A comprehensive identification and function analysis of the ATBS1 Interacting Factors (AIFs) gene family of Gossypium species in fiber development and under multiple stresses

•GhAIFs are highly expressed in the initiation and elongation phases of the fibers.•Exogenous hormones can significantly induce GhAIFs expression.•The majority of GhAIFs actively respond to cold stress.•GhAIFs were more abundantly expressed in cold resistant than sensitive materials. ATBS1 INTERACTING FACTORs (AIFs) are atypical basic helix-loop-helix (bHLH) proteins play important roles in the growth and development of plants. There are no comprehensive reports on the genomic identification and functional analysis of AIFs in cotton. In this study, 8, 11, 16, and 15 AIFs were identified in Gossypium arboreum L., Gossypium raimondii L., Gossypium hirsutum L., and Gossypium barbadense L., respectively. AIFs were also screened in other species: 3 in Theobroma cacao L., 4 in Populus trichocarpa C. and 5 in Zea mays L. Based on a neighbour-joining phylogenetic tree, 66 AIF proteins identified in these species were divided into 3 groups. Multiple sequence alignment analysis showed that the AIF protein sequences were relatively conserved. Analysis of gene chromosome position and gene replication showed that AIFs amplification in cotton might be due to fragment and tandem replication. And cold stress response and plant hormone cis-elements were identified in the promoter regions of GhAIFs. Published transcriptional data showed that GhAIFs were differentially expressed in various tissues, especially in floral organs and fibers. qRT-PCR results showed that most of GhAIFs were highly expressed at the fiber initiation stage. Analysis of the expression of selected GhAIFs under abiotic stress (GA, IAA, SA, ABA, and 4 °C treatment) suggested that GhAIFs might be involved in the regulation of abiotic stress. The comprehensive analysis of the AIF gene family in upland cotton provides a foundation for further studies on the function of atypical bHLH-GhAIFs family members and screening of fiber development, and stress-resistant candidate genes in cotton.