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Wachowska U, Pluskota W, Jastrzębski JP, Głowacka K, Szablewska-Stuper K, Balcerzak M. A method for reducing the concentrations of Fusarium graminearum trichothecenes in durum wheat grain with the use of Debaryomyces hansenii. Int J Food Microbiol 2023; 397:110211. [PMID: 37105049 DOI: 10.1016/j.ijfoodmicro.2023.110211] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/31/2023] [Accepted: 04/08/2023] [Indexed: 04/29/2023]
Abstract
Fusarium head blight (FHB), caused mainly by Fusarium graminearum, is one of the most dangerous diseases of durum wheat. This hemibiotrophic pathogen transitions from the biotrophic phase, during which it penetrates host tissues and secretes trichothecenes, to the necrotrophic phase which leads to the destruction of host tissues. Yeasts applied to spikes often reduce mycotoxin concentrations, but the underlying mechanisms have not been fully elucidated. Therefore, the aim of this study was to analyze the concentrations trichothecenes in durum wheat grain and changes in the F. graminearum transcriptome under the influence the Debaryomyces hansenii antagonistic yeast strain. Debaryomyces hansenii cells adhered to and formed cell aggregates/biofilm on the surface of spikes and pathogenic hyphae. Biological control suppressed the spread of F. graminearum by 90 % and decreased the content of deoxynivalenol (DON) in spikes by 31.2 %. Yeasts significantly reduced the expression of pathogen's genes encoding the rpaI subunit of RNA polymerase I and the activator of Hsp90 ATPase, but they had no effect on mRNA transcript levels of genes encoding the enzymes involved in the biosynthesis of trichothecenes. The yeast treatment reduced the number of F. graminearum operational taxonomic units (OTUs) nearly five-fold and increased the number of D. hansenii OTUs more than six-fold in the spike mycobiome. The mechanisms that suppress infections should be explored to develop effective biological methods for reducing the concentrations mycotoxins in wheat grain.
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Affiliation(s)
- Urszula Wachowska
- University of Warmia and Mazury, Department of Entomology, Phytopathology and Molecular Diagnostics, Poland.
| | - Wioletta Pluskota
- University of Warmia and Mazury, Department of Plant Physiology, Genetics and Biotechnology, Poland
| | - Jan Paweł Jastrzębski
- University of Warmia and Mazury, Department of Plant Physiology, Genetics and Biotechnology, Poland
| | - Katarzyna Głowacka
- University of Warmia and Mazury, Department of Plant Physiology, Genetics and Biotechnology, Poland
| | | | - Margaret Balcerzak
- Ottawa Research and Development Centre, Agriculture and Agri-Food, Canada
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Konkin D, Hsueh YC, Kirzinger M, Kubaláková M, Haldar A, Balcerzak M, Han F, Fedak G, Doležel J, Sharpe A, Ouellet T. Genomic sequencing of Thinopyrum elongatum chromosome arm 7EL, carrying fusarium head blight resistance, and characterization of its impact on the transcriptome of the introgressed line CS-7EL. BMC Genomics 2022; 23:228. [PMID: 35321662 PMCID: PMC8944066 DOI: 10.1186/s12864-022-08433-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 12/10/2020] [Accepted: 02/25/2022] [Indexed: 11/23/2022] Open
Abstract
Background The tall wheatgrass species Thinopyrum elongatum carries a strong fusarium head blight (FHB) resistance locus located on the long arm of chromosome 7 (7EL) as well as resistance to leaf and stem rusts, all diseases with a significant impact on wheat production. Towards understanding the contribution of Th. elongatum 7EL to improvement of disease resistance in wheat, the genomic sequence of the 7EL fragment present in the wheat Chinese Spring (CS) telosomic addition line CS-7EL was determined and the contribution and impact of 7EL on the rachis transcriptome during FHB infection was compared between CS and CS-7EL. Results We assembled the Th. elongatum 7EL chromosome arm using a reference-guided approach. Combining this assembly with the available reference sequence for CS hexaploid wheat provided a reliable reference for interrogating the transcriptomic differences in response to infection conferred by the 7EL fragment. Comparison of the transcriptomes of rachis tissues from CS and CS-7EL showed expression of Th. elongatum transcripts as well as modulation of wheat transcript expression profiles in the CS-7EL line. Expression profiles at 4 days after infection with Fusarium graminearum, the causal agent of FHB, showed an increased in expression of genes associated with an effective defense response, in particular glucan endo-1,3-beta-glucosidases and chitinases, in the FHB-resistant line CS-7EL while there was a larger increase in differential expression for genes associated with the level of fungal infection in the FHB-susceptible line CS. One hundred and seven 7EL transcripts were expressed in the smallest 7EL region defined to carry FHB resistance. Conclusion 7EL contributed to CS-7EL transcriptome by direct expression and through alteration of wheat transcript profiles. FHB resistance in CS-7EL was associated with transcriptome changes suggesting a more effective defense response. A list of candidate genes for the FHB resistance locus on 7EL has been established. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08433-8.
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Affiliation(s)
- David Konkin
- Aquatic and Crop Resource Development, National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada.
| | - Ya-Chih Hsueh
- Aquatic and Crop Resource Development, National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Morgan Kirzinger
- Aquatic and Crop Resource Development, National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Marie Kubaláková
- Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, CZ-77900, Olomouc, Czech Republic
| | - Aparna Haldar
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada.,Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Margaret Balcerzak
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
| | - Fangpu Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences No1, Beijing, China
| | - George Fedak
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, CZ-77900, Olomouc, Czech Republic
| | - Andrew Sharpe
- Global Institute for Food Security, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Thérèse Ouellet
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
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Haldar A, Tekieh F, Balcerzak M, Wolfe D, Lim D, Joustra K, Konkin D, Han F, Fedak G, Ouellet T. Introgression of Thinopyrum elongatum DNA fragments carrying resistance to fusarium head blight into Triticum aestivum cultivar Chinese Spring is associated with alteration of gene expression. Genome 2021; 64:1009-1020. [PMID: 33901415 DOI: 10.1139/gen-2020-0152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The tall wheatgrass species Thinopyrum elongatum carries on the long arm of chromosome 7E, a locus that contributes strongly to resistance to fusarium head blight (FHB), a devastating fungal disease affecting wheat crops in all temperate areas of the world. Introgression of Th. elongatum 7E chromatin into chromosome 7D of wheat was induced by the ph1b mutant of CS. Recombinants between chromosome 7E and wheat chromosome 7D, induced by the ph1b mutation, were monitored by a combination of molecular markers and phenotyping for FHB resistance. Progeny of up to five subsequent generations derived from two lineages, 64-8 and 32-5, were phenotyped for FHB symptoms and genotyped using published and novel 7D- and 7E-specific markers. Fragments from the distal end of 7EL, still carrying FHB resistance and estimated to be less than 114 and 66 Mbp, were identified as introgressed into wheat chromosome arm 7DL of progeny derived from 64-8 and 32-5, respectively. Gene expression analysis revealed variation in the expression levels of genes from the distal ends of 7EL and 7DL in the introgressed progeny. The 7EL introgressed material will facilitate the use of the 7EL FHB resistance locus in wheat breeding programs.
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Affiliation(s)
- Aparna Haldar
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada.,Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Farideh Tekieh
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada.,Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Margaret Balcerzak
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Danielle Wolfe
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - DaEun Lim
- Department of Biochemistry, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Kelsey Joustra
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada.,Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - David Konkin
- Aquatic and Crop Resource Development, National Research Council of Canada, Saskatoon, SK S7N 0W9, Canada
| | - Fangpu Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences No.1, Beijing, China
| | - George Fedak
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Thérèse Ouellet
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
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Brauer EK, Balcerzak M, Rocheleau H, Leung W, Schernthaner J, Subramaniam R, Ouellet T. Genome Editing of a Deoxynivalenol-Induced Transcription Factor Confers Resistance to Fusarium graminearum in Wheat. Mol Plant Microbe Interact 2020; 33:553-560. [PMID: 31790345 DOI: 10.1094/mpmi-11-19-0332-r] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Deoxynivalenol (DON) is a mycotoxin virulence factor that promotes growth of the Fusarium graminearum fungus in wheat floral tissues. To further our understanding of the effects of DON exposure on plant cell function, we characterized DON-induced transcriptional changes in wheat spikelets. Four hundred wheat genes were differentially expressed during infection with wild-type F. graminearum as compared with a Δtri5 mutant strain that is unable to produce DON. Most of these genes were more induced by the DON-producing strain and included genes involved in secondary metabolism, signaling, transport, and stress responses. DON induction was confirmed for a subset of the genes, including TaNFXL1, by treating tissues with DON directly. Previous work indicates that the NFXL1 ortholog represses trichothecene-induced defense responses and bacterial resistance in Arabidopsis, but the role of the NFXL family has not been studied in wheat. We observed greater DON-induced TaNFXL1 gene expression in a susceptible wheat genotype relative to the F. graminearum-resistant genotype Wuhan 1. Functional testing using both virus-induced gene silencing and CRISPR-mediated genome editing indicated that TaNFXL1 represses F. graminearum resistance. Together, this suggests that targeting the TaNFXL1 gene may help to develop disease resistance in cultivated wheat.
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Affiliation(s)
- Elizabeth K Brauer
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Margaret Balcerzak
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Hélène Rocheleau
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Winnie Leung
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Johann Schernthaner
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Rajagopal Subramaniam
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Thérèse Ouellet
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
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Cui X, Balcerzak M, Schernthaner J, Babic V, Datla R, Brauer EK, Labbé N, Subramaniam R, Ouellet T. Correction to: An optimised CRISPR/Cas9 protocol to create targeted mutations in homoeologous genes and an efficient genotyping protocol to identify edited events in wheat. Plant Methods 2019; 15:163. [PMID: 31892936 PMCID: PMC6936137 DOI: 10.1186/s13007-019-0539-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
[This corrects the article DOI: 10.1186/s13007-019-0500-2.].
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Affiliation(s)
- Xiucheng Cui
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
- Department of Biology, University of Ottawa, 75 Laurier Ave E, Ottawa, ON K1N 6N5 Canada
| | - Margaret Balcerzak
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
| | - Johann Schernthaner
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
| | - Vivijan Babic
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
| | - Raju Datla
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
| | - Elizabeth K. Brauer
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
| | - Natalie Labbé
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
| | - Rajagopal Subramaniam
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
| | - Thérèse Ouellet
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
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Hu X, Rocheleau H, McCartney C, Biselli C, Bagnaresi P, Balcerzak M, Fedak G, Yan Z, Valè G, Khanizadeh S, Ouellet T. Correction to: Identification and mapping of expressed genes associated with the 2DL QTL for fusarium head blight resistance in the wheat line Wuhan 1. BMC Genet 2019; 20:76. [PMID: 31619161 PMCID: PMC6796475 DOI: 10.1186/s12863-019-0777-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Following publication of the original article [1], we have been notified that some important information was omitted by the authors in the Copyright note. The Copyright note should read as below.
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Affiliation(s)
- Xinkun Hu
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada.,Triticeae Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Hélène Rocheleau
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
| | - Curt McCartney
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Unit 100, Morden, Manitoba, R6M 1Y5, Canada
| | - Chiara Biselli
- CREA, Council for Agricultural Research and Economics - Research Centre for Genomics and Bioinformatics, Via S. Protaso 302, I-29017, Fiorenzuola d'Arda, PC, Italy
| | - Paolo Bagnaresi
- CREA, Council for Agricultural Research and Economics - Research Centre for Genomics and Bioinformatics, Via S. Protaso 302, I-29017, Fiorenzuola d'Arda, PC, Italy
| | - Margaret Balcerzak
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
| | - George Fedak
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
| | - Zehong Yan
- Triticeae Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Giampiero Valè
- Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale, Vercelli, Italy
| | - Shahrokh Khanizadeh
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
| | - Thérèse Ouellet
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada.
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Hu X, Rocheleau H, McCartney C, Biselli C, Bagnaresi P, Balcerzak M, Fedak G, Yan Z, Valè G, Khanizadeh S, Ouellet T. Identification and mapping of expressed genes associated with the 2DL QTL for fusarium head blight resistance in the wheat line Wuhan 1. BMC Genet 2019; 20:47. [PMID: 31113363 PMCID: PMC6528218 DOI: 10.1186/s12863-019-0748-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 06/27/2018] [Accepted: 05/02/2019] [Indexed: 01/14/2023] Open
Abstract
Background Fusarium head blight (FHB) is a problem of great concern in small grain cereals, especially wheat. A quantitative trait locus (QTL) for FHB resistance (FHB_SFI) located on the long arm of chromosome 2D in the spring wheat genotype Wuhan 1 is a resistance locus which has potential to improve the FHB resistance of bread wheat since it confers effective resistance to wheat breeding lines. Recently, differentially expressed genes (DEG) have been identified by comparing near isogenic lines (NIL) carrying the susceptible and resistant alleles for the 2DL QTL, using RNA-Seq. In the present study, we aimed to identify candidate genes located within the genetic interval for the 2DL QTL for FHB resistance, as assessed by single floret inoculation (FHB_SFI), and possibly contributing to it. Results Combining previous and additional bioinformatics analyses, 26 DEG that were located on chromosome arm 2DL were selected for further characterization of their expression profile by RT-qPCR. Seven of those DEG showed a consistent differential expression profile between either three pairs of near isogenic lines or other genotypes carrying the R and S alleles for the 2DL QTL for FHB resistance. UN25696, which was identified in previous expression work using microarray was also confirmed to have a differential expression pattern. Those eight candidate genes were further characterized in 85 lines of a double haploid mapping population derived from the cross Wuhan 1/Nyubai, the population where the 2DL QTL was originally identified. The expression QTL for gene Traes_2DL_179570792 overlapped completely with the mapping interval for the 2DL QTL for FHB_SFI while the expression QTL for UN25696 mapped near the QTL, but did not overlap with it. None of the other genes had a significant eQTL on chromosome 2DL. Higher expression of Traes_2DL_179570792 and UN25696 was associated with the resistant allele at that locus. Conclusions Of the 26 DEG from the 2DL chromosome further characterized in this study, only two had an expression QTL located in or near the interval for the 2DL QTL. Traes_2DL_179570792 is the first expression marker identified as associated with the 2DL QTL. Electronic supplementary material The online version of this article (10.1186/s12863-019-0748-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xinkun Hu
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada.,Triticeae Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Hélène Rocheleau
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
| | - Curt McCartney
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Unit 100, Morden, Manitoba, R6M 1Y5, Canada
| | - Chiara Biselli
- CREA, Council for Agricultural Research and Economics - Research Centre for Genomics and Bioinformatics, Via S. Protaso 302, I-29017, Fiorenzuola d'Arda, PC, Italy
| | - Paolo Bagnaresi
- CREA, Council for Agricultural Research and Economics - Research Centre for Genomics and Bioinformatics, Via S. Protaso 302, I-29017, Fiorenzuola d'Arda, PC, Italy
| | - Margaret Balcerzak
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
| | - George Fedak
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
| | - Zehong Yan
- Triticeae Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Giampiero Valè
- Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale, Vercelli, Italy
| | - Shahrokh Khanizadeh
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
| | - Thérèse Ouellet
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada.
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Cui X, Balcerzak M, Schernthaner J, Babic V, Datla R, Brauer EK, Labbé N, Subramaniam R, Ouellet T. An optimised CRISPR/Cas9 protocol to create targeted mutations in homoeologous genes and an efficient genotyping protocol to identify edited events in wheat. Plant Methods 2019; 15:119. [PMID: 31673276 PMCID: PMC6814032 DOI: 10.1186/s13007-019-0500-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 10/03/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND Targeted genome editing using the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 system has been applied in a large number of plant species. Using a gene-specific single guide RNA (sgRNA) and the CRISPR/Cas9 system, small editing events such as deletions of few bases can be obtained. However larger deletions are required for some applications. In addition, identification and characterization of edited events can be challenging in plants with complex genomes, such as wheat. RESULTS In this study, we used the CRISPR/Cas9 system and developed a protocol that yielded high number of large deletions employing a pair of co-expressed sgRNA to target the same gene. The protocol was validated by targeting three genes, TaABCC6, TaNFXL1 and TansLTP9.4 in a wheat protoplast assay. Deletions of sequences located between the two sgRNA in each gene were the most frequent editing events observed for two of the three genes. A comparative assessment of editing frequencies between a codon-optimized Cas9 for expression in algae, crCas9, and a plant codon-optimized Cas9, pcoCas9, showed more consistent results with the vector expressing pcoCas9. Editing of TaNFXL1 by co-expression of sgRNA pair was investigated in transgenic wheat plants. Given the ploidy of bread wheat, a rapid, robust and inexpensive genotyping protocol was also adapted for hexaploid genomes and shown to be a useful tool to identify homoeolog-specific editing events in wheat. CONCLUSIONS Co-expressed pairs of sgRNA targeting single genes in conjunction with the CRISPR/Cas9 system produced large deletions in wheat. In addition, a genotyping protocol to identify editing events in homoeologs of TaNFXL1 was successfully adapted.
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Affiliation(s)
- Xiucheng Cui
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
- Department of Biology, University of Ottawa, 75 Laurier Ave E, Ottawa, ON K1N 6N5 Canada
| | - Margaret Balcerzak
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
| | - Johann Schernthaner
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
| | - Vivijan Babic
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
| | - Raju Datla
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
| | - Elizabeth K. Brauer
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
| | - Natalie Labbé
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
| | - Rajagopal Subramaniam
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
| | - Thérèse Ouellet
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
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Balcerzak M, Rudnik A, Jelińska M. Assessment of dietary exposure to inorganic chloride, phosphate, and sulphate bread additives by ion chromatography with conductometric detection. Acta Alimentaria 2018. [DOI: 10.1556/066.2018.47.1.12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- M. Balcerzak
- Department of Analytical Chemistry, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw. Poland
| | - A. Rudnik
- Department of Analytical Chemistry, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw. Poland
| | - M. Jelińska
- Department of Analytical Chemistry, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw. Poland
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Biselli C, Bagnaresi P, Faccioli P, Hu X, Balcerzak M, Mattera MG, Yan Z, Ouellet T, Cattivelli L, Valè G. Comparative Transcriptome Profiles of Near-Isogenic Hexaploid Wheat Lines Differing for Effective Alleles at the 2DL FHB Resistance QTL. Front Plant Sci 2018; 9:37. [PMID: 29434615 PMCID: PMC5797473 DOI: 10.3389/fpls.2018.00037] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 01/09/2018] [Indexed: 05/07/2023]
Abstract
Fusarium head blight (FHB), caused by the fungus Fusarium graminearum, represents one of the major wheat diseases worldwide, determining severe yield losses and reduction of grain quality due to the accumulation of mycotoxins. The molecular response associated with the wheat 2DL FHB resistance QTL was mined through a comprehensive transcriptomic analysis of the early response to F. graminearum infection, at 3 days post-inoculation, in spikelets and rachis. The analyses were conducted on two near isogenic lines (NILs) differing for the presence of the 2DL QTL (2-2618, resistant 2DL+ and 2-2890, susceptible null). The general response to fungal infection in terms of mRNAs accumulation trend was similar in both NILs, even though involving an higher number of DEGs in the susceptible NIL, and included down-regulation of the primary and energy metabolism, up-regulation of enzymes implicated in lignin and phenylpropanoid biosynthesis, activation of hormons biosynthesis and signal transduction pathways and genes involved in redox homeostasis and transcriptional regulation. The search for candidate genes with expression profiles associated with the 2DL QTL for FHB resistance led to the discovery of processes differentially modulated in the R and S NILs related to cell wall metabolism, sugar and JA signaling, signal reception and transduction, regulation of the redox status and transcription factors. Wheat FHB response-related miRNAs differentially regulated were also identified as putatively implicated in the superoxide dismutase activities and affecting genes regulating responses to biotic/abiotic stresses and auxin signaling. Altered gene expression was also observed for fungal non-codingRNAs. The putative targets of two of these were represented by the wheat gene WIR1A, involved in resistance response, and a gene encoding a jacalin-related lectin protein, which participate in biotic and abiotic stress response, supporting the presence of a cross-talk between the plant and the fungus.
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Affiliation(s)
- Chiara Biselli
- CREA–Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
- *Correspondence: Chiara Biselli
| | - Paolo Bagnaresi
- CREA–Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Primetta Faccioli
- CREA–Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Xinkun Hu
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Margaret Balcerzak
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Maria G. Mattera
- Plant Breeding Department, Institute for Sustainable Agriculture, Cordoba, Spain
- Department of Genetics–ETSIAM, University of Cordoba, Cordoba, Spain
| | - Zehong Yan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Therese Ouellet
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Luigi Cattivelli
- CREA–Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Giampiero Valè
- CREA–Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
- CREA–Research Centre for Cereal and Industrial Crops, Vercelli, Italy
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Harris LJ, Balcerzak M, Johnston A, Schneiderman D, Ouellet T. Host-preferential Fusarium graminearum gene expression during infection of wheat, barley, and maize. Fungal Biol 2015; 120:111-23. [PMID: 26693688 DOI: 10.1016/j.funbio.2015.10.010] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 09/22/2015] [Accepted: 10/19/2015] [Indexed: 11/25/2022]
Abstract
Fusarium graminearum is a broad host pathogen threatening cereal crops in temperate regions around the world. To better understand how F. graminearum adapts to different hosts, we have performed a comparison of the transcriptome of a single strain of F. graminearum during early infection (up to 4 d post-inoculation) of barley, maize, and wheat using custom oligomer microarrays. Our results showed high similarity between F. graminearum transcriptomes in infected wheat and barley spike tissues. Quantitative RT-PCR was used to validate the gene expression profiles of 24 genes. Host-specific expression of genes was observed in each of the three hosts. This included expression of distinct sets of genes associated with transport and secondary metabolism in each of the three crops, as well as host-specific patterns for particular gene categories such as sugar transporters, integral membrane protein PTH11-like proteins, and chitinases. This study identified 69 F. graminearum genes as preferentially expressed in developing maize kernels relative to wheat and barley spikes. These host-specific differences showcase the genomic flexibility of F. graminearum to adapt to a range of hosts.
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Affiliation(s)
- Linda J Harris
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario K1A 0C6, Canada.
| | - Margaret Balcerzak
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario K1A 0C6, Canada.
| | - Anne Johnston
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario K1A 0C6, Canada.
| | - Danielle Schneiderman
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario K1A 0C6, Canada.
| | - Thérèse Ouellet
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario K1A 0C6, Canada.
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Wójcik PI, Ouellet T, Balcerzak M, Dzwinel W. Identification of biomarker genes for resistance to a pathogen by a novel method for meta-analysis of single-channel microarray datasets. J Bioinform Comput Biol 2015; 13:1550013. [DOI: 10.1142/s0219720015500134] [Citation(s) in RCA: 6] [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: 11/18/2022]
Abstract
The search for fast and reliable methods allowing for extraction of biomarker genes, e.g. responsible for a plant resistance to a certain pathogen, is one of the most important and highly exploited data mining problem in bioinformatics. Here we describe a simple and efficient method suitable for combining results from multiple single-channel microarray experiments for meta-analysis. A new technique presented here makes use of the fuzzy set logic for the initial gene selection and of the machine learning algorithm AdaBoost to retrieve a set of genes where expression profiles are the most different between the resistant and susceptible classes. As a proof of concept, our method has been applied to the analysis of a gene expression dataset composed of many independent microarray experiments on wheat head tissue, to identify genes that are biomarkers of resistance to the fungus Fusarium graminearum. We used microarray data from many experiments performed on wheat lines of various resistance level. The resulting set of genes was validated by qPCR experiments.
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Affiliation(s)
- Piotr Iwo Wójcik
- Institute of Computer Science, AGH University of Science and Technology, Al. Mickiewicza 30, 30-059 Kraków, Poland
| | - Thérèse Ouellet
- Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, 960 Carling Ave, K1A 0C6 Ottawa, Canada
| | - Margaret Balcerzak
- Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, 960 Carling Ave, K1A 0C6 Ottawa, Canada
| | - Witold Dzwinel
- Institute of Computer Science, AGH University of Science and Technology, Al. Mickiewicza 30, 30-059 Kraków, Poland
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Balcerzak M, Harris LJ, Subramaniam R, Ouellet T. The feruloyl esterase gene family of Fusarium graminearum is differentially regulated by aromatic compounds and hosts. Fungal Biol 2012; 116:478-88. [DOI: 10.1016/j.funbio.2012.01.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Revised: 01/10/2012] [Accepted: 01/21/2012] [Indexed: 11/25/2022]
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Kolado W, Balcerzak M. The examination of migration of primary aromatic amines from laminated plastic food packaging materials into food simulants by spectrophotometric method. Acta Alimentaria 2009. [DOI: 10.1556/aalim.2008.0020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Balcerzak M, Radisson J, Azzar G, Farlay D, Boivin G, Pikula S, Buchet R. A comparative analysis of strategies for isolation of matrix vesicles. Anal Biochem 2006; 361:176-82. [PMID: 17194438 DOI: 10.1016/j.ab.2006.10.001] [Citation(s) in RCA: 21] [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] [Received: 07/31/2006] [Accepted: 10/02/2006] [Indexed: 10/24/2022]
Abstract
Matrix vesicles (MVs) are extracellular organelles involved in the initial steps of mineralization. MVs are isolated by two methods. The first isolation method of MVs starts with collagenase digestion of osseous tissues, followed by two differential centrifugations. The second isolation method does not use proteases but rather starts with differential centrifugation, followed by a fractionation on a sucrose gradient. The first method results in a homogeneous population of MVs with higher cholesterol/lipid content, alkaline phosphatase activity, and mineral formation rate as compared with MVs isolated by the second method. The second method leads to higher protein diversity as compared with MVs isolated according to the first method. Due to their distinct protein composition, lipid-to-protein and cholesterol-to-phospholipid ratios, and differences in rates of mineral formation, both types of isolated MVs are crucial for proteomic analysis and for understanding the regulation of mineralization process at the molecular level.
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Affiliation(s)
- M Balcerzak
- Department of Cellular Biochemistry, Nencki Insitute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
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Balcerzak M, Kaczmarczyk M. Rapid derivative spectrophotometric method for the determination of platinum in Pt-Ru/C catalyst using iodide media. ANAL SCI 2001; 17:1321-4. [PMID: 11759517 DOI: 10.2116/analsci.17.1321] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A rapid spectrophotometric method for the determination of platinum in 20% Pt-Ru (Pt:Ru (1:1)) carbon-supported catalyst has been developed. The samples of catalyst (0.85-12.60 mg) have been digested 1) in aqua regia after preliminary separation of carbon by burning or 2) directly in aqua regia in the presence of carbon. The detection of platinum was carried out in the obtained solutions after conversion of the metal into the iodide complex. The interfering effect of ruthenium on the detection of platinum was eliminated by the use of derivative spectrophotometry. Platinum was selectively determined by numerical calculation of the 4th-order-derivative absorption spectrum of the mixture of iodide complexes of both metals.
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Affiliation(s)
- M Balcerzak
- Department of Analytical Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland.
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Balcerzak M, Wyrzykowska E. Extraction preconcentration of platinum and ruthenium using high molecular weight amines prior to
simultaneous determination by derivative spectrophotometry. ACTA ACUST UNITED AC 1999. [DOI: 10.1051/analusis:1999150] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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Balcerzak M. Determination of platinum and ruthenium in Pt and Pt–Ru catalysts with carbon support by direct and derivative spectrophotometry. Talanta 1999; 48:39-47. [DOI: 10.1016/s0039-9140(98)00212-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/1998] [Revised: 05/13/1998] [Accepted: 05/22/1998] [Indexed: 11/29/2022]
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Balcerzak M, Świȩcicka E. Rapid simultaneous determination of ruthenium and osmium in aqueous solutions of their tetroxides by second-order derivative spectrophotometry. Anal Chim Acta 1997. [DOI: 10.1016/s0003-2670(97)00251-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Affiliation(s)
- M Balcerzak
- Department of Analytical Chemistry, Warsaw University of Technology, Poland
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Jarosz J, Balcerzak M, Skrzypek H. Involvement of larvicidal toxins in pathogenesis of insect parasitism with the rhabditoid nematodes,Steinernema feltiae andHeterorhabditis bacteriophora. ACTA ACUST UNITED AC 1991. [DOI: 10.1007/bf02377940] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Balcerzak M. Sensitive spectrophotometric determination of osmium with tin(II) chloride and rhodamine B after flotation using cyclohexane. Analyst 1988; 113:129-32. [PMID: 3358498 DOI: 10.1039/an9881300129] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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25
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Marczenko Z, Balcerzak M, Pasek H. Sensitive flotation-spectrophotometric determination of osmium based on the osmium(IV)-chloride-rhodamine 6 G system. Mikrochim Acta 1982. [DOI: 10.1007/bf01197986] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [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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Marczenko Z, Balcerzak M, Kuś S. Spectrophotometric determination of ruthenium and osmium. Talanta 1980; 27:1087-9. [DOI: 10.1016/0039-9140(80)80255-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/1979] [Revised: 06/10/1980] [Accepted: 06/16/1980] [Indexed: 10/18/2022]
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