (CIP), Lima, Peru
| | - Abhishek Rathore
- Statistics, Bioinformatics & Data Management (SBDM) Theme, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India
| | - Roma Rani Das
- Statistics, Bioinformatics & Data Management (SBDM) Theme, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India
| | - Ibnou Dieng
- Biometrics Unit, International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria
| | - Guillaume Bauchet
- Mueller Bioinformatics Laboratory, Boyce Thompson Institute for Plant Research, Ithaca, NY, USA
| | - Naama Menda
- Mueller Bioinformatics Laboratory, Boyce Thompson Institute for Plant Research, Ithaca, NY, USA
| | - Cyril Pommier
- BioinfOmics, Plant Bioinformatics Facility, Université Paris-Saclay, Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Versailles, France
| | - Felix Shaw
- Digital Biology, Earlham Institute, Norwich, Norfolk, UK
| | - David Lyon
- Mueller Bioinformatics Laboratory, Boyce Thompson Institute for Plant Research, Ithaca, NY, USA
| | - Leroy Mwanzia
- Performance, Innovation and Strategic Analysis, International Center for Tropical Agriculture (CIAT), Regional Office for Africa, Nairobi, Kenya
| | - Henry Juarez
- Research Informatics Unit (RIU), International Potato Center (CIP), Lima, Peru
| | - Enrico Bonaiuti
- Monitoring, Evaluation and Learning Team, International Center for Agricultural Research in the Dry Areas (ICARDA), Beirut, Lebanon
| | - Brian Chiputwa
- Research Methods Group (RMG), World Agroforestry (ICRAF), Nairobi, Kenya
| | - Olatunbosun Obileye
- Data Management Section, International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria
| | - Sandrine Auzoux
- UPR AIDA, The French Agricultural Research Centre for International Development (CIRAD), Sainte-Clotilde, Réunion, France
- Université de Montpellier, Montpellier, France
| | - Esther Dzalé Yeumo
- Unité Délégation à l’Information Scientifique et Technique - DIST, Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Versailles, France
| | - Lukas A. Mueller
- Mueller Bioinformatics Laboratory, Boyce Thompson Institute for Plant Research, Ithaca, NY, USA
| | | | | | - Erick Antezana
- Bayer Crop Science SA-NV, Diegem, Belgium
- Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Medha Devare
- Environment and Production Technology Division (EPTD), International Food Policy Research Institute (IFPRI), Washington, DC, USA
| | - Brian King
- CGIAR Platform for Big Data in Agriculture, International Center for Tropical Agriculture (CIAT), Cali, Colombia
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26
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Colmer J, O'Neill CM, Wells R, Bostrom A, Reynolds D, Websdale D, Shiralagi G, Lu W, Lou Q, Le Cornu T, Ball J, Renema J, Flores Andaluz G, Benjamins R, Penfield S, Zhou J. SeedGerm: a cost-effective phenotyping platform for automated seed imaging and machine-learning based phenotypic analysis of crop seed germination. New Phytol 2020; 228:778-793. [PMID: 32533857 DOI: 10.1111/nph.16736] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 05/25/2020] [Indexed: 05/26/2023]
Abstract
Efficient seed germination and establishment are important traits for field and glasshouse crops. Large-scale germination experiments are laborious and prone to observer errors, leading to the necessity for automated methods. We experimented with five crop species, including tomato, pepper, Brassica, barley, and maize, and concluded an approach for large-scale germination scoring. Here, we present the SeedGerm system, which combines cost-effective hardware and open-source software for seed germination experiments, automated seed imaging, and machine-learning based phenotypic analysis. The software can process multiple image series simultaneously and produce reliable analysis of germination- and establishment-related traits, in both comma-separated values (CSV) and processed images (PNG) formats. In this article, we describe the hardware and software design in detail. We also demonstrate that SeedGerm could match specialists' scoring of radicle emergence. Germination curves were produced based on seed-level germination timing and rates rather than a fitted curve. In particular, by scoring germination across a diverse panel of Brassica napus varieties, SeedGerm implicates a gene important in abscisic acid (ABA) signalling in seeds. We compared SeedGerm with existing methods and concluded that it could have wide utilities in large-scale seed phenotyping and testing, for both research and routine seed technology applications.
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Affiliation(s)
- Joshua Colmer
- Engineering biology, Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Carmel M O'Neill
- Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Rachel Wells
- Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Aaron Bostrom
- Engineering biology, Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Daniel Reynolds
- Engineering biology, Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Danny Websdale
- Engineering biology, Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Gagan Shiralagi
- Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Wei Lu
- College of Engineering, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Qiaojun Lou
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
| | - Thomas Le Cornu
- Engineering biology, Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Joshua Ball
- Engineering biology, Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Jim Renema
- Syngenta Seeds BV, Enkhuizen, 1601 BK, the Netherlands
| | | | | | - Steven Penfield
- Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Ji Zhou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Plant Phenomics Research Center, Jiangsu Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry, Nanjing Agricultural University, Nanjing, 210095, China
- Cambridge Crop Research, National Institute of Agricultural Botany, Cambridge, CB3 0LE, UK
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27
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Creydt M, Fischer M. Food Phenotyping: Recording and Processing of Non-Targeted Liquid Chromatography Mass Spectrometry Data for Verifying Food Authenticity. Molecules 2020; 25:E3972. [PMID: 32878155 PMCID: PMC7504784 DOI: 10.3390/molecules25173972] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 12/11/2022] Open
Abstract
Experiments based on metabolomics represent powerful approaches to the experimental verification of the integrity of food. In particular, high-resolution non-targeted analyses, which are carried out by means of liquid chromatography-mass spectrometry systems (LC-MS), offer a variety of options. However, an enormous amount of data is recorded, which must be processed in a correspondingly complex manner. The evaluation of LC-MS based non-targeted data is not entirely trivial and a wide variety of strategies have been developed that can be used in this regard. In this paper, an overview of the mandatory steps regarding data acquisition is given first, followed by a presentation of the required preprocessing steps for data evaluation. Then some multivariate analysis methods are discussed, which have proven to be particularly suitable in this context in recent years. The publication closes with information on the identification of marker compounds.
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Affiliation(s)
- Marina Creydt
- Hamburg School of Food Science-Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany;
- Center for Hybrid Nanostructures (CHyN), Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Markus Fischer
- Hamburg School of Food Science-Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany;
- Center for Hybrid Nanostructures (CHyN), Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
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28
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David E, Madec S, Sadeghi-Tehran P, Aasen H, Zheng B, Liu S, Kirchgessner N, Ishikawa G, Nagasawa K, Badhon MA, Pozniak C, de Solan B, Hund A, Chapman SC, Baret F, Stavness I, Guo W. Global Wheat Head Detection (GWHD) Dataset: A Large and Diverse Dataset of High-Resolution RGB-Labelled Images to Develop and Benchmark Wheat Head Detection Methods. Plant Phenomics 2020; 2020:3521852. [PMID: 33313551 PMCID: PMC7706323 DOI: 10.34133/2020/3521852] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 07/01/2020] [Indexed: 05/19/2023]
Abstract
The detection of wheat heads in plant images is an important task for estimating pertinent wheat traits including head population density and head characteristics such as health, size, maturity stage, and the presence of awns. Several studies have developed methods for wheat head detection from high-resolution RGB imagery based on machine learning algorithms. However, these methods have generally been calibrated and validated on limited datasets. High variability in observational conditions, genotypic differences, development stages, and head orientation makes wheat head detection a challenge for computer vision. Further, possible blurring due to motion or wind and overlap between heads for dense populations make this task even more complex. Through a joint international collaborative effort, we have built a large, diverse, and well-labelled dataset of wheat images, called the Global Wheat Head Detection (GWHD) dataset. It contains 4700 high-resolution RGB images and 190000 labelled wheat heads collected from several countries around the world at different growth stages with a wide range of genotypes. Guidelines for image acquisition, associating minimum metadata to respect FAIR principles, and consistent head labelling methods are proposed when developing new head detection datasets. The GWHD dataset is publicly available at http://www.global-wheat.com/and aimed at developing and benchmarking methods for wheat head detection.
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Affiliation(s)
- Etienne David
- Arvalis, Institut du végétal, 3 Rue Joseph et Marie Hackin, 75116 Paris, France
- UMR1114 EMMAH, INRAE, Centre PACA, Bâtiment Climat, Domaine Saint-Paul, 228 Route de l'Aérodrome, CS 40509, 84914 Avignon Cedex, France
| | - Simon Madec
- Arvalis, Institut du végétal, 3 Rue Joseph et Marie Hackin, 75116 Paris, France
- UMR1114 EMMAH, INRAE, Centre PACA, Bâtiment Climat, Domaine Saint-Paul, 228 Route de l'Aérodrome, CS 40509, 84914 Avignon Cedex, France
| | | | - Helge Aasen
- Institute of Agricultural Sciences, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | - Bangyou Zheng
- CSIRO Agriculture and Food, Queensland Biosciences Precinct, 306 Carmody Road, St Lucia, 4067 QLD, Australia
| | - Shouyang Liu
- UMR1114 EMMAH, INRAE, Centre PACA, Bâtiment Climat, Domaine Saint-Paul, 228 Route de l'Aérodrome, CS 40509, 84914 Avignon Cedex, France
- Plant Phenomics Research Center, Nanjing Agricultural University, Nanjing, China
| | - Norbert Kirchgessner
- Institute of Agricultural Sciences, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | - Goro Ishikawa
- Institute of Crop Science, National Agriculture and Food Research Organization, Japan
| | - Koichi Nagasawa
- Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization, Japan
| | | | - Curtis Pozniak
- Department of Plant Sciences, University of Saskatchewan, Canada
| | - Benoit de Solan
- Arvalis, Institut du végétal, 3 Rue Joseph et Marie Hackin, 75116 Paris, France
| | - Andreas Hund
- Institute of Agricultural Sciences, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | - Scott C. Chapman
- CSIRO Agriculture and Food, Queensland Biosciences Precinct, 306 Carmody Road, St Lucia, 4067 QLD, Australia
- School of Food and Agricultural Sciences, The University of Queensland, Gatton, 4343 QLD, Australia
| | - Frédéric Baret
- UMR1114 EMMAH, INRAE, Centre PACA, Bâtiment Climat, Domaine Saint-Paul, 228 Route de l'Aérodrome, CS 40509, 84914 Avignon Cedex, France
- Plant Phenomics Research Center, Nanjing Agricultural University, Nanjing, China
| | - Ian Stavness
- Department of Computer Science, University of Saskatchewan, Canada
| | - Wei Guo
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Midori-cho, Nishitokyo City, Tokyo, Japan
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Weise S, Lohwasser U, Oppermann M. Document or Lose It-On the Importance of Information Management for Genetic Resources Conservation in Genebanks. Plants (Basel) 2020; 9:E1050. [PMID: 32824806 DOI: 10.3390/plants9081050] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/13/2020] [Accepted: 08/14/2020] [Indexed: 12/19/2022]
Abstract
Genebanks play an important role in the long-term conservation of plant genetic resources and are complementary to the conservation of diversity in farmers' fields and in nature. In this context, documentation plays a critical role. Without well-structured documentation, it is not possible to make statements about the value of a resource, especially with regard to its potential for breeding and research. In particular, comprehensive information management is a prerequisite for the further development of genebank collections. This requires detailed information about the composition of a collection, thus allowing statements about which species and/or regions of origin are under-represented. This task is of strategic importance, especially due to the threats to crop plants and their wild relatives caused by advancing climate change. Both the actual conservation management and the fulfilment of legal obligations depend on information. Hence, documentation units have been established in almost all genebanks worldwide. They all face the challenge that knowledge about genebank accessions must be permanently managed and passed on across generations. International standards such as Multi-Crop Passport Descriptors (MCPD) have been established for the exchange of data between genebanks, and allow the operation of international information systems, such as the World Information and Early Warning System on Plant Genetic Resources for Food and Agriculture (WIEWS), the European Search Catalogue for Plant Genetic Resources (EURISCO) or Genesys.
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Brown D, Van den Bergh I, de Bruin S, Machida L, van Etten J. Data synthesis for crop variety evaluation. A review. Agron Sustain Dev 2020; 40:25. [PMID: 32863892 PMCID: PMC7440334 DOI: 10.1007/s13593-020-00630-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/23/2020] [Indexed: 05/12/2023]
Abstract
Crop varieties should fulfill multiple requirements, including agronomic performance and product quality. Variety evaluations depend on data generated from field trials and sensory analyses, performed with different levels of participation from farmers and consumers. Such multi-faceted variety evaluation is expensive and time-consuming; hence, any use of these data should be optimized. Data synthesis can help to take advantage of existing and new data, combining data from different sources and combining it with expert knowledge to produce new information and understanding that supports decision-making. Data synthesis for crop variety evaluation can partly build on extant experiences and methods, but it also requires methodological innovation. We review the elements required to achieve data synthesis for crop variety evaluation, including (1) data types required for crop variety evaluation, (2) main challenges in data management and integration, (3) main global initiatives aiming to solve those challenges, (4) current statistical approaches to combine data for crop variety evaluation and (5) existing data synthesis methods used in evaluation of varieties to combine different datasets from multiple data sources. We conclude that currently available methods have the potential to overcome existing barriers to data synthesis and could set in motion a virtuous cycle that will encourage researchers to share data and collaborate on data-driven research.
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Affiliation(s)
- David Brown
- Laboratory of Geo-Information Science and Remote Sensing, Wageningen University & Research, Droevendaalsesteeg 3, 6708 PB Wageningen, The Netherlands
- Bioversity International, Turrialba, 30501 Costa Rica
| | - Inge Van den Bergh
- Bioversity International, C/O KU Leuven, W. De Croylaan 42, P.O. Box 2455, 3001 Leuven, Belgium
| | - Sytze de Bruin
- Laboratory of Geo-Information Science and Remote Sensing, Wageningen University & Research, Droevendaalsesteeg 3, 6708 PB Wageningen, The Netherlands
| | - Lewis Machida
- Bioversity International, C/O International Institute of Tropical Agriculture (IITA), Nelson Mandela African Institute of Science and Technology, P.O. Box 447, Arusha, Tanzania
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31
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Papoutsoglou EA, Faria D, Arend D, Arnaud E, Athanasiadis IN, Chaves I, Coppens F, Cornut G, Costa BV, Ćwiek-Kupczyńska H, Droesbeke B, Finkers R, Gruden K, Junker A, King GJ, Krajewski P, Lange M, Laporte MA, Michotey C, Oppermann M, Ostler R, Poorter H, Ramı Rez-Gonzalez R, Ramšak Ž, Reif JC, Rocca-Serra P, Sansone SA, Scholz U, Tardieu F, Uauy C, Usadel B, Visser RGF, Weise S, Kersey PJ, Miguel CM, Adam-Blondon AF, Pommier C. Enabling reusability of plant phenomic datasets with MIAPPE 1.1. New Phytol 2020. [PMID: 32171029 DOI: 10.15454/1yxvzv] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Enabling data reuse and knowledge discovery is increasingly critical in modern science, and requires an effort towards standardising data publication practices. This is particularly challenging in the plant phenotyping domain, due to its complexity and heterogeneity. We have produced the MIAPPE 1.1 release, which enhances the existing MIAPPE standard in coverage, to support perennial plants, in structure, through an explicit data model, and in clarity, through definitions and examples. We evaluated MIAPPE 1.1 by using it to express several heterogeneous phenotyping experiments in a range of different formats, to demonstrate its applicability and the interoperability between the various implementations. Furthermore, the extended coverage is demonstrated by the fact that one of the datasets could not have been described under MIAPPE 1.0. MIAPPE 1.1 marks a major step towards enabling plant phenotyping data reusability, thanks to its extended coverage, and especially the formalisation of its data model, which facilitates its implementation in different formats. Community feedback has been critical to this development, and will be a key part of ensuring adoption of the standard.
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Affiliation(s)
- Evangelia A Papoutsoglou
- Plant Breeding, Wageningen University & Research, PO Box 386, Wageningen, 6700AJ, the Netherlands
| | - Daniel Faria
- BioData.pt, Instituto Gulbenkian de Ciência, 2780-156, Oeiras, Portugal
- INESC-ID, 1000-029, Lisboa, Portugal
| | - Daniel Arend
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Elizabeth Arnaud
- Bioversity International, Parc Scientifique Agropolis II, Montpellier Cedex 5, 34397, France
| | - Ioannis N Athanasiadis
- Geo-Information Science and Remote Sensing Laboratory, Wageningen University, Droevendaalsesteeg 3, Wageningen, 6708PB, the Netherlands
| | - Inês Chaves
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA) Avenida da República, 2780-157, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica (iBET), 2780-157, Oeiras, Portugal
| | - Frederik Coppens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium
| | | | - Bruno V Costa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA) Avenida da República, 2780-157, Oeiras, Portugal
- BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, 1749-016, Portugal
| | - Hanna Ćwiek-Kupczyńska
- Institute of Plant Genetics, Polish Academy of Sciences, ul. Strzeszyńska 34, 60-479, Poznań, Poland
| | - Bert Droesbeke
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium
| | - Richard Finkers
- Plant Breeding, Wageningen University & Research, PO Box 386, Wageningen, 6700AJ, the Netherlands
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, SI1000, Ljubljana, Slovenia
| | - Astrid Junker
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2577, Australia
| | - Paweł Krajewski
- Institute of Plant Genetics, Polish Academy of Sciences, ul. Strzeszyńska 34, 60-479, Poznań, Poland
| | - Matthias Lange
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Marie-Angélique Laporte
- Bioversity International, Parc Scientifique Agropolis II, Montpellier Cedex 5, 34397, France
| | - Célia Michotey
- Université Paris-Saclay, INRAE, URGI, Versailles, 78026, France
| | - Markus Oppermann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Richard Ostler
- Computational and Analytical Sciences, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Hendrik Poorter
- Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, D-52425, Jülich, Germany
- Department of Biological Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | | | - Živa Ramšak
- Department of Biotechnology and Systems Biology, National Institute of Biology, SI1000, Ljubljana, Slovenia
| | - Jochen C Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Philippe Rocca-Serra
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, Oxford, OX1 3QG, UK
| | - Susanna-Assunta Sansone
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, Oxford, OX1 3QG, UK
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - François Tardieu
- INRA, Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, UMR759, Montpellier, 34060, France
| | - Cristobal Uauy
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK
| | - Björn Usadel
- Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, D-52425, Jülich, Germany
- Institute for Biology I, BioSC, RWTH Aachen University, Worringer Weg 3, 52074, Aachen, Germany
| | - Richard G F Visser
- Plant Breeding, Wageningen University & Research, PO Box 386, Wageningen, 6700AJ, the Netherlands
| | - Stephan Weise
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | | | - Célia M Miguel
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA) Avenida da República, 2780-157, Oeiras, Portugal
- BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, 1749-016, Portugal
| | | | - Cyril Pommier
- Université Paris-Saclay, INRAE, URGI, Versailles, 78026, France
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Papoutsoglou EA, Faria D, Arend D, Arnaud E, Athanasiadis IN, Chaves I, Coppens F, Cornut G, Costa BV, Ćwiek‐Kupczyńska H, Droesbeke B, Finkers R, Gruden K, Junker A, King GJ, Krajewski P, Lange M, Laporte M, Michotey C, Oppermann M, Ostler R, Poorter H, Ramírez‐Gonzalez R, Ramšak Ž, Reif JC, Rocca‐Serra P, Sansone S, Scholz U, Tardieu F, Uauy C, Usadel B, Visser RGF, Weise S, Kersey PJ, Miguel CM, Adam‐Blondon A, Pommier C. Enabling reusability of plant phenomic datasets with MIAPPE 1.1. New Phytol 2020; 227:260-273. [PMID: 32171029 PMCID: PMC7317793 DOI: 10.1111/nph.16544] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 02/24/2020] [Indexed: 05/21/2023]
Abstract
Enabling data reuse and knowledge discovery is increasingly critical in modern science, and requires an effort towards standardising data publication practices. This is particularly challenging in the plant phenotyping domain, due to its complexity and heterogeneity. We have produced the MIAPPE 1.1 release, which enhances the existing MIAPPE standard in coverage, to support perennial plants, in structure, through an explicit data model, and in clarity, through definitions and examples. We evaluated MIAPPE 1.1 by using it to express several heterogeneous phenotyping experiments in a range of different formats, to demonstrate its applicability and the interoperability between the various implementations. Furthermore, the extended coverage is demonstrated by the fact that one of the datasets could not have been described under MIAPPE 1.0. MIAPPE 1.1 marks a major step towards enabling plant phenotyping data reusability, thanks to its extended coverage, and especially the formalisation of its data model, which facilitates its implementation in different formats. Community feedback has been critical to this development, and will be a key part of ensuring adoption of the standard.
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33
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Papoutsoglou EA, Faria D, Arend D, Arnaud E, Athanasiadis IN, Chaves I, Coppens F, Cornut G, Costa BV, Ćwiek-Kupczyńska H, Droesbeke B, Finkers R, Gruden K, Junker A, King GJ, Krajewski P, Lange M, Laporte MA, Michotey C, Oppermann M, Ostler R, Poorter H, Ramı Rez-Gonzalez R, Ramšak Ž, Reif JC, Rocca-Serra P, Sansone SA, Scholz U, Tardieu F, Uauy C, Usadel B, Visser RGF, Weise S, Kersey PJ, Miguel CM, Adam-Blondon AF, Pommier C. Enabling reusability of plant phenomic datasets with MIAPPE 1.1. New Phytol 2020. [PMID: 32171029 DOI: 10.15454/ah6u4a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Enabling data reuse and knowledge discovery is increasingly critical in modern science, and requires an effort towards standardising data publication practices. This is particularly challenging in the plant phenotyping domain, due to its complexity and heterogeneity. We have produced the MIAPPE 1.1 release, which enhances the existing MIAPPE standard in coverage, to support perennial plants, in structure, through an explicit data model, and in clarity, through definitions and examples. We evaluated MIAPPE 1.1 by using it to express several heterogeneous phenotyping experiments in a range of different formats, to demonstrate its applicability and the interoperability between the various implementations. Furthermore, the extended coverage is demonstrated by the fact that one of the datasets could not have been described under MIAPPE 1.0. MIAPPE 1.1 marks a major step towards enabling plant phenotyping data reusability, thanks to its extended coverage, and especially the formalisation of its data model, which facilitates its implementation in different formats. Community feedback has been critical to this development, and will be a key part of ensuring adoption of the standard.
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Affiliation(s)
- Evangelia A Papoutsoglou
- Plant Breeding, Wageningen University & Research, PO Box 386, Wageningen, 6700AJ, the Netherlands
| | - Daniel Faria
- BioData.pt, Instituto Gulbenkian de Ciência, 2780-156, Oeiras, Portugal
- INESC-ID, 1000-029, Lisboa, Portugal
| | - Daniel Arend
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Elizabeth Arnaud
- Bioversity International, Parc Scientifique Agropolis II, Montpellier Cedex 5, 34397, France
| | - Ioannis N Athanasiadis
- Geo-Information Science and Remote Sensing Laboratory, Wageningen University, Droevendaalsesteeg 3, Wageningen, 6708PB, the Netherlands
| | - Inês Chaves
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA) Avenida da República, 2780-157, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica (iBET), 2780-157, Oeiras, Portugal
| | - Frederik Coppens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium
| | | | - Bruno V Costa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA) Avenida da República, 2780-157, Oeiras, Portugal
- BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, 1749-016, Portugal
| | - Hanna Ćwiek-Kupczyńska
- Institute of Plant Genetics, Polish Academy of Sciences, ul. Strzeszyńska 34, 60-479, Poznań, Poland
| | - Bert Droesbeke
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium
| | - Richard Finkers
- Plant Breeding, Wageningen University & Research, PO Box 386, Wageningen, 6700AJ, the Netherlands
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, SI1000, Ljubljana, Slovenia
| | - Astrid Junker
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2577, Australia
| | - Paweł Krajewski
- Institute of Plant Genetics, Polish Academy of Sciences, ul. Strzeszyńska 34, 60-479, Poznań, Poland
| | - Matthias Lange
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Marie-Angélique Laporte
- Bioversity International, Parc Scientifique Agropolis II, Montpellier Cedex 5, 34397, France
| | - Célia Michotey
- Université Paris-Saclay, INRAE, URGI, Versailles, 78026, France
| | - Markus Oppermann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Richard Ostler
- Computational and Analytical Sciences, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Hendrik Poorter
- Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, D-52425, Jülich, Germany
- Department of Biological Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | | | - Živa Ramšak
- Department of Biotechnology and Systems Biology, National Institute of Biology, SI1000, Ljubljana, Slovenia
| | - Jochen C Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Philippe Rocca-Serra
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, Oxford, OX1 3QG, UK
| | - Susanna-Assunta Sansone
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, Oxford, OX1 3QG, UK
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - François Tardieu
- INRA, Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, UMR759, Montpellier, 34060, France
| | - Cristobal Uauy
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK
| | - Björn Usadel
- Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, D-52425, Jülich, Germany
- Institute for Biology I, BioSC, RWTH Aachen University, Worringer Weg 3, 52074, Aachen, Germany
| | - Richard G F Visser
- Plant Breeding, Wageningen University & Research, PO Box 386, Wageningen, 6700AJ, the Netherlands
| | - Stephan Weise
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | | | - Célia M Miguel
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA) Avenida da República, 2780-157, Oeiras, Portugal
- BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, 1749-016, Portugal
| | | | - Cyril Pommier
- Université Paris-Saclay, INRAE, URGI, Versailles, 78026, France
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Selby P, Abbeloos R, Backlund JE, Basterrechea Salido M, Bauchet G, Benites-Alfaro OE, Birkett C, Calaminos VC, Carceller P, Cornut G, Vasques Costa B, Edwards JD, Finkers R, Yanxin Gao S, Ghaffar M, Glaser P, Guignon V, Hok P, Kilian A, König P, Lagare JEB, Lange M, Laporte MA, Larmande P, LeBauer DS, Lyon DA, Marshall DS, Matthews D, Milne I, Mistry N, Morales N, Mueller LA, Neveu P, Papoutsoglou E, Pearce B, Perez-Masias I, Pommier C, Ramírez-González RH, Rathore A, Raquel AM, Raubach S, Rife T, Robbins K, Rouard M, Sarma C, Scholz U, Sempéré G, Shaw PD, Simon R, Soldevilla N, Stephen G, Sun Q, Tovar C, Uszynski G, Verouden M. BrAPI-an application programming interface for plant breeding applications. Bioinformatics 2020; 35:4147-4155. [PMID: 30903186 PMCID: PMC6792114 DOI: 10.1093/bioinformatics/btz190] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 11/23/2018] [Accepted: 03/20/2019] [Indexed: 12/04/2022] Open
Abstract
Motivation Modern genomic breeding methods rely heavily on very large amounts of phenotyping and genotyping data, presenting new challenges in effective data management and integration. Recently, the size and complexity of datasets have increased significantly, with the result that data are often stored on multiple systems. As analyses of interest increasingly require aggregation of datasets from diverse sources, data exchange between disparate systems becomes a challenge. Results To facilitate interoperability among breeding applications, we present the public plant Breeding Application Programming Interface (BrAPI). BrAPI is a standardized web service API specification. The development of BrAPI is a collaborative, community-based initiative involving a growing global community of over a hundred participants representing several dozen institutions and companies. Development of such a standard is recognized as critical to a number of important large breeding system initiatives as a foundational technology. The focus of the first version of the API is on providing services for connecting systems and retrieving basic breeding data including germplasm, study, observation, and marker data. A number of BrAPI-enabled applications, termed BrAPPs, have been written, that take advantage of the emerging support of BrAPI by many databases. Availability and implementation More information on BrAPI, including links to the specification, test suites, BrAPPs, and sample implementations is available at https://brapi.org/. The BrAPI specification and the developer tools are provided as free and open source.
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Affiliation(s)
- Peter Selby
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
| | | | | | | | | | - Omar E Benites-Alfaro
- International Potato Center (CIP), Lima, Peru.,International Food Policy Research Institute (IFPRI), Washington DC, USA
| | | | - Viana C Calaminos
- International Rice Research Institute (IRRI), Los Baños, Laguna, The Philippines
| | - Pierre Carceller
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | | | | | | | - Richard Finkers
- Department of Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - Star Yanxin Gao
- Institute of Biotechnology, Cornell University, Ithaca, New York, USA
| | - Mehmood Ghaffar
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Philip Glaser
- Institute of Biotechnology, Cornell University, Ithaca, New York, USA
| | | | - Puthick Hok
- Diversity Arrays Technology, Bruce, Australia
| | | | - Patrick König
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | | | - Matthias Lange
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | | | | | - David S LeBauer
- College of Agricultural and Life Sciences, The University of Arizona, Tucson, AZ, USA
| | | | - David S Marshall
- Information & Computational Sciences, The James Hutton Institute, Dundee, UK.,SRUC, Edinburgh, UK
| | | | - Iain Milne
- Information & Computational Sciences, The James Hutton Institute, Dundee, UK
| | | | | | | | - Pascal Neveu
- MISTEA, INRA, Montpellier SupAgro, Universite de Montpellier, Montpellier, France
| | - Evangelia Papoutsoglou
- Department of Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | | | | | - Cyril Pommier
- URGI, INRA, Université Paris-Saclay, Versailles, France
| | | | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Angel Manica Raquel
- International Rice Research Institute (IRRI), Los Baños, Laguna, The Philippines
| | - Sebastian Raubach
- Information & Computational Sciences, The James Hutton Institute, Dundee, UK
| | - Trevor Rife
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Kelly Robbins
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
| | | | - Chaitanya Sarma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Guilhem Sempéré
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.,INTERTRYP, Univ Montpellier, CIRAD, IRD, Montpellier, France
| | - Paul D Shaw
- Information & Computational Sciences, The James Hutton Institute, Dundee, UK
| | | | - Nahuel Soldevilla
- Integrated Breeding Program (IBP), CIMMYT, Texcoco, Mexico.,LeafNode Technology, Buenos Aires, Argentina
| | - Gordon Stephen
- Information & Computational Sciences, The James Hutton Institute, Dundee, UK
| | - Qi Sun
- Institute of Biotechnology, Cornell University, Ithaca, New York, USA
| | - Clarysabel Tovar
- Integrated Breeding Program (IBP), CIMMYT, Texcoco, Mexico.,LeafNode Technology, Buenos Aires, Argentina
| | | | - Maikel Verouden
- Wageningen University & Research, Biometris, Wageningen PB, The Netherlands
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35
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Nguyen GN, Norton SL. Genebank Phenomics: A Strategic Approach to Enhance Value and Utilization of Crop Germplasm. Plants (Basel) 2020; 9:E817. [PMID: 32610615 PMCID: PMC7411623 DOI: 10.3390/plants9070817] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 02/07/2023]
Abstract
Genetically diverse plant germplasm stored in ex-situ genebanks are excellent resources for breeding new high yielding and sustainable crop varieties to ensure future food security. Novel alleles have been discovered through routine genebank activities such as seed regeneration and characterization, with subsequent utilization providing significant genetic gains and improvements for the selection of favorable traits, including yield, biotic, and abiotic resistance. Although some genebanks have implemented cost-effective genotyping technologies through advances in DNA technology, the adoption of modern phenotyping is lagging. The introduction of advanced phenotyping technologies in recent decades has provided genebank scientists with time and cost-effective screening tools to obtain valuable phenotypic data for more traits on large germplasm collections during routine activities. The utilization of these phenotyping tools, coupled with high-throughput genotyping, will accelerate the use of genetic resources and fast-track the development of more resilient food crops for the future. In this review, we highlight current digital phenotyping methods that can capture traits during annual seed regeneration to enrich genebank phenotypic datasets. Next, we describe strategies for the collection and use of phenotypic data of specific traits for downstream research using high-throughput phenotyping technology. Finally, we examine the challenges and future perspectives of genebank phenomics.
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Affiliation(s)
- Giao N. Nguyen
- Australian Grains Genebank, Agriculture Victoria, 110 Natimuk Road, Horsham 3400, Australia;
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König P, Beier S, Basterrechea M, Schüler D, Arend D, Mascher M, Stein N, Scholz U, Lange M. BRIDGE - A Visual Analytics Web Tool for Barley Genebank Genomics. Front Plant Sci 2020; 11:701. [PMID: 32595658 PMCID: PMC7300248 DOI: 10.3389/fpls.2020.00701] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 05/04/2020] [Indexed: 05/05/2023]
Abstract
Genebanks harbor a large treasure trove of untapped plant genetic diversity. A growing world population and a changing climate require an increase in the production and development of stress resistant plant cultivars while decreasing the acreage. These requirements for improved plant cultivars can be supported by the broader exploitation of plant genetic resources (PGR) as inputs for genomics-assisted breeding. To support this process we have developed BRIDGE, a data warehouse and exploratory data analysis tool for genebank genomics of barley (Hordeum vulgare L.). Using efficient technologies for data storage, data transfer and web development, we facilitate access to digital genebank resources of barley by prioritizing the interactive and visual analysis of integrated genotypic and phenotypic data. The underlying data resulted from a barley genebank genomics study cataloging sequence and morphological data of 22,626 barley accessions, mainly from the German Federal ex situ genebank. BRIDGE consists of interactively coupled modules to visualize integrated, curated and quality checked data, such as variation data, results of dimensionality reduction and genome wide association studies (GWAS), phenotyping results, passport data as well as the geographic distribution of germplasm samples. The core component is a manager for custom collections of germplasm. A search module to find and select germplasm by passport and phenotypic attributes is included as well as modules to export genotypic data in gzip-compressed variant call format (VCF) files and phenotypic data in MIAPPE-compliant ISA-Tab files. BRIDGE is accessible at the following URL: https://bridge.ipk-gatersleben.de.
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Affiliation(s)
- Patrick König
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Sebastian Beier
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Martin Basterrechea
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Danuta Schüler
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Daniel Arend
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
- Center for Integrated Breeding Research, Georg-August University, Göttingen, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Matthias Lange
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
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Nédellec C, Ibanescu L, Bossy R, Sourdille P. WTO, an ontology for wheat traits and phenotypes in scientific publications. Genomics Inform 2020; 18:e14. [PMID: 32634868 PMCID: PMC7362939 DOI: 10.5808/gi.2020.18.2.e14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 06/09/2020] [Accepted: 06/10/2020] [Indexed: 11/20/2022] Open
Abstract
Phenotyping is a major issue for wheat agriculture to meet the challenges of adaptation of wheat varieties to climate change and chemical input reduction in crop. The need to improve the reuse of observations and experimental data has led to the creation of reference ontologies to standardize descriptions of phenotypes and to facilitate their comparison. The scientific literature is largely under-exploited, although extremely rich in phenotype descriptions associated with cultivars and genetic information. In this paper we propose the Wheat Trait Ontology (WTO) that is suitable for the extraction and management of scientific information from scientific papers, and its combination with data from genomic and experimental databases. We describe the principles of WTO construction and show examples of WTO use for the extraction and management of phenotype descriptions obtained from scientific documents.
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Affiliation(s)
- Claire Nédellec
- Paris-Saclay University, INRAE, MaIAGE, F-78350 Jouy-en-Josas, France
| | - Liliana Ibanescu
- Paris-Saclay University, INRAE, UMR MIA-Paris, AgroParisTech, F-75005, Paris, France
| | - Robert Bossy
- Paris-Saclay University, INRAE, MaIAGE, F-78350 Jouy-en-Josas, France
| | - Pierre Sourdille
- University Clermont-Auvergne, INRAE, UMR 1095 GDEC, F-63000 Clermont-Ferrand, France
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Abstract
Plant phenotyping enables noninvasive quantification of plant structure and function and interactions with environments. High-capacity phenotyping reaches hitherto inaccessible phenotypic characteristics. Diverse, challenging, and valuable applications of phenotyping have originated among scientists, prebreeders, and breeders as they study the phenotypic diversity of genetic resources and apply increasingly complex traits to crop improvement. Noninvasive technologies are used to analyze experimental and breeding populations. We cover the most recent research in controlled-environment and field phenotyping for seed, shoot, and root traits. Select field phenotyping technologies have become state of the art and show promise for speeding up the breeding process in early generations. We highlight the technologies behind the rapid advances in proximal and remote sensing of plants in fields. We conclude by discussing the new disciplines working with the phenotyping community: data science, to address the challenge of generating FAIR (findable, accessible, interoperable, and reusable) data, and robotics, to apply phenotyping directly on farms.
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Affiliation(s)
- Michelle Watt
- IBG-2: Plant Sciences, Institute of Bio- and Geosciences, Forschungszentrum Jülich, 52425 Jülich, Germany; ,
| | - Fabio Fiorani
- IBG-2: Plant Sciences, Institute of Bio- and Geosciences, Forschungszentrum Jülich, 52425 Jülich, Germany; ,
| | - Björn Usadel
- IBG-2: Plant Sciences, Institute of Bio- and Geosciences, Forschungszentrum Jülich, 52425 Jülich, Germany; ,
- Institute for Botany and Molecular Genetics, BioSC, RWTH Aachen University, 52074 Aachen, Germany
| | - Uwe Rascher
- IBG-2: Plant Sciences, Institute of Bio- and Geosciences, Forschungszentrum Jülich, 52425 Jülich, Germany; ,
| | - Onno Muller
- IBG-2: Plant Sciences, Institute of Bio- and Geosciences, Forschungszentrum Jülich, 52425 Jülich, Germany; ,
| | - Ulrich Schurr
- IBG-2: Plant Sciences, Institute of Bio- and Geosciences, Forschungszentrum Jülich, 52425 Jülich, Germany; ,
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Creydt M, Fischer M. Food authentication in real life: How to link nontargeted approaches with routine analytics? Electrophoresis 2020; 41:1665-1679. [PMID: 32249434 DOI: 10.1002/elps.202000030] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/19/2020] [Accepted: 03/23/2020] [Indexed: 12/20/2022]
Abstract
In times of increasing globalization and the resulting complexity of trade flows, securing food quality is an increasing challenge. The development of analytical methods for checking the integrity and, thus, the safety of food is one of the central questions for actors from science, politics, and industry. Targeted methods, for the detection of a few selected analytes, still play the most important role in routine analysis. In the past 5 years, nontargeted methods that do not aim at individual analytes but on analyte profiles that are as comprehensive as possible have increasingly come into focus. Instead of investigating individual chemical structures, data patterns are collected, evaluated and, depending on the problem, fed into databases that can be used for further nontargeted approaches. Alternatively, individual markers can be extracted and transferred to targeted methods. Such an approach requires (i) the availability of authentic reference material, (ii) the corresponding high-resolution laboratory infrastructure, and (iii) extensive expertise in processing and storing very large amounts of data. Probably due to the requirements mentioned above, only a few methods have really established themselves in routine analysis. This review article focuses on the establishment of nontargeted methods in routine laboratories. Challenges are summarized and possible solutions are presented.
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Affiliation(s)
- Marina Creydt
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Hamburg, Germany
| | - Markus Fischer
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Hamburg, Germany
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Azman Halimi R, Barkla BJ, Andrés-Hernandéz L, Mayes S, King GJ. Bridging the food security gap: an information-led approach to connect dietary nutrition, food composition and crop production. J Sci Food Agric 2020; 100:1495-1504. [PMID: 31756768 DOI: 10.1002/jsfa.10157] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 10/18/2019] [Accepted: 11/18/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Food security is recognized as a major global challenge, yet human food-chain systems are inherently not geared towards nutrition, with decisions on crop and cultivar choice not informed by dietary composition. Currently, food compositional tables and databases (FCT/FCDB) are the primary information sources for decisions relating to dietary intake. However, these only present single mean values representing major components. Establishment of a systematic controlled vocabulary to fill this gap requires representation of a more complex set of semantic relationships between terms used to describe nutritional composition and dietary function. RESULTS We carried out a survey of 11 FCT/FCDB and 177 peer-reviewed papers describing variation in nutritional composition and dietary function for food crops to identify a comprehensive set of terms to construct a controlled vocabulary. We used this information to generate a Crop Dietary Nutrition Data Framework (CDN-DF), which incorporates controlled vocabularies systematically organized into major classes representing nutritional components and dietary functions. We demonstrate the value of the CDN-DF for comparison of equivalent components between crop species or cultivars, for identifying data gaps and potential for formal meta-analysis. The CDN-DF also enabled us to explore relationships between nutritional components and the functional attributes of food. CONCLUSION We have generated a structured crop dietary nutrition data framework, which is generally applicable to the collation and comparison of data relevant to crop researchers, breeders, and other stakeholders, and will facilitate dialogue with nutritionists. It is currently guiding the establishment of a more robust formal ontology. © 2019 Society of Chemical Industry.
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Affiliation(s)
| | - Bronwyn J Barkla
- Southern Cross Plant Science, Southern Cross University, Lismore, Australia
| | | | - Sean Mayes
- School of Biosciences, University of Nottingham, Nottingham, UK
- Crop Improvement and Production, Crops For the Future, Semenyih, Malaysia
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, Australia
- School of Biosciences, University of Nottingham, Nottingham, UK
- Crop Improvement and Production, Crops For the Future, Semenyih, Malaysia
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Ćwiek-Kupczyńska H, Filipiak K, Markiewicz A, Rocca-Serra P, Gonzalez-Beltran AN, Sansone SA, Millet EJ, van Eeuwijk F, Ławrynowicz A, Krajewski P. Semantic concept schema of the linear mixed model of experimental observations. Sci Data 2020; 7:70. [PMID: 32109232 PMCID: PMC7046786 DOI: 10.1038/s41597-020-0409-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 02/13/2020] [Indexed: 11/24/2022] Open
Abstract
In the information age, smart data modelling and data management can be carried out to address the wealth of data produced in scientific experiments. In this paper, we propose a semantic model for the statistical analysis of datasets by linear mixed models. We tie together disparate statistical concepts in an interdisciplinary context through the application of ontologies, in particular the Statistics Ontology (STATO), to produce FAIR data summaries. We hope to improve the general understanding of statistical modelling and thus contribute to a better description of the statistical conclusions from data analysis, allowing their efficient exploration and automated processing.
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Affiliation(s)
- Hanna Ćwiek-Kupczyńska
- Institute of Plant Genetics, Polish Academy of Sciences, ul. Strzeszyńska 34, 60-479, Poznań, Poland
| | - Katarzyna Filipiak
- Institute of Mathematics, Poznań University of Technology, ul. Piotrowo 3a, 60-965, Poznań, Poland
| | - Augustyn Markiewicz
- Department of Mathematical and Statistical Methods, Poznań University of Life Sciences, ul. Wojska Polskiego 28, 60-637, Poznań, Poland
| | - Philippe Rocca-Serra
- Oxford e-Research Center, Department of Engineering Science, University of Oxford, Oxford, OX1 3QG, UK
| | - Alejandra N Gonzalez-Beltran
- Oxford e-Research Center, Department of Engineering Science, University of Oxford, Oxford, OX1 3QG, UK
- Scientific Computing Department, Science and Technology Facilities Council, UK Research & Innovation, Didcot, OX11 0QX, UK
| | - Susanna-Assunta Sansone
- Oxford e-Research Center, Department of Engineering Science, University of Oxford, Oxford, OX1 3QG, UK
| | - Emilie J Millet
- Biometris, Wageningen University & Research Centre, P.O. Box 16, 6700 AA, Wageningen, The Netherlands
| | - Fred van Eeuwijk
- Biometris, Wageningen University & Research Centre, P.O. Box 16, 6700 AA, Wageningen, The Netherlands
| | - Agnieszka Ławrynowicz
- Faculty of Computing and Telecommunications, Poznan University of Technology, ul. Piotrowo 3, 60-965, Poznań, Poland
| | - Paweł Krajewski
- Institute of Plant Genetics, Polish Academy of Sciences, ul. Strzeszyńska 34, 60-479, Poznań, Poland.
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Yang W, Feng H, Zhang X, Zhang J, Doonan JH, Batchelor WD, Xiong L, Yan J. Crop Phenomics and High-Throughput Phenotyping: Past Decades, Current Challenges, and Future Perspectives. Mol Plant 2020; 13:187-214. [PMID: 31981735 DOI: 10.1016/j.molp.2020.01.008] [Citation(s) in RCA: 232] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/06/2020] [Accepted: 01/10/2020] [Indexed: 05/18/2023]
Abstract
Since whole-genome sequencing of many crops has been achieved, crop functional genomics studies have stepped into the big-data and high-throughput era. However, acquisition of large-scale phenotypic data has become one of the major bottlenecks hindering crop breeding and functional genomics studies. Nevertheless, recent technological advances provide us potential solutions to relieve this bottleneck and to explore advanced methods for large-scale phenotyping data acquisition and processing in the coming years. In this article, we review the major progress on high-throughput phenotyping in controlled environments and field conditions as well as its use for post-harvest yield and quality assessment in the past decades. We then discuss the latest multi-omics research combining high-throughput phenotyping with genetic studies. Finally, we propose some conceptual challenges and provide our perspectives on how to bridge the phenotype-genotype gap. It is no doubt that accurate high-throughput phenotyping will accelerate plant genetic improvements and promote the next green revolution in crop breeding.
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Affiliation(s)
- Wanneng Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, P.R. China.
| | - Hui Feng
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Xuehai Zhang
- National Key Laboratory of Wheat and Maize Crops Science/College of Agronomy, Henan Agricultural University, Zhengzhou 450002, P.R. China
| | - Jian Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - John H Doonan
- The National Plant Phenomics Centre, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | | | - Lizhong Xiong
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, P.R. China
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Ghaffar M, Schüler D, König P, Arend D, Junker A, Scholz U, Lange M. Programmatic Access to FAIRified Digital Plant Genetic Resources. J Integr Bioinform 2020; 16:/j/jib.2019.16.issue-4/jib-2019-0060/jib-2019-0060.xml. [PMID: 31913851 PMCID: PMC7074143 DOI: 10.1515/jib-2019-0060] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 10/09/2019] [Indexed: 12/29/2022] Open
Abstract
Genetic variance within the genotype of population and its mapping to phenotype variance in a systematic and high throughput manner is of interest for biodiversity and breeding research. Beside the established and efficient high throughput genotype technologies, phenotype capabilities got increased focus in the last decade. This results in an increasing amount of phenotype data from well scaling, automated sensor platform. Thus, data stewardship is a central component to make experimental data from multiple domains interoperable and re-usable. To ensure a standard and comprehensive sharing of scientific and experimental data among domain experts, FAIR data principles are utilized for machine read-ability and scale-ability. In this context, BrAPI consortium, provides a comprehensive and commonly agreed FAIRed guidelines to offer a BrAPI layered scientific data in a RESTful manner. This paper presents the concepts, best practices and implementations to meet these challenges. As one of the worlds leading plant research institutes it is of vital interest for the IPK-Gatersleben to transform legacy data infrastructures into a bio-digital resource center for plant genetics resources (PGR). This paper also demonstrates the benefits of integrated database back-ends, established data stewardship processes, and FAIR data exposition in a machine-readable, highly scalable programmatic interfaces.
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Affiliation(s)
- Mehmood Ghaffar
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, 06466 Seeland, Germany
| | - Danuta Schüler
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, 06466 Seeland, Germany
| | - Patrick König
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, 06466 Seeland, Germany
| | - Daniel Arend
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, 06466 Seeland, Germany
| | - Astrid Junker
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, 06466 Seeland, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, 06466 Seeland, Germany
| | - Matthias Lange
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, 06466 Seeland, Germany
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Wegrzyn JL, Falk T, Grau E, Buehler S, Ramnath R, Herndon N. Cyberinfrastructure and resources to enable an integrative approach to studying forest trees. Evol Appl 2020; 13:228-241. [PMID: 31892954 PMCID: PMC6935593 DOI: 10.1111/eva.12860] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 08/11/2019] [Accepted: 08/14/2019] [Indexed: 12/19/2022] Open
Abstract
Sequencing technologies and bioinformatic approaches are now available to resolve the challenges associated with complex and heterozygous genomes. Increased access to less expensive and more effective instrumentation will contribute to a wealth of high-quality plant genomes in the next few years. In the meantime, more than 370 tree species are associated with public projects in primary repositories that are interrogating expression profiles, identifying variants, or analyzing targeted capture without a high-quality reference genome. Genomic data from these projects generates sequences that represent intermediate assemblies for transcriptomes and genomes. These data contribute to forest tree biology, but the associated sequence remains trapped in supplemental files that are poorly integrated in plant community databases and comparative genomic platforms. Successful implementation of life science cyberinfrastructure is improving data standards, ontologies, analytic workflows, and integrated database platforms for both model and non-model plant species. Unique to forest trees with large populations that are long-lived, outcrossing, and genetically diverse, the phenotypic and environmental metrics associated with georeferenced populations are just as important as the genomic data sampled for each individual. To address questions related to forest health and productivity, cyberinfrastructure must keep pace with the magnitude of genomic and phenomic sampling of larger populations. This review examines the current landscape of cyberinfrastructure, with an emphasis on best practices and resources to align community data with the Findable, Accessible, Interoperable, and Reusable (FAIR) guidelines.
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Affiliation(s)
- Jill L. Wegrzyn
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticut
| | - Taylor Falk
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticut
| | - Emily Grau
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticut
| | - Sean Buehler
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticut
| | - Risharde Ramnath
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticut
| | - Nic Herndon
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticut
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Rodrigues AM, Ribeiro-Barros AI, António C. Experimental Design and Sample Preparation in Forest Tree Metabolomics. Metabolites 2019; 9:E285. [PMID: 31766588 PMCID: PMC6950530 DOI: 10.3390/metabo9120285] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/15/2019] [Accepted: 11/20/2019] [Indexed: 02/07/2023] Open
Abstract
Appropriate experimental design and sample preparation are key steps in metabolomics experiments, highly influencing the biological interpretation of the results. The sample preparation workflow for plant metabolomics studies includes several steps before metabolite extraction and analysis. These include the optimization of laboratory procedures, which should be optimized for different plants and tissues. This is particularly the case for trees, whose tissues are complex matrices to work with due to the presence of several interferents, such as oleoresins, cellulose. A good experimental design, tree tissue harvest conditions, and sample preparation are crucial to ensure consistency and reproducibility of the metadata among datasets. In this review, we discuss the main challenges when setting up a forest tree metabolomics experiment for mass spectrometry (MS)-based analysis covering all technical aspects from the biological question formulation and experimental design to sample processing and metabolite extraction and data acquisition. We also highlight the importance of forest tree metadata standardization in metabolomics studies.
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Affiliation(s)
- Ana M. Rodrigues
- Plant Metabolomics Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal; (A.M.R.); (A.I.R.-B.)
| | - Ana I. Ribeiro-Barros
- Plant Metabolomics Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal; (A.M.R.); (A.I.R.-B.)
- Plant Stress and Biodiversity Laboratory, Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia, Universidade de Lisboa (ISA/ULisboa), 1349-017 Lisboa, Portugal
| | - Carla António
- Plant Metabolomics Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal; (A.M.R.); (A.I.R.-B.)
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Furbank RT, Jimenez-Berni JA, George-Jaeggli B, Potgieter AB, Deery DM. Field crop phenomics: enabling breeding for radiation use efficiency and biomass in cereal crops. New Phytol 2019; 223:1714-1727. [PMID: 30937909 DOI: 10.1111/nph.15817] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Accepted: 03/02/2019] [Indexed: 05/21/2023]
Abstract
Plant phenotyping forms the core of crop breeding, allowing breeders to build on physiological traits and mechanistic science to inform their selection of material for crossing and genetic gain. Recent rapid progress in high-throughput techniques based on machine vision, robotics, and computing (plant phenomics) enables crop physiologists and breeders to quantitatively measure complex and previously intractable traits. By combining these techniques with affordable genomic sequencing and genotyping, machine learning, and genome selection approaches, breeders have an opportunity to make rapid genetic progress. This review focuses on how field-based plant phenomics can enable next-generation physiological breeding in cereal crops for traits related to radiation use efficiency, photosynthesis, and crop biomass. These traits have previously been regarded as difficult and laborious to measure but have recently become a focus as cereal breeders find genetic progress from 'Green Revolution' traits such as harvest index become exhausted. Application of LiDAR, thermal imaging, leaf and canopy spectral reflectance, Chl fluorescence, and machine learning are discussed using wheat and sorghum phenotyping as case studies. A vision of how crop genomics and high-throughput phenotyping could enable the next generation of crop research and breeding is presented.
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Affiliation(s)
- Robert T Furbank
- ARC Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Australian National University, Canberra, 2601, ACT, Australia
- CSIRO Agriculture and Food, Canberra, 2601, ACT, Australia
| | - Jose A Jimenez-Berni
- CSIRO Agriculture and Food, Canberra, 2601, ACT, Australia
- Institute for Sustainable Agriculture (IAS), CSIC, Cordoba, 14004, Spain
| | - Barbara George-Jaeggli
- Queensland Alliance for Agriculture & Food Innovation, Centre for Crop Science, The University of Queensland, Hermitage Research Station, Warwick, 4370, QLD, Australia
- Agri-Science Queensland, Queensland Department of Agriculture & Fisheries, Hermitage Research Facility, Warwick, 4370, QLD, Australia
| | - Andries B Potgieter
- Queensland Alliance for Agriculture & Food Innovation, Centre for Crop Science, The University of Queensland, Tor Street, Toowoomba, 4350, QLD, Australia
| | - David M Deery
- CSIRO Agriculture and Food, Canberra, 2601, ACT, Australia
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Alvarez Prado S, Sanchez I, Cabrera-Bosquet L, Grau A, Welcker C, Tardieu F, Hilgert N. To clean or not to clean phenotypic datasets for outlier plants in genetic analyses? J Exp Bot 2019; 70:3693-3698. [PMID: 31020325 PMCID: PMC6685653 DOI: 10.1093/jxb/erz191] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 04/10/2019] [Indexed: 05/26/2023]
Abstract
Based on case studies, we discuss the extent to which genome-wide association studies (GWAS) are affected by outlier plants, i.e. those deviating from the expected distribution on a multi-criteria basis. Using a raw dataset consisting of daily measurements of leaf area, biomass, and plant height for thousands of plants, we tested three different cleaning methods for their effects on genetic analyses. No-cleaning resulted in the highest number of dubious quantitative trait loci, especially at loci with highly unbalanced allelic frequencies. A trade-off was identified between the risk of false-positives (with no-cleaning and/or a low threshold for minor allele frequency) and the risk of missing interesting rare alleles. Cleaning can lower the risk of the latter by making it possible to choose a higher threshold in GWAS.
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Affiliation(s)
| | - Isabelle Sanchez
- MISTEA, Université de Montpellier, INRA, Montpellier SupAgro, Montpellier, France
| | | | - Antonin Grau
- LEPSE, Université de Montpellier, INRA, Montpellier SupAgro, Montpellier, France
| | - Claude Welcker
- LEPSE, Université de Montpellier, INRA, Montpellier SupAgro, Montpellier, France
| | - François Tardieu
- LEPSE, Université de Montpellier, INRA, Montpellier SupAgro, Montpellier, France
| | - Nadine Hilgert
- MISTEA, Université de Montpellier, INRA, Montpellier SupAgro, Montpellier, France
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48
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Rodrigues J, Inzé D, Nelissen H, Saibo NJM. Source-Sink Regulation in Crops under Water Deficit. Trends Plant Sci 2019; 24:652-663. [PMID: 31109763 DOI: 10.1016/j.tplants.2019.04.005] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 04/12/2019] [Accepted: 04/13/2019] [Indexed: 05/21/2023]
Abstract
To meet the food demands of an increasing world population, it is necessary to improve crop production; a task that is made more challenging by the changing climate. Several recent reports show that increasing the capacity of plants to assimilate carbon (source strength), or to tap into the internal carbon reservoir (sink strength), has the potential to improve plant productivity in the field under water-deficit conditions. Here, we review the effects of water deficit on the source-sink communication, as well as the respective regulatory mechanisms underpinning plant productivity. We also highlight stress-tolerant traits that can contribute to harness source and sink strengths towards producing high-yielding and drought-tolerant crops, depending on the drought scenario.
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Affiliation(s)
- Joana Rodrigues
- Instituto de Tecnologia Química e Biológica António Xavier, UNL, 2780-157 Oeiras, Portugal; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Hilde Nelissen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium.
| | - Nelson J M Saibo
- Instituto de Tecnologia Química e Biológica António Xavier, UNL, 2780-157 Oeiras, Portugal.
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49
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Mascher M, Schreiber M, Scholz U, Graner A, Reif JC, Stein N. Genebank genomics bridges the gap between the conservation of crop diversity and plant breeding. Nat Genet 2019; 51:1076-81. [PMID: 31253974 DOI: 10.1038/s41588-019-0443-6] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 05/17/2019] [Indexed: 01/08/2023]
Abstract
Genebanks have the long-term mission of preserving plant genetic resources as an agricultural legacy for future crop improvement. Operating procedures for seed storage and plant propagation have been in place for decades, but there is a lack of effective means for the discovery and transfer of beneficial alleles from landraces and wild relatives into modern varieties. Here, we review the prospects of using molecular passport data derived from genomic sequence information as a universal monitoring tool at the single-plant level within and between genebanks. Together with recent advances in breeding methodologies, the transformation of genebanks into bio-digital resource centers will facilitate the selection of useful genetic variation and its use in breeding programs, thus providing easy access to past crop diversity. We propose linking catalogs of natural genetic variation and enquiries into biological mechanisms of plant performance as a long-term joint research goal of genebanks, plant geneticists and breeders.
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50
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Germeier CU, Unger S. Modeling Crop Genetic Resources Phenotyping Information Systems. Front Plant Sci 2019; 10:728. [PMID: 31281323 PMCID: PMC6597887 DOI: 10.3389/fpls.2019.00728] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 05/16/2019] [Indexed: 05/26/2023]
Abstract
Documentation of phenotype information is a priority need in biodiversity, crop modeling, breeding, ecology, and evolution research, for association studies, gene discovery, retrospective statistical analysis and data mining, QTL re-mapping, choosing cultivars, and planning crosses. Lack of access to phenotype information is still seen as a limiting factor for the use of plant genetic resources. Phenotype data are complex. Information on the context, under which they were collected, is indispensable, and the domain is continuously evolving. This study describes comprehensive data and object models supporting web interfaces for multi-site field phenotyping and data acquisition, which have been developed for Central Crop Databases within the European Cooperative Programme for Plant Genetic Resources over the years and which can be used as blueprints for phenotyping information systems. We start from the hypothesis, that entity relationship and object models useful for software development can picture domain expertise, similar as domain ontologies, and encourage a discussion of scientific information systems on modeling level. Starting from information requirements for statistical analysis, meta-analysis, and knowledge discovery, models are discussed in consideration of several standardization and modeling approaches including crop ontologies. Following an object-oriented modeling approach, we keep data and object models close together and to domain concepts. This will make database and software design better understandable and usable for domain experts and support a modular use of software artifacts to be shared across various domains of expertise. Classes and entities represent domain concepts with attributes naturally assigned to them. Field experiments with randomized plots, as typically used in the evaluation of plant genetic resources and in plant breeding, are in the focus. Phenotype observations, which can be listed as raw or aggregated data, are linked to explanatory metadata describing experimental treatments and agronomic interventions, observed traits and observation methodology, field plan and plot design, and the experiment site as a geographical entity. Based on clearly defined types, potential links to information systems in other domains (e.g., geographic information systems) can be better identified. Work flows are shown as web applications for the generation of field plans, field books, templates, upload of spreadsheet data, and images.
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Affiliation(s)
- Christoph U. Germeier
- Institute for Breeding Research on Agricultural Crops, Julius Kühn Institute, Federal Research Centre for Cultivated Plants, Quedlinburg, Germany
| | - Stefan Unger
- Data Processing Department, Julius Kühn Institute, Federal Research Centre for Cultivated Plants, Quedlinburg, Germany
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