Phenotyping SoyMAGIC population to uncover genetic control of drought tolerance

Objectives:

• Modify and expand the existing controlled environment phenotyping apparatus to 528 experimental units, so that 264 lines can be phenotyped simultaneously (under both water-replete and water-limited conditions).
• Complete single nucleotide polymorphism (SNP) sequencing of SoyMAGIC recombinant inbred lines (RILs).
• Complete drought tolerance phenotyping of 528 recombinant inbred lines chosen from the SoyMAGIC population.
• Use SNP-based genome wide association study (sGWAS) and IBD-based haplotype GWAS (hGWAS) quantitative trait locus (QTL) discovery methods to identify genomic regions underlying the traits associated with drought tolerance.

Impacts:

• Improved soybean genetics for drought tolerance.
• Accelerated development and commercial release of new superior soybean cultivars resilient to drought stress.
• The genomic toolkits to be created through this project will be invaluable for expediting the breeding process.

Scientific Summary:

Soil water deficits constitute a major limitation to soybean productivity in Ontario. Although yield losses due to drought stress vary greatly from year to year and even over short geographic distances within a year, a conservative estimate is that soybean growers just in Ontario’s ten southern-most counties lose about $190M in a typical year to drought-related yield loss. While water limitations will always suppress yields to some extent, breeding regionally-adapted drought-tolerant varieties is a promising strategy for reducing those losses. To do this using modern breeding approaches, it is necessary to identify regions of the soybean genome that control drought tolerance, which requires the phenotyping of hundreds of lines for which genotypic information is also available. Measuring “drought tolerance” of a line can be difficult and expensive to do, since i) applying and precisely controlling defined levels of soil water deficits is technically very challenging, and ii) assessing agronomically-relevant drought tolerance requires growing plants right through their life cycle so that yield and yield components can be measured.  

These technical challenges have recently been addressed through the development of a novel, low-cost and scalable controlled environment technique for maintaining precisely defined levels of soil water deficits in pot experiments. It has been shown to induce soybean responses to drought stress that are similar to those observed in the field and can be scaled up to permit low-cost phenotyping of hundreds of lines simultaneously. We will use this method to measure effects of drought stress on biomass, yield and yield components of 528 lines from the SoyMAGIC (multi-parent advanced generation intercross) population and then use different GWAS (genome-wide association study) approaches to discover genomic regions underlying the traits associated with drought tolerance. 

Using the SoyMAGIC population to identify drought-tolerant germplasm and discover durable genomic regions controlling variation in drought tolerance will allow the University of Guelph Ridgetown soybean breeding program to accelerate the development and commercial release of new superior cultivars resilient to drought stress.

External Funding Partners:

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

Natural Sciences and Engineering Research Council of Canada (NSERC)

Syngenta