Grapevine (Vitis) is cultivated worldwide for fresh consumption and for processing into wine and other products, commanding high economic value and serving as an indispensable horticultural crop for rural prosperity and a better life. The genus Vitis comprises two subgenera — Muscadinia Planch. and Euvitis Planch. — totaling more than 70 species, which can be grouped geographically into Eurasian, North American, and East Asian germplasm pools. As one of the earliest domesticated crops (~11,000 BCE), grapevine has experienced millennia of continuous domestication and breeding, processes that have eroded genetic diversity and eliminated many resistance alleles, leaving modern cultivars vulnerable to biotic and abiotic stresses. Although pangenomes of North American (Genome Biology, 2023) and European (Nature Genetics, 2024) grapevines have recently been published, a genus-level super-pangenome based on chromosome-scale assemblies of a large, diverse pane l— including East Asian wild species — has been lacking. Such a resource is essential for dissecting grapevine genetic diversity, conducting functional genomics, uncovering latent traits, and enabling precision breeding.

 

 

On 26 February 2025, the teams of Dr. Wenxiu Ye and Dr. Li Guo at the Shandong Laboratory of Advanced Agriculture Sciences in Weifang and Peking University Institute of Advanced Agricultural Sciences published a landmark study in Nature Genetics entitled “Super pangenome of Vitis empowers identification of downy mildew resistance genes for grapevine improvement.” For the first time, the study presents a haplotype-resolved super-pangenome of 72 Vitis accessions representing the Eurasian, North American, and East Asian germplasm pools, illuminating the genus’s rich diversity and complex breeding history. Integrating multi-omics data, the work pinpoints genetic variants and resistance genes associated with downy mildew, accelerating precision molecular breeding and heralding a new era of grapevine improvement and utilization.

 

Figure 1. Global geographic distribution of grapevine accessions and their fruit and leaf morphology.

 

The researchers first generated a complete haplotype-resolved genome of the wine cultivar Chardonnay (Vitis vinifera) and, for the first time in grapevine, defined centromere sequences using ChIP-seq. Comparative analysis revealed rapid centromere evolution, with marked haplotype-specific differences in satellite-repeat organization. Next, population genomics of 591 grapevine accessions guided the selection of 72 representative lines (25 wild and 47 cultivated) for chromosome-level haplotype assemblies (Figure 1). Quality metrics confirmed the high completeness and accuracy of these assemblies.

Figure 2. Haplotype-resolved phylogeny based on 144 phased genomes.

 

Owing to the high heterozygosity arising from frequent interspecific hybridization in Vitis, haplotype genomes are essential to accurately resolve heterozygous regions and reconstruct breeding histories. The study generated the first haplotype-resolved phylogeny, uncovering complex reticulate evolution and rich genetic diversity. North American and European accessions showed extensive within-pool admixture, whereas East Asian accessions exhibited limited intrapool crossing and few intercontinental exchanges (Figure 2). The largely untapped East Asian diversity underscores its vast potential for future breeding. The newly released East Asian wild genomes constitute a critical resource for grapevine improvement.

 

Analysis of the 72 accessions delineated >64,000 gene families — core, dispensable and private — whose accumulation curve approached saturation, indicating a near-closed Vitis pangenome. A systematic survey of the NLR immune-receptor family revealed significant differences in TIR-NBARC-LRR gene abundance between resistant wild and susceptible cultivated grapevines, suggesting a key role in downy-mildew resistance.

 

Figure 3. Super-pangenome gene-family landscape of 72 Vitis accessions.

 

The study further constructed the most comprehensive grapevine structural-variation (SV) map to date, facilitating the discovery of functional loci underlying resistance and resource-use efficiency (Figure 4). Whole-genome alignment of 67 Euvitis accessions identified 132,518 non-redundant SVs. Functional enrichment indicated involvement in leaf morphology, pathogen recognition, and biotic-stimulus perception. Comparison with known markers uncovered an SV tightly linked to the downy-mildew resistance locus Rpv3; distinct haplotypes across the three germplasm pools exhibited significant correlations with resistance, validating this SV as a diagnostic marker.

 

Figure 4. Structural-variant atlas of 72 Vitis accessions.

 

Finally, leveraging the SV map and the complete Chardonnay genome, the researchers built the first graph pangenome spanning European, Asian, and American germplasm. Integrating downy-mildew resistance phenotypes, stomatal phenotypes, and infection transcriptomes from 113 accessions, SV- and SNP-based eQTL analyses identified 63 SV-eQTLs and 1,808 SNP-eQTLs associated with resistance (Figure 5). Among the 63 resistance-linked SVs, the amino-acid transporter gene VvLHT8 was pinpointed. Functional assays demonstrated that VvLHT8 negatively regulates salicylic-acid biosynthesis and stomatal immunity, thereby suppressing resistance. These findings underscore the power of a high-quality pangenome coupled with multi-omics to mine agronomically important loci and genes.

 

Figure 5. Super-pangenome-guided SV-eQTL mapping and functional validation of VvLHT8.

 

In summary, this study delivers the most comprehensive genomic resource for the genus Vitis to date, enabling full dissection of genomic complexity and diversity and facilitating the efficient discovery and utilization of elite alleles — especially from wild germplasm. By integrating the super-pangenome with population transcriptomics and phenomics, the work deepens understanding of the genetic basis of key agronomic traits and provides theoretical foundations and new strategies for breeding “super grapevines.” The milestone advances grapevine genomics into a new phase and will accelerate high-quality development of China’s grape industry.

 

Dr. Wenxiu Ye and Dr. Li Guo (Shandong Laboratory of Advanced Agriculture Sciences in Weifang; Peking University Institute of Advanced Agricultural Sciences; Weifang Key Laboratory of Grapevine Improvement and Utilization) are co-corresponding authors. Dr. Li Guo, Mr. Xiangfeng Wang, Assistant Dr. Dilay Hazal Ayhan and Dr. Mohammad Saidur Rhaman, and visiting student Mr. Ming Yan are co-first authors. Academician Dr. Xing Wang Deng (Shandong Laboratory of Advanced Agriculture Sciences in Weifang; Peking University Institute of Advanced Agricultural Sciences) and Dr. Chonghuai Liu (Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences) provided critical support. Additional contributors include Dongyue Wang, Wei Zheng, Junjie Mei, Prof. Wei Ji (visiting scholar from Shanxi Agricultural University), Associate Prof. Jian Jiao (visiting scholar from Henan Agricultural University), Shaoying Chen, Jie Sun, Shu Yi, Dian Meng, Jing Wang, Mohammad Nasim Bhuiyan, Linling Guo, Qingxian Yang, Xuenan Zhang, Haisheng Sun, Dr. Guochen Qin, and Dr. Jianfu Jiang (Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences). The study was supported by the high-performance computing center and mass-spectrometry platform of Shandong Laboratory of Advanced Agriculture Sciences in Weifang and Peking University Institute of Advanced Agricultural Sciences, and funded by the Shandong Provincial Key R&D Program, Shandong Provincial Natural Science Foundation, Shandong Taishan Scholar Program, and Shandong Distinguished Young Scholar Fund.