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

SUMMARY 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.