Transcriptome analyses of the Dof-like gene family in grapevine reveal its involvement in berry, flower and seed development

Abstract

The Dof (DNA-binding with one finger) protein family spans a group of plant transcription factors involved in the regulation of several functions, such as plant responses to stress, hormones and light, phytochrome signaling and seed germination. Here we describe the Dof-like gene family in grapevine (Vitis vinifera L.), which consists of 25 genes coding for Dof. An extensive in silico characterization of the VviDofL gene family was performed. Additionally, the expression of the entire gene family was assessed in 54 grapevine tissues and organs using an integrated approach with microarray (cv Corvina) and real-time PCR (cv Pinot Noir) analyses. The phylogenetic analysis comparing grapevine sequences with those of Arabidopsis, tomato, poplar and already described Dof genes in other species allowed us to identify several duplicated genes. The diversification of grapevine DofL genes during evolution likely resulted in a broader range of biological roles. Furthermore, distinct expression patterns were identified between samples analyzed, corroborating such hypothesis. Our expression results indicate that several VviDofL genes perform their functional roles mainly during flower, berry and seed development, highlighting their importance for grapevine growth and production. The identification of similar expression profiles between both approaches strongly suggests that these genes have important regulatory roles that are evolutionally conserved between grapevine cvs Corvina and Pinot Noir.

Genome-wide identification and comparative evolutionary analysis of the Dof transcription factor family in physic nut and castor bean

“…The number of Dof family members in physic nut or castor is relatively smaller than most angiosperm plants reported thus far (Yanagisawa, 2002; Lijavetzky, Carbonero & Vicente-Carbajosa, 2003; Yang, Tuskan & Cheng, 2006; Ma et al, 2015; da Silva et al, 2016; Wu et al, 2016; Wen et al, 2016; Zou, Zhu & Zhang, 2019b). In fact, Dof proteins were characterized as a plant-specific transcription factor family that is present as a single member in unicellular algae (Moreno-Risueno et al, 2007), and the family members have highly expanded along with several WGD events, for example, the γ event for core eudicots and the τ event for monocots (Jiao et al, 2012, 2014).…”

“…Genome-wide surveys showed that the Dof gene family is present as a single member in most algae, however, the family has been highly expanded and diversified in terrestrial plants (Moreno-Risueno et al, 2007; Gupta et al, 2015). For example, there are 25 Dof genes present in grapevine ( Vitis vinifera ) (da Silva et al, 2016), 30 in rice ( Oryza sativa ) (Lijavetzky, Carbonero & Vicente-Carbajosa, 2003), 33 in pepper ( Capsicum annuum ) (Wu et al, 2016), 36 members in Arabidopsis thaliana (Yanagisawa, 2002), 36 in cucumber ( Cucumis sativus ) (Wen et al, 2016), 41 in poplar ( Populus trichocarpa ) (Yang, Tuskan & Cheng, 2006), 45 in cassava ( Manihot esculenta ) (Zou, Zhu & Zhang, 2019b), and 76 in Chinese cabbage ( Brassica rapa ) (Ma et al, 2015). Based on phylogenetic analysis of Dof domains, Dof proteins in model plants were classed into four subfamilies and several groups (Lijavetzky, Carbonero & Vicente-Carbajosa, 2003).…”

Genome-wide identification and expression analysis of GRAS family transcription factors in tea plant (Camellia sinensis)

“…Transcription factors (TFs) are critical components in physiological processes and regulatory networks of higher plants; TFs serve as a switch of gene regulation, promote or inhibit specific functional gene expression, and maintain the growth and development as well as stress responses of plants 19 – 21 . A large proportion of the plant genome is dedicated to TFs.…”

Genome-wide identification and characterization of Dof transcription factors in eggplant (Solanum melongenaL.)

“…Dof transcription factors are associated with a variety of biological processes in plant growth and development, including the responses to light and those in defence ( Park et al, 2003 ; Shaw et al, 2009 ; Zhang et al, 1995 ), germination and development of seeds ( Papi et al, 2002 ; Dong et al, 2007 ; Gabriele et al, 2010 ; Zou et al, 2013 ), control of flowering ( Imaizumi et al, 2005 ; Fornara et al, 2009 ), branching of shoots, and development of pollen, fruit and vascular tissues ( Konishi & Yanagisawa, 2007 ; Chen et al, 2012 ; Da Silva et al, 2016 ; Wu et al, 2016 ). Dof TFs also participate in carbon metabolism ( Yanagisawa, 2000 ) and various physiological processes such as nitrogen assimilation, phytochrome and cytochrome signalling, plant hormonal signalling, and biotic and abiotic stress tolerance ( Park et al, 2003 ; Ward et al, 2005 ; Kurai et al, 2011 ; Cai et al, 2013 ; Corrales et al, 2014 ; Wen et al, 2016 ).…”