Super pangenome of<i> Vitis</i> empowers identification of downy mildew resistance genes for grapevine improvement

Grapevine (Vitis) is one of the oldest domesticated fruit crops with great cultural and economic importance. Here, we assembled and annotated haplotype-resolved genomes of 72 global Vitis accessions including 25 wild and 47 cultivated grapevines, among which genomes for 60 grapevines are newly released. Haplotype-aware phylogenomics disentangled the mysterious hybridization history of grapevines, revealing enormous genetic diversity of Vitis genus. Pangenomic analysis reveals that European cultivars, more susceptible to the most destructive disease downy mildew (DM), have a smaller repertoire of resistance genes in NLR family encoding the TIR-NBARC-LRR domain. Through extensive structural variation (SV) characterization, phenotyping, DM-infection transcriptome profiling of 113 Vitis accessions, and SV-eQTL analysis, we have identified over 63 SVs and their relevant genes significantly associated with DM resistance, exemplified by a lysine histidine transporter, VvLHT8. This haplotype-resolved super pangenome of Vitis genus will accelerate breeding and enrich our understanding of the evolution and biology of grapevines.葡萄属（Vitis）是全球最古老的驯化果树作物之一，兼具重要的文化与经济价值。本研究组装并注释了72份全球葡萄属种质的单倍型解析基因组（haplotype-resolved genomes），其中包含25份野生葡萄与47份栽培葡萄，60份种质的基因组数据为本次研究新发布。借助单倍型感知系统发育基因组学分析，本研究解开了葡萄属长期以来扑朔迷离的杂交演化历史，揭示了葡萄属极为丰富的遗传多样性。泛基因组分析显示，对目前破坏性最强的病害——霜霉病（downy mildew, DM）更为易感的欧洲栽培品种，其编码TIR-NBARC-LRR结构域的NLR家族抗性基因库规模更小。本研究通过对113份葡萄属种质开展大规模结构变异（structural variation, SV）鉴定、表型组分析、霜霉病侵染转录组分析，以及结构变异-表达数量性状位点（SV-eQTL）分析，共鉴定出63个以上与霜霉病抗性显著相关的结构变异及其关联基因，其中以赖氨酸组氨酸转运蛋白VvLHT8为典型代表。这套葡萄属单倍型解析超级泛基因组将加速葡萄育种进程，并深化我们对葡萄演化与生物学特性的认知。