Genome structure variation analyses of peach reveal population dynamics and a 1.67 Mb causal inversion for fruit shape

• DOI: 10.1186/s13059-020-02239-1
• Publication Date: 2021-01-05T10:05:58Z
• Authors: Jiantao Guan; Yaoguang Xu; Yang Yu; Jun Fu; Fei Ren; Jiying Guo; Jianbo Zhao; Quan Jiang; Jianhua Wei; Hua Xie
• Keywords: Structural Variation; Functional Genomics; Human genetics

Abstract Background Structural variations (SVs), a major resource of genomic variation, can have profound consequences on phenotypic yet the impacts SVs remain largely unexplored in crops. Results Here, we generate high-quality de novo genome assembly for flat-fruit peach cultivar and produce comprehensive SV map peach, as high proportion sequence is occupied by heterozygous genome. We conduct population-level analyses that indicate undergone strong purifying selection during domestication, find evidence positive selection, with significant preference upstream intronic regions later improvement. perform SV-based GWAS identifies large 1.67-Mb inversion segregates perfectly shape. Mechanistically, this derived allele alters expression PpOFP2 gene positioned near proximal breakpoint inversion, confirm transgenic tomatoes causal Conclusions Thus, beyond introducing new genomics resources research, our study illustrates how focusing data drive basic functional discoveries plant science.