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Harnessing landrace diversity empowers wheat breeding

Nature (2024)Cite this article

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Abstract

Harnessing genetic diversity in major staple crops through the development of new breeding capabilities is essential to ensure food security1. Here we examined the genetic and phenotypic diversity of the A.E. Watkins landrace collection2 of bread wheat (Triticum aestivum), a major global cereal, through whole-genome re-sequencing (827 Watkins landraces and 208 modern cultivars) and in-depth field evaluation spanning a decade. We discovered that modern cultivars are derived from just two of the seven ancestral groups of wheat and maintain very long-range haplotype integrity. The remaining five groups represent untapped genetic sources, providing access to landrace-specific alleles and haplotypes for breeding. Linkage disequilibrium (LD) based haplotypes and association genetics analyses link Watkins genomes to the thousands of high-resolution quantitative trait loci (QTL), and significant marker–trait associations identified. Using these structured germplasm, genotyping and informatics resources, we revealed many Watkins-unique beneficial haplotypes that can confer superior traits in modern wheat. Furthermore, we assessed the phenotypic effects of 44,338 Watkins-unique haplotypes, introgressed from 143 prioritised QTL in the context of modern cultivars, bridging the gap between landrace diversity and current breeding. This study establishes a framework for systematically utilising genetic diversity in crop improvement to achieve sustainable food security.

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Author information

Author notes

  1. These authors contributed equally: Shifeng Cheng, Cong Feng, Luzie U. Wingen

Authors and Affiliations

  1. Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China

    Shifeng Cheng, Cong Feng, Hong Cheng, Mei Jiang, Zejian Huang, Baizhi Chen, Ruirui Han, Junliang Hou, Muhammad S. Iqbal, Hongbing Liu, Shiyan Liu, Lingling Ma, Zareen Sarfraz, Yan Shi, Bo Song, Abdul Waheed, Xingwei Wang, Yanping Wei, Shishi Wu, Yubing Wu, Wenfei Xian, Yawen Xu, Yunfeng Xu, Quan Yuan, Xin Zhang & Sanwen Huang

  2. John Innes Centre, Norwich Research Park, Norwich, UK

    Luzie U. Wingen, Michelle Leverington-Waite, Sarah Collier, Simon Orford, Xiaoming Wang, Rajani Awal, Tom O’Hara, Clare Lister, Ajay Siluveru, Jesús Quiroz-Chávez, Ricardo H. Ramírez-González, Lorelei Bilham, James K. M. Brown, Laetitia Chartrain, Kumar Gaurav, Amber N. Hafeez, Richard Horler, Ania Kowalski, Cathy Mumford, Charlie Philp, Darryl Playford, Burkhard Steuernagel, Brande B. H. Wulff, Paul Nicholson, Noam Chayut, Cristobal Uauy, Dale Sanders & Simon Griffiths

  3. Rothamsted Research, Harpenden, Hertfordshire, UK

    Andrew B. Riche, March Castle, Alison Lovegrove, Saroj Parmar, Peter R. Shewry, David Steele & Malcolm J. Hawkesford

  4. State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China

    Xiaoming Wang

  5. Functional Genomics, School of Biological Sciences, University of Bristol, Bristol, UK

    Gary Barker, Amanda Burridge, Alexandra M. Przewieslik-Allen, Mark Winfield & Keith J. Edwards

  6. RAGT, Grange Rd, Ickleton, Saffron Walden, UK

    Ruth Bryant, Chris Burt & David Schafer

  7. Limagrain UK Ltd., Woolpit, Bury St. Edmunds, Suffolk, UK

    Simon Berry & Phillip Tailby

  8. School of Life and Environmental Sciences, Faculty of Science, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, NSW, Australia

    Urmil Bansal & Harbans S. Bariana

  9. Western Sydney University, Richmond, New South Wales, Australia

    Harbans S. Bariana

  10. School of Biosciences, University of Nottingham, Sutton Bonington, UK

    Malcolm J. Bennett, John Foulkes & Oorbessy Gaju

  11. Department of Agricultural and Forest Sciences and Engineering, University of Lleida–AGROTECNIO-CERCA Center, Av. R. Roure 191, Lleida, Spain

    Breno Bicego & Gustavo Slafer

  12. Elsoms Wheat Ltd., Pinchbeck Rd, Spalding, UK

    Milika Buurman

  13. Debre Zeit Agricultural Research Center, Ethiopian Institute of Agricultural Research, Debre Zeit, Ethiopia

    Worku Denbel

  14. Wheat Research Department, Field Crops Research Institute, Agricultural Research Center, Giza, Egypt

    Ahmed F. Elkot

  15. Limagrain UK Limited, Rothwell, Market Rasen, UK

    Paul Fenwick

  16. Syngenta Seeds, Capital Park, CPC4, Fulbourn, Cambridge, UK

    David Feuerhelm

  17. School of Biology, University of Leeds, Leeds, UK

    Adam Gauley & Laura Dixon

  18. Agri-Food and Biosciences Institute, Belfast, Northern Ireland, BT9 5PX, UK

    Adam Gauley

  19. Qingdao Agricultural University, Qingdao, China

    Ruirui Han

  20. DSV, Top Dawkins Barn, Banbury, UK

    Matthew Kerton

  21. Institute of Field and Vegetable Crops, National Institute of the Republic of Serbia, Maksima Gorkog 30, Novi Sad, Republic of Serbia

    Ankica Kondic-Spica

  22. KWS UK Ltd., 56 Church St, Thriplow, Royston, UK

    Jacob Lage

  23. Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang, China

    Xiaolong Li

  24. National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, China

    Baoxing Song

  25. The Earlham Institute, Norwich Research Park, Norwich, UK

    Simon Tyrrell

  26. Egerton University, Njoro, Kenya

    Mercy N. Wamalwa

  27. Huazhong Agricultural University, Wuhan, China

    Yubing Wu, Yawen Xu & Xin Zhang

  28. Center for Desert Agriculture, Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia

    Brande B. H. Wulff

  29. Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany

    Wenfei Xian

  30. State Key Laboratory of Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China

    Sanwen Huang

Authors
  1. Shifeng Cheng
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  2. Cong Feng
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  3. Luzie U. Wingen
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  4. Hong Cheng
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  6. Mei Jiang
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  7. Michelle Leverington-Waite
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  9. Sarah Collier
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  10. Simon Orford
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  11. Xiaoming Wang
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Corresponding authors

Correspondence to Shifeng Cheng or Simon Griffiths.

Supplementary information

Supplementary Information

This file contains Supplementary notes 1 and 2; Supplementary Figures 1-11.

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Peer Review File

Supplementary Tables 1-10

This file contains Supplementary Tables 1-10.

Supplementary Tables 11-20

This file contains Supplementary Tables 11-20.

Supplementary Tables 21-33

This file contains Supplementary Tables 21-33.

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Cheng, S., Feng, C., Wingen, L.U. et al. Harnessing landrace diversity empowers wheat breeding. Nature (2024). https://doi.org/10.1038/s41586-024-07682-9

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