Coindre, E. | Search bioRxiv

bioRxiv2026

Linkage and association mapping coupled with pan-genome analyses of Vat homologs reveal QTLs and alleles for aphid resistance in melon

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 4R65aa-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.

genetics↗

bioRxiv2025

Robustness of high-throughput prediction of leaf ecophysiological traits using near infra-red spectroscopy and poro-fluorometry

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 (R{superscript 2} > 0.58), while the poro-fluorometer was efficient for predicting net CO2 assimilation (R{superscript 2} > 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 (R{superscript 2} > 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.

plant biology↗