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Summary  Cotton seeds are typically covered by lint and fuzz fibres. Natural ‘fuzzless’ mutants are an ideal model system for identifying genes that regulate cell initiation and elongation. Here, using a genome‐wide association study (GWAS), we identified a ~ 6.2 kb insertion, larINDEL  FZ  , located at the end of chromosome 8, composed of a ~ 5.0 kb repetitive sequence and a ~ 1.2 kb fragment translocated from chromosome 12 in fuzzless  Gossypium arboreum . The presence of larINDEL  FZ   was associated with a fuzzless seed and reduced trichome phenotypes in  G. arboreum . This distant insertion was predicted to be an enhancer, located ~ 18 kb upstream of the dominant‐repressor  GaFZ  ( Ga08G0121 ). Ectopic overexpression of  GaFZ  in  Arabidopsis thaliana  and  G. hirsutum  suggested that  GaFZ  negatively modulates fuzz and trichome development. Co‐expression and interaction analyses demonstrated that  GaFZ  might impact fuzz fibre/trichome development by repressing the expression of genes in the very‐long‐chain fatty acid elongation pathway. Thus, we identified a novel regulator of fibre/trichome development while providing insights into the importance of noncoding sequences in cotton.

Large‐fragment insertion activates gene GaFZ ( Ga08G0121 ) and is associated with the fuzz and trichome reduction in cotton ( Gossypium arboreum )