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

• Published in: Journal of integrative plant biology Vol. 66; no. 7; pp. 1408 - 1426
• Main Authors: Zhang, Tianhao, Peng, Wenjing, Xiao, Hua, Cao, Shuo, Chen, Zhuyifu, Su, Xiangnian, Luo, Yuanyuan, Liu, Zhongjie, Peng, Yanling, Yang, Xiping, Jiang, Guo‐Feng, Xu, Xiaodong, Ma, Zhiyao, Zhou, Yongfeng
• Format: Journal Article
• Language: English
• Published: China (Republic : 1949- ) Wiley Subscription Services, Inc 01.07.2024
• Subjects: Abiotic stress; Adaptation; Adaptive radiation; Climate adaptation; climate change; Coastal ecology; Coastal environments; Coastal processes; Gene flow; Gene regulation; Gene sequencing; Genes; Genetic analysis; Genomes; Genomics; grape breeding; Grapes; Grapevines; Haplotypes; Impact analysis; Indigenous species; local adaptation with gene flow; Phenotypic variations; Population; Population genetics; Population studies; Populations; Salinity tolerance; Salt tolerance; Single-nucleotide polymorphism; Subtropical zones; viticulture; Vitis; Vitis retordii; Whole genome sequencing; grape breeding; salt tolerance; viticulture; Vitis; local adaptation with gene flow; climate change
• ISSN: 1672-9072; 1744-7909
• DOI: 10.1111/jipb.13653

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. Population genomics and a haplotype‐resolved near telomere‐to‐telomere reference genome highlight the role of structural variation in local adaptation to saline coastal environments in woolly grape (Vitis retodrii) and identifies candidate genes for future breeding programs for grapevine and its rootstocks.