Spatial transcriptome and single-cell RNA sequencing reveal the molecular basis of cotton fiber initiation development

Plant J. 2025 Mar;121(6):e70064. doi: 10.1111/tpj.70064.

Abstract

Recent advances in single-cell transcriptomics have greatly expanded our knowledge of plant development and cellular responses. However, analyzing fiber cell differentiation in plants, particularly in cotton, remains a complex challenge. A spatial transcriptomic map of ovule from -1 DPA, 0 DPA, and 1 DPA in cotton was successfully constructed, which helps to explain the important role of sucrose synthesis and lipid metabolism during early fiber development. Additionally, single-cell RNA sequencing (scRNA-seq) further highlighted the cellular heterogeneity and identified clusters of fiber developmental marker genes. Integration of spatial and scRNA-seq data unveiled key genes SVB and SVBL involved in fiber initiation, suggesting functional redundancy between them. These findings provide a detailed molecular landscape of cotton fiber development, offering valuable insights for enhancing lint yield.

Keywords: Gossypium hirsutum L; SVB; SVBL; fiber differentiation; single‐cell transcriptomics; spatial transcriptome.

MeSH terms

  • Cotton Fiber*
  • Gene Expression Profiling
  • Gene Expression Regulation, Plant
  • Gossypium* / genetics
  • Gossypium* / growth & development
  • Gossypium* / metabolism
  • Ovule / genetics
  • Ovule / growth & development
  • Plant Proteins / genetics
  • Plant Proteins / metabolism
  • Sequence Analysis, RNA
  • Single-Cell Analysis
  • Transcriptome* / genetics

Substances

  • Plant Proteins