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Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

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Published on: March 12, 2021

Decoding crops one cell at a time: from cell atlases to single-cell genetics.

Hao Zhang¹, Robert J Schmitz¹

¹Department of Genetics, University of Georgia, Athens, GA 30602, USA.

Journal of Experimental Botany

|November 25, 2025

Summary

Single-cell and spatial transcriptomics reveal plant cell expression dynamics, aiding crop trait discovery. These technologies help identify genetic variants for improved crop traits by analyzing gene expression at the cellular level.

Keywords:

cellular heterogeneity cellular perturbation crops single-cell RNA-seq single-cell genetic screening spatial transcriptomics

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Area of Science:

Plant biology
Genomics
Agricultural science

Background:

Understanding crop traits is crucial for agriculture.
Technological advances are key to agricultural research.
Cellular heterogeneity and gene expression dynamics are vital for trait development.

Purpose of the Study:

To explore the application of single-cell and spatial transcriptomics in crop improvement.
To identify how specific cell types contribute to agricultural traits.
To accelerate the discovery of genetic variants for enhanced crop traits.

Main Methods:

Single-cell transcriptomics
Spatial transcriptomics
Integration with trait-associated loci
Analysis of cellular perturbations

Main Results:

Revealed tissue heterogeneity and spatial organization in plants.
Provided insights into cellular gene expression dynamics.
Enabled high-throughput discovery of genotype-gene expression relationships at the cellular level.

Conclusions:

Single-cell and spatial transcriptomics accelerate crop improvement by enabling detailed gene function studies.
These technologies allow for causal interrogation of sequence functions and regulatory networks at cell-type resolution.
Overcoming technical and biological barriers is essential for widespread application in plants.