Purifying selection on deleterious variants affected by the combination of subgenomes and gene expression in bread wheat
The genome-wide pattern of purifying selection on deleterious variants has attracted broad interest in breeding and evolutionary biology. Little is known about purifying selection in polyploid species with potential functional redundancy of duplicated homoeologs. Here, we examine the pattern of polymorphisms and the combined effects of both subgenome and gene expression on estimates of purifying selection in the allohexaploid bread wheat. We utilize the de novo annotated assemblies and transcriptome data of the 10+ Wheat Genome Project. Purifying selection is detected after filtering chromosomes harboring segregating foreign introgression by modern breeding. Interestingly, strong purifying selection is observed in the category of genes that are highly expressed in root tissues and are in the D subgenome, which is thought to contribute to the range expansion after allopolyploidization. We suggest that the combination of expressed tissues and subgenomes will inform the target of future wheat breeding to mitigate the effect of deleterious variants.
Authors
- Gwyneth Halstead-Nussloch
- Kazuki Murata (ORCID: https://orcid.org/0009-0002-4352-2688)
- Keith A. Gardner (ORCID: https://orcid.org/0000-0002-4890-301X)
- Kentaro K. Shimizu (ORCID: https://orcid.org/0000-0002-6483-1781)
- T. Kassa Mulualem
- Venkat Bandi (ORCID: https://orcid.org/0000-0002-4729-2261)
- Thomas Lux (ORCID: https://orcid.org/0000-0002-5543-1911)
- Anthony Hall (ORCID: https://orcid.org/0000-0002-1806-020X)
- Michael Bevan (ORCID: https://orcid.org/0000-0001-8264-2354)
- Curt A. McCartney (ORCID: https://orcid.org/0000-0002-9482-3133)
- Dal‐Hoe Koo (ORCID: https://orcid.org/0000-0003-4578-8519)
- Ian Small (ORCID: https://orcid.org/0000-0001-5300-1216)
- Tony Kuo (ORCID: https://orcid.org/0000-0003-2358-7919)
- Roman Briskine (ORCID: https://orcid.org/0000-0002-6831-3914)
- Simon G. Krattinger (ORCID: https://orcid.org/0000-0001-6912-7411)
- James Cockram
- Assaf Distelfeld (ORCID: https://orcid.org/0000-0003-1777-3053)
- A.S.M. Faridul Islam
- Bin Xiao Fu (ORCID: https://orcid.org/0000-0002-9439-7197)
- Uwe Scholz (ORCID: https://orcid.org/0000-0002-9682-1668)
- Moeko Okada (ORCID: https://orcid.org/0000-0002-4398-5917)
- Jemima Brinton (ORCID: https://orcid.org/0000-0001-7027-0450)
- Burkhard Steuernagel (ORCID: https://orcid.org/0000-0002-8284-7728)
- Masaomi Hatakeyama (ORCID: https://orcid.org/0000-0002-7409-9694)
- Pierre R. Fobert (ORCID: https://orcid.org/0000-0001-9397-7539)
- Benjamen White (ORCID: https://orcid.org/0000-0003-4391-3945)
- Liangliang Gao (ORCID: https://orcid.org/0000-0002-8562-0027)
- Haberer Georg
- Carl Gutwin
- David Swarbreck
- Brook Byrns
- Nils Stein
- Dario Copetti
- Toshiaki Tameshige
- Krystalee Wiebe
- Markus C. Kolodziej
- Martin Mascher
- Curtis Pozniak
- Nick Fradgley
- Dinushika Thambugala
- Cecile Monat
- Jasline Deek
- Darren Heavens
- Jun Sese
- Hiroyuki Kanamori
- Pierre J. Hucl
- Anne Fiebig
- Shuhei Nasuda
- Yusuke Nabeka
- Valentyna Klymiuk
- Timothy Paape
- Juan Gutierrez-Gonzalez
- Beat Keller
- Ricardo H. Ramirez-Gonzalez
- Jennifer Ens
- Sean Walkowiak
- BernardoClavijo
- Chu Shin Koh
- Gabriel Keeble-Gagnère
- Andrew G. Sharpe
- Luca Venturini
- Hiroyuki Tsuji
- Sylvie Cloutier
- Cristobal Uauy
- Jonathan Wright
- Axel Himmelbach
- Matthew Clark
- Arvind Bharti
- Lawrence Percival-Alwyn
- Allen K. Fritz
- Neil McKenzie
- Hikmet Budak
- Amidou N’ Diaye
- Emily Delorean
- KenChalmers
- Christine Fosker
- Jorge Nunez Siri
- Josquin Tibbets
- Ravi Singh
- Ksenia Krasileva
- Fuminori Kobayashi
- Jianzhong Wu
- Tomohiro Ban
- Alejandro C. Costamagna
- Sateesh Kagale
- Gary Muehlbauer
- Erik Legg
- Jesse A. Poland
- Kanako Kawaura
Institutions
- Kihara Institute for Biological Research (JP)
- Agricultural Research Service (US)
- University of Zurich (CH)
- Norwich Research Park (GB)
- Helmholtz Zentrum München (DE)
- University of Saskatchewan (CA)
- Earlham Institute (GB)
- Life Science Zurich (CH)
- Center for Advancing Health (US)
- Niigata University (JP)
- Yokohama City University (JP)
Publication Details
- Journal
- Cell Reports
- Published
- 2026-01-26
- DOI
- https://doi.org/10.1016/j.celrep.2025.116785
- Primary Topic
- Wheat and Barley Genetics and Pathology
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- National Science Foundation
- Genome Canada
- Ministry of Agriculture - Saskatchewan
- Western Grains Research Foundation
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
- Universität Zürich
- Genome Prairie
- Saskatchewan Wheat Development Commission
- Japan Society for the Promotion of Science
- Japan Science and Technology Agency
- Core Research for Evolutional Science and Technology