IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v13y2022i1d10.1038_s41467-021-27937-7.html
   My bibliography  Save this article

Signatures of selection in recently domesticated macadamia

Author

Listed:
  • Jishan Lin

    (Fujian Agriculture and Forestry University)

  • Wenping Zhang

    (Fujian Agriculture and Forestry University)

  • Xingtan Zhang

    (Fujian Agriculture and Forestry University)

  • Xiaokai Ma

    (Fujian Agriculture and Forestry University)

  • Shengcheng Zhang

    (Fujian Agriculture and Forestry University)

  • Shuai Chen

    (Fujian Agriculture and Forestry University)

  • Yibin Wang

    (Fujian Agriculture and Forestry University)

  • Haifeng Jia

    (Fujian Agriculture and Forestry University)

  • Zhenyang Liao

    (Fujian Agriculture and Forestry University)

  • Jing Lin

    (Fujian Agriculture and Forestry University)

  • Mengting Zhu

    (Fujian Agriculture and Forestry University)

  • Xiuming Xu

    (Fujian Agriculture and Forestry University)

  • Mingxing Cai

    (Fujian Agriculture and Forestry University)

  • Hui Zeng

    (China Academy of Tropical Agricultural Sciences)

  • Jifeng Wan

    (China Academy of Tropical Agricultural Sciences)

  • Weihai Yang

    (China Academy of Tropical Agricultural Sciences)

  • Tracie Matsumoto

    (Pacific Basin Agricultural Research Center)

  • Craig Hardner

    (The University of Queensland)

  • Catherine J. Nock

    (Southern Cross University)

  • Ray Ming

    (University of Illinois at Urbana-Champaign)

Abstract

Macadamia is a high value nut crop that is recently domesticated, ideal for testing the effect of artificial selection. Here, we sequence the genome of Hawaiian cultivar ‘Kau’ and assemble into 794 Mb in 14 pseudo-chromosomes with 37,728 genes. Genome analysis reveals a whole-genome duplication event, occurred 46.8 million years ago. Gene expansions occurred in gene families involves in fatty acid biosynthesis. Gene duplication of MADS-Box transcription factors in proanthocyanidin biosynthesis are relevant for seed coat development. Genome re-sequencing of 112 accessions reveals the origin of Hawaiian cultivars from Mount Bauple in southeast Queensland in Australia. Selective sweeps are detected in macadamia cultivars, including genes involved in fatty acid biosynthesis, seed coat development, and heat stress response. Such strong effects of artificial selection in few generations reveals the genomic basis for ‘one-step operation’ for clonal crop domestication. The knowledge gained could accelerate domestication of new crops from wild species.

Suggested Citation

  • Jishan Lin & Wenping Zhang & Xingtan Zhang & Xiaokai Ma & Shengcheng Zhang & Shuai Chen & Yibin Wang & Haifeng Jia & Zhenyang Liao & Jing Lin & Mengting Zhu & Xiuming Xu & Mingxing Cai & Hui Zeng & Ji, 2022. "Signatures of selection in recently domesticated macadamia," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-021-27937-7
    DOI: 10.1038/s41467-021-27937-7
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-021-27937-7
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-021-27937-7?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. Michael D. Purugganan & Dorian Q. Fuller, 2009. "The nature of selection during plant domestication," Nature, Nature, vol. 457(7231), pages 843-848, February.
    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. Oluwaseyi Shorinola & Rose Marks & Peter Emmrich & Chris Jones & Damaris Odeny & Mark A. Chapman, 2024. "Integrative and inclusive genomics to promote the use of underutilised crops," Nature Communications, Nature, vol. 15(1), pages 1-4, 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. repec:idb:brikps:64718 is not listed on IDEAS
    2. Serge Svizzero, 2018. "Plant domestication more rapid under optimizing behavior," Post-Print hal-02145462, HAL.
    3. Douglas Gollin, 2020. "Conserving genetic resources for agriculture: economic implications of emerging science," Food Security: The Science, Sociology and Economics of Food Production and Access to Food, Springer;The International Society for Plant Pathology, vol. 12(5), pages 919-927, October.
    4. Wolfgang Goettel & Hengyou Zhang & Ying Li & Zhenzhen Qiao & He Jiang & Dianyun Hou & Qijian Song & Vincent R. Pantalone & Bao-Hua Song & Deyue Yu & Yong-qiang Charles An, 2022. "POWR1 is a domestication gene pleiotropically regulating seed quality and yield in soybean," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    5. Matranga, Andrea, 2017. "The Ant and the Grasshopper: Seasonality and the Invention of Agriculture," MPRA Paper 76626, University Library of Munich, Germany.
    6. Eva Johansson & Faraz Muneer & Thomas Prade, 2023. "Plant Breeding to Mitigate Climate Change—Present Status and Opportunities with an Assessment of Winter Wheat Cultivation in Northern Europe as an Example," Sustainability, MDPI, vol. 15(16), pages 1-14, August.
    7. Brandon Schlautman & Spencer Barriball & Claudia Ciotir & Sterling Herron & Allison J. Miller, 2018. "Perennial Grain Legume Domestication Phase I: Criteria for Candidate Species Selection," Sustainability, MDPI, vol. 10(3), pages 1-23, March.
    8. Muhabbat Turdieva & Agnès Bernis-Fonteneau & Maira Esenalieva & Abdihalil Kayimov & Ashirmuhammed Saparmyradov & Khursandi Safaraliev & Kairkul Shalpykov & Paolo Colangelo & Devra I. Jarvis, 2024. "A Regional Perspective of Socio-Ecological Predictors for Fruit and Nut Tree Varietal Diversity Maintained by Farmer Communities in Central Asia," World, MDPI, vol. 5(1), pages 1-14, January.
    9. Serge Svizzero, 2017. "How the Neolithic Revolution Has Unfolded: Invention and Adoption or Change and Adaptation? Addressing the Diffusion Controversy about Initial Domestication," Working Papers hal-02145476, HAL.
    10. Jerzy H. Czembor & Elzbieta Czembor & Marcin Krystek & Juliusz Pukacki, 2023. "AgroGenome: Interactive Genomic-Based Web Server Developed Based on Data Collected for Accessions Stored in Polish Genebank," Agriculture, MDPI, vol. 13(1), pages 1-16, January.
    11. Rodríguez, Ricardo A. & Duncan, Janelle M. & Vanni, Michael J. & Melkikh, Alexey V. & Delgado, Juan D. & Riera, Rodrigo & Herrera, Ada M. & Camarena, Tomás & Quirós, Ángel & Fernández-Palacios, José M, 2017. "Exploring the analytical consequences of ecological subjects unwittingly neglected by the mainstream of evolutionary thought," Ecological Modelling, Elsevier, vol. 355(C), pages 70-83.
    12. Prabin Bajgain & James A. Anderson, 2021. "Multi-Allelic Haplotype-Based Association Analysis Identifies Genomic Regions Controlling Domestication Traits in Intermediate Wheatgrass," Agriculture, MDPI, vol. 11(7), pages 1-15, July.
    13. Muriel Gros-Balthazard & Claire Newton & Sarah Ivorra & Marie-Hélène Pierre & Jean-Christophe Pintaud & Jean-Frédéric Terral, 2016. "The Domestication Syndrome in Phoenix dactylifera Seeds: Toward the Identification of Wild Date Palm Populations," PLOS ONE, Public Library of Science, vol. 11(3), pages 1-21, March.
    14. Naihui Guo & Shengjia Tang & Yakun Wang & Wei Chen & Ruihu An & Zongliang Ren & Shikai Hu & Shaoqing Tang & Xiangjin Wei & Gaoneng Shao & Guiai Jiao & Lihong Xie & Ling Wang & Ying Chen & Fengli Zhao , 2024. "A mediator of OsbZIP46 deactivation and degradation negatively regulates seed dormancy in rice," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    15. An Huang & Paulo Santos & Russell Smyth, 2023. "Paddy and Prejudice: Evidence on the Agricultural Origins of Prejudice from China and 12 other Asian Societies," Monash Economics Working Papers 2023-02, Monash University, Department of Economics.

    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:13:y:2022:i:1:d:10.1038_s41467-021-27937-7. 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.