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Marker assisted breeding for SCN and white mould at University of Guelph soybean breeding program

Principal Investigator: Istvan Rajcan

Research Institution: University of Guelph

Timeline: April 2021 – March 2024  


  1. Targeted marker assisted selection in the significant bottlenecks in the soybean breeding process. This will be achieved by:

a) First, making crosses using materials with a known allelic composition for the trait of interest (soybean cyst nematode (SCN) and white mold (WM) resistance) to ascertain authentic hybridizations were performed as opposed to the seed being the result of seed obtained through self-pollination of the parent.

b) Second, using SCN and WM resistance markers to genotype F4 populations, with a focus on culling the plants and lines that do not contain gene(s) for disease-resistant breeding objectives.

  • Economic benefit. The drastic reduction in the number of plants containing the resistant alleles allows us to focus our efforts and resources only on the plants and progeny that hold the most promise for the traits of interest, such as SCN and WM resistance combined with high yield and seed quality in the new food-grade soybean varieties.


  • The use of high throughput marker assisted selection (MAS) for resistance traits of two major diseases, soybean cyst nematode and white mould, will facilitate the development of improved novel food grade soybean cultivars. The cultivars will have a better yield protection than was previously possible due to having been selected by MAS for disease resistance traits. This in turn will allow for a more environmentally sustainable soybean production in Ontario as a result of reduced losses in yield due to the major diseases, SCN and WM, and less use of pesticides, especially in the case of WM.

Scientific Summary:

This project aims to develop a paradigm shift whereas the selection of materials containing resistance genes will be entirely controlled by molecular markers used on F4 single plants. The University of Guelph uses a nursery in Costa Rica, Central America, to advance breeding materials from F2 to F4 generation. The University of Guelph’s populations from crosses done in previous winter arrive in Canada, from Costa Rica, annually at the F3: 4 seed stage typically in late April. The latter seeds are planted at the Woodstock station, where phenotypic selection occurs on a single individual plant basis for characteristics such as visual agronomic performance, maturity, number of pods per plant and absence of disease and lodging. The presence of resistance genes in the materials has not been used as a discriminating factor, which leads to selection of F4 plants that may end up being susceptible to SCN or WM.

A high discrepancy is currently present between breeding programs in the commercial (private) and public seed sectors. Over the last few decades, private breeding programs have added steps to their production chain and allocated budgets to allow genetic screening in their breeding program annually, making extensive use of MAS. The project aims at having an exclusive budget for carrying out marker-assisted selection earlier in the program, at F4 generation. This would allow us to select only the plants that carry the resistance alleles and discard the plants without any resistance to SCN and WM, which would not be useful for cultivar development. By focusing on the desired plants early on, we would save time and resources that would otherwise have to be spent on growing plant materials without much promise to develop superior disease resistant cultivars.

External Funding Partners:

The project was funded in part by the Ontario Agri-Food Innovation Alliance, a collaboration between the government of Ontario and the University of Guelph.