k-mer-based GWAS in a wheat collection reveals novel and diverse sources of powdery mildew resistance

2025/06/18 by Benjamin Jaegle, Yoav Voichek, Max Haupt +17 · 1 voice
Agricultural and Biological Sciences · Biochemistry, Genetics and Molecular Biology · #Wheat and Barley Genetics and Pathology #Genetic Mapping and Diversity in Plants and Animals #Genomics and Phylogenetic Studies

paper · pdf · doi:10.1186/s13059-025-03645-z

openalex publication_date 2025/06/18 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/31

Abstract

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.

Citations

• A One-Penny Imputed Genome from Next-Generation Reference Panels
• Multiple wheat genomes reveal global variation in modern breeding
• Twelve years of SAMtools and BCFtools
• rMVP: A Memory-Efficient, Visualization-Enhanced, and Parallel-Accelerated Tool for Genome-Wide Association Study
• Optical maps refine the bread wheat <i>Triticum aestivum</i> cv. Chinese Spring genome assembly
• GAPIT Version 3: Boosting Power and Accuracy for Genomic Association and Prediction
• Reap the crop wild relatives for breeding future crops

Discussions

• Nice paper of Jaegle et al. in Genome Biology : k-mer-based GWAS in a wheat collection reveals novel and diverse sources of powdery mildew resistance doi.org/10.1186/s130... [bsky, 1 points, 0 comments]

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