Genome-wide identification and expression analyses of the homeobox transcription factor family during ovule development in seedless and seeded grapes

Abstract

Seedless grapes are of considerable importance for the raisin and table grape industries. Previous transcriptome analyses of seed development in grape revealed that genes encoding homeobox transcription factors were differentially regulated in seedless compared with seeded grape during seed development. In the present study, we identified a total of 73 homeobox-like genes in the grapevine genome and analyzed the genomic content and expression profiles of these genes. Based on domain architecture and phylogenetic analyses grape homeobox genes can be classified into eleven subfamilies. An analysis of the exon-intron structures and conserved motifs provided further insight into the evolutionary relationships between these genes. Evaluation of synteny indicated that segmental and tandem duplications have contributed greatly to the expansion of the grape homeobox gene superfamily. Synteny analysis between the grape and Arabidopsis genomes provided a potential functional relevance for these genes. The tissue-specific expression patterns of homeobox genes suggested roles in both vegetative and reproductive tissues. Expression profiling of these genes during the course of ovule development in seeded and seedless cultivars suggested a potential role in ovule abortion associated with seedlessness. This study will facilitate the functional analysis of these genes and provide new resources for molecular breeding of seedless grapes.

Genome‐wide identification and expression analysis reveal the potential function of ethylene responsive factor gene family in response to Botrytis cinerea infection and ovule development in grapes (Vitis vinifera L.)

“…Duplication events that give rise to genes that occur on different chromosomes are identified as segmental duplications (Li et al . ), and are represented by coloured lines in Fig. , e .g.…”

“…VvERF protein secondary structure was predicted using Jpred 4.0 (http://www.compbio.dundee.ac.uk/jpred/), and phylogenetic trees including A. thaliana and grape ERF protein sequences, or with grape ERF proteins alone, were constructed based on the AP2 domain sequences using MEGA 6.0 software (Li et al . ). Sequence alignments were performed using the ‘muscle’ approach, and phylogenetic trees were constructed issuing the Neighbour‐Joining (NJ) method with 1000 bootstrap replications (Li et al .…”

“…Sequence alignments were performed using the ‘muscle’ approach, and phylogenetic trees were constructed issuing the Neighbour‐Joining (NJ) method with 1000 bootstrap replications (Li et al . ).…”

“…The processed data were log2 transformed, and the Multi Experiment Viewer (MeV 4.9) program (Li et al . ) was used to determine the expression values. The final results were displayed in the form of heat‐maps.…”

The grapevine homeobox gene VvHB58 influences seed and fruit development through multiple hormonal signaling pathways

“…Three members of the HD-ZIP I subfamily, VvHB62, VvHB54 and VvHB7, exhibited remarkable differences in the expression pattern during seed development between seeded and seedless grape cultivars, with relatively low expression levels in seeded cultivars [28]. Additionally, two members of the WOX family (a subfamily of the homeobox gene family), VvWOX3 and VvWOX11, were strongly activated during the torpedo and cotyledonary stages of somatic embryogenesis, but showed a relatively low expression level in the earlier developmental stages [29].…”