Nitrogen inputs can be an important cost consideration for farmers in terms of economic profit as well as environmental impact. Elucidating genetic regions that are associated with plant phenotype response to nitrogen stress can help in facilitating breeding approaches that can mitigate these costs. A diverse population of 272 maize lines was planted at a field site in Champaign, IL in two consecutive years in reduced nitrogen conditions. 302 phenotypes were recorded including: seed ionomic content, root structural traits derived from 2-dimensional images as well as a 3-dimensional representation generated from x-ray computed tomography (XRT) scans, root traits extrapolated from mini-rhizotron systems, drone images across the growing season and end of season agronomic traits such as biomass and yield. BLUP models were fit to obtain estimates of single year genotypic values as well as across years values both of which took into account year specific spatial variation. Individual years and combined years BLUP values were used as response variables in genome wide association studies (GWAS) to identify loci significantly associated with each set of values. Significant associations were identified for all phenotype categories.

Roots are the interface between the plant and the soil and play a central role in multiple ecosystem processes. With intensification of agricultural practices, rhizosphere processes are being disrupted and are causing degradation of the physical, chemical, and biotic properties of soil. Improvement of ecosystem service performance is rarely considered as a breeding trait due to the complexities and challenges of belowground evaluation. Advancements in root phenotyping and genetic tools are critical in accelerating ecosystem service improvement in cover crops. Here I will present root phenotyping approaches for assessing ecosystem service in a prospective cash cover crop; pennycress (Thlaspi arvense L.). In development is a large format mesocosm system that will allow 3D root system architecture analysis of multiple plants. Using this system, we will be assessing how variation in pennycress root system architecture can affect ecosystem service and abiotic stress tolerance with the plant to scale from single plant to canopy level traits.

The symbiosis between crops and arbuscular mycorrhizal fungi (AMF) have become an attractive route towards achieving carbon neutral agriculture and reducing the use of chemical fertilizers. Yet, our understanding of how active AMF infections influence the uptake, allocation, and exchange of carbon is limited. Here, we combine X-ray CT and PET imaging to observe and quantify the flow of carbon from leaves to roots to hyphae. Comparison of maize grown with and without AMF allows us to measure changes in the amount of 11CO2 taken up in leaves and subsequently the amount of 11C allocated to below-ground roots. Then, co-registered CT and PET images are used to identify hot spots which may indicate active AMF infection sites. Finally, analysis of 11C kinetics at these hot spots are used to assess the amount of carbon exchanged between maize roots and hyphae. By combining structural and biochemical information, we begin to deepen our understanding of the different types of changes in carbon flow in Maize-AMF systems and how we can improve sustainable agriculture efforts.