Genome-wide Identification, Phylogeny And Expression Analysis Of The SBP-box Transcription Factor Family Genes In Apple

Apple (Malus×domestica Borkh.) is economically one of the most important fruit cropsworldwide and the main fruit crop in the temperate regions of the world. The publication ofthe apple genome sequence provides important data for genome-wide identification of genesrelated with excellent agronomic traits, stress or pathogen resistance in apple, and is thefoundation of breeding novel apple cultivars that have excellent agronomic traits and arestress-or pathogen-resistant. Transcription factors play essential roles in the regulationnetworks of many significant developmental processes in plants. SQUAMOSA promoterbinding protein (SBP) is one type of plant-specific transcription factor and plays many crucialroles in development, hormone signaling and stress resistance in plants. To date, the roles ofSBP transcription factors have been substantially elucidated in many plants, whereas thefunction of SBP transcription factors in fruit crops remains unclear. In this study, all membersof apple SBP-box transcription factor family genes were identified in apple genome bybioinformatics approaches. Subsequently, domains, miR156target sites, phylogeny andevolution, gene structures and gene synteny of apple SBP-box genes were investigated.Moreover, expression patterns of apple SBP-box genes and miR156in various apple tissues ororgans and responses of apple SBP-box genes to various plant hormones were also analyzed,providing a basic understanding of the potential important roles of apple SBP transcriptionfactors. The major findings were as following:1. Genome-wide identification and annotation of SBP-box genes in apple.27putativeapple SBP-box genes were identified in apple genome and Genbank database, andnomenclature of them was carried out based on their chromosome orders.15of them hadmiR156target sites and were putative targets of miR156.2. Phylogenetic analysis of plant SBP proteins. According to the phylogenetic analysis ofSBP-domain proteins, plant SBP proteins were classified into eight groups, and apple SBPproteins were clustered into seven of the eight groups. The plant SBP proteins wereevolutionally divergent and diversified. 3. Gene duplications have played crutial roles in the expansion of apple SBP-box genefamily. Gene structure, gene chromosomal location and synteny analysis of MdSBP geneswithin the apple genome demonstrated that tandem and segmental duplications, as well aswhole genome duplications, have likely played critical roles in the expansion and evolution ofthe SBP-box gene family in apple, resulting in diversification of MdSBP genes quantitatively,structurally and functionally.4. Synteny of apple and Arabidopsis SBP-box genes. Synteny analysis between appleand Arabidopsis indicated that several paired homologs of MdSBP and AtSPL genes werelocated in syntenic genomic regions, indicating these syntenic orthologs likely share acommon ancestor and have similar biological roles. Thus we could confidently infer thefunctions of apple SBP-box genes based on their Arabidopsis homologs.5. Tissue-specific expression profiles of apple SBP-box genes and miR156, and theirfunction prediction. MdSBP genes exhibited diversified spatiotemporal expression patterns invarious apple tissues/organs. Most MdmiR156-targeted genes, which had relatively hightranscript levels in stems, leaves, apical buds and some floral organs, exhibited a moredifferential expression pattern than most MdmiR156-nontargeted genes. Whereas matureMdmiR156was generally expressed in a complementary fashion compared with their targetsand had relatively high expression levels in seeds of young fruit, seeds of mature fruit, flowerbuds, roots and stamens, especially in seeds of young fruit, suggesting its likely crucialfunction in seed development of apple. Based on comparative analysis of SBP-box genes andmiR156among different plant species and the tissue-specific expression profiles, wegenerally predicted the roles of MdSBP genes and MdmiR156in apple.6. Apple SBP-box genes were responsive to various plant hormones. Expression analysisof MdSBP genes in leaves upon different plant hormone (ethylene, salicylic acid, methyljasmonate, abscisic acid and gibberellin) treatments showed that many MdSBP genes wereresponsive to various plant hormones, indicating that MdSBP genes may be involved in theresponses to various plant hormone signaling in stress responses or in apple development.