Harnessing landrace diversity empowers wheat breeding

Shifeng Cheng (), Cong Feng, Luzie U. Wingen, Hong Cheng, Andrew B. Riche, Mei Jiang, Michelle Leverington-Waite, Zejian Huang, Sarah Collier, Simon Orford, Xiaoming Wang, Rajani Awal, Gary Barker, Tom O’Hara, Clare Lister, Ajay Siluveru, Jesús Quiroz-Chávez, Ricardo H. Ramírez-González, Ruth Bryant, Simon Berry, Urmil Bansal, Harbans S. Bariana, Malcolm J. Bennett, Breno Bicego, Lorelei Bilham, James K. M. Brown, Amanda Burridge, Chris Burt, Milika Buurman, March Castle, Laetitia Chartrain, Baizhi Chen, Worku Denbel, Ahmed F. Elkot, Paul Fenwick, David Feuerhelm, John Foulkes, Oorbessy Gaju, Adam Gauley, Kumar Gaurav, Amber N. Hafeez, Ruirui Han, Richard Horler, Junliang Hou, Muhammad S. Iqbal, Matthew Kerton, Ankica Kondic-Spica, Ania Kowalski, Jacob Lage, Xiaolong Li, Hongbing Liu, Shiyan Liu, Alison Lovegrove, Lingling Ma, Cathy Mumford, Saroj Parmar, Charlie Philp, Darryl Playford, Alexandra M. Przewieslik-Allen, Zareen Sarfraz, David Schafer, Peter R. Shewry, Yan Shi, Gustavo A. Slafer, Baoxing Song, Bo Song, David Steele, Burkhard Steuernagel, Phillip Tailby, Simon Tyrrell, Abdul Waheed, Mercy N. Wamalwa, Xingwei Wang, Yanping Wei, Mark Winfield, Shishi Wu, Yubing Wu, Brande B. H. Wulff, Wenfei Xian, Yawen Xu, Yunfeng Xu, Quan Yuan, Xin Zhang, Keith J. Edwards, Laura Dixon, Paul Nicholson, Noam Chayut, Malcolm J. Hawkesford, Cristobal Uauy, Dale Sanders, Sanwen Huang and Simon Griffiths ()
Additional contact information
Shifeng Cheng: Chinese Academy of Agricultural Sciences
Cong Feng: Chinese Academy of Agricultural Sciences
Luzie U. Wingen: John Innes Centre
Hong Cheng: Chinese Academy of Agricultural Sciences
Andrew B. Riche: Rothamsted Research
Mei Jiang: Chinese Academy of Agricultural Sciences
Michelle Leverington-Waite: John Innes Centre
Zejian Huang: Chinese Academy of Agricultural Sciences
Sarah Collier: John Innes Centre
Simon Orford: John Innes Centre
Xiaoming Wang: John Innes Centre
Rajani Awal: John Innes Centre
Gary Barker: University of Bristol
Tom O’Hara: John Innes Centre
Clare Lister: John Innes Centre
Ajay Siluveru: John Innes Centre
Jesús Quiroz-Chávez: John Innes Centre
Ricardo H. Ramírez-González: John Innes Centre
Ruth Bryant: RAGT
Simon Berry: Limagrain UK
Urmil Bansal: The University of Sydney Plant Breeding Institute
Harbans S. Bariana: The University of Sydney Plant Breeding Institute
Malcolm J. Bennett: University of Nottingham
Breno Bicego: University of Lleida–AGROTECNIO-CERCA Center
Lorelei Bilham: John Innes Centre
James K. M. Brown: John Innes Centre
Amanda Burridge: University of Bristol
Chris Burt: RAGT
Milika Buurman: Elsoms Wheat
March Castle: Rothamsted Research
Laetitia Chartrain: John Innes Centre
Baizhi Chen: Chinese Academy of Agricultural Sciences
Worku Denbel: Ethiopian Institute of Agricultural Research
Ahmed F. Elkot: Agricultural Research Center
Paul Fenwick: Limagrain UK
David Feuerhelm: Syngenta Seeds
John Foulkes: University of Nottingham
Oorbessy Gaju: University of Nottingham
Adam Gauley: University of Leeds
Kumar Gaurav: John Innes Centre
Amber N. Hafeez: John Innes Centre
Ruirui Han: Chinese Academy of Agricultural Sciences
Richard Horler: John Innes Centre
Junliang Hou: Chinese Academy of Agricultural Sciences
Muhammad S. Iqbal: Chinese Academy of Agricultural Sciences
Matthew Kerton: DSV UK
Ankica Kondic-Spica: National Institute of the Republic of Serbia
Ania Kowalski: John Innes Centre
Jacob Lage: KWS UK
Xiaolong Li: Zhejiang A&F University
Hongbing Liu: Chinese Academy of Agricultural Sciences
Shiyan Liu: Chinese Academy of Agricultural Sciences
Alison Lovegrove: Rothamsted Research
Lingling Ma: Chinese Academy of Agricultural Sciences
Cathy Mumford: John Innes Centre
Saroj Parmar: Rothamsted Research
Charlie Philp: John Innes Centre
Darryl Playford: John Innes Centre
Alexandra M. Przewieslik-Allen: University of Bristol
Zareen Sarfraz: Chinese Academy of Agricultural Sciences
David Schafer: RAGT
Peter R. Shewry: Rothamsted Research
Yan Shi: Chinese Academy of Agricultural Sciences
Gustavo A. Slafer: University of Lleida–AGROTECNIO-CERCA Center
Baoxing Song: Shandong Laboratory of Advanced Agriculture Sciences in Weifang
Bo Song: Chinese Academy of Agricultural Sciences
David Steele: Rothamsted Research
Burkhard Steuernagel: John Innes Centre
Phillip Tailby: Limagrain UK
Simon Tyrrell: The Earlham Institute
Abdul Waheed: Chinese Academy of Agricultural Sciences
Mercy N. Wamalwa: Egerton University
Xingwei Wang: Chinese Academy of Agricultural Sciences
Yanping Wei: Chinese Academy of Agricultural Sciences
Mark Winfield: University of Bristol
Shishi Wu: Chinese Academy of Agricultural Sciences
Yubing Wu: Chinese Academy of Agricultural Sciences
Brande B. H. Wulff: John Innes Centre
Wenfei Xian: Chinese Academy of Agricultural Sciences
Yawen Xu: Chinese Academy of Agricultural Sciences
Yunfeng Xu: Chinese Academy of Agricultural Sciences
Quan Yuan: Chinese Academy of Agricultural Sciences
Xin Zhang: Chinese Academy of Agricultural Sciences
Keith J. Edwards: University of Bristol
Laura Dixon: University of Leeds
Paul Nicholson: John Innes Centre
Noam Chayut: John Innes Centre
Malcolm J. Hawkesford: Rothamsted Research
Cristobal Uauy: John Innes Centre
Dale Sanders: John Innes Centre
Sanwen Huang: Chinese Academy of Agricultural Sciences
Simon Griffiths: John Innes Centre

Nature, 2024, vol. 632, issue 8026, 823-831

Abstract: 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, by whole-genome re-sequencing of 827 Watkins landraces and 208 modern cultivars and in-depth field evaluation spanning a decade. We found that modern cultivars are derived from 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-based haplotypes and association genetics analyses link Watkins genomes to the thousands of identified high-resolution quantitative trait loci and significant marker–trait associations. 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 prioritized quantitative trait loci in the context of modern cultivars, bridging the gap between landrace diversity and current breeding. This study establishes a framework for systematically utilizing genetic diversity in crop improvement to achieve sustainable food security.

Date: 2024
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DOI: 10.1038/s41586-024-07682-9

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