Genomic basis of root phenotypes for improved nitrogen acquisition in maize
Research collaboration to identify transposable elements (TEs) that regulate root growth angle and nitrogen acquisition efficiency in maize. The project seeks partners to support sequencing, personnel, and phenotyping equipment for a one-year validation study using contrasting maize genotypes.
Overview
This research program investigates how transposable elements (TEs) in the maize genome influence root growth angle and nitrogen (N) acquisition efficiency. By identifying nitrogen-responsive TEs, the project aims to uncover novel genomic targets for breeding maize varieties with improved nitrogen capture and reduced fertilizer requirements. The work addresses a critical agricultural challenge: reducing nitrogen runoff from heavily fertilized systems, such as those in the Midwestern U.S., while maintaining crop productivity. The project is seeking partnership support for sequencing costs, key personnel, and phenotyping equipment to advance the validation phase.
Technical specifications
Research approach:
- RNA sequencing of two maize genotypes with contrasting root architectures: B73 (steep-angled roots) and M162W (shallow-angled roots)
- Transcriptome analysis at four timepoints following exposure to high and low nitrogen conditions
- Validation of promising nitrogen-responsive TE candidates using a field-grown population of 200 B73xM162W progeny
- Integration of transcriptomic data with root phenotypic measurements to link TE activity to nitrogen acquisition traits
Scientific basis:
- Prior analysis of published RNA libraries identified 506 down-regulated and 684 up-regulated TEs under variable nitrogen conditions
- Differentially expressed TEs located near differentially expressed genes suggest direct regulatory relationships influencing root phenotypes
- TEs are stress-responsive and can modulate activity of nearby genes, inducing phenotypic changes relevant to nutrient acquisition
Technology readiness level
The project is currently at the hypothesis-validation stage. Preliminary evidence from mining publicly available RNA sequencing libraries supports the role of TEs in nitrogen-responsive gene regulation. The proposed one-year validation study will use controlled nitrogen treatments and field-based phenotyping to confirm candidate TEs and their phenotypic effects. The research is positioned to generate actionable genomic targets for maize breeding programs aimed at improving nitrogen use efficiency and reducing agricultural environmental impact.
About Iowa State University
Iowa State University is a large, comprehensive public land‑grant research university based in Ames, known for combining fundamental discovery with translational, industry‑relevant work. Companies collaborate through a research and technology park that co‑locates corporate R&D with faculty labs and startups, creating steady talent pipelines. Pilot‑scale facilities, field test sites, and a statewide extension network support prototyping, validation, and deployment with partners across the region. Research is supported by competitive federal funding, including awards from NSF, USDA, and DOE. A dedicated technology transfer office and affiliated research foundation streamline IP, licensing, and startup formation, with incubator space on site.
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