A spatially resolved multi-omic single-cell atlas of soybean development

Area of Science:

• Plant biology
• Genomics
• Molecular biology

Background:

• Cis-regulatory elements (CREs) are crucial for controlling gene expression.
• Understanding CREs in soybean is vital for crop improvement.

Purpose of the Study:

• To create a comprehensive atlas of gene expression and chromatin accessibility in soybean.
• To identify cell-type-specific CREs and transcription factor (TF) motifs.
• To investigate gene regulatory networks in soybean development and symbiotic nitrogen fixation.

Main Methods:

• Generation of a spatially resolved single-cell atlas of gene expression and chromatin accessibility across ten soybean tissues.
• Identification of distinct cell types and accessible chromatin regions (ACRs).
• Analysis of TF motifs enrichment and conservation in regulatory networks.

Main Results:

• Identification of 103 distinct soybean cell types and 303,199 ACRs.
• Discovery that nearly 40% of ACRs exhibit cell-type-specific patterns.
• Uncovered cell-type-specific TF motifs, developmental trajectories, and key regulators like DOF11 and a homeobox TF.

Conclusions:

• The study provides a valuable resource for analyzing gene regulatory programs in soybean.
• Identified key regulators for endosperm and embryo development, including sucrose transporters and homeobox TFs.
• Offers insights into the conservation of gene regulatory networks for nitrogen fixation in legumes.