About This Theme

Plant breeding links the traits (phenotypes) of individual plants with the differences between the DNA sequences (genotypes) of the individuals in order to select plants for breeding that may more reliably produce desirable traits in subsequent generations.

The phenometrics theme utilizes existing germplasm collections, both at the U of S and with P2IRC's partners, in combination with elegantly successful experimental designs developed for each crop, new precision phenotyping approaches, and characterizations of the phytomicrobiomes of leaves, roots, and rhizospheres.

Theme 2 will answer the question: how well are multi-scale digital phenotypic traits linked to genetic loci in target crops? We will incorporate the unique imaging capabilities of theme 2 with the power of theme 3's advanced computing resources to dissect genetically complex traits and transform our ability to breed crop plants by design.

Project 1.1
Arabidopsis Proof of Concept

Phenotype to Genotype in a Model System

The availability of a deep knowledge base and extensive genomic resources for the model plant Arabidopsis thaliana provides an ideal environment for researchers to develop new techniques and test new concepts prior to their applications in other species including crops such as canola, a close relative.

The availability of novel imaging technologies for phenotypic characterization of plants under controlled conditions now presents an opportunity for researchers to apply the efficiency of working in Arabidopsis thaliana to precisely investigate key biological phenomena that have profound impacts on crop traits.

This proposal will serve as a hypothesis-testing program to link phenotype to genotype, capitalizing on the depth of Arabidopsis thaliana sequence data, germplasm resources, and extensive phenotyping of mutants.

Project Lead
Isobel Parkin

Project 1.2
Crop Phenometrics Platform

Leveraging Field Phenomics for Advancing Key Rotational Crops

Supplying food for a growing population while increasing yield under changing climatic conditions requires improvement to selection efficiency in plant breeding.

This research will develop methodologies to acquire and process high-resolution imagery for wheat, canola, and lentil, which will be used to develop digital phenotypes that correlate with adaption and environmental stresses. Fifty diverse lines of each crop will be phenotyped for three seasons through the use of high-resolution ground and aerial imaging.

Digital data will be processed by the novel analysis algorithms developed by project 3.2 to create unique digital phenotypes (UDPs). Eventually, UDPs from large nested association mapping panels (>2500 lines/crop) will be associated with genomic regions and aid in complex trait dissection and integration with genomic selection models.

P2IRC's new image-based field phenotyping methodology will be used to replace and supplement current manual field phenotyping to the effect of greatly improving plant breeding efficiency.

Project Leads
Steve Shirtliffe
Scott Noble

Project 1.3
Plant Pedological Phenotype

The Soil Microbiome as a Plant Phenotype

This research will help crop breeders to identify the microbial communities and their associated characteristics that improve crop yields. The microbial communities corresponding with the roots of different wheat, canola, and lentil genotypes will be studied. Using the DNA extracted from these roots, specific microbes and whole microbiomes will be identified and correlated with highly yielding crop lines.

Project 1.3 research will link imagery of above and below ground plant physiologies with unique identifiers of their microbial communities and root chemistries to gain insight into associated crop performance metrics. P2IRC's field-based research will be complimented by this project's use of rhizoboxes and advanced imaging techniques to discretely focus on the mechanisms that plants utilize to interact with their microbial partners.

By understanding these unique identifiers and microbiomes as they relate to different crop genotypes, we will provide crop breeders around the world with targets that they can use to inform their designer breeding approaches in developing the next generations of wheat, canola, and lentil crops.

Project Leads
Steven Siciliano
Bobbi Helgason