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

文献类型： 外文期刊

作者： Luo, Yuanyuan 1 ; Liu, Zhenya 2 ; Jin, Zhongxin 3 ; Li, Peng 1 ; Tan, Xibei 1 ; Cao, Shuo 2 ; Wang, Xu 2 ; Liu, Zhongqi 2 ; Shi, Xiaoya 2 ; Huang, Siyang 2 ; Gu, Liyuan 1 ; Fan, Xiucai 1 ; Jiang, Jianfu 1 ; Sun, Lei 1 ; Zhou, Yongfeng 2 ; Liu, Chonghuai 1 ; Xu, Xiaodong 2 ; Ma, Zhiyao 2 ; Zhang, Ying 1 ;

作者机构： 1.Chinese Acad Agr Sci, Zhengzhou Fruit Res Inst, Zhengzhou 450000, Peoples R China

2.Chinese Acad Agr Sci, Minist Agr & Rural Affairs, Natl Key Lab Trop Crop Breeding, Guangdong Lab Lingnan Modern Agr,Shenzhen Branch,A, Shenzhen 518124, Peoples R China

3.Chinese Acad Trop Agr Sci, Trop Crops Genet Resources Inst, Natl Key Lab Trop Crop Breeding, Haikou 571101, Peoples R China

4.Chuxiong Yunguo Agr Technol Res Inst, Chuxiong, Peoples R China

5.Chinese Acad Agr Sci, Zhongyuan Res Ctr, Henan, Peoples R China

期刊名称：HORTICULTURE RESEARCH （ 影响因子：8.5； 五年影响因子：9.1 ）

ISSN： 2662-6810

年卷期： 2025 年 12 卷 2 期

页码：

收录情况： SCI

摘要： 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 F & ouml;ex, 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.

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