Single-cell transcriptome atlas reveals somatic cell embryogenic differentiation features during regeneration.

Area of Science:

• Plant biotechnology
• Developmental biology
• Genomics

Background:

• Somatic cell totipotency is crucial for plant regeneration but challenging to study.
• Somatic embryogenesis (SE) in plants offers a model for understanding cell totipotency.
• Identifying cell identity and gene regulation during SE is complex.

Purpose of the Study:

• To define the cellular landscape of cotton (Gossypium hirsutum L.) during embryogenic differentiation.
• To reveal gene regulatory mechanisms underlying somatic cell totipotency.
• To identify novel marker genes for plant regeneration.

Main Methods:

• High-throughput single-cell RNA sequencing (scRNA-seq) was employed.
• Bioinformatic analyses including RNA velocity and Scissor were used.
• Cotton (Gossypium hirsutum L.) nonembryogenic and primary embryogenic calli were analyzed.

Main Results:

• Four broad cell populations and six distinct clusters were identified in cotton calli.
• Specific cell clusters and states were enriched in nonembryogenic and embryogenic tissues.
• Energy metabolism, signal transduction, and transcription factors were enriched in embryogenic cells.
• The SE-ASSOCIATED LIPID TRANSFER PROTEIN (SELTP) gene was identified as a quantitative marker for embryogenic states.

Conclusions:

• This study provides a detailed cellular taxonomy and trajectory atlas for somatic cell differentiation in cotton.
• Novel marker genes, including SELTP, were identified for plant regeneration.
• The findings advance the understanding of somatic cell totipotency and gene regulation in plants.