Genome-Wide Characterization of the Fantastic Four Gene Family Identifies TaFAF-5D.5 Associated with Growth Habit Variation in Wheat

The Fantastic Four gene family encodes small, plant-specific regulatory proteins involved in developmental control; however, their roles in wheat remain poorly understood. In this study, we conducted a comprehensive genome-wide analysis of the Fantastic Four gene family in wheat. A total of 42 TaFAF genes were identified and systematically characterized in terms of their chromosomal distribution, phylogenetic relationships, gene structures, conserved motifs, and promoter cis-regulatory elements. Phylogenetic analysis classified TaFAF genes into four distinct clades, which exhibit high structural conservation but show divergent motif compositions. Expression profiling revealed tissue-specific expression patterns and suggested that a subset of TaFAF genes responded transcriptionally to heat stress in a genotype-dependent manner. Subcellular localization assays showed that representative Fantastic Four proteins were localized in the cytoplasm. Protein–protein interaction analyses indicated that TaFAF-1A.1 and TaFAF-5D.5 physically interact with the key flowering regulator TaFT1. Furthermore, haplotype analysis of TaFAF-5D.5 across 145 wheat accessions revealed a significant association with wheat growth habit, with a favorable haplotype preferentially enriched in winter wheat. Together, these results provide insights into the evolutionary diversification and functional relevance of the Fantastic Four genes and identify TaFAF-5D.5 as a candidate gene potentially associated with developmental adaptation and heat stress responses in wheat.