Purpose: Apple is one of the commercially most important fruits hosting a wide range of postharvest diseases that can threaten grower economy resulting in a yearly yield loss. Fungal diseases are the major problem in many countries, especially in organic culture as well as in countries with humid condition. Among the postharvest diseases, blue mold (caused by Penicillium expansum) is one of the most important. This disease is very destructive on apple, not only due to the economic damage but also because of mycotoxin patulin production. Research method: In the present study, we used wound inoculation and fruit trait data along with a large set of SNP data from the Axiom®Apple 480 K array to explore possible QTLs associated with rate of lesion decay, ripening period, fruit firmness and softening. Findings: Due to the very large number of SNPs in the present study, the significance threshold (5.63) was higher than in most other Genome-Wide Association Studies. However, some close to significant associations involving lesion decay were found on linkage group 3 (LG3), spanning a distance of 537 Kb (from 30,527,077 to 31,064,205). Interestingly, two SNPs associated with ripening period were also found on LG3 at the same position (30,494,523–30,885,771). Research limitations: This study could be extended with inclusion of more cultivars from different locations in order to minimize the impact of environment and to enhance the study power. Originality/Value: Although the genetic mechanism of blue mold resistance seems to be controlled by several genes in apple, our results indicate a possible association on LG3 which needs to be further investigated for candidate gene targeting. This finding may help to understand the genetic mechanism of blue mold disease in apple.

How selection and demography jointly shape the genomes of perennial crops remains an open question. Apple (M. domestica) is a compelling system because its domestication involved multiple wild progenitors and post-domestication admixture across Eurasia. We integrate 218 whole genomes (68 cultivated dessert/cider; 150 wild: M. sieversii, M. orientalis, M. sylvestris), RNA sequencing (RNA-seq), and a genome-wide association study of flowering time to resolve how these forces shaped the cultivated apple genome. Despite weak neutral differentiation and widespread admixture, dessert and cider apples form distinct gene pools that derive primarily from M. sieversii-M. orientalis rather than European M. sylvestris. We find no evidence of a domestication bottleneck, as expected in perennials. Demographic-aware selection scans reveal non-overlapping targets supported by RNA-seq; dessert shows more hard sweeps at fruit quality, disease resistance, and flowering genes, whereas cider shows proportionally more soft sweeps and balancing selection. Wild-to-crop introgression from M. sylvestris is extensive but heterogeneous; some introgressed tracts concentrate in hard-sweep regions and approach fixation (consistent with rapid, targeted uptake), whereas others persist at intermediate frequencies with soft-sweep signatures (consistent with diffuse, recurrent introgression of adaptive alleles). The lead chromosome 9 flowering-time association lies within an introgressed segment near a transposable element and is separated from sweep peaks, consistent with regulatory/polygenic control. Cultivated apples carry a lower deleterious load than wild relatives. These results provide a comprehensive genomic portrait of perennial fruit tree domestication, clarifying how selection and adaptive introgression shaped the cultivated apple genome and yielding actionable targets for breeding and conservation.

Abstract Apple scab, caused by Venturia inaequalis , remains one of the most damaging diseases in apple orchards, driving intensive pesticide use worldwide. Reducing this dependence requires the deployment of durable resistance, ideally through the combination of major resistance genes (R genes) with quantitative trait loci (QTL) that confer partial and potentially complementary protection. Yet, few apple scab QTLs have been functionally validated, and their underlying mechanisms remain largely unresolved. Here, we refined and functionally described, with transcriptomic data, five resistance QTLs in a biparental population of 1,970 individuals derived from the cross ‘TN 10-8’ × ‘Fiesta’. Using 43 newly developed KASP markers, QTL locations were substantially precised through high-resolution genotyping and phenotyping with two V. inaequalis isolates exhibiting contrasting virulence. Four QTL (qT1, qF11, qF17, qT13) were validated, while qF3 was not confirmed. Transcriptomic data comparison revealed the expression of candidate genes within the narrowed intervals, including receptor-like proteins in qT1, and RNAi- and signaling-related genes in qF11 and qF17, suggesting a diversified and complementary defense network. These findings refine the genetic architecture of apple scab resistance and suppose the existence of shared molecular pathways between major R gene, such as the well-described Rvi6 gene, and quantitative resistance, with for instance the QTL qT1. The identified loci and markers provide robust tools for marker-assisted and genomic breeding aimed at developing apple cultivars with complementary and potentially durable resistance pathways.

Gene pyramiding in crop varieties offers a promising strategy to achieve sustainable production and reduce reliance on pesticides. However, stacking resistance genes without understanding their biological functions may result in transient protection. Although numerous studies have mapped loci associated with resistance to biotic stresses, the underlying molecular mechanisms remain poorly characterised. Resistance genes are often involved in pest/pathogen recognition, whereas quantitative trait loci (QTLs) may act in other steps of plant immunity such as signalling and defence pathways. In parallel, specialised metabolites have attracted growing attention as key defence components, acting as antimicrobial or repellent agents. While both fields encounter challenges to precisely decipher plant defence mechanisms, making use of metabolomics on segregating populations could bypass some of these limitations. In this review, we introduce an approach based on the identification of metabolic QTLs within populations where resistance QTLs segregate, enabling the detection of genomic co-localisations between both types of QTLs. This integrative framework can reveal specific metabolic signatures associated with resistance, thus refining hypotheses on the mode of action of resistance QTLs. Ultimately, elucidating the genetic architecture of specialised metabolism in relation to quantitative resistance will inform on more effective combinations of defence mechanisms for breeding resistant varieties.

This work introduces WISER (whitening and successive least squares estimation refinement), an innovative and efficient method designed to enhance phenotype estimation by addressing population structure. WISER outperforms traditional methods such as least squares (LS) means and best linear unbiased prediction (BLUP) in phenotype estimation, offering a more accurate approach for omics-based selection and having the potential to improve association studies. Unlike existing approaches that correct for population structure, WISER provides a generalized framework applicable across diverse experimental setups, species, and omics datasets, including single nucleotide polymorphisms (SNPs), metabolomics, and near-infrared spectroscopy (NIRS) used as phenomic predictors. Central to WISER is the concept of whitening, a statistical transformation that removes correlations between variables and standardizes their variances. Within its framework, WISER extends classical methods that use eigen-information as fixed-effect covariates to correct for population structure, by relaxing their assumptions and implementing a true whitening matrix instead of a pseudo-whitening matrix. This approach corrects fixed effects (e.g., environmental effects) for the genetic covariance structure embedded within the experimental design, thereby minimizing confounding factors between fixed and genetic effects. To support its practical application, a user-friendly R package named wiser has been developed. The WISER method has been employed in analyses for genomic prediction and heritability estimation across four species and 33 traits using multiple datasets, including rice, maize, apple, and Scots pine. Results indicate that genomic predictive abilities based on WISER-estimated phenotypes consistently outperform the LS-means and BLUP approaches for phenotype estimation, regardless of the predictive model applied. This underscores WISER’s potential to advance omics analyses and related research fields by capturing stronger genetic signals.

The Biological Resource Center (BRC) ’Pome fruits and roses’ is hosted by INRAE near Angers, France. It includes collections of apple, pear, quince and rose. The apple, pear and quince collections are preserved in orchards on site and as DNA samples. Research accessions of the Rosa genus are preserved both in the field and as DNA samples, whereas traditional accessions are primarily maintained as DNA samples. Traditional roses accessions are preserved in the field by different private and public rose gardens in France. The main BRC’s mission is to preserve these biological resources while improving and optimizing its collections. It also aims to gather and enrich data associated with the conserved genetic accessions, in particular by recording and centralizing phenotypic and genetic characterization data. This ensures the provision of suitable biological material and data for research and selection purposes. Additionally, these data support genetic resources management, especially in the framework of the apple and pear French networks coordinated by BRC. Thanks to these data, pedigrees could be unravelled and association studies implemented.

How selection and demography shape genomes of long-lived crops remains largely unresolved. Using apple ( Malus domestica ) as a model, we integrate 218 whole genomes (68 cultivated dessert/cider; 150 wild: M. sieversii, M. orientalis, M. sylvestris ), RNA-seq, and a flowering-time GWAS to resolve how these forces forged the cultivated apple genome. Despite weak neutral differentiation and widespread admixture, dessert and cider apples form distinct gene pools that derive primarily from M. sieversii–M. orientalis rather than European M. sylvestris . We find no evidence of a strong domestication bottleneck, as expected in perennials. Demography-aware selection scans reveal largely non-overlapping targets: dessert shows more hard sweeps at genes linked to fruit quality, disease resistance, and flowering, whereas cider shows proportionally more soft sweeps and balancing selection; RNA-seq differential expression supports these candidates. Wild-to-crop introgression from M. sylvestris is extensive but heterogeneous by context: some introgressed tracts concentrate in hard-sweep regions and approach fixation (consistent with rapid, targeted uptake), whereas others persist at intermediate frequencies with soft-sweep signatures (consistent with diffuse, recurrent introgression of adaptive alleles). Extending to the phenotype, the lead chromosome 9 flowering-time association lies within an introgressed segment near a transposable element and is separated from sweep peaks, consistent with regulatory/polygenic control. Cultivated apples carry a lower predicted deleterious load than wild relatives. Together, these results provide one of the most comprehensive population genomic portraits of a perennial fruit tree domestication, clarifying how selection and adaptive introgression jointly shaped the cultivated apple genome architecture and yielding actionable targets for breeding and conservation. Significance statement Perennial crops are underexplored compared to annuals, leaving open the question of how selection, gene flow, and demography shape their genomes. Using the apple tree ( Malus domestica ), we analyzed 218 genomes, along with expression and trait data. Despite weak genome-wide differences, dessert and cider apples form distinct gene pools. Widespread gene flow from the European wild apple supplied adaptive alleles, with contrasting dynamics: in cider, a few introgressed DNA segments rose rapidly; in dessert, many variants shifted gradually. Cultivated apples also carry a lower predicted burden of harmful mutations than wild relatives. Together, these results redefine perennial domestication and pinpoint genomic targets to accelerate breeding and conservation. ### Competing Interest Statement The authors have declared no competing interest. Inserm, ATIP-CNRS IDEEV LabEx BASC Tamkeen, under the New York University, Abu Dhabi Research Institute grant AD, 454 European LEADER, 1.1.359 Proverbio PLEASURE, ANR-21-CE20-0005 Ministry of Research, Innovation and Digitization, CNCS/CCCDI-UEFISCDI, PN-IV-P8-8.1-PRE-HE-ORG-2024-0223, within PNCDI IV

Phytosanitary treatments are massively used in orchards to fight apple scab, a disease caused by the fungus Venturia inaequalis (Vi). To reduce these treatments, resistant varieties are largely deployed but their effectiveness can decrease over time. The combination of complementary molecular mechanisms within new varieties could enhance the durability of genetic resistance however, the underlying resistance mechanisms remain poorly understood. An apple pseudo-F1 progeny was previously widely investigated for its quantitative trait loci (QTL) controlling resistance to scab and at least three of them seem to act complementarily; notably, one of them is specific to some Vi isolates while the others have a broader spectra of action. The aim of this approach is to better understand the underlying molecular mechanisms and metabolites associated with resistance alleles by exploring apple leaf specialized metabolism. A total of three experiments was conducted: one experiment included non-inoculated leaves whereas in the two other experiments, leaf samples were collected five days after inoculation with two different Vi isolates, including one known to overcome one QTL. Metabolic content was extracted in aqueous methanol before performing an untargeted metabolomic analysis using an Orbitrap IDXTM mass spectrometer, allowing high-resolution mass spectrometry (HRMS) detection. This approach without a priori enables the detection of potentially new chemical families involved in resistance to apple scab. The current data article includes 1) the protocol of plant sample production with a table summarizing key elements of the experimental designs, 2) overview of the raw metabolomic profiles from all three experiments and 3) assessment of metabolic feature reproducibility between replicates in each dataset through Principal Component Analysis. The raw data files are available on the recherche.data.gouv repository (10.57745/XJBD8V). These datasets are valuable resources to further investigate the molecular mechanisms underlying genetic resistance to apple scab, with a focus on specialized metabolism. In the long term, it should improve apple breeding strategies by informing on how to combine appropriate genetic and biochemical factors in new varieties to ensure a more durable resistance.

The curation and preservation of Dutch apple germplasm depends on reliable accession level information. However, many accessions of Dutch heirloom apple cultivars maintained publicly by the “Centre for Genetic Resources, the Netherlands” (CGN) and privately by Dutch pomological societies lack information regarding true-to-typeness and pedigree ancestry. The aim of this study was to address this knowledge gap by genotyping 652 apple accessions maintained in the CGN collection and Dutch private collections, compare their genotypic information to each other and to a large database of apple cultivars from around the world to identify genotypic duplicates and pedigree relationships for the Dutch apple cultivars. Towards this aim, accessions were genotyped on the 20 K Illumina Infinium(R) apple SNP array and with 15 SSR markers. Each accession was assigned to a genotypic profile code (MUNQ codes, as used in previous studies) facilitating communication regarding genotypic duplicates. There were 211 (51.1

Heirloom Danish apple cultivars are historically and pomologically important, part of the cultural heritage, and have valuable adaptation to regional climate conditions. However, lack of information about their genetic identity and pedigree relatedness with other cultivars hampers proper cultivar identification, germplasm curation, genebank management, and future regional breeding efforts. Many Danish apple cultivars are maintained in the national collection “The Pometum”, maintaining around 850 apple accessions. Additional material is maintained in public or private Danish collections. However, no information exists regarding genotypic duplicates between these collections and germplasm collections in other countries, pedigree inferences across collections, and genotypically unique accessions at the genebank level. To provide such information, 976 accessions from Denmark were genotyped with simple sequence repeat (SSR) markers and the Illumina Infinium 20K single nucleotide polymorphism (SNP) array. The resulting genotypic data were compared to large databases of genotypic data from germplasm collections in multiple countries to identify genotypic duplicates and conduct pedigree reconstruction. The germplasm maintains 305 unique genotypic profiles which were not found in other germplasm collections. The study exposed previously unknown synonyms, accessions not true-to-type, and novel pedigree relationships involving accessions from multiple collection sites. The most frequent parents of Danish germplasm were ‘Hvid Vinter Pigeon’ and ‘Cox’s Orange Pippin’ whereas ‘Reinette Franche’ was the most common grandparent. The accession-level information will benefit germplasm curation, cultivar identification, genebank management, and future breeding efforts, and shed new light on cultivar history and origin.

Previous studies have highlighted the role of three quantitative trait loci (QTL, i.e. ‘qT1’, ‘qF11’ and ‘qF17’) in partial resistance to apple scab. 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.

Societal Impact StatementMany economically, culturally, and historically important apple cultivars are triploids, which have three copies of each chromosome instead of the more typical two copies in diploids. Despite their prevalence and importance, there have been conflicting reports regarding their origin and their ability to beget diploids. New genetic analysis methodologies outlined in this study have clarified the genetic origin of triploid apple cultivars and suggest that triploidy has been a dead end in historic apple pedigrees. The specific results of this study have resolved the pedigrees of many cultivars, including the famous English cultivar Cox's Orange Pippin and the oldest known US cultivar Roxbury Russet.Summary In apple (Malus × domestica), most cultivars are diploid, though a sizeable number are triploids, which tend to be stronger growing, more robust, and bear larger fruit. However, triploidy is also associated with strongly reduced fertility. Some recorded pedigrees for historical apple cultivars include triploids as parents of diploids, despite this reputation of poor fertility. This information, coupled with some initiatives using triploids in breeding efforts, result in confusion about how possible or common it is for triploids to be parents of diploid offspring. To date, no studies have systematically evaluated and identified pedigrees of triploid apple cultivars to resolve these contradictions. Here, we describe a method to make triploid genotype calls using Illumina Infinium single nucleotide polymorphism (SNP) array data through a novel Python script: ploidyClassifier. SNP data for 219 unique triploids was compared alongside 2498 unique diploid apple accessions to conduct pedigree reconstruction. Unreduced gamete‐donating parents were identified for over half of the triploid accessions. From those, reduced gamete‐donating parents were identified for nearly half. Full or partial pedigrees for many classic triploids were uncovered, including that of the oldest known American cultivar, ‘Roxbury Russet’. All tested pedigrees from literature that listed triploids as parents of diploids were deemed false, including that of the well‐known ‘Cox's Orange Pippin’, whose previously unreported second parent was also identified here as ‘Rosemary Russet’. These results together suggest that historic triploids are mostly or solely the product of diploid parentage and that triploidy has been a dead end in historic apple pedigrees.