Integrative analysis of the CLE gene family identifies GhTDIF and GhCLE14 as key regulators of cotton fiber secondary cell wall thickening.

Clavata3/embryo surrounding region-related (CLE) signaling peptides constitute a family of small peptides that play pivotal roles in plant growth and development as well as in responses to environmental cues, serving as key regulators of cell proliferation and differentiation across diverse plants. In this study, we conduct a genome-wide characterization of CLE genes in Gossypium hirsutum and identify two CLE genes highly expressed during the cotton fiber secondary wall thickening stage: GhTDIF and GhCLE14. Silencing of the GhCLE genes results in abnormal leaf morphology. Histological sectioning reveals a significant reduction in xylem cell number within leaf veins. Furthermore, mature fibers from silenced lines exhibit shortened length, reduced fiber twists, thinner cell walls, and decreased crystalline cellulose content. The expression of secondary cell wall (SCW) cellulose synthase genes ( GhCesAs) and the SCW biosynthesis-associated transcription factor GhMYB46_D13 is significantly downregulated in the silenced lines. Collectively, our findings demonstrate that GhCLE peptides play critical regulatory roles during cotton fiber development. This work not only expands the transcriptional regulatory network underlying CLE-mediated control of cotton fiber SCW biosynthesis but also provides a theoretical basis for the potential application of exogenous CLE peptides to improve fiber quality.