Genome-Wide Characterization and Expression Profiling of GASA Genes during Different Stages of Seed Development in Grapevine (Vitis vinifera L.) Predict Their Involvement in Seed Development

Abstract

Members of the plant-specific GASA (gibberellic acid-stimulated Arabidopsis) gene family have multiple potential roles in plant growth and development, particularly in flower induction and seed development. However, limited information is available about the functions of these genes in fruit plants, particularly in grapes. We identified 14 GASA genes in grapevine (Vitis vinifera L.) and performed comprehensive bioinformatics and expression analyses. In the bioinformatics analysis, the locations of genes on chromosomes, physiochemical properties of proteins, protein structure, and subcellular positions were described. We evaluated GASA proteins in terms of domain structure, exon-intron distribution, motif arrangements, promoter analysis, phylogenetic, and evolutionary history. According to the results, the GASA domain is conserved in all proteins and the proteins are divided into three well-conserved subgroups. Synteny analysis proposed that segmental and tandem duplication have played a role in the expansion of the GASA gene family in grapes, and duplicated gene pairs have negative selection pressure. Most of the proteins were predicted to be in the extracellular region, chloroplasts, and the vacuole. In silico promoter analysis suggested that the GASA genes may influence different hormone signaling pathways and stress-related mechanisms. Additionally, we performed a comparison of the expression between seedless (Thompson seedless) and seeded (Red globe) cultivars in different plant parts, including the ovule during different stages of development. Furthermore, some genes were differentially expressed in different tissues, signifying their role in grapevine growth and development. Several genes (VvGASA2 and 7) showed different expression levels in later phases of seed development in Red globe and Thompson seedless, suggesting their involvement in seed development. Our study presents the first genome-wide identification and expression profiling of grapevine GASA genes and provides the basis for functional characterization of GASA genes in grapes. We surmise that this information may provide new potential resources for the molecular breeding of grapes.

Keywords: Cis-elements; GASR; VvGAST; bioinformatics; grapevine; ovule abortion.

Figure 1

Predicted 3-D structures of GASA proteins.

Figure 2

Phylogenetic tree of GASA genes of Vitis vinifera, Malus domestica, and Arabidopsis thaliana. Blue-colored diamonds represent grapevine protein, green-colored squares represent apple proteins, and red-colored circles represent Arabidopsis proteins. Different colored oval shapes indicate different groups. Numbers near the tree branches indicate bootstrap values (BS) and BS values less than 50 are not shown.

Figure 3

Analysis of grapevine GASA genes. (A) Phylogenetic tree of grapevine GASA genes. Different boxes are colored to indicating different groups. Numbers near the tree branches indicate bootstrap values. (B) Motif analysis. The different colors of boxes denote different motif numbers. The length of box indicates motif length. (C) Exon-intron distribution. CDS denotes exons.

Figure 4

Chromosomal distribution and synteny analysis of grapevine GASA genes. Syntenic regions and chromosomal regions are depicted in different colors (Chr: chromosomes).

Figure 5

Real-time PCR analysis of grapevine GASA genes at different stages of seed development in seedless and seeded cultivar. Numbers on x-axis denote number of days after full bloom (DAF).

Figure 6

Real-time PCR analysis of different plant parts.

Figure 7

Cis-element prediction in the VvGASA promoters.