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

文献类型： 外文期刊

作者： Zhang, Tianhao 1 ; Peng, Wenjing 1 ; Xiao, Hua 1 ; Cao, Shuo 1 ; Chen, Zhuyifu 1 ; Su, Xiangnian 1 ; Luo, Yuanyuan 8 ; Liu, Zhongjie 1 ; Peng, Yanling 1 ; Yang, Xiping 2 ; Jiang, Guo-Feng 2 ; Xu, Xiaodong 1 ; Ma, Zhiyao 1 ; Zhou, Yongfeng 1 ;

作者机构： 1.Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Shenzhen Branch, Natl Key Lab Trop Crop Breeding,Guangdong Lab Ling, Shenzhen 518000, Peoples R China

2.Guangxi Univ, State Key Lab Conservat & Utilizat Subtrop Agrobio, Nanning 530004, Peoples R China

3.Guangxi Univ, Guangxi Coll, Guangxi Key Lab Forest Ecol & Conservat, Nanning 530004, Peoples R China

4.Guangxi Univ, Univ Key Lab Cultivat & Utilizat Subtrop Forest Pl, Coll Forestry, Nanning 530004, Peoples R China

5.Huazhong Agr Univ, Coll Informat, Wuhan 430070, Peoples R China

6.Guangxi Univ, Coll Agr, Guangxi Key Lab Sugarcane Biol, Nanning 530004, Peoples R China

7.Huazhong Agr Univ, Key Lab Hort Plant Biol, Minist Educ, Wuhan 430070, Peoples R China

8.Chinese Acad Agr Sci, Zhengzhou Fruit Res Inst, Zhengzhou 450009, Peoples R China

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

关键词： climate change; grape breeding; local adaptation with gene flow; salt tolerance; viticulture; Vitis

期刊名称：JOURNAL OF INTEGRATIVE PLANT BIOLOGY （ 影响因子：11.4； 五年影响因子：10.1 ）

ISSN： 1672-9072

年卷期： 2024 年

页码：

收录情况： SCI

摘要： 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.

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