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Mickael Malnoy - One of the best experts on this subject based on the ideXlab platform.

  • candidate gene mapping identifies genomic variations in the Fire Blight susceptibility genes hipm and dipm across the malus germplasm
    Scientific Reports, 2020
    Co-Authors: Richard Tegtmeier, Mickael Malnoy, Jugpreet Singh, Valerio Pompili, Diego Micheletti, Katchen Julliany Pereira Silva, Awais Khan
    Abstract:

    Development of apple (Malus domestica) cultivars resistant to Fire Blight, a devastating bacterial disease caused by Erwinia amylovora, is a priority for apple breeding programs. Towards this goal, the inactivation of members of the HIPM and DIPM gene families with a role in Fire Blight susceptibility (S genes) can help achieve sustainable tolerance. We have investigated the genomic diversity of HIPM and DIPM genes in Malus germplasm collections and used a candidate gene-based association mapping approach to identify SNPs (single nucleotide polymorphisms) with significant associations to Fire Blight susceptibility. A total of 87 unique SNP variants were identified in HIPM and DIPM genes across 93 Malus accessions. Thirty SNPs showed significant associations (p < 0.05) with Fire Blight susceptibility traits, while two of these SNPs showed highly significant (p < 0.001) associations across two different years. This research has provided knowledge about genetic diversity in Fire Blight S genes in diverse apple accessions and identified candidate HIPM and DIPM alleles that could be used to develop apple cultivars with decreased Fire Blight susceptibility via marker-assisted breeding or biotechnological approaches.

  • Status of Fire Blight resistance breeding in Malus
    Journal of Plant Pathology, 2020
    Co-Authors: Andreas Peil, Ofere Francis Emeriewen, Awais Khan, Sarah Kostick, Mickael Malnoy
    Abstract:

    Malus domestica (apple) is one of the most important fruit crops worldwide. Fire Blight, caused by Erwinia amylovora , is one of the most destructive bacterial diseases that impacts apple production systems worldwide. Although it is possible to manage Fire Blight using antibiotics such as streptomycin, kasugamycin or oxytetracycline, the quest for sustainable and eco-friendly production makes breeding for Fire Blight resistance the most promising and desirable approach. Breeding for resistance is a long, resource-intensive process due to the high susceptibility of most commercial apple cultivars, and the fact that most resistance sources being characterized are from wild genetic backgrounds with unpalatable fruits, and apple’s long generation times. Nevertheless, establishment of pre-breeding materials is crucial. This review highlights the status of breeding for Fire Blight resistance in Malus , taking into account, 1) major and minor resistance sources and their interaction with E. amylovora , 2) progress and challenges associated with using wild species as resistance sources, 3) progress and challenges associated with using elite cultivars as resistance sources, 4) advances in biotechnology for use in enhancing the production of durable Fire Blight resistant cultivars.

  • identification of novel strain specific and environment dependent minor qtls linked to Fire Blight resistance in apples
    Plant Molecular Biology Reporter, 2018
    Co-Authors: Elsa Desnoues, Mickael Malnoy, John L. Norelli, Kate Evans, Herb S Aldwinckle, Michael Wisniewski, Awais Khan
    Abstract:

    Since its first report almost 200 years ago, Fire Blight, caused by the gram-negative bacterium Erwinia amylovora, has threatened apple and pear production globally. Identifying novel genes and their functional alleles is a prerequisite to developing apple cultivars with enhanced Fire Blight resistance. Here, we report 13 strain-specific and environment-dependent minor QTLs linked to Fire Blight resistance from a segregating Malus sieversii × Malus × domestica mapping population. Interval mapping at 95% confidence and Kruskal–Wallis analysis at P value = 0.005 were used to identify QTLs for three strains of E. amylovora differing in virulence and pathogenicity. The QTLs identified explain a small to moderate part of resistance variability, and a majority was not common between years or E. amylovora strains. These QTLs are distributed in eight linkage groups of apples and comparison of their map position to previously identified Fire Blight resistance QTLs indicates that most are novel loci. Interaction between experimental conditions in the greenhouse and field, and between years, and differences in virulence levels of strains might be responsible for strain- and year-specific QTLs. The QTLs identified on LG10 for strain Ea273 in 2011 and strain LP101 in 2011, and on LG15 for strain LP101 could be the same QTLs identified previously with strain CFBP1430 in cultivar “Florina” and “Co-op16 × Co-op17” mapping population, respectively. We discuss the potential impact of newly identified minor Fire Blight QTLs and major gene-based resistance on the rate of mutation in pathogen populations to overcome resistance and durability of resistance.

  • identification of a major quantitative trait locus for resistance to Fire Blight in the wild apple species malus fusca
    Molecular Breeding, 2014
    Co-Authors: Ofere Francis Emeriewen, Klaus Richter, Mickael Malnoy, Magda-viola Hanke, Andrzej Kilian, E Zini, Andreas Peil
    Abstract:

    Fire Blight, caused by the Gram-negative bacterium Erwinia amylovora, is the most important bacterial disease affecting apple (Malus × domestica) and pear (Pyrus communis) production. The use of antibiotic treatment, though effective to some degree, is forbidden or strictly regulated in many European countries, and hence an alternative means of control is essential. The planting of Fire Blight-resistant cultivars seems to be a highly feasible strategy. In this study, we explored a segregating population derived from a cross between the wild apple species Malus fusca and the M. × domestica cultivar Idared. F1 progenies used for mapping were artificially inoculated with Erwinia amylovora strain Ea222_JKI at a concentration of 109 cfu/ml in three different years. The averages of percentage lesion length of all replicates of each genotype were used as numerical traits for statistical analysis. A Kruskal–Wallis analysis was used to determine marker–phenotype association and revealed a linkage group with Diversity Arrays Technology (DArT) markers significantly linked with Fire Blight. After locating the positions of the DArT markers on the Golden Delicious genome, simple sequence repeat (SSR) markers were developed from chromosome 10 to replace the DArT markers and to determine the quantitative trait locus (QTL) region. Multiple QTL mapping (MQM) revealed a strong QTL (Mfu10) on linkage group 10 of M. fusca explaining about 65.6 % of the phenotypic variation. This is the first report on a Fire Blight resistance QTL of M. fusca.

  • putative resistance gene markers associated with quantitative trait loci for Fire Blight resistance in malus robusta 5 accessions
    BMC Genetics, 2012
    Co-Authors: Susan E. Gardiner, Gennaro Fazio, Mickael Malnoy, John L. Norelli, Andreas Peil, Nihal De Silva, Deepa Bowatte, M B Horner, C M Carlisle, Claudia Wiedow
    Abstract:

    Breeding of Fire Blight resistant scions and rootstocks is a goal of several international apple breeding programs, as options are limited for management of this destructive disease caused by the bacterial pathogen Erwinia amylovora. A broad, large-effect quantitative trait locus (QTL) for Fire Blight resistance has been reported on linkage group 3 of Malus ‘Robusta 5’. In this study we identified markers derived from putative Fire Blight resistance genes associated with the QTL by integrating further genetic mapping studies with bioinformatics analysis of transcript profiling data and genome sequence databases. When several defined E.amylovora strains were used to inoculate three progenies from international breeding programs, all with ‘Robusta 5’ as a common parent, two distinct QTLs were detected on linkage group 3, where only one had previously been mapped. In the New Zealand ‘Malling 9’ X ‘Robusta 5’ population inoculated with E. amylovora ICMP11176, the proximal QTL co-located with SNP markers derived from a leucine-rich repeat, receptor-like protein ( MxdRLP1) and a closely linked class 3 peroxidase gene. While the QTL detected in the German ‘Idared’ X ‘Robusta 5’ population inoculated with E. amylovora strains Ea222_JKI or ICMP11176 was approximately 6 cM distal to this, directly below a SNP marker derived from a heat shock 90 family protein gene ( HSP90). In the US ‘Otawa3’ X ‘Robusta5’ population inoculated with E. amylovora strains Ea273 or E2002a, the position of the LOD score peak on linkage group 3 was dependent upon the pathogen strains used for inoculation. One of the five MxdRLP1 alleles identified in Fire Blight resistant and susceptible cultivars was genetically associated with resistance and used to develop a high resolution melting PCR marker. A resistance QTL detected on linkage group 7 of the US population co-located with another HSP90 gene-family member and a WRKY transcription factor previously associated with Fire Blight resistance. However, this QTL was not observed in the New Zealand or German populations. The results suggest that the upper region of ‘Robusta 5’ linkage group 3 contains multiple genes contributing to Fire Blight resistance and that their contributions to resistance can vary depending upon pathogen virulence and other factors. Mapping markers derived from putative Fire Blight resistance genes has proved a useful aid in defining these QTLs and developing markers for marker-assisted breeding of Fire Blight resistance.

Andreas Peil - One of the best experts on this subject based on the ideXlab platform.

  • Status of Fire Blight resistance breeding in Malus
    Journal of Plant Pathology, 2020
    Co-Authors: Andreas Peil, Ofere Francis Emeriewen, Awais Khan, Sarah Kostick, Mickael Malnoy
    Abstract:

    Malus domestica (apple) is one of the most important fruit crops worldwide. Fire Blight, caused by Erwinia amylovora , is one of the most destructive bacterial diseases that impacts apple production systems worldwide. Although it is possible to manage Fire Blight using antibiotics such as streptomycin, kasugamycin or oxytetracycline, the quest for sustainable and eco-friendly production makes breeding for Fire Blight resistance the most promising and desirable approach. Breeding for resistance is a long, resource-intensive process due to the high susceptibility of most commercial apple cultivars, and the fact that most resistance sources being characterized are from wild genetic backgrounds with unpalatable fruits, and apple’s long generation times. Nevertheless, establishment of pre-breeding materials is crucial. This review highlights the status of breeding for Fire Blight resistance in Malus , taking into account, 1) major and minor resistance sources and their interaction with E. amylovora , 2) progress and challenges associated with using wild species as resistance sources, 3) progress and challenges associated with using elite cultivars as resistance sources, 4) advances in biotechnology for use in enhancing the production of durable Fire Blight resistant cultivars.

  • engineering Fire Blight resistance into the apple cultivar gala using the fb_mr5 cc nbs lrr resistance gene of malus robusta 5
    Plant Biotechnology Journal, 2014
    Co-Authors: Giovanni A L Broggini, Henryk Flachowsky, Thomas D. Kost, Andrea Patocchi, Klaus Richter, Andreas Peil, Thomas Wohner, Johannes Fahrentrapp, Mariaviola Hanke, C. Gessler
    Abstract:

    Summary The Fire Blight susceptible apple cultivar Malus × domestica Borkh. cv. ‘Gala’ was transformed with the candidate Fire Blight resistance gene FB_MR5 originating from the crab apple accession Malus × robusta 5 (Mr5). A total of five different transgenic lines were obtained. All transgenic lines were shown to be stably transformed and originate from different transgenic events. The transgenic lines express the FB_MR5 either driven by the constitutive CaMV 35S promoter and the ocs terminator or by its native promoter and terminator sequences. Phenotyping experiments were performed with Mr5-virulent and Mr5-avirulent strains of Erwinia amylovora, the causal agent of Fire Blight. Significantly less disease symptoms were detected on transgenic lines after inoculation with two different Mr5-avirulent E. amylovora strains, while significantly more shoot necrosis was observed after inoculation with the Mr5-virulent mutant strain ZYRKD3_1. The results of these experiments demonstrated the ability of a single gene isolated from the native gene pool of apple to protect a susceptible cultivar from Fire Blight. Furthermore, this gene is confirmed to be the resistance determinant of Mr5 as the transformed lines undergo the same gene-for-gene interaction in the host–pathogen relationship Mr5–E. amylovora.

  • identification of a major quantitative trait locus for resistance to Fire Blight in the wild apple species malus fusca
    Molecular Breeding, 2014
    Co-Authors: Ofere Francis Emeriewen, Klaus Richter, Mickael Malnoy, Magda-viola Hanke, Andrzej Kilian, E Zini, Andreas Peil
    Abstract:

    Fire Blight, caused by the Gram-negative bacterium Erwinia amylovora, is the most important bacterial disease affecting apple (Malus × domestica) and pear (Pyrus communis) production. The use of antibiotic treatment, though effective to some degree, is forbidden or strictly regulated in many European countries, and hence an alternative means of control is essential. The planting of Fire Blight-resistant cultivars seems to be a highly feasible strategy. In this study, we explored a segregating population derived from a cross between the wild apple species Malus fusca and the M. × domestica cultivar Idared. F1 progenies used for mapping were artificially inoculated with Erwinia amylovora strain Ea222_JKI at a concentration of 109 cfu/ml in three different years. The averages of percentage lesion length of all replicates of each genotype were used as numerical traits for statistical analysis. A Kruskal–Wallis analysis was used to determine marker–phenotype association and revealed a linkage group with Diversity Arrays Technology (DArT) markers significantly linked with Fire Blight. After locating the positions of the DArT markers on the Golden Delicious genome, simple sequence repeat (SSR) markers were developed from chromosome 10 to replace the DArT markers and to determine the quantitative trait locus (QTL) region. Multiple QTL mapping (MQM) revealed a strong QTL (Mfu10) on linkage group 10 of M. fusca explaining about 65.6 % of the phenotypic variation. This is the first report on a Fire Blight resistance QTL of M. fusca.

  • Phytoalexin formation in Fire Blight-infected apple
    Trees, 2013
    Co-Authors: Cornelia Chizzali, Henryk Flachowsky, Klaus Richter, Andreas Peil, Mariam M. Gaid, Asma K. Belkheir, Till Beuerle, Robert Hänsch, Magda-viola Hanke, Benye Liu
    Abstract:

    Biosynthesis of phytoalexins is a plant defence strategy against pathogens. Shoots of the apple ( Malus  ×  domestica ) cultivar ‘Holsteiner Cox’ formed biphenyls and dibenzofurans when inoculated with the Fire Blight bacterium, Erwinia amylovora . The phytoalexins were only present in the transition zone of stems, whereas the leaves were devoid of the defence compounds. The scaffold of the phytoalexins is formed by biphenyl synthase (BIS), a type III polyketide synthase. In apple, BIS is encoded by a gene family, members of which fall into four subfamilies. Representative BIS cDNAs were cloned from Fire Blight-infected shoots of ‘Holsteiner Cox’ and functionally expressed. The preferred starter substrates were benzoyl-CoA and salicoyl-CoA, leading to the formation of 3,5-dihydroxybiphenyl and 4-hydroxycoumarin, respectively, in the presence of malonyl-CoA as extender molecule. The four subfamilies were differentially regulated after inoculation of shoots with E. amylovora . The BIS3 gene was expressed in stems, with maximum transcript levels in the transition zone. The BIS3 protein was immunochemically localized to the parenchyma of the bark. Dot-shaped immunofluorescence was restricted to the junctions between neighbouring cortical parenchyma cells. Leaves contained transcripts for BIS2 which, however, were not translated into immunodetectable BIS protein. The understanding of phytoalexin metabolism may aid in improving apple resistance to Fire Blight.

  • putative resistance gene markers associated with quantitative trait loci for Fire Blight resistance in malus robusta 5 accessions
    BMC Genetics, 2012
    Co-Authors: Susan E. Gardiner, Gennaro Fazio, Mickael Malnoy, John L. Norelli, Andreas Peil, Nihal De Silva, Deepa Bowatte, M B Horner, C M Carlisle, Claudia Wiedow
    Abstract:

    Breeding of Fire Blight resistant scions and rootstocks is a goal of several international apple breeding programs, as options are limited for management of this destructive disease caused by the bacterial pathogen Erwinia amylovora. A broad, large-effect quantitative trait locus (QTL) for Fire Blight resistance has been reported on linkage group 3 of Malus ‘Robusta 5’. In this study we identified markers derived from putative Fire Blight resistance genes associated with the QTL by integrating further genetic mapping studies with bioinformatics analysis of transcript profiling data and genome sequence databases. When several defined E.amylovora strains were used to inoculate three progenies from international breeding programs, all with ‘Robusta 5’ as a common parent, two distinct QTLs were detected on linkage group 3, where only one had previously been mapped. In the New Zealand ‘Malling 9’ X ‘Robusta 5’ population inoculated with E. amylovora ICMP11176, the proximal QTL co-located with SNP markers derived from a leucine-rich repeat, receptor-like protein ( MxdRLP1) and a closely linked class 3 peroxidase gene. While the QTL detected in the German ‘Idared’ X ‘Robusta 5’ population inoculated with E. amylovora strains Ea222_JKI or ICMP11176 was approximately 6 cM distal to this, directly below a SNP marker derived from a heat shock 90 family protein gene ( HSP90). In the US ‘Otawa3’ X ‘Robusta5’ population inoculated with E. amylovora strains Ea273 or E2002a, the position of the LOD score peak on linkage group 3 was dependent upon the pathogen strains used for inoculation. One of the five MxdRLP1 alleles identified in Fire Blight resistant and susceptible cultivars was genetically associated with resistance and used to develop a high resolution melting PCR marker. A resistance QTL detected on linkage group 7 of the US population co-located with another HSP90 gene-family member and a WRKY transcription factor previously associated with Fire Blight resistance. However, this QTL was not observed in the New Zealand or German populations. The results suggest that the upper region of ‘Robusta 5’ linkage group 3 contains multiple genes contributing to Fire Blight resistance and that their contributions to resistance can vary depending upon pathogen virulence and other factors. Mapping markers derived from putative Fire Blight resistance genes has proved a useful aid in defining these QTLs and developing markers for marker-assisted breeding of Fire Blight resistance.

Gennaro Fazio - One of the best experts on this subject based on the ideXlab platform.

  • putative resistance gene markers associated with quantitative trait loci for Fire Blight resistance in malus robusta 5 accessions
    BMC Genetics, 2012
    Co-Authors: Susan E. Gardiner, Gennaro Fazio, Mickael Malnoy, John L. Norelli, Andreas Peil, Nihal De Silva, Deepa Bowatte, M B Horner, C M Carlisle, Claudia Wiedow
    Abstract:

    Breeding of Fire Blight resistant scions and rootstocks is a goal of several international apple breeding programs, as options are limited for management of this destructive disease caused by the bacterial pathogen Erwinia amylovora. A broad, large-effect quantitative trait locus (QTL) for Fire Blight resistance has been reported on linkage group 3 of Malus ‘Robusta 5’. In this study we identified markers derived from putative Fire Blight resistance genes associated with the QTL by integrating further genetic mapping studies with bioinformatics analysis of transcript profiling data and genome sequence databases. When several defined E.amylovora strains were used to inoculate three progenies from international breeding programs, all with ‘Robusta 5’ as a common parent, two distinct QTLs were detected on linkage group 3, where only one had previously been mapped. In the New Zealand ‘Malling 9’ X ‘Robusta 5’ population inoculated with E. amylovora ICMP11176, the proximal QTL co-located with SNP markers derived from a leucine-rich repeat, receptor-like protein ( MxdRLP1) and a closely linked class 3 peroxidase gene. While the QTL detected in the German ‘Idared’ X ‘Robusta 5’ population inoculated with E. amylovora strains Ea222_JKI or ICMP11176 was approximately 6 cM distal to this, directly below a SNP marker derived from a heat shock 90 family protein gene ( HSP90). In the US ‘Otawa3’ X ‘Robusta5’ population inoculated with E. amylovora strains Ea273 or E2002a, the position of the LOD score peak on linkage group 3 was dependent upon the pathogen strains used for inoculation. One of the five MxdRLP1 alleles identified in Fire Blight resistant and susceptible cultivars was genetically associated with resistance and used to develop a high resolution melting PCR marker. A resistance QTL detected on linkage group 7 of the US population co-located with another HSP90 gene-family member and a WRKY transcription factor previously associated with Fire Blight resistance. However, this QTL was not observed in the New Zealand or German populations. The results suggest that the upper region of ‘Robusta 5’ linkage group 3 contains multiple genes contributing to Fire Blight resistance and that their contributions to resistance can vary depending upon pathogen virulence and other factors. Mapping markers derived from putative Fire Blight resistance genes has proved a useful aid in defining these QTLs and developing markers for marker-assisted breeding of Fire Blight resistance.

  • rootstock regulated gene expression patterns associated with Fire Blight resistance in apple
    BMC Genomics, 2012
    Co-Authors: Philip J Jensen, Noemi O Halbrendt, Gennaro Fazio, Izabela Makalowska, Naomi Altman, Craig A Praul, Siela N Maximova, Henry K Ngugi, Robert Michael Crassweller, James W Travis
    Abstract:

    Desirable apple varieties are clonally propagated by grafting vegetative scions onto rootstocks. Rootstocks influence many phenotypic traits of the scion, including resistance to pathogens such as Erwinia amylovora, which causes Fire Blight, the most serious bacterial disease of apple. The purpose of the present study was to quantify rootstock-mediated differences in scion Fire Blight susceptibility and to identify transcripts in the scion whose expression levels correlated with this response. Rootstock influence on scion Fire Blight resistance was quantified by inoculating three-year old, orchard-grown apple trees, consisting of 'Gala' scions grafted to a range of rootstocks, with E. amylovora. Disease severity was measured by the extent of shoot necrosis over time. 'Gala' scions grafted to G.30 or MM.111 rootstocks showed the lowest rates of necrosis, while 'Gala' on M.27 and B.9 showed the highest rates of necrosis. 'Gala' scions on M.7, S.4 or M.9F56 had intermediate necrosis rates. Using an apple DNA microarray representing 55,230 unique transcripts, gene expression patterns were compared in healthy, un-inoculated, greenhouse-grown 'Gala' scions on the same series of rootstocks. We identified 690 transcripts whose steady-state expression levels correlated with the degree of Fire Blight susceptibility of the scion/rootstock combinations. Transcripts known to be differentially expressed during E. amylovora infection were disproportionately represented among these transcripts. A second-generation apple microarray representing 26,000 transcripts was developed and was used to test these correlations in an orchard-grown population of trees segregating for Fire Blight resistance. Of the 690 transcripts originally identified using the first-generation array, 39 had expression levels that correlated with Fire Blight resistance in the breeding population. Rootstocks had significant effects on the Fire Blight susceptibility of 'Gala' scions, and rootstock-regulated gene expression patterns could be correlated with differences in susceptibility. The results suggest a relationship between rootstock-regulated Fire Blight susceptibility and sorbitol dehydrogenase, phenylpropanoid metabolism, protein processing in the endoplasmic reticulum, and endocytosis, among others. This study illustrates the utility of our rootstock-regulated gene expression data sets for candidate trait-associated gene data mining.

  • Rootstock-regulated gene expression patterns associated with Fire Blight resistance in apple
    BMC Genomics, 2012
    Co-Authors: Philip J Jensen, Noemi O Halbrendt, Gennaro Fazio, Izabela Makalowska, Naomi Altman, Craig A Praul, Siela N Maximova, Henry K Ngugi, Robert Michael Crassweller, James W Travis
    Abstract:

    Background Desirable apple varieties are clonally propagated by grafting vegetative scions onto rootstocks. Rootstocks influence many phenotypic traits of the scion, including resistance to pathogens such as Erwinia amylovora , which causes Fire Blight, the most serious bacterial disease of apple. The purpose of the present study was to quantify rootstock-mediated differences in scion Fire Blight susceptibility and to identify transcripts in the scion whose expression levels correlated with this response. Results Rootstock influence on scion Fire Blight resistance was quantified by inoculating three-year old, orchard-grown apple trees, consisting of 'Gala' scions grafted to a range of rootstocks, with E. amylovora . Disease severity was measured by the extent of shoot necrosis over time. 'Gala' scions grafted to G.30 or MM.111 rootstocks showed the lowest rates of necrosis, while 'Gala' on M.27 and B.9 showed the highest rates of necrosis. 'Gala' scions on M.7, S.4 or M.9F56 had intermediate necrosis rates. Using an apple DNA microarray representing 55,230 unique transcripts, gene expression patterns were compared in healthy, un-inoculated, greenhouse-grown 'Gala' scions on the same series of rootstocks. We identified 690 transcripts whose steady-state expression levels correlated with the degree of Fire Blight susceptibility of the scion/rootstock combinations. Transcripts known to be differentially expressed during E. amylovora infection were disproportionately represented among these transcripts. A second-generation apple microarray representing 26,000 transcripts was developed and was used to test these correlations in an orchard-grown population of trees segregating for Fire Blight resistance. Of the 690 transcripts originally identified using the first-generation array, 39 had expression levels that correlated with Fire Blight resistance in the breeding population. Conclusions Rootstocks had significant effects on the Fire Blight susceptibility of 'Gala' scions, and rootstock-regulated gene expression patterns could be correlated with differences in susceptibility. The results suggest a relationship between rootstock-regulated Fire Blight susceptibility and sorbitol dehydrogenase, phenylpropanoid metabolism, protein processing in the endoplasmic reticulum, and endocytosis, among others. This study illustrates the utility of our rootstock-regulated gene expression data sets for candidate trait-associated gene data mining.

  • Putative resistance gene markers associated with quantitative trait loci for Fire Blight resistance in Malus 'Robusta 5' accessions
    BMC Genetics, 2012
    Co-Authors: Susan E. Gardiner, Gennaro Fazio, Mickael Malnoy, John L. Norelli, Andreas Peil, Nihal De Silva, Mary Horner, Deepa Bowatte, Charmaine Carlisle, Claudia Wiedow
    Abstract:

    Background: Breeding of Fire Blight resistant scions and rootstocks is a goal of several international apple breeding programs, as options are limited for management of this destructive disease caused by the bacterial pathogen Erwinia amylovora. A broad, large-effect quantitative trait locus (QTL) for Fire Blight resistance has been reported on linkage group 3 of Malus 'Robusta 5'. In this study we identified markers derived from putative Fire Blight resistance genes associated with the QTL by integrating further genetic mapping studies with bioinformatics analysis of transcript profiling data and genome sequence databases. Results: When several defined E. amylovora strains were used to inoculate three progenies from international breeding programs, all with 'Robusta 5' as a common parent, two distinct QTLs were detected on linkage group 3, where only one had previously been mapped. In the New Zealand 'Malling 9' X 'Robusta 5' population inoculated with E. amylovora ICMP11176, the proximal QTL co-located with SNP markers derived from a leucine-rich repeat, receptor-like protein (MxdRLP1) and a closely linked class 3 peroxidase gene. While the QTL detected in the German 'Idared' X 'Robusta 5' population inoculated with E. amylovora strains Ea222_JKI or ICMP11176 was approximately 6 cM distal to this, directly below a SNP marker derived from a heat shock 90 family protein gene (HSP90). In the US 'Otawa3' X 'Robusta5' population inoculated with E. amylovora strains Ea273 or E2002a, the position of the LOD score peak on linkage group 3 was dependent upon the pathogen strains used for inoculation. One of the five MxdRLP1 alleles identified in Fire Blight resistant and susceptible cultivars was genetically associated with resistance and used to develop a high resolution melting PCR marker. A resistance QTL detected on linkage group 7 of the US population co-located with another HSP90 gene-family member and a WRKY transcription factor previously associated with Fire Blight resistance. However, this QTL was not observed in the New Zealand or German populations. Conclusions: The results suggest that the upper region of 'Robusta5' linkage group 3 contains multiple genes contributing to Fire Blight resistance and that their contributions to resistance can vary depending upon pathogen virulence and other factors. Mapping markers derived from putative Fire Blight resistance genes has proved a useful aid in defining these QTLs and developing markers for marker-assisted breeding of Fire Blight resistance.

  • Fire Blight resistance of budagovsky 9 apple rootstock
    Plant Disease, 2008
    Co-Authors: Nicole L Russo, Gennaro Fazio, T L Robinson, Herb S Aldwinckle
    Abstract:

    Erwinia amylovora, the causal agent of Fire Blight, can cause a fatal infection of apple rootstocks known as rootstock Blight. Budagovsky 9 (B.9) apple rootstock is reported to be highly susceptible when inoculated with E. amylovora, although results from multiple trials showed that B.9 is resistant to rootstock Blight infection in field plantings. Conflicting results could stem from genetic variation in the B.9 population, appearing as phenotypic differences in rootstock material. However, genetic testing, using 23 microsatellite loci, confirmed the clonal uniformity of B.9 in commerce. Variation in growth habit between B.9 rootstocks originating from two nurseries also has been discounted as a source of disease resistance. Instead, results indicate a possible novel resistance phenotype in B.9 rootstock. B.9 rootstock was susceptible to leaf inoculation by E. amylovora, statistically similar to the susceptible rootstock Malling 9 (M.9). Conversely, inoculation assays targeting woody 4- to 5-year-old tissue revealed a high level of resistance in B.9, whereas M.9 remained susceptible. Although the mechanism by which B.9 gains resistance to E. amylovora is unknown, it is reminiscent of age-related resistance, due to an observed gain of resistance in woody rootstock tissue over succulent shoot tissue. Durable Fire Blight resistance correlated with tissue development could be a valuable tool for rootstock breeders.

John L. Norelli - One of the best experts on this subject based on the ideXlab platform.

  • dissecting genetic resistance to Fire Blight in three pear populations
    Phytopathology, 2020
    Co-Authors: Jason D Zurn, John L. Norelli, Sara Montanari, Richard L Bell, Nahla V Bassil
    Abstract:

    Fire Blight, caused by the bacterial pathogen Erwinia amylovora, is a persistent problem for pear (Pyrus spp.) growers in the United States. Growing resistant cultivars is one of the best options for managing Fire Blight. The cultivars Potomac and Old Home and the selection NJA2R59T69 display resistance to Fire Blight. As such, three mapping populations (El Dorado × Potomac, Old Home × Bartlett, and NJA2R59T69 × Bartlett) were developed to identify genomic regions associated with resistance to Fire Blight. Progeny were phenotyped during 2017 and 2018 by inoculating multiple actively growing shoots of field-grown seedling trees with E. amylovora isolate E153n via the cut-leaf method. Genotyping was conducted using the recently developed Axiom Pear 70 K Genotyping Array and chromosomal linkage groups were created for each population. An integrated two-way pseudo-testcross approach was used to map quantitative trait loci (QTLs). Resistance QTLs were identified on chromosome 2 for each population. The QTLs identified in the El Dorado × Potomac and Old Home × Bartlett populations are in the same region as QTLs that were previously identified in Harrow Sweet and Moonglow. The QTL in NJA2R59T69 mapped proximally to the previously identified QTLs and originated from an unknown Asian or occidental source. Future research will focus on further characterizing the resistance regions and developing tools for DNA-informed breeding.

  • identification of novel strain specific and environment dependent minor qtls linked to Fire Blight resistance in apples
    Plant Molecular Biology Reporter, 2018
    Co-Authors: Elsa Desnoues, Mickael Malnoy, John L. Norelli, Kate Evans, Herb S Aldwinckle, Michael Wisniewski, Awais Khan
    Abstract:

    Since its first report almost 200 years ago, Fire Blight, caused by the gram-negative bacterium Erwinia amylovora, has threatened apple and pear production globally. Identifying novel genes and their functional alleles is a prerequisite to developing apple cultivars with enhanced Fire Blight resistance. Here, we report 13 strain-specific and environment-dependent minor QTLs linked to Fire Blight resistance from a segregating Malus sieversii × Malus × domestica mapping population. Interval mapping at 95% confidence and Kruskal–Wallis analysis at P value = 0.005 were used to identify QTLs for three strains of E. amylovora differing in virulence and pathogenicity. The QTLs identified explain a small to moderate part of resistance variability, and a majority was not common between years or E. amylovora strains. These QTLs are distributed in eight linkage groups of apples and comparison of their map position to previously identified Fire Blight resistance QTLs indicates that most are novel loci. Interaction between experimental conditions in the greenhouse and field, and between years, and differences in virulence levels of strains might be responsible for strain- and year-specific QTLs. The QTLs identified on LG10 for strain Ea273 in 2011 and strain LP101 in 2011, and on LG15 for strain LP101 could be the same QTLs identified previously with strain CFBP1430 in cultivar “Florina” and “Co-op16 × Co-op17” mapping population, respectively. We discuss the potential impact of newly identified minor Fire Blight QTLs and major gene-based resistance on the rate of mutation in pathogen populations to overcome resistance and durability of resistance.

  • Fire Blight resistance in wild accessions of malus sieversii
    Plant Disease, 2017
    Co-Authors: Julia M Harshman, Kate Evans, Haley Allen, Ryan Potts, Jade Flamenco, Herb S Aldwinckle, Michael Wisniewski, John L. Norelli
    Abstract:

    Fire Blight (Erwinia amylovora) is a devastating bacterial disease in apple that results in severe economic losses. Epidemics are becoming more common as susceptible cultivars and rootstocks are being planted, and control is becoming more difficult as antibiotic-resistant strains develop. Resistant germplasm currently being utilized by breeding programs tend to have small fruit size and poor flavor characteristics. Malus sieversii, a progenitor species of domestic apple, is notable for its relatively large, palatable fruit and some accessions have been reported to be resistant to Fire Blight. In this study, nearly 200 accessions of M. sieversii and appropriate controls were inoculated with E. amylovora in both Washington and West Virginia to identify Fire Blight resistant accessions. Twelve accessions were identified with resistance comparable to highly resistant and resistant controls. Several accessions exhibited a unique resistance response, not previously reported in domestic apple (M. × domestica), characterized by low incidence of infection but high severity once infection was initiated. Several of these M. sieversii accessions will be used as parents in future crosses in the Washington State University apple breeding program.

  • putative resistance gene markers associated with quantitative trait loci for Fire Blight resistance in malus robusta 5 accessions
    BMC Genetics, 2012
    Co-Authors: Susan E. Gardiner, Gennaro Fazio, Mickael Malnoy, John L. Norelli, Andreas Peil, Nihal De Silva, Deepa Bowatte, M B Horner, C M Carlisle, Claudia Wiedow
    Abstract:

    Breeding of Fire Blight resistant scions and rootstocks is a goal of several international apple breeding programs, as options are limited for management of this destructive disease caused by the bacterial pathogen Erwinia amylovora. A broad, large-effect quantitative trait locus (QTL) for Fire Blight resistance has been reported on linkage group 3 of Malus ‘Robusta 5’. In this study we identified markers derived from putative Fire Blight resistance genes associated with the QTL by integrating further genetic mapping studies with bioinformatics analysis of transcript profiling data and genome sequence databases. When several defined E.amylovora strains were used to inoculate three progenies from international breeding programs, all with ‘Robusta 5’ as a common parent, two distinct QTLs were detected on linkage group 3, where only one had previously been mapped. In the New Zealand ‘Malling 9’ X ‘Robusta 5’ population inoculated with E. amylovora ICMP11176, the proximal QTL co-located with SNP markers derived from a leucine-rich repeat, receptor-like protein ( MxdRLP1) and a closely linked class 3 peroxidase gene. While the QTL detected in the German ‘Idared’ X ‘Robusta 5’ population inoculated with E. amylovora strains Ea222_JKI or ICMP11176 was approximately 6 cM distal to this, directly below a SNP marker derived from a heat shock 90 family protein gene ( HSP90). In the US ‘Otawa3’ X ‘Robusta5’ population inoculated with E. amylovora strains Ea273 or E2002a, the position of the LOD score peak on linkage group 3 was dependent upon the pathogen strains used for inoculation. One of the five MxdRLP1 alleles identified in Fire Blight resistant and susceptible cultivars was genetically associated with resistance and used to develop a high resolution melting PCR marker. A resistance QTL detected on linkage group 7 of the US population co-located with another HSP90 gene-family member and a WRKY transcription factor previously associated with Fire Blight resistance. However, this QTL was not observed in the New Zealand or German populations. The results suggest that the upper region of ‘Robusta 5’ linkage group 3 contains multiple genes contributing to Fire Blight resistance and that their contributions to resistance can vary depending upon pathogen virulence and other factors. Mapping markers derived from putative Fire Blight resistance genes has proved a useful aid in defining these QTLs and developing markers for marker-assisted breeding of Fire Blight resistance.

  • Fire Blight: Applied Genomic Insights of the Pathogen and Host
    Annual Review of Phytopathology, 2012
    Co-Authors: Mickael Malnoy, Theo H M Smits, John L. Norelli, Stefan Martens, Marie Anne Barny, George W. Sundin, Brion Duffy
    Abstract:

    The enterobacterial phytopathogen Erwinia amylovora causes Fire Blight, an invasive disease that threatens a wide range of commercial and ornamental Rosaceae host plants. The response elicited by E. amylovora in its host during disease development is similar to the hypersensitive reaction that typically leads to resistance in an incompatible host-pathogen interaction, yet no gene-for-gene resistance has been described for this host-pathogen system. Comparative genomic analysis has found an unprecedented degree of genetic uniformity among strains of E. amylovora, suggesting that the pathogen has undergone a recent genetic bottleneck. The genome of apple, an important host of E. amylovora, has been sequenced, creating new opportunities for the study of interactions between host and pathogen during Fire Blight development and for the identification of resistance genes. This review includes recent advances in the genomics of both host and pathogen.

Awais Khan - One of the best experts on this subject based on the ideXlab platform.

  • genome wide association mapping identifies novel loci underlying Fire Blight resistance in apple
    The Plant Genome, 2021
    Co-Authors: Ranjita Thapa, Jugpreet Singh, Benjamin Gutierrez, Jie Arro, Awais Khan
    Abstract:

    Fire Blight, caused by epiphytotic gram-negative bacteria Erwinia amylovora, is the most destructive bacterial disease of apple (Malus spp.). Genetic mechanisms of Fire Blight resistance have mainly been studied using traditional biparental quantitative trait loci (QTL) mapping approaches. Here, we use large-scale historic shoot and blossom Fire Blight data collected over multiple years and genotyping-by-sequencing (GBS) markers to identify significant marker-trait associations in a diverse set of 566 apple [Malus domestica (Suckow) Borkh.] accessions. There was large variation in Fire Blight resistance and susceptibility in these accessions. We identified 23 and 38 QTL significantly (p < .001) associated with shoot and blossom Blight resistance, respectively. The QTL are distributed across all 17 chromosomes of apple. Four shoot Blight and 19 blossom Blight QTL identified in this study colocalized with previously identified QTL associated with resistance to Fire Blight or apple scab. Using transcriptomics data of two apple cultivars with contrasting Fire Blight responses, we also identified candidate genes for Fire Blight resistance that are differentially expressed between resistant and susceptible cultivars and located within QTL intervals for Fire Blight resistance. However, further experiments are needed to confirm and validate these marker-trait associations and develop diagnostic markers before use in marker-assisted breeding to develop apple cultivars with decreased Fire Blight susceptibility.

  • candidate gene mapping identifies genomic variations in the Fire Blight susceptibility genes hipm and dipm across the malus germplasm
    Scientific Reports, 2020
    Co-Authors: Richard Tegtmeier, Mickael Malnoy, Jugpreet Singh, Valerio Pompili, Diego Micheletti, Katchen Julliany Pereira Silva, Awais Khan
    Abstract:

    Development of apple (Malus domestica) cultivars resistant to Fire Blight, a devastating bacterial disease caused by Erwinia amylovora, is a priority for apple breeding programs. Towards this goal, the inactivation of members of the HIPM and DIPM gene families with a role in Fire Blight susceptibility (S genes) can help achieve sustainable tolerance. We have investigated the genomic diversity of HIPM and DIPM genes in Malus germplasm collections and used a candidate gene-based association mapping approach to identify SNPs (single nucleotide polymorphisms) with significant associations to Fire Blight susceptibility. A total of 87 unique SNP variants were identified in HIPM and DIPM genes across 93 Malus accessions. Thirty SNPs showed significant associations (p < 0.05) with Fire Blight susceptibility traits, while two of these SNPs showed highly significant (p < 0.001) associations across two different years. This research has provided knowledge about genetic diversity in Fire Blight S genes in diverse apple accessions and identified candidate HIPM and DIPM alleles that could be used to develop apple cultivars with decreased Fire Blight susceptibility via marker-assisted breeding or biotechnological approaches.

  • Comparative evaluation of lateral flow immunoassays, LAMP, and quantitative PCR for diagnosis of Fire Blight in apple orchards
    Journal of Plant Pathology, 2020
    Co-Authors: Jugpreet Singh, Della Cobb-smith, Elizabeth Higgins, Awais Khan
    Abstract:

    Fire Blight remains a serious threat to commercial apple production in the USA and worldwide. Other diseases and spray damage can result in Fire Blight-like symptoms that can lead to misdiagnosis and affect disease management strategies. Accurate and timely detection of the Fire Blight pathogen, Erwinia amylovora , is extremely important to deploy appropriate and timely measures to reduce Fire Blight epidemics in commercial apple orchards. We tested two commercial lateral flow immunoassays (AgriStrip®, and Pocket Diagnostics kit), Loop mediated isothermal amplification (LAMP), and quantitative PCR (qPCR) to diagnose E. amylovora infected samples in lab and field settings. The AgriStrip® and Pocket Diagnostics kits were able to detect actively growing bacteria up to ×10^6 cfu/ml bacterial concentration. Pocket Diagnostics kit had less specificity and showed positive tests for E. pyrifolia in addition to E. amylovora . The LAMP assay showed high specificity for E. amylovora and was able to detect up to ×10^3 cfu/ml bacterial concentrations. The qPCR assay was also able to detect bacterial cells up to ×10^−3 cfu/ml bacterial concentration with highly specific E. amylovora detection. Grower surveys and comparative cost-benefit analysis indicated that immunoassay kits are less expensive, easier to use, and require less technical expertise for on-site Fire Blight diagnosis than LAMP and qPCR. However, the choice of a specific diagnostic assay depends on the time, sensitivity, and specificity required for the detection of Fire Blight and its management.

  • Status of Fire Blight resistance breeding in Malus
    Journal of Plant Pathology, 2020
    Co-Authors: Andreas Peil, Ofere Francis Emeriewen, Awais Khan, Sarah Kostick, Mickael Malnoy
    Abstract:

    Malus domestica (apple) is one of the most important fruit crops worldwide. Fire Blight, caused by Erwinia amylovora , is one of the most destructive bacterial diseases that impacts apple production systems worldwide. Although it is possible to manage Fire Blight using antibiotics such as streptomycin, kasugamycin or oxytetracycline, the quest for sustainable and eco-friendly production makes breeding for Fire Blight resistance the most promising and desirable approach. Breeding for resistance is a long, resource-intensive process due to the high susceptibility of most commercial apple cultivars, and the fact that most resistance sources being characterized are from wild genetic backgrounds with unpalatable fruits, and apple’s long generation times. Nevertheless, establishment of pre-breeding materials is crucial. This review highlights the status of breeding for Fire Blight resistance in Malus , taking into account, 1) major and minor resistance sources and their interaction with E. amylovora , 2) progress and challenges associated with using wild species as resistance sources, 3) progress and challenges associated with using elite cultivars as resistance sources, 4) advances in biotechnology for use in enhancing the production of durable Fire Blight resistant cultivars.

  • root system traits impact early Fire Blight susceptibility in apple malus domestica
    BMC Plant Biology, 2019
    Co-Authors: Jugpreet Singh, Jack Fabrizio, Elsa Desnoues, Julliany Pereira Silva, Wolfgang Busch, Awais Khan
    Abstract:

    Although it is known that resistant rootstocks facilitate management of Fire Blight disease, incited by Erwinia amylovora, the role of rootstock root traits in providing systemic defense against E. amylovora is unclear. In this study, the hypothesis that rootstocks of higher root vigor provide higher tolerance to Fire Blight infection in apples is tested. Several apple scion genotypes grafted onto a single rootstock genotype and non-grafted ‘M.7’ rootstocks of varying root vigor are used to assess phenotypic and molecular relationships between root traits of rootstocks and Fire Blight susceptibility of apple scion cultivars. It is observed that different root traits display significant (p < 0.05) negative correlations with Fire Blight susceptibility. In fact, root surface area partially dictates differential levels of Fire Blight susceptibility of ‘M.7’ rootstocks. Furthermore, contrasting changes in gene expression patterns of diverse molecular pathways accompany observed differences in levels of root-driven Fire Blight susceptibility. It is noted that a singular co-expression gene network consisting of genes from defense, carbohydrate metabolism, protein kinase activity, oxidation-reduction, and stress response pathways modulates root-dependent Fire Blight susceptibility in apple. In particular, WRKY75 and UDP-glycotransferase are singled-out as hub genes deserving of further detailed analysis. It is proposed that low root mass may incite resource-limiting conditions to activate carbohydrate metabolic pathways, which reciprocally interact with plant immune system genes to elicit differential levels of Fire Blight susceptibility.