Genome-wide identification of GhAAI genes reveals that GhAAI66 triggers a phase transition to induce early flowering

Plants undergo a phase transition from vegetative to reproductive development that triggers floral induction. Genes containing an AAI (alpha-amylase inhibitor) domain form a large gene family, but there have been no comprehensive analyses of this gene family in any plant species. Here, we identified 336 AAI genes from nine plant species including 122 AAI genes in cotton (Gossypium hirsutum). The AAI gene family has evolutionarily conserved amino acid residues throughout the plant kingdom. Phylogenetic analysis classified AAI genes into five major clades with significant polyploidization and showing effects of genome duplication. Our study identified 42 paralogous and 216 orthologous gene pairs resulting from segmental and whole-genome duplication, respectively, demonstrating significant contributions of gene duplication to expansion of the cotton AAI gene family. Further, GhAAI66 was preferentially expressed in flower tissue and as responses to phytohormone treatments. Ectopic expression of GhAAI66 in Arabidopsis and silencing in cotton revealed that GhAAI66 triggers a phase transition to induce early flowering. Further, GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis of RNA sequencing data and qRT-PCR (quantitative reverse transcription-PCR) analysis indicated that GhAAI66 integrates multiple flower signaling pathways including gibberellin, jasmonic acid, and floral integrators to trigger an early flowering cascade in Arabidopsis. Therefore, characterization of the AAI family provides invaluable insights for improving cotton breeding.