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The PIN-FORMED (PIN) protein, the most important polar auxin transporter, plays a critical role in the distribution of auxin and controls multiple biological processes. However, characterizations and functions of this gene family have not been identified in cotton. Here, we identified the  PIN  family in  Gossypium hirsutum ,  Gossypium arboreum , and  Gossypium raimondii . This gene family was divided into seven subgroups. A chromosomal distribution analysis showed that  GhPIN  genes were evenly distributed in eight chromosomes and that the whole genome and dispersed duplications were the main duplication events for  GhPIN  expansion. qRT-PCR analysis showed a tissue-specific expression pattern for  GhPIN . Likely due to the  cis -element variations in their promoters, transcripts of  PIN6  and  PIN8  genes from the At (tetraploid genome orginated from  G. arboreum ) subgenome and  PIN1a  from the Dt (tetraploid genome orginated from  G. raimondii ) subgenome in  G. hirsutum  was significantly increased compared to the transcripts in the diploids. The differential regulation of these  PIN  genes after the polyploidization may be conducive to fiber initiation and elongation. Exogenously applied auxin polar transport inhibitor significantly suppressed fiber growth, which is consistent with the essential function of these  PIN  genes for regulating cotton fiber development. Furthermore, the overexpression of  GhPIN1a_Dt ,  GhPIN6_At , and  GhPIN8_At  in  Arabidopsis  promoted the density and length of trichomes in leaves.

A Genome-Scale Analysis of the PIN Gene Family Reveals Its Functions in Cotton Fiber Development