OzOat Diversity Panel: A Global Genome-to-Phenome Resource for Oat Breeding

Full description

The OzOat diversity panel is a curated collection of approximately 319 oat accessions representing global genetic diversity and the breeding history of Australian oats. The panel spans material from historical landraces (circa 1892) to modern cultivars, including key international introductions and donor lines. Designed to maximise recombination and capture broad phenotypic diversity, the OzOat panel underpins gene discovery and marker development for a wide range of traits. High-density SNP genotyping, transcriptome sequencing, and curated pedigree information provide a powerful genome-to-phenome platform for accelerating genetic discovery and breeding innovation. Combined these resources enable the development of oat varieties with improved resilience, productivity, and quality tailored to Australian farming systems. Links to genomic, pedigree, and marker–trait association datasets generated as part of the GRDC project: Optimising genetic control of oat phenology for Australia (CSP2007-002RTX) are provided within this DAP entry.
Lineage: GRDC project: Optimising genetic control of oat phenology for Australia CSP2007-002RTX supported the foundational work to establish the panel, concepts, GWAS/TWAS pipelines underpinning the 'OzOat' panel. The types of data generated include:

SNP data:
- Genomic SNPs from DArTSeq SNP platform
- SNP Haplotype file combining DArTSeq SNPs 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 Oat Sang_v0 and Oat OT3098_v1 (PepsiCo) reference genomes.

Phenotype data:
1. Controlled environment (long day, long day with vernalisation, short day) conditions at Adelaide University (Scott Boden), for the complete OzOat panel.
2. Field experiments were conducted at Wagga Wagga, New South Wales (147.3°E, 35.1°S, elevation ~210 m) in 2021 and 2022. A subset of the OzOat panel were evaluated. In 2021, 80 oat genotypes were sown at two sowing dates (7 May and 2 June), and in 2022, 60 genotypes were sown at three sowing dates (14 April, 3 May, and 24 May).

Pedigree:
The Helium Pedigree Visualisation Framework (Shaw et al. 2014) was utilised to view over 1000 international accessions spanning diversity relevant to the history of Australian oat breeding. From this list, 319 oat lines were selected to form the OzOat panel. A Helium-compatible csv file contains all known ancestors for these 1000 oat accessions, lines selected for inclusion in the OzOat panel are highlighted in green. Pedigrees were obtained from the “Pedigrees of Oat Lines” POOL database (Tinker and Deyl, 2005), from Fitzsimmons et al. (1983) and directly from oat breeders (Dr Pamela Zwer and Dr Bruce Winter, personal communication).

Fitzsimmons, R. W., Roberts, G. L., and Wrigley, C. W. (1983). Australian Oat varieties (Melbourne: CSIRO Publishing). doi: 10.1071/9780643105447
Shaw, P. D., Graham, M., Kennedy, J., Milne, I., and Marshall, DF (2014). Helium: visualization of large scale plant pedigrees. BMC Bioinf. 15, 259. doi: 10.1186/1471-2105-15-259
Tinker, N. A., and Deyl, J. K. (2005). A curated internet database of oat pedigrees. Crop Sci. 45, 2269–2272. doi: 10.2135/cropsci2004.0687