Guo Li, Wang Xiangfeng, Ayhan Dilay Hazal, Rhaman Mohammad Saidur, Yan Ming, Jiang Jianfu, Wang Dongyue, Zheng Wei, Mei Junjie, Ji Wei, Jiao Jian, Chen Shaoying, Sun Jie, Yi Shu, Meng Dian, Wang Jing, Bhuiyan Mohammad Nasim, Qin Guochen, Guo Linling, Yang Qingxian, Zhang Xuenan, Sun Haisheng, Liu Chonghuai, Deng Xing Wang, Ye Wenxiu
Shandong Key Laboratory of Precision Molecular Crop Design and Breeding, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, China.
Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China.
Nat Genet. 2025 Mar;57(3):741-753. doi: 10.1038/s41588-025-02111-7. Epub 2025 Feb 26.
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 the enormous genetic diversity of the Vitis genus. Pangenomic analysis reveals that European cultivars, more susceptible to the destructive disease downy mildew (DM), have a smaller repertoire of resistance genes in the 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-expression quantitative trait loci 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 the Vitis genus will accelerate breeding and enrich our understanding of the evolution and biology of grapevines.
葡萄（葡萄属）是最古老的驯化水果作物之一，具有重要的文化和经济价值。在此，我们组装并注释了72个全球葡萄品种的单倍型解析基因组，其中包括25个野生葡萄和47个栽培葡萄，其中60个葡萄品种的基因组是新发布的。单倍型感知系统发育基因组学解开了葡萄神秘的杂交历史，揭示了葡萄属巨大的遗传多样性。泛基因组分析表明，更容易感染毁灭性霜霉病（DM）的欧洲栽培品种，在编码TIR-NBARC-LRR结构域的NLR家族中，抗性基因库较小。通过对113个葡萄品种进行广泛的结构变异（SV）表征、表型分析、DM感染转录组分析以及SV-表达数量性状位点分析，我们鉴定出超过63个与DM抗性显著相关的SV及其相关基因，以赖氨酸组氨酸转运蛋白VvLHT8为例。这个葡萄属的单倍型解析超级泛基因组将加速育种进程，并丰富我们对葡萄进化和生物学的理解。
