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Vélëz H, Af Sätra JS, Odilbekov F, Bourras S, Garkava-Gustavsson L, Dalman K. Transformation and gene-disruption in the apple-pathogen, Neonectria ditissima. Hereditas 2022; 159:31. [PMID: 35953844 PMCID: PMC9373326 DOI: 10.1186/s41065-022-00244-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 07/25/2022] [Indexed: 11/18/2022] Open
Abstract
Background Apple production in Sweden and elsewhere is being threatened by the fungus, Neonectria ditissima, which causes a disease known as European canker. The disease can cause extensive damage and the removal of diseased wood and heavily infected trees can be laborious and expensive. Currently, there is no way to eradicate the fungus from infected trees and our knowledge of the infection process is limited. Thus, to target and modify genes efficiently, the genetic transformation technique developed for N. ditissima back in 2003 was modified. Results The original protocol from 2003 was upgraded to use enzymes currently available in the market for making protoplasts. The protoplasts were viable, able to uptake foreign DNA, and able to regenerate back into a mycelial colony, either as targeted gene-disruption mutants or as ectopic mutants expressing the green fluorescent protein (GFP). Conclusions A new genetic transformation protocol has been established and the inclusion of hydroxyurea in the buffer during the protoplast-generation step greatly increased the creation of knockout mutants via homologous recombination. Pathogenicity assays using the GFP-mutants showed that the mutants were able to infect the host and cause disease. Supplementary Information The online version contains supplementary material available at 10.1186/s41065-022-00244-x.
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Affiliation(s)
- Heriberto Vélëz
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, 75007, Uppsala, Sweden.
| | - Jonas Skytte Af Sätra
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 190, SE-23422, Lomma, Sweden
| | - Firuz Odilbekov
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 190, SE-23422, Lomma, Sweden
| | - Salim Bourras
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, 75007, Uppsala, Sweden
| | - Larisa Garkava-Gustavsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 190, SE-23422, Lomma, Sweden.
| | - Kerstin Dalman
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, 750 07, Uppsala, Sweden
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Gutierrez‐Beltran E, Elander PH, Dalman K, Dayhoff GW, Moschou PN, Uversky VN, Crespo JL, Bozhkov PV. Tudor staphylococcal nuclease is a docking platform for stress granule components and is essential for SnRK1 activation in Arabidopsis. EMBO J 2021; 40:e105043. [PMID: 34287990 PMCID: PMC8447601 DOI: 10.15252/embj.2020105043] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 06/23/2021] [Accepted: 07/01/2021] [Indexed: 12/19/2022] Open
Abstract
Tudor staphylococcal nuclease (TSN; also known as Tudor-SN, p100, or SND1) is a multifunctional, evolutionarily conserved regulator of gene expression, exhibiting cytoprotective activity in animals and plants and oncogenic activity in mammals. During stress, TSN stably associates with stress granules (SGs), in a poorly understood process. Here, we show that in the model plant Arabidopsis thaliana, TSN is an intrinsically disordered protein (IDP) acting as a scaffold for a large pool of other IDPs, enriched for conserved stress granule components as well as novel or plant-specific SG-localized proteins. While approximately 30% of TSN interactors are recruited to stress granules de novo upon stress perception, 70% form a protein-protein interaction network present before the onset of stress. Finally, we demonstrate that TSN and stress granule formation promote heat-induced activation of the evolutionarily conserved energy-sensing SNF1-related protein kinase 1 (SnRK1), the plant orthologue of mammalian AMP-activated protein kinase (AMPK). Our results establish TSN as a docking platform for stress granule proteins, with an important role in stress signalling.
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Affiliation(s)
- Emilio Gutierrez‐Beltran
- Instituto de Bioquímica Vegetal y FotosíntesisConsejo Superior de Investigaciones Científicas (CSIC)‐Universidad de SevillaSevillaSpain
- Departamento de Bioquímica Vegetal y Biología MolecularFacultad de BiologíaUniversidad de SevillaSevillaSpain
| | - Pernilla H Elander
- Department of Molecular SciencesUppsala BioCenterSwedish University of Agricultural Sciences and Linnean Center for Plant BiologyUppsalaSweden
| | - Kerstin Dalman
- Department of Molecular SciencesUppsala BioCenterSwedish University of Agricultural Sciences and Linnean Center for Plant BiologyUppsalaSweden
| | - Guy W Dayhoff
- Department of ChemistryCollege of Art and SciencesUniversity of South FloridaTampaFLUSA
| | - Panagiotis N Moschou
- Institute of Molecular Biology and BiotechnologyFoundation for Research and Technology ‐ HellasHeraklionGreece
- Department of Plant BiologyUppsala BioCenterSwedish University of Agricultural Sciences and Linnean Center for Plant BiologyUppsalaSweden
- Department of BiologyUniversity of CreteHeraklionGreece
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of MedicineUniversity of South FloridaTampaFLUSA
- Institute for Biological Instrumentation of the Russian Academy of SciencesFederal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”PushchinoRussia
| | - Jose L Crespo
- Instituto de Bioquímica Vegetal y FotosíntesisConsejo Superior de Investigaciones Científicas (CSIC)‐Universidad de SevillaSevillaSpain
| | - Peter V Bozhkov
- Department of Molecular SciencesUppsala BioCenterSwedish University of Agricultural Sciences and Linnean Center for Plant BiologyUppsalaSweden
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Dauphinee AN, Cardoso C, Dalman K, Ohlsson JA, Fick SB, Robert S, Hicks GR, Bozhkov PV, Minina EA. Chemical Screening Pipeline for Identification of Specific Plant Autophagy Modulators. Plant Physiol 2019; 181:855-866. [PMID: 31488572 PMCID: PMC6836817 DOI: 10.1104/pp.19.00647] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/14/2019] [Indexed: 05/18/2023]
Abstract
Autophagy is a major catabolic process in eukaryotes with a key role in homeostasis, programmed cell death, and aging. In plants, autophagy is also known to regulate agronomically important traits such as stress resistance, longevity, vegetative biomass, and seed yield. Despite its significance, there is still a shortage of reliable tools modulating plant autophagy. Here, we describe the first robust pipeline for identification of specific plant autophagy-modulating compounds. Our screening protocol comprises four phases: (1) high-throughput screening of chemical compounds in cell cultures of tobacco (Nicotiana tabacum); (2) confirmation of the identified hits in planta using Arabidopsis (Arabidopsis thaliana); (3) further characterization of the effect using conventional molecular biology methods; and (4) verification of chemical specificity on autophagy in planta. The methods detailed here streamline the identification of specific plant autophagy modulators and aid in unraveling the molecular mechanisms of plant autophagy.
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Affiliation(s)
- Adrian N Dauphinee
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala SE-750 07, Sweden
| | - Catarina Cardoso
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala SE-750 07, Sweden
- Plant Genetics, School of Life Science Weihenstephan, Technical University of Munich, 85354 Freising, Germany
| | - Kerstin Dalman
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala SE-750 07, Sweden
| | - Jonas A Ohlsson
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala SE-750 07, Sweden
| | | | - Stéphanie Robert
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 83 Umea, Sweden
| | - Glenn R Hicks
- Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, California, 92521
| | - Peter V Bozhkov
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala SE-750 07, Sweden
| | - Elena A Minina
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala SE-750 07, Sweden
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany
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Minina EA, Moschou PN, Vetukuri RR, Sanchez-Vera V, Cardoso C, Liu Q, Elander PH, Dalman K, Beganovic M, Lindberg Yilmaz J, Marmon S, Shabala L, Suarez MF, Ljung K, Novák O, Shabala S, Stymne S, Hofius D, Bozhkov PV. Transcriptional stimulation of rate-limiting components of the autophagic pathway improves plant fitness. J Exp Bot 2018; 69:1415-1432. [PMID: 29365132 PMCID: PMC6019011 DOI: 10.1093/jxb/ery010] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [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: 09/12/2017] [Accepted: 12/14/2017] [Indexed: 05/02/2023]
Abstract
Autophagy is a major catabolic process whereby autophagosomes deliver cytoplasmic content to the lytic compartment for recycling. Autophagosome formation requires two ubiquitin-like systems conjugating Atg12 with Atg5, and Atg8 with lipid phosphatidylethanolamine (PE), respectively. Genetic suppression of these systems causes autophagy-deficient phenotypes with reduced fitness and longevity. We show that Atg5 and the E1-like enzyme, Atg7, are rate-limiting components of Atg8-PE conjugation in Arabidopsis. Overexpression of ATG5 or ATG7 stimulates Atg8 lipidation, autophagosome formation, and autophagic flux. It also induces transcriptional changes opposite to those observed in atg5 and atg7 mutants, favoring stress resistance and growth. As a result, ATG5- or ATG7-overexpressing plants exhibit increased resistance to necrotrophic pathogens and oxidative stress, delayed aging and enhanced growth, seed set, and seed oil content. This work provides an experimental paradigm and mechanistic insight into genetic stimulation of autophagy in planta and shows its efficiency for improving plant productivity.
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Affiliation(s)
- Elena A Minina
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
- Correspondence: and
| | - Panagiotis N Moschou
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Ramesh R Vetukuri
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Victoria Sanchez-Vera
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Catarina Cardoso
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Qinsong Liu
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Pernilla H Elander
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Kerstin Dalman
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Mirela Beganovic
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | | | - Sofia Marmon
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Lana Shabala
- School of Land and Food, University of Tasmania, Private Bag, Hobart, TAS, Australia
| | - Maria F Suarez
- Departamento de Biologia Molecular y Bioquimica, Facultad de Ciencias, Universidad de Malaga, Campus de Teatinos, Malaga, Spain
| | - Karin Ljung
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umea, Sweden
| | - Ondřej Novák
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany Academy of Sciences of the Czech Republic (AS CR), Olomouc, Czech Republic
- Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Sergey Shabala
- School of Land and Food, University of Tasmania, Private Bag, Hobart, TAS, Australia
| | - Sten Stymne
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Daniel Hofius
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Peter V Bozhkov
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
- Correspondence: and
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Reza SH, Delhomme N, Street NR, Ramachandran P, Dalman K, Nilsson O, Minina EA, Bozhkov PV. Transcriptome analysis of embryonic domains in Norway spruce reveals potential regulators of suspensor cell death. PLoS One 2018; 13:e0192945. [PMID: 29499063 PMCID: PMC5834160 DOI: 10.1371/journal.pone.0192945] [Citation(s) in RCA: 10] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 01/09/2018] [Indexed: 01/04/2023] Open
Abstract
The terminal differentiation and elimination of the embryo-suspensor is the earliest manifestation of programmed cell death (PCD) during plant ontogenesis. Molecular regulation of suspensor PCD remains poorly understood. Norway spruce (Picea abies) embryos provide a powerful model for studying embryo development because of their large size, sequenced genome, and the possibility to obtain a large number of embryos at a specific developmental stage through somatic embryogenesis. Here, we have carried out global gene expression analysis of the Norway spruce embryo-suspensor versus embryonal mass (a gymnosperm analogue of embryo proper) using RNA sequencing. We have identified that suspensors have enhanced expression of the NAC domain-containing transcription factors, XND1 and ANAC075, previously shown to be involved in the initiation of developmental PCD in Arabidiopsis. The analysis has also revealed enhanced expression of Norway spruce homologues of the known executioners of both developmental and stress-induced cell deaths, such as metacaspase 9 (MC9), cysteine endopeptidase-1 (CEP1) and ribonuclease 3 (RNS3). Interestingly, a spruce homologue of bax inhibitor-1 (PaBI-1, for Picea abies BI-1), an evolutionarily conserved cell death suppressor, was likewise up-regulated in the embryo-suspensor. Since Arabidopsis BI-1 so far has been implicated only in the endoplasmic reticulum (ER)-stress induced cell death, we investigated its role in embryogenesis and suspensor PCD using RNA interference (RNAi). We have found that PaBI-1-deficient lines formed a large number of abnormal embryos with suppressed suspensor elongation and disturbed polarity. Cytochemical staining of suspensor cells has revealed that PaBI-1 deficiency suppresses vacuolar cell death and induces necrotic type of cell death previously shown to compromise embryo development. This study demonstrates that a large number of cell-death components are conserved between angiosperms and gymnosperms and establishes a new role for BI-1 in the progression of vacuolar cell death.
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Affiliation(s)
- Salim H. Reza
- Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, SE, Sweden
- Department of Molecular Sciences, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, SE, Sweden
- * E-mail: (SHR); (EAM); (PVB)
| | - Nicolas Delhomme
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Nathaniel R. Street
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Prashanth Ramachandran
- Department of Organismal Biology, Uppsala BioCenter, Linnean Center for Plant Biology, Uppsala University, Uppsala, SE, Sweden
| | - Kerstin Dalman
- Department of Molecular Sciences, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, SE, Sweden
| | - Ove Nilsson
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Elena A. Minina
- Department of Molecular Sciences, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, SE, Sweden
- * E-mail: (SHR); (EAM); (PVB)
| | - Peter V. Bozhkov
- Department of Molecular Sciences, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, SE, Sweden
- * E-mail: (SHR); (EAM); (PVB)
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Dalman K, Wind JJ, Nemesio-Gorriz M, Hammerbacher A, Lundén K, Ezcurra I, Elfstrand M. Overexpression of PaNAC03, a stress induced NAC gene family transcription factor in Norway spruce leads to reduced flavonol biosynthesis and aberrant embryo development. BMC Plant Biol 2017; 17:6. [PMID: 28061815 PMCID: PMC5219727 DOI: 10.1186/s12870-016-0952-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Accepted: 12/15/2016] [Indexed: 05/20/2023]
Abstract
BACKGROUND The NAC family of transcription factors is one of the largest gene families of transcription factors in plants and the conifer NAC gene family is at least as large, or possibly larger, as in Arabidopsis. These transcription factors control both developmental and stress induced processes in plants. Yet, conifer NACs controlling stress induced processes has received relatively little attention. This study investigates NAC family transcription factors involved in the responses to the pathogen Heterobasidion annosum (Fr.) Bref. sensu lato. RESULTS The phylogeny and domain structure in the NAC proteins can be used to organize functional specificities, several well characterized stress-related NAC proteins are found in III-3 in Arabidopsis (Jensen et al. Biochem J 426:183-196, 2010). The Norway spruce genome contain seven genes with similarity to subgroup III-3 NACs. Based on the expression pattern PaNAC03 was selected for detailed analyses. Norway spruce lines overexpressing PaNAC03 exhibited aberrant embryo development in response to maturation initiation and 482 misregulated genes were identified in proliferating cultures. Three key genes in the flavonoid biosynthesis pathway: a CHS, a F3'H and PaLAR3 were consistently down regulated in the overexpression lines. In accordance, the overexpression lines showed reduced levels of specific flavonoids, suggesting that PaNAC03 act as a repressor of this pathway, possibly by directly interacting with the promoter of the repressed genes. However, transactivation studies of PaNAC03 and PaLAR3 in Nicotiana benthamiana showed that PaNAC03 activated PaLAR3A, suggesting that PaNAC03 does not act as an independent negative regulator of flavan-3-ol production through direct interaction with the target flavonoid biosynthetic genes. CONCLUSIONS PaNAC03 and its orthologs form a sister group to well characterized stress-related angiosperm NAC genes and at least PaNAC03 is responsive to biotic stress and appear to act in the control of defence associated secondary metabolite production.
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Affiliation(s)
- Kerstin Dalman
- Department of Forest Mycology and Plant Pathology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Department of Chemistry and Biotechnology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Julia Johanna Wind
- KTH Biotechnology, Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Miguel Nemesio-Gorriz
- Department of Forest Mycology and Plant Pathology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Almuth Hammerbacher
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
- Department of Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Karl Lundén
- Department of Forest Mycology and Plant Pathology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ines Ezcurra
- KTH Biotechnology, Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Malin Elfstrand
- Department of Forest Mycology and Plant Pathology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Department of Forest Mycology and Plant Pathology, SLU, PO. Box 7026, Uppsala, 75007 Sweden
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Nemesio-Gorriz M, Blair PB, Dalman K, Hammerbacher A, Arnerup J, Stenlid J, Mukhtar SM, Elfstrand M. Identification of Norway Spruce MYB-bHLH-WDR Transcription Factor Complex Members Linked to Regulation of the Flavonoid Pathway. Front Plant Sci 2017; 8:305. [PMID: 28337212 PMCID: PMC5343035 DOI: 10.3389/fpls.2017.00305] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 02/20/2017] [Indexed: 05/16/2023]
Abstract
Transcription factors (TFs) forming MYB-bHLH-WDR complexes are known to regulate the biosynthesis of specialized metabolites in angiosperms through an intricate network. These specialized metabolites participate in a wide range of biological processes including plant growth, development, reproduction as well as in plant immunity. Studying the regulation of their biosynthesis is thus essential. While MYB (TFs) have been previously shown to control specialized metabolism (SM) in gymnosperms, the identity of their partners, in particular bHLH or WDR members, has not yet been revealed. To gain knowledge about MYB-bHLH-WDR transcription factor complexes in gymnosperms and their regulation of SW, we identified two bHLH homologs of AtTT8, six homologs of the MYB transcription factor AtTT2 and one WDR ortholog of AtTTG1 in Norway spruce. We investigated the expression levels of these genes in diverse tissues and upon treatments with various stimuli including methyl-salicylate, methyl-jasmonate, wounding or fungal inoculation. In addition, we also identified protein-protein interactions among different homologs of MYB, bHLH and WDR. Finally, we generated transgenic spruce cell lines overexpressing four of the Norway spruce AtTT2 homologs and observed differential regulation of genes in the flavonoid pathway and flavonoid contents.
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Affiliation(s)
- Miguel Nemesio-Gorriz
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural SciencesUppsala, Sweden
- *Correspondence: Miguel Nemesio-Gorriz
| | - Peter B. Blair
- Department of Biology, University of Alabama at BirminghamBirmingham, AL, USA
| | - Kerstin Dalman
- Department of Chemistry and Biotechnology, Swedish University of Agricultural SciencesUppsala, Sweden
| | - Almuth Hammerbacher
- Department of Microbiology, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
| | - Jenny Arnerup
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural SciencesUppsala, Sweden
| | - Jan Stenlid
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural SciencesUppsala, Sweden
| | - Shahid M. Mukhtar
- Department of Biology, University of Alabama at BirminghamBirmingham, AL, USA
| | - Malin Elfstrand
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural SciencesUppsala, Sweden
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Van der Nest MA, Olson A, Lind M, Vélëz H, Dalman K, Brandström Durling M, Karlsson M, Stenlid J. Distribution and evolution of het gene homologs in the basidiomycota. Fungal Genet Biol 2013; 64:45-57. [PMID: 24380733 DOI: 10.1016/j.fgb.2013.12.007] [Citation(s) in RCA: 17] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 12/04/2013] [Accepted: 12/20/2013] [Indexed: 12/24/2022]
Abstract
In filamentous fungi a system known as somatic incompatibility (SI) governs self/non-self recognition. SI is controlled by a regulatory signaling network involving proteins encoded at the het (heterokaryon incompatible) loci. Despite the wide occurrence of SI, the molecular identity and structure of only a small number of het genes and their products have been characterized in the model fungi Neurospora crassa and Podospora anserina. Our aim was to identify and study the distribution and evolution of putative het gene homologs in the Basidiomycota. For this purpose we used the information available for the model fungi to identify homologs of het genes in other fungi, especially the Basidiomycota. Putative het-c, het-c2 and un-24 homologs, as well as sequences containing the NACHT, HET or WD40 domains present in the het-e, het-r, het-6 and het-d genes were identified in certain members of the Ascomycota and Basidiomycota. The widespread phylogenetic distribution of certain het genes may reflect the fact that the encoded proteins are involved in fundamental cellular processes other than SI. Although homologs of het-S were previously known only from the Sordariomycetes (Ascomycota), we also identified a putative homolog of this gene in Gymnopus luxurians (Basidiomycota, class Agaricomycetes). Furthermore, with the exception of un-24, all of the putative het genes identified occurred mostly in a multi-copy fashion, some with lineage and species-specific expansions. Overall our results indicated that gene duplication followed by gene loss and/or gene family expansion, as well as multiple events of domain fusion and shuffling played an important role in the evolution of het gene homologs of Basidiomycota and other filamentous fungi.
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Affiliation(s)
- M A Van der Nest
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden.
| | - A Olson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
| | - M Lind
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
| | - H Vélëz
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
| | - K Dalman
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
| | - M Brandström Durling
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
| | - M Karlsson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
| | - J Stenlid
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
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Dalman K, Himmelstrand K, Olson Å, Lind M, Brandström-Durling M, Stenlid J. A genome-wide association study identifies genomic regions for virulence in the non-model organism Heterobasidion annosum s.s. PLoS One 2013; 8:e53525. [PMID: 23341945 PMCID: PMC3547014 DOI: 10.1371/journal.pone.0053525] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [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: 09/03/2012] [Accepted: 12/03/2012] [Indexed: 12/02/2022] Open
Abstract
The dense single nucleotide polymorphisms (SNP) panels needed for genome wide association (GWA) studies have hitherto been expensive to establish and use on non-model organisms. To overcome this, we used a next generation sequencing approach to both establish SNPs and to determine genotypes. We conducted a GWA study on a fungal species, analysing the virulence of Heterobasidion annosum s.s., a necrotrophic pathogen, on its hosts Picea abies and Pinus sylvestris. From a set of 33,018 single nucleotide polymorphisms (SNP) in 23 haploid isolates, twelve SNP markers distributed on seven contigs were associated with virulence (P<0.0001). Four of the contigs harbour known virulence genes from other fungal pathogens and the remaining three harbour novel candidate genes. Two contigs link closely to virulence regions recognized previously by QTL mapping in the congeneric hybrid H. irregulare × H. occidentale. Our study demonstrates the efficiency of GWA studies for dissecting important complex traits of small populations of non-model haploid organisms with small genomes.
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Affiliation(s)
- Kerstin Dalman
- Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
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Olson Å, Aerts A, Asiegbu F, Belbahri L, Bouzid O, Broberg A, Canbäck B, Coutinho PM, Cullen D, Dalman K, Deflorio G, van Diepen LTA, Dunand C, Duplessis S, Durling M, Gonthier P, Grimwood J, Fossdal CG, Hansson D, Henrissat B, Hietala A, Himmelstrand K, Hoffmeister D, Högberg N, James TY, Karlsson M, Kohler A, Kües U, Lee YH, Lin YC, Lind M, Lindquist E, Lombard V, Lucas S, Lundén K, Morin E, Murat C, Park J, Raffaello T, Rouzé P, Salamov A, Schmutz J, Solheim H, Ståhlberg J, Vélëz H, de Vries RP, Wiebenga A, Woodward S, Yakovlev I, Garbelotto M, Martin F, Grigoriev IV, Stenlid J. Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen. New Phytol 2012; 194:1001-1013. [PMID: 22463738 DOI: 10.1111/j.1469-8137.2012.04128.x] [Citation(s) in RCA: 152] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Parasitism and saprotrophic wood decay are two fungal strategies fundamental for succession and nutrient cycling in forest ecosystems. An opportunity to assess the trade-off between these strategies is provided by the forest pathogen and wood decayer Heterobasidion annosum sensu lato. We report the annotated genome sequence and transcript profiling, as well as the quantitative trait loci mapping, of one member of the species complex: H. irregulare. Quantitative trait loci critical for pathogenicity, and rich in transposable elements, orphan and secreted genes, were identified. A wide range of cellulose-degrading enzymes are expressed during wood decay. By contrast, pathogenic interaction between H. irregulare and pine engages fewer carbohydrate-active enzymes, but involves an increase in pectinolytic enzymes, transcription modules for oxidative stress and secondary metabolite production. Our results show a trade-off in terms of constrained carbohydrate decomposition and membrane transport capacity during interaction with living hosts. Our findings establish that saprotrophic wood decay and necrotrophic parasitism involve two distinct, yet overlapping, processes.
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Affiliation(s)
- Åke Olson
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Box 7026, Ullsväg 26, 750 05 Uppsala, Sweden
| | - Andrea Aerts
- US DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Fred Asiegbu
- Department of Forest Ecology, PO Box 27 Latokartanonkaari 7, 00014 University of Helsinki, Helsinki, Finland
| | - Lassaad Belbahri
- Laboratory of Soil Biology, University of Neuchâtel, Rue Emile Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Ourdia Bouzid
- Microbiology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Anders Broberg
- Department of Chemistry, Swedish University of Agricultural Sciences, Box 7015, 750 05 Uppsala, Sweden
| | - Björn Canbäck
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Box 7026, Ullsväg 26, 750 05 Uppsala, Sweden
| | - Pedro M Coutinho
- AFMB UMR 6098 CNRS/UI/UII, Case 932, 163 Avenue de Luminy 13288 Marseille cedex 9, France
| | - Dan Cullen
- Forest Products Laboratory, Madison, WI 53726, USA
| | - Kerstin Dalman
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Box 7026, Ullsväg 26, 750 05 Uppsala, Sweden
| | - Giuliana Deflorio
- Department of Plant and Soil Science, Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, St. Machar Drive, Aberdeen, AB24 3UU, Scotland UK
| | - Linda T A van Diepen
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Christophe Dunand
- Laboratory of Cell Surfaces and Plant Signalisation 24, University Paul Sabatier (Toulouse III), UMR5546- CNRS, Chemin de Borde-Rouge, BP 42617, Auzeville 31326 Castanet-Tolosan, France
| | - Sébastien Duplessis
- UMR INRA-UHP 'Interactions Arbres/Micro-Organismes' IFR 110 'Genomique, Ecophysiologie et Ecologie Fonctionnelles' INRA-Nancy 54280 Champenoux, France
| | - Mikael Durling
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Box 7026, Ullsväg 26, 750 05 Uppsala, Sweden
| | - Paolo Gonthier
- Department of Exploitation and Protection of Agricultural and Forest Resources (Di. Va. P. R. A.) - Plant Pathology, University of Torino, Via L. da Vinci 44, I-10095 Grugliasco, Italy
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, 601 Genome Way Huntsville, AL 35806, USA
| | - Carl Gunnar Fossdal
- Norwegian Forest and Landscape Institute, Høgskoleveien 8, NO-1432 Ås, Norway
| | - David Hansson
- Department of Chemistry, Swedish University of Agricultural Sciences, Box 7015, 750 05 Uppsala, Sweden
| | - Bernard Henrissat
- AFMB UMR 6098 CNRS/UI/UII, Case 932, 163 Avenue de Luminy 13288 Marseille cedex 9, France
| | - Ari Hietala
- Norwegian Forest and Landscape Institute, Høgskoleveien 8, NO-1432 Ås, Norway
| | - Kajsa Himmelstrand
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Box 7026, Ullsväg 26, 750 05 Uppsala, Sweden
| | - Dirk Hoffmeister
- Pharmaceutical Biology, Friedrich-Schiller-Universität Jena, Winzerlaer Str. 2, 07745 Jena, Germany
| | - Nils Högberg
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Box 7026, Ullsväg 26, 750 05 Uppsala, Sweden
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Magnus Karlsson
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Box 7026, Ullsväg 26, 750 05 Uppsala, Sweden
| | - Annegret Kohler
- UMR INRA-UHP 'Interactions Arbres/Micro-Organismes' IFR 110 'Genomique, Ecophysiologie et Ecologie Fonctionnelles' INRA-Nancy 54280 Champenoux, France
| | - Ursula Kües
- Büsgen-Institute, Section Molecular Wood Biotechnology and Technical Mycology, University of Göttingen, Büsgenweg 2, D-37077 Göttingen, Germany
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea
| | - Yao-Cheng Lin
- VIB Department of Plant Systems Biology, Ghent University, Bioinformatics and Evolutionary Genomics, Technologiepark 927, B-9052 Gent, Belgium
| | - Mårten Lind
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Box 7026, Ullsväg 26, 750 05 Uppsala, Sweden
| | | | - Vincent Lombard
- AFMB UMR 6098 CNRS/UI/UII, Case 932, 163 Avenue de Luminy 13288 Marseille cedex 9, France
| | - Susan Lucas
- US DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Karl Lundén
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Box 7026, Ullsväg 26, 750 05 Uppsala, Sweden
| | - Emmanuelle Morin
- UMR INRA-UHP 'Interactions Arbres/Micro-Organismes' IFR 110 'Genomique, Ecophysiologie et Ecologie Fonctionnelles' INRA-Nancy 54280 Champenoux, France
| | - Claude Murat
- UMR INRA-UHP 'Interactions Arbres/Micro-Organismes' IFR 110 'Genomique, Ecophysiologie et Ecologie Fonctionnelles' INRA-Nancy 54280 Champenoux, France
| | - Jongsun Park
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea
| | - Tommaso Raffaello
- Department of Forest Ecology, PO Box 27 Latokartanonkaari 7, 00014 University of Helsinki, Helsinki, Finland
| | - Pierre Rouzé
- VIB Department of Plant Systems Biology, Ghent University, Bioinformatics and Evolutionary Genomics, Technologiepark 927, B-9052 Gent, Belgium
| | - Asaf Salamov
- US DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, 601 Genome Way Huntsville, AL 35806, USA
| | - Halvor Solheim
- Norwegian Forest and Landscape Institute, Høgskoleveien 8, NO-1432 Ås, Norway
| | - Jerry Ståhlberg
- Department of Molecular Biology, Swedish University of Agricultural Sciences, Box 590, Husargatan 3, 751 24 Uppsala, Sweden
| | - Heriberto Vélëz
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Box 7026, Ullsväg 26, 750 05 Uppsala, Sweden
| | - Ronald P de Vries
- Microbiology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Ad Wiebenga
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Steve Woodward
- Department of Plant and Soil Science, Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, St. Machar Drive, Aberdeen, AB24 3UU, Scotland UK
| | - Igor Yakovlev
- Norwegian Forest and Landscape Institute, Høgskoleveien 8, NO-1432 Ås, Norway
| | | | - Francis Martin
- UMR INRA-UHP 'Interactions Arbres/Micro-Organismes' IFR 110 'Genomique, Ecophysiologie et Ecologie Fonctionnelles' INRA-Nancy 54280 Champenoux, France
| | | | - Jan Stenlid
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Box 7026, Ullsväg 26, 750 05 Uppsala, Sweden
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Beste L, Nahar N, Dalman K, Fujioka S, Jonsson L, Dutta PC, Sitbon F. Synthesis of hydroxylated sterols in transgenic Arabidopsis plants alters growth and steroid metabolism. Plant Physiol 2011; 157:426-440. [PMID: 21746809 PMCID: PMC3165889 DOI: 10.1104/pp.111.171199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Accepted: 07/04/2011] [Indexed: 05/29/2023]
Abstract
To explore mechanisms in plant sterol homeostasis, we have here increased the turnover of sterols in Arabidopsis (Arabidopsis thaliana) and potato (Solanum tuberosum) plants by overexpressing four mouse cDNA encoding cholesterol hydroxylases (CHs), hydroxylating cholesterol at the C-7, C-24, C-25, or C-27 positions. Compared to the wild type, the four types of Arabidopsis transformant showed varying degrees of phenotypic alteration, the strongest one being in CH25 lines, which were dark-green dwarfs resembling brassinosteroid-related mutants. Gas chromatography-mass spectrometry analysis of extracts from wild-type Arabidopsis plants revealed trace levels of α and β forms of 7-hydroxycholesterol, 7-hydroxycampesterol, and 7-hydroxysitosterol. The expected hydroxycholesterol metabolites in CH7-, CH24-, and CH25 transformants were identified and quantified using gas chromatography-mass spectrometry. Additional hydroxysterol forms were also observed, particularly in CH25 plants. In CH24 and CH25 lines, but not in CH7 ones, the presence of hydroxysterols was correlated with a considerable alteration of the sterol profile and an increased sterol methyltransferase activity in microsomes. Moreover, CH25 lines contained clearly reduced levels of brassinosteroids, and displayed an enhanced drought tolerance. Equivalent transformations of potato plants with the CH25 construct increased hydroxysterol levels, but without the concomitant alteration of growth and sterol profiles observed in Arabidopsis. The results suggest that an increased hydroxylation of cholesterol and/or other sterols in Arabidopsis triggers compensatory processes, acting to maintain sterols at adequate levels.
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Beste L, Nahar N, Dalman K, Fujioka S, Jonsson L, Dutta PC, Sitbon F. Synthesis of hydroxylated sterols in transgenic Arabidopsis plants alters growth and steroid metabolism. Plant Physiol 2011; 157:426-40. [PMID: 21746809 DOI: 10.1104/pp.110.171199] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [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
To explore mechanisms in plant sterol homeostasis, we have here increased the turnover of sterols in Arabidopsis (Arabidopsis thaliana) and potato (Solanum tuberosum) plants by overexpressing four mouse cDNA encoding cholesterol hydroxylases (CHs), hydroxylating cholesterol at the C-7, C-24, C-25, or C-27 positions. Compared to the wild type, the four types of Arabidopsis transformant showed varying degrees of phenotypic alteration, the strongest one being in CH25 lines, which were dark-green dwarfs resembling brassinosteroid-related mutants. Gas chromatography-mass spectrometry analysis of extracts from wild-type Arabidopsis plants revealed trace levels of α and β forms of 7-hydroxycholesterol, 7-hydroxycampesterol, and 7-hydroxysitosterol. The expected hydroxycholesterol metabolites in CH7-, CH24-, and CH25 transformants were identified and quantified using gas chromatography-mass spectrometry. Additional hydroxysterol forms were also observed, particularly in CH25 plants. In CH24 and CH25 lines, but not in CH7 ones, the presence of hydroxysterols was correlated with a considerable alteration of the sterol profile and an increased sterol methyltransferase activity in microsomes. Moreover, CH25 lines contained clearly reduced levels of brassinosteroids, and displayed an enhanced drought tolerance. Equivalent transformations of potato plants with the CH25 construct increased hydroxysterol levels, but without the concomitant alteration of growth and sterol profiles observed in Arabidopsis. The results suggest that an increased hydroxylation of cholesterol and/or other sterols in Arabidopsis triggers compensatory processes, acting to maintain sterols at adequate levels.
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Affiliation(s)
- Lisa Beste
- Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
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Lind M, Dalman K, Stenlid J, Karlsson B, Olson A. Identification of quantitative trait loci affecting virulence in the basidiomycete Heterobasidion annosum s.l. Curr Genet 2007; 52:35-44. [PMID: 17569047 DOI: 10.1007/s00294-007-0137-y] [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: 01/29/2007] [Revised: 05/21/2007] [Accepted: 05/25/2007] [Indexed: 10/23/2022]
Abstract
Identification of virulence factors of phytopathogens is important for the fundamental understanding of infection and disease progress in plants and for the development of control strategies. We have identified quantitative trait loci (QTL) for virulence on 1-year-old Pinus sylvestris and 2-year-old Picea abies seedlings and positioned them on a genetic linkage map of the necrotrophic phytopathogen Heterobasidion annosum sensu lato (s.l.), a major root rot pathogen on conifers. The virulence of 102 progeny isolates was analysed using two measurements: lesion lengths and fungal growth in sapwood from a cambial infection site. We found negative virulence effects of hybridization although this was contradicted on a winter-hardened spruce. On P. abies, both measurements identified several partially overlapping QTLs on linkage group (LG) 15 of significant logarithm of odds (LOD) values ranging from 2.31 to 3.85. On P. sylvestris, the lesion length measurement also identified a QTL (LOD 3.09) on LG 15. Moreover, QTLs on two separate smaller LGs, with peak LOD values of 2.78 and 4.58 were identified for fungal sapwood growth and lesion lengths, respectively. The QTL probably represent loci important for specific as well as general aspects of virulence on P. sylvestris and P. abies.
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Affiliation(s)
- Mårten Lind
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, PO Box 7026, 75007 Uppsala, Sweden
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