Genomic Organization of the B3-Domain Transcription Factor Family in Grapevine (Vitis vinifera L.) and Expression during Seed Development in Seedless and Seeded Cultivars

Abstract

Members of the plant-specific B3-domain transcription factor family have important and varied functions, especially with respect to vegetative and reproductive growth. Although B3 genes have been studied in many other plants, there is limited information on the genomic organization and expression of B3 genes in grapevine (Vitis vinifera L.). In this study, we identified 50 B3 genes in the grapevine genome and analyzed these genes in terms of chromosomal location and syntenic relationships, intron-exon organization, and promoter cis-element content. We also analyzed the presumed proteins in terms of domain structure and phylogenetic relationships. Based on the results, we classified these genes into five subfamilies. The syntenic relationships suggest that approximately half of the genes resulted from genome duplication, contributing to the expansion of the B3 family in grapevine. The analysis of cis-element composition suggested that most of these genes may function in response to hormones, light, and stress. We also analyzed expression of members of the B3 family in various structures of grapevine plants, including the seed during seed development. Many B3 genes were expressed preferentially in one or more structures of the developed plant, suggesting specific roles in growth and development. Furthermore, several of the genes were expressed differentially in early developing seeds from representative seeded and seedless cultivars, suggesting a role in seed development or abortion. The results of this study provide a foundation for functional analysis of B3 genes and new resources for future molecular breeding of grapevine.

Keywords: B3 superfamily; Vitis vinifera; expression analysis; ovule abortion; transcription factor.

Figure 1

Phylogenetic analysis of B3 proteins from grapevine, tomato and Arabidopsis. Diamonds represent tomato protein, circles represent grapevine proteins, and squares represent Arabidopsis proteins.

Figure 2

Structural analysis of grapevine B3 genes. (A) Phylogenetic analysis and classification. Different boxes are colored indicating different subfamilies. Numbers near the tree branches indicate bootstrap values. (B) Domain analysis. (C) Exon–intron structures. Exons are marked as yellow boxes, and introns are represented by black lines.

Figure 3

Synteny analysis and chromosomal distribution of grapevine B3 genes. Colored bars connecting two chromosomal regions denote syntenic regions; the corresponding genes on two chromosomes were regarded as segmental duplications. Chr: chromosomes.

Figure 4

Synteny analysis of B3 genes between Arabidopsis and grapevine. Relative positions were depicted according to the grape and Arabidopsis chromosomes; colored lines represent syntenic regions.

Figure 5

Expression profile analysis of B3 genes during progressive stages of seed development in seeded (Red Globe) and seedless (Thompson Seedless) cultivars. (A) Heat map of semiquantitative RT-PCR analysis. (B) Real-time PCR analysis. Numbers indicate the number of days after full bloom (DAF).

Figure 6

Expression analysis of grapevine B3 genes in various structures of seeded and seedless cultivars. (A) Heat map of Semiquantitative RT-PCR analysis. (B) Real-time PCR analysis.

Figure 7

Predicted cis-elements in B3 gene promoters. The 1.5 kb sequences of 50 grape B3 genes were analyzed with the PlantCARE program.

Figure 8

Gene ontology analysis of B3 proteins in three categories (Biological process, molecular function and cellular component) using Blast2Go program. Different colors which are indicated near the graphics represent distinct biological process, molecular function or cellular component.