OzWheat v1.0 GWAS platform datasets

Full description

Genomic/pedigree and marker-trait association data associated with the following publication; Hyles, J., Eagles, H., et al. (2024). OzWheat; a genome-to-phenome platform to resolve complex traits for wheat pre-breeding and research.
Lineage: Project OD-107742 () supported the foundational work to establish the panel, concepts, GWAS/TWAS pipelines underpinning the 'OzWheat' panel. Multiple projects have supported the development and application of this resource (below).

SNP data:
- Genomic SNPs from Illumina 90K Infinium iSelect Array SNP and transcriptome derived SNPs as described in Hyles et al. 2025 and Dillon et al. 2025.
- 90K data was generated in collaboration with AgVic under the GRDC DAV00127 project, and through OD-105738 and OD-107742.
- Transcript SNPs were generated in CSIRO strategic investment projects OD-107742 and OD-211556.
- SNP Haplotype file combining 90K and transcriptome SNPs generated after removal of missing or poor-quality data (genotypes with >50% missing data removed, SNPs with >20% missing data removed). Monomorphic markers and those with a minor allele frequency less than 5% were also removed. File sorted by physical chromosome position of SNP in IWGSC Chinese Spring Ref Seq v1.0.

Phenotype data:
Phenotype data was generated in projects OD-107742, OD-211556 and OD-217714, with the exception of phenotype data at the Narrabri site being collected under a University of Sydney PhD research project (Jessica Hyles).

Association results:
Marker:trait association analysis was performed in project OD-220968 using concepts and analytical pipelines developed in OD-107742.

Pedigree:
Pedigree curation as described in Hyles et al. 2024.

RShiny application was developed in Scientific Research Collaboration projects; ERRFP-1147, ERRFP-1380.