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Bernád V, Al-Tamimi N, Langan P, Gillespie G, Dempsey T, Henchy J, Harty M, Ramsay L, Houston K, Macaulay M, Shaw PD, Raubach S, Mcdonnel KP, Russell J, Waugh R, Khodaeiaminjan M, Negrão S. Unlocking the genetic diversity and population structure of the newly introduced two-row spring European HerItage Barley collecTion (ExHIBiT). Front Plant Sci 2024; 15:1268847. [PMID: 38571708 PMCID: PMC10987740 DOI: 10.3389/fpls.2024.1268847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 02/28/2024] [Indexed: 04/05/2024]
Abstract
In the last century, breeding programs have traditionally favoured yield-related traits, grown under high-input conditions, resulting in a loss of genetic diversity and an increased susceptibility to stresses in crops. Thus, exploiting understudied genetic resources, that potentially harbour tolerance genes, is vital for sustainable agriculture. Northern European barley germplasm has been relatively understudied despite its key role within the malting industry. The European Heritage Barley collection (ExHIBiT) was assembled to explore the genetic diversity in European barley focusing on Northern European accessions and further address environmental pressures. ExHIBiT consists of 363 spring-barley accessions, focusing on two-row type. The collection consists of landraces (~14%), old cultivars (~18%), elite cultivars (~67%) and accessions with unknown breeding history (~1%), with 70% of the collection from Northern Europe. The population structure of the ExHIBiT collection was subdivided into three main clusters primarily based on the accession's year of release using 26,585 informative SNPs based on 50k iSelect single nucleotide polymorphism (SNP) array data. Power analysis established a representative core collection of 230 genotypically and phenotypically diverse accessions. The effectiveness of this core collection for conducting statistical and association analysis was explored by undertaking genome-wide association studies (GWAS) using 24,876 SNPs for nine phenotypic traits, four of which were associated with SNPs. Genomic regions overlapping with previously characterised flowering genes (HvZTLb) were identified, demonstrating the utility of the ExHIBiT core collection for locating genetic regions that determine important traits. Overall, the ExHIBiT core collection represents the high level of untapped diversity within Northern European barley, providing a powerful resource for researchers and breeders to address future climate scenarios.
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Affiliation(s)
- Villő Bernád
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Nadia Al-Tamimi
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Patrick Langan
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Gary Gillespie
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Timothy Dempsey
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Joey Henchy
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Mary Harty
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Luke Ramsay
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Kelly Houston
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Malcolm Macaulay
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Paul D. Shaw
- Department of Information and Computational Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Sebastian Raubach
- Department of Information and Computational Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Kevin P. Mcdonnel
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
- School of Biosystems Engineering, University College Dublin, Dublin, Ireland
| | - Joanne Russell
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- Division of Plant Sciences, University of Dundee at The James Hutton Institute, Dundee, United Kingdom
| | | | - Sónia Negrão
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
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Raubach S, Schreiber M, Shaw PD. GridScore: a tool for accurate, cross-platform phenotypic data collection and visualization. BMC Bioinformatics 2022; 23:214. [PMID: 35668357 PMCID: PMC9169276 DOI: 10.1186/s12859-022-04755-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 05/30/2022] [Indexed: 11/17/2022] Open
Abstract
Background Plant breeding and crop research rely on experimental phenotyping trials. These trials generate data for large numbers of traits and plant varieties that needs to be captured efficiently and accurately to support further research and downstream analysis. Traditionally scored by hand, phenotypic data is nowadays collected using spreadsheets or specialized apps. While many solutions exist, which increase efficiency and reduce errors, none offer the same familiarity as printed field plans which have been used for decades and offer an intuitive overview over the trial setup, previously recorded data and plots still requiring scoring. Results We introduce GridScore which utilizes cutting-edge web technologies to reproduce the familiarity of printed field plans while enhancing the phenotypic data collection process by adding advanced features like georeferencing, image tagging and speech recognition. GridScore is a cross-platform open-source plant phenotyping app that combines barcode-based systems with a guided data collection approach while offering a top-down view onto the data collected in a field layout. GridScore is compared to existing tools across a wide spectrum of criteria including support for barcodes, multiple platforms, and visualizations. Conclusion Compared to its competition, GridScore shows strong performance across the board offering a complete manual phenotyping experience.
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Affiliation(s)
- Sebastian Raubach
- Department of Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland.
| | - Miriam Schreiber
- Department of Life Science, University of Dundee, Dundee, Scotland
| | - Paul D Shaw
- Department of Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland
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Arrieta M, Macaulay M, Colas I, Schreiber M, Shaw PD, Waugh R, Ramsay L. An Induced Mutation in HvRECQL4 Increases the Overall Recombination and Restores Fertility in a Barley HvMLH3 Mutant Background. Front Plant Sci 2021; 12:706560. [PMID: 34868104 PMCID: PMC8633572 DOI: 10.3389/fpls.2021.706560] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 09/28/2021] [Indexed: 05/16/2023]
Abstract
Plant breeding relies on the meiotic recombination or crossing over to generate the new combinations of the alleles along and among the chromosomes. However, crossing over is constrained in the crops such as barley by a combination of the low frequency and biased distribution. In this study, we attempted to identify the genes that limit the recombination by performing a suppressor screen for the restoration of fertility to the semi-fertile barley mutant desynaptic10 (des10), carrying a mutation in the barley ortholog of MutL-Homolog 3 (HvMLH3), a member of the MutL-homolog (MLH) family of DNA mismatch repair genes. des10 mutants exhibit reduced recombination and fewer chiasmata, resulting in the loss of obligate crossovers (COs) leading to chromosome mis-segregation. We identified several candidate suppressor lines and confirmed their restored fertility in an Hvmlh3 background in the subsequent generations. We focus on one of the candidate suppressor lines, SuppLine2099, which showed the most complete restoration of fertility. We characterized this line by using a target-sequence enrichment and sequencing (TENSEQ) capture array representing barley orthologs of 46 meiotic genes. We found that SuppLine2099 contained a C/T change in the anti-CO gene RecQ-like helicase 4 (RECQL4) resulting in the substitution of a non-polar glycine to a polar aspartic acid (G700D) amino acid in the conserved helicase domain. Single nucleotide polymorphism (SNP) genotyping of F3 populations revealed a significant increase in the recombination frequency in lines with Hvrecql4 in the Hvmlh3 background that was associated with the restoration of fertility. The genotyping also indicated that there was nearly double the recombination levels in homozygous Hvrecql4 lines compared to the wild type (WT). However, we did not observe any significant change in the distribution of CO events. Our results confirm the anti-CO role of RECQL4 in a large genome cereal and establish the possibility of testing the utility of increasing recombination in the context of traditional crop improvement.
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Affiliation(s)
- Mikel Arrieta
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Malcolm Macaulay
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Isabelle Colas
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Miriam Schreiber
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Paul D. Shaw
- Information and Computational Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- Division of Plant Sciences, The University of Dundee at The James Hutton Institute, Dundee, United Kingdom
- *Correspondence: Robbie Waugh
| | - Luke Ramsay
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- Luke Ramsay
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4
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McCouch S, Navabi ZK, Abberton M, Anglin NL, Barbieri RL, Baum M, Bett K, Booker H, Brown GL, Bryan GJ, Cattivelli L, Charest D, Eversole K, Freitas M, Ghamkhar K, Grattapaglia D, Henry R, Valadares Inglis MC, Islam T, Kehel Z, Kersey PJ, King GJ, Kresovich S, Marden E, Mayes S, Ndjiondjop MN, Nguyen HT, Paiva SR, Papa R, Phillips PWB, Rasheed A, Richards C, Rouard M, Amstalden Sampaio MJ, Scholz U, Shaw PD, Sherman B, Staton SE, Stein N, Svensson J, Tester M, Montenegro Valls JF, Varshney R, Visscher S, von Wettberg E, Waugh R, Wenzl P, Rieseberg LH. Mobilizing Crop Biodiversity. Mol Plant 2020; 13:1341-1344. [PMID: 32835887 DOI: 10.1016/j.molp.2020.08.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 08/19/2020] [Accepted: 08/19/2020] [Indexed: 05/10/2023]
Affiliation(s)
- Susan McCouch
- Plant Breeding and Genetics, School of Integrated Plant Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Zahra Katy Navabi
- DivSeek, Global Institute for Food Security, 110 Gymnasium Place, University of Saskatchewan, Saskatoon, SK, S7N 0W9, Canada; Global Institute for Food Security, 110 Gymnasium Place, University of Saskatchewan, Saskatoon, SK, S7N 4J8, Canada
| | - Michael Abberton
- International Institute of Tropical Agriculture (IITA), PMB 5320, Oyo Rd, Ibadan, Nigeria
| | - Noelle L Anglin
- International Potato Center (CIP) 1895 Avenida La Molina, Lima Peru 12, Lima 15023, Peru
| | - Rosa Lia Barbieri
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, Final Av W5 Norte, Caixa Postal 02372, 70770-917 - Brasília DF, Brazil
| | - Michael Baum
- International Center for Agricultural Research in the Dry Areas (ICARDA), Station Exp. INRA-Quich. Rue Hafiane Cherkaoui. Agdal. Rabat - Instituts, 10111, Rabat, Morocco
| | - Kirstin Bett
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Dr., Saskatoon, SK S7N 5A8, Canada
| | - Helen Booker
- Department of Plant Agriculture, University of Guelph, Rm 316, Crop Science Bldg, 50 Stone Rd E, Guelph, ON N1G 2W1, Canada
| | - Gerald L Brown
- Genome Prairie, 111 Research Drive, Suite 101, Saskatoon, SK, S7N 3R2, Canada
| | - Glenn J Bryan
- The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Luigi Cattivelli
- CREA, Research Centre for Genomics and Bioinformatics, via San Protaso 302, Fiorenzuola d'Arda, 29017, Italy
| | - David Charest
- Genome British Columbia, 400-575 West 8th Avenue, Vancouver, BC, V5Z 0C4, Canada
| | - Kellye Eversole
- International Wheat Genome Sequencing Consortium, 2841 NE Marywood Ct, Lee's Summit, MO, 64086, USA
| | - Marcelo Freitas
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, Final Av W5 Norte, Caixa Postal 02372, 70770-917 - Brasília DF, Brazil
| | - Kioumars Ghamkhar
- Forage Science, Grasslands Research Centre, AgResearch, Palmerston North, 4410, New Zealand
| | - Dario Grattapaglia
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, Final Av W5 Norte, Caixa Postal 02372, 70770-917 - Brasília DF, Brazil
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072, Australia
| | - Maria Cleria Valadares Inglis
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, Final Av W5 Norte, Caixa Postal 02372, 70770-917 - Brasília DF, Brazil
| | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Zakaria Kehel
- International Center for Agricultural Research in the Dry Areas (ICARDA), Station Exp. INRA-Quich. Rue Hafiane Cherkaoui. Agdal. Rabat - Instituts, 10111, Rabat, Morocco
| | - Paul J Kersey
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Graham J King
- Southern Cross University, PO Box 157, Lismore, NSW 2480, Australia
| | - Stephen Kresovich
- Feed the Future Innovation Lab for Crop Improvement, 431 Weill Hall, Cornell University, Ithaca, NY, 14853, USA
| | - Emily Marden
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6R 2A5, Canada
| | - Sean Mayes
- Crops For the Future (UK) CIC 76-80 Baddow Road, Chelmsford, Essex, CM2 7PJ, UK
| | - Marie Noelle Ndjiondjop
- Africa Rice Center (AfricaRice), Mbe Research Station, Bouaké, 01 BP 2511 Bouaké, Côte d'Ivoire
| | - Henry T Nguyen
- University of Missouri, Division of Plant Sciences, 25 Agriculture Lab Bldg, College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, MO 65211, USA
| | - Samuel Rezende Paiva
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, Final Av W5 Norte, Caixa Postal 02372, 70770-917 - Brasília DF, Brazil
| | - Roberto Papa
- Università Politecnica delle Marche, D3A-Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Via Brecce Bianche, 60131, Ancona, Italy
| | - Peter W B Phillips
- Johnson Shoyama Graduate School of Public Policy, University of Saskatchewan, 101 Diefenbaker Place, Saskatoon, S7N 5B8, Canada
| | - Awais Rasheed
- CIMMYT-China office, Beijing 100081, Beijing, P.R. China
| | - Christopher Richards
- USDA-ARS National Laboratory for Genetic Resources Preservation, 1111 South Mason St, Fort Collins, CO, 80521, USA
| | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier, Cedex 5, France
| | - Maria Jose Amstalden Sampaio
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, Final Av W5 Norte, Caixa Postal 02372, 70770-917 - Brasília DF, Brazil
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Corrensstr. 3, D-06466 Seeland, Germany
| | - Paul D Shaw
- The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Brad Sherman
- Law School, University of Queensland, St Lucia, QLD, 4072, Australia
| | - S Evan Staton
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6R 2A5, Canada
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Corrensstr. 3, D-06466 Seeland, Germany; CiBreed - Center for Integrated Breeding Research, Department of Crop Sciences, Georg-August University Göttingen, Von Siebold Straße 8, D-37075 Göttingen, Germany
| | | | - Mark Tester
- King Abdullah University of Science & Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Jose Francisco Montenegro Valls
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, Final Av W5 Norte, Caixa Postal 02372, 70770-917 - Brasília DF, Brazil
| | - Rajeev Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru - 502 324, Telangana State, India
| | - Stephen Visscher
- Global Institute for Food Security, 110 Gymnasium Place, University of Saskatchewan, Saskatoon, SK, S7N 4J8, Canada
| | - Eric von Wettberg
- University of Vermont, 63 Carrigan Drive, Jeffords Hall, Burlington, VT, 05405, USA
| | - Robbie Waugh
- The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, UK; School of Agriculture and Wine & Waite Research Institute, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Peter Wenzl
- Centro Internacional de Agricultura Tropical (CIAT), Km 17 Recta Cali-Palmira, 763537 Cali, Colombia
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6R 2A5, Canada.
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Looseley ME, Ramsay L, Bull H, Swanston JS, Shaw PD, Macaulay M, Booth A, Russell JR, Waugh R, Thomas WTB. Association mapping of malting quality traits in UK spring and winter barley cultivar collections. Theor Appl Genet 2020; 133:2567-2582. [PMID: 32506274 PMCID: PMC7419451 DOI: 10.1007/s00122-020-03618-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 05/18/2020] [Indexed: 05/10/2023]
Abstract
Historical malting quality data was collated from UK national and recommended list trial data and used in a GWAS. 25 QTL were identified, with the majority from spring barley cultivar sets. In Europe, the most economically significant use of barley is the production of malt for use in the brewing and distilling industries. As such, selection for traits related to malting quality is of great commercial interest. In order to study the genetic basis of variation for malting quality traits in UK cultivars, a historical set of trial data was collated from national and recommended list trials from the period 1988 to 2016. This data was used to estimate variety means for 20 quality related traits in 451 spring barley cultivars, and 407 winter cultivars. Genotypes for these cultivars were generated using iSelect 9k and 50k genotyping platforms, and a genome wide association scan performed to identify malting quality quantitative trait loci (QTL). 24 QTL were identified in spring barley cultivars, and 2 from the winter set. A number of these correspond to known malting quality related genes but the remainder represents novel genetic variation that is accessible to breeders for the genetic improvement of new cultivars.
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Affiliation(s)
- Mark E Looseley
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
- Xelect Ltd, Horizon House, Abbey Walk, St Andrews, Fife, KY16 9LB, Scotland, UK
| | - Luke Ramsay
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK.
| | - Hazel Bull
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
- Syngenta UK Ltd., Market Stainton, Market Rasen, Lincolnshire, LN8 5LJ, UK
| | - J Stuart Swanston
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Paul D Shaw
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Malcolm Macaulay
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Allan Booth
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Joanne R Russell
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Robbie Waugh
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
- Plant Sciences Division, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, Scotland, UK
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6
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Selby P, Abbeloos R, Backlund JE, Basterrechea Salido M, Bauchet G, Benites-Alfaro OE, Birkett C, Calaminos VC, Carceller P, Cornut G, Vasques Costa B, Edwards JD, Finkers R, Yanxin Gao S, Ghaffar M, Glaser P, Guignon V, Hok P, Kilian A, König P, Lagare JEB, Lange M, Laporte MA, Larmande P, LeBauer DS, Lyon DA, Marshall DS, Matthews D, Milne I, Mistry N, Morales N, Mueller LA, Neveu P, Papoutsoglou E, Pearce B, Perez-Masias I, Pommier C, Ramírez-González RH, Rathore A, Raquel AM, Raubach S, Rife T, Robbins K, Rouard M, Sarma C, Scholz U, Sempéré G, Shaw PD, Simon R, Soldevilla N, Stephen G, Sun Q, Tovar C, Uszynski G, Verouden M. BrAPI-an application programming interface for plant breeding applications. Bioinformatics 2020; 35:4147-4155. [PMID: 30903186 PMCID: PMC6792114 DOI: 10.1093/bioinformatics/btz190] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 11/23/2018] [Accepted: 03/20/2019] [Indexed: 12/04/2022] Open
Abstract
Motivation Modern genomic breeding methods rely heavily on very large amounts of phenotyping and genotyping data, presenting new challenges in effective data management and integration. Recently, the size and complexity of datasets have increased significantly, with the result that data are often stored on multiple systems. As analyses of interest increasingly require aggregation of datasets from diverse sources, data exchange between disparate systems becomes a challenge. Results To facilitate interoperability among breeding applications, we present the public plant Breeding Application Programming Interface (BrAPI). BrAPI is a standardized web service API specification. The development of BrAPI is a collaborative, community-based initiative involving a growing global community of over a hundred participants representing several dozen institutions and companies. Development of such a standard is recognized as critical to a number of important large breeding system initiatives as a foundational technology. The focus of the first version of the API is on providing services for connecting systems and retrieving basic breeding data including germplasm, study, observation, and marker data. A number of BrAPI-enabled applications, termed BrAPPs, have been written, that take advantage of the emerging support of BrAPI by many databases. Availability and implementation More information on BrAPI, including links to the specification, test suites, BrAPPs, and sample implementations is available at https://brapi.org/. The BrAPI specification and the developer tools are provided as free and open source.
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Affiliation(s)
- Peter Selby
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
| | | | | | | | | | - Omar E Benites-Alfaro
- International Potato Center (CIP), Lima, Peru.,International Food Policy Research Institute (IFPRI), Washington DC, USA
| | | | - Viana C Calaminos
- International Rice Research Institute (IRRI), Los Baños, Laguna, The Philippines
| | - Pierre Carceller
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | | | | | | | - Richard Finkers
- Department of Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - Star Yanxin Gao
- Institute of Biotechnology, Cornell University, Ithaca, New York, USA
| | - Mehmood Ghaffar
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Philip Glaser
- Institute of Biotechnology, Cornell University, Ithaca, New York, USA
| | | | - Puthick Hok
- Diversity Arrays Technology, Bruce, Australia
| | | | - Patrick König
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | | | - Matthias Lange
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | | | | | - David S LeBauer
- College of Agricultural and Life Sciences, The University of Arizona, Tucson, AZ, USA
| | | | - David S Marshall
- Information & Computational Sciences, The James Hutton Institute, Dundee, UK.,SRUC, Edinburgh, UK
| | | | - Iain Milne
- Information & Computational Sciences, The James Hutton Institute, Dundee, UK
| | | | | | | | - Pascal Neveu
- MISTEA, INRA, Montpellier SupAgro, Universite de Montpellier, Montpellier, France
| | - Evangelia Papoutsoglou
- Department of Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | | | | | - Cyril Pommier
- URGI, INRA, Université Paris-Saclay, Versailles, France
| | | | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Angel Manica Raquel
- International Rice Research Institute (IRRI), Los Baños, Laguna, The Philippines
| | - Sebastian Raubach
- Information & Computational Sciences, The James Hutton Institute, Dundee, UK
| | - Trevor Rife
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Kelly Robbins
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
| | | | - Chaitanya Sarma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Guilhem Sempéré
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.,INTERTRYP, Univ Montpellier, CIRAD, IRD, Montpellier, France
| | - Paul D Shaw
- Information & Computational Sciences, The James Hutton Institute, Dundee, UK
| | | | - Nahuel Soldevilla
- Integrated Breeding Program (IBP), CIMMYT, Texcoco, Mexico.,LeafNode Technology, Buenos Aires, Argentina
| | - Gordon Stephen
- Information & Computational Sciences, The James Hutton Institute, Dundee, UK
| | - Qi Sun
- Institute of Biotechnology, Cornell University, Ithaca, New York, USA
| | - Clarysabel Tovar
- Integrated Breeding Program (IBP), CIMMYT, Texcoco, Mexico.,LeafNode Technology, Buenos Aires, Argentina
| | | | - Maikel Verouden
- Wageningen University & Research, Biometris, Wageningen PB, The Netherlands
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7
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Darrier B, Russell J, Milner SG, Hedley PE, Shaw PD, Macaulay M, Ramsay LD, Halpin C, Mascher M, Fleury DL, Langridge P, Stein N, Waugh R. A Comparison of Mainstream Genotyping Platforms for the Evaluation and Use of Barley Genetic Resources. Front Plant Sci 2019; 10:544. [PMID: 31105733 PMCID: PMC6499090 DOI: 10.3389/fpls.2019.00544] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 04/09/2019] [Indexed: 05/18/2023]
Abstract
We compared the performance of two commonly used genotyping platforms, genotyping-by-sequencing (GBS) and single nucleotide polymorphism-arrays (SNP), to investigate the extent and pattern of genetic variation within a collection of 1,000 diverse barley genotypes selected from the German Federal ex situ GenBank hosted at IPK Gatersleben. Each platform revealed equivalent numbers of robust bi-allelic SNPs (39,733 and 37,930 SNPs for the 50K SNP-array and GBS datasets respectively). A small overlap of 464 SNPs was common to both platforms, indicating that the methodologies we used selectively access informative polymorphism in different portions of the barley genome. Approximately half of the GBS dataset was comprised of SNPs with minor allele frequencies (MAFs) below 1%, illustrating the power of GBS to detect rare alleles in diverse germplasm collections. While desired for certain applications, the highly robust calling of alleles at the same SNPs across multiple populations is an advantage of the SNP-array, allowing direct comparisons of data from related or unrelated studies. Overall MAFs and diversity statistics (π) were higher for the SNP-array data, potentially reflecting the conscious removal of markers with a low MAF in the ascertainment population. A comparison of similarity matrices revealed a positive correlation between both approaches, supporting the validity of using either for entire GenBank characterization. To explore the potential of each dataset for focused genetic analyses we explored the outcomes of their use in genome-wide association scans for row type, growth habit and non-adhering hull, and discriminant analysis of principal components for the drivers of sub-population differentiation. Interpretation of the results from both types of analysis yielded broadly similar conclusions indicating that choice of platform used for such analyses should be determined by the research question being asked, group preferences and their capabilities to extract and interpret the different types of output data easily and quickly. Access to the requisite infrastructure for running, processing, analyzing, querying, storing, and displaying either datatype is an additional consideration. Our investigations reveal that for barley the cost per genotyping assay is less for SNP-arrays than GBS, which translates to a cost per informative datapoint being significantly lower for the SNP-array.
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Affiliation(s)
- Benoit Darrier
- School of Agriculture and Wine, The University of Adelaide, Adelaide, SA, Australia
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Joanne Russell
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Sara G. Milner
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Pete E. Hedley
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Paul D. Shaw
- Information and Computational Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Malcolm Macaulay
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Luke D. Ramsay
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Claire Halpin
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Delphine L. Fleury
- School of Agriculture and Wine, The University of Adelaide, Adelaide, SA, Australia
| | - Peter Langridge
- School of Agriculture and Wine, The University of Adelaide, Adelaide, SA, Australia
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
- Center of Integrated Breeding Research, Georg-August University, Göttingen, Germany
| | - Robbie Waugh
- School of Agriculture and Wine, The University of Adelaide, Adelaide, SA, Australia
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- *Correspondence: Robbie Waugh,
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Looseley ME, Griffe LL, Büttner B, Wright KM, Middlefell-Williams J, Bull H, Shaw PD, Macaulay M, Booth A, Schweizer G, Russell JR, Waugh R, Thomas WTB, Avrova A. Resistance to Rhynchosporium commune in a collection of European spring barley germplasm. Theor Appl Genet 2018; 131:2513-2528. [PMID: 30151748 DOI: 10.1007/s00122-018-3168-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 08/17/2018] [Indexed: 05/02/2023]
Abstract
Association analyses of resistance to Rhynchosporium commune in a collection of European spring barley germplasm detected 17 significant resistance quantitative trait loci. The most significant association was confirmed as Rrs1. Rhynchosporium commune is a fungal pathogen of barley which causes a highly destructive and economically important disease known as rhynchosporium. Genome-wide association mapping was used to investigate the genetic control of host resistance to R. commune in a collection of predominantly European spring barley accessions. Multi-year disease nursery field trials revealed 8 significant resistance quantitative trait loci (QTL), whilst a separate association mapping analysis using historical data from UK national and recommended list trials identified 9 significant associations. The most significant association identified in both current and historical data sources, collocated with the known position of the major resistance gene Rrs1. Seedling assays with R. commune single-spore isolates expressing the corresponding avirulence protein NIP1 confirmed that this locus is Rrs1. These results highlight the significant and continuing contribution of Rrs1 to host resistance in current elite spring barley germplasm. Varietal height was shown to be negatively correlated with disease severity, and a resistance QTL was identified that co-localised with the semi-dwarfing gene sdw1, previously shown to contribute to disease escape. The remaining QTL represent novel resistances that are present within European spring barley accessions. Associated markers to Rrs1 and other resistance loci, identified in this study, represent a set of tools that can be exploited by breeders for the sustainable deployment of varietal resistance in new cultivars.
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Affiliation(s)
- Mark E Looseley
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK.
| | - Lucie L Griffe
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
- RAGT Seeds Ltd, Grange Road, Ickleton, Saffron Walden, Essex, CB10 1TA, UK
| | - Bianca Büttner
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, Am Gereuth 2, 85354, Freising, Germany
| | - Kathryn M Wright
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | | | - Hazel Bull
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
- Syngenta UK Ltd, Market Stainton, Market Rasen, Lincolnshire, LN8 5LJ, UK
| | - Paul D Shaw
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Malcolm Macaulay
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Allan Booth
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Günther Schweizer
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, Am Gereuth 2, 85354, Freising, Germany
| | - Joanne R Russell
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Robbie Waugh
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | | | - Anna Avrova
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
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Affiliation(s)
- Cheol-Sik Yoon
- Department of Plant Pathology, University of Illinois, 1102 S. Goodwin, Urbana, Illinois 61801
| | - Dean A. Glawe
- Department of Plant Pathology, University of Illinois and Illinois Natural History Survey, 1102 S. Goodwin. Urbana, Illinois 61801
| | - Paul D. Shaw
- Department of Plant Pathology, University of Illinois, 1102 S. Goodwin, Urbana, Illinois 61801
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Bayer MM, Rapazote-Flores P, Ganal M, Hedley PE, Macaulay M, Plieske J, Ramsay L, Russell J, Shaw PD, Thomas W, Waugh R. Development and Evaluation of a Barley 50k iSelect SNP Array. Front Plant Sci 2017; 8:1792. [PMID: 29089957 PMCID: PMC5651081 DOI: 10.3389/fpls.2017.01792] [Citation(s) in RCA: 137] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 10/02/2017] [Indexed: 05/18/2023]
Abstract
High-throughput genotyping arrays continue to be an attractive, cost-effective alternative to sequencing based approaches. We have developed a new 50k Illumina Infinium iSelect genotyping array for barley, a cereal crop species of major international importance. The majority of SNPs on the array have been extracted from variants called in exome capture data of a wide range of European barley germplasm. We used the recently published barley pseudomolecule assembly to map the exome capture data, which allowed us to generate markers with accurate physical positions and detailed gene annotation. Markers from an existing and widely used barley 9k Infinium iSelect array were carried over onto the 50k chip for backward compatibility. The array design featured 49,267 SNP markers that converted into 44,040 working assays, of which 43,461 were scorable in GenomeStudio. Of the working assays, 6,251 are from the 9k iSelect platform. We validated the SNPs by comparing the genotype calls from the new array to legacy datasets. Rates of agreement averaged 98.1 and 93.9% respectively for the legacy 9k iSelect SNP set (Comadran et al., 2012) and the exome capture SNPs. To test the utility of the 50k chip for genetic mapping, we genotyped a segregating population derived from a Golden Promise × Morex cross (Liu et al., 2014) and mapped over 14,000 SNPs to genetic positions which showed a near exact correspondence to their known physical positions. Manual adjustment of the cluster files used by the interpreting software for genotype scoring improved results substantially, but migration of cluster files between sites led to a deterioration of results, suggesting that local adjustment of cluster files is required on a site-per-site basis. Information relating to the markers on the chip is available online at https://ics.hutton.ac.uk/50k.
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Affiliation(s)
- Micha M. Bayer
- The James Hutton Institute, Dundee, United Kingdom
- *Correspondence: Micha M. Bayer
| | | | | | | | | | | | - Luke Ramsay
- The James Hutton Institute, Dundee, United Kingdom
| | | | - Paul D. Shaw
- The James Hutton Institute, Dundee, United Kingdom
| | | | - Robbie Waugh
- The James Hutton Institute, Dundee, United Kingdom
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Shaw PD, Graham M, Kennedy J, Milne I, Marshall DF. Helium: visualization of large scale plant pedigrees. BMC Bioinformatics 2014; 15:259. [PMID: 25085009 PMCID: PMC4133633 DOI: 10.1186/1471-2105-15-259] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 07/10/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Plant breeders use an increasingly diverse range of data types to identify lines with desirable characteristics suitable to be taken forward in plant breeding programmes. There are a number of key morphological and physiological traits, such as disease resistance and yield that need to be maintained and improved upon if a commercial variety is to be successful. Computational tools that provide the ability to integrate and visualize this data with pedigree structure, will enable breeders to make better decisions on the lines that are used in crossings to meet both the demands for increased yield/production and adaptation to climate change. RESULTS We have used a large and unique set of experimental barley (H. vulgare) data to develop a prototype pedigree visualization system. We then used this prototype to perform a subjective user evaluation with domain experts to guide and direct the development of an interactive pedigree visualization tool called Helium. CONCLUSIONS We show that Helium allows users to easily integrate a number of data types along with large plant pedigrees to offer an integrated environment in which they can explore pedigree data. We have also verified that users were happy with the abstract representation of pedigrees that we have used in our visualization tool.
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Affiliation(s)
- Paul D Shaw
- Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK.
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Milne I, Stephen G, Bayer M, Cock PJA, Pritchard L, Cardle L, Shaw PD, Marshall D. Using Tablet for visual exploration of second-generation sequencing data. Brief Bioinform 2012; 14:193-202. [PMID: 22445902 DOI: 10.1093/bib/bbs012] [Citation(s) in RCA: 641] [Impact Index Per Article: 53.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The advent of second-generation sequencing (2GS) has provided a range of significant new challenges for the visualization of sequence assemblies. These include the large volume of data being generated, short-read lengths and different data types and data formats associated with the diversity of new sequencing technologies. This article illustrates how Tablet-a high-performance graphical viewer for visualization of 2GS assemblies and read mappings-plays an important role in the analysis of these data. We present Tablet, and through a selection of use cases, demonstrate its value in quality assurance and scientific discovery, through features such as whole-reference coverage overviews, variant highlighting, paired-end read mark-up, GFF3-based feature tracks and protein translations. We discuss the computing and visualization techniques utilized to provide a rich and responsive graphical environment that enables users to view a range of file formats with ease. Tablet installers can be freely downloaded from http://bioinf.hutton.ac.uk/tablet in 32 or 64-bit versions for Windows, OS X, Linux or Solaris. For further details on the Tablet, contact tablet@hutton.ac.uk.
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Affiliation(s)
- Iain Milne
- Information & Computational Sciences, The James Hutton Institute JHI, Dundee DD2 5DA, Scotland, UK.
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Obukowicz M, Shaw PD. Construction of tn3-containing plasmids from plant-pathogenic pseudomonads and an examination of their biological properties. Appl Environ Microbiol 2010; 49:468-73. [PMID: 16346739 PMCID: PMC238431 DOI: 10.1128/aem.49.2.468-473.1985] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Indigenous plasmids isolated from Pseudomonas tabaci ATCC 11528(pJP1), Pseudomonas angulata 45(pJP30), and P. tabaci BR2(pBPW1) (M. Obukowicz and P. D. Shaw, J. Bacteriol. 155:438-442, 1983) were labeled with Tn3, and the strains were subsequently cured of their respective plasmids. Plasmid-containing and cured isolates caused plant symptoms that were nearly indistinguishable, and the same amount of tabtoxin was produced by P. tabaci strains ATCC 11528 and BR2.
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Affiliation(s)
- M Obukowicz
- Department of Plant Pathology, University of Illinois, Urbana, Illinois 61801
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Harbour GC, Tymiak AA, Rinehart KL, Shaw PD, Hughes R, Mizsak SA, Coats JH, Zurenko GE, Li LH, Kuentzel SL. Ptilocaulin and isoptilocaulin, antimicrobial and cytotoxic cyclic guanidines from the Caribbean sponge Ptilocaulis aff. P. spiculifer (Lamarck, 1814). J Am Chem Soc 2002. [DOI: 10.1021/ja00408a071] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Siuda JF, VanBlaricom GR, Shaw PD, Johnson RD, White RH, Hager LP, Rinehart KL. 1-Iodo-3,3-dibromo-2-heptanone, 1,1,3,3-tetrabromo-2-heptanone, and related compounds from the red alga Bonnemaisonia hamifera. J Am Chem Soc 2002. [DOI: 10.1021/ja00837a066] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Cha C, Gao P, Chen YC, Shaw PD, Farrand SK. Production of acyl-homoserine lactone quorum-sensing signals by gram-negative plant-associated bacteria. Mol Plant Microbe Interact 1998; 11:1119-29. [PMID: 9805399 DOI: 10.1094/mpmi.1998.11.11.1119] [Citation(s) in RCA: 392] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Many gram-negative bacteria regulate expression of specialized gene sets in response to population density. This regulatory mechanism, called autoinduction or quorum-sensing, is based on the production by the bacteria of a small, diffusible signal molecule called the autoinducer. In the most well-studied systems the autoinducers are N-acylated derivatives of L-homoserine lactone (acyl-HSL). Signal specificity is conferred by the length, and the nature of the substitution at C-3, of the acyl side-chain. We evaluated four acyl-HSL bioreporters, based on tra of Agrobacterium tumefaciens, lux of Vibrio fischeri, las of Pseudomonas aeruginosa, and pigment production by Chromobacterium violaceum, for their ability to detect sets of 3-oxo acyl-HSLs, 3-hydroxy acyl-HSLs, and alkanoyl-HSLs with chain lengths ranging from C4 to C12. The traG::lacZ fusion reporter from the A. tumefaciens Ti plasmid was the single most sensitive and versatile detector of the four. Using this reporter, we screened 106 isolates representing seven genera of bacteria that associate with plants. Most of the Agrobacterium, Rhizobium, and Pantoea isolates and about half of the Erwinia and Pseudomonas isolates gave positive reactions. Only a few isolates of Xanthomonas produced a detectable signal. We characterized the acyl-HSLs produced by a subset of the isolates by thin-layer chromatography. Among the pseudomonads and erwinias, most produced a single dominant activity chromatographing with the properties of N-(3-oxo-hexanoyl)-L-HSL. However, a few of the erwinias, and the P. fluorescens and Ralstonia solanacearum isolates, produced quite different signals, including 3-hydroxy forms, as well as active compounds that chromatographed with properties unlike any of our standards. The few positive xanthomonas, and almost all of the agrobacteria, produced small amounts of a compound with the chromatographic properties of N-(3-oxo-octanoyl)-L-HSL. Members of the genus Rhizobium showed the greatest diversity, with some producing as few as one and others producing as many as seven detectable signals. Several isolates produced extremely nonpolar compounds indicative of very long acyl side-chains. Production of these compounds suggests that quorum-sensing is common as a gene regulatory mechanism among gram-negative plant-associated bacteria.
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Affiliation(s)
- C Cha
- Department of Crop Sciences, University of Illinois at Urbana-Champaign 61801, USA
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Liu L, Shaw PD. A possible role for acetylated intermediates in diaminopimelate and tabtoxinine-beta-lactam biosynthesis in Pseudomonas syringae pv. tabaci BR2.024. J Bacteriol 1997; 179:5922-7. [PMID: 9294453 PMCID: PMC179485 DOI: 10.1128/jb.179.18.5922-5927.1997] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The deduced product of an open reading frame (ORF3) located in the tabtoxinine-beta-lactam (T beta L) biosynthetic region of Pseudomonas syringae pv. tabaci BR2.024 (BR2.024) has significant sequence homology to the dapD products of other bacteria. dapD encodes L-2,3,4,5-tetrahydrodipicolinate succinyl coenzyme A succinyltransferase (THDPA-ST), an enzyme in the diaminopimelate (DAP) and lysine biosynthetic pathway. Complementation studies, in vitro transcription-translation experiments, and enzymatic assays indicated that ORF3 encodes a product with THDPA-ST activity in Escherichia coli dapD mutant beta 274. However, a BR2.024 mutant with an insert in ORF3 was prototrophic, and only basal THDPA-ST activity was detected in extracts of both parent and mutant. This finding suggested that ORF3 was not required for DAP biosynthesis and that it did not encode a product with THDPA-ST activity. The results of enzymatic studies, indicating that BR2.024 uses acetylated intermediates for DAP biosynthesis, are consistent with the hypothesis that BR2.024 does not need THDPA-ST for DAP biosynthesis. The ORF3 mutant produced reduced levels of tabtoxin, indicating that ORF3 may have a role in T beta L biosynthesis. We have named the gene tabB and have proposed a possible function for the gene product.
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Affiliation(s)
- L Liu
- Department of Crop Sciences, University of Illinois, Urbana-Champaign 61801, USA
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Shaw PD, Ping G, Daly SL, Cha C, Cronan JE, Rinehart KL, Farrand SK. Detecting and characterizing N-acyl-homoserine lactone signal molecules by thin-layer chromatography. Proc Natl Acad Sci U S A 1997; 94:6036-41. [PMID: 9177164 PMCID: PMC20996 DOI: 10.1073/pnas.94.12.6036] [Citation(s) in RCA: 578] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Many Gram-negative bacteria regulate gene expression in response to their population size by sensing the level of acyl-homoserine lactone signal molecules which they produce and liberate to the environment. We have developed an assay for these signals that couples separation by thin-layer chromatography with detection using Agrobacterium tumefaciens harboring lacZ fused to a gene that is regulated by autoinduction. With the exception of N-butanoyl-L-homoserine lactone, the reporter detected acyl-homoserine lactones with 3-oxo-, 3-hydroxy-, and 3-unsubstituted side chains of all lengths tested. The intensity of the response was proportional to the amount of the signal molecule chromatographed. Each of the 3-oxo- and the 3-unsubstituted derivatives migrated with a unique mobility. Using the assay, we showed that some bacteria produce as many as five detectable signal molecules. Structures could be assigned tentatively on the basis of mobility and spot shape. The dominant species produced by Pseudomonas syringae pv. tabaci chromatographed with the properties of N-(3-oxohexanoyl)-L-homoserine lactone, a structure that was confirmed by mass spectrometry. An isolate of Pseudomonas fluorescens produced five detectable species, three of which had novel chromatographic properties. These were identified as the 3-hydroxy- forms of N-hexanoyl-, N-octanoyl-, and N-decanoyl-L-homoserine lactone. The assay can be used to screen cultures of bacteria for acyl-homoserine lactones, for quantifying the amounts of these molecules produced, and as an analytical and preparative aid in determining the structures of these signal molecules.
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Affiliation(s)
- P D Shaw
- Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA
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Liu L, Shaw PD. Characterization of dapB, a gene required by Pseudomonas syringae pv. tabaci BR2.024 for lysine and tabtoxinine-beta-lactam biosynthesis. J Bacteriol 1997; 179:507-13. [PMID: 8990304 PMCID: PMC178722 DOI: 10.1128/jb.179.2.507-513.1997] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The dapB gene, which encodes L-2,3-dihydrodipicolinate reductase, the second enzyme of the lysine branch of the aspartic amino acid family, was cloned and sequenced from a tabtoxin-producing bacterium, Pseudomonas syringae pv. tabaci BR2.024. The deduced amino acid sequence shared 60 to 90% identity to known dapB gene products from gram-negative bacteria and 19 to 21% identity to the dapB products from gram-positive bacteria. The consensus sequence for the NAD(P)H binding site [(V/I)(A/G)(V/I)XGXXGXXG)] and the proposed substrate binding site (HHRHK) were conserved in the polypeptide. A BR2.024 dapB mutant is a diaminopimelate auxotroph and tabtoxin negative. The addition of a mixture of L-,L-, D,D-, and meso-diaminopimelate to defined media restored growth but not tabtoxin production. Cloned DNA fragments containing the parental dapB gene restored the ability to grow in defined media and tabtoxin production to the dapB mutant. These results indicate that the dapB gene is required for both lysine and tabtoxin biosynthesis, thus providing the first genetic evidence that the biosynthesis of tabtoxin proceeds in part along the lysine biosynthetic pathway. These data also suggest that L-2,3,4,5-tetrahydrodipicolinate is a common intermediate for both lysine and tabtoxin biosynthesis.
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Affiliation(s)
- L Liu
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 61801, USA
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Engst K, Shaw PD. Identification of a lysA-like gene required for tabtoxin biosynthesis and pathogenicity in Pseudomonas syringae pv. tabaci strain PTBR2.024. Mol Plant Microbe Interact 1992; 5:322-9. [PMID: 1515668 DOI: 10.1094/mpmi-5-322] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
Pseudomonas syringae pv. tabaci strain PTBR2.024 produces tabtoxin and causes wildfire disease on tobacco and green bean. PTBR7.000, a Tn5 mutant of PTBR2.024, does not produce tabtoxin, is nonpathogenic on tobacco, and is prototrophic. A 3-kb fragment from a genomic library of the parent strain PTBR2.024 complemented both mutant phenotypes. This 3-kb fragment contains two open reading frames (ORFs), ORF1 and ORF2, and two truncated ORFs, ORF3 and ORF4. The Tn5 insert in PTBR7.000 was mapped to ORF2, and complementation studies showed that an intact ORF2 was sufficient to restore tabtoxin production and pathogenicity. The deduced amino acid sequences of ORF2 and truncated ORF3 contain significant homology to bacterial lysine biosynthetic enzymes, diaminopimelate decarboxylase, and delta 1-piperidine-2,6-dicarboxylate succinyl transferase, respectively. ORF2, however, is not required for lysine biosynthesis. We designated the sequence corresponding to ORF2 as gene tabA and propose that the product of tabA is an enzyme in the tabtoxin biosynthetic pathway that recognizes a substrate analogue of a compound in the lysine biosynthetic pathway.
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Affiliation(s)
- K Engst
- Department of Plant Pathology, University of Illinois, Urbana-Champaign 61801
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Abstract
Nonpathogenic mutants of Xanthomonas campestris pv. glycines 8ra were generated with N-methyl-N-nitro-N'-nitrosoguanidine to identify and characterize pathogenicity genes of the bacterium. A total of 16 nonpathogenic mutants were isolated from 2,000 colonies. One mutant, NP1, was chosen for further study. NP1 did not multiply in soybean cotyledons. A genomic library of strain 8ra was constructed in the cosmid pLAFR3, and the cosmids were tested for complementation in NP1. One cosmid clone, pIH1, which contained a 31-kb insert, complemented mutant NP1. A restriction map of pIH1 was constructed, and deletion analyses identified a 10-kb HindIII fragment that restored pathogenicity to NP1. Southern hybridization analysis indicated that DNA sequences in the 10-kb HindIII fragment are conserved among other X. campestris pathovars tested. Three regions responsible for restoring pathogenicity have been identified by Tn3-HoHo1 mutagenesis. A 2.7-kb ClaI fragment was sequenced, and two possible open reading frames (ORF1 and ORF2) were found. Results indicated that ORF2 but not ORF1 may be expressed in Escherichia coli and in X. campestris pv. glycines. The carboxy terminus of the potential polypeptide encoded by ORF2 has an amino acid sequence similar to that of the gamma subunit of oxaloacetate decarboxylase, which is involved in sodium ion transport in Klebsiella pneumoniae.
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Affiliation(s)
- I Hwang
- Department of Plant Pathology, University of Illinois, Urbana-Champaign
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Abstract
Pseudomonas syringae pv. tabaci BR2 produces tabtoxin and causes wildfire disease on tobacco and bean plants. Approximately 2,700 Tn5 insertion mutants of a plasmid-free strain, PTBR 2.024, were generated by using suicide plasmid pGS9. Of these Tn5 mutants, 8 were no longer pathogenic on tobacco plants and 10 showed reduced symptoms. All of the eight nonpathogenic mutants caused typical wildfire disease symptoms on bean plants. Two of the nonpathogenic mutants failed to produce tabtoxin. The eight nonpathogenic mutants have Tn5 insertions into different EcoRI and SalI restriction fragments. The EcoRI fragments containing Tn5 from the eight nonpathogenic mutants were cloned into vector pTZ18R or pLAFR3. A genomic library of the parent strain was constructed in the broad-host-range cosmid pLAFR3. Three different cosmid clones that hybridized to the cloned Tn5-containing fragment from one of the nonpathogenic mutants, PTBR 4.000, were isolated from the genomic library. These clones contained six contiguous EcoRI fragments (a total of 57 kilobases [kb]). A 7.2-kb EcoRI fragment common to all three restored pathogenicity to mutant PTBR 4.000. None of the six EcoRI fragments hybridized to Tn5-containing fragments from the other seven mutants. The 7.2-kb fragment was conserved in P. syringae pv. tabaci and P. syringae pv. angulata, but not in other pathovars or strains. Because the mutants retained pathogenicity on bean plants and because of the conservation of the 7.2-kb EcoRI fragment only in pathovars of tobacco, we suggest that genes on the fragment might be related to host specificity.
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Affiliation(s)
- Y P Salch
- Department of Plant Pathology, University of Illinois at Urbana-Champaign 61801
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Abstract
Thirty isolates of Pseudomonas syringae pv. tabaci, pv. angulata (pathogens on tobacco), pv. coronafaciens, and pv. striafaciens (pathogens on oats) were examined for plasmid DNAs. The strains were obtained from plants throughout the world, some over 50 years ago. Of the 22 tobacco pathogens, 16 contain predominantly one type of plasmid, the pJP27.00 type. The remaining six tobacco-specific strains do not harbor detectable plasmids. The oat pathogens contain one, two, or three plasmids. DNA homology studies indicate that the plasmid DNAs are highly conserved. More importantly, the plasmids harbored by strains isolated from one host plant are conserved most stringently; e.g., the plasmids from the tobacco pathogens are, with one exception, indistinguishable by restriction endonuclease digestion and Southern hybridization. There is also extensive homology among plasmids indigenous to the oat-specific P. syringae pv. coronafaciens and pv. striafaciens strains.
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Obukowicz M, Shaw PD. Tn3 labeling of a cryptic plasmid found in the plant pathogenic bacterium Pseudomonas tabaci and mobilization of RSF1010 by donation. J Bacteriol 1983; 155:438-42. [PMID: 6305922 PMCID: PMC217702 DOI: 10.1128/jb.155.1.438-442.1983] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
pBPW1, a conjugative cryptic plasmid isolated from the plant pathogenic bacterium Pseudomonas tabaci BR2, was labeled with Tn3. pBPW1::Tn3 and RSF1010 mobilization into Pseudomonas mellea recipients were separate events, not involving recombination of the two plasmids during conjugation.
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Nagaraja KV, Shaw PD. Inhibition of wheat germ RNA polymerase II by 2, 6-dibromobenzoquinone and related compounds from Aplysina fistularis. Arch Biochem Biophys 1982; 215:544-50. [PMID: 7092240 DOI: 10.1016/0003-9861(82)90114-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Abstract
Cell-free extracts of Streptomyces bikiniensis contain an adenosine 5'-triphosphate-dependent kinase which inactivates streptomycin (Sm) and dihydrostreptomycin by phosphorylation. The products have been identified as streptomycin 6-phosphate and dihydrostreptomycin 6-phosphate. Activity was not present in logarithmic-phase cells, which were susceptible to 25 mug of Sm per ml. In stationary-phase cells, activity appeared 12 h before detectable Sm in the medium. These cells were resistant to more than 200 mug of Sm per ml. Certain S. bikiniensis isolates selected from cultures treated with acriflavine or ethidium bromide lost the ability to produce Sm and became susceptible to 10 mug of Sm per ml throughout their growth. Cell-free extracts of the dye-treated isolates did not inactivate Sm and lacked streptomycin kinase activity at all stages in development. Ribosomes from resistant cells bound the same amount of [(3)H]dihydrostreptomycin as ribosomes from susceptible cells, and there was no correlation between the uptake of [(3)H]dihydrostreptomycin and resistance. The Sm-inactivating enzyme was identified as streptomycin-6-kinase. These results suggest that phosphorylation by streptomycin-6-kinase is a major factor in resistance in S. bikiniensis.
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Newitter DA, Schlissel ER, Shaw PD. Teaching aid with a simulated periodontal membrane. J Dent Educ 1979; 43:306-7. [PMID: 86550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Newitter DA, Schlissel ER, Shaw PD. Teaching aid with a simulated periodontal membrane. J Dent Educ 1979. [DOI: 10.1002/j.0022-0337.1979.43.5.tb01266.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Abstract
The treatment of Streptomyces bikiniensis with ethidium bromide or acriflavine resulted in the loss of the ability to produce streptomycin in 2 approximately 16% of the colonies isolated from the treated spores. These isolates had also lost their resistance to streptomycin. Treatment with the dyes caused partial to total loss of the ability to produce aerial mycelium by S. bikiniensis, but the isolates regained this ability upon repeated transfer to fresh medium. The dyes did not appear to effect pigment production by S. bikiniensis.
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Carter JH, Du Bus RH, Dyer JR, Floyd JC, Rice KC, Shaw PD. Biosynthesis of viomycin. II. Origin of beta-lysine and viomycidine. Biochemistry 1974; 13:1227-33. [PMID: 4360783 DOI: 10.1021/bi00703a027] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Carter JH, Du Bus RH, Dyer JR, Floyd JC, Rice KC, Shaw PD. Biosynthesis of viomycin. I. Origin of alpha, beta-diaminopropionic acid and serine. Biochemistry 1974; 13:1221-7. [PMID: 4360782 DOI: 10.1021/bi00703a026] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Gruner BJ, DeAngelo AB, Shaw PD. The isolation and some properties of an enzyme system which catalyzes the degradation of -nitropropionic acid. Arch Biochem Biophys 1972; 148:107-14. [PMID: 4400520 DOI: 10.1016/0003-9861(72)90121-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Abstract
The metabolism of inorganic nitrogen compounds was studied in extracts of Penicillium atrovenetum which had been grown under conditions in which beta-nitropropionic acid (BNP) synthesis varied from 0 to 12.5 mumoles per ml. None of the extracts was able to oxidize ammonium ion or nitrite. An enzyme was detected which catalyzed the oxidation of hydroxylamine with cytochrome c as the electron acceptor. The activity of this enzyme was not related to the ability of the organism to produce BNP. Nitrate and nitrite reductase activities were detected only in P. atrovenetum cultures grown on nitrate as a nitrogen source. These results indicated that BNP synthesis is probably not directly associated with the metabolism of inorganic nitrogen compounds and that an organic pathway for the formation of the nitro group is more likely. The activities of certain enzymes related to the metabolism of aspartic acid were investigated. Aspartate ammonia-lyase activity could not be detected in P. atrovenetum extracts. Aspartate aminotransferase and glutamate dehydrogenase activities were found in the extracts but were highest in the cultures which did not produce BNP. beta-Nitroacrylic acid reductase activity was highest in extracts of cultures which were actively synthesizing BNP.
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Taber WA, Gottlieb D, Shaw PD. Antibiotics. Mycologia 1968. [DOI: 10.2307/3757406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Shaw PD, McCloskey JA. Biosynthesis of nitro compounds. II. Studies on potential precursors for the nitro group of beta-nitropropionic acid. Biochemistry 1967; 6:2247-60. [PMID: 6058115 DOI: 10.1021/bi00859a047] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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