IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v12y2021i1d10.1038_s41467-021-27432-z.html
   My bibliography  Save this article

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
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-021-27432-z
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-021-27432-z?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. 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.
    2. 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.
    3. 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.
    4. 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.
    5. John Doebley & Adrian Stec & Lauren Hubbard, 1997. "The evolution of apical dominance in maize," Nature, Nature, vol. 386(6624), pages 485-488, April.
    6. 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.
    7. 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.
    8. 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.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Yongjun Fang & Xiaohu Xiao & Jishan Lin & Qiang Lin & Jiang Wang & Kaiye Liu & Zhonghua Li & Jianfeng Xing & Zhenglin Liu & Baiyu Wang & Yiying Qi & Xiangyu Long & Xia Zeng & Yanshi Hu & Jiyan Qi & Yu, 2024. "Pan-genome and phylogenomic analyses highlight Hevea species delineation and rubber trait evolution," Nature Communications, Nature, vol. 15(1), pages 1-14, December.

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Octavio R. Salazar & Ke Chen & Vanessa J. Melino & Muppala P. Reddy & Eva Hřibová & Jana Čížková & Denisa Beránková & Juan Pablo Arciniegas Vega & Lina María Cáceres Leal & Manuel Aranda & Lukasz Jare, 2024. "SOS1 tonoplast neo-localization and the RGG protein SALTY are important in the extreme salinity tolerance of Salicornia bigelovii," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
    2. Haifei Hu & Junliang Zhao & William J. W. Thomas & Jacqueline Batley & David Edwards, 2025. "The role of pangenomics in orphan crop improvement," Nature Communications, Nature, vol. 16(1), pages 1-9, December.
    3. Abdul Hameed & Sadiq Hussain & Aysha Rasheed & Muhammad Zaheer Ahmed & Sahar Abbas, 2024. "Exploring the Potentials of Halophytes in Addressing Climate Change-Related Issues: A Synthesis of Their Biological, Environmental, and Socioeconomic Aspects," World, MDPI, vol. 5(1), pages 1-22, January.
    4. Syed Riaz Ahmed & Zeba Ali & Iram Ijaz & Zafran Khan & Nimra Gul & Soha Pervaiz & Hesham F. Alharby & Daniel K. Y. Tan & Muhammad Sayyam Tariq & Maria Ghaffar & Amir Bibi & Khalid Rehman Hakeem, 2023. "Multi-Trait Selection of Quinoa Ideotypes at Different Levels of Cutting and Spacing," Sustainability, MDPI, vol. 15(14), pages 1-23, July.
    5. Gyaneshwer Chaubey & Anurag Kadian & Saroj Bala & Vadlamudi Raghavendra Rao, 2015. "Genetic Affinity of the Bhil, Kol and Gond Mentioned in Epic Ramayana," PLOS ONE, Public Library of Science, vol. 10(6), pages 1-11, June.
    6. Estavoyer, Maxime & François, Olivier, 2022. "Theoretical analysis of principal components in an umbrella model of intraspecific evolution," Theoretical Population Biology, Elsevier, vol. 148(C), pages 11-21.
    7. Seung Young Lee & Hyun-Sook Lee & Chang-Min Lee & Su-Kyung Ha & Hyang-Mi Park & So-Myeong Lee & Youngho Kwon & Ji-Ung Jeung & Youngjun Mo, 2023. "Multi-Environment Trials and Stability Analysis for Yield-Related Traits of Commercial Rice Cultivars," Agriculture, MDPI, vol. 13(2), pages 1-13, January.
    8. Hyosik Jang & Ian M Ehrenreich, 2012. "Genome-Wide Characterization of Genetic Variation in the Unicellular, Green Alga Chlamydomonas reinhardtii," PLOS ONE, Public Library of Science, vol. 7(7), pages 1-9, July.
    9. Lee, Anthony J. & Hibbs, Courtney & Wright, Margaret J. & Martin, Nicholas G. & Keller, Matthew C. & Zietsch, Brendan P., 2017. "Assessing the accuracy of perceptions of intelligence based on heritable facial features," Intelligence, Elsevier, vol. 64(C), pages 1-8.
    10. Thompson Katherine L. & Linnen Catherine R. & Kubatko Laura, 2016. "Tree-based quantitative trait mapping in the presence of external covariates," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 15(6), pages 473-490, December.
    11. Chew, Soo Hong & Ebstein, Richard P. & Lu, Yunfeng, 2023. "Rice culture and the cushion hypothesis: Experimental evidence from incentivized risk taking tasks," Economics Letters, Elsevier, vol. 223(C).
    12. Jacobo Pardo-Seco & Alberto Gómez-Carballa & Jorge Amigo & Federico Martinón-Torres & Antonio Salas, 2014. "A Genome-Wide Study of Modern-Day Tuscans: Revisiting Herodotus's Theory on the Origin of the Etruscans," PLOS ONE, Public Library of Science, vol. 9(9), pages 1-11, September.
    13. Rujia Chen & Ning Xiao & Yue Lu & Tianyun Tao & Qianfeng Huang & Shuting Wang & Zhichao Wang & Mingli Chuan & Qing Bu & Zhou Lu & Hanyao Wang & Yanze Su & Yi Ji & Jianheng Ding & Ahmed Gharib & Huixin, 2023. "A de novo evolved gene contributes to rice grain shape difference between indica and japonica," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    14. Jiguo Cao & Liangliang Wang & Zhongwen Huang & Junyi Gai & Rongling Wu, 2017. "Functional Mapping of Multiple Dynamic Traits," Journal of Agricultural, Biological and Environmental Statistics, Springer;The International Biometric Society;American Statistical Association, vol. 22(1), pages 60-75, March.
    15. Ilja M Nolte & Chris Wallace & Stephen J Newhouse & Daryl Waggott & Jingyuan Fu & Nicole Soranzo & Rhian Gwilliam & Panos Deloukas & Irina Savelieva & Dongling Zheng & Chrysoula Dalageorgou & Martin F, 2009. "Common Genetic Variation Near the Phospholamban Gene Is Associated with Cardiac Repolarisation: Meta-Analysis of Three Genome-Wide Association Studies," PLOS ONE, Public Library of Science, vol. 4(7), pages 1-10, July.
    16. Hoicheong Siu & Li Jin & Momiao Xiong, 2012. "Manifold Learning for Human Population Structure Studies," PLOS ONE, Public Library of Science, vol. 7(1), pages 1-18, January.
    17. Elodie Persyn & Richard Redon & Lise Bellanger & Christian Dina, 2018. "The impact of a fine-scale population stratification on rare variant association test results," PLOS ONE, Public Library of Science, vol. 13(12), pages 1-17, December.
    18. Andre Krumel Portella & Afroditi Papantoni & Catherine Paquet & Spencer Moore & Keri Shiels Rosch & Stewart Mostofsky & Richard S Lee & Kimberly R Smith & Robert Levitan & Patricia Pelufo Silveira & S, 2020. "Predicted DRD4 prefrontal gene expression moderates snack intake and stress perception in response to the environment in adolescents," PLOS ONE, Public Library of Science, vol. 15(6), pages 1-20, June.
    19. Lindsay Fernández-Rhodes & Jennifer R Malinowski & Yujie Wang & Ran Tao & Nathan Pankratz & Janina M Jeff & Sachiko Yoneyama & Cara L Carty & V Wendy Setiawan & Loic Le Marchand & Christopher Haiman &, 2018. "The genetic underpinnings of variation in ages at menarche and natural menopause among women from the multi-ethnic Population Architecture using Genomics and Epidemiology (PAGE) Study: A trans-ethnic ," PLOS ONE, Public Library of Science, vol. 13(7), pages 1-21, July.
    20. Peña-Malavera Andrea & Bruno Cecilia & Fernandez Elmer & Balzarini Monica, 2014. "Comparison of algorithms to infer genetic population structure from unlinked molecular markers," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 13(4), pages 391-402, August.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-27432-z. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.