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Genome re-sequencing reveals the history of apple and supports a two-stage model for fruit enlargement

Author

Listed:
  • Naibin Duan

    (Shandong Agricultural University
    Shandong Academy of Agricultural Sciences)

  • Yang Bai

    (Cornell University)

  • Honghe Sun

    (Cornell University)

  • Nan Wang

    (Shandong Agricultural University)

  • Yumin Ma

    (Shandong Academy of Agricultural Sciences)

  • Mingjun Li

    (Northwest A&F University)

  • Xin Wang

    (Cornell University)

  • Chen Jiao

    (Cornell University)

  • Noah Legall

    (Cornell University)

  • Linyong Mao

    (Cornell University)

  • Sibao Wan

    (Cornell University)

  • Kun Wang

    (Chinese Academy of Agricultural Sciences)

  • Tianming He

    (Xinjiang Agricultural University)

  • Shouqian Feng

    (Shandong Agricultural University)

  • Zongying Zhang

    (Shandong Agricultural University)

  • Zhiquan Mao

    (Shandong Agricultural University)

  • Xiang Shen

    (Shandong Agricultural University)

  • Xiaoliu Chen

    (Shandong Agricultural University)

  • Yuanmao Jiang

    (Shandong Agricultural University)

  • Shujing Wu

    (Shandong Agricultural University)

  • Chengmiao Yin

    (Shandong Agricultural University)

  • Shunfeng Ge

    (Shandong Agricultural University)

  • Long Yang

    (Shandong Agricultural University)

  • Shenghui Jiang

    (Shandong Agricultural University)

  • Haifeng Xu

    (Shandong Agricultural University)

  • Jingxuan Liu

    (Shandong Agricultural University)

  • Deyun Wang

    (Shandong Agricultural University)

  • Changzhi Qu

    (Shandong Agricultural University)

  • Yicheng Wang

    (Shandong Agricultural University)

  • Weifang Zuo

    (Shandong Agricultural University)

  • Li Xiang

    (Shandong Agricultural University)

  • Chang Liu

    (Mudanjiang Branch of Heilongjiang Academy of Agricultural Science)

  • Daoyuan Zhang

    (Chinese Academy of Sciences)

  • Yuan Gao

    (Chinese Academy of Agricultural Sciences)

  • Yimin Xu

    (Cornell University)

  • Kenong Xu

    (Cornell University)

  • Thomas Chao

    (Plant Genetic Resources Unit)

  • Gennaro Fazio

    (Plant Genetic Resources Unit)

  • Huairui Shu

    (Shandong Agricultural University)

  • Gan-Yuan Zhong

    (Plant Genetic Resources Unit)

  • Lailiang Cheng

    (Cornell University)

  • Zhangjun Fei

    (Cornell University
    Robert W. Holley Center for Plant and Health)

  • Xuesen Chen

    (Shandong Agricultural University)

Abstract

Human selection has reshaped crop genomes. Here we report an apple genome variation map generated through genome sequencing of 117 diverse accessions. A comprehensive model of apple speciation and domestication along the Silk Road is proposed based on evidence from diverse genomic analyses. Cultivated apples likely originate from Malus sieversii in Kazakhstan, followed by intensive introgressions from M. sylvestris. M. sieversii in Xinjiang of China turns out to be an “ancient” isolated ecotype not directly contributing to apple domestication. We have identified selective sweeps underlying quantitative trait loci/genes of important fruit quality traits including fruit texture and flavor, and provide evidences supporting a model of apple fruit size evolution comprising two major events with one occurring prior to domestication and the other during domestication. This study outlines the genetic basis of apple domestication and evolution, and provides valuable information for facilitating marker-assisted breeding and apple improvement.

Suggested Citation

  • Naibin Duan & Yang Bai & Honghe Sun & Nan Wang & Yumin Ma & Mingjun Li & Xin Wang & Chen Jiao & Noah Legall & Linyong Mao & Sibao Wan & Kun Wang & Tianming He & Shouqian Feng & Zongying Zhang & Zhiqua, 2017. "Genome re-sequencing reveals the history of apple and supports a two-stage model for fruit enlargement," Nature Communications, Nature, vol. 8(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:8:y:2017:i:1:d:10.1038_s41467-017-00336-7
    DOI: 10.1038/s41467-017-00336-7
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    Cited by:

    1. Xiaoyun Xin & Peirong Li & Xiuyun Zhao & Yangjun Yu & Weihong Wang & Guihua Jin & Jiao Wang & Liling Sun & Deshuang Zhang & Fenglan Zhang & Shuancang Yu & Tongbing Su, 2024. "Temperature-dependent jumonji demethylase modulates flowering time by targeting H3K36me2/3 in Brassica rapa," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    2. Ting Wang & Shiyao Duan & Chen Xu & Yi Wang & Xinzhong Zhang & Xuefeng Xu & Liyang Chen & Zhenhai Han & Ting Wu, 2023. "Pan-genome analysis of 13 Malus accessions reveals structural and sequence variations associated with fruit traits," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    3. Thomas Davies & Sophie Watts & Kendra McClure & Zoë Migicovsky & Sean Myles, 2022. "Phenotypic divergence between the cultivated apple (Malus domestica) and its primary wild progenitor (Malus sieversii)," PLOS ONE, Public Library of Science, vol. 17(3), pages 1-11, March.
    4. Xiaofeng Cai & Xuepeng Sun & Chenxi Xu & Honghe Sun & Xiaoli Wang & Chenhui Ge & Zhonghua Zhang & Quanxi Wang & Zhangjun Fei & Chen Jiao & Quanhua Wang, 2021. "Genomic analyses provide insights into spinach domestication and the genetic basis of agronomic traits," Nature Communications, Nature, vol. 12(1), pages 1-12, December.

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