Comparative proteomic analysis reveals the mechanisms governing cotton fiber differentiation and initiation

► We compared the ovule proteomes of wild-type and fiberless mutant (fl) during fiber differentiation and initiation in cotton. ► The fl proteome is consistent with increased ROS generation, decreased stress response and lowered ROS scavenging capability. ► ROS homeostasis may be a central regulatory mechanism for cotton fiber morphogenesis. ► Post-transcriptional and post-translational regulation may be pivotal in this process. ► Carbohydrate metabolism, starch accumulation and the content of some carbohydrates were lower in fl mutant than in WT.