Integrating physiology and transcriptomics reveals the mechanisms underlying the differences in cotton ( Gossypium hirsutum L.) growth and development under different photoperiods

Photoperiod is a crucial environmental factor that regulates plant growth and flowering. While the photoperiodic flowering pathway has been extensively studied, the mechanisms underlying photoperiodic regulation of cotton ( Gossypium hirsutum L.) growth and development remain unclear. In this study, we selected different genotypes of cotton varieties, XJ12 and XJ21-11, to investigate the effects of long-day (LD) and short-day (SD) conditions on cotton photosynthesis, dry matter accumulation, flowering time, and related gene expression, utilizing physiological index measurements, transcriptomics, and WGCNA analysis. The results indicated that LD treatment significantly enhanced photosynthetic parameters and dry matter weight in both cotton varieties, with the net photosynthetic rate (Pn) being 154.79% and 111.86% higher under LD compared to SD treatment. Additionally, the flowering time of the two varieties was advanced by 12 and 13 days, respectively, under LD treatment relative to SD treatment. LD conditions promoted gene expression in sucrose and starch metabolism, facilitating cotton growth. Furthermore, LD inhibited the expression of genes associated with flavonoid biosynthesis, thereby altering the secondary metabolism of cotton, and activated transcription factors through signaling pathways (including phytohormone signaling and MAPK signaling pathways) and biological clock rhythms, which induced earlier flowering in cotton. This study provides new insights into the molecular mechanism of the effect of photoperiod on cotton growth and development.