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

IF 8.7 1区农林科学 Q1 Agricultural and Biological Sciences

Horticulture Research Pub Date : 2024-11-07 DOI:10.1093/hr/uhae306

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

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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, V. 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 Vitis 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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分阶段 T2T 基因组组装有助于挖掘葡萄抗病基因

葡萄是一种重要的水果作物，其生产面临着病害的严重威胁，造成了巨大的经济损失。野生葡萄近缘种是恢复抗病基因座的宝贵资源。然而，野生葡萄基因组中可用的抗病基因位点在很大程度上仍未被开发。在这项研究中，我们组装了两个分期基因组，包括一个高抗性的中国野生葡萄 Vitis davidii Föex 和一个易感栽培品种 V. vinifera L. cv. "Manicure Finger"。我们共检测到 36,688 个结构变异（SVs），与杂合 SVs 相关的基因在等位基因特异性表达（ASE）方面表现出丰富性。此外，我们还发现了八个R基因亚群，并发现74.2%的R基因与转座元件（TE）重叠。在 R 基因中，与栽培品种相比，野生葡萄基因组中的 NBS 型基因表现出更高的表达谱。此外，我们还在野生葡萄基因组中发现了五个特定的 NBS 型 R 基因簇，这些基因在栽培品种中是不存在的。通过基因图谱绘制，我们在大维葡萄树基因组的基础上确定了四个与葡萄白腐病抗性相关的数量性状位点（QTL），其中六个 NBS 型 R 基因在野生葡萄和栽培葡萄之间表现出不同的表达。总之，我们的研究揭示了葡萄基因组中抗性基因的结构，为进一步的育种计划提供了宝贵的遗传资源。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Horticulture Research Biochemistry, Genetics and Molecular Biology-Biochemistry

CiteScore

11.20

自引率

6.90%

发文量

367

审稿时长

20 weeks

期刊介绍： Horticulture Research, an open access journal affiliated with Nanjing Agricultural University, has achieved the prestigious ranking of number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2022. As a leading publication in the field, the journal is dedicated to disseminating original research articles, comprehensive reviews, insightful perspectives, thought-provoking comments, and valuable correspondence articles and letters to the editor. Its scope encompasses all vital aspects of horticultural plants and disciplines, such as biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.