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Yanarella CF, Fattel L, Kristmundsdóttir ÁÝ, Lopez MD, Edwards JW, Campbell DA, Abel CA, Lawrence-Dill CJ. Wisconsin diversity panel phenotypes: spoken descriptions of plants and supporting data. BMC Res Notes 2024; 17:33. [PMID: 38263080 PMCID: PMC10807131 DOI: 10.1186/s13104-024-06694-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 01/11/2024] [Indexed: 01/25/2024] Open
Abstract
OBJECTIVES Phenotyping plants in a field environment can involve a variety of methods including the use of automated instruments and labor-intensive manual measurement and scoring. Researchers also collect language-based phenotypic descriptions and use controlled vocabularies and structures such as ontologies to enable computation on descriptive phenotype data, including methods to determine phenotypic similarities. In this study, spoken descriptions of plants were collected and observers were instructed to use their own vocabulary to describe plant features that were present and visible. Further, these plants were measured and scored manually as part of a larger study to investigate whether spoken plant descriptions can be used to recover known biological phenomena. DATA DESCRIPTION Data comprise phenotypic observations of 686 accessions of the maize Wisconsin Diversity panel, and 25 positive control accessions that carry visible, dramatic phenotypes. The data include the list of accessions planted, field layout, data collection procedures, student participants' (whose personal data are protected for ethical reasons) and volunteers' observation transcripts, volunteers' audio data files, terrestrial and aerial images of the plants, Amazon Web Services method selection experimental data, and manually collected phenotypes (e.g., plant height, ear and tassel features, etc.; measurements and scores). Data were collected during the summer of 2021 at Iowa State University's Agricultural Engineering and Agronomy Research Farms.
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Deng CH, Naithani S, Kumari S, Cobo-Simón I, Quezada-Rodríguez EH, Skrabisova M, Gladman N, Correll MJ, Sikiru AB, Afuwape OO, Marrano A, Rebollo I, Zhang W, Jung S. Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences. Database (Oxford) 2023; 2023:baad088. [PMID: 38079567 PMCID: PMC10712715 DOI: 10.1093/database/baad088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 10/17/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023]
Abstract
Large-scale genotype and phenotype data have been increasingly generated to identify genetic markers, understand gene function and evolution and facilitate genomic selection. These datasets hold immense value for both current and future studies, as they are vital for crop breeding, yield improvement and overall agricultural sustainability. However, integrating these datasets from heterogeneous sources presents significant challenges and hinders their effective utilization. We established the Genotype-Phenotype Working Group in November 2021 as a part of the AgBioData Consortium (https://www.agbiodata.org) to review current data types and resources that support archiving, analysis and visualization of genotype and phenotype data to understand the needs and challenges of the plant genomic research community. For 2021-22, we identified different types of datasets and examined metadata annotations related to experimental design/methods/sample collection, etc. Furthermore, we thoroughly reviewed publicly funded repositories for raw and processed data as well as secondary databases and knowledgebases that enable the integration of heterogeneous data in the context of the genome browser, pathway networks and tissue-specific gene expression. Based on our survey, we recommend a need for (i) additional infrastructural support for archiving many new data types, (ii) development of community standards for data annotation and formatting, (iii) resources for biocuration and (iv) analysis and visualization tools to connect genotype data with phenotype data to enhance knowledge synthesis and to foster translational research. Although this paper only covers the data and resources relevant to the plant research community, we expect that similar issues and needs are shared by researchers working on animals. Database URL: https://www.agbiodata.org.
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Affiliation(s)
- Cecilia H Deng
- Molecular and Digital Breeding, New Cultivar Innovation, The New Zealand Institute for Plant and Food Research Limited, 120 Mt Albert Road, Auckland 1025, New Zealand
| | - Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Sunita Kumari
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, New York, NY 11724, USA
| | - Irene Cobo-Simón
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
- Institute of Forest Science (ICIFOR-INIA, CSIC), Madrid, Spain
| | - Elsa H Quezada-Rodríguez
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana-Xochimilco, Ciudad de México, México
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Maria Skrabisova
- Department of Biochemistry, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Nick Gladman
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, New York, NY 11724, USA
- U.S. Department of Agriculture-Agricultural Research Service, NEA Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, NY 14853, USA
| | - Melanie J Correll
- Agricultural and Biological Engineering Department, University of Florida, 1741 Museum Rd, Gainesville, FL 32611, USA
| | | | | | - Annarita Marrano
- Phoenix Bioinformatics, 39899 Balentine Drive, Suite 200, Newark, CA 94560, USA
| | | | - Wentao Zhang
- National Research Council Canada, 110 Gymnasium Pl, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Sook Jung
- Department of Horticulture, Washington State University, 303c Plant Sciences Building, Pullman, WA 99164-6414, USA
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Imbert B, Kreplak J, Flores RG, Aubert G, Burstin J, Tayeh N. Development of a knowledge graph framework to ease and empower translational approaches in plant research: a use-case on grain legumes. Front Artif Intell 2023; 6:1191122. [PMID: 37601035 PMCID: PMC10435283 DOI: 10.3389/frai.2023.1191122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 07/10/2023] [Indexed: 08/22/2023] Open
Abstract
While the continuing decline in genotyping and sequencing costs has largely benefited plant research, some key species for meeting the challenges of agriculture remain mostly understudied. As a result, heterogeneous datasets for different traits are available for a significant number of these species. As gene structures and functions are to some extent conserved through evolution, comparative genomics can be used to transfer available knowledge from one species to another. However, such a translational research approach is complex due to the multiplicity of data sources and the non-harmonized description of the data. Here, we provide two pipelines, referred to as structural and functional pipelines, to create a framework for a NoSQL graph-database (Neo4j) to integrate and query heterogeneous data from multiple species. We call this framework Orthology-driven knowledge base framework for translational research (Ortho_KB). The structural pipeline builds bridges across species based on orthology. The functional pipeline integrates biological information, including QTL, and RNA-sequencing datasets, and uses the backbone from the structural pipeline to connect orthologs in the database. Queries can be written using the Neo4j Cypher language and can, for instance, lead to identify genes controlling a common trait across species. To explore the possibilities offered by such a framework, we populated Ortho_KB to obtain OrthoLegKB, an instance dedicated to legumes. The proposed model was evaluated by studying the conservation of a flowering-promoting gene. Through a series of queries, we have demonstrated that our knowledge graph base provides an intuitive and powerful platform to support research and development programmes.
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Affiliation(s)
- Baptiste Imbert
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Jonathan Kreplak
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Raphaël-Gauthier Flores
- Université Paris-Saclay, INRAE, URGI, Versailles, France
- Université Paris-Saclay, INRAE, BioinfOmics, Plant Bioinformatics Facility, Versailles, France
| | - Grégoire Aubert
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Judith Burstin
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Nadim Tayeh
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
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4
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Cope KR, Prates ET, Miller JI, Demerdash ON, Shah M, Kainer D, Cliff A, Sullivan KA, Cashman M, Lane M, Matthiadis A, Labbé J, Tschaplinski TJ, Jacobson DA, Kalluri UC. Exploring the role of plant lysin motif receptor-like kinases in regulating plant-microbe interactions in the bioenergy crop Populus. Comput Struct Biotechnol J 2022; 21:1122-1139. [PMID: 36789259 PMCID: PMC9900275 DOI: 10.1016/j.csbj.2022.12.052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 12/18/2022] [Accepted: 12/30/2022] [Indexed: 01/02/2023] Open
Abstract
For plants, distinguishing between mutualistic and pathogenic microbes is a matter of survival. All microbes contain microbe-associated molecular patterns (MAMPs) that are perceived by plant pattern recognition receptors (PRRs). Lysin motif receptor-like kinases (LysM-RLKs) are PRRs attuned for binding and triggering a response to specific MAMPs, including chitin oligomers (COs) in fungi, lipo-chitooligosaccharides (LCOs), which are produced by mycorrhizal fungi and nitrogen-fixing rhizobial bacteria, and peptidoglycan in bacteria. The identification and characterization of LysM-RLKs in candidate bioenergy crops including Populus are limited compared to other model plant species, thus inhibiting our ability to both understand and engineer microbe-mediated gains in plant productivity. As such, we performed a sequence analysis of LysM-RLKs in the Populus genome and predicted their function based on phylogenetic analysis with known LysM-RLKs. Then, using predictive models, molecular dynamics simulations, and comparative structural analysis with previously characterized CO and LCO plant receptors, we identified probable ligand-binding sites in Populus LysM-RLKs. Using several machine learning models, we predicted remarkably consistent binding affinity rankings of Populus proteins to CO. In addition, we used a modified Random Walk with Restart network-topology based approach to identify a subset of Populus LysM-RLKs that are functionally related and propose a corresponding signal transduction cascade. Our findings provide the first look into the role of LysM-RLKs in Populus-microbe interactions and establish a crucial jumping-off point for future research efforts to understand specificity and redundancy in microbial perception mechanisms.
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Affiliation(s)
- Kevin R. Cope
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Erica T. Prates
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - John I. Miller
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Omar N.A. Demerdash
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Manesh Shah
- Genome Science and Technology, The University of Tennessee–Knoxville, Knoxville, TN 37996, USA
| | - David Kainer
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Ashley Cliff
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville 37996, USA
| | - Kyle A. Sullivan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Mikaela Cashman
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Matthew Lane
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville 37996, USA
| | - Anna Matthiadis
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jesse Labbé
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | | | - Daniel A. Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA,The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville 37996, USA
| | - Udaya C. Kalluri
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA,Corresponding author.
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Sheng M, Ma X, Wang J, Xue T, Li Z, Cao Y, Yu X, Zhang X, Wang Y, Xu W, Su Z. KNOX II transcription factor HOS59 functions in regulating rice grain size. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:863-880. [PMID: 35167131 DOI: 10.1111/tpj.15709] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 01/30/2022] [Accepted: 02/10/2022] [Indexed: 06/14/2023]
Abstract
Plant Knotted1-like homeobox (KNOX) genes encode homeodomain-containing transcription factors. In rice (Oryza sativa L.), little is known about the downstream target genes of KNOX Class II subfamily proteins. Here we generated chromatin immunoprecipitation (ChIP)-sequencing datasets for HOS59, a member of the rice KNOX Class II subfamily, and characterized the genome-wide binding sites of HOS59. We conducted trait ontology (TO) analysis of 9705 identified downstream target genes, and found that multiple TO terms are related to plant structure morphology and stress traits. ChIP-quantitative PCR (qPCR) was conducted to validate some key target genes. Meanwhile, our IP-MS datasets showed that HOS59 was closely associated with BELL family proteins, some grain size regulators (OsSPL13, OsSPL16, OsSPL18, SLG, etc.), and some epigenetic modification factors such as OsAGO4α and OsAGO4β, proteins involved in small interfering RNA-mediated gene silencing. Furthermore, we employed CRISPR/Cas9 editing and transgenic approaches to generate hos59 mutants and overexpression lines, respectively. Compared with wild-type plants, the hos59 mutants have longer grains and increased glume cell length, a loose plant architecture, and drooping leaves, while the overexpression lines showed smaller grain size, erect leaves, and lower plant height. The qRT-PCR results showed that mutation of the HOS59 gene led to upregulation of some grain size-related genes such as OsSPL13, OsSPL18, and PGL2. In summary, our results indicate that HOS59 may be a repressor of the downstream target genes, negatively regulating glume cell length, rice grain size, plant architecture, etc. The identified downstream target genes and possible interaction proteins of HOS59 improve our understanding of the KNOX regulatory networks.
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Affiliation(s)
- Minghao Sheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xuelian Ma
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jiyao Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tianxi Xue
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Zhongqiu Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yaxin Cao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xinyue Yu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xinyi Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yonghong Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wenying Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Zhen Su
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
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6
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Thessen AE, Walls RL, Vogt L, Singer J, Warren R, Buttigieg PL, Balhoff JP, Mungall CJ, McGuinness DL, Stucky BJ, Yoder MJ, Haendel MA. Transforming the study of organisms: Phenomic data models and knowledge bases. PLoS Comput Biol 2020; 16:e1008376. [PMID: 33232313 PMCID: PMC7685442 DOI: 10.1371/journal.pcbi.1008376] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The rapidly decreasing cost of gene sequencing has resulted in a deluge of genomic data from across the tree of life; however, outside a few model organism databases, genomic data are limited in their scientific impact because they are not accompanied by computable phenomic data. The majority of phenomic data are contained in countless small, heterogeneous phenotypic data sets that are very difficult or impossible to integrate at scale because of variable formats, lack of digitization, and linguistic problems. One powerful solution is to represent phenotypic data using data models with precise, computable semantics, but adoption of semantic standards for representing phenotypic data has been slow, especially in biodiversity and ecology. Some phenotypic and trait data are available in a semantic language from knowledge bases, but these are often not interoperable. In this review, we will compare and contrast existing ontology and data models, focusing on nonhuman phenotypes and traits. We discuss barriers to integration of phenotypic data and make recommendations for developing an operationally useful, semantically interoperable phenotypic data ecosystem.
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Affiliation(s)
- Anne E. Thessen
- Environmental and Molecular Toxicology, Oregon State University, Corvallis, Oregon, United States of America
- Ronin Institute for Independent Scholarship, Monclair, New Jersey, United States of America
| | - Ramona L. Walls
- Bio5 Institute, University of Arizona, Tucson, Arizona, United States of America
| | - Lars Vogt
- TIB Leibniz Information Centre for Science and Technology, Hannover, Germany
| | | | | | - Pier Luigi Buttigieg
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
| | - James P. Balhoff
- Renaissance Computing Institute, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Christopher J. Mungall
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | | | - Brian J. Stucky
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, United States of America
| | - Matthew J. Yoder
- Illinois Natural History Survey, Champaign, Illinois, United States of America
| | - Melissa A. Haendel
- Environmental and Molecular Toxicology, Oregon State University, Corvallis, Oregon, United States of America
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7
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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. THE NEW PHYTOLOGIST 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] [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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8
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Dai X, Xu Z, Liang Z, Tu X, Zhong S, Schnable JC, Li P. Non-homology-based prediction of gene functions in maize (Zea mays ssp. mays). THE PLANT GENOME 2020; 13:e20015. [PMID: 33016608 DOI: 10.1002/tpg2.20015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 12/22/2019] [Accepted: 02/12/2020] [Indexed: 06/11/2023]
Abstract
Advances in genome sequencing and annotation have eased the difficulty of identifying new gene sequences. Predicting the functions of these newly identified genes remains challenging. Genes descended from a common ancestral sequence are likely to have common functions. As a result, homology is widely used for gene function prediction. This means functional annotation errors also propagate from one species to another. Several approaches based on machine learning classification algorithms were evaluated for their ability to accurately predict gene function from non-homology gene features. Among the eight supervised classification algorithms evaluated, random-forest-based prediction consistently provided the most accurate gene function prediction. Non-homology-based functional annotation provides complementary strengths to homology-based annotation, with higher average performance in Biological Process GO terms, the domain where homology-based functional annotation performs the worst, and weaker performance in Molecular Function GO terms, the domain where the accuracy of homology-based functional annotation is highest. GO prediction models trained with homology-based annotations were able to successfully predict annotations from a manually curated "gold standard" GO annotation set. Non-homology-based functional annotation based on machine learning may ultimately prove useful both as a method to assign predicted functions to orphan genes which lack functionally characterized homologs, and to identify and correct functional annotation errors which were propagated through homology-based functional annotations.
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Affiliation(s)
- Xiuru Dai
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, 273100, China
- Quantitative Life Sciences Initiative, Center for Plant Science Innovation, and Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Zheng Xu
- Department of Mathematics and Statistics, Wright State University, Dayton, OH, 45435, USA
| | - Zhikai Liang
- Quantitative Life Sciences Initiative, Center for Plant Science Innovation, and Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Xiaoyu Tu
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Silin Zhong
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - James C Schnable
- Quantitative Life Sciences Initiative, Center for Plant Science Innovation, and Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Pinghua Li
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, 273100, China
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9
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McWhite CD, Papoulas O, Drew K, Cox RM, June V, Dong OX, Kwon T, Wan C, Salmi ML, Roux SJ, Browning KS, Chen ZJ, Ronald PC, Marcotte EM. A Pan-plant Protein Complex Map Reveals Deep Conservation and Novel Assemblies. Cell 2020; 181:460-474.e14. [PMID: 32191846 DOI: 10.1016/j.cell.2020.02.049] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 01/08/2020] [Accepted: 02/21/2020] [Indexed: 01/11/2023]
Abstract
Plants are foundational for global ecological and economic systems, but most plant proteins remain uncharacterized. Protein interaction networks often suggest protein functions and open new avenues to characterize genes and proteins. We therefore systematically determined protein complexes from 13 plant species of scientific and agricultural importance, greatly expanding the known repertoire of stable protein complexes in plants. By using co-fractionation mass spectrometry, we recovered known complexes, confirmed complexes predicted to occur in plants, and identified previously unknown interactions conserved over 1.1 billion years of green plant evolution. Several novel complexes are involved in vernalization and pathogen defense, traits critical for agriculture. We also observed plant analogs of animal complexes with distinct molecular assemblies, including a megadalton-scale tRNA multi-synthetase complex. The resulting map offers a cross-species view of conserved, stable protein assemblies shared across plant cells and provides a mechanistic, biochemical framework for interpreting plant genetics and mutant phenotypes.
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Affiliation(s)
- Claire D McWhite
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Ophelia Papoulas
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Kevin Drew
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Rachael M Cox
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Viviana June
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Oliver Xiaoou Dong
- Department of Plant Pathology and The Genome Center, University of California, Davis, Davis, CA 95616, USA; Joint Bioenergy Institute, Emeryville, CA 94608, USA
| | - Taejoon Kwon
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulju-gun, Ulsan 44919, Republic of Korea
| | - Cuihong Wan
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA; Hubei Key Lab of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, No. 152 Luoyu Road, Wuhan 430079, P.R. China
| | - Mari L Salmi
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Stanley J Roux
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Karen S Browning
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Z Jeffrey Chen
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Pamela C Ronald
- Department of Plant Pathology and The Genome Center, University of California, Davis, Davis, CA 95616, USA; Joint Bioenergy Institute, Emeryville, CA 94608, USA
| | - Edward M Marcotte
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA.
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10
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Fabris M, Abbriano RM, Pernice M, Sutherland DL, Commault AS, Hall CC, Labeeuw L, McCauley JI, Kuzhiuparambil U, Ray P, Kahlke T, Ralph PJ. Emerging Technologies in Algal Biotechnology: Toward the Establishment of a Sustainable, Algae-Based Bioeconomy. FRONTIERS IN PLANT SCIENCE 2020; 11:279. [PMID: 32256509 PMCID: PMC7090149 DOI: 10.3389/fpls.2020.00279] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 02/24/2020] [Indexed: 05/18/2023]
Abstract
Mankind has recognized the value of land plants as renewable sources of food, medicine, and materials for millennia. Throughout human history, agricultural methods were continuously modified and improved to meet the changing needs of civilization. Today, our rapidly growing population requires further innovation to address the practical limitations and serious environmental concerns associated with current industrial and agricultural practices. Microalgae are a diverse group of unicellular photosynthetic organisms that are emerging as next-generation resources with the potential to address urgent industrial and agricultural demands. The extensive biological diversity of algae can be leveraged to produce a wealth of valuable bioproducts, either naturally or via genetic manipulation. Microalgae additionally possess a set of intrinsic advantages, such as low production costs, no requirement for arable land, and the capacity to grow rapidly in both large-scale outdoor systems and scalable, fully contained photobioreactors. Here, we review technical advancements, novel fields of application, and products in the field of algal biotechnology to illustrate how algae could present high-tech, low-cost, and environmentally friendly solutions to many current and future needs of our society. We discuss how emerging technologies such as synthetic biology, high-throughput phenomics, and the application of internet of things (IoT) automation to algal manufacturing technology can advance the understanding of algal biology and, ultimately, drive the establishment of an algal-based bioeconomy.
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Affiliation(s)
- Michele Fabris
- Climate Change Cluster (C3), University of Technology Sydney, Ultimo, NSW, Australia
- CSIRO Synthetic Biology Future Science Platform, Brisbane, QLD, Australia
| | - Raffaela M. Abbriano
- Climate Change Cluster (C3), University of Technology Sydney, Ultimo, NSW, Australia
| | - Mathieu Pernice
- Climate Change Cluster (C3), University of Technology Sydney, Ultimo, NSW, Australia
| | - Donna L. Sutherland
- Climate Change Cluster (C3), University of Technology Sydney, Ultimo, NSW, Australia
| | - Audrey S. Commault
- Climate Change Cluster (C3), University of Technology Sydney, Ultimo, NSW, Australia
| | - Christopher C. Hall
- Climate Change Cluster (C3), University of Technology Sydney, Ultimo, NSW, Australia
| | - Leen Labeeuw
- Climate Change Cluster (C3), University of Technology Sydney, Ultimo, NSW, Australia
| | - Janice I. McCauley
- Climate Change Cluster (C3), University of Technology Sydney, Ultimo, NSW, Australia
| | | | - Parijat Ray
- Climate Change Cluster (C3), University of Technology Sydney, Ultimo, NSW, Australia
| | - Tim Kahlke
- Climate Change Cluster (C3), University of Technology Sydney, Ultimo, NSW, Australia
| | - Peter J. Ralph
- Climate Change Cluster (C3), University of Technology Sydney, Ultimo, NSW, Australia
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11
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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. MOLECULAR PLANT 2020; 13:187-214. [PMID: 31981735 DOI: 10.1016/j.molp.2020.01.008] [Citation(s) in RCA: 239] [Impact Index Per Article: 59.8] [Reference Citation Analysis] [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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12
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Braun IR, Lawrence-Dill CJ. Automated Methods Enable Direct Computation on Phenotypic Descriptions for Novel Candidate Gene Prediction. FRONTIERS IN PLANT SCIENCE 2020; 10:1629. [PMID: 31998331 PMCID: PMC6965352 DOI: 10.3389/fpls.2019.01629] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 11/19/2019] [Indexed: 06/01/2023]
Abstract
Natural language descriptions of plant phenotypes are a rich source of information for genetics and genomics research. We computationally translated descriptions of plant phenotypes into structured representations that can be analyzed to identify biologically meaningful associations. These representations include the entity-quality (EQ) formalism, which uses terms from biological ontologies to represent phenotypes in a standardized, semantically rich format, as well as numerical vector representations generated using natural language processing (NLP) methods (such as the bag-of-words approach and document embedding). We compared resulting phenotype similarity measures to those derived from manually curated data to determine the performance of each method. Computationally derived EQ and vector representations were comparably successful in recapitulating biological truth to representations created through manual EQ statement curation. Moreover, NLP methods for generating vector representations of phenotypes are scalable to large quantities of text because they require no human input. These results indicate that it is now possible to computationally and automatically produce and populate large-scale information resources that enable researchers to query phenotypic descriptions directly.
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Affiliation(s)
- Ian R. Braun
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, United States
- Interdepartmental Bioinformatics and Computational Biology, Iowa State University, Ames, IA, United States
| | - Carolyn J. Lawrence-Dill
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, United States
- Interdepartmental Bioinformatics and Computational Biology, Iowa State University, Ames, IA, United States
- Department of Agronomy, Iowa State University, Ames, IA, United States
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13
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Baker T, Whitehead B, Musker R, Keizer J. Global agricultural concept space: lightweight semantics for pragmatic interoperability. NPJ Sci Food 2019; 3:16. [PMID: 31552293 PMCID: PMC6751214 DOI: 10.1038/s41538-019-0048-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 07/16/2019] [Indexed: 11/10/2022] Open
Abstract
Progress on research and innovation in food technology depends increasingly on the use of structured vocabularies—concept schemes, thesauri, and ontologies—for discovering and re-using a diversity of data sources. Here, we report on GACS Core, a concept scheme in the larger Global Agricultural Concept Space (GACS), which was formed by mapping between the most frequently used concepts of AGROVOC, CAB Thesaurus, and NAL Thesaurus and serves as a target for mapping near-equivalent concepts from other vocabularies. It provides globally unique identifiers, which can be used as keywords in bibliographic databases, tags for web content, for building lightweight facet schemes, and for annotating spreadsheets, databases, and image metadata using synonyms and variant labels in 25 languages. The minimal semantics of GACS allows terms defined with more precision in ontologies, or less precision in controlled vocabularies, to be linked together making it easier to discover and integrate semantically diverse data sources.
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Affiliation(s)
| | | | | | - Johannes Keizer
- Global Open Data for Agriculture and Nutrition (GODAN) Secretariat, Wallingford, UK
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14
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Evolutionary characteristics of intergenic transcribed regions indicate rare novel genes and widespread noisy transcription in the Poaceae. Sci Rep 2019; 9:12122. [PMID: 31431676 PMCID: PMC6702216 DOI: 10.1038/s41598-019-47797-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 07/19/2019] [Indexed: 01/19/2023] Open
Abstract
Extensive transcriptional activity occurring in intergenic regions of genomes has raised the question whether intergenic transcription represents the activity of novel genes or noisy expression. To address this, we evaluated cross-species and post-duplication sequence and expression conservation of intergenic transcribed regions (ITRs) in four Poaceae species. Among 43,301 ITRs across the four species, 34,460 (80%) are species-specific. ITRs found across species tend to be more divergent in expression and have more recent duplicates compared to annotated genes. To assess if ITRs are functional (under selection), machine learning models were established in Oryza sativa (rice) that could accurately distinguish between phenotype genes and pseudogenes (area under curve-receiver operating characteristic = 0.94). Based on the models, 584 (8%) and 4391 (61%) rice ITRs are classified as likely functional and nonfunctional with high confidence, respectively. ITRs with conserved expression and ancient retained duplicates, features that were not part of the model, are frequently classified as likely-functional, suggesting these characteristics could serve as pragmatic rules of thumb for identifying candidate sequences likely to be under selection. This study also provides a framework to identify novel genes using comparative transcriptomic data to improve genome annotation that is fundamental for connecting genotype to phenotype in crop and model systems.
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15
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Cooper L, Meier A, Laporte MA, Elser JL, Mungall C, Sinn BT, Cavaliere D, Carbon S, Dunn NA, Smith B, Qu B, Preece J, Zhang E, Todorovic S, Gkoutos G, Doonan JH, Stevenson DW, Arnaud E, Jaiswal P. The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics. Nucleic Acids Res 2019; 46:D1168-D1180. [PMID: 29186578 PMCID: PMC5753347 DOI: 10.1093/nar/gkx1152] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 11/21/2017] [Indexed: 01/08/2023] Open
Abstract
The Planteome project (http://www.planteome.org) provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. The Planteome project is developing a plant gene annotation platform; Planteome Noctua, to facilitate community engagement. All the Planteome ontologies are publicly available and are maintained at the Planteome GitHub site (https://github.com/Planteome) for sharing, tracking revisions and new requests. The annotated data are freely accessible from the ontology browser (http://browser.planteome.org/amigo) and our data repository.
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Affiliation(s)
- Laurel Cooper
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Austin Meier
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | | | - Justin L Elser
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Chris Mungall
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | | | - Seth Carbon
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Nathan A Dunn
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Barry Smith
- Department of Philosophy, University at Buffalo, Buffalo, NY 14260, USA
| | - Botong Qu
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR 97331, USA
| | - Justin Preece
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Eugene Zhang
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR 97331, USA
| | - Sinisa Todorovic
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR 97331, USA
| | - Georgios Gkoutos
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - John H Doonan
- National Plant Phenomics Centre, Institute of Biological, Environmental, and Rural Sciences, Aberystwyth University, Aberystwyth SY23 3DA, UK
| | | | - Elizabeth Arnaud
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
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16
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Walls RL, Cooper L, Elser J, Gandolfo MA, Mungall CJ, Smith B, Stevenson DW, Jaiswal P. The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species. FRONTIERS IN PLANT SCIENCE 2019; 10:631. [PMID: 31214208 PMCID: PMC6558174 DOI: 10.3389/fpls.2019.00631] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/26/2019] [Indexed: 06/09/2023]
Abstract
The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover development stages for all plants, particularly the land plants (bryophytes through angiosperms). As a case study to illustrate the general approach, we examine variation in gene expression across embryo development stages in Arabidopsis and maize, demonstrating how the PO can be used to compare patterns of expression across stages and in developmentally different species. Although many genes appear to be active throughout embryo development, we identified a small set of uniquely expressed genes for each stage of embryo development and also between the two species. Evaluating the different sets of genes expressed during embryo development in Arabidopsis or maize may inform future studies of the divergent developmental pathways observed in monocotyledonous versus dicotyledonous species. The PO and its annotation database (http://www.planteome.org) make plant data for any species more discoverable and accessible through common formats, thus providing support for applications in plant pathology, image analysis, and comparative development and evolution.
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Affiliation(s)
- Ramona L. Walls
- CyVerse, Bio5 Institute, The University of Arizona, Tucson, AZ, United States
| | - Laurel Cooper
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Justin Elser
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Maria Alejandra Gandolfo
- Liberty Hyde Bailey Hortorium, Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Christopher J. Mungall
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Barry Smith
- Department of Philosophy, University at Buffalo, Buffalo, NY, United States
| | | | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
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17
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Pan Q, Wei J, Guo F, Huang S, Gong Y, Liu H, Liu J, Li L. Trait ontology analysis based on association mapping studies bridges the gap between crop genomics and Phenomics. BMC Genomics 2019; 20:443. [PMID: 31159731 PMCID: PMC6547493 DOI: 10.1186/s12864-019-5812-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 05/20/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Trait ontology (TO) analysis is a powerful system for functional annotation and enrichment analysis of genes. However, given the complexity of the molecular mechanisms underlying phenomes, only a few hundred gene-to-TO relationships in plants have been elucidated to date, limiting the pace of research in this "big data" era. RESULTS Here, we curated all the available trait associated sites (TAS) information from 79 association mapping studies of maize (Zea mays L.) and rice (Oryza sativa L.) lines with diverse genetic backgrounds and built a large-scale TAS-derived TO system for functional annotation of genes in various crops. Our TO system contains information for up to 18,042 genes (6345 in maize at the 25 k level and 11,697 in rice at the 50 k level), including gene-to-TO relationships, which covers over one fifth of the annotated gene sets for maize and rice. A comparison of Gene Ontology (GO) vs. TO analysis demonstrated that the TAS-derived TO system is an efficient alternative tool for gene functional annotation and enrichment analysis. We therefore combined information from the TO, GO, metabolic pathway, and co-expression network databases and constructed the TAS system, which is publicly available at http://tas.hzau.edu.cn . TAS provides a user-friendly interface for functional annotation of genes, enrichment analysis, genome-wide extraction of trait-associated genes, and crosschecking of different functional annotation databases. CONCLUSIONS TAS bridges the gap between genomic and phenomic information in crops. This easy-to-use tool will be useful for geneticists, biologists, and breeders in the agricultural community, as it facilitates the dissection of molecular mechanisms conferring agronomic traits in an easy, genome-wide manner.
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Affiliation(s)
- Qingchun Pan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Junfeng Wei
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Feng Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Suiyong Huang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yong Gong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hao Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jianxiao Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
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18
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Mir RR, Reynolds M, Pinto F, Khan MA, Bhat MA. High-throughput phenotyping for crop improvement in the genomics era. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 282:60-72. [PMID: 31003612 DOI: 10.1016/j.plantsci.2019.01.007] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 12/10/2018] [Accepted: 01/09/2019] [Indexed: 05/24/2023]
Abstract
Tremendous progress has been made with continually expanding genomics technologies to unravel and understand crop genomes. However, the impact of genomics data on crop improvement is still far from satisfactory, in large part due to a lack of effective phenotypic data; our capacity to collect useful high quality phenotypic data lags behind the current capacity to generate high-throughput genomics data. Thus, the research bottleneck in plant sciences is shifting from genotyping to phenotyping. This article review the current status of efforts made in the last decade to systematically collect phenotypic data to alleviate this 'phenomics bottlenecks' by recording trait data through sophisticated non-invasive imaging, spectroscopy, image analysis, robotics, high-performance computing facilities and phenomics databases. These modern phenomics platforms and tools aim to record data on traits like plant development, architecture, plant photosynthesis, growth or biomass productivity, on hundreds to thousands of plants in a single day, as a phenomics revolution. It is believed that this revolution will provide plant scientists with the knowledge and tools necessary for unlocking information coded in plant genomes. Efforts have been also made to present the advances made in the last 10 years in phenomics platforms and their use in generating phenotypic data on different traits in several major crops including rice, wheat, barley, and maize. The article also highlights the need for phenomics databases and phenotypic data sharing for crop improvement. The phenomics data generated has been used to identify genes/QTL through QTL mapping, association mapping and genome-wide association studies (GWAS) for genomics-assisted breeding (GAB) for crop improvement.
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Affiliation(s)
- Reyazul Rouf Mir
- Division of Genetics & Plant Breeding, Faculty of Agriculture (FoA), Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Wadura Campus, Sopore-193201, Kashmir, India.
| | - Mathew Reynolds
- Global Wheat Program, International Maize and Wheat Improvement Centre (CIMMYT), Mexico, D.F., Mexico
| | - Francisco Pinto
- Global Wheat Program, International Maize and Wheat Improvement Centre (CIMMYT), Mexico, D.F., Mexico
| | - Mohd Anwar Khan
- Division of Genetics & Plant Breeding, Faculty of Agriculture (FoA), Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Wadura Campus, Sopore-193201, Kashmir, India
| | - Mohd Ashraf Bhat
- Division of Genetics & Plant Breeding, Faculty of Agriculture (FoA), Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Wadura Campus, Sopore-193201, Kashmir, India
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19
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Venkatesan A, Tagny Ngompe G, Hassouni NE, Chentli I, Guignon V, Jonquet C, Ruiz M, Larmande P. Agronomic Linked Data (AgroLD): A knowledge-based system to enable integrative biology in agronomy. PLoS One 2018; 13:e0198270. [PMID: 30500839 PMCID: PMC6269127 DOI: 10.1371/journal.pone.0198270] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 09/03/2018] [Indexed: 12/22/2022] Open
Abstract
Recent advances in high-throughput technologies have resulted in a tremendous increase in the amount of omics data produced in plant science. This increase, in conjunction with the heterogeneity and variability of the data, presents a major challenge to adopt an integrative research approach. We are facing an urgent need to effectively integrate and assimilate complementary datasets to understand the biological system as a whole. The Semantic Web offers technologies for the integration of heterogeneous data and their transformation into explicit knowledge thanks to ontologies. We have developed the Agronomic Linked Data (AgroLD- www.agrold.org), a knowledge-based system relying on Semantic Web technologies and exploiting standard domain ontologies, to integrate data about plant species of high interest for the plant science community e.g., rice, wheat, arabidopsis. We present some integration results of the project, which initially focused on genomics, proteomics and phenomics. AgroLD is now an RDF (Resource Description Format) knowledge base of 100M triples created by annotating and integrating more than 50 datasets coming from 10 data sources-such as Gramene.org and TropGeneDB-with 10 ontologies-such as the Gene Ontology and Plant Trait Ontology. Our evaluation results show users appreciate the multiple query modes which support different use cases. AgroLD's objective is to offer a domain specific knowledge platform to solve complex biological and agronomical questions related to the implication of genes/proteins in, for instances, plant disease resistance or high yield traits. We expect the resolution of these questions to facilitate the formulation of new scientific hypotheses to be validated with a knowledge-oriented approach.
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Affiliation(s)
- Aravind Venkatesan
- Institut de Biologie Computationnelle (IBC), Univ. of Montpellier, Montpellier, France
- LIRMM, Univ. of Montpellier & CNRS, Montpellier, France
| | - Gildas Tagny Ngompe
- Institut de Biologie Computationnelle (IBC), Univ. of Montpellier, Montpellier, France
- LIRMM, Univ. of Montpellier & CNRS, Montpellier, France
| | - Nordine El Hassouni
- Institut de Biologie Computationnelle (IBC), Univ. of Montpellier, Montpellier, France
- UMR AGAP, CIRAD, Montpellier, France
- South Green Bioinformatics Platform, Montpellier, France
| | - Imene Chentli
- Institut de Biologie Computationnelle (IBC), Univ. of Montpellier, Montpellier, France
- LIRMM, Univ. of Montpellier & CNRS, Montpellier, France
| | - Valentin Guignon
- South Green Bioinformatics Platform, Montpellier, France
- Bioversity International, Montpellier, France
| | - Clement Jonquet
- Institut de Biologie Computationnelle (IBC), Univ. of Montpellier, Montpellier, France
- LIRMM, Univ. of Montpellier & CNRS, Montpellier, France
| | - Manuel Ruiz
- Institut de Biologie Computationnelle (IBC), Univ. of Montpellier, Montpellier, France
- UMR AGAP, CIRAD, Montpellier, France
- South Green Bioinformatics Platform, Montpellier, France
- AGAP, Univ. of Montpellier, CIRAD, INRA, INRIA, SupAgro, Montpellier, France
| | - Pierre Larmande
- Institut de Biologie Computationnelle (IBC), Univ. of Montpellier, Montpellier, France
- LIRMM, Univ. of Montpellier & CNRS, Montpellier, France
- South Green Bioinformatics Platform, Montpellier, France
- DIADE, IRD, Univ. of Montpellier, Montpellier, France
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20
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Understanding Forest Health with Remote Sensing, Part III: Requirements for a Scalable Multi-Source Forest Health Monitoring Network Based on Data Science Approaches. REMOTE SENSING 2018. [DOI: 10.3390/rs10071120] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Forest ecosystems fulfill a whole host of ecosystem functions that are essential for life on our planet. However, an unprecedented level of anthropogenic influences is reducing the resilience and stability of our forest ecosystems as well as their ecosystem functions. The relationships between drivers, stress, and ecosystem functions in forest ecosystems are complex, multi-faceted, and often non-linear, and yet forest managers, decision makers, and politicians need to be able to make rapid decisions that are data-driven and based on short and long-term monitoring information, complex modeling, and analysis approaches. A huge number of long-standing and standardized forest health inventory approaches already exist, and are increasingly integrating remote-sensing based monitoring approaches. Unfortunately, these approaches in monitoring, data storage, analysis, prognosis, and assessment still do not satisfy the future requirements of information and digital knowledge processing of the 21st century. Therefore, this paper discusses and presents in detail five sets of requirements, including their relevance, necessity, and the possible solutions that would be necessary for establishing a feasible multi-source forest health monitoring network for the 21st century. Namely, these requirements are: (1) understanding the effects of multiple stressors on forest health; (2) using remote sensing (RS) approaches to monitor forest health; (3) coupling different monitoring approaches; (4) using data science as a bridge between complex and multidimensional big forest health (FH) data; and (5) a future multi-source forest health monitoring network. It became apparent that no existing monitoring approach, technique, model, or platform is sufficient on its own to monitor, model, forecast, or assess forest health and its resilience. In order to advance the development of a multi-source forest health monitoring network, we argue that in order to gain a better understanding of forest health in our complex world, it would be conducive to implement the concepts of data science with the components: (i) digitalization; (ii) standardization with metadata management after the FAIR (Findability, Accessibility, Interoperability, and Reusability) principles; (iii) Semantic Web; (iv) proof, trust, and uncertainties; (v) tools for data science analysis; and (vi) easy tools for scientists, data managers, and stakeholders for decision-making support.
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Lu-Irving P, Marx HE, Dlugosch KM. Leveraging contemporary species introductions to test phylogenetic hypotheses of trait evolution. CURRENT OPINION IN PLANT BIOLOGY 2018; 42:95-102. [PMID: 29754025 DOI: 10.1016/j.pbi.2018.04.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 04/18/2018] [Accepted: 04/22/2018] [Indexed: 06/08/2023]
Abstract
Plant trait evolution is a topic of interest across disciplines and scales. Phylogenetic studies are powerful for generating hypotheses about the mechanisms that have shaped plant traits and their evolution. Introduced plants are a rich source of data on contemporary trait evolution. Introductions could provide especially useful tests of a variety of evolutionary hypotheses because the environments selecting on evolving traits are still present. We review phylogenetic and contemporary studies of trait evolution and identify areas of overlap and areas for further integration. Emerging tools which can promote integration include broadly focused repositories of trait data, and comparative models of trait evolution that consider both intra and interspecific variation.
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Affiliation(s)
- Patricia Lu-Irving
- Department of Ecology and Evolutionary Biology, University of Arizona, PO Box 210088, Tucson, AZ 85721, USA.
| | - Hannah E Marx
- Department of Ecology and Evolutionary Biology, University of Arizona, PO Box 210088, Tucson, AZ 85721, USA
| | - Katrina M Dlugosch
- Department of Ecology and Evolutionary Biology, University of Arizona, PO Box 210088, Tucson, AZ 85721, USA
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22
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Friesner J, Assmann SM, Bastow R, Bailey-Serres J, Beynon J, Brendel V, Buell CR, Bucksch A, Busch W, Demura T, Dinneny JR, Doherty CJ, Eveland AL, Falter-Braun P, Gehan MA, Gonzales M, Grotewold E, Gutierrez R, Kramer U, Krouk G, Ma S, Markelz RJC, Megraw M, Meyers BC, Murray JAH, Provart NJ, Rhee S, Smith R, Spalding EP, Taylor C, Teal TK, Torii KU, Town C, Vaughn M, Vierstra R, Ware D, Wilkins O, Williams C, Brady SM. The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology. PLANT PHYSIOLOGY 2017; 175:1499-1509. [PMID: 29208732 PMCID: PMC5717721 DOI: 10.1104/pp.17.01490] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 10/31/2017] [Indexed: 05/20/2023]
Abstract
Training for experimental plant biologists needs to combine bioinformatics, quantitative approaches, computational biology, and training in the art of collaboration, best achieved through fully integrated curriculum development.
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Affiliation(s)
- Joanna Friesner
- Agricultural Sustainability Institute and Department of Neurobiology, Physiology, and Behavior, University of California, Davis, California 95616
| | - Sarah M Assmann
- Biology Department, Penn State University, University Park, Pennsylvania 16802
| | - Ruth Bastow
- GARNet, School of Biosciences, Cardiff University, Cardiff CF10 3AT, United Kingdom
| | - Julia Bailey-Serres
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, California 92521
| | - Jim Beynon
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Volker Brendel
- Department of Biology and Department of Computer Science, Indiana University, Bloomington, Indiana 47405
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Alexander Bucksch
- Department of Plant Biology, Warnell School of Forestry and Natural Resources, and Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602
| | - Wolfgang Busch
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria; Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037
| | - Taku Demura
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan; RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Jose R Dinneny
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Colleen J Doherty
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695
| | | | - Pascal Falter-Braun
- Institute of Network Biology, Department of Environmental Science, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Malia A Gehan
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
| | | | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Rodrigo Gutierrez
- FONDAP Center for Genome Regulation, Millennium Nucleus Center for Plant Systems and Synthetic Biology, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile 8331150
| | - Ute Kramer
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Gabriel Krouk
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, CNRS, INRA, Montpellier SupAgro, Université Montpellier, Institut de Biologie Intégrative des Plantes "Claude Grignon," Place Viala, 34060 Montpellier cedex, France
| | - Shisong Ma
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - R J Cody Markelz
- Department of Plant Biology, University of California, Davis, California 95616
| | - Molly Megraw
- Department of Botany and Plant Pathology, Department of Computer Science, and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132; Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211
| | - James A H Murray
- School of Biosciences, Cardiff University, Cardiff CF10 3AX, Wales, United Kingdom
| | - Nicholas J Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Sue Rhee
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Roger Smith
- Syngenta Crop Protection, Research Triangle Park, North Carolina 27709
| | - Edgar P Spalding
- Department of Botany, University of Wisconsin, Madison, Wisconsin 53706
| | - Crispin Taylor
- American Society of Plant Biologists, Rockville, Maryland 20855
| | | | - Keiko U Torii
- Howard Hughes Medical Institute and Department of Biology, University of Washington, Seattle, Washington 98195
| | - Chris Town
- J. Craig Venter Institute, Rockville, Maryland 20850
| | - Matthew Vaughn
- Life Sciences Computing, Texas Advanced Computing Center, Austin, Texas 78758
| | - Richard Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724; U.S. Department of Agriculture Agricultural Research Service, Ithaca, New York 14853
| | - Olivia Wilkins
- Department of Plant Science, McGill University, Montreal, Quebec H9X 3V9, Canada
| | - Cranos Williams
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, North Carolina 27695
| | - Siobhan M Brady
- Department of Plant Biology, Genome Center, University of California, Davis, California 95616
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Das S, Tyagi W, Rai M, Yumnam JS. Understanding Fe 2+ toxicity and P deficiency tolerance in rice for enhancing productivity under acidic soils. Biotechnol Genet Eng Rev 2017; 33:97-117. [PMID: 28927358 DOI: 10.1080/02648725.2017.1370888] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Plants experience low phosphorus (P) and high iron (Fe) levels in acidic lowland soils that lead to reduced crop productivity. A better understanding of the relationship between these two stresses at molecular and physiological level will lead to development of suitable strategies to increase crop productivity in such poor soils. Tolerance for most abiotic stresses including P deficiency and Fe toxicity is a quantitative trait in rice. Recent studies in the areas of physiology, genetics, and overall metabolic pathways in response to P deficiency of rice plants have improved our understanding of low P tolerance. Phosphorous uptake and P use efficiency are the two key traits for improving P deficiency tolerance. In the case of Fe toxicity tolerance, QTLs have been reported but the identity and role played by underlying genes is just emerging. Details pertaining to Fe deficiency tolerance in rice are well worked out including genes involved in Fe sensing and uptake. But, how rice copes with Fe toxicity is not clearly understood. This review focuses on the progress made in understanding these key environmental stresses. Finally, an opinion on the key genes which can be targeted for this stress is provided.
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Affiliation(s)
- Sudip Das
- a School of Crop Improvement, College of Post-Graduate (CPGS), Central Agricultural University , Imphal , India
| | - Wricha Tyagi
- a School of Crop Improvement, College of Post-Graduate (CPGS), Central Agricultural University , Imphal , India
| | - Mayank Rai
- a School of Crop Improvement, College of Post-Graduate (CPGS), Central Agricultural University , Imphal , India
| | - Julia S Yumnam
- a School of Crop Improvement, College of Post-Graduate (CPGS), Central Agricultural University , Imphal , India
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Wang D, Wang S, Chao J, Wu X, Sun Y, Li F, Lv J, Gao X, Liu G, Wang Y. Morphological phenotyping and genetic analyses of a new chemical-mutagenized population of tobacco (Nicotiana tabacum L.). PLANTA 2017; 246:149-163. [PMID: 28401357 DOI: 10.1007/s00425-017-2690-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Accepted: 04/01/2017] [Indexed: 06/07/2023]
Abstract
MAIN CONCLUSION A novel tobacco mutant library was constructed, screened, and characterized as a crucial genetic resource for functional genomics and applied research. A comprehensive mutant library is a fundamental resource for investigating gene functions, especially after the completion of genome sequencing. A new tobacco mutant population induced by ethyl methane sulfonate mutagenesis was developed for functional genomics applications. We isolated 1607 mutant lines and 8610 mutant plants with altered morphological phenotypes from 5513 independent M2 families that consisted of 69,531 M2 plants. The 2196 mutations of abnormal phenotypes in the M2 putative mutants were classified into four groups with 17 major categories and 51 subcategories. More than 60% of the abnormal phenotypes observed fell within the five major categories including plant height, leaf shape, leaf surface, leaf color, and flowering time. The 465 M2 mutants exhibited multiple phenotypes, and 1054 of the 2196 mutations were pleiotropic. Verification of the phenotypes in advanced generations indicated that 70.63% of the M3 lines, 84.87% of the M4 lines, and 95.75% of the M5 lines could transmit original mutant phenotypes of the corresponding M2, M3, and M4 mutant plants. Along with the increased generation of mutants, the ratios of lines inheriting OMPs increased and lines with emerging novel mutant phenotypes decreased. Genetic analyses of 18 stably heritable mutants showed that two mutants were double recessive, five were monogenic recessive, eight presented monogenic dominant inheritance, and three presented semi-dominant inheritance. The pleiotropy pattern, saturability evaluation, research prospects of genome, and phenome of the mutant populations were also discussed. Simultaneously, this novel mutant library provided a fundamental resource for investigating gene functions in tobacco.
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Affiliation(s)
- Dawei Wang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, No. 11 Keyuanjingsi Road, Laoshan District, Qingdao, 266101, China
- Key Laboratory for Tobacco Gene Resources, State Tobacco Monopoly Administration, Qingdao, 266101, China
| | - Shaomei Wang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, No. 11 Keyuanjingsi Road, Laoshan District, Qingdao, 266101, China
| | - Jiangtao Chao
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, No. 11 Keyuanjingsi Road, Laoshan District, Qingdao, 266101, China
- Key Laboratory for Tobacco Gene Resources, State Tobacco Monopoly Administration, Qingdao, 266101, China
| | - Xinru Wu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, No. 11 Keyuanjingsi Road, Laoshan District, Qingdao, 266101, China
- Key Laboratory for Tobacco Gene Resources, State Tobacco Monopoly Administration, Qingdao, 266101, China
| | - Yuhe Sun
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, No. 11 Keyuanjingsi Road, Laoshan District, Qingdao, 266101, China
- Key Laboratory for Tobacco Gene Resources, State Tobacco Monopoly Administration, Qingdao, 266101, China
| | - Fengxia Li
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, No. 11 Keyuanjingsi Road, Laoshan District, Qingdao, 266101, China
- Key Laboratory for Tobacco Gene Resources, State Tobacco Monopoly Administration, Qingdao, 266101, China
| | - Jing Lv
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, No. 11 Keyuanjingsi Road, Laoshan District, Qingdao, 266101, China
- Key Laboratory for Tobacco Gene Resources, State Tobacco Monopoly Administration, Qingdao, 266101, China
| | - Xiaoming Gao
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, No. 11 Keyuanjingsi Road, Laoshan District, Qingdao, 266101, China
- Key Laboratory for Tobacco Gene Resources, State Tobacco Monopoly Administration, Qingdao, 266101, China
| | - Guanshan Liu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, No. 11 Keyuanjingsi Road, Laoshan District, Qingdao, 266101, China.
- Key Laboratory for Tobacco Gene Resources, State Tobacco Monopoly Administration, Qingdao, 266101, China.
| | - Yuanying Wang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, No. 11 Keyuanjingsi Road, Laoshan District, Qingdao, 266101, China.
- Key Laboratory for Tobacco Gene Resources, State Tobacco Monopoly Administration, Qingdao, 266101, China.
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Hoehndorf R, Alshahrani M, Gkoutos GV, Gosline G, Groom Q, Hamann T, Kattge J, de Oliveira SM, Schmidt M, Sierra S, Smets E, Vos RA, Weiland C. The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants. J Biomed Semantics 2016; 7:65. [PMID: 27842607 PMCID: PMC5109718 DOI: 10.1186/s13326-016-0107-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 11/01/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The systematic analysis of a large number of comparable plant trait data can support investigations into phylogenetics and ecological adaptation, with broad applications in evolutionary biology, agriculture, conservation, and the functioning of ecosystems. Floras, i.e., books collecting the information on all known plant species found within a region, are a potentially rich source of such plant trait data. Floras describe plant traits with a focus on morphology and other traits relevant for species identification in addition to other characteristics of plant species, such as ecological affinities, distribution, economic value, health applications, traditional uses, and so on. However, a key limitation in systematically analyzing information in Floras is the lack of a standardized vocabulary for the described traits as well as the difficulties in extracting structured information from free text. RESULTS We have developed the Flora Phenotype Ontology (FLOPO), an ontology for describing traits of plant species found in Floras. We used the Plant Ontology (PO) and the Phenotype And Trait Ontology (PATO) to extract entity-quality relationships from digitized taxon descriptions in Floras, and used a formal ontological approach based on phenotype description patterns and automated reasoning to generate the FLOPO. The resulting ontology consists of 25,407 classes and is based on the PO and PATO. The classified ontology closely follows the structure of Plant Ontology in that the primary axis of classification is the observed plant anatomical structure, and more specific traits are then classified based on parthood and subclass relations between anatomical structures as well as subclass relations between phenotypic qualities. CONCLUSIONS The FLOPO is primarily intended as a framework based on which plant traits can be integrated computationally across all species and higher taxa of flowering plants. Importantly, it is not intended to replace established vocabularies or ontologies, but rather serve as an overarching framework based on which different application- and domain-specific ontologies, thesauri and vocabularies of phenotypes observed in flowering plants can be integrated.
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Affiliation(s)
- Robert Hoehndorf
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, 4700 KAUST, Thuwal, 23955–6900 Kingdom of Saudi Arabia
- Computer, Electrical and Mathematical Sciences & Engineering Division (CEMSE), King Abdullah University of Science and Technology, 4700 KAUST, Thuwal, 23955–6900 Kingdom of Saudi Arabia
| | - Mona Alshahrani
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, 4700 KAUST, Thuwal, 23955–6900 Kingdom of Saudi Arabia
- Computer, Electrical and Mathematical Sciences & Engineering Division (CEMSE), King Abdullah University of Science and Technology, 4700 KAUST, Thuwal, 23955–6900 Kingdom of Saudi Arabia
| | - Georgios V. Gkoutos
- College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences, Centre for Computational Biology, University of Birmingham, Birmingham, B15 2TT United Kingdom
- Institute of Translational Medicine, University Hospitals Birmingham, NHS Foundation Trust, Birmingham, B15 2TT United Kingdom
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 2AX United Kingdom
| | - George Gosline
- Royal Botanical Gardens, Kew, Richmond, Surrey, TW9 3AB United Kingdom
| | - Quentin Groom
- Botanic Garden Meise, Nieuwelaan 38, Meise, 1860 Belgium
| | - Thomas Hamann
- Naturalis Biodiversity Center, P.O. Box 9517, Leiden, 2300 RA The Netherlands
| | - Jens Kattge
- Max Planck Institute for Biogeochemistry, Hans Knoell Str. 10, Jena, 07745 Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, 04103 Germany
| | | | - Marco Schmidt
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, Frankfurt am Main, 60325 Germany
| | - Soraya Sierra
- Naturalis Biodiversity Center, P.O. Box 9517, Leiden, 2300 RA The Netherlands
| | - Erik Smets
- Naturalis Biodiversity Center, P.O. Box 9517, Leiden, 2300 RA The Netherlands
| | - Rutger A. Vos
- Naturalis Biodiversity Center, P.O. Box 9517, Leiden, 2300 RA The Netherlands
| | - Claus Weiland
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, Frankfurt am Main, 60325 Germany
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Pauli D, Chapman SC, Bart R, Topp CN, Lawrence-Dill CJ, Poland J, Gore MA. The Quest for Understanding Phenotypic Variation via Integrated Approaches in the Field Environment. PLANT PHYSIOLOGY 2016; 172:622-634. [PMID: 27482076 PMCID: PMC5047081 DOI: 10.1104/pp.16.00592] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 07/28/2016] [Indexed: 05/18/2023]
Abstract
Field-based, high-throughput phenotyping enables the detailed characterization of plant populations under relevant conditions, providing valuable biological insight into the life history of plants.
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Affiliation(s)
- Duke Pauli
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853 (D.P., M.A.G.);Commonwealth Scientific and Industrial Research Organization Agriculture and Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia, Queensland 4067 Australia (S.C.C.);Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (R.B., C.N.T.);Department of Genetics, Development, and Cell Biology and Department of Agronomy, Iowa State University, Ames, Iowa 50011 (C.J.L.-D.); andWheat Genetics Resource Center, Department of Plant Pathology, and Department of Agronomy, Kansas State University, Manhattan, Kansas 66506 (J.P.)
| | - Scott C Chapman
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853 (D.P., M.A.G.);Commonwealth Scientific and Industrial Research Organization Agriculture and Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia, Queensland 4067 Australia (S.C.C.);Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (R.B., C.N.T.);Department of Genetics, Development, and Cell Biology and Department of Agronomy, Iowa State University, Ames, Iowa 50011 (C.J.L.-D.); andWheat Genetics Resource Center, Department of Plant Pathology, and Department of Agronomy, Kansas State University, Manhattan, Kansas 66506 (J.P.)
| | - Rebecca Bart
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853 (D.P., M.A.G.);Commonwealth Scientific and Industrial Research Organization Agriculture and Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia, Queensland 4067 Australia (S.C.C.);Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (R.B., C.N.T.);Department of Genetics, Development, and Cell Biology and Department of Agronomy, Iowa State University, Ames, Iowa 50011 (C.J.L.-D.); andWheat Genetics Resource Center, Department of Plant Pathology, and Department of Agronomy, Kansas State University, Manhattan, Kansas 66506 (J.P.)
| | - Christopher N Topp
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853 (D.P., M.A.G.);Commonwealth Scientific and Industrial Research Organization Agriculture and Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia, Queensland 4067 Australia (S.C.C.);Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (R.B., C.N.T.);Department of Genetics, Development, and Cell Biology and Department of Agronomy, Iowa State University, Ames, Iowa 50011 (C.J.L.-D.); andWheat Genetics Resource Center, Department of Plant Pathology, and Department of Agronomy, Kansas State University, Manhattan, Kansas 66506 (J.P.)
| | - Carolyn J Lawrence-Dill
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853 (D.P., M.A.G.);Commonwealth Scientific and Industrial Research Organization Agriculture and Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia, Queensland 4067 Australia (S.C.C.);Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (R.B., C.N.T.);Department of Genetics, Development, and Cell Biology and Department of Agronomy, Iowa State University, Ames, Iowa 50011 (C.J.L.-D.); andWheat Genetics Resource Center, Department of Plant Pathology, and Department of Agronomy, Kansas State University, Manhattan, Kansas 66506 (J.P.)
| | - Jesse Poland
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853 (D.P., M.A.G.);Commonwealth Scientific and Industrial Research Organization Agriculture and Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia, Queensland 4067 Australia (S.C.C.);Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (R.B., C.N.T.);Department of Genetics, Development, and Cell Biology and Department of Agronomy, Iowa State University, Ames, Iowa 50011 (C.J.L.-D.); andWheat Genetics Resource Center, Department of Plant Pathology, and Department of Agronomy, Kansas State University, Manhattan, Kansas 66506 (J.P.)
| | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853 (D.P., M.A.G.);Commonwealth Scientific and Industrial Research Organization Agriculture and Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia, Queensland 4067 Australia (S.C.C.);Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (R.B., C.N.T.);Department of Genetics, Development, and Cell Biology and Department of Agronomy, Iowa State University, Ames, Iowa 50011 (C.J.L.-D.); andWheat Genetics Resource Center, Department of Plant Pathology, and Department of Agronomy, Kansas State University, Manhattan, Kansas 66506 (J.P.)
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27
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Thessen AE, Bunker DE, Buttigieg PL, Cooper LD, Dahdul WM, Domisch S, Franz NM, Jaiswal P, Lawrence-Dill CJ, Midford PE, Mungall CJ, Ramírez MJ, Specht CD, Vogt L, Vos RA, Walls RL, White JW, Zhang G, Deans AR, Huala E, Lewis SE, Mabee PM. Emerging semantics to link phenotype and environment. PeerJ 2015; 3:e1470. [PMID: 26713234 PMCID: PMC4690371 DOI: 10.7717/peerj.1470] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 11/12/2015] [Indexed: 11/20/2022] Open
Abstract
Understanding the interplay between environmental conditions and phenotypes is a fundamental goal of biology. Unfortunately, data that include observations on phenotype and environment are highly heterogeneous and thus difficult to find and integrate. One approach that is likely to improve the status quo involves the use of ontologies to standardize and link data about phenotypes and environments. Specifying and linking data through ontologies will allow researchers to increase the scope and flexibility of large-scale analyses aided by modern computing methods. Investments in this area would advance diverse fields such as ecology, phylogenetics, and conservation biology. While several biological ontologies are well-developed, using them to link phenotypes and environments is rare because of gaps in ontological coverage and limits to interoperability among ontologies and disciplines. In this manuscript, we present (1) use cases from diverse disciplines to illustrate questions that could be answered more efficiently using a robust linkage between phenotypes and environments, (2) two proof-of-concept analyses that show the value of linking phenotypes to environments in fishes and amphibians, and (3) two proposed example data models for linking phenotypes and environments using the extensible observation ontology (OBOE) and the Biological Collections Ontology (BCO); these provide a starting point for the development of a data model linking phenotypes and environments.
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Affiliation(s)
- Anne E. Thessen
- Ronin Institute for Independent Scholarship, Monclair, NJ, United States
- The Data Detektiv, Waltham, MA, United States
| | - Daniel E. Bunker
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ, United States
| | - Pier Luigi Buttigieg
- HGF-MPG Group for Deep Sea Ecology and Technology, Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar-und Meeresforschung, Bremerhaven, Germany
| | - Laurel D. Cooper
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Wasila M. Dahdul
- Department of Biology, University of South Dakota, Vermillion, SD, United States
| | - Sami Domisch
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
| | - Nico M. Franz
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Carolyn J. Lawrence-Dill
- Departments of Genetics, Development and Cell Biology and Agronomy, Iowa State University, Ames, IA, United States
| | | | | | - Martín J. Ramírez
- Division of Arachnology, Museo Argentino de Ciencias Naturales–CONICET, Buenos Aires, Argentina
| | - Chelsea D. Specht
- Departments of Plant and Microbial Biology & Integrative Biology, University of California, Berkeley, CA, United States
| | - Lars Vogt
- Institut für Evolutionsbiologie und Ökologie, Universität Bonn, Bonn, Germany
| | | | - Ramona L. Walls
- iPlant Collaborative, University of Arizona, Tucson, AZ, United States
| | - Jeffrey W. White
- US Arid Land Agricultural Research Center, United States Department of Agriculture—ARS, Maricopa, AZ, United States
| | - Guanyang Zhang
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Andrew R. Deans
- Department of Entomology, Pennsylvania State University, University Park, PA, United States
| | - Eva Huala
- Phoenix Bioinformatics, Redwood City, CA, United States
| | - Suzanna E. Lewis
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Paula M. Mabee
- Department of Biology, University of South Dakota, Vermillion, SD, United States
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Andorf CM, Cannon EK, Portwood JL, Gardiner JM, Harper LC, Schaeffer ML, Braun BL, Campbell DA, Vinnakota AG, Sribalusu VV, Huerta M, Cho KT, Wimalanathan K, Richter JD, Mauch ED, Rao BS, Birkett SM, Sen TZ, Lawrence-Dill CJ. MaizeGDB update: new tools, data and interface for the maize model organism database. Nucleic Acids Res 2015; 44:D1195-201. [PMID: 26432828 PMCID: PMC4702771 DOI: 10.1093/nar/gkv1007] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 09/24/2015] [Indexed: 11/24/2022] Open
Abstract
MaizeGDB is a highly curated, community-oriented database and informatics service to researchers focused on the crop plant and model organism Zea mays ssp. mays. Although some form of the maize community database has existed over the last 25 years, there have only been two major releases. In 1991, the original maize genetics database MaizeDB was created. In 2003, the combined contents of MaizeDB and the sequence data from ZmDB were made accessible as a single resource named MaizeGDB. Over the next decade, MaizeGDB became more sequence driven while still maintaining traditional maize genetics datasets. This enabled the project to meet the continued growing and evolving needs of the maize research community, yet the interface and underlying infrastructure remained unchanged. In 2015, the MaizeGDB team completed a multi-year effort to update the MaizeGDB resource by reorganizing existing data, upgrading hardware and infrastructure, creating new tools, incorporating new data types (including diversity data, expression data, gene models, and metabolic pathways), and developing and deploying a modern interface. In addition to coordinating a data resource, the MaizeGDB team coordinates activities and provides technical support to the maize research community. MaizeGDB is accessible online at http://www.maizegdb.org.
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Affiliation(s)
- Carson M Andorf
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011, USA Department of Computer Science, Iowa State University, Ames, IA 50011, USA
| | - Ethalinda K Cannon
- Department of Electrical and Computer Engineering, Iowa State University, Ames, IA 50011, USA
| | - John L Portwood
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011, USA
| | - Jack M Gardiner
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Lisa C Harper
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011, USA
| | - Mary L Schaeffer
- USDA-ARS Plant Genetics Research Unit, University of Missouri, Columbia, MO 65211, USA Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA
| | - Bremen L Braun
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011, USA
| | - Darwin A Campbell
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011, USA Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | | | | | - Miranda Huerta
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - Kyoung Tak Cho
- Department of Computer Science, Iowa State University, Ames, IA 50011, USA
| | - Kokulapalan Wimalanathan
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA Bioinformatics and Computational Biology, Iowa State University, Ames, IA 50011, USA
| | - Jacqueline D Richter
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Emily D Mauch
- Interdepartmental Genetics and Genomics, Iowa State University, Ames, IA 50011, USA
| | - Bhavani S Rao
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Scott M Birkett
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Taner Z Sen
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011, USA Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Carolyn J Lawrence-Dill
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011, USA Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA Department of Agronomy, Iowa State University, Ames, IA 50011, USA
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29
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Großkinsky DK, Svensgaard J, Christensen S, Roitsch T. Plant phenomics and the need for physiological phenotyping across scales to narrow the genotype-to-phenotype knowledge gap. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:5429-40. [PMID: 26163702 DOI: 10.1093/jxb/erv345] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Plants are affected by complex genome×environment×management interactions which determine phenotypic plasticity as a result of the variability of genetic components. Whereas great advances have been made in the cost-efficient and high-throughput analyses of genetic information and non-invasive phenotyping, the large-scale analyses of the underlying physiological mechanisms lag behind. The external phenotype is determined by the sum of the complex interactions of metabolic pathways and intracellular regulatory networks that is reflected in an internal, physiological, and biochemical phenotype. These various scales of dynamic physiological responses need to be considered, and genotyping and external phenotyping should be linked to the physiology at the cellular and tissue level. A high-dimensional physiological phenotyping across scales is needed that integrates the precise characterization of the internal phenotype into high-throughput phenotyping of whole plants and canopies. By this means, complex traits can be broken down into individual components of physiological traits. Since the higher resolution of physiological phenotyping by 'wet chemistry' is inherently limited in throughput, high-throughput non-invasive phenotyping needs to be validated and verified across scales to be used as proxy for the underlying processes. Armed with this interdisciplinary and multidimensional phenomics approach, plant physiology, non-invasive phenotyping, and functional genomics will complement each other, ultimately enabling the in silico assessment of responses under defined environments with advanced crop models. This will allow generation of robust physiological predictors also for complex traits to bridge the knowledge gap between genotype and phenotype for applications in breeding, precision farming, and basic research.
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Affiliation(s)
- Dominik K Großkinsky
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Højbakkegård Allé 13, 2630 Taastrup, Denmark
| | - Jesper Svensgaard
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Højbakkegård Allé 13, 2630 Taastrup, Denmark
| | - Svend Christensen
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Højbakkegård Allé 13, 2630 Taastrup, Denmark
| | - Thomas Roitsch
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Højbakkegård Allé 13, 2630 Taastrup, Denmark Global Change Research Centre, Czech Globe AS CR, v.v.i.., Drásov 470, Cz-664 24 Drásov, Czech Republic
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30
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Krajewski P, Chen D, Ćwiek H, van Dijk ADJ, Fiorani F, Kersey P, Klukas C, Lange M, Markiewicz A, Nap JP, van Oeveren J, Pommier C, Scholz U, van Schriek M, Usadel B, Weise S. Towards recommendations for metadata and data handling in plant phenotyping. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:5417-27. [PMID: 26044092 DOI: 10.1093/jxb/erv271] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Recent methodological developments in plant phenotyping, as well as the growing importance of its applications in plant science and breeding, are resulting in a fast accumulation of multidimensional data. There is great potential for expediting both discovery and application if these data are made publicly available for analysis. However, collection and storage of phenotypic observations is not yet sufficiently governed by standards that would ensure interoperability among data providers and precisely link specific phenotypes and associated genomic sequence information. This lack of standards is mainly a result of a large variability of phenotyping protocols, the multitude of phenotypic traits that are measured, and the dependence of these traits on the environment. This paper discusses the current situation of standardization in the area of phenomics, points out the problems and shortages, and presents the areas that would benefit from improvement in this field. In addition, the foundations of the work that could revise the situation are proposed, and practical solutions developed by the authors are introduced.
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Affiliation(s)
- Paweł Krajewski
- Institute of Plant Genetics, Polish Academy of Sciences, ul. Strzeszyńska 34, Poznań, Poland
| | - Dijun Chen
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, D-06466 Stadt Seeland, Germany
| | - Hanna Ćwiek
- Institute of Plant Genetics, Polish Academy of Sciences, ul. Strzeszyńska 34, Poznań, Poland
| | - Aalt D J van Dijk
- Applied Bioinformatics, Bioscience, Plant Sciences Group, Wageningen University and Research Centre (WUR), Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Fabio Fiorani
- Forschungszentrum Jülich, IBG-2 Plant Sciences, Jülich, Germany
| | - Paul Kersey
- The European Molecular Biology Laboratory-The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Christian Klukas
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, D-06466 Stadt Seeland, Germany
| | - Matthias Lange
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, D-06466 Stadt Seeland, Germany
| | | | - Jan Peter Nap
- Applied Bioinformatics, Bioscience, Plant Sciences Group, Wageningen University and Research Centre (WUR), Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Jan van Oeveren
- Keygene N.V., Agro Business Park 90, 6708 PW Wageningen, The Netherlands
| | | | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, D-06466 Stadt Seeland, Germany
| | - Marco van Schriek
- Keygene N.V., Agro Business Park 90, 6708 PW Wageningen, The Netherlands
| | - Björn Usadel
- Forschungszentrum Jülich, IBG-2 Plant Sciences, Jülich, Germany RWTH Aachen, Worringer Weg 3, Institute of Biology I, Aachen, Germany
| | - Stephan Weise
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, D-06466 Stadt Seeland, Germany
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