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Andrew Leakey's Laboratory

An Integrated Phenomics Approach to Identifying the Genetic Basis for Maize Root Structure and Control of Plant Nutrient Relations

PI: Christopher Topp (Danforth Plant Science Center)

CoPIs: Andrew Leakey (University of Illinois), Ivan Baxter (USDA-ARS)

Funding Source:  NSF / Danforth Plant Science Center

Twitter LogoProject twitter feed: @rootsinthefield

Realizing the enormous potential of root systems to boost and stabilize crop yields under stress and to reduce unsustainable levels of fertilizer use will require a thorough understanding of their genetics and physiology. Image based phenotyping has enabled high-throughput and accurate measurements of roots, but despite an expansive list of new and promising methods, each has inherent tradeoffs that greatly limited their individual power to connect genotype to phenotype. Our proposed work brings to bear an integrated root phenomic and physiological profiling approach to resolve the genetic basis and functional consequences of maize root architecture in powerful genetic resources. We will profile the root architecture of two maize populations in four complementary ways: 3D imaging of young plants in a gel based system, optical and X-ray based imaging of root crowns excavated from the field, and minirhizotron imaging of roots growing across the entire soil profile in the field. Quantitative genetic analyses from each of these methods combined with RNA-Seq will allow us to identify the genetic loci controlling these traits including candidate genes. Additionally, this integrated analysis of identical genotypes and, with the exception of gel imaging, identical field plots, will generate the most comprehensive comparison of root phenotyping methods to date. One population will be selected from screening of the NAM parent lines in the first two years of the project, the other population will be the Illinois Protein Strain Recombinant Inbreds (IPSRIs). Over five years, this approach will address the following aims: 

1. Identify genes driving phenotypic variation of root architecture. Root architecture QTL will be identified using four experimental approaches and compared in two maize populations with high genetic resolution. Candidate gene identification will be supported by RNA-Seq analysis and validated using existing transposon-tagging lines, or through transgenic overexpression/RNAi lines;

2. Identify genes controlling phenotypic plasticity of root architecture to nitrogen supply. Root plasticity, or growth conditioned by the environment, allows a plant to fine tune its architecture based on changing resource availabilities. We will identify and characterize parent lines from the Maize NAM population that differ in their nitrogen plasticity response from the hub parent B73. By profiling the corresponding RIL population and the IPSRIs for the root traits in a high/low nitrogen contrast field environment we will be able to genetically pinpoint the root architecture response to nitrogen availability. 

3. Determine the functional impacts of root architecture on plant nitrogen status, elemental content and seed quality.  We will use several different techniques to analyze the functional consequences of different root architectures on whole plant physiology. Elemental profiling will be used to analyze the ability of the plant to take up mineral nutrients. We will also profile amino acids, seed protein, and oil levels and selected lines will be grown in larger plots to analyze total plant N and nitrogen use efficiency

This proposal represents the first large-scale multi-modality root phenotyping experiment to detect QTL and will build important bridges linking disparate bodies of literature concerning root architecture. On the technological side, the activities proposed here will develop, refine, and integrate phenomics methodologies spanning lab to field. On the biological side, we will generate links between root traits in the field and their functional consequences for nutrient uptake and whole plant physiology. Concurrently, we will probe deeply the genetic basis of these traits to identify genes and develop a better understanding about how plants control root growth and function.

Ultimately, this research could lead to improvements in our ability to grow plants with fewer nutrient inputs and reduce the environmental costs of agriculture. Our proposed educational activities are collectively designed to help plug “leaks” at a number of key educational stages.  The program will include (1) an ASPB-funded outreach program at an Urbana middle school that will also be expanded to a St. Louis middle school; (2) research opportunities for high school and undergraduate students and (3) a DIY phenomics and 3D printing workshop for high school ‘Maker’ groups in St. Louis.