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Genomic analyses provide insights into spinach domestication and the genetic basis of agronomic traits

Author

Listed:
  • Xiaofeng Cai

    (Shanghai Normal University
    Qinghai University)

  • Xuepeng Sun

    (Cornell University
    Zhejiang A&F University)

  • Chenxi Xu

    (Shanghai Normal University)

  • Honghe Sun

    (Cornell University
    Cornell University)

  • Xiaoli Wang

    (Shanghai Normal University)

  • Chenhui Ge

    (Shanghai Normal University)

  • Zhonghua Zhang

    (Qingdao Agricultural University)

  • Quanxi Wang

    (Harbin Normal University)

  • Zhangjun Fei

    (Cornell University
    USDA-ARS, Robert W. Holley Center for Agriculture and Health)

  • Chen Jiao

    (Cornell University
    Zhejiang University)

  • Quanhua Wang

    (Shanghai Normal University)

Abstract

Spinach is a nutritious leafy vegetable belonging to the family Chenopodiaceae. Here we report a high-quality chromosome-scale reference genome assembly of spinach and genome resequencing of 305 cultivated and wild spinach accessions. Reconstruction of ancestral Chenopodiaceae karyotype indicates substantial genome rearrangements in spinach after its divergence from ancestral Chenopodiaceae, coinciding with high repeat content in the spinach genome. Population genomic analyses provide insights into spinach genetic diversity and population differentiation. Genome-wide association studies of 20 agronomical traits identify numerous significantly associated regions and candidate genes for these traits. Domestication sweeps in the spinach genome are identified, some of which are associated with important traits (e.g., leaf phenotype, bolting and flowering), demonstrating the role of artificial selection in shaping spinach phenotypic evolution. This study provides not only insights into the spinach evolution and domestication but also valuable resources for facilitating spinach breeding.

Suggested Citation

  • 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.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-27432-z
    DOI: 10.1038/s41467-021-27432-z
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    1. John Doebley & Adrian Stec & Lauren Hubbard, 1997. "The evolution of apical dominance in maize," Nature, Nature, vol. 386(6624), pages 485-488, April.
    2. Nick Patterson & Alkes L Price & David Reich, 2006. "Population Structure and Eigenanalysis," PLOS Genetics, Public Library of Science, vol. 2(12), pages 1-20, December.
    3. 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.
    4. Juliane C. Dohm & André E. Minoche & Daniela Holtgräwe & Salvador Capella-Gutiérrez & Falk Zakrzewski & Hakim Tafer & Oliver Rupp & Thomas Rosleff Sörensen & Ralf Stracke & Richard Reinhardt & Alexand, 2014. "The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)," Nature, Nature, vol. 505(7484), pages 546-549, January.
    5. David E. Jarvis & Yung Shwen Ho & Damien J. Lightfoot & Sandra M. Schmöckel & Bo Li & Theo J. A. Borm & Hajime Ohyanagi & Katsuhiko Mineta & Craig T. Michell & Noha Saber & Najeh M. Kharbatia & Ryan R, 2017. "The genome of Chenopodium quinoa," Nature, Nature, vol. 542(7641), pages 307-312, February.
    6. David E. Jarvis & Yung Shwen Ho & Damien J. Lightfoot & Sandra M. Schmöckel & Bo Li & Theo J. A. Borm & Hajime Ohyanagi & Katsuhiko Mineta & Craig T. Michell & Noha Saber & Najeh M. Kharbatia & Ryan R, 2017. "Correction: Corrigendum: The genome of Chenopodium quinoa," Nature, Nature, vol. 545(7655), pages 510-510, May.
    7. Chenxi Xu & Chen Jiao & Honghe Sun & Xiaofeng Cai & Xiaoli Wang & Chenhui Ge & Yi Zheng & Wenli Liu & Xuepeng Sun & Yimin Xu & Jie Deng & Zhonghua Zhang & Sanwen Huang & Shaojun Dai & Beiquan Mou & Qu, 2017. "Draft genome of spinach and transcriptome diversity of 120 Spinacia accessions," Nature Communications, Nature, vol. 8(1), pages 1-10, August.
    8. Xuehui Huang & Nori Kurata & Xinghua Wei & Zi-Xuan Wang & Ahong Wang & Qiang Zhao & Yan Zhao & Kunyan Liu & Hengyun Lu & Wenjun Li & Yunli Guo & Yiqi Lu & Congcong Zhou & Danlin Fan & Qijun Weng & Chu, 2012. "A map of rice genome variation reveals the origin of cultivated rice," Nature, Nature, vol. 490(7421), pages 497-501, October.
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