Leveraging natural diversity to discover SNP effects on promoter function

Overview

This innovative research leverages natural genetic variation in maize to directly link SNP variants identified through Genome-Wide Association Studies (GWAS) with changes in gene expression and subsequent phenotypic outcomes. By utilizing the high-quality genomic resources available in maize, the project aims to demonstrate the predictive power of associating specific SNPs with gene expression changes. The approach involves testing regulatory sequence variants using transient expression systems and measuring gene expression differences through RNA sequencing. This methodology promises to uncover novel regulatory mechanisms and provides a pathway for precision manipulation of gene expression in major crops.

Technical specifications

• Utilization of GWAS: Identifies SNP variants affecting promoter regions, particularly those associated with leaf morphology.
• Transient Expression Systems: Utilizes N. benthamiana and maize protoplasts to test the effects of SNPs on promoter function using a fluorescent ratiometric reporter system.
• CRISPR-Edited Lines: Top candidate SNPs will be tested by creating CRISPR-edited maize lines and phenotyping seedling leaf dimensions.
• RNA Sequencing: Measures differential gene expression in planta to correlate with transient expression results and infer gene network responses.

Technology readiness level

This research is currently at Technology Readiness Level 3, with experimental proof of concept demonstrated through initial GWAS analysis and transient expression testing. Future validation includes further experimental testing and CRISPR editing to solidify the link between SNPs and phenotypic changes.