About This Theme

The advent of high-throughput advanced imaging modalities has yielded new opportunities to gather structural and functional data from plants.

This research will develop applications for advanced imaging technologies to relate phenotype to genotype, exploring the uses of:

  • X-ray for in-line phase contrast, fluorescence imaging, absorption spectroscopy, and subtraction imaging;
  • Positron emission tomography (PET) using molecular tracers; and
  • Mass spectrometry (MS) of plant tissues.

Through integration and collaboration with Theme 3, methods will be developed for gathering information and determining how the resulting data can be correlated with the allelic variation captured in genomic databases.

Project 2.1
Application of Advanced Imaging Technologies to Relate Phenotype to Genotype

A great deal is known about crop genetics, however, how this genetic information is linked to plant phenotypes and performance is largely unknown. The goal of this research is to develop linkages between genotype and phenotype through imaging to help deliver the superior phenotypic performance and adaptibility needed to meet global food demand. 

This research will answer the question of how advanced imaging methods can accelerate marker development and enhance the design of superior plant varieties, working in collaboration with Theme 1 researchers. Through the adaption of existing methods and the development of new imaging technologies, synchrotron imaging, spectroscopy, X-rays, and PET-based imaging will be used to unlock novel phenotypic information about live and intact plant structures and interactions of soil-root systems.

Individual project sub-themes, each working with different imaging technologies, will develop methods for the physical imaging and compositional analyses needed to discover and describe the genetic materials that will provide breeders with improved field performance. The structural and functional biomolecular markers of different plant genotypes will be used to develop a structure-function-genome model, a novel and rapid method of identifying traits targeted for specific crop performance. Chemical tools, such as Abscisic acid analogs, will be developed to affect abiotic stress responses and link the physiological responses of plants to their related genetic expressions.

Project Leads
Sue Abrams
Chris Phenix
Chithra Karunakaran
Derek Peak

Project 2.2
In Situ Phenotypic Characterization of Plants

In collaboration with international robotics centres of excellence, this project will use a 'phenomobile', a field-based high-throughput mobile phenotyping platform with a novel navigation system and an array of integrated field sensors, for the rapid assessment of multiple quantitative plant traits. A key concept for this research is to integrate streams of data from multiple adaptable sensors, working under different environmental scenarios, to increase both the accuracy and number of traits that can be quantified for field-grown plants.

Proximal sensing tools and GPS referencing will be integrated to utilize mobile platforms that are low cost, flexible, and applicable to contrasting crop species. The field platform will be customized and tested in a laboratory setting and evaluated in crop breeding nurseries in Saskatchewan.

The proposed sensor unit is comprised of a front-end reconfigurable platform including multiple field sensors that are capable of measuring key phenotypic traits of the selected crops. The objective is to collect data related to the selected traits on a regular basis (daily, weekly, or some combination with frequency and time of the day to be determined) so that unique digital signatures with time correlation can be extracted from the data. The developed sensor systems and algorithms will be applied to examine multiple quantitative traits with focus on wheat, canola, and lentils.

Project Leads
Reza Fotouhi
Aryan Saadat Mehr

Project 2.3
High-Throughput Data Acquisition for 3D Structural Imaging and Characterization of Plant Phenotypes

Many of the available imaging techniques are not designed for high-throughput data acquisition. This project will work to identify which current technologies have the most promise and which have the greatest limitations to evaluate how limitations might be resolved using next generation technologies. Imaging above and below ground requires directed, intense beams of diagnostic radiation with optimized detectors and software. We will assess the potential of laser-based betatron x-rays and neutron beams for high-throughput 3D structural imaging and characterization of plant phenotypes.

This project capitalizes on the unique Betatron Beam Line (BBL) operated at the Advanced Laser Light Source (ALLC) facility and a team of experts at INRS to optimize imaging parameters and design a dedicated imaging system. Our neutron effort relies on expertise and methods under development at the Canadian Neutron Beam Centre (CNBC) at Canadian Nuclear Laboratories (CNL).

Project Leads
Emil Hallin
Jean-Claude Kieffer
Kishor Wasan