k-mer-based GWAS in a wheat collection reveals novel and diverse sources of powdery mildew resistance
Wheat genetic resources hold the diversity required to mitigate agricultural challenges from climate change and reduced inputs. Using DArTseq, we genotype 461 wheat landraces and cultivars and evaluate them for powdery mildew resistance. By developing a k-mer-based GWAS approach with fully assembled genomes of Triticum aestivum and its progenitors, we uncover 25% more resistance-associated k-mers than single-reference methods, outperforming SNP-based GWAS in both loci detection and mapping precision. In total, we detect 34 powdery mildew resistance loci, including 27 potentially novel regions. Our approach underscores the importance of integrating multiple reference genomes to unlock the potential of wheat germplasm.
Authors
- Małgorzata Jasińska (ORCID: https://orcid.org/0000-0002-0090-0012)
- Rebecca Leber (ORCID: https://orcid.org/0009-0005-7382-6406)
- Victoria Widrig (ORCID: https://orcid.org/0000-0002-1285-3815)
- Benjamin Jaegle (ORCID: https://orcid.org/0000-0002-2679-1328)
- Matthias Heuberger (ORCID: https://orcid.org/0000-0003-3283-9233)
- Kevin Gauthier (ORCID: https://orcid.org/0009-0009-5236-4694)
- Alexandros G. Sotiropoulos (ORCID: https://orcid.org/0000-0002-3591-0851)
- Maja Boczkowska (ORCID: https://orcid.org/0000-0001-8691-410X)
- Nils Stein (ORCID: https://orcid.org/0000-0003-3011-8731)
- Max Haupt (ORCID: https://orcid.org/0000-0003-1528-4571)
- Boulos Chalhoub (ORCID: https://orcid.org/0000-0002-9268-5486)
- Yipu Li
- Gerhard Herren (ORCID: https://orcid.org/0000-0002-3963-4815)
- Yoav Voichek (ORCID: https://orcid.org/0000-0001-8460-7018)
- Beat Keller (ORCID: https://orcid.org/0000-0003-2379-9225)
- Javier Sánchez‐Martín (ORCID: https://orcid.org/0000-0002-0284-7219)
- Paulina Bolc (ORCID: https://orcid.org/0000-0001-7006-7372)
- Esther Jung (ORCID: https://orcid.org/0009-0007-1727-9377)
- Beate Schierscher
- Sarah Serex
Institutions
- Gregor Mendel Institute of Molecular Plant Biology (AT)
- Universidad de Salamanca (ES)
- University of Southern Queensland (AU)
- University of Zurich (CH)
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK) (DE)
- Agroscope (CH)
- Martin Luther University Halle-Wittenberg (DE)
Publication Details
- Journal
- Genome biology
- Published
- 2025-06-18
- DOI
- https://doi.org/10.1186/s13059-025-03645-z
- Citations
- 5
- Primary Topic
- Wheat and Barley Genetics and Pathology
- Type
- article
- Field-Weighted Citation Impact
- 8.75
Funders
- National Science Foundation
- European Commission
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
- Ministerio de Ciencia e Innovación
- Universität Zürich
- Agroscope
- Agencia Estatal de Investigación