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Gao Y, Zhou Q, Luo J, Xia C, Zhang Y, Yue Z. Crop-GPA: an integrated platform of crop gene-phenotype associations. NPJ Syst Biol Appl 2024; 10:15. [PMID: 38346982 PMCID: PMC10861494 DOI: 10.1038/s41540-024-00343-7] [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: 08/11/2023] [Accepted: 01/22/2024] [Indexed: 02/15/2024] Open
Abstract
With the increasing availability of large-scale biology data in crop plants, there is an urgent demand for a versatile platform that fully mines and utilizes the data for modern molecular breeding. We present Crop-GPA ( https://crop-gpa.aielab.net ), a comprehensive and functional open-source platform for crop gene-phenotype association data. The current Crop-GPA provides well-curated information on genes, phenotypes, and their associations (GPAs) to researchers through an intuitive interface, dynamic graphical visualizations, and efficient online tools. Two computational tools, GPA-BERT and GPA-GCN, are specifically developed and integrated into Crop-GPA, facilitating the automatic extraction of gene-phenotype associations from bio-crop literature and predicting unknown relations based on known associations. Through usage examples, we demonstrate how our platform enables the exploration of complex correlations between genes and phenotypes in crop plants. In summary, Crop-GPA serves as a valuable multi-functional resource, empowering the crop research community to gain deeper insights into the biological mechanisms of interest.
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Affiliation(s)
- Yujia Gao
- School of Information and Artificial Intelligence, Anhui Beidou Precision Agriculture Information Engineering Research Center, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Qian Zhou
- School of Information and Artificial Intelligence, Anhui Beidou Precision Agriculture Information Engineering Research Center, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Jiaxin Luo
- School of Information and Artificial Intelligence, Anhui Beidou Precision Agriculture Information Engineering Research Center, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Chuan Xia
- School of Information and Artificial Intelligence, Anhui Beidou Precision Agriculture Information Engineering Research Center, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Youhua Zhang
- School of Information and Artificial Intelligence, Anhui Beidou Precision Agriculture Information Engineering Research Center, Anhui Agricultural University, Hefei, Anhui, 230036, China.
| | - Zhenyu Yue
- School of Information and Artificial Intelligence, Anhui Beidou Precision Agriculture Information Engineering Research Center, Anhui Agricultural University, Hefei, Anhui, 230036, China.
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2
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Dumschott K, Dörpholz H, Laporte MA, Brilhaus D, Schrader A, Usadel B, Neumann S, Arnaud E, Kranz A. Ontologies for increasing the FAIRness of plant research data. FRONTIERS IN PLANT SCIENCE 2023; 14:1279694. [PMID: 38098789 PMCID: PMC10720748 DOI: 10.3389/fpls.2023.1279694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 11/15/2023] [Indexed: 12/17/2023]
Abstract
The importance of improving the FAIRness (findability, accessibility, interoperability, reusability) of research data is undeniable, especially in the face of large, complex datasets currently being produced by omics technologies. Facilitating the integration of a dataset with other types of data increases the likelihood of reuse, and the potential of answering novel research questions. Ontologies are a useful tool for semantically tagging datasets as adding relevant metadata increases the understanding of how data was produced and increases its interoperability. Ontologies provide concepts for a particular domain as well as the relationships between concepts. By tagging data with ontology terms, data becomes both human- and machine- interpretable, allowing for increased reuse and interoperability. However, the task of identifying ontologies relevant to a particular research domain or technology is challenging, especially within the diverse realm of fundamental plant research. In this review, we outline the ontologies most relevant to the fundamental plant sciences and how they can be used to annotate data related to plant-specific experiments within metadata frameworks, such as Investigation-Study-Assay (ISA). We also outline repositories and platforms most useful for identifying applicable ontologies or finding ontology terms.
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Affiliation(s)
- Kathryn Dumschott
- Institute of Bio- and Geosciences (IBG-4: Bioinformatics) & Bioeconomy Science Center (BioSC), CEPLAS, Forschungszentrum Jülich, Jülich, Germany
| | - Hannah Dörpholz
- Institute of Bio- and Geosciences (IBG-4: Bioinformatics) & Bioeconomy Science Center (BioSC), CEPLAS, Forschungszentrum Jülich, Jülich, Germany
| | - Marie-Angélique Laporte
- Digital Solutions Team, Digital Inclusion Lever, Bioversity International, Montpellier Office, Montpellier, France
| | - Dominik Brilhaus
- Data Science and Management & Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Andrea Schrader
- Data Science and Management & Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Björn Usadel
- Institute of Bio- and Geosciences (IBG-4: Bioinformatics) & Bioeconomy Science Center (BioSC), CEPLAS, Forschungszentrum Jülich, Jülich, Germany
- Institute for Biological Data Science & Cluster of Excellence on Plant Sciences (CEPLAS), Faculty of Mathematics and Life Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Steffen Neumann
- Program Center MetaCom, Leibniz Institute of Plant Biochemistry, Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Germany
| | - Elizabeth Arnaud
- Digital Solutions Team, Digital Inclusion Lever, Bioversity International, Montpellier Office, Montpellier, France
| | - Angela Kranz
- Institute of Bio- and Geosciences (IBG-4: Bioinformatics) & Bioeconomy Science Center (BioSC), CEPLAS, Forschungszentrum Jülich, Jülich, Germany
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3
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Li Z, Zhang Y, Ding CH, Chen Y, Wang H, Zhang J, Ying S, Wang M, Zhang R, Liu J, Xie Y, Tang T, Diao H, Ye L, Zhuang Y, Teng W, Zhang B, Huang L, Tong Y, Zhang W, Li G, Benhamed M, Dong Z, Gou JY, Zhang Y. LHP1-mediated epigenetic buffering of subgenome diversity and defense responses confers genome plasticity and adaptability in allopolyploid wheat. Nat Commun 2023; 14:7538. [PMID: 37985755 PMCID: PMC10661560 DOI: 10.1038/s41467-023-43178-2] [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: 03/30/2023] [Accepted: 10/25/2023] [Indexed: 11/22/2023] Open
Abstract
Polyploidization is a major driver of genome diversification and environmental adaptation. However, the merger of different genomes may result in genomic conflicts, raising a major question regarding how genetic diversity is interpreted and regulated to enable environmental plasticity. By analyzing the genome-wide binding of 191 trans-factors in allopolyploid wheat, we identified like heterochromatin protein 1 (LHP1) as a master regulator of subgenome-diversified genes. Transcriptomic and epigenomic analyses of LHP1 mutants reveal its role in buffering the expression of subgenome-diversified defense genes by controlling H3K27me3 homeostasis. Stripe rust infection releases latent subgenomic variations by eliminating H3K27me3-related repression. The simultaneous inactivation of LHP1 homoeologs by CRISPR-Cas9 confers robust stripe rust resistance in wheat seedlings. The conditional repression of subgenome-diversified defenses ensures developmental plasticity to external changes, while also promoting neutral-to-non-neutral selection transitions and adaptive evolution. These findings establish an LHP1-mediated buffering system at the intersection of genotypes, environments, and phenotypes in polyploid wheat. Manipulating the epigenetic buffering capacity offers a tool to harness cryptic subgenomic variations for crop improvement.
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Affiliation(s)
- Zijuan Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, 200032, Shanghai, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Yuyun Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, 200032, Shanghai, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Ci-Hang Ding
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, China
| | - Yan Chen
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, 510006, Guangzhou, China
| | - Haoyu Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, 200032, Shanghai, China
- Henan University, School of Life Science, 457000, Kaifeng, Henan, China
| | - Jinyu Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, 200032, Shanghai, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Songbei Ying
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Meiyue Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Rongzhi Zhang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
- Ministry of Agriculture, Key Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River Valley, Jinan, China
- National Engineering Research Center for Wheat and Maize, Jinan, Shandong, China
| | - Jinyi Liu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, 200032, Shanghai, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Yilin Xie
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, 200032, Shanghai, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Tengfei Tang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, 200032, Shanghai, China
- Henan University, School of Life Science, 457000, Kaifeng, Henan, China
| | - Huishan Diao
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Luhuan Ye
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, 200032, Shanghai, China
| | - Yili Zhuang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, 200032, Shanghai, China
| | - Wan Teng
- University of the Chinese Academy of Sciences, 100049, Beijing, China
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, 100101, Beijing, China
| | - Bo Zhang
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 810008, Xining, China
| | - Lin Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, 611130, Wenjiang, Chengdu, China
| | - Yiping Tong
- University of the Chinese Academy of Sciences, 100049, Beijing, China
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, 100101, Beijing, China
| | - Wenli Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No.1 Weigang, 210095, Nanjing, Jiangsu, China
| | - Genying Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
- Ministry of Agriculture, Key Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River Valley, Jinan, China
- National Engineering Research Center for Wheat and Maize, Jinan, Shandong, China
| | - Moussa Benhamed
- Université Paris Cité, Institute of Plant Sciences Paris-Saclay (IPS2), F-75006, Paris, France.
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France.
| | - Zhicheng Dong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, 510006, Guangzhou, China.
| | - Jin-Ying Gou
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, China.
| | - Yijing Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China.
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4
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Darwish E, Ghosh R, Bentzer J, Tsardakas Renhuldt N, Proux-Wera E, Kamal N, Spannagl M, Hause B, Sirijovski N, Van Aken O. The dynamics of touch-responsive gene expression in cereals. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:282-302. [PMID: 37159480 DOI: 10.1111/tpj.16269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 04/24/2023] [Accepted: 04/29/2023] [Indexed: 05/11/2023]
Abstract
Wind, rain, herbivores, obstacles, neighbouring plants, etc. provide important mechanical cues to steer plant growth and survival. Mechanostimulation to stimulate yield and stress resistance of crops is of significant research interest, yet a molecular understanding of transcriptional responses to touch is largely absent in cereals. To address this, we performed whole-genome transcriptomics following mechanostimulation of wheat, barley, and the recent genome-sequenced oat. The largest transcriptome changes occurred ±25 min after touching, with most of the genes being upregulated. While most genes returned to basal expression level by 1-2 h in oat, many genes retained high expression even 4 h post-treatment in barley and wheat. Functional categories such as transcription factors, kinases, phytohormones, and Ca2+ regulation were affected. In addition, cell wall-related genes involved in (hemi)cellulose, lignin, suberin, and callose biosynthesis were touch-responsive, providing molecular insight into mechanically induced changes in cell wall composition. Furthermore, several cereal-specific transcriptomic footprints were identified that were not observed in Arabidopsis. In oat and barley, we found evidence for systemic spreading of touch-induced signalling. Finally, we provide evidence that both the jasmonic acid-dependent and the jasmonic acid-independent pathways underlie touch-signalling in cereals, providing a detailed framework and marker genes for further study of (a)biotic stress responses in cereals.
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Affiliation(s)
- Essam Darwish
- Department of Biology, Lund University, Sölvegatan 35, 223 62, Lund, Sweden
- Plant Physiology Section, Agricultural Botany Department, Faculty of Agriculture, Cairo University, Cairo, Egypt
| | - Ritesh Ghosh
- Department of Biology, Lund University, Sölvegatan 35, 223 62, Lund, Sweden
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Johan Bentzer
- ScanOats Industrial Research Centre, Department of Chemistry, Division of Pure and Applied Biochemistry, Lund University, Lund, Sweden
| | - Nikos Tsardakas Renhuldt
- ScanOats Industrial Research Centre, Department of Chemistry, Division of Pure and Applied Biochemistry, Lund University, Lund, Sweden
| | - Estelle Proux-Wera
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Box 1031, SE-17121, Solna, Sweden
| | - Nadia Kamal
- PGSB - Plant Genome and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Manuel Spannagl
- PGSB - Plant Genome and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Bettina Hause
- Leibniz Institute of Plant Biochemistry, Weinberg 3, D06120, Halle, Germany
| | - Nick Sirijovski
- ScanOats Industrial Research Centre, Department of Chemistry, Division of Pure and Applied Biochemistry, Lund University, Lund, Sweden
| | - Olivier Van Aken
- Department of Biology, Lund University, Sölvegatan 35, 223 62, Lund, Sweden
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5
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Acién JM, Cañizares E, Candela H, González-Guzmán M, Arbona V. From Classical to Modern Computational Approaches to Identify Key Genetic Regulatory Components in Plant Biology. Int J Mol Sci 2023; 24:ijms24032526. [PMID: 36768850 PMCID: PMC9916757 DOI: 10.3390/ijms24032526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/19/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023] Open
Abstract
The selection of plant genotypes with improved productivity and tolerance to environmental constraints has always been a major concern in plant breeding. Classical approaches based on the generation of variability and selection of better phenotypes from large variant collections have improved their efficacy and processivity due to the implementation of molecular biology techniques, particularly genomics, Next Generation Sequencing and other omics such as proteomics and metabolomics. In this regard, the identification of interesting variants before they develop the phenotype trait of interest with molecular markers has advanced the breeding process of new varieties. Moreover, the correlation of phenotype or biochemical traits with gene expression or protein abundance has boosted the identification of potential new regulators of the traits of interest, using a relatively low number of variants. These important breakthrough technologies, built on top of classical approaches, will be improved in the future by including the spatial variable, allowing the identification of gene(s) involved in key processes at the tissue and cell levels.
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Affiliation(s)
- Juan Manuel Acién
- Departament de Biologia, Bioquímica i Ciències Naturals, Universitat Jaume I, 12071 Castelló de la Plana, Spain
| | - Eva Cañizares
- Departament de Biologia, Bioquímica i Ciències Naturals, Universitat Jaume I, 12071 Castelló de la Plana, Spain
| | - Héctor Candela
- Instituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Spain
| | - Miguel González-Guzmán
- Departament de Biologia, Bioquímica i Ciències Naturals, Universitat Jaume I, 12071 Castelló de la Plana, Spain
- Correspondence: (M.G.-G.); (V.A.); Tel.: +34-964-72-9415 (M.G.-G.); +34-964-72-9401 (V.A.)
| | - Vicent Arbona
- Departament de Biologia, Bioquímica i Ciències Naturals, Universitat Jaume I, 12071 Castelló de la Plana, Spain
- Correspondence: (M.G.-G.); (V.A.); Tel.: +34-964-72-9415 (M.G.-G.); +34-964-72-9401 (V.A.)
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6
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Schulthess AW, Kale SM, Zhao Y, Gogna A, Rembe M, Philipp N, Liu F, Beukert U, Serfling A, Himmelbach A, Oppermann M, Weise S, Boeven PHG, Schacht J, Longin CFH, Kollers S, Pfeiffer N, Korzun V, Fiebig A, Schüler D, Lange M, Scholz U, Stein N, Mascher M, Reif JC. Large-scale genotyping and phenotyping of a worldwide winter wheat genebank for its use in pre-breeding. Sci Data 2022; 9:784. [PMID: 36572688 PMCID: PMC9792552 DOI: 10.1038/s41597-022-01891-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 12/07/2022] [Indexed: 12/27/2022] Open
Abstract
Plant genetic resources (PGR) stored at genebanks are humanity's crop diversity savings for the future. Information on PGR contrasted with modern cultivars is key to select PGR parents for pre-breeding. Genotyping-by-sequencing was performed for 7,745 winter wheat PGR samples from the German Federal ex situ genebank at IPK Gatersleben and for 325 modern cultivars. Whole-genome shotgun sequencing was carried out for 446 diverse PGR samples and 322 modern cultivars and lines. In 19 field trials, 7,683 PGR and 232 elite cultivars were characterized for resistance to yellow rust - one of the major threats to wheat worldwide. Yield breeding values of 707 PGR were estimated using hybrid crosses with 36 cultivars - an approach that reduces the lack of agronomic adaptation of PGR and provides better estimates of their contribution to yield breeding. Cross-validations support the interoperability between genomic and phenotypic data. The here presented data are a stepping stone to unlock the functional variation of PGR for European pre-breeding and are the basis for future breeding and research activities.
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Affiliation(s)
- Albert W. Schulthess
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Sandip M. Kale
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany ,grid.418674.80000 0004 0533 4528Present Address: Carlsberg Research Laboratory, Copenhagen, Denmark
| | - Yusheng Zhao
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Abhishek Gogna
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Maximilian Rembe
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Norman Philipp
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Fang Liu
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany ,grid.9227.e0000000119573309Present Address: Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Ulrike Beukert
- grid.13946.390000 0001 1089 3517Julius Kühn Institute (Federal Research Centre for Cultivated Plants), Quedlinburg, Germany
| | - Albrecht Serfling
- grid.13946.390000 0001 1089 3517Julius Kühn Institute (Federal Research Centre for Cultivated Plants), Quedlinburg, Germany
| | - Axel Himmelbach
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Markus Oppermann
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Stephan Weise
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | | | | | - C. Friedrich H. Longin
- grid.9464.f0000 0001 2290 1502State Plant Breeding Institute, University of Hohenheim, Stuttgart, Germany
| | - Sonja Kollers
- grid.425691.dKWS SAAT SE & Co. KGaA, Einbeck, Germany
| | | | - Viktor Korzun
- grid.425691.dKWS SAAT SE & Co. KGaA, Einbeck, Germany
| | - Anne Fiebig
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Danuta Schüler
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Matthias Lange
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Uwe Scholz
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Nils Stein
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany ,grid.7450.60000 0001 2364 4210Center for Integrated Breeding Research (CiBreed), Georg-August-University, Göttingen, Germany
| | - Martin Mascher
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany ,grid.421064.50000 0004 7470 3956German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Jochen C. Reif
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
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7
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Feser M, König P, Fiebig A, Arend D, Lange M, Scholz U. On the way to plant data commons - a genotyping use case. J Integr Bioinform 2022; 19:jib-2022-0033. [PMID: 36065132 PMCID: PMC9800039 DOI: 10.1515/jib-2022-0033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/04/2022] [Accepted: 08/11/2022] [Indexed: 01/09/2023] Open
Abstract
Over the last years it has been observed that the progress in data collection in life science has created increasing demand and opportunities for advanced bioinformatics. This includes data management as well as the individual data analysis and often covers the entire data life cycle. A variety of tools have been developed to store, share, or reuse the data produced in the different domains such as genotyping. Especially imputation, as a subfield of genotyping, requires good Research Data Management (RDM) strategies to enable use and re-use of genotypic data. To aim for sustainable software, it is necessary to develop tools and surrounding ecosystems, which are reusable and maintainable. Reusability in the context of streamlined tools can e.g. be achieved by standardizing the input and output of the different tools and adapting to open and broadly used file formats. By using such established file formats, the tools can also be connected with others, improving the overall interoperability of the software. Finally, it is important to build strong communities that maintain the tools by developing and contributing new features and maintenance updates. In this article, concepts for this will be presented for an imputation service.
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Affiliation(s)
- Manuel Feser
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466Seeland, Germany
| | - Patrick König
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466Seeland, Germany
| | - Anne Fiebig
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466Seeland, Germany
| | - Daniel Arend
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466Seeland, Germany
| | - Matthias Lange
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466Seeland, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466Seeland, Germany
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Zheng S, Szymański J, Shahaf N, Malitsky S, Meir S, Wang X, Aharoni A, Rogachev I. Metabolic diversity in a collection of wild and cultivated Brassica rapa subspecies. Front Mol Biosci 2022; 9:953189. [DOI: 10.3389/fmolb.2022.953189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/29/2022] [Indexed: 11/18/2022] Open
Abstract
Brassica rapa (B. rapa) and its subspecies contain many bioactive metabolites that are important for plant defense and human health. This study aimed at investigating the metabolite composition and variation among a large collection of B. rapa genotypes, including subspecies and their accessions. Metabolite profiling of leaves of 102 B. rapa genotypes was performed using ultra-performance liquid chromatography coupled with a photodiode array detector and quadrupole time-of-flight mass spectrometry (UPLC-PDA-QTOF-MS/MS). In total, 346 metabolites belonging to different chemical classes were tentatively identified; 36 out of them were assigned with high confidence using authentic standards and 184 were those reported in B. rapa leaves for the first time. The accumulation and variation of metabolites among genotypes were characterized and compared to their phylogenetic distance. We found 47 metabolites, mostly representing anthocyanins, flavonols, and hydroxycinnamic acid derivatives that displayed a significant correlation to the phylogenetic relatedness and determined four major phylometabolic branches; 1) Chinese cabbage, 2) yellow sarson and rapid cycling, 3) the mizuna-komatsuna-turnip-caitai; and 4) a mixed cluster. These metabolites denote the selective pressure on the metabolic network during B. rapa breeding. We present a unique study that combines metabolite profiling data with phylogenetic analysis in a large collection of B. rapa subspecies. We showed how selective breeding utilizes the biochemical potential of wild B. rapa leading to highly diverse metabolic phenotypes. Our work provides the basis for further studies on B. rapa metabolism and nutritional traits improvement.
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9
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pISA-tree - a data management framework for life science research projects using a standardised directory tree. Sci Data 2022; 9:685. [DOI: 10.1038/s41597-022-01805-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 10/24/2022] [Indexed: 11/12/2022] Open
Abstract
AbstractWe developed pISA-tree, a straightforward and flexible data management solution for organisation of life science project-associated research data and metadata. pISA-tree was initiated by end-user requirements thus its strong points are practicality and low maintenance cost. It enables on-the-fly creation of enriched directory tree structure (project/Investigation/Study/Assay) based on the ISA model, in a standardised manner via consecutive batch files. Templates-based metadata is generated in parallel at each level enabling guided submission of experiment metadata. pISA-tree is complemented by two R packages, pisar and seekr. pisar facilitates integration of pISA-tree datasets into bioinformatic pipelines and generation of ISA-Tab exports. seekr enables synchronisation with the FAIRDOMHub repository. Applicability of pISA-tree was demonstrated in several national and international multi-partner projects. The system thus supports findable, accessible, interoperable and reusable (FAIR) research and is in accordance with the Open Science initiative. Source code and documentation of pISA-tree are available at https://github.com/NIB-SI/pISA-tree.
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10
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Genomics-informed prebreeding unlocks the diversity in genebanks for wheat improvement. Nat Genet 2022; 54:1544-1552. [DOI: 10.1038/s41588-022-01189-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 08/18/2022] [Indexed: 11/06/2022]
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11
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Kale SM, Schulthess AW, Padmarasu S, Boeven PHG, Schacht J, Himmelbach A, Steuernagel B, Wulff BBH, Reif JC, Stein N, Mascher M. A catalogue of resistance gene homologs and a chromosome-scale reference sequence support resistance gene mapping in winter wheat. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1730-1742. [PMID: 35562859 PMCID: PMC9398310 DOI: 10.1111/pbi.13843] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/06/2022] [Accepted: 04/23/2022] [Indexed: 06/15/2023]
Abstract
A resistance gene atlas is an integral component of the breeder's arsenal in the fight against evolving pathogens. Thanks to high-throughput sequencing, catalogues of resistance genes can be assembled even in crop species with large and polyploid genomes. Here, we report on capture sequencing and assembly of resistance gene homologs in a diversity panel of 907 winter wheat genotypes comprising ex situ genebank accessions and current elite cultivars. In addition, we use accurate long-read sequencing and chromosome conformation capture sequencing to construct a chromosome-scale genome sequence assembly of cv. Attraktion, an elite variety representative of European winter wheat. We illustrate the value of our resource for breeders and geneticists by (i) comparing the resistance gene complements in plant genetic resources and elite varieties and (ii) conducting genome-wide associations scans (GWAS) for the fungal diseases yellow rust and leaf rust using reference-based and reference-free GWAS approaches. The gene content under GWAS peaks was scrutinized in the assembly of cv. Attraktion.
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Affiliation(s)
- Sandip M. Kale
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
| | - Albert W. Schulthess
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
| | - Sudharsan Padmarasu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
| | | | | | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
| | | | - Brande B. H. Wulff
- John Innes CentreNorwich Research ParkNorwichUK
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - Jochen C. Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
- Center for Integrated Breeding Research (CiBreed)Georg‐August‐University GöttingenGöttingenGermany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
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12
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Li X, Xu X, Chen M, Xu M, Wang W, Liu C, Yu L, Liu W, Yang W. The field phenotyping platform's next darling: Dicotyledons. FRONTIERS IN PLANT SCIENCE 2022; 13:935748. [PMID: 36092402 PMCID: PMC9449727 DOI: 10.3389/fpls.2022.935748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
The genetic information and functional properties of plants have been further identified with the completion of the whole-genome sequencing of numerous crop species and the rapid development of high-throughput phenotyping technologies, laying a suitable foundation for advanced precision agriculture and enhanced genetic gains. Collecting phenotypic data from dicotyledonous crops in the field has been identified as a key factor in the collection of large-scale phenotypic data of crops. On the one hand, dicotyledonous plants account for 4/5 of all angiosperm species and play a critical role in agriculture. However, their morphology is complex, and an abundance of dicot phenotypic information is available, which is critical for the analysis of high-throughput phenotypic data in the field. As a result, the focus of this paper is on the major advancements in ground-based, air-based, and space-based field phenotyping platforms over the last few decades and the research progress in the high-throughput phenotyping of dicotyledonous field crop plants in terms of morphological indicators, physiological and biochemical indicators, biotic/abiotic stress indicators, and yield indicators. Finally, the future development of dicots in the field is explored from the perspectives of identifying new unified phenotypic criteria, developing a high-performance infrastructure platform, creating a phenotypic big data knowledge map, and merging the data with those of multiomic techniques.
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Affiliation(s)
- Xiuni Li
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Chengdu, China
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest, Ministry of Agriculture, Chengdu, China
| | - Xiangyao Xu
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Chengdu, China
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest, Ministry of Agriculture, Chengdu, China
| | - Menggen Chen
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Chengdu, China
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest, Ministry of Agriculture, Chengdu, China
| | - Mei Xu
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Chengdu, China
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest, Ministry of Agriculture, Chengdu, China
| | - Wenyan Wang
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Chengdu, China
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest, Ministry of Agriculture, Chengdu, China
| | - Chunyan Liu
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Chengdu, China
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest, Ministry of Agriculture, Chengdu, China
| | - Liang Yu
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Chengdu, China
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest, Ministry of Agriculture, Chengdu, China
| | - Weiguo Liu
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Chengdu, China
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest, Ministry of Agriculture, Chengdu, China
| | - Wenyu Yang
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Chengdu, China
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest, Ministry of Agriculture, Chengdu, China
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13
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Guo Y, Himmelbach A, Weiss E, Stein N, Mascher M. Six-rowed wild-growing barleys are hybrids of diverse origins. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:849-858. [PMID: 35678640 DOI: 10.1111/tpj.15861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/25/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Crop-wild gene flow is common when domesticated plants and their wild relatives grow close to each other. The resultant hybrid forms appear as semi-domesticates and were sometimes considered as missing links between crops and their wild progenitors. Wild-growing barleys in Central and Eastern Asia, named Hordeum agriocrithon, show hallmark characters of both wild and domesticated forms. Their spikes disintegrate at maturity to disperse without human intervention, but bear lateral grains, which were favored by early farmers and are absent from other wild barleys. As an intermediate form, H. agriocrithon has been proposed several times as a progenitor of domesticated barley. Here, we used genome-wide marker data and whole-genome resequencing to show that all H. agriocrithon accessions of a major germplasm collection are hybrid forms that arose multiple times by admixture of diverse domesticated and wild populations. Although H. agriocrithon barleys have not played a special role in barley domestication, future analysis of the adaptative potential of bi-directional crop-wild gene flow in extant barleys may prove a fertile research field.
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Affiliation(s)
- Yu Guo
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Ehud Weiss
- The Martin (Szusz) Department of Land of Israel Studies and Archaeology, Bar-Ilan University, Ramat-Gan, Israel
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
- Center for Integrated Breeding Research (CiBreed), Georg-August-University Göttingen, Göttingen, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
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14
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Navrátilová P, Toegelová H, Tulpová Z, Kuo Y, Stein N, Doležel J, Houben A, Šimková H, Mascher M. Prospects of telomere-to-telomere assembly in barley: Analysis of sequence gaps in the MorexV3 reference genome. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1373-1386. [PMID: 35338551 PMCID: PMC9241371 DOI: 10.1111/pbi.13816] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 02/11/2022] [Accepted: 03/20/2022] [Indexed: 05/06/2023]
Abstract
The first gapless, telomere-to-telomere (T2T) sequence assemblies of plant chromosomes were reported recently. However, sequence assemblies of most plant genomes remain fragmented. Only recent breakthroughs in accurate long-read sequencing have made it possible to achieve highly contiguous sequence assemblies with a few tens of contigs per chromosome, that is a number small enough to allow for a systematic inquiry into the causes of the remaining sequence gaps and the approaches and resources needed to close them. Here, we analyse sequence gaps in the current reference genome sequence of barley cv. Morex (MorexV3). Optical map and sequence raw data, complemented by ChIP-seq data for centromeric histone variant CENH3, were used to estimate the abundance of centromeric, ribosomal DNA, and subtelomeric repeats in the barley genome. These estimates were compared with copy numbers in the MorexV3 pseudomolecule sequence. We found that almost all centromeric sequences and 45S ribosomal DNA repeat arrays were absent from the MorexV3 pseudomolecules and that the majority of sequence gaps can be attributed to assembly breakdown in long stretches of satellite repeats. However, missing sequences cannot fully account for the difference between assembly size and flow cytometric genome size estimates. We discuss the prospects of gap closure with ultra-long sequence reads.
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Affiliation(s)
- Pavla Navrátilová
- Institute of Experimental Botany of the Czech Academy of SciencesOlomoucCzech Republic
| | - Helena Toegelová
- Institute of Experimental Botany of the Czech Academy of SciencesOlomoucCzech Republic
| | - Zuzana Tulpová
- Institute of Experimental Botany of the Czech Academy of SciencesOlomoucCzech Republic
| | - Yi‐Tzu Kuo
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
- Center for Integrated Breeding Research (CiBreed)Georg‐August‐University GöttingenGöttingenGermany
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of SciencesOlomoucCzech Republic
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
| | - Hana Šimková
- Institute of Experimental Botany of the Czech Academy of SciencesOlomoucCzech Republic
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
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15
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Arend D, Psaroudakis D, Memon JA, Rey-Mazón E, Schüler D, Szymanski JJ, Scholz U, Junker A, Lange M. From data to knowledge - big data needs stewardship, a plant phenomics perspective. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:335-347. [PMID: 35535481 DOI: 10.1111/tpj.15804] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 05/02/2022] [Accepted: 05/06/2022] [Indexed: 06/14/2023]
Abstract
The research data life cycle from project planning to data publishing is an integral part of current research. Until the last decade, researchers were responsible for all associated phases in addition to the actual research and were assisted only at certain points by IT or bioinformaticians. Starting with advances in sequencing, the automation of analytical methods in all life science fields, including in plant phenotyping, has led to ever-increasing amounts of ever more complex data. The tasks associated with these challenges now often exceed the expertise of and infrastructure available to scientists, leading to an increased risk of data loss over time. The IPK Gatersleben has one of the world's largest germplasm collections and two decades of experience in crop plant research data management. In this article we show how challenges in modern, data-driven research can be addressed by data stewards. Based on concrete use cases, data management processes and best practices from plant phenotyping, we describe which expertise and skills are required and how data stewards as an integral actor can enhance the quality of a necessary digital transformation in progressive research.
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Affiliation(s)
- Daniel Arend
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, D-06466 Seeland, OT Gatersleben, Germany
| | - Dennis Psaroudakis
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, D-06466 Seeland, OT Gatersleben, Germany
| | - Junaid Altaf Memon
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, D-06466 Seeland, OT Gatersleben, Germany
| | - Elena Rey-Mazón
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, D-06466 Seeland, OT Gatersleben, Germany
| | - Danuta Schüler
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, D-06466 Seeland, OT Gatersleben, Germany
| | - Jedrzej Jakub Szymanski
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, D-06466 Seeland, OT Gatersleben, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, D-06466 Seeland, OT Gatersleben, Germany
| | - Astrid Junker
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, D-06466 Seeland, OT Gatersleben, Germany
| | - Matthias Lange
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, D-06466 Seeland, OT Gatersleben, Germany
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16
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Langstroff A, Heuermann MC, Stahl A, Junker A. Opportunities and limits of controlled-environment plant phenotyping for climate response traits. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1-16. [PMID: 34302493 PMCID: PMC8741719 DOI: 10.1007/s00122-021-03892-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 06/17/2021] [Indexed: 05/19/2023]
Abstract
Rising temperatures and changing precipitation patterns will affect agricultural production substantially, exposing crops to extended and more intense periods of stress. Therefore, breeding of varieties adapted to the constantly changing conditions is pivotal to enable a quantitatively and qualitatively adequate crop production despite the negative effects of climate change. As it is not yet possible to select for adaptation to future climate scenarios in the field, simulations of future conditions in controlled-environment (CE) phenotyping facilities contribute to the understanding of the plant response to special stress conditions and help breeders to select ideal genotypes which cope with future conditions. CE phenotyping facilities enable the collection of traits that are not easy to measure under field conditions and the assessment of a plant's phenotype under repeatable, clearly defined environmental conditions using automated, non-invasive, high-throughput methods. However, extrapolation and translation of results obtained under controlled environments to field environments is ambiguous. This review outlines the opportunities and challenges of phenotyping approaches under controlled environments complementary to conventional field trials. It gives an overview on general principles and introduces existing phenotyping facilities that take up the challenge of obtaining reliable and robust phenotypic data on climate response traits to support breeding of climate-adapted crops.
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Affiliation(s)
- Anna Langstroff
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Heinrich Buff-Ring 26, 35392, Giessen, Germany
| | - Marc C Heuermann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, OT Gatersleben, 06466, Seeland, Germany
| | - Andreas Stahl
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Heinrich Buff-Ring 26, 35392, Giessen, Germany
- Institute for Resistance Research and Stress Tolerance, Federal Research Centre for Cultivated Plants, Julius Kühn-Institut (JKI), Erwin-Baur-Strasse 27, 06484, Quedlinburg, Germany
| | - Astrid Junker
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, OT Gatersleben, 06466, Seeland, Germany.
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17
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Lange M, Alako BTF, Cochrane G, Ghaffar M, Mascher M, Habekost PK, Hillebrand U, Scholz U, Schorch F, Freitag J, Scholz AH. Quantitative monitoring of nucleotide sequence data from genetic resources in context of their citation in the scientific literature. Gigascience 2021; 10:giab084. [PMID: 34966925 PMCID: PMC8716361 DOI: 10.1093/gigascience/giab084] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 08/04/2021] [Accepted: 11/29/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Linking nucleotide sequence data (NSD) to scientific publication citations can enhance understanding of NSD provenance, scientific use, and reuse in the community. By connecting publications with NSD records, NSD geographical provenance information, and author geographical information, it becomes possible to assess the contribution of NSD to infer trends in scientific knowledge gain at the global level. FINDINGS We extracted and linked records from the European Nucleotide Archive to citations in open-access publications aggregated at Europe PubMed Central. A total of 8,464,292 ENA accessions with geographical provenance information were associated with publications. We conducted a data quality review to uncover potential issues in publication citation information extraction and author affiliation tagging and developed and implemented best-practice recommendations for citation extraction. We constructed flat data tables and a data warehouse with an interactive web application to enable ad hoc exploration of NSD use and summary statistics. CONCLUSIONS The extraction and linking of NSD with associated publication citations enables transparency. The quality review contributes to enhanced text mining methods for identifier extraction and use. Furthermore, the global provision and use of NSD enable scientists worldwide to join literature and sequence databases in a multidimensional fashion. As a concrete use case, we visualized statistics of country clusters concerning NSD access in the context of discussions around digital sequence information under the United Nations Convention on Biological Diversity.
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Affiliation(s)
- Matthias Lange
- Leibniz Institute of Plant Genetics and Crop Plant Research, Department Breeding Research, OT Gatersleben, Corrensstrasse 3, 06466 Seeland, Germany
| | - Blaise T F Alako
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Mehmood Ghaffar
- Leibniz Institute of Plant Genetics and Crop Plant Research, Department Breeding Research, OT Gatersleben, Corrensstrasse 3, 06466 Seeland, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research, Department Breeding Research, OT Gatersleben, Corrensstrasse 3, 06466 Seeland, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
| | - Pia-Katharina Habekost
- Leibniz Institute of Plant Genetics and Crop Plant Research, Department Breeding Research, OT Gatersleben, Corrensstrasse 3, 06466 Seeland, Germany
- The Harz University of Applied Science, Department of Automation and Computer Science, Friedrichstraße 57, 38855 Wernigerode, Germany
| | - Upneet Hillebrand
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Department Research - Microbial Ecology and Diversity, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research, Department Breeding Research, OT Gatersleben, Corrensstrasse 3, 06466 Seeland, Germany
| | - Florian Schorch
- Leibniz Institute of Plant Genetics and Crop Plant Research, Department Breeding Research, OT Gatersleben, Corrensstrasse 3, 06466 Seeland, Germany
- The Harz University of Applied Science, Department of Automation and Computer Science, Friedrichstraße 57, 38855 Wernigerode, Germany
| | - Jens Freitag
- Leibniz Institute of Plant Genetics and Crop Plant Research, Department Breeding Research, OT Gatersleben, Corrensstrasse 3, 06466 Seeland, Germany
| | - Amber Hartman Scholz
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Department Research - Microbial Ecology and Diversity, Inhoffenstraße 7B, 38124 Braunschweig, Germany
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18
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Zhang Y, Li Z, Zhang Y, Lin K, Peng Y, Ye L, Zhuang Y, Wang M, Xie Y, Guo J, Teng W, Tong Y, Zhang W, Xue Y, Lang Z, Zhang Y. Evolutionary rewiring of the wheat transcriptional regulatory network by lineage-specific transposable elements. Genome Res 2021; 31:2276-2289. [PMID: 34503979 PMCID: PMC8647832 DOI: 10.1101/gr.275658.121] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 09/01/2021] [Indexed: 01/03/2023]
Abstract
More than 80% of the wheat genome consists of transposable elements (TEs), which act as major drivers of wheat genome evolution. However, their contributions to the regulatory evolution of wheat adaptations remain largely unclear. Here, we created genome-binding maps for 53 transcription factors (TFs) underlying environmental responses by leveraging DAP-seq in Triticum urartu, together with epigenomic profiles. Most TF binding sites (TFBSs) located distally from genes are embedded in TEs, whose functional relevance is supported by purifying selection and active epigenomic features. About 24% of the non-TE TFBSs share significantly high sequence similarity with TE-embedded TFBSs. These non-TE TFBSs have almost no homologous sequences in non-Triticeae species and are potentially derived from Triticeae-specific TEs. The expansion of TE-derived TFBS linked to wheat-specific gene responses, suggesting TEs are an important driving force for regulatory innovations. Altogether, TEs have been significantly and continuously shaping regulatory networks related to wheat genome evolution and adaptation.
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Affiliation(s)
- Yuyun Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Zijuan Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu'e Zhang
- University of the Chinese Academy of Sciences, Beijing, 100049, China
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Kande Lin
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yuan Peng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
- Shanghai Center for Plant Stress Biology, National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Luhuan Ye
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yili Zhuang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Meiyue Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yilin Xie
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Jingyu Guo
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- Henan University, School of Life Science, Kaifeng, Henan 457000, China
| | - Wan Teng
- University of the Chinese Academy of Sciences, Beijing, 100049, China
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yiping Tong
- University of the Chinese Academy of Sciences, Beijing, 100049, China
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yongbiao Xue
- University of the Chinese Academy of Sciences, Beijing, 100049, China
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, and National Centre for Bioinformation, Beijing 100101 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Zhaobo Lang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
- Shanghai Center for Plant Stress Biology, National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yijing Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
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19
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Mayer G, Müller W, Schork K, Uszkoreit J, Weidemann A, Wittig U, Rey M, Quast C, Felden J, Glöckner FO, Lange M, Arend D, Beier S, Junker A, Scholz U, Schüler D, Kestler HA, Wibberg D, Pühler A, Twardziok S, Eils J, Eils R, Hoffmann S, Eisenacher M, Turewicz M. Implementing FAIR data management within the German Network for Bioinformatics Infrastructure (de.NBI) exemplified by selected use cases. Brief Bioinform 2021; 22:bbab010. [PMID: 33589928 PMCID: PMC8425304 DOI: 10.1093/bib/bbab010] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 12/21/2020] [Accepted: 01/06/2021] [Indexed: 12/21/2022] Open
Abstract
This article describes some use case studies and self-assessments of FAIR status of de.NBI services to illustrate the challenges and requirements for the definition of the needs of adhering to the FAIR (findable, accessible, interoperable and reusable) data principles in a large distributed bioinformatics infrastructure. We address the challenge of heterogeneity of wet lab technologies, data, metadata, software, computational workflows and the levels of implementation and monitoring of FAIR principles within the different bioinformatics sub-disciplines joint in de.NBI. On the one hand, this broad service landscape and the excellent network of experts are a strong basis for the development of useful research data management plans. On the other hand, the large number of tools and techniques maintained by distributed teams renders FAIR compliance challenging.
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Affiliation(s)
- Gerhard Mayer
- Ruhr University Bochum, Faculty of Medicine, Medizinisches Proteom-Center, Bochum, Germany
- Ruhr University Bochum, Center for Protein Diagnostics (ProDi), Medical Proteome Analysis, Bochum, Germany
- Ulm University, Institute of Medical Systems Biology, Ulm, Germany
| | - Wolfgang Müller
- Heidelberg Institute for Theoretical Studies (HITS gGmbH), Scientific Databases and Visualization Group, Heidelberg, Germany
| | - Karin Schork
- Ruhr University Bochum, Faculty of Medicine, Medizinisches Proteom-Center, Bochum, Germany
- Ruhr University Bochum, Center for Protein Diagnostics (ProDi), Medical Proteome Analysis, Bochum, Germany
| | - Julian Uszkoreit
- Ruhr University Bochum, Faculty of Medicine, Medizinisches Proteom-Center, Bochum, Germany
- Ruhr University Bochum, Center for Protein Diagnostics (ProDi), Medical Proteome Analysis, Bochum, Germany
| | - Andreas Weidemann
- Heidelberg Institute for Theoretical Studies (HITS gGmbH), Scientific Databases and Visualization Group, Heidelberg, Germany
| | - Ulrike Wittig
- Heidelberg Institute for Theoretical Studies (HITS gGmbH), Scientific Databases and Visualization Group, Heidelberg, Germany
| | - Maja Rey
- Heidelberg Institute for Theoretical Studies (HITS gGmbH), Scientific Databases and Visualization Group, Heidelberg, Germany
| | | | - Janine Felden
- Jacobs University Bremen gGmbH, Bremen, Germany
- University of Bremen, MARUM - Center for Marine Environmental Sciences, Bremen, Germany
| | - Frank Oliver Glöckner
- Jacobs University Bremen gGmbH, Bremen, Germany
- University of Bremen, MARUM - Center for Marine Environmental Sciences, Bremen, Germany
- Alfred Wegener Institute - Helmholtz Center for Polar- and Marine Research, Bremerhaven, Germany
| | - Matthias Lange
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Daniel Arend
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Sebastian Beier
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Astrid Junker
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Danuta Schüler
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Hans A Kestler
- Ulm University, Institute of Medical Systems Biology, Ulm, Germany
- Leibniz Institute on Ageing - Fritz Lipmann Institute, Jena
| | - Daniel Wibberg
- Bielefeld University, Center for Biotechnology (CeBiTec), Bielefeld, Germany
| | - Alfred Pühler
- Bielefeld University, Center for Biotechnology (CeBiTec), Bielefeld, Germany
| | - Sven Twardziok
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Center for Digital Health, Berlin, Germany
| | - Jürgen Eils
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Center for Digital Health, Berlin, Germany
| | - Roland Eils
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Center for Digital Health, Berlin, Germany
- Heidelberg University Hospital and BioQuant, Health Data Science Unit, Heidelberg, Germany
| | - Steve Hoffmann
- Leibniz Institute on Ageing - Fritz Lipmann Institute, Jena
| | - Martin Eisenacher
- Ruhr University Bochum, Faculty of Medicine, Medizinisches Proteom-Center, Bochum, Germany
- Ruhr University Bochum, Center for Protein Diagnostics (ProDi), Medical Proteome Analysis, Bochum, Germany
| | - Michael Turewicz
- Ruhr University Bochum, Faculty of Medicine, Medizinisches Proteom-Center, Bochum, Germany
- Ruhr University Bochum, Center for Protein Diagnostics (ProDi), Medical Proteome Analysis, Bochum, Germany
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20
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Mascher M, Wicker T, Jenkins J, Plott C, Lux T, Koh CS, Ens J, Gundlach H, Boston LB, Tulpová Z, Holden S, Hernández-Pinzón I, Scholz U, Mayer KFX, Spannagl M, Pozniak CJ, Sharpe AG, Šimková H, Moscou MJ, Grimwood J, Schmutz J, Stein N. Long-read sequence assembly: a technical evaluation in barley. THE PLANT CELL 2021; 33:1888-1906. [PMID: 33710295 PMCID: PMC8290290 DOI: 10.1093/plcell/koab077] [Citation(s) in RCA: 139] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 02/28/2021] [Indexed: 05/19/2023]
Abstract
Sequence assembly of large and repeat-rich plant genomes has been challenging, requiring substantial computational resources and often several complementary sequence assembly and genome mapping approaches. The recent development of fast and accurate long-read sequencing by circular consensus sequencing (CCS) on the PacBio platform may greatly increase the scope of plant pan-genome projects. Here, we compare current long-read sequencing platforms regarding their ability to rapidly generate contiguous sequence assemblies in pan-genome studies of barley (Hordeum vulgare). Most long-read assemblies are clearly superior to the current barley reference sequence based on short-reads. Assemblies derived from accurate long reads excel in most metrics, but the CCS approach was the most cost-effective strategy for assembling tens of barley genomes. A downsampling analysis indicated that 20-fold CCS coverage can yield very good sequence assemblies, while even five-fold CCS data may capture the complete sequence of most genes. We present an updated reference genome assembly for barley with near-complete representation of the repeat-rich intergenic space. Long-read assembly can underpin the construction of accurate and complete sequences of multiple genomes of a species to build pan-genome infrastructures in Triticeae crops and their wild relatives.
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Affiliation(s)
- Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Seeland 06466, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Leipzig 04103, Germany
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zürich, Zürich 8008, Switzerland
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806
| | | | - Thomas Lux
- PGSB–Plant Genome and Systems Biology, Helmholtz Center Munich–German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Chu Shin Koh
- Global Institute for Food Security, University of Saskatchewan, Saskatoon SK S7N 4L8, Canada
| | - Jennifer Ens
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon SK S7N 5A8, Canada
| | - Heidrun Gundlach
- PGSB–Plant Genome and Systems Biology, Helmholtz Center Munich–German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Lori B Boston
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806
| | - Zuzana Tulpová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc 78371, Czech Republic
| | - Samuel Holden
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, UK
| | | | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Seeland 06466, Germany
| | - Klaus F X Mayer
- PGSB–Plant Genome and Systems Biology, Helmholtz Center Munich–German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Manuel Spannagl
- PGSB–Plant Genome and Systems Biology, Helmholtz Center Munich–German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Curtis J Pozniak
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon SK S7N 5A8, Canada
| | - Andrew G Sharpe
- Global Institute for Food Security, University of Saskatchewan, Saskatoon SK S7N 4L8, Canada
| | - Hana Šimková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc 78371, Czech Republic
| | - Matthew J Moscou
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, UK
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Seeland 06466, Germany
- Center for Integrated Breeding Research (CiBreed), Georg-August-University Göttingen, Göttingen 37073, Germany
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21
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Marsh JI, Hu H, Gill M, Batley J, Edwards D. Crop breeding for a changing climate: integrating phenomics and genomics with bioinformatics. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1677-1690. [PMID: 33852055 DOI: 10.1007/s00122-021-03820-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 03/18/2021] [Indexed: 05/05/2023]
Abstract
Safeguarding crop yields in a changing climate requires bioinformatics advances in harnessing data from vast phenomics and genomics datasets to translate research findings into climate smart crops in the field. Climate change and an additional 3 billion mouths to feed by 2050 raise serious concerns over global food security. Crop breeding and land management strategies will need to evolve to maximize the utilization of finite resources in coming years. High-throughput phenotyping and genomics technologies are providing researchers with the information required to guide and inform the breeding of climate smart crops adapted to the environment. Bioinformatics has a fundamental role to play in integrating and exploiting this fast accumulating wealth of data, through association studies to detect genomic targets underlying key adaptive climate-resilient traits. These data provide tools for breeders to tailor crops to their environment and can be introduced using advanced selection or genome editing methods. To effectively translate research into the field, genomic and phenomic information will need to be integrated into comprehensive clade-specific databases and platforms alongside accessible tools that can be used by breeders to inform the selection of climate adaptive traits. Here we discuss the role of bioinformatics in extracting, analysing, integrating and managing genomic and phenomic data to improve climate resilience in crops, including current, emerging and potential approaches, applications and bottlenecks in the research and breeding pipeline.
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Affiliation(s)
- Jacob I Marsh
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, 6009, Australia
| | - Haifei Hu
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, 6009, Australia
| | - Mitchell Gill
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, 6009, Australia
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, 6009, Australia
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, 6009, Australia.
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22
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Cagirici HB, Budak H, Sen TZ. Genome-wide discovery of G-quadruplexes in barley. Sci Rep 2021; 11:7876. [PMID: 33846409 PMCID: PMC8041835 DOI: 10.1038/s41598-021-86838-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 03/19/2021] [Indexed: 12/04/2022] Open
Abstract
G-quadruplexes (G4s) are four-stranded nucleic acid structures with closely spaced guanine bases forming square planar G-quartets. Aberrant formation of G4 structures has been associated with genomic instability. However, most plant species are lacking comprehensive studies of G4 motifs. In this study, genome-wide identification of G4 motifs in barley was performed, followed by a comparison of genomic distribution and molecular functions to other monocot species, such as wheat, maize, and rice. Similar to the reports on human and some plants like wheat, G4 motifs peaked around the 5′ untranslated region (5′ UTR), the first coding domain sequence, and the first intron start sites on antisense strands. Our comparative analyses in human, Arabidopsis, maize, rice, and sorghum demonstrated that the peak points could be erroneously merged into a single peak when large window sizes are used. We also showed that the G4 distributions around genic regions are relatively similar in the species studied, except in the case of Arabidopsis. G4 containing genes in monocots showed conserved molecular functions for transcription initiation and hydrolase activity. Additionally, we provided examples of imperfect G4 motifs.
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Affiliation(s)
- H Busra Cagirici
- Crop Improvement and Genetics Research Unit, Western Regional Research Center, U.S. Department of Agriculture - Agricultural Research Service, 800 Buchanan St, Albany, CA, 94710, USA
| | - Hikmet Budak
- Montana BioAg Inc., Missoula, MT, USA.,Agrogen, LLC., Omaha, NE, USA
| | - Taner Z Sen
- Crop Improvement and Genetics Research Unit, Western Regional Research Center, U.S. Department of Agriculture - Agricultural Research Service, 800 Buchanan St, Albany, CA, 94710, USA.
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23
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Citron Watermelon Potential to Improve Crop Diversification and Reduce Negative Impacts of Climate Change. SUSTAINABILITY 2021. [DOI: 10.3390/su13042269] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Citron watermelon (Citrullus lanatus var. citroides (L.H. Bailey) Mansf. ex Greb.) is an underexploited and under-researched crop species with the potential to contribute to crop diversification in Sub-Saharan Africa. The species is cultivated in the drier parts of Southern Africa, mainly by smallholder farmers who maintain a wide range of landrace varieties. Understanding the molecular and morpho-physiological basis for drought adaptation in citron watermelon under these dry environments can aid in the identification of suitable traits for drought-tolerance breeding and improve food system resilience among smallholder farmers, thus adding to crop diversification. This paper reviews the literature on drought adaptation of Citrullus lanatus spp. (C3 xerophytes), using the systematic review approach. The review discusses the potential role of citron watermelon in adding to crop diversification, alternative food uses, and potential by-products that can be processed from the crop, and it analyzes the role of Sub-Saharan African farmers play as key actors in conserving citron watermelon germplasm and biodiversity. Finally, the review provides a summary of significant findings and identifies critical knowledge gaps for further research.
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24
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Blätke MA, Szymanski JJ, Gladilin E, Scholz U, Beier S. Editorial: Advances in Applied Bioinformatics in Crops. FRONTIERS IN PLANT SCIENCE 2021; 12:640394. [PMID: 33679855 PMCID: PMC7928291 DOI: 10.3389/fpls.2021.640394] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 01/20/2021] [Indexed: 06/12/2023]
Affiliation(s)
- Mary-Ann Blätke
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Jedrzej Jakub Szymanski
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Evgeny Gladilin
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Uwe Scholz
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Sebastian Beier
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
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25
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Zhang Y, Wang J, Du J, Zhao Y, Lu X, Wen W, Gu S, Fan J, Wang C, Wu S, Wang Y, Liao S, Zhao C, Guo X. Dissecting the phenotypic components and genetic architecture of maize stem vascular bundles using high-throughput phenotypic analysis. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:35-50. [PMID: 32569428 PMCID: PMC7769239 DOI: 10.1111/pbi.13437] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 06/03/2020] [Accepted: 06/15/2020] [Indexed: 05/27/2023]
Abstract
High-throughput phenotyping is increasingly becoming an important tool for rapid advancement of genetic gain in breeding programmes. Manual phenotyping of vascular bundles is tedious and time-consuming, which lags behind the rapid development of functional genomics in maize. More robust and automated techniques of phenotyping vascular bundles traits at high-throughput are urgently needed for large crop populations. In this study, we developed a standard process for stem micro-CT data acquisition and an automatic CT image process pipeline to obtain vascular bundle traits of stems including geometry-related, morphology-related and distribution-related traits. Next, we analysed the phenotypic variation of stem vascular bundles between natural population subgroup (480 inbred lines) based on 48 comprehensively phenotypic information. Also, the first database for stem micro-phenotypes, MaizeSPD, was established, storing 554 pieces of basic information of maize inbred lines, 523 pieces of experimental information, 1008 pieces of CT scanning images and processed images, and 24 192 pieces of phenotypic data. Combined with genome-wide association studies (GWASs), a total of 1562 significant single nucleotide polymorphism (SNPs) were identified for 30 stem micro-phenotypic traits, and 84 unique genes of 20 traits such as VBNum, VBAvArea and PZVBDensity were detected. Candidate genes identified by GWAS mainly encode enzymes involved in cell wall metabolism, transcription factors, protein kinase and protein related to plant signal transduction and stress response. The results presented here will advance our knowledge about phenotypic trait components of stem vascular bundles and provide useful information for understanding the genetic controls of vascular bundle formation and development.
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Affiliation(s)
- Ying Zhang
- Beijing Key Lab of Digital PlantNational Engineering Research Center for Information Technology in AgricultureBeijing Research Center for Information Technology in AgricultureBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Jinglu Wang
- Beijing Key Lab of Digital PlantNational Engineering Research Center for Information Technology in AgricultureBeijing Research Center for Information Technology in AgricultureBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Jianjun Du
- Beijing Key Lab of Digital PlantNational Engineering Research Center for Information Technology in AgricultureBeijing Research Center for Information Technology in AgricultureBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Yanxin Zhao
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular BreedingMaize Research CenterBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Xianju Lu
- Beijing Key Lab of Digital PlantNational Engineering Research Center for Information Technology in AgricultureBeijing Research Center for Information Technology in AgricultureBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Weiliang Wen
- Beijing Key Lab of Digital PlantNational Engineering Research Center for Information Technology in AgricultureBeijing Research Center for Information Technology in AgricultureBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Shenghao Gu
- Beijing Key Lab of Digital PlantNational Engineering Research Center for Information Technology in AgricultureBeijing Research Center for Information Technology in AgricultureBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Jiangchuan Fan
- Beijing Key Lab of Digital PlantNational Engineering Research Center for Information Technology in AgricultureBeijing Research Center for Information Technology in AgricultureBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Chuanyu Wang
- Beijing Key Lab of Digital PlantNational Engineering Research Center for Information Technology in AgricultureBeijing Research Center for Information Technology in AgricultureBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Sheng Wu
- Beijing Key Lab of Digital PlantNational Engineering Research Center for Information Technology in AgricultureBeijing Research Center for Information Technology in AgricultureBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Yongjian Wang
- Beijing Key Lab of Digital PlantNational Engineering Research Center for Information Technology in AgricultureBeijing Research Center for Information Technology in AgricultureBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Shengjin Liao
- Beijing Key Lab of Digital PlantNational Engineering Research Center for Information Technology in AgricultureBeijing Research Center for Information Technology in AgricultureBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Chunjiang Zhao
- Beijing Key Lab of Digital PlantNational Engineering Research Center for Information Technology in AgricultureBeijing Research Center for Information Technology in AgricultureBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Xinyu Guo
- Beijing Key Lab of Digital PlantNational Engineering Research Center for Information Technology in AgricultureBeijing Research Center for Information Technology in AgricultureBeijing Academy of Agriculture and Forestry SciencesBeijingChina
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Li M, Hensel G, Melzer M, Junker A, Tschiersch H, Ruwe H, Arend D, Kumlehn J, Börner T, Stein N. Mutation of the ALBOSTRIANS Ohnologous Gene HvCMF3 Impairs Chloroplast Development and Thylakoid Architecture in Barley. FRONTIERS IN PLANT SCIENCE 2021; 12:732608. [PMID: 34659298 PMCID: PMC8517540 DOI: 10.3389/fpls.2021.732608] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/10/2021] [Indexed: 05/12/2023]
Abstract
Gene pairs resulting from whole genome duplication (WGD), so-called ohnologous genes, are retained if at least one member of the pair undergoes neo- or sub-functionalization. Phylogenetic analyses of the ohnologous genes ALBOSTRIANS (HvAST/HvCMF7) and ALBOSTRIANS-LIKE (HvASL/HvCMF3) of barley (Hordeum vulgare) revealed them as members of a subfamily of genes coding for CCT motif (CONSTANS, CONSTANS-LIKE and TIMING OF CAB1) proteins characterized by a single CCT domain and a putative N-terminal chloroplast transit peptide. Recently, we showed that HvCMF7 is needed for chloroplast ribosome biogenesis. Here we demonstrate that mutations in HvCMF3 lead to seedlings delayed in development. They exhibit a yellowish/light green - xantha - phenotype and successively develop pale green leaves. Compared to wild type, plastids of mutant seedlings show a decreased PSII efficiency, impaired processing and reduced amounts of ribosomal RNAs; they contain less thylakoids and grana with a higher number of more loosely stacked thylakoid membranes. Site-directed mutagenesis of HvCMF3 identified a previously unknown functional domain, which is highly conserved within this subfamily of CCT domain containing proteins. HvCMF3:GFP fusion constructs were localized to plastids and nucleus. Hvcmf3Hvcmf7 double mutants exhibited a xantha-albino or albino phenotype depending on the strength of molecular lesion of the HvCMF7 allele. The chloroplast ribosome deficiency is discussed as the primary observed defect of the Hvcmf3 mutants. Based on our observations, the genes HvCMF3 and HvCMF7 have similar but not identical functions in chloroplast development of barley supporting our hypothesis of neo-/sub-functionalization between both ohnologous genes.
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Affiliation(s)
- Mingjiu Li
- Genomics of Genetic Resources, Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
| | - Goetz Hensel
- Plant Reproductive Biology, Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
| | - Michael Melzer
- Structural Cell Biology, Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
| | - Astrid Junker
- Acclimation Dynamics and Phenotyping, Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
| | - Henning Tschiersch
- Heterosis Research Group, Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
| | - Hannes Ruwe
- Molecular Genetics, Institute of Biology, Humboldt University, Berlin, Germany
| | - Daniel Arend
- Research Group Bioinformatics and Information Technology, Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
| | - Jochen Kumlehn
- Plant Reproductive Biology, Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
| | - Thomas Börner
- Molecular Genetics, Institute of Biology, Humboldt University, Berlin, Germany
- *Correspondence: Thomas Börner,
| | - Nils Stein
- Genomics of Genetic Resources, Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
- Department of Crop Sciences, Center for Integrated Breeding Research, Georg-August-University, Göttingen, Germany
- Nils Stein,
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DEFECTIVE ENDOSPERM-D1 (Dee-D1) is crucial for endosperm development in hexaploid wheat. Commun Biol 2020; 3:791. [PMID: 33361776 PMCID: PMC7758331 DOI: 10.1038/s42003-020-01509-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 11/20/2020] [Indexed: 11/09/2022] Open
Abstract
Hexaploid wheat (Triticum aestivum L.) is a natural allopolyploid and provides a usable model system to better understand the genetic mechanisms that underlie allopolyploid speciation through the hybrid genome doubling. Here we aimed to identify the contribution of chromosome 1D in the development and evolution of hexaploid wheat. We identified and mapped a novel DEFECTIVE ENDOSPERM–D1 (Dee-D1) locus on 1DL that is involved in the genetic control of endosperm development. The absence of Dee-D1 leads to non-viable grains in distant crosses and alters grain shape, which negatively affects grain number and thousand-grain weight. Dee-D1 can be classified as speciation locus with a positive effect on the function of genes which are involved in endosperm development in hybrid genomes. The presence of Dee-D1 is necessary for the normal development of endosperm, and thus play an important role in the evolution and improvement of grain yield in hexaploid wheat. Natalia Tikhenko et al. investigate the genetic contribution of the wheat chromosome 1D to its development and evolution. They find a novel locus, DEFECTIVE ENDOSPERM-D1, on the long arm of 1D that is required for normal endosperm development as its absence leads to non-viable grains and altered grain shape.
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Dreissig S, Maurer A, Sharma R, Milne L, Flavell AJ, Schmutzer T, Pillen K. Natural variation in meiotic recombination rate shapes introgression patterns in intraspecific hybrids between wild and domesticated barley. THE NEW PHYTOLOGIST 2020; 228:1852-1863. [PMID: 32659029 DOI: 10.1111/nph.16810] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 07/05/2020] [Indexed: 06/11/2023]
Abstract
Meiotic recombination rates vary considerably between species, populations and individuals. The genetic exchange between homologous chromosomes plays a major role in evolution by breaking linkage between advantageous and deleterious alleles in the case of introgressions. Identifying recombination rate modifiers is thus of both fundamental and practical interest to understand and utilize variation in meiotic recombination rates. We investigated recombination rate variation in a large intraspecific hybrid population (named HEB-25) derived from a cross between domesticated barley and 25 wild barley accessions. We observed quantitative variation in total crossover number with a maximum of a 1.4-fold difference between subpopulations and increased recombination rates across pericentromeric regions. The meiosis-specific α-kleisin cohesin subunit REC8 was identified as a candidate gene influencing crossover number and patterning. Furthermore, we quantified wild barley introgression patterns and revealed how local and genome-wide recombination rate variation shapes patterns of introgression. The identification of allelic variation in REC8 in combination with the observed changes in crossover patterning suggest a difference in how chromatin loops are tethered to the chromosome axis, resulting in reduced crossover suppression across pericentromeric regions. Local and genome-wide recombination rate variation is shaping patterns of introgressions and thereby directly influences the consequences of linkage drag.
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Affiliation(s)
- Steven Dreissig
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Straße 3, Halle (Saale), 06120, Germany
| | - Andreas Maurer
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Straße 3, Halle (Saale), 06120, Germany
| | - Rajiv Sharma
- Division of Plant Sciences, University of Dundee at JHI, Invergowrie Dundee, DD2 5DA, Scotland, UK
| | - Linda Milne
- The James Hutton Institute (JHI), Invergowrie Dundee, DD2 5DA, Scotland, UK
| | - Andrew John Flavell
- Division of Plant Sciences, University of Dundee at JHI, Invergowrie Dundee, DD2 5DA, Scotland, UK
| | - Thomas Schmutzer
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Straße 3, Halle (Saale), 06120, Germany
| | - Klaus Pillen
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Straße 3, Halle (Saale), 06120, Germany
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29
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Jayakodi M, Padmarasu S, Haberer G, Bonthala VS, Gundlach H, Monat C, Lux T, Kamal N, Lang D, Himmelbach A, Ens J, Zhang XQ, Angessa TT, Zhou G, Tan C, Hill C, Wang P, Schreiber M, Boston LB, Plott C, Jenkins J, Guo Y, Fiebig A, Budak H, Xu D, Zhang J, Wang C, Grimwood J, Schmutz J, Guo G, Zhang G, Mochida K, Hirayama T, Sato K, Chalmers KJ, Langridge P, Waugh R, Pozniak CJ, Scholz U, Mayer KFX, Spannagl M, Li C, Mascher M, Stein N. The barley pan-genome reveals the hidden legacy of mutation breeding. Nature 2020; 588:284-289. [PMID: 33239781 PMCID: PMC7759462 DOI: 10.1038/s41586-020-2947-8] [Citation(s) in RCA: 248] [Impact Index Per Article: 62.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 09/09/2020] [Indexed: 12/25/2022]
Abstract
Genetic diversity is key to crop improvement. Owing to pervasive genomic structural variation, a single reference genome assembly cannot capture the full complement of sequence diversity of a crop species (known as the 'pan-genome'1). Multiple high-quality sequence assemblies are an indispensable component of a pan-genome infrastructure. Barley (Hordeum vulgare L.) is an important cereal crop with a long history of cultivation that is adapted to a wide range of agro-climatic conditions2. Here we report the construction of chromosome-scale sequence assemblies for the genotypes of 20 varieties of barley-comprising landraces, cultivars and a wild barley-that were selected as representatives of global barley diversity. We catalogued genomic presence/absence variants and explored the use of structural variants for quantitative genetic analysis through whole-genome shotgun sequencing of 300 gene bank accessions. We discovered abundant large inversion polymorphisms and analysed in detail two inversions that are frequently found in current elite barley germplasm; one is probably the product of mutation breeding and the other is tightly linked to a locus that is involved in the expansion of geographical range. This first-generation barley pan-genome makes previously hidden genetic variation accessible to genetic studies and breeding.
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Affiliation(s)
- Murukarthick Jayakodi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Sudharsan Padmarasu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Georg Haberer
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Venkata Suresh Bonthala
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Heidrun Gundlach
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Cécile Monat
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Thomas Lux
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Nadia Kamal
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Daniel Lang
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Jennifer Ens
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Xiao-Qi Zhang
- Western Barley Genetics Alliance, State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Western Australia, Australia
| | - Tefera T Angessa
- Western Barley Genetics Alliance, State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Western Australia, Australia
| | - Gaofeng Zhou
- Western Barley Genetics Alliance, State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Western Australia, Australia
- Agriculture and Food, Department of Primary Industries and Regional Development, South Perth, Western Australia, Australia
| | - Cong Tan
- Western Barley Genetics Alliance, State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Western Australia, Australia
| | - Camilla Hill
- Western Barley Genetics Alliance, State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Western Australia, Australia
| | - Penghao Wang
- Western Barley Genetics Alliance, State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Western Australia, Australia
| | | | - Lori B Boston
- HudsonAlpha, Institute for Biotechnology, Huntsville, AL, USA
| | | | - Jerry Jenkins
- HudsonAlpha, Institute for Biotechnology, Huntsville, AL, USA
| | - Yu Guo
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Anne Fiebig
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | | | - Dongdong Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, China
| | - Jing Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, China
| | - Chunchao Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, China
| | - Jane Grimwood
- HudsonAlpha, Institute for Biotechnology, Huntsville, AL, USA
| | - Jeremy Schmutz
- HudsonAlpha, Institute for Biotechnology, Huntsville, AL, USA
| | - Ganggang Guo
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, China
| | - Guoping Zhang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Keiichi Mochida
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Takashi Hirayama
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Kenneth J Chalmers
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, South Australia, Australia
| | - Peter Langridge
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, South Australia, Australia
| | - Robbie Waugh
- The James Hutton Institute, Dundee, UK
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, South Australia, Australia
- School of Life Sciences, University of Dundee, Dundee, UK
| | - Curtis J Pozniak
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Klaus F X Mayer
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
- School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Manuel Spannagl
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Chengdao Li
- Western Barley Genetics Alliance, State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Western Australia, Australia.
- Agriculture and Food, Department of Primary Industries and Regional Development, South Perth, Western Australia, Australia.
- Hubei Collaborative Innovation Centre for Grain Industry, Yangtze University, Jingzhou, China.
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.
- Center for Integrated Breeding Research (CiBreed), Georg-August-University Göttingen, Göttingen, Germany.
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30
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Arend D, König P, Junker A, Scholz U, Lange M. The on-premise data sharing infrastructure e!DAL: Foster FAIR data for faster data acquisition. Gigascience 2020; 9:giaa107. [PMID: 33090199 PMCID: PMC7580168 DOI: 10.1093/gigascience/giaa107] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/09/2020] [Accepted: 09/19/2020] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND The FAIR data principle as a commitment to support long-term research data management is widely accepted in the scientific community. Although the ELIXIR Core Data Resources and other established infrastructures provide comprehensive and long-term stable services and platforms for FAIR data management, a large quantity of research data is still hidden or at risk of getting lost. Currently, high-throughput plant genomics and phenomics technologies are producing research data in abundance, the storage of which is not covered by established core databases. This concerns the data volume, e.g., time series of images or high-resolution hyper-spectral data; the quality of data formatting and annotation, e.g., with regard to structure and annotation specifications of core databases; uncovered data domains; or organizational constraints prohibiting primary data storage outside institional boundaries. RESULTS To share these potentially dark data in a FAIR way and master these challenges the ELIXIR Germany/de.NBI service Plant Genomic and Phenomics Research Data Repository (PGP) implements a "bring the infrastructure to the data" approach, which allows research data to be kept in place and wrapped in a FAIR-aware software infrastructure. This article presents new features of the e!DAL infrastructure software and the PGP repository as a best practice on how to easily set up FAIR-compliant and intuitive research data services. Furthermore, the integration of the ELIXIR Authentication and Authorization Infrastructure (AAI) and data discovery services are introduced as means to lower technical barriers and to increase the visibility of research data. CONCLUSION The e!DAL software matured to a powerful and FAIR-compliant infrastructure, while keeping the focus on flexible setup and integration into existing infrastructures and into the daily research process.
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Affiliation(s)
- Daniel Arend
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, D-06466 Seeland, Germany
| | - Patrick König
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, D-06466 Seeland, Germany
| | - Astrid Junker
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, D-06466 Seeland, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, D-06466 Seeland, Germany
| | - Matthias Lange
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, D-06466 Seeland, Germany
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Analysis of wild tomato introgression lines elucidates the genetic basis of transcriptome and metabolome variation underlying fruit traits and pathogen response. Nat Genet 2020; 52:1111-1121. [PMID: 32989321 DOI: 10.1038/s41588-020-0690-6] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 08/13/2020] [Indexed: 02/07/2023]
Abstract
Wild tomato species represent a rich gene pool for numerous desirable traits lost during domestication. Here, we exploited an introgression population representing wild desert-adapted species and a domesticated cultivar to establish the genetic basis of gene expression and chemical variation accompanying the transfer of wild-species-associated fruit traits. Transcriptome and metabolome analysis of 580 lines coupled to pathogen sensitivity assays resulted in the identification of genomic loci associated with levels of hundreds of transcripts and metabolites. These associations occurred in hotspots representing coordinated perturbation of metabolic pathways and ripening-related processes. Here, we identify components of the Solanum alkaloid pathway, as well as genes and metabolites involved in pathogen defense and linking fungal resistance with changes in the fruit ripening regulatory network. Our results outline a framework for understanding metabolism and pathogen resistance during tomato fruit ripening and provide insights into key fruit quality traits.
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32
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Sielemann K, Hafner A, Pucker B. The reuse of public datasets in the life sciences: potential risks and rewards. PeerJ 2020; 8:e9954. [PMID: 33024631 PMCID: PMC7518187 DOI: 10.7717/peerj.9954] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/25/2020] [Indexed: 12/13/2022] Open
Abstract
The 'big data' revolution has enabled novel types of analyses in the life sciences, facilitated by public sharing and reuse of datasets. Here, we review the prodigious potential of reusing publicly available datasets and the associated challenges, limitations and risks. Possible solutions to issues and research integrity considerations are also discussed. Due to the prominence, abundance and wide distribution of sequencing data, we focus on the reuse of publicly available sequence datasets. We define 'successful reuse' as the use of previously published data to enable novel scientific findings. By using selected examples of successful reuse from different disciplines, we illustrate the enormous potential of the practice, while acknowledging the respective limitations and risks. A checklist to determine the reuse value and potential of a particular dataset is also provided. The open discussion of data reuse and the establishment of this practice as a norm has the potential to benefit all stakeholders in the life sciences.
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Affiliation(s)
- Katharina Sielemann
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Graduate School DILS, Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Bielefeld University, Bielefeld, Germany
| | - Alenka Hafner
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Current Affiliation: Intercollege Graduate Degree Program in Plant Biology, Penn State University, University Park, State College, PA, United States of America
| | - Boas Pucker
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Evolution and Diversity, Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
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33
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Li Z, Guo R, Li M, Chen Y, Li G. A review of computer vision technologies for plant phenotyping. COMPUTERS AND ELECTRONICS IN AGRICULTURE 2020; 176:105672. [PMID: 0 DOI: 10.1016/j.compag.2020.105672] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
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34
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Bachmann-Pfabe S, Dehmer KJ. Evaluation of Wild Potato Germplasm for Tuber Starch Content and Nitrogen Utilization Efficiency. PLANTS 2020; 9:plants9070833. [PMID: 32630783 PMCID: PMC7411790 DOI: 10.3390/plants9070833] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 06/29/2020] [Accepted: 07/01/2020] [Indexed: 01/03/2023]
Abstract
Potato wild relatives provide a considerable source of variation for important traits in cultivated potato (Solanum tuberosum L.) breeding. This study evaluates the variation of tuber starch content and nitrogen utilization efficiency (NutE) in wild potato germplasm. For the experiments regarding starch content, 28 accessions of ten different tuber-bearing wild Solanum-species were chosen, and in vitro plantlets were raised from seeds. Twenty plantlets (= genotypes) per accession were then cultivated in the greenhouse until natural senescence and tuber starch content was determined. The average tuber starch content across all genotypes tested was 21.7% of fresh mass. Contents above 28% of fresh mass were found in 50 genotypes, belonging to the species S. chacoense, S. commersonii, S. jamesii, and S. pinnatisectum. Subsequently, 22 wild genotypes revealing high tuber starch contents and four modern varieties of cultivated potato were studied as in vitro plantlets under optimal and low N supply (30 and 7.5 mmol L-1 N). Low N supply lead to a genotype-dependent reduction of shoot dry mass between 13 and 46%. The majority of the wild types also reduced root dry mass by 26 to 62%, while others maintained root growth and even exceeded the NutE of the varieties under low N supply. Thus, wild potato germplasm appears superior to cultivars in terms of tuber starch contents and N utilization efficiency, which should be investigated in further studies.
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35
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Ruban A, Schmutzer T, Wu DD, Fuchs J, Boudichevskaia A, Rubtsova M, Pistrick K, Melzer M, Himmelbach A, Schubert V, Scholz U, Houben A. Supernumerary B chromosomes of Aegilops speltoides undergo precise elimination in roots early in embryo development. Nat Commun 2020; 11:2764. [PMID: 32488019 PMCID: PMC7265534 DOI: 10.1038/s41467-020-16594-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 05/13/2020] [Indexed: 12/17/2022] Open
Abstract
Not necessarily all cells of an organism contain the same genome. Some eukaryotes exhibit dramatic differences between cells of different organs, resulting from programmed elimination of chromosomes or their fragments. Here, we present a detailed analysis of programmed B chromosome elimination in plants. Using goatgrass Aegilops speltoides as a model, we demonstrate that the elimination of B chromosomes is a strictly controlled and highly efficient root-specific process. At the onset of embryo differentiation B chromosomes undergo elimination in proto-root cells. Independent of centromere activity, B chromosomes demonstrate nondisjunction of chromatids and lagging in anaphase, leading to micronucleation. Chromatin structure and DNA replication differ between micronuclei and primary nuclei and degradation of micronucleated DNA is the final step of B chromosome elimination. This process might allow root tissues to survive the detrimental expression, or overexpression of B chromosome-located root-specific genes with paralogs located on standard chromosomes. B chromosomes are supernumerary chromosomes exhibiting dramatic differences between different organs in same species. Here, the authors show programmed B chromosome elimination in goatgrass starts at the onset of embryo differentiation by nondisjunction of chromatids, anaphase lagging, and ends with the degradation of micronucleated DNA.
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Affiliation(s)
- Alevtina Ruban
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, OT Gatersleben, Germany.,KWS SAAT SE & Co. KGaA, 37574, Einbeck, Germany
| | - Thomas Schmutzer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, OT Gatersleben, Germany.,Martin Luther University Halle-Wittenberg, Institute for Agricultural and Nutritional Sciences, 06099, Halle (Saale), Germany
| | - Dan D Wu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, OT Gatersleben, Germany.,Triticeae Research Institute, Sichuan Agricultural University, 611130, Wenjiang, China
| | - Joerg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, OT Gatersleben, Germany
| | - Anastassia Boudichevskaia
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, OT Gatersleben, Germany.,KWS SAAT SE & Co. KGaA, 37574, Einbeck, Germany
| | - Myroslava Rubtsova
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, OT Gatersleben, Germany.,SAATEN-UNION BIOTEC GmbH, 06466 Seeland, OT Gatersleben, Germany
| | - Klaus Pistrick
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, OT Gatersleben, Germany
| | - Michael Melzer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, OT Gatersleben, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, OT Gatersleben, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, OT Gatersleben, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, OT Gatersleben, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, OT Gatersleben, Germany.
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Bernhardt N, Brassac J, Dong X, Willing EM, Poskar CH, Kilian B, Blattner FR. Genome-wide sequence information reveals recurrent hybridization among diploid wheat wild relatives. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:493-506. [PMID: 31821649 DOI: 10.1111/tpj.14641] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 11/13/2019] [Accepted: 11/28/2019] [Indexed: 05/07/2023]
Abstract
Many conflicting hypotheses regarding the relationships among crops and wild species closely related to wheat (the genera Aegilops, Amblyopyrum, and Triticum) have been postulated. The contribution of hybridization to the evolution of these taxa is intensely discussed. To determine possible causes for this, and provide a phylogeny of the diploid taxa based on genome-wide sequence information, independent data were obtained from genotyping-by-sequencing and a target-enrichment experiment that returned 244 low-copy nuclear loci. The data were analyzed using Bayesian, likelihood and coalescent-based methods. D statistics were used to test if incomplete lineage sorting alone or together with hybridization is the source for incongruent gene trees. Here we present the phylogeny of all diploid species of the wheat wild relatives. We hypothesize that most of the wheat-group species were shaped by a primordial homoploid hybrid speciation event involving the ancestral Triticum and Am. muticum lineages to form all other species except Ae. speltoides. This hybridization event was followed by multiple introgressions affecting all taxa except Triticum. Mostly progenitors of the extant species were involved in these processes, while recent interspecific gene flow seems insignificant. The composite nature of many genomes of wheat-group taxa results in complicated patterns of diploid contributions when these lineages are involved in polyploid formation, which is, for example, the case for tetraploid and hexaploid wheats. Our analysis provides phylogenetic relationships and a testable hypothesis for the genome compositions in the basic evolutionary units within the wheat group of Triticeae.
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Affiliation(s)
- Nadine Bernhardt
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany
| | - Jonathan Brassac
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany
| | - Xue Dong
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- Plant Germplasm and Genomics Centre, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China
| | - Eva-Maria Willing
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - C Hart Poskar
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany
| | - Benjamin Kilian
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany
- Global Crop Diversity Trust, 53113, Bonn, Germany
| | - Frank R Blattner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany
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Hoseinzadeh P, Ruge-Wehling B, Schweizer P, Stein N, Pidon H. High Resolution Mapping of a Hordeum bulbosum-Derived Powdery Mildew Resistance Locus in Barley Using Distinct Homologous Introgression Lines. FRONTIERS IN PLANT SCIENCE 2020; 11:225. [PMID: 32194602 PMCID: PMC7063055 DOI: 10.3389/fpls.2020.00225] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 02/13/2020] [Indexed: 05/17/2023]
Abstract
Powdery mildew caused by Blumeria graminis f. sp. hordei (Bgh) is one of the main foliar diseases in barley (Hordeum vulgare L.; Hv). Naturally occurring resistance genes used in barley breeding are a cost effective and environmentally sustainable strategy to minimize the impact of pathogens, however, the primary gene pool of H. vulgare contains limited diversity owing to recent domestication bottlenecks. To ensure durable resistance against this pathogen, more genes are required that could be unraveled by investigation of secondary barley gene-pool. A large set of Hordeum bulbosum (Hb) introgression lines (ILs) harboring a diverse set of desirable resistance traits have been developed and are being routinely used as source of novel diversity in gene mapping studies. Nevertheless, this strategy is often compromised by a lack of recombination between the introgressed fragment and the orthologous chromosome of the barley genome. In this study, we fine-mapped a Hb gene conferring resistance to barley powdery mildew. The initial genotyping of two Hb ILs mapping populations with differently sized 2HS introgressions revealed severely reduced interspecific recombination in the region of the introgressed segment, preventing precise localization of the gene. To overcome this difficulty, we developed an alternative strategy, exploiting intraspecific recombination by crossing two Hv/Hb ILs with collinear Hb introgressions, one of which carries a powdery mildew resistance gene, while the other doesn't. The intraspecific recombination rate in the Hb-introgressed fragment of 2HS was approximately 20 times higher than it was in the initial simple ILs mapping populations. Using high-throughput genotyping-by-sequencing (GBS), we allocated the resistance gene to a 1.4 Mb interval, based on an estimate using the Hv genome as reference, in populations of only 103 and 146 individuals, respectively, similar to what is expected at this locus in barley. The most likely candidate resistance gene within this interval is part of the coiled-coil nucleotide-binding-site leucine-rich-repeat (CC-NBS-LLR) gene family, which is over-represented among genes conferring strong dominant resistance to pathogens. The reported strategy can be applied as a general strategic approach for identifying genes underlying traits of interest in crop wild relatives.
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Affiliation(s)
- Parastoo Hoseinzadeh
- Genomics of Genetic Resources, Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Brigitte Ruge-Wehling
- Institute for Breeding Research on Agricultural Crops, Julius Kühn Institute (JKI), Sanitz, Germany
| | - Patrick Schweizer
- Pathogen-Stress Genomics, Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Nils Stein
- Genomics of Genetic Resources, Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- Department of Crop Sciences, Center for Integrated Breeding Research (CiBreed), Georg-August-University, Göttingen, Germany
| | - Hélène Pidon
- Genomics of Genetic Resources, Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
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Vos RA, Katayama T, Mishima H, Kawano S, Kawashima S, Kim JD, Moriya Y, Tokimatsu T, Yamaguchi A, Yamamoto Y, Wu H, Amstutz P, Antezana E, Aoki NP, Arakawa K, Bolleman JT, Bolton E, Bonnal RJP, Bono H, Burger K, Chiba H, Cohen KB, Deutsch EW, Fernández-Breis JT, Fu G, Fujisawa T, Fukushima A, García A, Goto N, Groza T, Hercus C, Hoehndorf R, Itaya K, Juty N, Kawashima T, Kim JH, Kinjo AR, Kotera M, Kozaki K, Kumagai S, Kushida T, Lütteke T, Matsubara M, Miyamoto J, Mohsen A, Mori H, Naito Y, Nakazato T, Nguyen-Xuan J, Nishida K, Nishida N, Nishide H, Ogishima S, Ohta T, Okuda S, Paten B, Perret JL, Prathipati P, Prins P, Queralt-Rosinach N, Shinmachi D, Suzuki S, Tabata T, Takatsuki T, Taylor K, Thompson M, Uchiyama I, Vieira B, Wei CH, Wilkinson M, Yamada I, Yamanaka R, Yoshitake K, Yoshizawa AC, Dumontier M, Kosaki K, Takagi T. BioHackathon 2015: Semantics of data for life sciences and reproducible research. F1000Res 2020; 9:136. [PMID: 32308977 PMCID: PMC7141167 DOI: 10.12688/f1000research.18236.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/05/2020] [Indexed: 01/08/2023] Open
Abstract
We report on the activities of the 2015 edition of the BioHackathon, an annual event that brings together researchers and developers from around the world to develop tools and technologies that promote the reusability of biological data. We discuss issues surrounding the representation, publication, integration, mining and reuse of biological data and metadata across a wide range of biomedical data types of relevance for the life sciences, including chemistry, genotypes and phenotypes, orthology and phylogeny, proteomics, genomics, glycomics, and metabolomics. We describe our progress to address ongoing challenges to the reusability and reproducibility of research results, and identify outstanding issues that continue to impede the progress of bioinformatics research. We share our perspective on the state of the art, continued challenges, and goals for future research and development for the life sciences Semantic Web.
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Affiliation(s)
- Rutger A. Vos
- Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | | | - Hiroyuki Mishima
- Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Shin Kawano
- Database Center for Life Science, Tokyo, Japan
| | | | | | - Yuki Moriya
- Database Center for Life Science, Tokyo, Japan
| | | | | | | | - Hongyan Wu
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | | | - Erick Antezana
- Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Nobuyuki P. Aoki
- Faculty of Science and Engineering, SOKA University, Tokyo, Japan
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Tokyo, Japan
| | - Jerven T. Bolleman
- SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Lausanne, Switzerland
| | - Evan Bolton
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, USA
| | - Raoul J. P. Bonnal
- Istituto Nazionale Genetica Molecolare, Romeo ed Enrica Invernizzi, Milan, Italy
| | | | - Kees Burger
- Dutch Techcentre for Life Sciences, Utrecht, The Netherlands
| | - Hirokazu Chiba
- National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan
| | - Kevin B. Cohen
- Computational Bioscience Program, University of Colorado School of Medicine, Denver, USA
- Université Paris-Saclay, LIMSI, CNRS, Paris, France
| | | | | | - Gang Fu
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, USA
| | | | | | | | - Naohisa Goto
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Tudor Groza
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, Australia
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, Australia
| | - Colin Hercus
- Novocraft Technologies Sdn. Bhd., Selangor, Malaysia
| | - Robert Hoehndorf
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Kotone Itaya
- Institute for Advanced Biosciences, Keio University, Tokyo, Japan
| | - Nick Juty
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | | | - Jee-Hyub Kim
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Akira R. Kinjo
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Masaaki Kotera
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Kouji Kozaki
- The Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan
| | | | - Tatsuya Kushida
- National Bioscience Database Center, Japan Science and Technology Agency, Tokyo, Japan
| | - Thomas Lütteke
- Institute of Veterinary Physiology and Biochemistry, Justus-Liebig University Giessen, Giessen, Germany
- Gesellschaft für innovative Personalwirtschaftssysteme mbH (GIP GmbH), Offenbach, Germany
| | | | | | - Attayeb Mohsen
- National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Hiroshi Mori
- Center for Information Biology, National Institute of Genetics, Mishima, Japan
| | - Yuki Naito
- Database Center for Life Science, Tokyo, Japan
| | | | | | | | - Naoki Nishida
- Department of Systems Science, Osaka University, Osaka, Japan
| | - Hiroyo Nishide
- National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan
| | - Soichi Ogishima
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Tazro Ohta
- Database Center for Life Science, Tokyo, Japan
| | - Shujiro Okuda
- Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, USA
| | | | - Philip Prathipati
- National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Pjotr Prins
- University Medical Center Utrecht, Utrecht, The Netherlands
- University of Tennessee Health Science Center, Memphis, USA
| | - Núria Queralt-Rosinach
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Shinya Suzuki
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Tsuyosi Tabata
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | | | - Kieron Taylor
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Mark Thompson
- Leiden University Medical Center, Leiden, The Netherlands
| | - Ikuo Uchiyama
- National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan
| | - Bruno Vieira
- WurmLab, School of Biological & Chemical Sciences, Queen Mary University of London, London, UK
| | - Chih-Hsuan Wei
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, USA
| | - Mark Wilkinson
- Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | | | | | - Kazutoshi Yoshitake
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | | | - Michel Dumontier
- Institute of Data Science, Maastricht University, Maastricht, The Netherlands
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Toshihisa Takagi
- National Bioscience Database Center, Japan Science and Technology Agency, Tokyo, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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Ghaffar M, Schüler D, König P, Arend D, Junker A, Scholz U, Lange M. Programmatic Access to FAIRified Digital Plant Genetic Resources. J Integr Bioinform 2020; 16:/j/jib.2019.16.issue-4/jib-2019-0060/jib-2019-0060.xml. [PMID: 31913851 PMCID: PMC7074143 DOI: 10.1515/jib-2019-0060] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 10/09/2019] [Indexed: 12/29/2022] Open
Abstract
Genetic variance within the genotype of population and its mapping to phenotype variance in a systematic and high throughput manner is of interest for biodiversity and breeding research. Beside the established and efficient high throughput genotype technologies, phenotype capabilities got increased focus in the last decade. This results in an increasing amount of phenotype data from well scaling, automated sensor platform. Thus, data stewardship is a central component to make experimental data from multiple domains interoperable and re-usable. To ensure a standard and comprehensive sharing of scientific and experimental data among domain experts, FAIR data principles are utilized for machine read-ability and scale-ability. In this context, BrAPI consortium, provides a comprehensive and commonly agreed FAIRed guidelines to offer a BrAPI layered scientific data in a RESTful manner. This paper presents the concepts, best practices and implementations to meet these challenges. As one of the worlds leading plant research institutes it is of vital interest for the IPK-Gatersleben to transform legacy data infrastructures into a bio-digital resource center for plant genetics resources (PGR). This paper also demonstrates the benefits of integrated database back-ends, established data stewardship processes, and FAIR data exposition in a machine-readable, highly scalable programmatic interfaces.
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Affiliation(s)
- Mehmood Ghaffar
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, 06466 Seeland, Germany
| | - Danuta Schüler
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, 06466 Seeland, Germany
| | - Patrick König
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, 06466 Seeland, Germany
| | - Daniel Arend
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, 06466 Seeland, Germany
| | - Astrid Junker
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, 06466 Seeland, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, 06466 Seeland, Germany
| | - Matthias Lange
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, 06466 Seeland, Germany
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40
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Monat C, Padmarasu S, Lux T, Wicker T, Gundlach H, Himmelbach A, Ens J, Li C, Muehlbauer GJ, Schulman AH, Waugh R, Braumann I, Pozniak C, Scholz U, Mayer KFX, Spannagl M, Stein N, Mascher M. TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools. Genome Biol 2019; 20:284. [PMID: 31849336 DOI: 10.1101/631648] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 11/25/2019] [Indexed: 05/29/2023] Open
Abstract
Chromosome-scale genome sequence assemblies underpin pan-genomic studies. Recent genome assembly efforts in the large-genome Triticeae crops wheat and barley have relied on the commercial closed-source assembly algorithm DeNovoMagic. We present TRITEX, an open-source computational workflow that combines paired-end, mate-pair, 10X Genomics linked-read with chromosome conformation capture sequencing data to construct sequence scaffolds with megabase-scale contiguity ordered into chromosomal pseudomolecules. We evaluate the performance of TRITEX on publicly available sequence data of tetraploid wild emmer and hexaploid bread wheat, and construct an improved annotated reference genome sequence assembly of the barley cultivar Morex as a community resource.
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Affiliation(s)
- Cécile Monat
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Sudharsan Padmarasu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Thomas Lux
- PGSB - Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Heidrun Gundlach
- PGSB - Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Jennifer Ens
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Chengdao Li
- Western Barley Genetics Alliance, School of Veterinary and Life Sciences (VLS), Murdoch University, Murdoch, WA, Australia
- Hubei Collaborative Innovation Center for Grain Industry/School of Agriculture, Yangtze University, Jingzhou, China
| | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics & Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA
| | - Alan H Schulman
- Green Technology, Natural Resources Institute (Luke), Viikki Plant Science Centre, and Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Robbie Waugh
- The James Hutton Institute, Dundee, UK
- School of Life Sciences, University of Dundee, Dundee, UK
| | | | - Curtis Pozniak
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Klaus F X Mayer
- PGSB - Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany
- School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
| | - Manuel Spannagl
- PGSB - Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.
- Department of Crop Sciences, Center for Integrated Breeding Research (CiBreed), Georg-August-University Göttingen, Göttingen, Germany.
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
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41
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Monat C, Padmarasu S, Lux T, Wicker T, Gundlach H, Himmelbach A, Ens J, Li C, Muehlbauer GJ, Schulman AH, Waugh R, Braumann I, Pozniak C, Scholz U, Mayer KFX, Spannagl M, Stein N, Mascher M. TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools. Genome Biol 2019; 20:284. [PMID: 31849336 PMCID: PMC6918601 DOI: 10.1186/s13059-019-1899-5] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 11/25/2019] [Indexed: 11/24/2022] Open
Abstract
Chromosome-scale genome sequence assemblies underpin pan-genomic studies. Recent genome assembly efforts in the large-genome Triticeae crops wheat and barley have relied on the commercial closed-source assembly algorithm DeNovoMagic. We present TRITEX, an open-source computational workflow that combines paired-end, mate-pair, 10X Genomics linked-read with chromosome conformation capture sequencing data to construct sequence scaffolds with megabase-scale contiguity ordered into chromosomal pseudomolecules. We evaluate the performance of TRITEX on publicly available sequence data of tetraploid wild emmer and hexaploid bread wheat, and construct an improved annotated reference genome sequence assembly of the barley cultivar Morex as a community resource.
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Affiliation(s)
- Cécile Monat
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Sudharsan Padmarasu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Thomas Lux
- PGSB - Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Heidrun Gundlach
- PGSB - Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Jennifer Ens
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Chengdao Li
- Western Barley Genetics Alliance, School of Veterinary and Life Sciences (VLS), Murdoch University, Murdoch, WA, Australia
- Hubei Collaborative Innovation Center for Grain Industry/School of Agriculture, Yangtze University, Jingzhou, China
| | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics & Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA
| | - Alan H Schulman
- Green Technology, Natural Resources Institute (Luke), Viikki Plant Science Centre, and Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Robbie Waugh
- The James Hutton Institute, Dundee, UK
- School of Life Sciences, University of Dundee, Dundee, UK
| | | | - Curtis Pozniak
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Klaus F X Mayer
- PGSB - Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany
- School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
| | - Manuel Spannagl
- PGSB - Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.
- Department of Crop Sciences, Center for Integrated Breeding Research (CiBreed), Georg-August-University Göttingen, Göttingen, Germany.
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
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A Deep Learning Semantic Segmentation-Based Approach for Field-Level Sorghum Panicle Counting. REMOTE SENSING 2019. [DOI: 10.3390/rs11242939] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Small unmanned aerial systems (UAS) have emerged as high-throughput platforms for the collection of high-resolution image data over large crop fields to support precision agriculture and plant breeding research. At the same time, the improved efficiency in image capture is leading to massive datasets, which pose analysis challenges in providing needed phenotypic data. To complement these high-throughput platforms, there is an increasing need in crop improvement to develop robust image analysis methods to analyze large amount of image data. Analysis approaches based on deep learning models are currently the most promising and show unparalleled performance in analyzing large image datasets. This study developed and applied an image analysis approach based on a SegNet deep learning semantic segmentation model to estimate sorghum panicles counts, which are critical phenotypic data in sorghum crop improvement, from UAS images over selected sorghum experimental plots. The SegNet model was trained to semantically segment UAS images into sorghum panicles, foliage and the exposed ground using 462, 250 × 250 labeled images, which was then applied to field orthomosaic to generate a field-level semantic segmentation. Individual panicle locations were obtained after post-processing the segmentation output to remove small objects and split merged panicles. A comparison between model panicle count estimates and manually digitized panicle locations in 60 randomly selected plots showed an overall detection accuracy of 94%. A per-plot panicle count comparison also showed high agreement between estimated and reference panicle counts (Spearman correlation ρ = 0.88, mean bias = 0.65). Misclassifications of panicles during the semantic segmentation step and mosaicking errors in the field orthomosaic contributed mainly to panicle detection errors. Overall, the approach based on deep learning semantic segmentation showed good promise and with a larger labeled dataset and extensive hyper-parameter tuning, should provide even more robust and effective characterization of sorghum panicle counts.
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Wibberg D, Batut B, Belmann P, Blom J, Glöckner FO, Grüning B, Hoffmann N, Kleinbölting N, Rahn R, Rey M, Scholz U, Sharan M, Tauch A, Trojahn U, Usadel B, Kohlbacher O. The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR. F1000Res 2019; 8. [PMID: 33163154 PMCID: PMC7607484 DOI: 10.12688/f1000research.20244.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/04/2020] [Indexed: 12/25/2022] Open
Abstract
The German Network for Bioinformatics Infrastructure (de.NBI) is a national and academic infrastructure funded by the German Federal Ministry of Education and Research (BMBF). The de.NBI provides (i) service, (ii) training, and (iii) cloud computing to users in life sciences research and biomedicine in Germany and Europe and (iv) fosters the cooperation of the German bioinformatics community with international network structures. The de.NBI members also run the German node (ELIXIR-DE) within the European ELIXIR infrastructure. The de.NBI / ELIXIR-DE training platform, also known as special interest group 3 (SIG 3) ‘Training & Education’, coordinates the bioinformatics training of de.NBI and the German ELIXIR node. The network provides a high-quality, coherent, timely, and impactful training program across its eight service centers. Life scientists learn how to handle and analyze biological big data more effectively by applying tools, standards and compute services provided by de.NBI. Since 2015, more than 300 training courses were carried out with about 6,000 participants and these courses received recommendation rates of almost 90% (status as of July 2020). In addition to face-to-face training courses, online training was introduced on the de.NBI website in 2016 and guidelines for the preparation of e-learning material were established in 2018. In 2016, ELIXIR-DE joined the ELIXIR training platform. Here, the de.NBI / ELIXIR-DE training platform collaborates with ELIXIR in training activities, advertising training courses via TeSS and discussions on the exchange of data for training events essential for quality assessment on both the technical and administrative levels. The de.NBI training program trained thousands of scientists from Germany and beyond in many different areas of bioinformatics.
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Affiliation(s)
- Daniel Wibberg
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, 33501, Germany
| | - Bérénice Batut
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, 79110, Germany
| | - Peter Belmann
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, 33501, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, 35392, Germany
| | - Frank Oliver Glöckner
- Alfred-Wegener-Institut - Helmholtz Zentrum für Polar- und Meeresforschung and Jacobs University Bremen, Campus Ring 1, Bremen, 28759, Germany
| | - Björn Grüning
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, 79110, Germany
| | - Nils Hoffmann
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, 44227, Germany
| | - Nils Kleinbölting
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, 33501, Germany
| | - René Rahn
- Algorithmic Bioinformatics, Department of Mathematics and Computer Science, Freie Universität Berlin, Takustraße 9, Berlin, 14195, Germany
| | - Maja Rey
- Scientific Databases and Visualization Group, Heidelberg Institute for Theoretical Studies (HITS) gGmbH, Schloss-Wolfsbrunnenweg 35, Heidelberg, 69118, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, 06466, Germany
| | - Malvika Sharan
- The Heidelberg Center for Human Bioinformatics (HD-HuB), European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, 69117, Germany
| | - Andreas Tauch
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, 33501, Germany
| | - Ulrike Trojahn
- The Heidelberg Center for Human Bioinformatics (HD-HuB), European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, 69117, Germany
| | - Björn Usadel
- IBG-2 Plant Sciences, Forschungszentrum Jülich, Jülich, 52428, Germany
| | - Oliver Kohlbacher
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, Tübingen, 72076, Germany.,Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, 72076, Germany.,Translational Bioinformatics, University Hospital Tubingen, Tübingen, 72076, Germany.,Biomolecular Interactions, Max Planck Institute for Development Biology, Tübingen, 72076, Germany
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44
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Liu Z, Marella CBN, Hartmann A, Hajirezaei MR, von Wirén N. An Age-Dependent Sequence of Physiological Processes Defines Developmental Root Senescence. PLANT PHYSIOLOGY 2019; 181:993-1007. [PMID: 31515448 PMCID: PMC6836830 DOI: 10.1104/pp.19.00809] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 09/02/2019] [Indexed: 05/22/2023]
Abstract
Aging-related processes in plant tissues are associated with changes in developmental and physiological processes relevant for stress tolerance and plant performance. While senescence-regulated processes have been extensively characterized in leaves, they remain poorly described in roots. Here, we investigated the physiological processes and molecular determinants underlying the senescence of seminal roots in hydroponically grown barley (Hordeum vulgare). Transcriptome profiling in apical and basal root tissues revealed that several NAC-, WRKY-, and APETALA2 (AP2)-type transcription factors were upregulated just before the arrest of root elongation, when root cortical cell lysis and nitrate uptake, as well as cytokinin concentrations ceased. At this time point, root abscisic acid levels peaked, suggesting that abscisic acid is involved in root aging-related processes characterized by expression changes of genes involved in oxidative stress responses. This temporal sequence of aging-related processes in roots is highly reminiscent of typical organ senescence, with the exception of evidence for the retranslocation of nutrients from roots. Supported by the identification of senescence-related transcription factors, some of which are not expressed in leaves, our study indicates that roots undergo an intrinsic genetically determined senescence program, predominantly influenced by plant age.
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Affiliation(s)
- Zhaojun Liu
- Molecular Plant Nutrition, Department Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstrasse 3, 06466 Gatersleben, Germany
| | - Chakravarthy B N Marella
- Molecular Plant Nutrition, Department Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstrasse 3, 06466 Gatersleben, Germany
| | - Anja Hartmann
- Molecular Plant Nutrition, Department Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstrasse 3, 06466 Gatersleben, Germany
| | - Mohammad R Hajirezaei
- Molecular Plant Nutrition, Department Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstrasse 3, 06466 Gatersleben, Germany
| | - Nicolaus von Wirén
- Molecular Plant Nutrition, Department Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstrasse 3, 06466 Gatersleben, Germany vonwiren@ipk-gatersleben
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45
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Bustos‐Korts D, Dawson IK, Russell J, Tondelli A, Guerra D, Ferrandi C, Strozzi F, Nicolazzi EL, Molnar‐Lang M, Ozkan H, Megyeri M, Miko P, Çakır E, Yakışır E, Trabanco N, Delbono S, Kyriakidis S, Booth A, Cammarano D, Mascher M, Werner P, Cattivelli L, Rossini L, Stein N, Kilian B, Waugh R, van Eeuwijk FA. Exome sequences and multi-environment field trials elucidate the genetic basis of adaptation in barley. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:1172-1191. [PMID: 31108005 PMCID: PMC6851764 DOI: 10.1111/tpj.14414] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 04/30/2019] [Accepted: 05/13/2019] [Indexed: 05/25/2023]
Abstract
Broadening the genetic base of crops is crucial for developing varieties to respond to global agricultural challenges such as climate change. Here, we analysed a diverse panel of 371 domesticated lines of the model crop barley to explore the genetics of crop adaptation. We first collected exome sequence data and phenotypes of key life history traits from contrasting multi-environment common garden trials. Then we applied refined statistical methods, including some based on exomic haplotype states, for genotype-by-environment (G×E) modelling. Sub-populations defined from exomic profiles were coincident with barley's biology, geography and history, and explained a high proportion of trial phenotypic variance. Clear G×E interactions indicated adaptation profiles that varied for landraces and cultivars. Exploration of circadian clock-related genes, associated with the environmentally adaptive days to heading trait (crucial for the crop's spread from the Fertile Crescent), illustrated complexities in G×E effect directions, and the importance of latitudinally based genic context in the expression of large-effect alleles. Our analysis supports a gene-level scientific understanding of crop adaption and leads to practical opportunities for crop improvement, allowing the prioritisation of genomic regions and particular sets of lines for breeding efforts seeking to cope with climate change and other stresses.
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Affiliation(s)
- Daniela Bustos‐Korts
- BiometrisWageningen University and Research CentrePO Box 166700 ACWageningenThe Netherlands
| | - Ian K. Dawson
- Cell and Molecular SciencesJames Hutton InstituteInvergowrie, DundeeUK
| | - Joanne Russell
- Cell and Molecular SciencesJames Hutton InstituteInvergowrie, DundeeUK
| | - Alessandro Tondelli
- CREA – Research Centre for Genomics and BioinformaticsVia S. Protaso 30229017Fiorenzuola d'ArdaItaly
| | - Davide Guerra
- CREA – Research Centre for Genomics and BioinformaticsVia S. Protaso 30229017Fiorenzuola d'ArdaItaly
| | - Chiara Ferrandi
- PTP Science ParkVia Einstein, Loc. Cascina Codazza26900LodiItaly
| | | | | | - Marta Molnar‐Lang
- Agricultural InstituteCentre for Agricultural ResearchHungarian Academy of Sciences2462MartonvásárHungary
| | - Hakan Ozkan
- University of ÇukurovaFaculty of AgricultureDepartment of Field Crops01330AdanaTurkey
| | - Maria Megyeri
- Agricultural InstituteCentre for Agricultural ResearchHungarian Academy of Sciences2462MartonvásárHungary
| | - Peter Miko
- Agricultural InstituteCentre for Agricultural ResearchHungarian Academy of Sciences2462MartonvásárHungary
| | - Esra Çakır
- University of ÇukurovaFaculty of AgricultureDepartment of Field Crops01330AdanaTurkey
| | - Enes Yakışır
- Bahri Dagdas International Agricultural Research InstituteKonyaTurkey
| | - Noemi Trabanco
- Università degli Studi di Milano – DiSAAVia Celoria 220133MilanoItaly
| | - Stefano Delbono
- CREA – Research Centre for Genomics and BioinformaticsVia S. Protaso 30229017Fiorenzuola d'ArdaItaly
| | | | - Allan Booth
- Cell and Molecular SciencesJames Hutton InstituteInvergowrie, DundeeUK
| | - Davide Cammarano
- Cell and Molecular SciencesJames Hutton InstituteInvergowrie, DundeeUK
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)06466SeelandGermany
| | - Peter Werner
- KWS UK Ltd56 Church StreetThriplow, RoystonSG8 7REUK
| | - Luigi Cattivelli
- CREA – Research Centre for Genomics and BioinformaticsVia S. Protaso 30229017Fiorenzuola d'ArdaItaly
| | - Laura Rossini
- Università degli Studi di Milano – DiSAAVia Celoria 220133MilanoItaly
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)06466SeelandGermany
| | - Benjamin Kilian
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)06466SeelandGermany
- Present address:
Global Crop Diversity TrustPlatz der Vereinten Nationen 753113BonnGermany
| | - Robbie Waugh
- Cell and Molecular SciencesJames Hutton InstituteInvergowrie, DundeeUK
- Division of Plant SciencesSchool of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHUK
| | - Fred A. van Eeuwijk
- BiometrisWageningen University and Research CentrePO Box 166700 ACWageningenThe Netherlands
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46
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Philipp N, Weise S, Oppermann M, Börner A, Keilwagen J, Kilian B, Arend D, Zhao Y, Graner A, Reif JC, Schulthess AW. Historical phenotypic data from seven decades of seed regeneration in a wheat ex situ collection. Sci Data 2019; 6:137. [PMID: 31358775 PMCID: PMC6662709 DOI: 10.1038/s41597-019-0146-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 07/08/2019] [Indexed: 11/16/2022] Open
Abstract
Genebanks are valuable sources of genetic diversity, which can help to cope with future problems of global food security caused by a continuously growing population, stagnating yields and climate change. However, the scarcity of phenotypic and genotypic characterization of genebank accessions severely restricts their use in plant breeding. To warrant the seed integrity of individual accessions during periodical regeneration cycles in the field phenotypic characterizations are performed. This study provides non-orthogonal historical data of 12,754 spring and winter wheat accessions characterized for flowering time, plant height, and thousand grain weight during 70 years of seed regeneration at the German genebank. Supported by historical weather observations outliers were removed following a previously described quality assessment pipeline. In this way, ready-to-use processed phenotypic data across regeneration years were generated and further validated. We encourage international and national genebanks to increase their efforts to transform into bio-digital resource centers. A first important step could consist in unlocking their historical data treasures that allows an educated choice of accessions by scientists and breeders.
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Affiliation(s)
- Norman Philipp
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Seeland/OT, Gatersleben, Germany
| | - Stephan Weise
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Seeland/OT, Gatersleben, Germany
| | - Markus Oppermann
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Seeland/OT, Gatersleben, Germany
| | - Andreas Börner
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Seeland/OT, Gatersleben, Germany
| | - Jens Keilwagen
- Institute for Biosafety in Plant Biotechnology, Julius Kühn-Institut (JKI) - Federal Research Centre for Cultivated Plants, 06484, Quedlinburg, Germany
| | - Benjamin Kilian
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113, Bonn, Germany
| | - Daniel Arend
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Seeland/OT, Gatersleben, Germany
| | - Yusheng Zhao
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Seeland/OT, Gatersleben, Germany
| | - Andreas Graner
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Seeland/OT, Gatersleben, Germany
| | - Jochen C Reif
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Seeland/OT, Gatersleben, Germany.
| | - Albert W Schulthess
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Seeland/OT, Gatersleben, Germany
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47
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Zhao C, Zhang Y, Du J, Guo X, Wen W, Gu S, Wang J, Fan J. Crop Phenomics: Current Status and Perspectives. FRONTIERS IN PLANT SCIENCE 2019; 10:714. [PMID: 31214228 PMCID: PMC6557228 DOI: 10.3389/fpls.2019.00714] [Citation(s) in RCA: 136] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 05/14/2019] [Indexed: 05/19/2023]
Abstract
Reliable, automatic, multifunctional, and high-throughput phenotypic technologies are increasingly considered important tools for rapid advancement of genetic gain in breeding programs. With the rapid development in high-throughput phenotyping technologies, research in this area is entering a new era called 'phenomics.' The crop phenotyping community not only needs to build a multi-domain, multi-level, and multi-scale crop phenotyping big database, but also to research technical systems for phenotypic traits identification and develop bioinformatics technologies for information extraction from the overwhelming amounts of omics data. Here, we provide an overview of crop phenomics research, focusing on two parts, from phenotypic data collection through various sensors to phenomics analysis. Finally, we discussed the challenges and prospective of crop phenomics in order to provide suggestions to develop new methods of mining genes associated with important agronomic traits, and propose new intelligent solutions for precision breeding.
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48
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Pucker B, Holtgräwe D, Stadermann KB, Frey K, Huettel B, Reinhardt R, Weisshaar B. A chromosome-level sequence assembly reveals the structure of the Arabidopsis thaliana Nd-1 genome and its gene set. PLoS One 2019; 14:e0216233. [PMID: 31112551 PMCID: PMC6529160 DOI: 10.1371/journal.pone.0216233] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 04/16/2019] [Indexed: 01/27/2023] Open
Abstract
In addition to the BAC-based reference sequence of the accession Columbia-0 from the year 2000, several short read assemblies of THE plant model organism Arabidopsis thaliana were published during the last years. Also, a SMRT-based assembly of Landsberg erecta has been generated that identified translocation and inversion polymorphisms between two genotypes of the species. Here we provide a chromosome-arm level assembly of the A. thaliana accession Niederzenz-1 (AthNd-1_v2c) based on SMRT sequencing data. The best assembly comprises 69 nucleome sequences and displays a contig length of up to 16 Mbp. Compared to an earlier Illumina short read-based NGS assembly (AthNd-1_v1), a 75 fold increase in contiguity was observed for AthNd-1_v2c. To assign contig locations independent from the Col-0 gold standard reference sequence, we used genetic anchoring to generate a de novo assembly. In addition, we assembled the chondrome and plastome sequences. Detailed analyses of AthNd-1_v2c allowed reliable identification of large genomic rearrangements between A. thaliana accessions contributing to differences in the gene sets that distinguish the genotypes. One of the differences detected identified a gene that is lacking from the Col-0 gold standard sequence. This de novo assembly extends the known proportion of the A. thaliana pan-genome.
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Affiliation(s)
- Boas Pucker
- Bielefeld University, Faculty of Biology & Center for Biotechnology, Bielefeld, Germany
| | - Daniela Holtgräwe
- Bielefeld University, Faculty of Biology & Center for Biotechnology, Bielefeld, Germany
| | - Kai Bernd Stadermann
- Bielefeld University, Faculty of Biology & Center for Biotechnology, Bielefeld, Germany
| | - Katharina Frey
- Bielefeld University, Faculty of Biology & Center for Biotechnology, Bielefeld, Germany
| | - Bruno Huettel
- Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Richard Reinhardt
- Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Bernd Weisshaar
- Bielefeld University, Faculty of Biology & Center for Biotechnology, Bielefeld, Germany
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49
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Bolger AM, Poorter H, Dumschott K, Bolger ME, Arend D, Osorio S, Gundlach H, Mayer KFX, Lange M, Scholz U, Usadel B. Computational aspects underlying genome to phenome analysis in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:182-198. [PMID: 30500991 PMCID: PMC6849790 DOI: 10.1111/tpj.14179] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 11/06/2018] [Accepted: 11/16/2018] [Indexed: 05/18/2023]
Abstract
Recent advances in genomics technologies have greatly accelerated the progress in both fundamental plant science and applied breeding research. Concurrently, high-throughput plant phenotyping is becoming widely adopted in the plant community, promising to alleviate the phenotypic bottleneck. While these technological breakthroughs are significantly accelerating quantitative trait locus (QTL) and causal gene identification, challenges to enable even more sophisticated analyses remain. In particular, care needs to be taken to standardize, describe and conduct experiments robustly while relying on plant physiology expertise. In this article, we review the state of the art regarding genome assembly and the future potential of pangenomics in plant research. We also describe the necessity of standardizing and describing phenotypic studies using the Minimum Information About a Plant Phenotyping Experiment (MIAPPE) standard to enable the reuse and integration of phenotypic data. In addition, we show how deep phenotypic data might yield novel trait-trait correlations and review how to link phenotypic data to genomic data. Finally, we provide perspectives on the golden future of machine learning and their potential in linking phenotypes to genomic features.
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Affiliation(s)
- Anthony M. Bolger
- Institute for Biology I, BioSCRWTH Aachen UniversityWorringer Weg 352074AachenGermany
| | - Hendrik Poorter
- Forschungszentrum Jülich (FZJ) Institute of Bio‐ and Geosciences (IBG‐2) Plant SciencesWilhelm‐Johnen‐Straße52428JülichGermany
- Department of Biological SciencesMacquarie UniversityNorth RydeNSW2109Australia
| | - Kathryn Dumschott
- Institute for Biology I, BioSCRWTH Aachen UniversityWorringer Weg 352074AachenGermany
| | - Marie E. Bolger
- Forschungszentrum Jülich (FZJ) Institute of Bio‐ and Geosciences (IBG‐2) Plant SciencesWilhelm‐Johnen‐Straße52428JülichGermany
| | - Daniel Arend
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenCorrensstraße 306466SeelandGermany
| | - Sonia Osorio
- Department of Molecular Biology and BiochemistryInstituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”Universidad de Málaga‐Consejo Superior de Investigaciones CientíficasCampus de Teatinos29071MálagaSpain
| | - Heidrun Gundlach
- Plant Genome and Systems Biology (PGSB)Helmholtz Zentrum München (HMGU)Ingolstädter Landstraße 185764NeuherbergGermany
| | - Klaus F. X. Mayer
- Plant Genome and Systems Biology (PGSB)Helmholtz Zentrum München (HMGU)Ingolstädter Landstraße 185764NeuherbergGermany
| | - Matthias Lange
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenCorrensstraße 306466SeelandGermany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenCorrensstraße 306466SeelandGermany
| | - Björn Usadel
- Institute for Biology I, BioSCRWTH Aachen UniversityWorringer Weg 352074AachenGermany
- Forschungszentrum Jülich (FZJ) Institute of Bio‐ and Geosciences (IBG‐2) Plant SciencesWilhelm‐Johnen‐Straße52428JülichGermany
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50
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Schreiber M, Himmelbach A, Börner A, Mascher M. Genetic diversity and relationship between domesticated rye and its wild relatives as revealed through genotyping-by-sequencing. Evol Appl 2019; 12:66-77. [PMID: 30622636 PMCID: PMC6304746 DOI: 10.1111/eva.12624] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 02/19/2018] [Indexed: 12/20/2022] Open
Abstract
Rye (Secale cereale L.) is a cereal grass that is an important food crop in Central and Eastern Europe. In contrast to its close relatives wheat and barley, it was not a founder crop of Neolithic agriculture, but is considered a secondary domesticate that may have become a crop plant only after a transitory phase as a weed. As a minor crop of only local importance, genomic resources in rye are underdeveloped, and few population genetic studies using genomewide markers have been published to date. We collected genotyping-by-sequencing data for 603 individuals from 101 genebank accessions of domesticated rye and its wild progenitor S. cereale subsp. vavilovii and related species in the genus Secale. Variant detection in the context of a recently published draft sequence assembly of cultivated rye yielded 55,744 single nucleotide polymorphisms with present genotype calls in 90% of samples. Analysis of population structure recapitulated the taxonomy of the genus Secale. We found only weak genetic differentiation between wild and domesticated rye with likely gene flow between the two groups. Moreover, incomplete lineage sorting was frequent between Secale species because of either ongoing gene flow or recent speciation. Our study highlights the necessity of gauging the representativeness of ex situ germplasm collections for domestication studies and motivates a more in-depth analysis of the interplay between sequence divergence and reproductive isolation in the genus Secale.
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Affiliation(s)
- Mona Schreiber
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
| | - Andreas Börner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
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