Systematic analysis of the Aux/IAA gene family in pineapple reveals insights into their structural diversity, expression dynamics, and interaction networks

The Aux/IAA protein is integral to the modulation of auxin signaling, which is essential for plant growth and development. However, systematic analysis on the Aux/IAA gene family in pineapple (Ananas comosus L.) remains unexplored. We systematically identified 20 AcAux/IAA genes in pineapple, classifying them into eight evolutionary groups. Structural analysis revealed conserved domains (I-IV) and intron-exon patterns, with most genes harboring hormone/stress-responsive cis-elements. Subcellular localization confirmed nuclear targeting of all AcIAA-GFP fusion proteins. Tissue-specific expression profiling identified AcIAA1/6/19 as root-enriched, AcIAA2/8 as floral-specific, and AcIAA7 as leaf-preferential. During fruit development, AcIAA9/17–19 peaked at ripening stage, while AcIAA1/3–4/6/11–12/15 declined progressively. Yeast two-hybrid assays uncovered 68 AcIAA-AcARF interactions, with AcARF6/14 showing broad binding capacity, while AcIAA1/17/20 exhibited no interactions. These findings present insights into pineapple Aux/IAA genes, revealing their structural diversity, spatiotemporal expression dynamics, and interaction networks with AcARFs, and highlight their potential roles in organ development and fruit ripening. This study establishes a foundation for future functional analyses aimed at elucidating the molecular mechanisms underlying auxin signaling, which governs fruit yield and quality in pineapples.