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 ...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.展开更多
基金supported by the Science Fund Program for Distinguished Young Scholars of the National Natural Science Foundation of China(Overseas)to Yongfeng ZhouNational Natural Science Foundation of China(Nos.32300191,32372662)+1 种基金Guangxi University,Bama Institute of Integration of Industry and Education,postgraduate joint training project(Project Nos.20210020,20210039)the National Key Research and Development Program of China(grants 2023YFF1000100 and 2023YFD2200700).
文摘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.
