Functional characterization of cis-regulatory variation underlying trait diversity in maize

• Applicant: Thomas Hartwig, Ph.D.
• Subject Area: Plant Genetics and Genomics
• Term: since 2021
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 458854361

Natural variation has enormous potential for trait enhancement in crops. However, most of the functional variation localizes to non-gene coding regions, making it difficult to pinpoint beneficial alleles. One of the most successful approaches to do so are genome-wide association studies (GWAS). However, they usually lack the resolution to identify the polymorphism that actually causes the difference in phenotype and fail to reveal the underlying molecular mechanism. This proposal aims to advance our understanding of how non-coding polymorphisms affect phenotypes in maize. For this goal, we propose an approach we name F1-mediated identification of non-coding cis-element-impacting SNPs (FIND-CIS). The idea behind FIND-CIS is to identify functional polymorphisms by their ability to affect the binding of transcription factors (TFs). Instead of performing FIND-CIS in different inbred lines, we use the F1 generation to compare diverse genomes and quantify the effect polymorphisms have on TF binding. We also propose a bioinformatic analysis to distinguish causal and non-causal variation. As a proof of concept we plan to apply the FIND-CIS approach to the drought stress response in maize. The goal is to better understand how variation affects the drought response in maize and to identify targets for future genome editing approaches to ultimately develop more tolerant varieties.

• DFG Programme: Research Grants