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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #402116

Research Project: Mapping Crop Genome Functions for Biology-Enabled Germplasm Improvement

Location: Plant, Soil and Nutrition Research

Title: Direct and predicted motif analysis of GRAS family transcription factors in sorghum and other important crop species

item Gladman, Nicholas
item KUMARI, SUNITA - Cold Spring Harbor Laboratory
item FAHEY, AUDREY - Cold Spring Harbor Laboratory
item REGULSKI, MICHAEL - Cold Spring Harbor Laboratory
item Ware, Doreen

Submitted to: Maize Genetics Conference Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: 3/16/2023
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Identifying non-coding regions that control gene expression has become an essential aspect of understanding gene regulatory networks that can play a role in crop improvements such as crop manipulation, stress response, and plant evolution. Recently, the expansion of high-quality reference genomes and chromatin profiling techniques have opened up direct and comparative accounting of transcription factor (TF) binding locations that could modulate proximal or distal gene expression. While a full complement of open chromatin, epigenetic, and TF-binding experiments provide information for likely candidate regulatory regions, using TF-binding approaches such as ChIP-seq or DAP-seq can provide additional valuable insight and targets for reverse genetic approaches such as EMS-induced or natural SNP variant screens or CRISPR editing techniques (e.g. promoter bashing). Here, we present the first ever DAP-seq profiles of three GRAS family TFs (SHR, SCL23, and SLC3) in the agriculturally important crop Sorghum bicolor. The binding location of the three GRAS TFs display unique and shared gene targets and categories of previously-characterized DNA-binding motifs as well as novel sequences that could potentially be GRAS family-specific recognition motifs and have been associated with gametogenesis, floral development, light signaling, hormone signaling, and root development. These results provide unique insight into the GRAS family of TFs and novel regulatory targets for further molecular characterization. This project was funded by the USDA-ARS award number 8062-21000-044-000D.