Harnessing landrace diversity empowers wheat breeding

Harnessing genetic diversity in major staple crops through the development of new breeding capabilities is essential to ensure food security. Here we examined the genetic and phenotypic diversity of the A. E. Watkins landrace collection 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.

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, Simon Griffiths