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User Stories

User Story 1 – Identifying virus resistant PGRs using Pretzel

Overview of Key Steps To Visualise Results in Pretzel

  1. Project genetic map QTL into Cameor v1 genome assembly

  2. Integrate genes and KASP markers

  3. Identify sbm-1 gene with BLAST search

  4. Examine WGS genotypes around the sbm-1 gene to identify haplotype shared by resistant accessions

  5. Identify Multispecies Pulse 30K SNP array marker(s) that tag the haplotype

  6. Examine PGRs from the AGG using the identified marker(s) to identify PGRs likely carrying the PSbMV resistance allele

User Story 2 - Filtering AGG wheat accessions for stripe rust resistance gene Yr34/Yr48

In this User Story we will achieve the following in Prezel:

  1. Explore and compare Yellow Rust QTLs on chromosome 5A from Cheng at al. 2024 and Tong et al. 2024 (a meta study collecting QTLs from many other studies) defined in different versions of the wheat genome reference assembly (IWGSC RefSeq v1.0 and IWGSC RefSeq v2.1)

  2. Identify the Yr34/Yr48 region of 5AL based on results in Qureshi et al. 2018

  3. Define the Wheat Barley 40K SNP array haplotype carried by wheat accession WAWHT2046 (AGG accession: AGG91389WHEA), the original accession where Yr34 was discovered in Bariana et al. 2006, in the Yr34/Yr48 region

  4. Filter for AGG accessions matching the Yr34/Yr48 haplotype

User Story 3 - From SSRs to pan genomes with Pretzel: Two decades of wheat yield QTLs on chromosome 7A

There are three main parts to this User Story:

  • In the first part, we will learn how to navigate the wheat pan genome in Pretzel, and visualise some well known results such as the 5B/7B translocation in ArinaLrFor and SY Mattis as well as the Thinopyrum ponticum introgression in LongReach Lancer at the end of 3DL.

  • In the second part, we will briefly summarise results from the last 20 years around yield on chromosome 7A. We will use Pretzel to integrate a range of QTL studies and ultimately identify the WAPO1 gene.

  • Finally, we will combine the first two parts to:

    • Reproduce results reported in Kuzay et al. 2019 and Voss-Fels et al. 2019 relating to haplotypes carried by the 10+ Wheat Genomes in the WAPO1 region of chromosome 7A;
    • Extend these results to classify wheat PGR accessions in the AGG;
    • Identify wheat PGR accessions in the AGG carrying rare haplotypes in the WAPO1 region.

Details for all publications cited are listed in the references.