An integrated peach genome structural variation map uncovers genes associated with fruit traits
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RESEARCH
Open Access
An integrated peach genome structural variation map uncovers genes associated with fruit traits Jian Guo1,2†, Ke Cao1†, Cecilia Deng3, Yong Li1, Gengrui Zhu1, Weichao Fang1, Changwen Chen1, Xinwei Wang1, Jinlong Wu1, Liping Guan1, Shan Wu4, Wenwu Guo2, Jia-Long Yao3*, Zhangjun Fei4,5* and Lirong Wang1* * Correspondence: jia-long.yao@ plantandfood.co.nz; zf25@cornell. edu; [email protected] † Jian Guo and Ke Cao contributed equally to this work. 3 The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland 1142, New Zealand 4 Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, USA 1 Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China Full list of author information is available at the end of the article
Abstract Background: Genome structural variations (SVs) have been associated with key traits in a wide range of agronomically important species; however, SV profiles of peach and their functional impacts remain largely unexplored. Results: Here, we present an integrated map of 202,273 SVs from 336 peach genomes. A substantial number of SVs have been selected during peach domestication and improvement, which together affect 2268 genes. Genome-wide association studies of 26 agronomic traits using these SVs identify a number of candidate causal variants. A 9-bp insertion in Prupe.4G186800, which encodes a NAC transcription factor, is shown to be associated with early fruit maturity, and a 487-bp deletion in the promoter of PpMYB10.1 is associated with flesh color around the stone. In addition, a 1.67 Mb inversion is highly associated with fruit shape, and a gene adjacent to the inversion breakpoint, PpOFP1, regulates flat shape formation. Conclusions: The integrated peach SV map and the identified candidate genes and variants represent valuable resources for future genomic research and breeding in peach. Keywords: SVs, GWAS, Peach, Fruit, Fruit shape
Introduction Structural variations (SVs), comprising insertions/deletions (indels), duplications, inversions, and translocations, are widely present in genomes [1–4]. In humans, SVs provide an extensive source of genetic variation for the identification of genes involved in important biological processes [5]. In many plant species, SVs have been reported to regulate agronomic traits such as fruit shape in tomato (Solanum lycopersicum) [6], nematode resistance in soybean (Glycine max) [7], reproductive morphology in cucumber (Cucumis sativus) [8], asexual reproduction in citrus [9], and fruit texture in peach (Prunus persica) [10]. Recent rapid advances in next-generation sequencing technologies have facilitated genome-wide detection of SVs in large crop populations [11, 12]. © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s)
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