A highly diversified NLR cluster in melon contains homologs that confer powdery mildew and aphid resistance

Abstract

Podosphaera xanthii is the main causal agent of powdery mildew (PM) on Cucurbitaceae. In Cucumis melo, the Pm-w resistance gene, which confers resistance to P. xanthii, is located on chromosome 5 in a cluster of nucleotide-binding leucine-rich repeat receptors (NLRs). We used positional cloning and transgenesis, to isolate the Pm-w^{WMR 29} gene encoding a coiled-coil NLR (CC-NLR). Pm-w^{WMR 29} conferred high level of resistance to race 1 of PM and intermediate level of resistance to race 3 of PM. Pm-w^{WMR 29} turned out to be a homolog of the Aphis gossypii resistance gene Vat-1^{PI 161375}. We confirmed that Pm-w^{WMR 29} did not confer resistance to aphids, while Vat-1^{PI 161375} did not confer resistance to PM. We showed that both homologs were included in a highly diversified cluster of NLRs, the Vat cluster. Specific Vat-1^{PI 161375} and Pm-w^{WMR 29} markers were present in 10% to 13% of 678 accessions representative of wild and cultivated melon types worldwide. Phylogenic reconstruction of 34 protein homologs of Vat-1^{PI 161375} and Pm-w^WMR 29 identified in 24 melon accessions revealed an ancestor with four R65aa—a specific motif in the LRR domain, evolved towards aphid and virus resistance, while an ancestor with five R65aa evolved towards PM resistance. The complexity of the cluster comprising the Vat/Pm-w genes and its diversity in melon suggest that Vat homologs may contribute to the recognition of a broad range of yet to be identified pests and pathogens.

Acknowledgements

We thank Virginie Chareyron and the A2M Experimental Unit of INRAE for taking care of the plants and the aphid resistance tests. We thank Joel Chadoeuf for his statistical analysis advice. We thank Marc Bardin for helpful discussions. We thank David Manley for improving the English in this paper. This work was supported by the Biology and Plant Breeding Division of INRAE.

Author Contributions

N.B. designed the homologs diversity analysis in the Vat/Pm-w cluster and she performed phylogenetic analysis of Vat homologs in relation with phenotypic data. She supervised aphid resistance phenotyping, and she analyzed the diversity data (phenotypic and genomic data) with V.C. She realized all the statistical analysis. She supervised the manuscript building. V.C. performed comple-mentation experiments of Pm-w and the molecular analysis of the Vat cluster in melon, she annotated the Vat-related sequences of all genotypes studied and validated their expression in collabo-ration with VR. She analyzed the phenotypic data with NB. V.R.-R. carried out the molecular analysis of Vat homologs, extracted DNA of the melon collection and designed and genotyped the markers for both alleles and participated to the manual annota-tion of Vat-related sequence. N.G., P.M., and M.P. performed the powdery mildew and aphid resistance phenotyping. M.C. and C.T. performed the fine mapping of Pm-w and screened the BAC library. A.B. supervised the positional cloning and the BAC library pro-duction and screening. C.D. supervised the positional cloning of Pm-w^{WR 29} in collaboration with A.B., supervised the complemen-tation experiments and the frequency analysis of Pm-w^{WR 29} and Vat-1^{PI 161375} markers in a worldwide melon collection. N.B., V.C. and C.D. wrote the manuscript. All authors read the manuscript.

Data Availability

The data underlying this article are available in the article and in its online supplementary material.

Conflict of interest statement

The authors have declared that no competing interests exist.

Supplementary data

Supplementary data is available at Horticulture Research online.

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