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Research Article
Lawrence B. Smart
Cornell University
Corresponding Author
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Background: Melampsora spp. rusts are the greatest pathogen threat to shrub willow (Salix spp.) bioenergy crops. Genetic resistance is key to limit the effects of these foliar diseases on host response and biomass yield, however, the genetic basis of host resistance has not been characterized. The addition of new genomic resources for Salix provides greater power to investigate the interaction between S. purpurea and M. americana, species commonly found in the Northeast US. Here, we utilize 3' RNA-seq to investigate host-pathogen interactions following controlled inoculations of M. americana on resistant and susceptible F2 S. purpurea genotypes identified in a recent QTL mapping study. Differential gene expression, network analysis, and eQTL mapping was used to contrast the response to inoculation and to identify associated candidate genes.
Results: Controlled inoculation in a replicated greenhouse study identified 19 and 105 differentially expressed genes between resistant and susceptible genotypes at 42 and 66 HPI, respectively. Defense response gene networks were activated in both resistant and susceptible genotypes and enriched for many of the same defense response genes, yet the hub genes of these common response modules showed greater mean expression among the resistant plants. Further, eight and six eQTL hotspots were identified at 42 and 66 HPI, respectively. The combined results of the three analyses highlight 124 candidate genes in the host for further analysis while analysis of pathogen RNA showed differential expression of 22 genes, two of which are candidate pathogen effectors.
Conclusions: We identified two differentially expressed M. americana transcripts and 124 S. purpurea genes that are good candidates for future studies to confirm their role in conferring resistance.
Keywords
Salix purpurea, Melampsora americana, shrub willow, leaf rust, transcriptome, 3' RNA-seq, WGCNA, Differential expression, eQTL
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Competing interest reported. LB Smart is an inventor of patented cultivar ‘Fish Creek’, for which he receives royalties based on cutting sales. The other authors have no competing interests.
This is a list of supplementary files associated with this preprint. Click to download.
- AdditionalFigure1.pdf
- AdditionalFigure2.pdf
- AdditionalFigure3.pdf
- AdditionalTable1DifferentialExpressionSuscVResGOResults.xlsx
- AdditionalTable2DifferentialExpressionInocVCtrlGOResults.xlsx
- AdditionalTable3NetworkAnalysisResistantModulesGOResults.xlsx
- AdditionalTable4NetworkAnalysisSusceptibleModulesGOResults.xlsx
- AdditionalTable5eQTLHotspotsGOResults.xlsx
- AdditionalTable6CandidateGeneList.xlsx
- AdditionalTable7MamericanaEffectorPredictionSummary.xlsx
- AdditionalTable8SignalPPredictionSummary.xlsx
- AdditionalTable9EffectorPv2.0PredictionSummary.xlsx
- WilkersonCrowellRusteQTLAdditionalfileslegends.docx
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This preprint is under consideration at BMC Genomics. A preprint is a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research Article
Lawrence B. Smart
Cornell University
Corresponding Author
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Under Review
Version 1
Posted 16 Jun, 2021
No community comments so far
Reviews received
Received 02 Jul, 2021
Reviewers agreed
On 17 Jun, 2021
Reviewers invited
Invitations sent on 17 Jun, 2021
Editor assigned
On 17 Jun, 2021
Editor invited
On 14 Jun, 2021
Submission checks complete
On 14 Jun, 2021
First submitted
On 04 Jun, 2021
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background: Melampsora spp. rusts are the greatest pathogen threat to shrub willow (Salix spp.) bioenergy crops. Genetic resistance is key to limit the effects of these foliar diseases on host response and biomass yield, however, the genetic basis of host resistance has not been characterized. The addition of new genomic resources for Salix provides greater power to investigate the interaction between S. purpurea and M. americana, species commonly found in the Northeast US. Here, we utilize 3' RNA-seq to investigate host-pathogen interactions following controlled inoculations of M. americana on resistant and susceptible F2 S. purpurea genotypes identified in a recent QTL mapping study. Differential gene expression, network analysis, and eQTL mapping was used to contrast the response to inoculation and to identify associated candidate genes.
Results: Controlled inoculation in a replicated greenhouse study identified 19 and 105 differentially expressed genes between resistant and susceptible genotypes at 42 and 66 HPI, respectively. Defense response gene networks were activated in both resistant and susceptible genotypes and enriched for many of the same defense response genes, yet the hub genes of these common response modules showed greater mean expression among the resistant plants. Further, eight and six eQTL hotspots were identified at 42 and 66 HPI, respectively. The combined results of the three analyses highlight 124 candidate genes in the host for further analysis while analysis of pathogen RNA showed differential expression of 22 genes, two of which are candidate pathogen effectors.
Conclusions: We identified two differentially expressed M. americana transcripts and 124 S. purpurea genes that are good candidates for future studies to confirm their role in conferring resistance.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
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