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Development of breeding strategies for organic soybean production systems in Canada

Principal Investigator: Istvan Rajcan

Research Institution: University of Guelph

Timeline: April 2018 – March 2022


  • Grow the F7, F8 and F9 breeding lines from breeding populations (crosses) that are the result of selection of organic (O) and conventional (C) farms in replicated yield trials using two O field locations in Ontario.
  • Grow selected early maturing soybean breeding lines and cultivars from the Guelph and Manitoba programs in several O locations in Manitoba.
  • Evaluate weed competitiveness, root morphology and other agronomic traits including yield in the above trials to determine the “winners” in O vs. C production systems.
  • Characterize the phenotypic traits that lead to the winning genotypes in contrasting production systems. Isolate the DNA and perform molecular analysis using single nucleotide polymorphism (SNP) markers by genotyping-by-sequencing (GBS) to characterize the genomic regions associated with yield, agronomic, morphological, and physiological traits between the O and C production systems. 


  • Results provide organic soybean growers with valuable information on the adaptation of current commercial soybean cultivars to the organic soybean production system in their fields in two provinces, Ontario and Manitoba.
  • New knowledge of the comparative genetic control of yield and agronomic traits in conventional and organic production systems. Plant breeders will benefit from knowing which regions (QTL) of soybean chromosomes determine high yield under O vs. C production systems.

Scientific Summary:

The main objective of this proposal was to build knowledge on how to efficiently develop, through plant breeding, new soybean cultivars for O growers to maximize competitiveness, efficiency, and volume of production. This was achieved by growing breeding populations of soybean that have been developed from bi-parental food grade crosses and selected in previous years on contrasting O and C farms.

For the first time in Canada, a detailed description of comparative performance of soybean cultivars grown on O vs. C production systems over several years and locations is available to the O agriculture sector. This research will also be published in peer reviewed journals for use by the wider scientific research community. The differences in the phenotypes of the same soybean cultivars and RILs between the O and C farms were studied to improve the understanding of underlying factors in agronomic performance between the two systems. Genomic regions on soybean chromosomes associated with enhanced performance on O vs. C farms were also determined to develop molecular markers that can be used for selection under each production system.


The cultivar trials were grown in Ontario in 2019, 2020 and 2021 at O and C field sites as described below. They consisted of 52 cultivars in the maturity groups 0 and 1. Only a partial data analysis of years is complete and the completed portions are outlined below.

In 2019, the cultivar trials were grown in Elora and Woodstock as the C sites and New Hamburg and Arthur, ON, as O sites. The O site in Moorefield had to be dropped due to conditions being too wet resulting in the loss of the trial. However, the data from the other locations were sound.

The 2020 C trial locations were Elora and Woodstock, and the O trial locations were planted in New Hamburg and Moorfield, ON. The field samples from the 2020 field trials were processed and analyzed. Fifty-two cultivars from the 00 to 1 maturity groups were grown in C and O environments in 2020. The purpose of these trials was to access root surface area, nodule dry mass, and yield. Root samples of each cultivar were taken using a soil core device. The samples were analyzed, and data processed in the winter of 2021. Root surface area was measured using an optical scanner, nodule mass was measured using a high-accuracy scale, and yield was determined using a scale when cultivar plots were harvested. Significant crossover effects were observed for all traits of interest between locations, location type, and cultivars, suggesting differential phenotypes obtained for traits under observation between the O and C field sites. This in turn suggests a differential gene expression between the two production systems for the group of cultivars that have been developed using only the C production system. In addition, it also indicates that there is genetic variation among individual C-developed soybean cultivars that can be used on O farms.  

Surface area and nodule dry mass was greatest in organic locations, but these traits were not correlated to yield under the conditions in this study. The yield of the cultivars showed significant cross-over effects between O and C sites in 2020. Several cultivars were identified that had stable or greater relative yield performance between the two sets of production system environments. These high-performing cultivars have value in future organic soybean breeding ventures that could develop new, novel genetic combinations that further enhance suitability in organic production systems.

In 2021, field experiments in Manitoba were planted in the eastern (Glenlea) and western (Carman) Red River Valley in Manitoba’s soybean heartland. Both locations were in O production as resources, including seed source, were limited and prevented having them in both O and C field trials. Despite extreme drought and heat, the experiments were carried out successfully, providing an excellent opportunity to evaluate soybeans under water/heat stress conditions.

In 2021 in Ontario, the cultivar trial consisting of 52 soybean cultivars was planted at two O field locations at New Hamburg and Rockwood and two C locations at Elora and Woodstock, Ontario. Despite the clean field conditions at Rockwood at the start, the weeds soon became unmanageable after crop emergence. Lacking the opportunity to control them with chemicals and having row spacing for field plots too narrow to allow for the farmer’s equipment to control the weeds mechanically resulted in this site being dropped.  The site at New Hamburg was kept in slightly better shape with fewer weeds. This allowed for biomass samples to be collected on shoots and roots from each entry. The extremely cold and wet conditions in the fall did not allow for the site to be harvested. However, the rest of the data were collected. The C sites in Elora and Woodstock were planted, managed, and harvested without an issue.

The 2021 field results showed that there was significant effect (p<0.01) of production type (O vs. C) for the following traits:

  • Leaf tissue nitrogen (N) content. The cultivars differed in their N content among themselves as well as between O vs. P environments.
  • Leaf tissue phosphorus (P) content. Cultivars significantly differed among themselves, but overall, they accumulated less P in O than in C systems (
  • Leaf potassium (K) content. While the production type was significantly different between O and C, the cultivars did not differ among themselves for K content.
  • Linkage maps have been generated using DNA markers produced by Genotyping-by-Sequencing (GBS) and will be used for QTL analysis of genomic regions associated with plant performance for different traits under observation between the O vs. C environments. It is anticipated that we will discover some O-specific QTL, some C-specific and some universal QTL for yield and other traits when comparing between the O and C environments.

The 2021 results were consistent with 2019 and 2020 for the above traits.

Seed yield of the 52 cultivars depended on the production system. Some cultivars performed better in O and others in C production systems. This is illustrated in Figure 1 showing the differential performance of cultivars between the C field sites (Elora and Woodstock) and O field sites (New Hamburg and Moorefield) in 2020 below.

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Figure 1. Cross-over effects for the yield of 52 soybean cultivars in 2020 in Ontario. Elora and WRS (Woodstock Research Station) were conventional (C) field sites and Moore (Moorefield) and NH (New Hamburg) were the O sites.

Furthermore, the results of the root biomass and nodulation traits showed a significant difference in root biomass and nodulation between the O and C production systems on the set of 52 soybean cultivars, which were bred entirely using the C production system. The root biomass and nodulation were significantly greater in O than in C.

The yield between the O and C environments significantly differed for the cultivars studied. Some cultivars seemed particularly adapted to O (OAC Acclaim, OAC Strive, DH4173, Panorama, and Tala) whereas others are better adapted to C (OAC Prodigy, OAC Ginty, S05-T6, OAC 13-O5C, OAC 13-61C-ChCdn and OAC Malory). However, there were several cultivars that showed stable adaptation and superior performance in both O and C, such as: OAC Wallace, DH530, OAC Drayton, OAC Bounty, OAC Eve and OAC Prescott. These results suggest that testing cultivars and breeding populations on organic sites may lead to the development of new soybean cultivars specifically adapted for organic production systems which can be grown by organic farmers.

Additional work with recombinant inbred line (RIL) populations allowed the study of the impact of selection under O vs. C to determine if the production system affected the selections made, and furthermore, what underlying genetics, in terms of QTL, were responsible for the differential selection. The recombinant inbred line (RIL) populations consisted of two F7 RIL populations as follows: Pop 1: 131 RIL from the cross OAC Sunny x S05-T6, and Pop 2 with 146 RIL from the cross OAC Calypso x DH618. The crosses were made under a previous project with the intent to expose them to O and C environments during selection, rather than looking at finished cultivars that were only selected after development under the C environment.

The Pop 1 and Pop 2 population trials were planted in a randomized complete block (RCB) design with 2 replications/location at 4 Ontario locations (2 O and 2 C) in 2020 as mentioned above. Data were collected on the following traits: yield, plant height, lodging, maturity, pubescence, and hilum colour. Leaf tissue samples were collected in the growth room for DNA extraction. The DNA was extracted from all the RILs and parents and shipped to IBIS institute at Laval University (Genome Quebec Lab) for genotyping-by-sequencing (GBS).

In 2021, the two RIL populations were grown at the same Ontario field locations in O and C production systems as the cultivar trials, New Hamburg and Rockwood for O and Elora and Woodstock for C. The issues experienced at the O locations (dropping Rockwood) were the same as described above for the cultivar trials. However, we were able to collect all data except for yield from the New Hamburg O location, whereas both C locations provided data for all traits under observation.

The DNA samples were sent to Genome Quebec’s lab at Laval University for Genotyping-by-Sequencing (GBS) in fall 2022 and marker data were received in January 2023. GBS data were filtered for all 285 genotypes from Pop 1 and Pop 2, including the four parental genotypes. Due to delays in getting the bioinformatics data (January 2023), the Ph.D. candidate, Mr. Xin Lu, has started to generate linkage maps only recently as the molecular data were not available until January. The GBS data will be used to map QTL for yield, agronomic and physiological traits, including root traits. The large number of samples from several field sites and 285 genotype samples in replicates has required an incredibly large number of hours to wash the roots, weigh, and image analyze them. The root trait data were collected by March 2023. During the rest of the student’s project, the phenotypic data will be overlaid on the linkage map to identify QTL that are specific to O vs. C production systems. This in turn will help to determine what genomic regions affect traits of interest the same across both production systems, O and C, or in a production-system-dependant fashion. We expect that many QTL for yield, agronomic and physiological traits will differ in the RIL populations between O and C.

External Funding Partners:

This research is part of the national Organic Science Cluster 3 program managed by the Organic Federation of Canada in collaboration with the Organic Agricultural Centre of Canada (OACC) at Dalhousie University.

Funding for this program was provided by the AgriScience Program under Agriculture and Agri-Food Canada’s Canadian Agricultural Partnership.

Manitoba Pulse and Soybean Growers

Field Farms Marketing

Organic Council of Ontario

Project Related Publications:

Isaac, ME., Nimmo, V., Gaudin, ACM., Leptin, A., Schmidt, JE., Kallenbach, CM., Martin, A., Entz, M., Carkner, M., Rajcan, I., Boyle, TD and Lu X. 2021. Crop Domestication, Root Trait Syndromes and Soil Nutrient Acquisition in Organic Agroecosystems: A Systematic Review. Front. Sustain. Food Syst. 5:716480.

Boyle, T., Najafabadi,M. Y., and Rajcan, I. 2023. Comparative assessment of early season soybean cultivars in organic and conventional production system for morphological and agronomic traits. Crop Science.63:227-247.