The genome of Vitis vinifera cv. Mgaloblishvili reveals resistance and susceptibility factors to downy mildew in the Rpv29 and Rpv31 loci

Abstract

Mgaloblishvili, a grapevine variety from Georgia (Southern Caucasus), exhibits a unique resistance mechanism against downy mildew. Mgaloblishvili resistance mechanism, involving pathogen recognition, activation of ethylene signalling pathway, and structural and chemical defences, is mediated by the resistance loci Rpv29, Rpv30, and Rpv31. Mgaloblishvili genome was sequenced using PacBio HiFi, resulting in a chromosome-scale diploid assembly of 986 Mbp, including 58 912 predicted protein-coding genes across two phased chromosome sets. Comparative analysis with the susceptible PN40024 genome allowed us to identify differences in structure, gene content, and gene expression, as well as the impact of structural variants (SVs) and single nucleotide polymorphisms (SNPs) between Mgaloblishvili and PN40024 loci. Resistance haplotypes were identified through DNA sequencing of a self-pollinated Mgaloblishvili population. Compared to orthologous regions in PN40024, the Rpv29 locus in Mgaloblishvili exhibits reduced gene content, while the Rpv31 locus has similar gene content. In both Mgaloblishvili and PN40024, most genes within these loci are associated with plant defence pathways. While genes in both genotypes perform similar functions, SVs and SNPs were identified as key determinants of the structural differences between the genomes. Defining the Rpv30 locus was challenging due to ambiguous marker localization. DNA sequencing allowed us to identify resistance haplotypes for both Rpv30 and Rpv31 on Mgaloblishvili haplotype 2, though insights into the Rpv29 locus remain limited. Our results indicate that Mgaloblishvili’s resistance is driven by numerous small SVs and SNPs, which lead to the loss of susceptibility factors and unique transcriptional regulation of defence-related genes.

Acknowledgements

This work was partially supported by the USDA NIFA Award #2022-51181-38240 and ‘Grape for vine: recycling grape wastes to protect grapevine from fungal pathogens (Grape4vine)’ project financed by Fondazione Cariplo (Ref. 2022-0617). The Authors thank the Agriculture, Environment, and Bioenergy Doctorate programme of the University of Milan. The authors acknowledge support from the University of Milan through the APC initiative.

Author contributions

G.D.L., D.C., S.L.T., O.F., and D.M. conceived the experiments. V.R., A.M., M.M., A.H.J.W., and R.F.B. performed the experiments. V.R., A.M., and M.M. analysed the data. V.R. wrote the manuscript. V.R., G.D.L., D.C., A.M., M.M., S.L.T., O.F., and D.M. revised the manuscript. All the authors accepted the final version.

Data availability

Sequencing data are accessible through NCBI under the BioProject ID PRJNA1087404. New genome assembly of Mgaloblishvili and annotation files are available at Zenodo under the DOI: 10.5281/zenodo.10815333 and at www.grapegenomics.com.

Conflict of interest statement

The authors declare no conflict of interests.

Supplementary data

Supplementary data is available at Horticulture Research online.

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