Objective
1. Assemble available large scale public multiomic datasets for canola and wheat from local, national and international efforts.
2. Develop a new Integrated Multiomic Platform (IMP) data interface focused on fast and intuitive visualization tools to enable easy interpretation and interaction with the integrated data sets in both crops.
3. Generate high throughput transcriptome data (RNA-Seq) from planned field trials of wheat and canola diversity panels (250 lines each, including NAM founder lines).
4. Carry out TWAS (transcriptome-wide association study) and integrate with existing GWAS (genome-wide) studies and other multiomic data sets available in IMP to identify highly resolved QTLs and eQTLs associated with trains of interest.
5. Generate high throughput transcriptome data from field trials of selected NAM subpopulations (chosen based on output from Obj 4) for validation of QTLs and eQTLs and assemble catalogues of candidate genes impacting traits of interest.
Project Description
The ‘Identification and exploitation of genome structural variants (SVs) for trait improvement in Prairie crops’ (ADF20200117 – co-funded by SODC) project led by GIFS has successfully spent the last four years developing resources to establish the range of SVs that exists within canola and wheat germplasm. Circa 2020 this variation had been identified as an important feature of plant genomes, underlying multiple key agronomic traits, but somewhat neglected because of difficulty in accurately identifying SVs with short-read data and existing software tools. The project used state-of-the-art long-read sequencing technology in the Omics and Precision Analytics Laboratory at GIFS and new bioinformatics tools supported by the Data Management and Analytics platform also at GIFS, to enable routine and accurate identification of SVs with a comparatively low-cost approach and identified functional variants contributing to multiple phenotypes such as adaptation, disease resistance, and other crop improvement traits. There now exists an opportunity to build upon the outputs from the SV project that will formally ended May 31st 2025 and to fill an information gap within the Canadian canola and wheat breeding research communities. The gap is not so much a lack of ‘omics data for these crops but rather the ability to access it in a coherent and intuitive fashion. Therefore, we propose to build a new Integrated Multiomic Platform (IMP) for canola and wheat, with a focus on developing a high-performance public portal interface for the representation and visualization of a large array of multiomic data sets now available for these crops, including those generated from the SV project as well as other local, national and international efforts. Lack of tools to readily interrogate these data sets in an integrated fashion limits their practical application to breeding programs and creates an immediate risk to rapid variety development for two of the most important crops for Saskatchewan and Canada. The project will make use of the existing significant experience within GIFS and USask delivering portals for accessing and representing data both internally and externally for a variety of different needs to develop the IMP. This experience includes:
1) Sequencing Information Management System (SIMS) that enables internal and external clients to access sequence datasets generated by the OPAL platform at GIFS/ view metrics about the data and download it in a secure fashion.
2) Breeding Acceleration platform that enables researchers to shorten the breeding cycle in crop and livestock breeding programs through the application of genomic selection, speed breeding and genomic modelling.
