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Ficht A, Konkin DJ, Cram D, Sidebottom C, Tan Y, Pozniak C, Rajcan I. Genomic selection for agronomic traits in a winter wheat breeding program. Theor Appl Genet 2023; 136:38. [PMID: 36897431 DOI: 10.1007/s00122-023-04294-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 12/19/2022] [Indexed: 06/18/2023]
Abstract
rAMP-seq based genomic selection for agronomic traits has been shown to be a useful tool for winter wheat breeding programs by increasing the rate of genetic gain. Genomic selection (GS) is an effective strategy to employ in a breeding program that focuses on optimizing quantitative traits, which results in the ability for breeders to select the best genotypes. GS was incorporated into a breeding program to determine the potential for implementation on an annual basis, with emphasis on selecting optimal parents and decreasing the time and costs associated with phenotyping large numbers of genotypes. The design options for applying repeat amplification sequencing (rAMP-seq) in bread wheat were explored, and a low-cost single primer pair strategy was implemented. A total of 1870 winter wheat genotypes were phenotyped and genotyped using rAMP-seq. The optimization of training to testing population size showed that the 70:30 ratio provided the most consistent prediction accuracy. Three GS models were tested, rrBLUP, RKHS and feed-forward neural networks using the University of Guelph Winter Wheat Breeding Program (UGWWBP) and Elite-UGWWBP populations. The models performed equally well for both populations and did not differ in prediction accuracy (r) for most agronomic traits, with the exception of yield, where RKHS performed the best with an r = 0.34 and 0.39 for each population, respectively. The ability to operate a breeding program where multiple selection strategies, including GS, are utilized will lead to higher efficiency in the program and ultimately lead to a higher rate of genetic gain.
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Affiliation(s)
- Alexandra Ficht
- Department of Plant Agriculture, University of Guelph, Crop Science Building, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - David J Konkin
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, Saskatoon, Canada
| | - Dustin Cram
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, Saskatoon, Canada
| | - Christine Sidebottom
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, Saskatoon, Canada
| | - Yifang Tan
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, Saskatoon, Canada
| | - Curtis Pozniak
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Room 2E64, Agriculture Building, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Istvan Rajcan
- Department of Plant Agriculture, University of Guelph, Crop Science Building, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada.
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2
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Zhang W, Boyle K, Gao P, Polley B, Brost JM, Francis T, Sidebottom C, McCallum B, Kutcher HR, Randhawa H, Fetch T, Ferrie AMR, Fobert PR. Systematic characterization of multi-rust resistance genes from a 'Parula x Thatcher' population with high-density genetic map. Phytopathology 2023. [PMID: 36656304 DOI: 10.1094/phyto-06-22-0238-fi] [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] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Pyramiding multiple resistant genes has been proposed as the most effective way to control wheat rust diseases globally. Identifying the most effective pyramids is challenged by the large pool of rust resistance genes, and limited information about their mechanisms of resistance and interactions. Here, using a high-density genetic map, a double haploid population, and multi-rust field testing, we aimed to systematically characterize the most effective gene pyramids for rust resistance from the durable multi-rust resistant CIMMYT cultivar, Parula. We revealed the Parula resistance gene pyramid contains Lr34/Yr18/Sr57 (Lr34), Lr46/Yr29/Sr58 (Lr46), Lr27/Yr30/Sr2 (Sr2) and Lr68. The efficacy, magnitude of effect and interactions with each other varied for the three rust diseases. A subpopulation mapping approach was applied to characterize the complex interactions of the resistance genes by controlling for the effect of Lr34. Using this approach, we found Lr34 and Lr68 have a strong additive effect for leaf rust, while no additive effects were observed for any rusts between Lr34 and Lr46. Lr34 combined synergistically with Sr12 from Thatcher for stem rust, while the additive effect of Lr34 and Sr2 was dependent on the type of rust and environment. Two novel leaf rust QTL from Parula were identified in this study, a stable QTL QLr-7BS, and QLr-5AS, which showed Lr34 dependent expression. With these findings, we propose combining 2-3 high value genes from Canadian wheat (e.g. Sr12 from Thatcher) with a foundational multi-APR cassette for desirable and durable resistance to all three rusts in Canadian wheat.
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Affiliation(s)
- Wentao Zhang
- National Research Council Canada, 6356, Aquatic and Crop Resource Development Research Centre, 110 Gymnasium Pl, Saskatoon, Saskatchewan, Canada, S7N0W9;
| | - Kerry Boyle
- National Research Council Canada, 6356, Aquatic and Crop Resource Development Research Centre, Saskatoon, Saskatchewan, Canada;
| | - Peng Gao
- National Research Council Canada, 6356, Aquatic and Crop Resource Development Research Centre, Saskatoon, Saskatchewan, Canada;
| | - Brittany Polley
- National Research Council Canada, 6356, Aquatic and Crop Resource Development Research Centre, Saskatoon, Saskatchewan, Canada;
| | - Jennifer M Brost
- National Research Council Canada, 6356, Aquatic and Crop Resource Development Research Centre, Saskatoon, Saskatchewan, Canada;
| | - Tammy Francis
- National Research Council Canada Saskatoon, 85071, Industrial Research Assistance Program, Saskatoon, Saskatchewan, Canada;
| | - Christine Sidebottom
- National Research Council Canada Saskatoon, 85071, Aquatic and Crop Resource Development, Saskatoon, Saskatchewan, Canada;
| | - Brent McCallum
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, Morden, Manitoba, Canada;
| | - Hadley Randal Kutcher
- University of Saskatchewan, 7235, Crop Development Centre/Department of Plant Sciences, Saskatoon, Saskatchewan, Canada;
| | - Harpinder Randhawa
- Agriculture and Agri-Food Canada Lethbridge Research and Development Centre, 98670, Lethbridge Research and Development Centre, Lethbridge, Alberta, Canada;
| | - Tom Fetch
- Agriculture and Agri-Food Canada, Brandon Research and Development Centre, Brandon, Manitoba, Canada;
| | - Alison M R Ferrie
- National Research Council Canada, 6356, Aquatic and Crop Resource Development Research Centre, Saskatoon, Saskatchewan, Canada;
| | - Pierre R Fobert
- National Research Council Canada, 6356, Aquatic and Crop Resource Development Research Centre, Ottawa, Ottawa, Ontario, Canada;
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Gao P, Quilichini TD, Yang H, Li Q, Nilsen KT, Qin L, Babic V, Liu L, Cram D, Pasha A, Esteban E, Condie J, Sidebottom C, Zhang Y, Huang Y, Zhang W, Bhowmik P, Kochian LV, Konkin D, Wei Y, Provart NJ, Kagale S, Smith M, Patterson N, Gillmor CS, Datla R, Xiang D. Evolutionary divergence in embryo and seed coat development of U's Triangle Brassica species illustrated by a spatiotemporal transcriptome atlas. New Phytol 2022; 233:30-51. [PMID: 34687557 DOI: 10.1111/nph.17759] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 07/19/2021] [Indexed: 06/13/2023]
Abstract
The economically valuable Brassica species include the six related members of U's Triangle. Despite the agronomic and economic importance of these Brassicas, the impacts of evolution and relatively recent domestication events on the genetic landscape of seed development have not been comprehensively examined in these species. Here we present a 3D transcriptome atlas for the six species of U's Triangle, producing a unique resource that captures gene expression data for the major subcompartments of the seed, from the unfertilized ovule to the mature embryo and seed coat. This comprehensive dataset for seed development in tetraploid and ancestral diploid Brassicas provides new insights into evolutionary divergence and expression bias at the gene and subgenome levels during the domestication of these valued crop species. Comparisons of gene expression associated with regulatory networks and metabolic pathways operating in the embryo and seed coat during seed development reveal differences in storage reserve accumulation and fatty acid metabolism among the six Brassica species. This study illustrates the genetic underpinnings of seed traits and the selective pressures placed on seed production, providing an immense resource for continued investigation of Brassica polyploid biology, genomics and evolution.
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Affiliation(s)
- Peng Gao
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, S7N 4L8, Canada
| | - Teagen D Quilichini
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Hui Yang
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Qiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Kirby T Nilsen
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, 2701 Grand Valley Road, Brandon, MB, R7C 1A1, Canada
| | - Li Qin
- College of Art & Science, University of Saskatchewan, 9 Campus Dr, Saskatoon, SK, S7N 5A5, Canada
| | - Vivijan Babic
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Li Liu
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, S7N 4L8, Canada
| | - Dustin Cram
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Asher Pasha
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks St., Toronto, ON, M5S 3B2, Canada
| | - Eddi Esteban
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks St., Toronto, ON, M5S 3B2, Canada
| | - Janet Condie
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Christine Sidebottom
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Yan Zhang
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Yi Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Wentao Zhang
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Pankaj Bhowmik
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Leon V Kochian
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, S7N 4L8, Canada
| | - David Konkin
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Yangdou Wei
- College of Art & Science, University of Saskatchewan, 9 Campus Dr, Saskatoon, SK, S7N 5A5, Canada
| | - Nicholas J Provart
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks St., Toronto, ON, M5S 3B2, Canada
| | - Sateesh Kagale
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Mark Smith
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Nii Patterson
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - C Stewart Gillmor
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados del IPN (CINVESTAV-IPN), Irapuato, Guanajuato, 36821, México
| | - Raju Datla
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, S7N 4L8, Canada
| | - Daoquan Xiang
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
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Sari E, Knox RE, Ruan Y, Henriquez MA, Kumar S, Burt AJ, Cuthbert RD, Konkin DJ, Walkowiak S, Campbell HL, Singh AK, Ross J, Lokuruge P, Hsueh E, Boyle K, Sidebottom C, Condie J, Yates S, Pozniak CJ, Fobert PR. Historic recombination in a durum wheat breeding panel enables high-resolution mapping of Fusarium head blight resistance quantitative trait loci. Sci Rep 2020; 10:7567. [PMID: 32372012 PMCID: PMC7200731 DOI: 10.1038/s41598-020-64399-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 04/15/2020] [Indexed: 11/09/2022] Open
Abstract
The durum wheat line DT696 is a source of moderate Fusarium head blight (FHB) resistance. Previous analysis using a bi-parental population identified two FHB resistance quantitative trait loci (QTL) on chromosome 5A: 5A1 was co-located with a plant height QTL, and 5A2 with a major maturity QTL. A Genome-Wide Association Study (GWAS) of DT696 derivative lines from 72 crosses based on multi-environment FHB resistance, plant height, and maturity phenotypic data was conducted to improve the mapping resolution and further elucidate the genetic relationship of height and maturity with FHB resistance. The Global Tetraploid Wheat Collection (GTWC) was exploited to identify durum wheat lines with DT696 allele and additional recombination events. The 5A2 QTL was confirmed in the derivatives, suggesting the expression stability of the 5A2 QTL in various genetic backgrounds. The GWAS led to an improved mapping resolution rendering the 5A2 interval 10 Mbp shorter than the bi-parental QTL mapping interval. Haplotype analysis using SNPs within the 5A2 QTL applied to the GTWC identified novel haplotypes and recombination breakpoints, which could be exploited for further improvement of the mapping resolution. This study suggested that GWAS of derivative breeding lines is a credible strategy for improving mapping resolution.
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Affiliation(s)
- Ehsan Sari
- Aquatic and Crop Resource Development Centre, National Research Council, Saskatoon, SK, Canada.,Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Ron E Knox
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada.
| | - Yuefeng Ruan
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada.
| | - Maria Antonia Henriquez
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| | - Santosh Kumar
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, MB, Canada
| | - Andrew J Burt
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Richard D Cuthbert
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - David J Konkin
- Aquatic and Crop Resource Development Centre, National Research Council, Saskatoon, SK, Canada
| | - Sean Walkowiak
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada.,Canadian Grain Commission, Winnipeg, MB, Canada
| | - Heather L Campbell
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Asheesh K Singh
- Department of Agronomy, Iowa State University, Ames, Iowa, United States of America
| | - Jay Ross
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Prabhath Lokuruge
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Emma Hsueh
- Aquatic and Crop Resource Development Centre, National Research Council, Saskatoon, SK, Canada
| | - Kerry Boyle
- Aquatic and Crop Resource Development Centre, National Research Council, Saskatoon, SK, Canada
| | - Christine Sidebottom
- Aquatic and Crop Resource Development Centre, National Research Council, Saskatoon, SK, Canada
| | - Janet Condie
- Aquatic and Crop Resource Development Centre, National Research Council, Saskatoon, SK, Canada
| | - Shawn Yates
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Curtis J Pozniak
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Pierre R Fobert
- Aquatic and Crop Resource Development Centre, National Research Council, Ottawa, ON, Canada
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5
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Clarke WE, Higgins EE, Plieske J, Wieseke R, Sidebottom C, Khedikar Y, Batley J, Edwards D, Meng J, Li R, Lawley CT, Pauquet J, Laga B, Cheung W, Iniguez-Luy F, Dyrszka E, Rae S, Stich B, Snowdon RJ, Sharpe AG, Ganal MW, Parkin IAP. A high-density SNP genotyping array for Brassica napus and its ancestral diploid species based on optimised selection of single-locus markers in the allotetraploid genome. Theor Appl Genet 2016; 129:1887-99. [PMID: 27364915 PMCID: PMC5025514 DOI: 10.1007/s00122-016-2746-7] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 06/18/2016] [Indexed: 05/18/2023]
Abstract
The Brassica napus Illumina array provides genome-wide markers linked to the available genome sequence, a significant tool for genetic analyses of the allotetraploid B. napus and its progenitor diploid genomes. A high-density single nucleotide polymorphism (SNP) Illumina Infinium array, containing 52,157 markers, was developed for the allotetraploid Brassica napus. A stringent selection process employing the short probe sequence for each SNP assay was used to limit the majority of the selected markers to those represented a minimum number of times across the highly replicated genome. As a result approximately 60 % of the SNP assays display genome-specificity, resolving as three clearly separated clusters (AA, AB, and BB) when tested with a diverse range of B. napus material. This genome specificity was supported by the analysis of the diploid ancestors of B. napus, whereby 26,504 and 29,720 markers were scorable in B. oleracea and B. rapa, respectively. Forty-four percent of the assayed loci on the array were genetically mapped in a single doubled-haploid B. napus population allowing alignment of their physical and genetic coordinates. Although strong conservation of the two positions was shown, at least 3 % of the loci were genetically mapped to a homoeologous position compared to their presumed physical position in the respective genome, underlying the importance of genetic corroboration of locus identity. In addition, the alignments identified multiple rearrangements between the diploid and tetraploid Brassica genomes. Although mostly attributed to genome assembly errors, some are likely evidence of rearrangements that occurred since the hybridisation of the progenitor genomes in the B. napus nucleus. Based on estimates for linkage disequilibrium decay, the array is a valuable tool for genetic fine mapping and genome-wide association studies in B. napus and its progenitor genomes.
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Affiliation(s)
- Wayne E Clarke
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Erin E Higgins
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Joerg Plieske
- TraitGenetics GmbH, Am Schwabeplan 1b, Stadt Seeland OT, 06466, Gatersleben, Germany
| | - Ralf Wieseke
- TraitGenetics GmbH, Am Schwabeplan 1b, Stadt Seeland OT, 06466, Gatersleben, Germany
| | - Christine Sidebottom
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, S7N 0W9, Canada
| | - Yogendra Khedikar
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Jacqueline Batley
- School of Plant Biology and The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
| | - Dave Edwards
- School of Plant Biology and The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
| | - Jinling Meng
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ruiyuan Li
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, 430070, China
| | | | - Jérôme Pauquet
- BIOGEMMA 6, chemin des Panedautes, 31700, Mondonville, France
- SYNGENTA France SAS, 346, route des Pasquiers, 84260, Sarrians, France
| | | | - Wing Cheung
- DNA Landmarks Inc, 84 Rue Richelieu, St-Jean-sur-Richelieu, QC, J3B 6X3, Canada
| | - Federico Iniguez-Luy
- Genomics and Bioinformatics Unit, Agri Aquaculture Nutritional Genomic Center (CGNA), Conicyt-Regional, Gore La Araucania, R10C1001, Temuco, Chile
| | - Emmanuelle Dyrszka
- Syngenta France SAS, 12 Chemin de l'hobit, B.P. 27, 31790, Saint-Sauveur, France
| | | | - Benjamin Stich
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Rod J Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Andrew G Sharpe
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, S7N 0W9, Canada
| | - Martin W Ganal
- TraitGenetics GmbH, Am Schwabeplan 1b, Stadt Seeland OT, 06466, Gatersleben, Germany
| | - Isobel A P Parkin
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada.
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6
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Singh R, Bollina V, Higgins EE, Clarke WE, Eynck C, Sidebottom C, Gugel R, Snowdon R, Parkin IAP. Single-nucleotide polymorphism identification and genotyping in Camelina sativa. Mol Breed 2015; 35:35. [PMID: 25620879 PMCID: PMC4300397 DOI: 10.1007/s11032-015-0224-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 11/18/2014] [Indexed: 05/09/2023]
Abstract
Camelina sativa, a largely relict crop, has recently returned to interest due to its potential as an industrial oilseed. Molecular markers are key tools that will allow C. sativa to benefit from modern breeding approaches. Two complementary methodologies, capture of 3' cDNA tags and genomic reduced-representation libraries, both of which exploited second generation sequencing platforms, were used to develop a low density (768) Illumina GoldenGate single nucleotide polymorphism (SNP) array. The array allowed 533 SNP loci to be genetically mapped in a recombinant inbred population of C. sativa. Alignment of the SNP loci to the C. sativa genome identified the underlying sequenced regions that would delimit potential candidate genes in any mapping project. In addition, the SNP array was used to assess genetic variation among a collection of 175 accessions of C. sativa, identifying two sub-populations, yet low overall gene diversity. The SNP loci will provide useful tools for future crop improvement of C. sativa.
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Affiliation(s)
- Ravinder Singh
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, S7N 0X2 Canada
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, 180 009 JK India
| | - Venkatesh Bollina
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, S7N 0X2 Canada
| | - Erin E. Higgins
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, S7N 0X2 Canada
| | - Wayne E. Clarke
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, S7N 0X2 Canada
| | - Christina Eynck
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, S7N 0X2 Canada
| | - Christine Sidebottom
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, S7N 0W9 Canada
| | - Richard Gugel
- Plant Gene Resources Canada, 107 Science Place, Saskatoon, S7N 0X2 Canada
| | - Rod Snowdon
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Isobel A. P. Parkin
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, S7N 0X2 Canada
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7
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Clarke WE, Parkin IA, Gajardo HA, Gerhardt DJ, Higgins E, Sidebottom C, Sharpe AG, Snowdon RJ, Federico ML, Iniguez-Luy FL. Genomic DNA enrichment using sequence capture microarrays: a novel approach to discover sequence nucleotide polymorphisms (SNP) in Brassica napus L. PLoS One 2013; 8:e81992. [PMID: 24312619 PMCID: PMC3849492 DOI: 10.1371/journal.pone.0081992] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 10/20/2013] [Indexed: 12/24/2022] Open
Abstract
Targeted genomic selection methodologies, or sequence capture, allow for DNA enrichment and large-scale resequencing and characterization of natural genetic variation in species with complex genomes, such as rapeseed canola (Brassica napus L., AACC, 2n=38). The main goal of this project was to combine sequence capture with next generation sequencing (NGS) to discover single nucleotide polymorphisms (SNPs) in specific areas of the B. napus genome historically associated (via quantitative trait loci –QTL– analysis) to traits of agronomical and nutritional importance. A 2.1 million feature sequence capture platform was designed to interrogate DNA sequence variation across 47 specific genomic regions, representing 51.2 Mb of the Brassica A and C genomes, in ten diverse rapeseed genotypes. All ten genotypes were sequenced using the 454 Life Sciences chemistry and to assess the effect of increased sequence depth, two genotypes were also sequenced using Illumina HiSeq chemistry. As a result, 589,367 potentially useful SNPs were identified. Analysis of sequence coverage indicated a four-fold increased representation of target regions, with 57% of the filtered SNPs falling within these regions. Sixty percent of discovered SNPs corresponded to transitions while 40% were transversions. Interestingly, fifty eight percent of the SNPs were found in genic regions while 42% were found in intergenic regions. Further, a high percentage of genic SNPs was found in exons (65% and 64% for the A and C genomes, respectively). Two different genotyping assays were used to validate the discovered SNPs. Validation rates ranged from 61.5% to 84% of tested SNPs, underpinning the effectiveness of this SNP discovery approach. Most importantly, the discovered SNPs were associated with agronomically important regions of the B. napus genome generating a novel data resource for research and breeding this crop species.
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Affiliation(s)
- Wayne E. Clarke
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Isobel A. Parkin
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Humberto A. Gajardo
- Genomics and Bioinformatics Unit, Agriaquaculture Nutritional Genomic Center (CGNA), Temuco, Louisiana, United States of America Araucanía, Chile
| | | | - Erin Higgins
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Christine Sidebottom
- Plant Biotechnology Institute, National Research Council Canada, Saskatoon, Saskatchewan, Canada
| | - Andrew G. Sharpe
- Plant Biotechnology Institute, National Research Council Canada, Saskatoon, Saskatchewan, Canada
| | - Rod J. Snowdon
- Department of Plant Breeding, Justus Liebig University, Giessen, Germany
| | - Maria L. Federico
- Genomics and Bioinformatics Unit, Agriaquaculture Nutritional Genomic Center (CGNA), Temuco, Louisiana, United States of America Araucanía, Chile
| | - Federico L. Iniguez-Luy
- Genomics and Bioinformatics Unit, Agriaquaculture Nutritional Genomic Center (CGNA), Temuco, Louisiana, United States of America Araucanía, Chile
- * E-mail:
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Parkin IA, Clarke WE, Sidebottom C, Zhang W, Robinson SJ, Links MG, Karcz S, Higgins EE, Fobert P, Sharpe AG. Towards unambiguous transcript mapping in the allotetraploid Brassica napusThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”. Genome 2010; 53:929-38. [DOI: 10.1139/g10-053] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The architecture of the Brassica napus genome is marked by its evolutionary origins. The genome of B. napus was formed from the hybridization of two closely related diploid Brassica species, both of which evolved from an hexaploid ancestor. The extensive whole genome duplication events in its near and distant past result in the allotetraploid genome of B. napus maintaining multiple copies of most genes, which predicts a highly complex and redundant transcriptome that can confound any expression analyses. A stringent assembly of 142 399 B. napus expressed sequence tags allowed the development of a well-differentiated set of reference transcripts, which were used as a foundation to assess the efficacy of available tools for identifying and distinguishing transcripts in B. napus ; including microarray hybridization and 3′ anchored sequence tag capture. Microarray platforms cannot distinguish transcripts derived from the two progenitors or close homologues, although observed differential expression appeared to be biased towards unique transcripts. The use of 3′ capture enhanced the ability to unambiguously identify homologues within the B. napus transcriptome but was limited by tag length. The ability to comprehensively catalogue gene expression in polyploid species could be transformed by the application of cost-efficient next generation sequencing technologies that will capture millions of long sequence tags.
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Affiliation(s)
- Isobel A.P. Parkin
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
- Department of Computing Science, 176 Thorvaldson Building, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada
- National Research Council Plant Biotechnology Institute, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
- Department of Veterinary Microbiology, WCVM, University of Saskatchewan, 52 Campus Drive, Saskatoon, SK S7N 5B4, Canada
| | - Wayne E. Clarke
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
- Department of Computing Science, 176 Thorvaldson Building, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada
- National Research Council Plant Biotechnology Institute, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
- Department of Veterinary Microbiology, WCVM, University of Saskatchewan, 52 Campus Drive, Saskatoon, SK S7N 5B4, Canada
| | - Christine Sidebottom
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
- Department of Computing Science, 176 Thorvaldson Building, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada
- National Research Council Plant Biotechnology Institute, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
- Department of Veterinary Microbiology, WCVM, University of Saskatchewan, 52 Campus Drive, Saskatoon, SK S7N 5B4, Canada
| | - Wentao Zhang
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
- Department of Computing Science, 176 Thorvaldson Building, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada
- National Research Council Plant Biotechnology Institute, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
- Department of Veterinary Microbiology, WCVM, University of Saskatchewan, 52 Campus Drive, Saskatoon, SK S7N 5B4, Canada
| | - Stephen J. Robinson
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
- Department of Computing Science, 176 Thorvaldson Building, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada
- National Research Council Plant Biotechnology Institute, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
- Department of Veterinary Microbiology, WCVM, University of Saskatchewan, 52 Campus Drive, Saskatoon, SK S7N 5B4, Canada
| | - Matthew G. Links
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
- Department of Computing Science, 176 Thorvaldson Building, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada
- National Research Council Plant Biotechnology Institute, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
- Department of Veterinary Microbiology, WCVM, University of Saskatchewan, 52 Campus Drive, Saskatoon, SK S7N 5B4, Canada
| | - Steve Karcz
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
- Department of Computing Science, 176 Thorvaldson Building, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada
- National Research Council Plant Biotechnology Institute, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
- Department of Veterinary Microbiology, WCVM, University of Saskatchewan, 52 Campus Drive, Saskatoon, SK S7N 5B4, Canada
| | - Erin E. Higgins
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
- Department of Computing Science, 176 Thorvaldson Building, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada
- National Research Council Plant Biotechnology Institute, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
- Department of Veterinary Microbiology, WCVM, University of Saskatchewan, 52 Campus Drive, Saskatoon, SK S7N 5B4, Canada
| | - Pierre Fobert
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
- Department of Computing Science, 176 Thorvaldson Building, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada
- National Research Council Plant Biotechnology Institute, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
- Department of Veterinary Microbiology, WCVM, University of Saskatchewan, 52 Campus Drive, Saskatoon, SK S7N 5B4, Canada
| | - Andrew G. Sharpe
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
- Department of Computing Science, 176 Thorvaldson Building, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada
- National Research Council Plant Biotechnology Institute, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
- Department of Veterinary Microbiology, WCVM, University of Saskatchewan, 52 Campus Drive, Saskatoon, SK S7N 5B4, Canada
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Sidebottom C, Buckley S, Pudney P, Twigg S, Jarman C, Holt C, Telford J, McArthur A, Worrall D, Hubbard R, Lillford P. Heat-stable antifreeze protein from grass. Nature 2000; 406:256. [PMID: 10917518 DOI: 10.1038/35018639] [Citation(s) in RCA: 198] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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10
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Edwards ME, Dickson CA, Chengappa S, Sidebottom C, Gidley MJ, Reid JS. Molecular characterisation of a membrane-bound galactosyltransferase of plant cell wall matrix polysaccharide biosynthesis. Plant J 1999; 19:691-7. [PMID: 10571854 DOI: 10.1046/j.1365-313x.1999.00566.x] [Citation(s) in RCA: 117] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Galactomannan biosynthesis in vitro is catalysed by membrane preparations from developing fenugreek seed endosperms. Two enzymes interact: a GDP-mannose dependent (1-->4)-beta-D-mannan synthase and a UDP-galactose dependent (1-->6)-alpha-D-galactosyltransferase. The statistical distribution of galactosyl substituents along the mannan backbone, and the degree of galactose substitution of the primary product of galactomannan biosynthesis appear to be regulated by the specificity of the galactosyltransferase. We now report the detergent solubilisation of the fenugreek galactosyltransferase with retention of activity, the identification on gels of a putative 51 kDa galactosyltransferase protein, and the isolation, cloning and sequencing of the corresponding cDNA. The solubilised galactosyltransferase has an absolute requirement for added acceptor substrates. Beta-(1-->4)-linked D-manno-oligosaccharides with chain lengths greater than or equal to 5 acted as acceptors, as did galactomannans of low to medium galactose-substitution. The putative galactosyltransferase cDNA encodes a 51282 Da protein, with a single transmembrane alpha helix near the N terminus. We have also confirmed the identity of the galactosyltransferase by inserting the cDNA in frame into the genome of the methylotrophic yeast Pichia pastoris under the control of an AOX promoter and the yeast alpha secretion factor and observing the secretion of galactomannan alpha-galactosyltransferase activity. Particularly high activities were observed when a truncated sequence, lacking the membrane-spanning helix, was expressed.
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Affiliation(s)
- M E Edwards
- University of Stirling, Department of Biological Sciences, Stirling, UK
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11
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Sidebottom C. IEC 60601-1, the 3rd edition: what will change? Biomed Instrum Technol 1999; 33:334-6. [PMID: 10459420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
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12
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Worrall D, Elias L, Ashford D, Smallwood M, Sidebottom C, Lillford P, Telford J, Holt C, Bowles D. A carrot leucine-rich-repeat protein that inhibits ice recrystallization. Science 1998; 282:115-7. [PMID: 9756474 DOI: 10.1126/science.282.5386.115] [Citation(s) in RCA: 193] [Impact Index Per Article: 7.4] [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: 11/02/2022]
Abstract
Many organisms adapted to live at subzero temperatures express antifreeze proteins that improve their tolerance to freezing. Although structurally diverse, all antifreeze proteins interact with ice surfaces, depress the freezing temperature of aqueous solutions, and inhibit ice crystal growth. A protein purified from carrot shares these functional features with antifreeze proteins of fish. Expression of the carrot complementary DNA in tobacco resulted in the accumulation of antifreeze activity in the apoplast of plants grown at greenhouse temperatures. The sequence of carrot antifreeze protein is similar to that of polygalacturonase inhibitor proteins and contains leucine-rich repeats.
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Affiliation(s)
- D Worrall
- The Plant Laboratory, Biology Department, University of York, Post Office Box 373, York, YO1 5YW, UK
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13
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Allen AK, Bolwell GP, Brown DS, Sidebottom C, Slabas AR. Potato lectin: a three-domain glycoprotein with novel hydroxyproline-containing sequences and sequence similarities to wheat-germ agglutinin. Int J Biochem Cell Biol 1996; 28:1285-91. [PMID: 9022287 DOI: 10.1016/s1357-2725(96)00043-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [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]
Abstract
Potato (Solanum tuberosum) tuber lectin is a chitin-binding, hydroxyproline-rich glycoprotein, which may be involved in the defence mechanism of the plant. We had previously obtained evidence that it consists of at least two very dissimilar domains. The aim was to use a combination of accurate determinations of molecular weight and protein sequencing to gain more accurate information on the domains. Accurate determinations of the molecular weight of the lectin by a MALDI mass spectrometer have shown that the subunit molecular weight is 65,500 (+/- 1100) and that of a totally deglycosylated sample is 31,250 (+/- 30). This means that the lectin is 52.3 (+/- 1)% carbohydrate with a considerable number of glycoforms being present. Partial sequences and other analyses are consistent with the existence of three distinct domains. These are: (1) an N-terminal region which is rich in proline but poor in hydroxyproline; (2) a glycosylated region with a glycosylated molecular weight of 45,300 (+/- 1100) and a deglycosylated molecular weight of 11,050 (+/- 50) which is extremely rich in glycosylated hydroxyproline residues with a similar sequence to extensins; and (3) a cystine-rich domain which has the sugar binding site shows partial conservation of a repeated motif common to many chitin-binding proteins of the hevin family including wheat-germ agglutinin. The closest similarity seems to be to the sequence of potato basic chitinase.
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Affiliation(s)
- A K Allen
- Department of Biochemistry, Charing Cross and Westminster Medical School, (University of London), U.K
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14
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Edwards A, Marshall J, Denyer K, Sidebottom C, Visser RG, Martin C, Smith AM. Evidence that a 77-kilodalton protein from the starch of pea embryos is an isoform of starch synthase that is both soluble and granule bound. Plant Physiol 1996; 112:89-97. [PMID: 8819321 PMCID: PMC157927 DOI: 10.1104/pp.112.1.89] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
In this paper we provide further evidence about the nature of a 77-kD starch synthase (SSII) that is both soluble and bound to the starch granules in developing pea (Pisum sativum L.) embryos. Mature SSII gives rise to starch synthase activity when expressed in a strain of Escherichia coli lacking glycogen synthase. In transgenic potatoes (Solanum tuberosum L.) expressing SSII, the protein is both soluble and bound to the starch granules. These results confirm that SSII is a starch synthase and indicate that partitioning between the soluble and granule-bound fraction of storage organs is an intrinsic property of the protein. A 60-kD isoform of starch synthase found both in the soluble and granule-bound fraction of the pea embryos is probably derived by the processing of SSII and is a different gene product from GBSSI, the exclusively granule-bound 59-kD isoform of starch synthase that is similar to starch synthases encoded by the waxy genes of cereals and the amf gene of potatoes. Consistent with this, expression in E. coli of an N-terminally truncated version of SSII gives rise to starch synthase activity.
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Affiliation(s)
- A Edwards
- John Innes Centre, Norwich, United Kingdom
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15
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Marshall J, Sidebottom C, Debet M, Martin C, Smith AM, Edwards A. Identification of the major starch synthase in the soluble fraction of potato tubers. Plant Cell 1996; 8:1121-35. [PMID: 8768372 PMCID: PMC161188 DOI: 10.1105/tpc.8.7.1121] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The major isoform of starch synthase from the soluble fraction of developing potato tubers has been purified and used to prepare an antibody and isolate a cDNA. The protein is 140 kD, and it is distinctly different in predicted primary amino acid sequence from other isoforms of the enzyme thus far described. Immunoinhibition and immunoblotting experiments and analysis of tubers in which activity of the isoform was reduced through expression of antisense mRNA revealed that the isoform accounts for approximately 80% of the activity in the soluble fraction of the tuber and that it is also bound to starch granules. Severe reductions in activity had no discernible effect on starch content or amylose-to-amylopectin ratio of starch in tubers. However, they caused a profound change in the morphology of starch granules, indicative of important underlying changes in the structure of starch polymers within the granule.
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Affiliation(s)
- J Marshall
- John Innes Centre, Norwich, United Kingdom
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16
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Edwards A, Marshall J, Sidebottom C, Visser RG, Smith AM, Martin C. Biochemical and molecular characterization of a novel starch synthase from potato tubers. Plant J 1995; 8:283-94. [PMID: 7670507 DOI: 10.1046/j.1365-313x.1995.08020283.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
An isoform of starch synthase from potato tubers which is present both in the stroma of the plastid and tightly bound to starch granules has been identified biochemically and a cDNA has been isolated. The protein encoded by the cDNA is 79.9 kDa and has a putative transit peptide and a distinct N-terminal domain which is predicted to be highly flexible. It is similar in both amino acid sequence and predicted structure to the granule-bound starch synthase II (GBSSII) of pea embryos. When expressed in Escherichia coli, the mature protein has starch synthase activity. The importance of the isoform has been assessed by biochemical measurements and antisense transformation experiments in which the amount of the isoform in the tuber is severely and specifically reduced. Both approaches indicate that the isoform contributes a maximum of 15% of the total starch synthase activity of the tuber. It is suggested that this isoform and the GBSSII of pea embryos represent a widely distributed class of isoforms of starch synthase. The contribution to total starch synthase activity of members of this class probably varies considerably from one type of storage organ to another.
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17
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Abstract
Characterization of Pisum (pea) seed trypsin inhibitors (TI) and their corresponding cDNAs indicates that the pea TI gene family contains two genes. The existence of multiple TI isoforms can be attributed to post-translational modifications of primary gene products. Post-translational processing at the C-terminus during the desiccation stage of seed development results in the appearance of TI isoforms with increased affinity for the target enzyme, trypsin.
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18
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Carling D, Aguan K, Woods A, Verhoeven AJ, Beri RK, Brennan CH, Sidebottom C, Davison MD, Scott J. Mammalian AMP-activated protein kinase is homologous to yeast and plant protein kinases involved in the regulation of carbon metabolism. J Biol Chem 1994; 269:11442-8. [PMID: 7908907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
In mammals, an AMP-activated protein kinase (AMPK) phosphorylates both acetyl-CoA carboxylase and 3-hydroxy-3-methylglutaryl-CoA reductase in vitro and has been proposed to play a major role in the regulation of lipid metabolism in vivo. We report here the primary sequence of rat AMPK and show that antibodies raised against synthetic peptides based on the deduced sequence of AMPK immunoprecipitate AMPK activity from rat liver extracts. AMPK has a remarkable degree of sequence identity to the proteins encoded by the yeast SNF1 gene and the plant RKIN1 gene. SNF1 protein kinase activity is essential for release of genes from glucose repression in Saccharomyces cerevisiae. Expression of cRKIN1 in yeast snf1 mutants restores SNF1 function. These results indicate that AMPK, SNF1, and RKIN1 form part of a family of protein kinases that have been highly conserved throughout evolution. Our results suggest that AMPK may be involved in the regulation of a wide range of metabolic pathways.
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Affiliation(s)
- D Carling
- Medical Research Council of Molecular Medicine, Royal Postgraduate Medical School, London, United Kingdom
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Denyer K, Sidebottom C, Hylton CM, Smith AM. Soluble isoforms of starch synthase and starch-branching enzyme also occur within starch granules in developing pea embryos. Plant J 1993; 4:191-198. [PMID: 8220472 DOI: 10.1046/j.1365-313x.1993.04010191.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Developing wild-type pea embryos contain two major isoforms of starch synthase and two isoforms of starch-branching enzyme. One of the starch synthases and both starch-branching enzymes occur both in the soluble fraction and tightly bound to starch granules. The other starch synthase, which is very similar to the waxy proteins of other species, is exclusively granule-bound., It is inactive when solubilized in a native form from starch granules, but activity is recovered when the SDS-denatured protein is reconstituted from polyacrylamide gels. Evidence is presented which indicates that all of these proteins become incorporated within the structure of the granule as it grows. It is proposed that the granule-bound waxy protein is active in vivo at the granule surface, whereas the remaining proteins are active in the soluble fraction of the amyloplast. The proteins become trapped within the granule matrix as the polymers they synthesize crystallize around them, and they probably play no further part in polymer synthesis.
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Affiliation(s)
- K Denyer
- John Innes Institute, Norwich, UK
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20
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de Silva J, Jarman CD, Arrowsmith DA, Stronach MS, Chengappa S, Sidebottom C, Reid JS. Molecular characterization of a xyloglucan-specific endo-(1-->4)-beta-D-glucanase (xyloglucan endo-transglycosylase) from nasturtium seeds. Plant J 1993; 3:701-711. [PMID: 8374619 DOI: 10.1111/j.1365-313x.1993.00701.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
A novel xyloglucan-specific endo-(1-->4)-beta-D-glucanase, involved in the post-germinative mobilization of xyloglucan storage reserves, has previously been isolated from nasturtium (Tropaeolum majus L.) seed. Its mode of action has been shown, in vitro, to be one of transglycosylation except at low substrate (glycosylacceptor) concentrations when hydrolysis predominates. Here it is shown that this nasturtium seed xyloglucan endo-transglycosylase is encoded by a single gene which is transcribed and processed to a 1.5 kb mRNA. The isolation and DNA sequence analysis of a cDNA copy of the nasturtium xyloglucan endo-transglycosylase transcript is described. The cDNA encodes a 33.5 kDa precursor polypeptide which is subsequently processed to a 31 kDa mature protein. The precursor incorporates an N-terminal signal sequence which probably contains information relevant to the targeting of the enzyme to the cell wall. The computer-predicted isoelectric point (5.14) and low (approximately 0%) alpha-helix content of the deduced mature protein are in excellent agreement with the experimental data obtained using the purified enzyme. The deduced protein sequence lacks homology with known plant endo-(1-->4)-beta-D-glucanases, consistent with the unique properties of the enzyme. Database searches have revealed that a Brassica protein (meri-5) of previously unknown function, but abundantly expressed in expanding tissue, shares structural identity with the nasturtium xyloglucan endo-transglycosylase. The expression of a xyloglucan endo-transglycosylase in expanding tissue would be consistent with the contention that enzymes of this type are involved in cell wall loosening.
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Affiliation(s)
- J de Silva
- Colworth Laboratory, Sharnbrook, Bedford, UK
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21
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Foulds IJ, Lea VJ, Sidebottom C, James CM, Boulton RE, Brears T, Slabas AR, Jack PL, Stratford R. Cloning and sequence analysis of the coat protein gene of barley mild mosaic virus. Virus Res 1993; 27:79-89. [PMID: 8447180 DOI: 10.1016/0168-1702(93)90114-3] [Citation(s) in RCA: 8] [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: 01/30/2023]
Abstract
The sequence of the 3' 1462nts of RNA-1 of a UK isolate of the fungal-transmitted virus barley mild mosaic (BaMMV) has been determined. An open reading frame encoding the coat protein gene was identified within this region using amino acid sequence information obtained by cyanogen bromide cleavage of virus particles. The amino acid sequence of the full-length coat protein was deduced from the nucleotide sequence. Amino acid sequence comparisons revealed highest homology to the coat protein of barley yellow mosaic virus. In addition, a significant, but limited, number of the amino acid residues that are conserved between aphid-transmitted potyviruses were also conserved between BaMMV and potyviruses.
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Affiliation(s)
- I J Foulds
- Plant Breeding International, Trumpington, Cambridge, UK
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22
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Millar DJ, Slabas AR, Sidebottom C, Smith CG, Allen AK, Bolwell GP. A major stress-inducible Mr-42000 wall glycoprotein of French bean (Phaseolus vulgaris L.). Planta 1992; 187:176-184. [PMID: 24178040 DOI: 10.1007/bf00201935] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/09/1991] [Indexed: 06/02/2023]
Abstract
A major wall protein of suspension-cultured cells of French bean has been isolated and characterised. It can be prepared from walls or the culture filtrate and in composition it is particularly rich in proline, valine and glutamic acid/glutamine and contains appreciable amounts of hydroxyproline. The N-terminus shows some glycosylation, while following chemical deglycosylation the first 38 residues were found to be identical to those of proline-rich proteins from soybean. However, the composition of the highly purified Mr-42000 bean protein differs considerably from the soybean proteins and must contain its own specific domains. An antibody was raised and used to demonstrate the inducibility of the Mr-42000 bean protein in response to elicitor action. The protein was found to be mainly localised in the intercellular spaces of the cortical cells of bean hypocotyls and at the wall-plasmalemma interface of xylem vessels, another potentially accessible compartment for pathogens. Following wounding, the protein was found to be generally distributed in the wall of epidermal and cortical cells of the hypocotyls. The Mr-42000 protein is cross reactive with antibodies raised to glycoproteins of the Rhizobium infection thread and the chitin-binding hydroxyproline-rich glycoprotein, potato lectin. These common epitopes together with the previously demonstrated chitin-binding properties of the bean protein indicate a role in host-microbial interactions. Furthermore, the Mr-42000 protein itself bound to the growing hyphal tips of the bean pathogen, Colletotrichum lindemuthianum.
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Affiliation(s)
- D J Millar
- Department of Biological Sciences, City of London Polytechnic, Old Castle Street, E1 7NT, London, UK
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23
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Millar DJ, Allen AK, Smith CG, Sidebottom C, Slabas AR, Bolwell GP. Chitin-binding proteins in potato (Solanum tuberosum L.) tuber. Characterization, immunolocalization and effects of wounding. Biochem J 1992; 283 ( Pt 3):813-21. [PMID: 1590771 PMCID: PMC1130959 DOI: 10.1042/bj2830813] [Citation(s) in RCA: 18] [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: 12/27/2022]
Abstract
Tubers of potato (Solanum tuberosum L.) contain a number of chitin-binding proteins which have possible functions in defence against pathogens. A major protein of the tuber is the chitin-binding lectin which has been further characterized with respect to its antigenicity and N-terminal amino acid sequence. By using an antiserum monospecific for tuber lectin in unwounded potato the protein was found in the cytoplasm and vacuole, unusually for a hydroxyproline-rich glycoprotein, but consistent with its soluble nature in subcellular extracts. Little increased synthesis of the lectin precursor or the post-translationally modified form could be demonstrated in excised potato tuber discs. However, after wounding there is increased synthesis of another hydroxyproline-containing glycoprotein of Mr 57,000, which binds to chitin and shares common epitopes with the lectin. In comparison with the tuber lectin, this novel glycoprotein contains less hydroxyproline, but from its overall composition it is clearly not an underhydroxylated form of the tuber lectin. It differed in its N-terminal amino acid sequence and was much less glycosylated, although arabinose was still present. Synthesis of the Mr-57,000 polypeptide began after the initial burst of protein synthesis and increased, reaching a peak at 24 h after wounding. The protein was produced with its enzymes of post-translational modification, prolyl hydroxylase and arabinosyltransferase, concomitantly with the marker enzymes for wounding, phenylalanine ammonia-lyase and membrane-bound phenol oxidase and peroxidase.
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Affiliation(s)
- D J Millar
- Department of Biological Sciences, City of London Polytechnic, U.K
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Slabas AR, Chase D, Nishida I, Murata N, Sidebottom C, Safford R, Sheldon PS, Kekwick RG, Hardie DG, Mackintosh RW. Molecular cloning of higher-plant 3-oxoacyl-(acyl carrier protein) reductase. Sequence identities with the nodG-gene product of the nitrogen-fixing soil bacterium Rhizobium meliloti. Biochem J 1992; 283 ( Pt 2):321-6. [PMID: 1575676 PMCID: PMC1131036 DOI: 10.1042/bj2830321] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.2] [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: 12/27/2022]
Abstract
cDNA clones encoding the fatty-acid- biosynthetic enzyme NADPH-linked 3-oxoacyl-(acyl carrier protein) (ACP) reductase were isolated from a Brassica napus (rape) developing seed library and from an Arabidopsis thaliana (thale cress) leaf library. The N-terminal end of the coding region shows features typical of a stromal-targeting plastid-transit peptide. The deduced amino acid sequences have 41% and 55% identity respectively with the nodG-gene product of Rhizobium meliloti, one of the host-specific genes that restrict infectivity of this bacterium to a small range of host plants. The probability that the nodG-gene product is a oxoreductase strengthens the hypothesis that some of the host-specific nod-gene products are enzymes which synthesize polyketides that uniquely modify the Rhizobium nodulation signal molecule.
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Affiliation(s)
- A R Slabas
- School of Biological Sciences, University of Durham, U.K
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Abstract
3-Oxoacyl-[ACP] reductase (E.C. 1.1.1.100, alternatively known as beta-ketoacyl-[ACP] reductase), a component of fatty acid synthetase has been purified from seeds of rape by ammonium sulphate fractionation, Procion Red H-E3B chromatography, FPLC gel filtration and high performance hydroxyapatite chromatography. The purified enzyme appears on SDS-PAGE as a number of 20-30 kDa components and has a strong tendency to exist in a dimeric form, particularly when dithiothreitol is not present to reduce disulphide bonds. Cleveland mapping and cross-reactivity with antiserum raised against avocado 3-oxoacyl-[ACP] reductase both indicate that the multiple components have similar primary structures. On gel filtration the enzyme appears to have a molecular mass of 120 kDa suggesting that the native structure is tetrameric. The enzyme has a strong preference for the acetoacetyl ester of acyl carrier protein (Km = 3 microM) over the corresponding esters of the model substrates N-acetyl cysteamine (Km = 35 mM) and CoA (Km = 261 microM). It is inactivated by dilution but this can be partly prevented by the inclusion of NADPH. Using an antiserum prepared against avocado 3-oxoacyl-[ACP] reductase, the enzyme has been visualised inside the plastids of rape embryo and leaf tissues by immunoelectron microscopy. Amino acid sequencing of two peptides prepared by digestion of the purified enzyme with trypsin showed strong similarities with 3-oxoacyl-[ACP] reductase from avocado pear and the Nod G gene product from Rhizobium meliloti.
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Affiliation(s)
- P S Sheldon
- Department of Biochemistry, University of Birmingham, Edgbaston, UK
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Sheldon PS, Kekwick RG, Sidebottom C, Smith CG, Slabas AR. 3-Oxoacyl-(acyl-carrier protein) reductase from avocado (Persea americana) fruit mesocarp. Biochem J 1990; 271:713-20. [PMID: 2244875 PMCID: PMC1149621 DOI: 10.1042/bj2710713] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.0] [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: 12/30/2022]
Abstract
The NADPH-linked 3-oxoacyl-(acyl-carrier protein) (ACP) reductase (EC 1.1.1.100), also known as 'beta-ketoacyl-ACP reductase', has been purified from the mesocarp of mature avocado pears (Persea americana). The enzyme is inactivated by low ionic strength and low temperature. On SDS/PAGE under reducing conditions, purified 3-oxoacyl-ACP reductase migrated as a single polypeptide giving a molecular mass of 28 kDa. Gel-filtration chromatography gave an apparent native molecular mass of 130 kDa, suggesting that the enzyme is tetrameric. The enzyme is inactivated by dilution, but some protection is afforded by the presence of NADPH. Kinetic constants have been determined using synthetic analogues as well as the natural ACP substrate. It exhibits a broad pH optimum around neutrality. Phenylglyoxal inactivates the enzyme, and partial protection is given by 1 mM-NADPH. Antibodies have been raised against the protein, which were used to localize it using immunogold electron microscopy. It is localized in plastids. N-Terminal amino-acid-sequence analysis was performed on the enzyme, and it shows close structural similarity with cytochrome f. Internal amino-acid-sequence data, derived from tryptic peptides, shows similarity with the putative gene products encoded by the nodG gene from the nitrogen-fixing bacterium Rhizobium meliloti and the gra III act III genes from Streptomyces spp.
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Affiliation(s)
- P S Sheldon
- Department of Biochemistry, University of Birmingham, U.K
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Domoney C, Firmin JL, Sidebottom C, Ealing PM, Slabas A, Casey R. Lipoxygenase heterogeneity in Pisum sativum. Planta 1990; 181:35-43. [PMID: 24196672 DOI: 10.1007/bf00202322] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/1989] [Accepted: 09/28/1989] [Indexed: 05/16/2023]
Abstract
Antibodies raised against two pea (Pisum sativum L. cv. Birte) seed lipoxygenases have been used to analyze lipoxygenase heterogeneity in seeds and in other organs. At least seven different polypeptides were identified in vivo; five of these were identified as precursors synthesized in vitro. The developmental appearance of the seed polypeptides has been analyzed and 'early' and 'late' forms were identified. Limited N-terminal sequence data indicated further heterogeneity when compared with sequences predicted from cDNAs.
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Affiliation(s)
- C Domoney
- John Innes Institute, Colney Lane, NR4 7UH, Norwich, UK
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Cottingham I, Austin A, Sidebottom C, Slabas A. Purified enoy-[acyl-carrier-protein] reductase from rape seed (Brassica napus) contains two closely related polypeptides which differ by a six-amino-acid N-terminal extension. ACTA ACUST UNITED AC 1988. [DOI: 10.1016/0167-4838(88)90072-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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