Genome structure variation analyses of peach reveal population dynamics and a 1.67\u2009Mb causal inversion for fruit shape

Jiantao Guan,Fei Ren,Jianbo Zhao,Jun Fu,Yang Yu,Yaoguang Xu,Quan Jiang,Hua Xie,Jiying Guo,Jianhua Wei

doi:10.1186/s13059-020-02239-1

Jiantao Guan, Fei Ren + Show 8 more

Open Access

https://doi.org/10.1186/s13059-020-02239-1

Copy DOI

Abstract

BackgroundStructural 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.ResultsHere, 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.ConclusionsThus, beyond introducing new genomics resources for peach research, our study illustrates how focusing on SV data can drive basic functional discoveries in plant science.

Highlights

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
Genome assembly and annotation of RYP1 The genome of Rui You Pan 1 (RYP1) was de novo assembled using 140.84 Gb PacBio long reads (~ 589.74× coverage) and 35.37 Gb Illumina short reads (~ 147.97× coverage) using the pipeline detailed in Additional file 1: Fig. S1 and Additional file 2: Table S1
We assembled the PacBio long reads from RYP1 into contigs using the Canu pipeline [40] and improved contigs into 87 super contigs by employing the Highly Efficient Repeat Assembly (HERA) algorithm [41]

Summary

Introduction

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. Guan et al Genome Biology (2021) 22:13 flanking noncoding regions of loci/genes linked to agriculturally important traits, e.g. grain size [11, 12], fruit shape [13], fruit weight [2], and fruit color [14, 15]. Despite these significant advances, the contribution of SVs, especially large chromosomal rearrangements, to specific traits remains largely uncharacterized in plant organisms. Understanding the genomic context of SVs (and especially heterozygous SVs) can help elucidate the basis of phenotypic diversity

Methods

Results

Discussion

Conclusion