Durable resistance to oat crown rust

Australian oat production is limited by crown rust disease caused by Puccinia coronata f. sp. avenae (Pca). This project seeks to generate resources and knowledge to advance our understanding of the disease and develop strategies to minimise yield losses to Pca.\n\n\nLineage: Description of files\n-\tDArTseq: Raw data obtained for collections of oat genotypes described in the publication Nguyen et al., 2024 (https://doi.org/10.1094/PHYTO-10-23-0353-R); and Nguyen et al., 2025 Accepted in Crop Science. Five seeds from each oat line were sent to Diversity Arrays Technology Pty Ltd. for DNA extraction and genotyping using their proprietary genome complexity reduction-based sequencing technology. To identify single nucleotide polymorphism (SNP) markers, the sequences obtained from DArTSeq were aligned against the reference genome sequence Avena sativa OT3098 v2 (PepsiCo, https://wheat.pw.usda.gov/jb?data=/ggds/oat-ot3098v2-pepsico), deposited in the GrainGenes database, using BLAST (Altschul et al. 1990) with an expected value (E) threshold of less than 5e-7 and sequence identity greater than 70%. Only markers that matched a genomic location were kept. The SNP dataset was filtered in dartR (v2.9.7) by first removing loci with all missing data, then excluding monomorphic loci to retain only polymorphic markers. A call rate filter removed loci with over 50% missing data and markers with a minor allele frequency below 0.01 were discarded. \n-\tHypoxia induced necrosis. The OzOat panel was screened for the hypoxia-induced necrosis phenotype typical of Sr2-mediated resistance. Petroleum jelly (Vaseline; Unilever) was applied with the thumb and forefinger to both sides of an ∼2-cm section of a fully expanded leaf of plants at various growth stages that were maintained in a glasshouse at 25°C during the day (16 h) and 18°C at night. Responses were monitored visually over subsequent days and scored early at ~6 weeks after sowing and late at anthesis \n-\tRaw field trial data 2023-2024. Oat lines were tested for disease resistance under field conditions (GS7 RILs, postulated carriers of Adult Plant resistance, OzOat panel). Briefly,field infection data was collected from field trials in Australia at Manjimup, WA (33.24° S, 116.16° E), in 2023 and 2024, and Cobbitty, NSW (33.99° S, 150.69° E), in 2024. Data for oat collection was recorded in Manjimup (2023) and Cobbitty (2024). In all trials, lines were planted 1-row wide x ~0.5m long. In the Manjimup trials in 2023 and 2024 (MJ23 and MJ24), rust pathotypes (triplet codes as described by Park 2000) 0001-2 and 0005-0 were used, while in the Cobbitty trial 2024 (CB24), the pathotypes “4473-4,6,10, Bett, Barc”, “0767-3,4,5,6,10,Wa,Vo”, and “3707-1,4,5,6,7,10,12,Wa,Nu,Gw,Ge,Dr,Al” were utilised. Around the flowering between Zadoks growth stage GS59 - GS80 (Zadoks et al. 1974), rust infection severity was scored using the 0-to-100 modified Cobb scale (Peterson et al. 1948) in Manjimup, whereas in Cobbitty, severity was rated on a 1–9 scale.\n-\tShort read sequencing data of Pca isolates. Genome sequencing of 137 isolates using short reads. DNA extractions for Illumina sequencing were performed with the G-Biosciences OmniPrep. Genomic DNA isolation kit using 20–40 mg of rust spores as input. Libraries were generated using either the Illumina DNA PCR-Free Prep or the IDT Prism library preparation protocol depending on sample needs. Libraries were sequenced to 15-30X depth, 150 bp paired end reads with Illumina Novaseq by Azenta or the Australian Genome Research Facility. Download available at short reads are available on NCBI under BioProject PRJNA1063754 (see Henningsen EC, et al (2024). PLoS genetics, 20(11), e1011493. https://doi.org/10.1371/journal.pgen.1011493.\n-\tVirulence profiles of collection of Pca isolates. See https://doi.org/10.1371/journal.pgen.1011