Genomics & molecular marker assisted mapping approach to identify disease resistance genes in flax

Posted on 27.07.2018 | Last Modified 26.07.2023
Lead Researcher (PI): Helen Booker
Institution: University of Saskatchewan
Total WGRF Funding: $374,471
Co-Funders: Agriculture Development Fund
Start Date: 2017
Project Length: 5 Years

To develop genomics and molecular marker tools to improve the efficiency of flax breeding for disease resistance (pasmo, fusarium wilt, powdery mildew) and to address breeding bottlenecks impacting flax improvement.

Project Summary:

A total of 105 accessions were selected for pasmo resistance from the screening of more than 3,400 accessions available at the Plant Genetic Resource Canada (PGRC) collections. Crosses were made between the best pasmo resistant accessions and an advanced CDC breeding line. Recombinant inbred populations (RILs) were developed following a modified speed breeding approach to accelerate generation advancement under controlled conditions. Introgression of the resistance into current cultivars is in progress.

A QTL-sequence analysis pipeline was developed and updated. The pipeline was published in a scientific journal ( The pipeline including its user guide is publicly available on GitHub ( This guide includes a description of the pipeline, installation instructions, a step-by-step guide to use the pipeline, and examples of the output. The usefulness of the new pipeline was demonstrated in Aurore × Adelie (AA), Aurore x Oliver (AO), and Bison x Novelty (BNv) recombinant inbred line (RIL) populations that allowed the identification of loci associated with fusarium wilt and powdery mildew resistance.

QTL analyses using the GBS-SNP data and 703 RILs of BNv population using both JoinMap and MapQTL confirmed the presence of a single major QTL located at 4 Mbp of Chr1. Two additional QTL each explaining 3% of the variability for wilt resistance were identified on Chr8 and Chr14, with several minor QTLs located on other chromosomes. These results were consistent using the mean disease scores over the three timepoints taken each year from Morden (2019) and Saskatoon (2019 and 2020) as well as the summed disease scores for each year. These results strongly support a major QTL for FW resistance in Bison on Chr1.

Additional assessments of the BNv population for reaction to fusarium wilt were completed in 2022 at the AAFC-Morden and Saskatoon wilt nurseries. Results from 2019, 2020 and 2022 showed the consistency of the reaction of the RILs and the checks to fusarium wilt. The assessments also identified transgressive segregants within the RILs in all environments. Several RILs were identified that consistently had scores lower than the resistant check regardless of the environments. These RILs are potential sources for improvement of resistance to fusarium wilt in the flax cultivars.

Evaluation of the RWP8 locus associated with powdery mildew resistance in the AA and AO RIL populations was completed. Initially, we identified that the locus contained two clusters of tandemly repeated genes with a high level of homology to the Arabidopsis RPW8 genes. One cluster contained two genes while the other contained three genes. Further investigation, however, led us to believe that the two clusters are haplotypes; Adelie having a single cluster containing three genes (Lus10000834.g, Lus10000835.g, and Lus10000836.g) and Aurore and CDC Bethune having a single cluster with two genes (Lus10009328.g and Lus10009329.g). Different approaches including Oxford Nanopore technology to sequence this region in Adelie and Aurore were completed. The results confirmed the presence of at least one gene from each haplotype in all cultivars. The sequencing results indicated the absence of some key genes in Adelie that may be responsible for its resistance to powdery mildew.

Key Messages:

  • Identified accessions and inbred lines with improved resistance to pasmo, fusarium wilt and powdery mildew for use in flax breeding for genetic improvement of disease resistance.
  • Development of an improved QTL-seq pipeline that is user friendly and can be used by researchers globally to identify loci and genes associated with important traits in different populations.
  • Developed DNA markers associated with reaction to fusarium wilt and powdery mildew allowing for assisted selection for disease resistance in the breeding program.
  • Identified potential gene and genetic mechanism leading to resistance to powdery mildew in flax.