Phased T2T genome assemblies facilitate the mining of disease-resistance genes in Vitis davidii Open Access

Abstract

Grape is an important fruit crop, and its production faces significant threat from diseases, resulting in substantial economic loss. Wild grape relatives are valuable resources for the restoration of disease-resistance loci. However, available resistance loci in wild grape genomes remain largely unexplored. In this study, we assembled two phased genomes, including a high-resistant Chinese wild grape, Vitis davidii Föex, and a susceptible cultivar, Vitis vinifera L. cv. ‘Manicure Finger’. We detected a total of 36 688 structural variations (SVs), with the genes associated with heterozygous SVs showing an enrichment in allele-specific expression (ASE). Furthermore, we identified eight subgroups of R genes and found that 74.2% of R genes overlap with transposable elements (TEs). Among R genes, NBS-type genes exhibit higher expression profiles in the wild grape genome compared with those in the grape cultivar. Additionally, five specific NBS-type R gene clusters were identified in the wild grape genome that are absent in the cultivar. Through genetic mapping, we identified four quantitative trait loci (QTLs) associated with grape white rot resistance based on the V. davidii genome, within which six NBS-type R genes exhibit differential expression between wild and cultivated grapes. Overall, our study revealed the landscape of resistance genes in grape genomes, providing valuable genetic resources for further breeding programs.

Acknowledgements

This study was funded by the National Key Research and Development Program of China (2021YFD1200200), the Agricultural Science and Technology Innovation Program (CAAS-ASTIP-2021-ZFRI), the National Natural Science Foundation of China (31872057), and the China Agriculture Research System (CARS-29).

Author contributions

Y.Z. conceived and designed the project. Y.L., S.C., X.W., Z.L., X.S., and S.H. performed the genome assembly and gene annotation. P.L. and X.T. performed transcriptome analysis. C.L., X.F., J.J., L.S., and G.L. assisted in grape culture and sample collection. Z.L., Z.M., X.X., Z.J., and Y.Z. assisted in bioinformatics analyses and data visualization. Y.L. and Y.Z. wrote and purified the manuscript.

Data availability

All the raw sequencing data generated for this project have been deposited in the National Genomics Data Center (NGDC) Genome Sequence Archive (GSA) (https://ngdc.cncb.ac.cn/gsa/) with the number of CRA017609. The assembly and annotation as well as the sequences of centromeres and heterozygous regions have been deposited in Zenodo (https://zenodo.org/records/12671741).

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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