Phenotyping data coupled with RNA sequencing of apple genotypes exhibiting contrasted quantitative trait loci architecture for apple scab (Venturia inaequalis) resistance.

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Underlying molecular mechanisms of these loci are yet unknown. Exploring differential gene expression between apple genotypes carrying contrasting combinations of these QTLs could depict original candidate genes and pathways implicated. We therefore carried out RNA sequencing just before and five days after inoculation of the pathogenic fungi Venturia inaequalis, in sixteen genotypes from a pseudo-F1 progeny segregating for resistant or susceptible alleles of the three QTLs. The current dataset includes i) transcriptomic profile description, ii) analysis of differentially expressed genes related to none or combined QTLs, infected or not with Venturia inaequalis and iii) disease phenotyping of the same genetic materials. The raw data files have been deposited in the Gene Expression Omnibus (GEO) repository with the accession number GSE250309. These outputs represent the first step towards elucidating the genetic basis of quantitative apple scab resistance. In the long term, this data set will improve apple breeding strategies on how to combine qualitative (used so far) and quantitative resistances to apple scab, with the aim of diversifying selective pressures on the pathogen.", "claims": [{"id": "claim-method", "statement": "Transcript levels were calculated in CPM and DEGs were defined as exhibiting at least 1.5-fold change in transcript abundance and statistical levels of p < 0.05 relative to a control, using DESeq2, including a Benjamini–Hochberg procedure to control the false discovery rate (FDR) [16].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39239265", "locator": "sections[8] \"Leaf sampling RNA extraction/sequencing and transcriptomic analysis\" paragraph 2", "quote": "Transcript levels were calculated in CPM and DEGs were defined as exhibiting at least 1.5-fold change in transcript abundance and statistical levels of p < 0.05 relative to a control, using DESeq2, including a Benjamini–Hochberg procedure to control the false discovery rate (FDR) [16]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Modulation of apple leaf transcriptome by QTLs and infection by Venturia inaequalis (Original data) (Gene Expression Omnibus).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39239265", "locator": "sections[13] \"Data Availability\" paragraph 2", "quote": "Modulation of apple leaf transcriptome by QTLs and infection by Venturia inaequalis (Original data) (Gene Expression Omnibus)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:39239265"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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