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Functional annotation revealed that the candidate genes related to fuzz initiation were significantly involved in the asparagine biosynthetic process, cell wall biosynthesis, and stress response. The expression trends of sixteen genes randomly selected from the RNA-seq data were almost consistent with the results of qRT-PCR. Our study revealed several potential candidate genes and pathways related to fuzz initiation induced by high temperature. This provides a new view of temperature-induced tissue and organ development in Gossypium barba