Structural and Functional Analysis of the GRAS Gene Family in Grapevine Indicates a Role of GRAS Proteins in the Control of Development and Stress Responses

Abstract

GRAS transcription factors are involved in many processes of plant growth and development (e.g., axillary shoot meristem formation, root radial patterning, nodule morphogenesis, arbuscular development) as well as in plant disease resistance and abiotic stress responses. However, little information is available concerning this gene family in grapevine (Vitis vinifera L.), an economically important woody crop. We performed a model curation of GRAS genes identified in the latest genome annotation leading to the identification of 52 genes. Gene models were improved and three new genes were identified that could be grapevine- or woody-plant specific. Phylogenetic analysis showed that GRAS genes could be classified into 13 groups that mapped on the 19 V. vinifera chromosomes. Five new subfamilies, previously not characterized in other species, were identified. Multiple sequence alignment showed typical GRAS domain in the proteins and new motifs were also described. As observed in other species, both segmental and tandem duplications contributed significantly to the expansion and evolution of the GRAS gene family in grapevine. Expression patterns across a variety of tissues and upon abiotic and biotic conditions revealed possible divergent functions of GRAS genes in grapevine development and stress responses. By comparing the information available for tomato and grapevine GRAS genes, we identified candidate genes that might constitute conserved transcriptional regulators of both climacteric and non-climacteric fruit ripening. Altogether this study provides valuable information and robust candidate genes for future functional analysis aiming at improving the quality of fleshy fruits.

Genome-wide identification and expression of GRAS gene family members in cassava

“…This number is lower than that in Malus domestica (127) [28], Populus (106) [20], and maize (86) [27] but higher than that in Arabidopsis (34) [20], rice (60) [20], Chinese cabbage (48) [19], Prunus mume (46) [21], tobacco (53) [22], castor (48) [23], grapevine (52) [24], Medicago truncatula (68) [25,26], pepper (50) [29], and tea plant (52) [30]. This variation in GRAS gene numbers might be related to gene duplication events or genome size [24]. Four groups of tandem duplicated MeGRAS genes and 34 pairs of segmental duplicated MeGRAS genes were detected in this study.…”

“…GRAS genes have recently been studied in various plant species, i.e., Arabidopsis [18], rice [18], Chinese cabbage [19], Populus [20], Prunus mume [21], tobacco [22], castor bean [23], grapevine [24], Medicago truncatula [25,26], maize [27], Malus domestica [28], pepper [29], and tea plant [30]. According to previous studies in Arabidopsis and rice [18], the GRAS family members can be classified into eight subfamilies: the DELLA, HAM, LAS, PAT1, SCR, SHR, SCL3, and LISCL subfamilies.…”

Transcriptome-Wide Identification, Evolutionary Analysis, and GA Stress Response of the GRAS Gene Family in Panax ginseng C. A. Meyer

“…These nine members may have similar functions. It has been reported that the HAM and LS families In order to help with PgGRAS classification and decipher the evolution history of the PgGRAS gene family in ginseng, we built two evolutionary trees and applied 67 genes (Ginseng and Arabidopsis) (Figure 2a; Tables S2 and S3) and 172 genes (Ginseng, Arabidopsis, Tomato and Rice) (Figure 2b; Tables S2 and S3), respectively [46,47]. As shown in Figure 2, we identified a total of 15 sub-families of the GRAS genes.…”

Genome-wide characterisation and expression profile of the grapevine ATL ubiquitin ligase family reveal biotic and abiotic stress-responsive and development-related members

“…The publication of the grapevine ( Vitis vinifera ) genome sequence in 2007 facilitated the functional analysis of a number of gene families characterised in other species to determine whether these could be used to improve the performance of this economically important fruit crop33343536373839. The E3 ubiquitin ligase family has not been investigated thus far, and only one grapevine RING-type E3 ubiquitin ligase has been functionally characterised: the EIRP1 protein from the wild species V. pseudoreticulata .…”