Transcriptome‐wide analysis of the MADS‐box gene family in the orchid Erycina pusilla

• Published in: Plant biotechnology journal 2016-01, Vol.14 (1), p.284-298
• Main Authors: Lin, Choun‐Sea, Hsu, Chen‐Tran, Liao, De‐Chih, Chang, Wan‐Jung, Chou, Ming‐Lun, Huang, Yao‐Ting, Chen, Jeremy J. W, Ko, Swee‐Suak, Chan, Ming‐Tsair, Shih, Ming‐Che
• Format: Article
• Language: English
• Subjects: Amino Acid Motifs; Amino Acid Sequence; Arabidopsis - genetics; bacteria artificial chromosome; Bacterial artificial chromosomes; breeding; Classification; clones; Correlation analysis; Crops; Databases, Genetic; Erycina; Evolution; Exons - genetics; Flowering; Flowers; Flowers - genetics; Gene expression; Gene Expression Profiling; Gene Expression Regulation, Plant; Gene sequencing; Genes; Genes, Plant; Horticulture; in situ hybridization; industry; Information dissemination; Introns; Introns - genetics; Localization; MADS box proteins; MADS Domain Proteins - chemistry; MADS Domain Proteins - genetics; MADS Domain Proteins - metabolism; Mathematical models; meristems; Multigene Family; next‐generation sequencing; Nuclei; Nucleotide Motifs; Orchidaceae; Orchidaceae - genetics; Organ Specificity - genetics; ornamental horticulture; Phylogenetics; Phylogeny; Plant breeding; Position (location); Protein Domains; Proteins; Subcellular Fractions - metabolism; subcellular localization; Transcription factors; transcriptome
• ISSN: 1467-7644; 1467-7652
• DOI: 10.1111/pbi.12383

Orchids exhibit a range of unique flower shapes and are a valuable ornamental crop. MADS‐box transcription factors are key regulatory components in flower initiation and development. Changing the flower shape and flowering time can increase the value of the orchid in the ornamental horticulture industry. In this study, 28 MADS‐box genes were identified from the transcriptome database of the model orchid Erycina pusilla. The full‐length genomic sequences of these MADS‐box genes were obtained from BAC clones. Of these, 27 were MIKC‐type EpMADS (two truncated forms) and one was a type I EpMADS. Eleven EpMADS genes contained introns longer than 10 kb. Phylogenetic analysis classified the 24 MIKCᶜ genes into nine subfamilies. Three specific protein motifs, AG, FUL and SVP, were identified and used to classify three subfamilies. The expression profile of each EpMADS gene correlated with its putative function. The phylogenetic analysis was highly correlated with the protein domain identification and gene expression results. Spatial expression of EpMADS6, EpMADS12 and EpMADS15 was strongly detected in the inflorescence meristem, floral bud and seed via in situ hybridization. The subcellular localization of the 28 EpMADS proteins was also investigated. Although EpMADS27 lacks a complete MADS‐box domain, EpMADS27‐YFP was localized in the nucleus. This characterization of the orchid MADS‐box family genes provides useful information for both orchid breeding and studies of flowering and evolution.