Genome-wide identification and analysis of the apple (Malus × domestica Borkh.) TIFY gene family

TIFY transcription factors comprise a plant-specific family involved in the regulation of diverse developmental processes and responses to phytohormones. However, little is known about these genes in woody species, and so, we characterized the 30-member TIFY gene family of apple (Malus × domestica Borkh.). Synteny analysis indicated that segmental, tandem, and whole genome duplications have contributed to the expansion and evolution of the family. Moreover, synteny analysis between the apple and Arabidopsis genomes demonstrated that several apple TIFY genes were found in the corresponding syntenic blocks of Arabidopsis, suggesting that the genes were established prior to the divergence of the corresponding taxonomic lineages. Additionally, phylogenetic analysis, as well as a comparison of exon–intron and protein structures, provided insights into both the evolutionary relationships and the putative functions of the family members. Tissue-specific expression analysis of specific subfamily genes revealed diverse spatiotemporal expression patterns, while expression profiles under abiotic stress and various hormone treatments indicated that the majority of the apple TIFY genes were responsive to high salinity, drought, abscisic acid, and methyl jasmonate but not salicylic acid or ethylene. This genome-wide identification and characterization of evolutionary relationships and expression profiles of apple TIFY genes will not only be useful for further analysis of this gene family and its role in stress response but may also aid in future agricultural improvement of apple stress tolerance.