A high-density single nucleotide polymorphism (SNP) array is essential to enable faster progress in plant breeding for new cultivar development. In this regard, we have developed an Axiom 60K almond SNP array by resequencing 81 almond accessions. For the validation of the array, a set of 210 accessions were genotyped and 82.8% of the SNPs were classified in the best recommended SNPs. The rate of missing data was between 0.4% and 2.7% for the almond accessions and less than 15.5% for the few peach and wild accessions, suggesting that this array can be used for peach and interspecific peach × almond genetic studies. The values of the two SNPs linked to the RMja (nematode resistance) and SK (bitterness) genes were consistent. We also genotyped 49 hybrids from an almond F2 progeny and could build a genetic map with a set of 1159 SNPs. Error rates, less than 1%, were evaluated by comparing replicates and by detection of departures from Mendelian inheritance in the F2 progeny. This almond array is commercially available and should be a cost-effective genotyping tool useful in the search for new genes and quantitative traits loci (QTL) involved in the control of agronomic traits.

Cucumber crops face high pressure from pathogens, including various viral species. Mapping quantitative trait loci (QTL) for vegetable resistance to viruses has primarily been conducted after mechanical inoculation in controlled environments, but not in crop field conditions. Moreover, viruses that cannot be mechanically inoculated, e.g. the cucurbit aphid-borne yellows virus (CABYV), have been overlooked in resistance studies. Here, we aimed to identify QTLs reducing epidemics of two prevalent cucumber viruses: CABYV and the cucumber mosaic virus (CMV). We evaluated the resistance of 256 elite cucumber lines and landraces in crop field conditions by screening for the presence of both viruses six-times during the season. We mapped twelve QTLs reducing CABYV epidemics and seven QTLs reducing CMV epidemics by combining multiloci genome-wide association studies and local score approach analyses. We also examined the attractiveness of this cucumber panel for Aphis gossypii, a major cucumber virus vector. We identified five QTLs that reduced the attractiveness, including one co-localizing with a QTL reducing CABYV epidemics. Interestingly, some accessions deemed CMV-resistant after mechanical inoculation in controlled environments showed high infection rates in crop field conditions. Only one QTL for CMV resistance was detected in both conditions, indicating that these phenotypes are regulated by independent QTLs. Local linkage disequilibrium study findings suggested that certain QTLs reducing epidemics were introduced early into elite lines through serendipity or selection. QTLs could be pyramided with other low-effect QTLs through genomic selection to obtain cucumber cultivars with enhanced field resistance to viruses.

Selecting varieties with limited canopy warming can help adapt crops to climate change, but underlying traits and their genetic bases remain poorly understood. Using a diversity panel of 279 Vitis vinifera L. cultivars, we investigated genetic variation in leaf temperature (Tleaf) and questioned which morpho-physiological traits involved in leaf energy balance are genetically controlled and drive these variations. Specifically, we measured Tleaf, stomatal conductance, leaf inclination, area, unfolding, reflectance, and transmittance under irrigated field conditions. Substantial genetic variability was found for Tleaf and all morpho-physiological traits, which have been little explored together from a genetic perspective. Empirically, stomatal conductance had the strongest influence on genetic variations in Tleaf, followed by transmittance, although theoretically, based on energy balance, leaf traits with their observed ranges of variation could all impact Tleaf with similar amplitude. Genome-wide association studies revealed independent genetic control for Tleaf, stomatal conductance, leaf inclination, and transmittance, suggesting multiple independent genetic levers. Screening these genomic regions highlighted relevant candidate genes respectively involved in thermal dissipation (PetC), stomatal development (YODA, LOB), phototropism (YY1), and trichome initiation (GTL1). We disclosed allelic combinations jointly favouring leaf cooling, water saving, and light interception. Our results provide novel insights for breeding climate-resilient grapevines.

Understanding the genetic architecture of ecophysiological traits related to carbon gain and water loss is crucial to develop cultivars tolerant to abiotic stresses and that maintain productivity in the context of climate change. This can be achieved both through experiments in the greenhouse on potted plants under controlled conditions and in the field. However, the stability of genetic determinism of ecophysiological traits across environmental conditions has rarely been evaluated. We studied a grapevine diversity panel grown both in a greenhouse and in the field, to investigate the impact of growing conditions on leaf ecophysiological traits related to leaf morphology, fluorescence, gas exchange and water use efficiency. The correlation structure between traits was conserved within each environment even though, for most traits, cultivars ranking was not conserved between both environments. However, a set of cultivars, sharing the same functioning pattern in terms of gas exchange and fluorescence in both environments, was identified. Single-and multi-environment Genome-Wide Association Studies (GWAS), based on a dense genotyping matrix, were used to dissect the genetic architecture of leaf traits. The Quantitative Trait Loci (QTLs) identified through single-environment analyses differed substantially from those detected using multi-environment ones. Multi-environment approaches highlighted shared QTLs across environments for gas exchange and fluorescence traits. Candidate genes associated with carbon- and water-related functions were further identified in these genomic regions. Despite the weak correlation between greenhouse and field trait values, combining both environments enabled the identification of robust genetic regions associated with ecophysiological traits of interest.

Water scarcity is a major threat to crop production and quality. Improving drought tolerance through variety selection requires a deeper understanding of plant ecophysiological responses, but large-scale phenotyping remains a bottleneck. This study assessed the potential of high-throughput tools (spectroscopy and poro-fluorometry) to predict leaf morphological and ecophysiological traits in a grapevine diversity panel grown in pots under well-watered outdoor conditions and under three contrasting soil water treatments in a greenhouse. We found a certain complementarity between measuring devices. Spectrometers could accurately predict leaf mass per area, water content, and water quantity (R² > 0.58), while the poro-fluorometer was efficient for predicting net CO₂ assimilation (R² > 0.72), regardless of the water treatment. The prediction of leaf mass per area using spectrometers appeared to be quite robust across both outdoor and greenhouse experiments, while the prediction of water use efficiency was dependent on the water treatment, with much better predictions under moderate (R² > 0.73) than severe water deficit. Calibrated models were then applied to the full diversity panel using only high-throughput measurements to estimate trait values and their broad-sense heritability. Leaf mass per area, also measured directly, showed similar heritability whether based on observed or predicted data. Heritability estimates for predicted traits reached up to 0.5. Overall, our findings support the use of spectroscopy and poro-fluorometry as reliable, non-destructive tools for high-throughput phenotyping, enabling genetic studies on drought-related traits in grapevine.

A bstract: Aphids threaten crop productivity through phloem feeding and the transmission of plant viruses. Aphis gossypii , in particular, is a widespread and damaging pest of worldwide cultivated melon. Resistance to its emerging CUC1 clone in Europe remains poorly characterized. Here, we dissected the genetic architecture of melon resistance to CUC1 using complementary traits that capture multiple stages of the aphid-melon interaction: plant attractiveness to aphids, acceptance, aphid colonization, and multiplication. Genome-wide association studies (GWAS) in a diversity panel of 174 accessions identified a quantitative trait locus (QTL) for attractiveness on chromosome 6, while analyses in a complementary panel of 212 accessions revealed QTLs for plant acceptance by aphids on chromosomes 3, 8, and 12. Colonization and multiplication traits further highlighted resistance QTLs on chromosomes 5 and 12, the latter supported by both SNP-based GWAS and bulk-segregant analysis. Pan-NLRome k-mer- and graph- based GWAS, together with Vat presence/absence association analyses, provided allele-level resolution of the QTL on chromosome 5, corresponding to the Vat region. Leveraging allelic diversity at this locus, we functionally characterized 20 Vat homologs with four R65aa motifs within their leucine-rich repeat (LRR) domain and demonstrated the capacity of R65aa-type Vat alleles to confer clone-specific resistance. Resistance-conferring alleles limited virus multiplication, such as Cucumber mosaic virus (CMV), when transmitted by five A. gossypii clones, including CUC1. Together, our results revealed multiple genetic determinants underlying quantitative resistance to the A. gossypii CUC1 clone in melon and highlighted the central role of Vat homologs in resistance to both A. gossypii and the viruses it vectors. These findings provide strategic targets for pyramiding resistance loci acting at different stages of the pest life cycle to enhance durable protection against these biotic threats.