J Integr Plant Biol ›› 2024, Vol. 66 ›› Issue (7): 1408-1426.DOI: 10.1111/jipb.13653

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  • 收稿日期:2023-09-27 接受日期:2024-03-04 出版日期:2024-07-01 发布日期:2024-07-12

Population genomics highlights structural variations in local adaptation to saline coastal environments in woolly grape

Tianhao Zhang1,2,3,4†, Wenjing Peng1,2,5†, Hua Xiao1, Shuo Cao1,6, Zhuyifu Chen1, Xiangnian Su1,2,3, Yuanyuan Luo7, Zhongjie Liu1, Yanling Peng1, Xiping Yang2,5, Guo‐Feng Jiang2,3*, Xiaodong Xu1*, Zhiyao Ma1* and Yongfeng Zhou1,8*   

  1. 1. National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
    2. State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangxi University, Nanning 530004, China
    3. Guangxi Key Laboratory of Forest Ecology and Conservation, Guangxi Colleges and Universities Key Laboratory for Cultivation and Utilization of Subtropical Forest Plantation, College of Forestry, Guangxi University, Nanning 530004, China
    4. College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
    5. Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China
    6. Key Laboratory of Horticultural Plant Biology Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
    7. Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
    8. National Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
    †These authors contributed equally to this work.
    *Correspondences: Guo‐Feng Jiang (gfjiang@gxu.edu.cn); Xiaodong Xu (xuxiaodong@caas.cn); Zhiyao Ma (mazhiyao@caas.cn); Yongfeng Zhou (zhouyongfeng@caas.cn, Dr. Zhou is fully responsible for the distributions of all materials associated with this article)
  • Received:2023-09-27 Accepted:2024-03-04 Online:2024-07-01 Published:2024-07-12

Abstract: Structural variations (SVs) are a feature of plant genomes that has been largely unexplored despite their significant impact on plant phenotypic traits and local adaptation to abiotic and biotic stress. In this study, we employed woolly grape (Vitis retordii), a species native to the tropical and subtropical regions of East Asia with both coastal and inland habitats, as a valuable model for examining the impact of SVs on local adaptation. We assembled a haplotype-resolved chromosomal reference genome for woolly grape, and conducted population genetic analyses based on whole- genome sequencing (WGS) data from coastal and inland populations. The demographic analyses revealed recent bottlenecks in all populations and asymmetric gene flow from the inland to the coastal population. In total, 1,035 genes associated with plant adaptive regulation for salt stress, radiation, and environmental adaptation were detected underlying local selection by SVs and SNPs in the coastal population, of which 37.29% and 65.26% were detected by SVs and SNPs, respectively. Candidate genes such as FSD2, RGA1, and AAP8 associated with salt tolerance were found to be highly differentiated and selected during the process of local adaptation to coastal habitats in SV regions. Our study highlights the importance of SVs in local adaptation; candidate genes related to salt stress and climatic adaptation to tropical and subtropical environments are important genomic resources for future breeding programs of grapevine and its rootstocks.

Key words: climate change, grape breeding, local adaptation with gene flow, salt tolerance, viticulture, Vitis

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