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

AO_SCPLOWBSTRACTC_SCPLOWAphids 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.