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; Brande B.H. Wulff

doi:10.1038/s41586-024-07682-9

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 BerryUrmil 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, Brande B.H. Wulff

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

11 Scopus citations

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.

Original language	English (US)
Pages (from-to)	823-831
Number of pages	9
Journal	NATURE
Volume	632
Issue number	8026
DOIs	https://doi.org/10.1038/s41586-024-07682-9
State	Published - Aug 22 2024

Bibliographical note

Publisher Copyright:
© The Author(s) 2024.

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This output contributes to the following UN Sustainable Development Goals (SDGs)

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Cheng, S., Feng, C., Wingen, L. U., Cheng, H., Riche, A. B., Jiang, M., Leverington-Waite, M., Huang, Z., Collier, S., Orford, S., Wang, X., Awal, R., Barker, G., O’Hara, T., Lister, C., Siluveru, A., Quiroz-Chávez, J., Ramírez-González, R. H., Bryant, R., ... Wulff, B. B. H. (2024). Harnessing landrace diversity empowers wheat breeding. NATURE, 632(8026), 823-831. https://doi.org/10.1038/s41586-024-07682-9

@article{be755cfcde714f66bce750b63a46217e,

title = "Harnessing landrace diversity empowers wheat breeding",

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.",

author = "Shifeng Cheng and Cong Feng and Wingen, {Luzie U.} and Hong Cheng and Riche, {Andrew B.} and Mei Jiang and Michelle Leverington-Waite and Zejian Huang and Sarah Collier and Simon Orford and Xiaoming Wang and Rajani Awal and Gary Barker and Tom O{\textquoteright}Hara and Clare Lister and Ajay Siluveru and Jes{\'u}s Quiroz-Ch{\'a}vez and Ram{\'i}rez-Gonz{\'a}lez, {Ricardo H.} and Ruth Bryant and Simon Berry and Urmil Bansal and Bariana, {Harbans S.} and Bennett, {Malcolm J.} and Breno Bicego and Lorelei Bilham and Brown, {James K.M.} and Amanda Burridge and Chris Burt and Milika Buurman and March Castle and Laetitia Chartrain and Baizhi Chen and Worku Denbel and Elkot, {Ahmed F.} and Paul Fenwick and David Feuerhelm and John Foulkes and Oorbessy Gaju and Adam Gauley and Kumar Gaurav and Hafeez, {Amber N.} and Ruirui Han and Richard Horler and Junliang Hou and Iqbal, {Muhammad S.} and Matthew Kerton and Ankica Kondic-Spica and Ania Kowalski and Jacob Lage and Wulff, {Brande B.H.}",

note = "Publisher Copyright: {\textcopyright} The Author(s) 2024.",

year = "2024",

month = aug,

day = "22",

doi = "10.1038/s41586-024-07682-9",

language = "English (US)",

volume = "632",

pages = "823--831",

journal = "NATURE",

issn = "0028-0836",

publisher = "Nature Research",

number = "8026",

}

Cheng, S, Feng, C, Wingen, LU, Cheng, H, Riche, AB, Jiang, M, Leverington-Waite, M, Huang, Z, Collier, S, Orford, S, Wang, X, Awal, R, Barker, G, O’Hara, T, Lister, C, Siluveru, A, Quiroz-Chávez, J, Ramírez-González, RH, Bryant, R, Berry, S, Bansal, U, Bariana, HS, Bennett, MJ, Bicego, B, Bilham, L, Brown, JKM, Burridge, A, Burt, C, Buurman, M, Castle, M, Chartrain, L, Chen, B, Denbel, W, Elkot, AF, Fenwick, P, Feuerhelm, D, Foulkes, J, Gaju, O, Gauley, A, Gaurav, K, Hafeez, AN, Han, R, Horler, R, Hou, J, Iqbal, MS, Kerton, M, Kondic-Spica, A, Kowalski, A, Lage, J & Wulff, BBH 2024, 'Harnessing landrace diversity empowers wheat breeding', NATURE, vol. 632, no. 8026, pp. 823-831. https://doi.org/10.1038/s41586-024-07682-9

TY - JOUR

T1 - Harnessing landrace diversity empowers wheat breeding

AU - Cheng, Shifeng

AU - Feng, Cong

AU - Wingen, Luzie U.

AU - Cheng, Hong

AU - Riche, Andrew B.

AU - Jiang, Mei

AU - Leverington-Waite, Michelle

AU - Huang, Zejian

AU - Collier, Sarah

AU - Orford, Simon

AU - Wang, Xiaoming

AU - Awal, Rajani

AU - Barker, Gary

AU - O’Hara, Tom

AU - Lister, Clare

AU - Siluveru, Ajay

AU - Quiroz-Chávez, Jesús

AU - Ramírez-González, Ricardo H.

AU - Bryant, Ruth

AU - Berry, Simon

AU - Bansal, Urmil

AU - Bariana, Harbans S.

AU - Bennett, Malcolm J.

AU - Bicego, Breno

AU - Bilham, Lorelei

AU - Brown, James K.M.

AU - Burridge, Amanda

AU - Burt, Chris

AU - Buurman, Milika

AU - Castle, March

AU - Chartrain, Laetitia

AU - Chen, Baizhi

AU - Denbel, Worku

AU - Elkot, Ahmed F.

AU - Fenwick, Paul

AU - Feuerhelm, David

AU - Foulkes, John

AU - Gaju, Oorbessy

AU - Gauley, Adam

AU - Gaurav, Kumar

AU - Hafeez, Amber N.

AU - Han, Ruirui

AU - Horler, Richard

AU - Hou, Junliang

AU - Iqbal, Muhammad S.

AU - Kerton, Matthew

AU - Kondic-Spica, Ankica

AU - Kowalski, Ania

AU - Lage, Jacob

AU - Wulff, Brande B.H.

PY - 2024/8/22

Y1 - 2024/8/22

N2 - 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.

AB - 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.

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U2 - 10.1038/s41586-024-07682-9

DO - 10.1038/s41586-024-07682-9

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AN - SCOPUS:85200166912

SN - 0028-0836

VL - 632

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EP - 831

JO - NATURE

JF - NATURE

IS - 8026

ER -

Harnessing landrace diversity empowers wheat breeding

Abstract

Bibliographical note

ASJC Scopus subject areas

UN SDGs

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