Single-cell and spatial transcriptomics reveal the regulatory continuum from initial substrates to storage compounds...

Area of Science:

• Plant Biology
• Genomics
• Developmental Biology

Background:

• Wheat grain development is crucial for yield and quality but involves complex interactions between maternal and filial tissues.
• Understanding the regulatory mechanisms requires methods that capture both cellular identity and spatial information.

Purpose of the Study:

• To create a high-resolution spatiotemporal atlas of wheat grain development at the milk stage.
• To dissect the regulatory architecture of wheat grain development by integrating single-nucleus and spatial transcriptomics.

Main Methods:

• Integration of single-nucleus RNA sequencing (snRNA-seq) and spatial transcriptomics.
• Construction of a spatiotemporal atlas of wheat grain development at 25 days after flowering (DAF).

Main Results:

• Resolved 13 transcriptionally and spatially distinct cell populations within the wheat grain.
• Uncovered pervasive subgenome-biased transcription, with significant B subgenome dominance in grain tissues.
• Identified stage-specific maternal-filial communication and hormone signaling crosstalk (auxin, ABA, GA).
• Discovered NAC transcription factors as key regulators of storage metabolism, programmed cell death, and grain maturation.

Conclusions:

• The integration of snRNA-seq and spatial transcriptomics is powerful for resolving regulatory complexity in polyploid crop organs.
• This study provides a foundational resource for understanding wheat grain development and enhancing crop yield and quality.