Genetics and Improvement of Fruit and Vegetables

Diaporthe amygdali Delacr. is a phytopathogenic fungus of considerable agronomic importance, responsible for branch canker in almond (Prunus dulcis [Mill.] D.A. Webb) and peach (Prunus persica L.) trees. It represents a major phytosanitary threat to almond cultivation in Europe, particularly in Mediterranean regions. Almond is currently among the most rapidly expanding perennial crops, with cultivated areas increasing as a result of the introduction of new cultivars and the adoption of improved agronomic practices. The objectives of this study were to isolate and identify fungal pathogens from infected almond samples collected in France through multilocus phylogenetic analyses (ITS, tef1-α, his3, tub2, cal genes) combined with morphological characterization; evaluate the susceptibility of 18 almond genotypes, using 'Ferragnès' and 'Texas' as reference standards for susceptibility and tolerance, respectively; and compare three field inoculation methods. All isolates were identified as D. amygdali. The varietal screening identified marked differences in resistance among the tested cultivars. In particular, 'Ferrastar', 'R1877', 'R1413', and 'R1542' exhibited high levels of resistance, whereas 'Tuono', 'Guara', and 'R1568' showed susceptibility comparable to that of 'Ferragnès', which was used as the susceptible control. Among the inoculation methods evaluated, the mycelial plug technique proved to be the most consistent and reliable, outperforming both conidial suspension inoculation and the toothpick method coated with mycelium. These findings further confirm the genetic resistance of the cultivars 'Ferrastar' and 'Ardèchoise' to branch canker across different growing conditions, supporting their suitability for use in breeding and genetic improvement programs.

• The three stresses significantly inhibited root growth through distinct mechanisms: NC reduced branch number and total length, NH diminished surface area and diameter, while NB synergistically suppressed root volume. • these stresses activated antioxidant enzymes and elevated oxidative markers, indicating stress-specific defense strategies. • 39 metabolic pathways were enriched which included biosynthesis of secondary metabolites and plant hormone signal transduction were enriched under salt stress. Notably, alkali stress resulted in extensive pathway enrichment [7527 differentially expressed genes (DEGs)], sharing the three most significantly enriched pathways with salt stress treatment. The combination of saline and alkali stress specifically activated the glutathione metabolic pathway, with 56.6 % of DEGs encoding glutathione S-transferases (GSTs), pivotal for detoxification and redox homeostasis. • A coordinated network involving the upregulation of SlGRAS1/2/4 transcription factors (161.97 % induction under NH) and GSH biosynthetic genes (GSH1, GR) underpinned pH adaptation. Meanwhile, non-additive effects were observed in NB, with a lower suppression of SlGRAS10 (−25.12 %) than under NH (−66.25 %). To explore the physiological and molecular mechanisms underlying tomato root responses to salt stress, alkali stress, and combined saline-alkaline stress. Here, the tomato cultivar ‘M82’ was cultivated with the following four treatments: (1) 1x Hoagland nutrient solution (control; CK); (2) 1x Hoagland nutrient solution + 100 mmol/L NaCl (NC); (3) 1x Hoagland nutrient solution + 100 mmol/L NaHCO 3 (NH); and (4) 1x Hoagland nutrient solution + 50 mmol/LNaCl+50 mmol/L NaHCO 3 (NB). The root morphological traits, physiological parameters, transcriptomic profiles, and metabolomic signatures of the plants under these treatments were analyzed. In this experiment, the three stresses significantly inhibited root growth through distinct mechanisms: NC reduced branch number and total length, NH diminished surface area and diameter, while NB synergistically suppressed root volume. In addition, these stresses activated antioxidant enzymes and elevated oxidative markers, indicating stress-specific defense strategies. Furthermore, a combined analysis of the transcriptome and metabolome of roots revealed that 39 metabolic pathways were enriched which included biosynthesis of secondary metabolites and plant hormone signal transduction were enriched under salt stress. Notably, alkali stress resulted in extensive pathway enrichment [7527 differentially expressed genes (DEGs)], sharing the three most significantly enriched pathways with salt stress treatment. The combination of saline and alkali stress specifically activated the glutathione metabolic pathway, with 56.6 % of DEGs encoding glutathione S-transferases (GSTs), pivotal for detoxification and redox homeostasis. Besides, the study found that a coordinated network involving the upregulation of SlGRAS1/2/4 transcription factors (161.97 % induction under NH) and GSH biosynthetic genes (GSH1, GR) underpinned pH adaptation. Meanwhile, non-additive effects were observed in NB, with a lower suppression of SlGRAS10 (−25.12 %) than under NH (−66.25 %), suggesting a cross-talk that buffers oxidative damage. These findings provide novel insights for breeding saline-alkaline-resilient crops and designing stress management strategies targeting glutathione metabolism.

The Pseudomonas syringae species complex is an important group of ubiquitous bacteria containing plant-pathogenic strains of which many strains cause damage and economic losses to a wide range of crops. Efforts to elucidate host range determinants have focused on the effector repertoires in the type 3 secretion system (T3SS). However, recently, we showed that the inability of a P. syringae pv. actinidiae strain to trigger effector-triggered immunity (ETI) in Arabidopsis thaliana is due to an inefficient T3SS and not to the absence of a recognised effector. We thus compared the T3SS efficiency of several P. syringae strains belonging to different phylogroups. We assessed the temporal dynamics of their ability to induce ion leakage, an indicator of the hypersensitive response (HR), in A. thaliana Col-0, as a proxy for T3SS function. Though not a direct measurement of T3SS efficiency, the use of a robust statistical model allowed us to reveal that P. syringae strains DC3000 avrB and M6 avrB consistently triggered a strong HR while other strains induced it at significantly different intensities depending on temperature. Among thermosensitive strains, both low and warm temperature dependencies for T3SS efficiency were observed, irrespective of their invitro growth optimum, even among quasiclonal strains. These results reveal a strong, strain-specific regulatory role of temperature in effector injection and reinforce the importance of environmental factors in the outcome of plant-bacteria interactions. Moreover, this work highlights the need to study bacterial virulence beyond model strains such as DC3000 and B728a that are not representative of the diversity of the P. syringae species complex.

Eggplant (Solanum melongena L.) is a major Solanaceous crop of Asian origin, but genomic resources remain limited compared to related species. Here, a core collection of 368 accessions spanning global diversity of S. melongena and wild relatives is phenotyped for agronomic, disease resistance and fruit metabolomic traits and resequenced. Additionally, 40 chromosome-level assemblies of S. melongena, its progenitor S. insanum and the allied species S. incanum enable the construction of two graph-based pangenomes, capturing broad genetic variation. We demonstrate the power of these datasets by identifying major loci controlling prickliness and resistance to Fusarium oxysporum f. sp. melongenae, driven by SVs affecting the LONELY GUY 3 gene and a resistance gene cluster, respectively, as well as a mutation in a GDSL-like esterase/lipase gene altering the levels of dicaffeoyl-quinic acids. These findings provide a cornerstone for pangenome-assisted breeding, enabling detailed analyses of genetic diversity, domestication history, and trait evolution in eggplant.

ABSTRACTSeed immune responses are an underexplored area in host–pathogen interactions, leaving seed–pathogen interactions poorly understood despite their considerable economic impact. This study examined tomato seed defences by assessing the antimicrobial activity (AA) of seed exudates during germination. Results showed genotype‐dependent and constitutive defence responses from seeds showing AA in exudates. Seed priming with a panel of elicitors such as methyl jasmonate (MeJA) enhanced AA in certain genotypes, highlighting an inducible defence response. Both constitutive and inducible (elicitor‐dependent) seed defences were genotype‐dependent and more effective against the non‐host pathogen Alternaria brassicicola (Abra43), while host pathogens seemed resistant to exudates' AA, suggesting that they developed strategies to neutralise exudates' AA. Multi‐omic analyses revealed distinct hormonal and molecular pathways involved in constitutive and inducible defences. By characterising exudates and correlating genotype‐ and elicitor‐specific AA, candidate antimicrobial compounds were identified. As proof of concept, we functionally validated the AA of a putative defensin (Solyc07g007755) whose expression was highly correlated with the observed AA of the seed exudate against Abra43, demonstrating the potential of our dataset for the development of phytosanitary strategies to protect seeds during germination.

ABSTRACTUnderstanding crop domestication offers crucial insights into the evolutionary processes that drive population divergence and adaptation. It also informs the identification of genetically diverse wild germplasm, which is essential for breeding and conservation efforts. While domestication has been extensively studied in many Mediterranean fruit trees, the evolutionary history of the almond (Prunus dulcis) remains comparatively underexplored. To address this, we analyzed 209 wild and cultivated almond accessions sampled across Eurasia and genotyped with 23 microsatellite markers. Using population genetics and coalescent‐based inference, we reconstructed the domestication history of P. dulcis and its relationships with wild relatives. Bayesian clustering revealed four genetically distinct clusters of cultivated almonds: Turkish, Caucasian–Central Asian, Southern Spanish, and European/North American. These groups were differentiated from wild almond species—including Prunus turcomanica, Prunus orientalis, Prunus fenzliana, and Prunus spinosissima—each forming its gene pool across the Middle East and Central Asia. Approximate Bayesian Computation (ABC) supported a single domestication event in the Middle East, originating from either P. orientalis or P. turcomanica, with subsequent gene flow from P. fenzliana and P. spinosissima into the Turkish and Central Asian cultivated gene pools, respectively. We also inferred reciprocal introgression from cultivated almonds back into wild populations. Notably, sharka resistance—caused by plum pox virus (PPV)—was identified in three P. dulcis clusters and P. fenzliana, suggesting that resistance may have arisen independently or been maintained through crop–wild introgression. Together, our results highlight a complex and protracted domestication history for almond, shaped by contributions from multiple wild relatives and recurrent gene flow. These findings enhance our understanding of perennial crop evolution and underscore the value of wild germplasm in breeding programs aimed at increasing resilience in fruit trees.

Abstract Cucumber mosaic virus (CMV) is a major plant pathogen with a worldwide distribution and the widest host range among all known plant viruses. It affects numerous crop species and can cause symptoms that significantly reduce yield. CMV is primarily transmitted by aphids and more sporadically through seeds. It is frequently studied in laboratory settings with the aim of developing effective control strategies. In many experiments, infected plants are placed in direct contact with healthy ones assuming that CMV cannot be transmitted in this way. However, this has not been formally demonstrated. Therefore, this study aimed to assess whether CMV can be transmitted through plant-to-plant contact. Infected plants were first rubbed against healthy ones and then left in contact for 28 days. Target plants were subsequently tested using DAS-ELISA to detect potential transmission. We applied this protocol in two separate tests totalizing 15 combinations of plant species including pepper (Capsicum annuum) and five weed species (Capsella bursa-pastoris, Cerastium glomeratum, Stellaria media, Stachys arvensis and Trifolium repens). We found that CMV could be transmitted through contact between pepper and all tested weed species except T.repens. These findings highlight the importance of verifying whether a virus is capable of contact transmission before carrying out experiments in controlled conditions. In case of transmission, appropriate precautions will be crucial to avoid unintended transmissions.

Composite hypothesis testing using summary statistics is a well-established approach for assessing the effect of a single marker or gene across multiple traits or omics levels. Numerous procedures have been developed for this task and have been successfully applied to identify complex patterns of association between traits, conditions, or phenotypes. However, existing methods often struggle with scalability in large datasets or fail to account for dependencies between traits or omics levels, limiting their ability to control false positives effectively. To overcome these challenges, we present the qch_copula approach, which integrates mixture models with a copula function to capture dependencies between traits or omics and provides rigorously defined P-values for any composite hypothesis. Through a comprehensive benchmark against eight state-of-the-art methods, we demonstrate that qch_copula controls Type I error rates effectively while enhancing the detection of joint association patterns. Compared to other mixture model-based approaches, our method notably reduces memory usage during the EM algorithm, allowing the analysis of up to 20 traits and 105−106 markers. The effectiveness of qch_copula is further validated through two application cases in human and plant genetics. The method is available in the R package qch, accessible on CRAN.

The construction of accurate whole genome sequences is pivotal for characterizing the genetic diversity of plant species, identifying genes controlling important traits, or understanding their evolutionary dynamics. Here, we generated the nuclear, mitochondrial, and chloroplast high-quality assemblies of 5 melon (Cucumis melo L.) accessions representing 5 botanical groups, using the Oxford Nanopore sequencing technology. The accessions here studied included varied origins, fruit shapes, sizes, and resistance traits, providing a holistic view of melon genomic diversity. The final chromosome-level genome assemblies ranged in size from 359 to 365 Mb, with approximately 25× coverage for 4 of them multiplexed in half of a PromethION flowcell, and 48× coverage for the fifth, sequenced individually in another half of a PromethION flowcell. Contigs N50 ranged from 7 to 15 Mb for all the assemblies, and very long contigs reaching sizes of 20–25 Mb, almost compatible with complete chromosomes, were assembled in all the accessions. Quality assessment through Benchmarking Universal Single-Copy Orthologs (BUSCO) and Merqury indicated the high completeness and accuracy of the assemblies, with BUSCO values exceeding 96% for all accessions, and Merqury QV values ranging between 41 and 47. We focused on the complex NLR resistance gene regions to validate the accuracy of the assemblies in highly complex and repetitive regions. Through Nanopore adaptive sampling, we generated accurately targeted assemblies of these regions with significantly higher coverage, enabling the comparison to our whole genome assemblies. Overall, these chromosome-level assembled genomes constitute a valuable resource for research focused on melon diversity, disease resistance, evolution, and breeding applications.