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Genome composition due to long-term selection by soybean breeders

Principal Investigator: Istvan Rajcan

Research Institution: University of Guelph

Timeline: December 2013 – December 2017

Objectives:

  • Determine the changes in the soybean genome due to long-term breeder selection.
  • Develop molecular-based strategies that can be applied to facilitate the development of new and improved soybean cultivars with maximum genetic potential to be used in a public and private soybean breeding program.

 Impacts:

  • The determination of different genes contributing to high productivity/yield in Canadian soybeans coming from different parent sources may lead to improved soybean cultivars with maximum genetic potential to be commercially available.
  • The understanding of genetic control of seed compositional traits such as oil, protein, isoflavones and fatty acids will allow for the development of breeding strategies for their further improvement.
  • An assessment of the genetic diversity in Canadian soybean germplasm developed over 50 years of breeding will help to determine genetic vulnerability due to a narrow gene pool.

Scientific Summary:

The value of Canadian soybeans is over $1 billion annually. Soybean breeding in Canada began at the University of Guelph in the 1920’s. Since then, soybean production has enjoyed tremendous expansion throughout Canada, initially from mainly Ontario and now well into Quebec and western Canada. The continued improvement of soybean cultivars relies on sufficient genetic variation between parents to produce progeny variable for traits of interest upon which improvement can be made. As phenotypic variation is positively associated with genetic diversity, it is important for a soybean breeding program to maintain a sufficient level of genetic diversity for continued genetic gain resulting in development of commercial cultivars. In addition, developing soybean cultivars for niche markets has been an important objective for Canadian soybean breeders. Therefore, genetic diversity for yield and value-added traits, such as food grade quality or nutraceutical compounds, is essential. Recent advancements in genomic technologies provide unprecedented capabilities in investigating genome changes in soybean, especially for relevant traits.

By applying genomic technologies to pedigrees of a breeding program, the specific changes in the soybean genome due to long-term breeder selection can be studied. By genotyping the members of a pedigree, changes in genetic diversity over generations of breeding activity can be characterized. In addition to the overall effects of selection, specific genomic changes known as “signatures of selection” can also be detected. The selection signatures appear to be frequent in genomic regions controlling traits of agronomic importance. An improved understanding of the factors involved in breeding for most important traits in soybean and development of genomics tools that will facilitate it will help to maintain Ontario soybean growers’ competitiveness by further enhancing genetic gains in yield and other important traits.

The research project focused on a comprehensive investigation into the genomic landscape of two commercially successful public soybean breeding programs. This was done to gain insight into how long term selection within the programs has affected (or if it has affected) the ability to make future gains in variety development for Canadian producers. Through both multi-location field trials and the latest in genomic technologies, significant findings into how the genome has been modified by breeder selection have been uncovered. Important parameters associated with plant breeding were studied such as genetic diversity, selection, genotype-phenotype associations and long-term changes in various trait values. The results have shown that there were significant changes in traits targeted for improvement by the breeding programs. In addition, the specific transmission of genes/alleles over multiple generations is now known. The results from the research now serve as a platform for new tools for Canadian soybean variety development and improvement. This will continue to create excellent opportunities for Canadian seed companies to build their business and export seeds from Canada to increase the profits and benefits to their own business and that of Canada.

Funding Partners:

Huron Commodities Inc.

National Sciences and Engineering Research Council of Canada’s Collaborative Research and Development program (NSERC-CRD)

SeCan

Project Related Publications:

Bruce, R.W., Torkamaneh, D., Grainger, C.M., Belzile, F., Eskandari, M. and I. Rajcan. 2020. Haplotype diversity underlying quantitative traits in Canadian soybean breeding Germplasm. Theor. Appl. Genetics 133:1967–1976.

Bruce, R., Torkamaneh, D., Grainger, C., Belzile, F., Eskandari, M., and I. Rajcan. 2019. Genome-wide genetic diversity is maintained through decades of soybean breeding. Theor. Appl. Gen. 132:3089–3100.

Bruce, R., Grainger, C., Ficht, A. Eskandar, M. and I. Rajcan. 2019. Trends in Soybean Trait Improvement over Generations of Selective Breeding. Crop Sci. Crop Sci. 59: 1870-1879.

Bruce, R., Grainger, C., Torkamaneh, D., Belzile, F., Eskandari, M., and I. Rajcan. 2018. Analysis of historical genetic diversity in the University of Guelph soybean breeding programs. Poster. Plant and Animal Genome Conference XXIV, San Diego, CA, USA, January 13 to 17, 2018.

Ficht, A. and I. Rajcan. 2018. Genetic analysis of sucrose concentration in soybean using genotyping-by- sequencing. Poster. Plant and Animal Genome Conference XXIV, San Diego, CA, USA, January 13 to 17, 2018.

Bruce, R., Grainger, C., Torkamaneh, D., Belzile, F., Eskandari, M., and I.Rajcan. 2016. A pedigree-based germplasm panel for assessing genomic change in a public soybean breeding program. Poster presented at Soy2016: 16th Biennial Conference of the Molecular and Cellular Biology of the Soybean. August 7th to 10th, 2016. Columbus, OH, USA.

Rajcan, I. 2016. Soybean Breeding in Canada: Value-added and genomics perspectives. INVITED TALK. INTA, Cordoba, Cordoba, Argentina, February 12th, 2016.

Rajcan, I. 2016. Soybean Breeding in Canada: Value-added and genomics perspectives. INVITED TALK. INTA, Parana, Entre Rios, Argentina, February 11th, 2016.

Rajcan, I. 2016. Soybean Breeding from Value-added and Genomics Perspectives. INVITED TALK. EMBRAPA SOJA, Londrina, Parana, Brazil, February 8th, 2016.

Bruce, R., Grainger, C., Eskandari, M., and I. Rajcan. 2016. Genetic and Phenotypic Diversity of a Public Soybean Breeding Program. Poster. Plant and Animal Genome Conference XXIV, San Diego, CA, USA, January 9 – 13, 2016.

Rajcan, I. 2015. Soybean Breeding from Value-added and Genomics Perspectives. INVITED TALK. Universität für Bodenkultur Wien (Vienna Agricultural University), Department für Nutzpflanzen- wissenschaften, Vienna, Austria, November 18, 2015.

Bruce, R., Grainger, C.M., Rajcan, I. and M. Eskandari. 2014. Dynamics of genomic change and marker- trait associations in two soybean breeding programs at the University of Guelph. ASA-CSSA-SSSA International Annual Meeting, Long Beach, CA, USA, Nov. 2-5, 2014.

Bruce, R., Grainger, C.M., Eskandari, M., and I. Rajcan. 2014. Dynamics of genomic change and marker- trait associations in two soybean breeding programs at the University of Guelph. Soy 2014, 15th Biennial Conference of Molecular & Cellular Biology of the Soybean, Minneapolis, MN, USA, August 3-6, 2014.

Grainger, C.M, Bruce, R., Eskandari, M, and I. Rajcan. 2014. Integrating Genomics into a Public Plant Breeding Program using a Pedigree-Based Approach. Soy 2014, Minneapolis, MN, USA, August 3-6, 2014.

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