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Canadian Field Crop Genetics Improvement Cluster, Activity 6: Breeding soybeans for adaptation to environment and emerging pests and concurrent development of molecular marker selection tools: Development of high yielding early maturity soybeans

Principal Investigator: Louise O’Donoughue

Research Institution: CEROM

Timeline: April 2013 – March 2018


  • Develop soybean cultivars, mostly for animal feed, adapted to maturity group (MG) 00 and less.
  • Characterize the genetic basis of maturity in eastern Canadian soybean germplasm.
  • Develop molecular marker selection tools to manipulate genes in the breeding program.
  • Evaluate a new genomic selection strategy for yield and early maturity.


  • Advances in sequencing and genotyping technologies to identify earliness (E) genes allows researchers to select for these genes before the field season begins.
  • Using the new marker selection strategy called genomic selection researchers can now assess traits, such as yield, to aid in breeding very early maturity soybeans thereby helping to address the negative relationship between yield and maturity.
  • By implementing the use of new selection tools in soybean breeding programs researchers are now able to more efficiently breed for early maturity, high yielding soybeans.
  • As a result of a better understanding of genetics and selection tools, soybean breeders can respond faster to emerging issues in soybeans to produce varieties adapted to current and potential growing regions in Canada.

Scientific Summary:

Many areas of Canada have suitable conditions for soybean production, but are hindered by the lack of very early, short season varieties. Eastern and northern Quebec, northern Ontario, Manitoba and the Maritimes are key areas where soybean production is a possibility.

Selecting soybeans for early maturity is currently done by phenotypic selection after plants are mature. Advances in sequencing and genotyping technologies means soybean lines can now be characterized by earliness (E) genes using markers to select for these genes before the field season begins.

The recent development of a new marker strategy called genomic selection, which can assess traits like yield, may hold promise for breeding very early maturity soybeans and address the negative relationship between yield and maturity.

This research project looked at the rapid integration of new selection tools into practical soybean breeding programs, leading to more efficient breeding for very early maturity, high yielding soybean varieties. A better understanding of the genetic basis for maturity in soybeans, and the development of selection tools to allow breeders to respond more quickly to emerging issues will help breeders produce varieties adapted to all existing and potential soybean growing regions in Canada.

Developing very early maturity soybeans also has the potential to open new markets and opportunities for farmers across Canada and allow for diversified crop rotations in short season environments.


Variety development:

There are several combinations of genes that can lead to early maturity or short season soybean cultivars, and this project looked for gene combinations that are better suited to different environments (soil, climate).

Five advanced lines have been tested in Quebec provincial trials (MG 000 to 00), three of the lines were also tested in Manitoba. Three new early maturity soybean cultivars are expected to be available for commercial registration in 2018.

Genetic characterization:

The full eastern Canadian soybean gene collection (100 lines, four Egenes) was characterized and the early parental collection for E1 to E4 loci was completed. One of the key findings of this project was that some early maturity genes have been underutilized in the Canadian gene pool. Loci have also been identified that were not previously reported for maturity, flowering and time to pod filling. These new loci will be studied further under the Genome Canada Soyagen project.

New selection tools:

A fully equipped marker assisted selection/molecular biology lab, including a liquid handling robot, has been developed as part of this project. A haploid typing tool was also developed through this project that streamlines the characterization of gene collections – reviewing Canadian and global gene banks for genotypic data that will help make faster selections for early maturity breeding programs.

Genomic selection:

After discovering the prediction model intended for this project was less than optimal, this research objective was changed. From two target populations in Quebec, 200 previously genotyped lines were randomly selected, and phenotypic data was collected on yield, maturity, flowering time, seed weight, and oil and protein content. Phenotypic and genotypic data are being used to evaluate the efficiency of different prediction models. Results are expected after the field season of 2018.


In characterizing existing early maturity genes in the Canadian gene pool, researchers discovered some sources of early maturity soybean genes that hadn’t been used or were underutilized in current breeding programs, and some germplasm has been exchanged with Agriculture and Agri-Food Canada researchers. Another surprising discovery was finding early maturing loci in the global gene bank that were previously unknown.

Two advanced soybean lines have been identified that performed well and were superior to checks over two years of testing in Quebec and Manitoba, and if there is commercial interest in these lines they will be registered and licensed for commercialization.

Additional Opportunities:

This Growing Forward 2 activity has already been leveraged through the Genome Canada Soyagen project to build on this breeding work.

The results of this project in eastern Canada can be adapted and are useful for other environments across the country to develop material suitable for growing conditions in western Canada. Some of the early maturity gene combinations identified under this project are now being grown in eight environments across Canada (Quebec, Ontario, Manitoba and Saskatchewan) to verify if some of them are suited to other environments in Canada.

External Funding Partners:

This research activity was part of the Canadian Field Crop Genetics Improvement Cluster led by the Canadian Field Crop Research Alliance (CFCRA).

Funding for this project was provided in part by Agriculture and Agri-Food Canada through the Growing Forward 2 (GF2) AgriInnovation Program and in part by CFCRA members. Grain Farmers of Ontario is a founding member of the CFCRA.

Project Related Publications:

Copley, T.R., Duceppe, M.O. and O’Donoughue, L. 2018. Identification of novel loci associated with maturity and yield traits in early maturity soybean plant introduction lines. BMC Genomics 19(1):167.

Tardivel A., Sonah H., Belzile F., and O’Donoughue, L. 2014. Rapid identification of alleles at the soybean maturity gene E3 using genotyping by sequencing and a haplotype-based approach. The Plant Genome (10): 3835.

Torkamaneh, D. and Belzile, F. 2015. Scanning and Filling: Ultra-Dense SNP genotyping combining genotyping-by-sequencing, SNP array and whole-genome resequencing data. PLOS ONE (10): 1371.