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

Tianhao Zhang ¹Wenjing Peng ²Hua Xiao ³Shuo Cao ⁴Zhuyifu Chen ³Xiangnian Su ¹Yuanyuan Luo ⁵Zhongjie Liu ³Yanling Peng ³Xiping Yang ⁶Guo-Feng Jiang ⁷Xiaodong Xu ³Zhiyao Ma ³Yongfeng Zhou⁸

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作者信息

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;State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources,Guangxi University,Nanning 530004,China;Guangxi Key Laboratory of Forest Ecology and Conservation,Guangxi Colleges and Univ
2. 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;State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources,Guangxi University,Nanning 530004,China;Guangxi Key Laboratory of Sugarcane Biology,College of Agriculture,Guangxi Universi
3. 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
4. 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;Key Laboratory of Horticultural Plant Biology Ministry of Education,Huazhong Agricultural University,Wuhan 430070,China
5. Zhengzhou Fruit Research Institute,Chinese Academy of Agricultural Sciences,Zhengzhou 450009,China
6. State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources,Guangxi University,Nanning 530004,China;Guangxi Key Laboratory of Sugarcane Biology,College of Agriculture,Guangxi University,Nanning 530004,China
7. State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources,Guangxi University,Nanning 530004,China;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
8. 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;National Key Laboratory of Tropical Crop Breeding,Tropical Crops Genetic Resources Institute,Chinese Academy of Tropical Agricultural Sciences,Haikou 571101,China
折叠

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 re-tordii),a species native to the tropical and sub-tropical regions of East Asia with both coastal and inland habitats,as a valuable model for examining the impact of SVs on local adaptation.We as-sembled a haplotype-resolved chromosomal ref-erence 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 asso-ciated 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 toler-ance 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;candi-date genes related to salt stress and climatic adaptation to tropical and subtropical environ-ments 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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基金项目

Science Fund Program for Distinguished Young Scholars of the National Natural Science Foundation of China(Overseas)()

National Natural Science Foundation of China(32300191)

National Natural Science Foundation of China(32372662)

Guangxi University,Bama Institute of Integration of Industry and Education,postgraduate joint training project(20210020)

Guangxi University,Bama Institute of Integration of Industry and Education,postgraduate joint training project(20210039)

National Key Research and Development Program of China(2023YFF1000100)

National Key Research and Development Program of China(2023YFD2200700)

出版年

2024

植物学报(英文版)

中国植物学会

植物学报(英文版)

CSTPCDCSCD

影响因子：0.921

ISSN：1672-9072

参考文献量107

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