title: Genome-wide identification and analysis of the MADS-box gene family in apple.
abstract: The MADS-box gene family is one of the most widely studied families in plants and has diverse developmental roles in flower pattern formation, gametophyte cell division and fruit differentiation. Although the genome-wide analysis of this family has been performed in some species, little is known regarding MADS-box genes in apple (Malus domestica). In this study, 146 MADS-box genes were identified in the apple genome and were phylogenetically clustered into six subgroups (MIKC(c), MIKC*, Mα, Mβ, Mγ and Mδ) with the MADS-box genes from Arabidopsis and rice. The predicted apple MADS-box genes were distributed across all 17 chromosomes at different densities. Additionally, the MADS-box domain, exon length, gene structure and motif compositions of the apple MADS-box genes were analysed. Moreover, the expression of all of the apple MADS-box genes was analysed in the root, stem, leaf, flower tissues and five stages of fruit development. All of the apple MADS-box genes, with the exception of some genes in each group, were expressed in at least one of the tissues tested, which indicates that the MADS-box genes are involved in various aspects of the physiological and developmental processes of the apple. To the best of our knowledge, this report describes the first genome-wide analysis of the apple MADS-box gene family, and the results should provide valuable information for understanding the classification, cloning and putative functions of this family.
authors.affiliation: Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning 125100, PR China.
authors.forename: Yi
authors.initials: Y
authors.lastname: Tian
authors.affiliation: Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning 125100, PR China.
authors.forename: Qinglong
authors.initials: Q
authors.lastname: Dong
authors.affiliation: Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning 125100, PR China.
authors.forename: Zhirui
authors.initials: Z
authors.lastname: Ji
authors.affiliation: Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning 125100, PR China.
authors.forename: Fumei
authors.initials: F
authors.lastname: Chi
authors.affiliation: Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning 125100, PR China. Electronic address: Congph@163.com.
authors.forename: Peihua
authors.initials: P
authors.lastname: Cong
authors.affiliation: Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning 125100, PR China. Electronic address: zszhouqrj@163.com.
authors.forename: Zongshan
authors.initials: Z
authors.lastname: Zhou
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000235:genetics; D002875:Chromosomes / Q000648:ultrastructure; D005091:Exons; D035264:Flowers / Q000235:genetics; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D007438:Introns; D026161:MADS Domain Proteins / Q000235:genetics*; D027845:Malus / Q000235:genetics*; D008969:Molecular Sequence Data; D005810:Multigene Family; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid
chemical_list: D026161:MADS Domain Proteins
keywords: Apple; Expression analysis; Gene family; MADS-box; Phylogenetic analysis