title: Genome-wide identification and analysis of the SBP-box family genes in apple (Malus × domestica Borkh.).
abstract: SQUAMOSA promoter binding protein (SBP)-box genes encode a family of plant-specific transcription factors and play many crucial roles in plant development. In this study, 27 SBP-box gene family members were identified in the apple (Malus × domestica Borkh.) genome, 15 of which were suggested to be putative targets of MdmiR156. Plant SBPs were classified into eight groups according to the phylogenetic analysis of SBP-domain proteins. Gene structure, gene chromosomal location and synteny analyses of MdSBP genes within the apple genome demonstrated that tandem and segmental duplications, as well as whole genome duplications, have likely contributed to the expansion and evolution of the SBP-box gene family in apple. Additionally, synteny analysis between apple and Arabidopsis indicated that several paired homologs of MdSBP and AtSPL genes were located in syntenic genomic regions. Tissue-specific expression analysis of MdSBP genes in apple demonstrated their diversified spatiotemporal expression patterns. Most MdmiR156-targeted MdSBP genes, which had relatively high transcript levels in stems, leaves, apical buds and some floral organs, exhibited a more differential expression pattern than most MdmiR156-nontargeted MdSBP genes. Finally, expression analysis of MdSBP genes in leaves upon various plant hormone treatments showed that many MdSBP genes were responsive to different plant hormones, indicating that MdSBP genes may be involved in responses to hormone signaling during stress or in apple development.
authors.affiliation: State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Li
authors.forename: Hongmin
authors.initials: H
authors.lastname: Hou
authors.forename: Xiaoqin
authors.initials: X
authors.lastname: Li
authors.forename: Jiang
authors.initials: J
authors.lastname: Xiang
authors.forename: Xiangjing
authors.initials: X
authors.lastname: Yin
authors.forename: Hua
authors.initials: H
authors.lastname: Gao
authors.forename: Yi
authors.initials: Y
authors.lastname: Zheng
authors.forename: Carole L
authors.initials: CL
authors.lastname: Bassett
authors.forename: Xiping
authors.initials: X
authors.lastname: Wang
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D032461:Chromosomes, Plant; D019143:Evolution, Molecular; D020440:Gene Duplication; D015870:Gene Expression; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018745:Genome, Plant; D027845:Malus / Q000235:genetics* / Q000378:metabolism; D005810:Multigene Family; D010802:Phylogeny; D063245:Plant Development / Q000235:genetics*; D010937:Plant Growth Regulators / Q000378:metabolism / Q000494:pharmacology; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D018514:Plant Structures; D015398:Signal Transduction; D013312:Stress, Physiological / Q000235:genetics; D026801:Synteny; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D010937:Plant Growth Regulators; D010940:Plant Proteins; D014157:Transcription Factors
keywords: ABA; Apple; Eth; GA; Gene expression; Hormone response; MdmiR156; MeJA; NLS; Phylogeny; SA; SBP; SBP-box gene; SPL; SQUAMOSA promoter binding protein; SQUAMOSA promoter binding protein-like; Synteny; aa; abscisic acid; amino acid(s); ethylene; gibberellin; methyl jasmonate; miRNA; microRNA; nuclear localization signal; salicylic acid