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

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  

Objectives:

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

a) Targeted use when making crosses using materials with a known allelic composition for the trait of interest, which is resistance to soybean cyst nematode (SCN) and white mold (WM). This enables identification of authentic hybridizations as opposed to seed being the result of seed obtained through self-pollination of the parent, enabling the breeding program to focus on seed generated through authentic hybridizations.

b) 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-resistance breeding objectives.

  • Economic benefit: The drastic reduction in the number of plants missing 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.

Impacts:

  • 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 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 because 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 aimed to develop a paradigm shift whereby 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 made in the previous winter arrive in Canada, from Costa Rica, annually at the F3: 4 seed stage, typically in early May of each year. 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 led to selection of F4 plants that could be susceptible to SCN or WM.

Currently, a high discrepancy is present between breeding programs in the commercial (private) and public seed sectors. Over the last few decades, private breeding programs 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 aimed to have an exclusive budget for carrying out marker-assisted selection earlier in the program, at F4 generation. This allowed 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 saved time and resources that would otherwise have been spent on growing plant materials without much promise to develop superior disease resistant cultivars.

Results:

This project achieved both objectives outlined above. 62 crosses were made using SCN resistant parents hybridized with high yielding, high-quality food grade soybean parents and 10 crosses were made between partially resistant parents to WM and high yielding and high-quality food grade soybean parents.

The progeny of the above crosses were subjected to single seed descent for two generations in Costa Rica over the past two years to produce F4 and F5 generations for selection. A total of 4010 F5 single rows were tested for agronomic traits in the field in Woodstock, ON, in 2023. The visually-selected 654 rows (based on agronomic appearance) were sampled for marker assisted selection (MAS) using two in-house developed KASP markers SCN 1-2 and SCN 4-2 to determine the presence of the resistance allele at the Rhg1 locus along with the copy number (SCN 4-2) for the resistance gene. From these, 298 F5 recombinant inbred lines (RILs) were selected from as many rows to be tested for yield and agronomic traits in Preliminary Yield Trials at F6 generation in Woodstock and Elora, ON, in 2024.

In addition, eight populations from the third year of crossing under the project were selected for MAS using KASP markers SCN 1-2 and SCN 2-4 as single selected F4 plants. From the total of 1,967 single F4 plants, we selected 986 that carried the resistant marker allele at the Rhg1 locus. These plants were threshed separately and will be grown in single F5 rows in the field at Woodstock, ON, in 2024, for agronomic assessment and selection.

Out of 11 crosses made for WM resistance, we grew 281 F5 rows in 2023. The crosses included WM resistant parents, such as PI 391589B (WM), P1603148 (WM) and Maple Donovan crossed to elite high-yielding parents. From these F5 rows, we visually selected 128 based on their agronomic performance in the field to be grown as F6 lines in the Preliminary Yield Trials plots at Woodstock and Elora in 2024. The entries will be subjected to MAS for the presence of a major WM resistance on Chromosome 1, which explains approximately 50% of the phenotypic variation for the trait. In addition, since some of the crosses also included SCN resistant parents, the progeny was subjected to MAS for SCN resistance on top of WM resistance. The results allowed us to select a total of 134 WM resistant F5 RILs, 37 WM and SCN resistant RILs and 8 SCN resistant only RILs. All these selected RILs will be tested as F6 RILs in the Preliminary Yield Trials in the field in Woodstock and Elora in 2024.

This project has allowed the soybean breeding program at the University of Guelph, Guelph Campus to increase the efficiency of MAS for the development of high yielding, high-quality SCN and WM resistant food grade soybean cultivars for Ontario soybean growers.

External Funding Partners:

The project was funded in part by the Ontario Agri-Food Innovation Alliance, Tier 1 grant.