We conducted a genome-wide association study (GWAS) to identify genetic resistance to Wheat streak mosaic virus (WSMV) in Aegilops tauschii, the diploid progenitor of the wheat D subgenome. A panel of 250 accessions was screened in replicated batches under controlled inoculation in the greenhouse at Kansas State University. Both visual tolerance scores and viral titer accumulation were recorded to capture variation in disease response.

Whole-genome sequencing data provided high-density SNP markers for association mapping. Using multiple GWAS models, we detected significant loci linked to both tolerance and reduced viral titers, highlighting novel loci underlying WSMV resistance.

This work represents the first large-scale GWAS for WSMV in Ae. tauschii and establishes a foundation for dissecting tolerance mechanisms. The identified loci and resistant accessions represent valuable resources for pre-breeding and marker-assisted selection. These findings underscore the importance of Ae. tauschii diversity for improving wheat resilience against viral diseases. This repository includes genotypic data (SNP matrices) and codes for phylogenetic tree construction, PCA, and comprehensive phenotypic and genotypic data analyses.

Dataset DOI: 10.5061/dryad.2547d7x4r

Description of the data and file structure

Aegilops tauschii, the D-genome donor of bread wheat (Triticum aestivum), represents a critical genetic resource for wheat improvement. It harbors a wide range of natural variation for agronomically important traits, including resistance and tolerance to biotic and abiotic stresses. Wheat streak mosaic virus (WSMV) is a major viral disease that reduces wheat yield worldwide. Identifying novel genetic variation for WSMV tolerance in Aegilops tauschii provides opportunities for the development of improved, resilient wheat cultivars.

In this study, a diverse panel of 250 Ae. tauschii accessions was comprehensively phenotyped for WSMV tolerance and genotyped using whole-genome-sequencing based high-density SNP markers. The dataset includes SNP matrices, phenotypic measurements, and accompanying scripts for phylogenetic tree construction, principal component analysis (PCA), and downstream phenotypic and genotypic data analyses. These resources will support further evolutionary, genomic, and breeding research, while also enabling reproducibility and reuse by the broader scientific community.

Any datasets that could not be accommodated within the manuscript’s supplementary materials are provided in this repository. The files and their descriptions are available in the table below.

Files and Descriptions

Ae.tauschii.WGS-panel_SNP.matrix.hmp.txt.zip: Compressed SNP matrix file for the full Ae. tauschii panel. This matrix was used for phylogenetic tree and PCA

Lineage_1_hapmap.file_GWAS.SNP.matrix.hmp.txt.zip: Hapmap-format SNP matrix for Lineage 1 accessions used in GWAS

Lineage_2_hapmap.file_GWAS.SNP.matrix.hmp.txt.zip: Hapmap-format SNP matrix for Lineage 2 accessions used in GWAS

audpc.severity.dist.Rmd: R Markdown script for analyzing and visualizing AUDPC-based severity distribution

Virus.titer.dist.lineage.and.dpi.Rmd: R Markdown script for analyzing virus titer distribution across lineages and time points (dpi).

titer.vs.audpc.corr.heat.map.Rmd: R Markdown script for generating correlation heatmaps between AUDPC and virus titer data.

colorful.manhattan.and.SNP.density.titer.tauschii.Rmd: R Markdown script for Manhattan plots and SNP density analysis related to virus titer in Ae. tauschii

Correlation_Plot.Rmd: R Markdown script for generating correlation plot

Heat_map_of_WSMV_symptom_from_common_accession_in_WSMV_single_and_mixed_infection.Rmd: R Markdown script for generating heatmap for WSMV symptom from common accession

HeatMap_250Accessions_WSMV.Rmd: R Markdown script for generating heatmap for WSMV

Heatmap_pair_line_plot_for_checking_the_behavious_of_accessions_for_WSMV_titer_in_single_and_mixed_infection.Rmd: R Markdown script for generating heatmap pair line plot

Paired_line_plot_to_compare_WSMV_symptom_in_single_and_mixed_infection.Rmd: R Markdown script for generating plot to compare WSMV symptoms

Titer_Trend.Rmd: R Markdown script for studying titer trend

Violin_plot_script_for_symptom_scores.Rmd: R Markdown script for generating symptom scores

Violin_Plot_Viral_Titer.Rmd: R Markdown script for generating virus titer data

Disease_progress_curve_comparing_single_vs_mixed_infection_symptom.Rmd: R Markdown script for generating disease progress curve

Heat_map_of_WSMV_virus-titer_from_common_accession_in_WSMV_single_and_mixed_infection.Rmd: R Markdown script for WSMV titer heatmap for common accessions in single and mixed infection

Code/software

The software required to run this dataset includes R and associated free packages, which are explained in the provided R Markdown (.Rmd) files. For GWAS analyses, the GAPIT package is needed, and all essential models must be loaded beforehand. Both the SNP matrix and the corresponding phenotypic data are required to perform GWAS.

Access information

The raw Illumina fastq data used in this study include previously published (https://www.nature.com/articles/s41587-021-01058-4) data which is available under the NCBI BioProject accession number PRJNA685125. Seventeen other accessions we sequenced in this study were deposited at NCBI under the BioProject accession number PRJNA1259393.

Dataset: Phenotyping and genotyping of a diverse Aegilops tauschii panel for Wheat streak mosaic virus (WSMV) tolerance

Data files

Abstract

Description of the data and file structure

Files and Descriptions

Code/software

Access information

Dataset: Phenotyping and genotyping of a diverse Aegilops tauschii panel for Wheat streak mosaic virus (WSMV) tolerance

Data files

Abstract

README: Dataset: Phenotyping and genotyping of a diverse Aegilops tauschii panel for Wheat streak mosaic virus (WSMV) tolerance

Description of the data and file structure

Files and Descriptions

Code/software

Access information