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

文献类型： 外文期刊

作者： Guan, Jiantao 1 ; Xu, Yaoguang 1 ; Yu, Yang 1 ; Fu, Jun 1 ; Ren, Fei 3 ; Guo, Jiying 3 ; Zhao, Jianbo 3 ; Jiang, Quan 3 ; We 1 ;

作者机构： 1.Beijing Acad Agr & Forestry Sci, Beijing Agrobiotechnol Res Ctr, Beijing, Peoples R China

2.Beijing Key Lab Agr Genet Resources & Biotechnol, Beijing, Peoples R China

3.Beijing Acad Agr & Forestry Sci, Inst Forestry & Pomol, Beijing, Peoples R China

关键词： Peach genome assembly; Structure variation; Population dynamics; Genome-wide association study; Large heterozygous inversion; PpOFP2; Fruit shape

期刊名称：GENOME BIOLOGY （ 影响因子：13.583； 五年影响因子：17.433 ）

ISSN： 1474-760X

年卷期： 2021 年 22 卷 1 期

页码：

收录情况： SCI

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

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