Leon V. Kochian
USDA-ARS

I. Introduction
In the introduction slides, I will talk about how terrestrial plants must adapt to their soil environment, as they cannot move and thus must deal with the sometimes harsh soil environment in which they must grow. Will mention adaption to drought, insufficient mineral nutrients, and excesses of minerals and metals in the soil that reach toxic levels. There is a significant level of variation and genetic control for these plant responses to soil-based abiotic stresses and will show one or more well-known examples such as aluminum (Al) tolerance in crop plants.
II. Role of Root System Architecture in Crop Adaptation to Marginal Soils
1.Will talk about the growing awareness by crop scientists that the spatial distribution of roots in the soil, a trait called root system architecture (RSA), plays an important role in many root-based plant traits such as efficient acquisition of limiting mineral nutrients and water. 2.Plants need to place their roots within the soil profile where they can do the most good, and the ability of plants to do this is genetically controlled. 3.Will show recent examples of work in this field to improve crop adaptation to low P soils and maybe for water acquisition under drought.
III. The application and integration of advances in genetic mapping with crop genomics and physiology research.
1.Will talk about the power of integrating genome-wide and traditional QTL mapping approaches with molecular and physiological research in this area. 2.Will briefly explain genome-wide association mapping, where one phenotypes a “diversity” panel of your favorite crop species for your trait of interest (such as drought tolerance or tolerance to low P). The panel is also genotyped with many thousands of markers. Sophisticated statistical approaches are then used to identify discrete regions of the crop plant’s genome where QTL important for variation in the trait of interests exist and are due to specific genes. It is then possible to sometimes clone the genes underlying variation in that trait.
IV. Kochian Lab’s Research on Root System Architecture in Rice
1.Describe the rice diversity panel we use for genome-wide association mapping. 2.Introduce Randy’s RootReader 2D system. How we grow the plants, photograph the roots, and computationally analyze the root images. 3.Show example of genome-wide association analysis of rice Al tolerance. 4.Then describe in much more detail the RootReader 3D system. Show how we grow the plants in the gellan gum-nutrient media cylinders. Then describe how we image the roots, and use RootReader 3D to analyze the images and reconstruct the many 2D images of a specific root system into the 3D root system model. Then describe how the software automatically calculates 19 different root traits for each root system 3D reconstruction. 5.Show the results from both genome-wide association mapping of our rice diversity panel described above and also QTL mapping using a bi-parental mapping containing ~170 recombinant inbred lines (RILs), for the 19 RSA traits. 6.Describe in more detail several interesting QTL for root traits that may be important for water uptake under drought conditions and P uptake in a low P soil and how we will be analyzing these TL to clone the gene underlying the QTL and see if the root traits contribute to drought tolerance or P efficiency (tolerance to low P soil conditions). 7.Finish up with our new hydroponic-based 3D RSA plant growth system developed primarily by Jon Shaff. Involves growing plants in glass cylinders containing nutrient solution with a specially-made colored plastic mesh system. Show how we can grow rice, maize, sorghum or any plant species in this system, image the root systems growing through the mesh, and then computationally remove the images of the mesh and supports form the mesh, leavening the root system image for reconstruction of 3D RSA. See photos left. 8.Describe the advantages of this hydroponic-system: a) can grow any plant species in this system as some crop species don’t grow well in the gel; b) Can significantly increase the size of the growth cylinders thus allowing us to grow older plants; c) can impose stresses more easily like P or N deficiency.