A Climate-Smart Canadian Wheat Cluster for a Productive and Profitable Canadian Wheat Sector: Activity 12 – A collaborative approach to genomic selection in winter wheat to accelerate improvement of complex traits

Objectives:

• To create a set of common genomic selection (GS) tools to enhance the capacity of breeding programs to rapidly develop climate-resilient winter wheat varieties that protect the environment and fit the domestic and export market for Canadian eastern soft red (CESRW) and hard red (CEHRW) classes.
• To establish a framework to facilitate the exchange of data and germplasm between winter wheat breeding programs, to be used in conjunction with common genomic selection tools to promote more efficient collaboration among breeding programs.

Impacts:

• The implementation of these new tools will mean the more rapid development of high-yielding, disease-resistant, quality winter wheat varieties for eastern Canada that can stand up to the challenges of climate change.
• The increased collaboration between the participating public winter wheat breeding programs will increase efficiency in breeding efforts across the region, ensuring that more beneficial traits can be integrated into the next generation of varieties.

Scientific Summary:

Genomic selection (GS) is a plant breeding strategy that makes use of next-generation sequencing (NGS) technologies to generate genome-wide genotyping data of breeding lines that are then used to derive mathematical models to estimate the breeding values of traits. In contrast to marker-assisted selection (MAS), it is well suited to predict complex traits that are quantitative in nature and strongly affected by environment. By predicting the performance of lines or crosses with genomic information, the implementation of GS into wheat variety development programs can significantly improve the rate of genetic gain (the increase in performance that is achieved per cycle) – recent studies have demonstrated increases from 20-300%, depending on the trait. GS is therefore a very promising strategy to accelerate genetic improvement of many complex traits that limit the production of winter wheat in Eastern Canada, such as yield, winter survival, lodging, and Fusarium head blight (FHB) resistance. While GS has gained acceptance within many breeding programs, one often overlooked outcome is the promotion of germplasm sharing between programs, achieved by identifying promising material for a new environment or purpose, especially to adapt to climate change and reduce greenhouse gases (GHG).

Our project proposes to develop a uniform GS methodology that could be easily implemented across the four Eastern Canadian winter wheat public breeding programs (University of Guelph (UG)-Guelph, UG-Ridgetown, Agriculture & Agri-Food Canada (AAFC)-Ottawa, CÉROM) to predict complex traits of interest to growers (yield, FHB resistance, winter survival, grain quality, straw strength) and, in doing so, facilitate and accelerate the exchange of germplasm between programs and avoid overlaps. Our primary objective will be to create of a set of common genomic selection tools to enhance the capacity of breeding programs to develop climate-resilient winter wheat varieties for the domestic and export markets of soft red (CESRW) and hard red (CEHRW) classes. To ensure these tools can be used to their full potential, a secondary objective is to establish a framework to facilitate the exchange of data and germplasm between winter wheat breeding programs to promote more efficient collaboration in that sphere.

To achieve this, each participating program will select a population (training set) representative of their germplasm pool to be genotyped using genotyping-by-sequencing (GBS), a highly efficient NGS-based technology for wheat. A bioinformatic pipeline will be optimized for the generation of high-quality single nucleotide polymorphism (SNP) marker data from those sets. Existing phenotypic data from the participating programs will be capitalized upon to develop GS models for each of the individual program sets and then be cross-validated using a 4/5-fold scheme (wherein 80% of the panel is used to predict the remaining 20%). Meanwhile, new high-quality phenotype data for agronomic, Fusarium, and end-use quality data will be generated in a series of trials across four sites in Ontario and Québec, so that lines from all programs can be evaluated across many environments. With this new phenotypic data, new global models can be developed and optimized to generate genomic-estimated breeding values (GEBVs) for all genotyped material for each target environment. These models, as well as the bioinformatic tools, will be made available to all participating programs via an online portal, so that each participating program can access, update and improve them with new data, continuously improving their ability to select for the complex traits that are essential for the success of winter wheat producers and the entire value chain.

This project will have meaningful long-term impacts on the cereal sector in Eastern Canada, as new high-yielding, disease-resistant, stress-tolerant cultivars will be more profitable and enticing to producers and increase the supply of locally produced grain for end users. Aside from profitability, increased winter wheat acreage will have significant positive effects on soil quality, reduce erosion, break diseases cycles, and increase carbon sequestration. Winter wheat is currently underutilized in eastern Canada, falling behind in acreage to corn and soybeans, and it is critical that variety development keep pace with producers’ needs and a changing climate. A genomics-enhanced collaborative approach to selection will enhance the speed and flexibility at which breeding programs can react to new challenges, bringing increased resiliency to the sector. The future of variety development in a changing world may well depend on the timely manner with which we embrace genomics technologies and use it to share our collective resources. We believe our project will ensure a brighter future for wheat producers across Eastern Canada.

External Funding Partners:

This activity was funded in part by the Government of Canada under the Sustainable Canadian Agricultural Partnership’s AgriScience Program, with industry support from the Canadian Field Crop Research Alliance (CFCRA). Grain Farmers of Ontario is a founding member of the CFCRA.