Genome-Wide Identification and Expression Profile of Dof Transcription Factor Gene Family in Pepper (Capsicum annuum L.)

Abstract

Dof (DNA-binding One Zinc Finger) transcription factor family is unique to plants and has diverse roles associated with plant-specific phenomena, such as light, phytohormone and defense responses as well as seed development and germination. Although, genome-wide analysis of this family has been performed in many species, information regarding Dof genes in the pepper, Capsicum annuum L., is extremely limited. In this study, exhaustive searches of pepper genome revealed 33 potential CaDofs that were phylogenetically clustered into four subgroups. Twenty-nine of the 33 Dof genes could be mapped on 11 chromosomes, except for chromosome 7. The intron/exon organizations and conserved motif compositions of these genes were also analyzed. Additionally, phylogenetic analysis and classification of the Dof transcription factor family in eight plant species revealed that S. lycopersicum and C. annuum as well as O. sativa and S. bicolor Dof proteins may have evolved conservatively. Moreover, comprehensive expression analysis of CaDofs using a RNA-seq atlas and quantitative real-time polymerase chain reaction (qRT-PCR) revealed that these genes exhibit a variety of expression patterns. Most of the CaDofs were expressed in at least one of the tissues tested, whereas several genes were identified as being highly responsive to heat and salt stresses. Overall, this study describes the first genome-wide analysis of the pepper Dof family, whose genes exhibited different expression patterns in all primary fruit developmental stages and tissue types, as in response to abiotic stress. In particular, some Dof genes might be used as biomarkers for heat and salt stress. The results could expand our understanding of the roles of Dof genes in pepper.

Genome-Wide Identification and Characterization of the <i>Dof</i> Transcription Factor Gene Family in <i>Phaseolus vulgaris</i> L.

“…As shown in Figure 7, the expression levels of the PvDof10, PvDof30, PvDof36, PvDof12 and PvDof27 genes belonging to classes A and C were relatively higher in young pod and stem tissues, indicating that they may play important roles in the development of these tissues in bean. Wang et al [14] reported that CaDofs28, CaDofs10, CaDofs14, and CaDof16 were primarily expressed in the stems of Capsicum annuum, which is perhaps unsurprising given that the stem contains abundant vascular tissue; Kim et al [53] also observed, in Arabidopsis, that the AtDof5.1 gene was highly expressed in vascular tissues. These expression profiles suggest that PvDof genes may be involved in various physiological functions during plant development.…”

“…Transcription factors (TFs) are responsible for regulating the expression of genes involved in plant-specific cis-regulatory elements in the promoter regions [3]. Yanagisawa and Schmidt [4] were the first to isolate the TF in maize, with an array of Dof TF genes subsequently isolated and functionally characterized in many plants, including Arabidopsis thaliana and Orizasativa [5] [6], Sorghum bicolor (L.) Moench [7], Brachypodium distachyon [8], Solanum lycopersicum [9], Ricinus communis L. [10], Cajanus cajan [11], Phyllostachys heterocycla [12], Chrysanthemum morifolium [13], Capsicum annuum [14] and Populus trichocarpa [15].…”

Transcriptome-Based Analysis of Dof Family Transcription Factors and Their Responses to Abiotic Stress in Tea Plant (Camellia sinensis)

“…The transgenic rice plants hosting OsDof12 gene exhibit a change of plant architecture [27]. Meanwhile, the expression of CaDofs in response to abiotic stress was observed in pepper [28]. …”

Allele specific expression of Dof genes responding to hormones and abiotic stresses in sugarcane

“…We performed phylogenetic analysis with MEGA5.0. Sequence of Dof proteins from Arabidopsis and sorghum were obtained from literature [23]. The phylogenetic tree image was enhanced by the Evolview online program (http:// www.evolgenius.info/evolview).…”