Genome-wide identification reveals the regulatory roles of the TATA-box binding protein associated factor (TAF) gene family in cotton oil accumulation

Abstract TBP-associated factors (TAFs), along with the TATA-box binding protein (TBP), com-pose transcription factor IID (TFIID), which is an essential complex for transcription initiation and regulation. TAFs are involved in regulating plant development. However, genome-wide identification and expression pattern analysis of TAFs in cotton remain unreported. In this study, a total of 124 TAF genes were identified in four Gossypium species. TAFs were divided into six subgroups based on the phylogenetic tree analysis. Analysis of collinearity and selection pressure indicated that TAF gene pairs have undergone strong purifying selection during evolution. Gene expression analysis of GhTAFs revealed that TAFs are expressed at all stages of cotton seed and fiber development. Furthermore, a set of key GhTAF genes was identified, which are specifically or constitutively highly expressed across multiple stages of cotton seed and fiber development. Based on WGCNA, we identified Ghir_D11G035840 as a candidate gene involved in lipid accumulation regulation, and further constructed a putative co-expression interaction network for this gene to elucidate its functional connections. Overexpression of Ghir_D11G035840 in Arabidopsis thaliana resulted in a significant increase in seed oil content, thereby confirming its functional role in regulating oil accumulation. Furthermore, a putative interaction network derived from the co-expression network revealed that Ghir_D11G035840 may interact with numerous genes to regulate both ovule development and lipid synthesis. These results provide valuable genetic resources and a theoretical basis for subsequent investigations into the molecular mechanisms underlying cotton seed oil synthesis and fiber quality formation using functional genomics approaches.