OzWheat v1.0 GWAS platform datasets

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. \nLineage: 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).\n\nSNP data:\n- 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.\n- 90K data was generated in collaboration with AgVic under the GRDC DAV00127 project, and through OD-105738 and OD-107742. \n- Transcript SNPs were generated in CSIRO strategic investment projects OD-107742 and OD-211556.\n- 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. \n\nPhenotype data:\nPhenotype 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).\n\nAssociation results:\nMarker:trait association analysis was performed in project OD-220968 using concepts and analytical pipelines developed in OD-107742.\n\nPedigree: \nPedigree curation as described in Hyles et al. 2024.\n\nRShiny application was developed in Scientific Research Collaboration projects; ERRFP-1147, ERRFP-1380.

本数据集关联以下发表论文中的基因组/系谱与标记-性状关联数据；引用文献：Hyles, J., Eagles, H. 等（2024）《OzWheat：用于解析小麦预育种与研究复杂性状的基因组-表型组平台》。
项目谱系：项目OD-107742（）为构建该种质面板、核心研究理念以及支撑“OzWheat”面板的全基因组关联分析（Genome-Wide Association Study, GWAS）/转录组全基因组关联分析（Transcriptome-Wide Association Study, TWAS）流程的基础工作提供了支持。另有多项项目为该资源的开发与应用提供了支撑（详见下文）。

单核苷酸多态性（Single Nucleotide Polymorphism, SNP）数据：
- 基因组SNP数据源自Illumina 90K Infinium iSelect芯片，以及转录组来源的SNP数据，相关细节参见Hyles等人2025年与Dillon等人2025年的研究。
- 90K芯片数据由维多利亚州农业厅（Agriculture Victoria, AgVic）合作完成，依托谷物研发公司（Grains Research and Development Corporation, GRDC）DAV00127项目，以及OD-105738与OD-107742项目生成。
- 转录组SNP数据由澳大利亚联邦科学与工业研究组织（Commonwealth Scientific and Industrial Research Organisation, CSIRO）战略投资项目OD-107742与OD-211556生成。
- 整合90K芯片与转录组SNP的SNP单倍型文件：经缺失数据或低质量数据过滤后生成，具体过滤规则为移除缺失率>50%的基因型、缺失率>20%的SNP位点，同时移除单态性标记与次要等位基因频率低于5%的位点。文件按SNP在国际小麦基因组测序联盟（International Wheat Genome Sequencing Consortium, IWGSC）中国春参考基因组序列v1.0中的物理染色体位置进行排序。

表型数据：由项目OD-107742、OD-211556与OD-217714生成，仅Narrabri试验点的表型数据由悉尼大学博士研究项目（负责人Jessica Hyles）采集。

标记-性状关联分析：由项目OD-220968执行，采用OD-107742项目中开发的研究理念与分析流程。

系谱整理：详见Hyles等人2024年的研究。

RShiny应用由科研合作项目ERRFP-1147、ERRFP-1380开发完成。