Abstract
BackgroundSeedless grapes are greatly appreciated for fresh and dry fruit consumption. Parthenocarpy and stenospermocarpy have been described as the main phenomena responsible for seedlessness in Vitis vinifera. However, the key genes underpinning molecular and cellular processes that play a significant role in seed development are not well characterized. To identify important regulators and mechanisms that may be altered in the seedless phenotype, we performed a comprehensive transcriptional analysis to compare the transcriptomes of a popular seeded wine cultivar (wild-type) and its seedless somatic variant (mutant) at three key developmental stages.ResultsThe transcriptomes revealed by Illumina mRNA-Seq technology had approximately 98% of grapevine annotated transcripts and about 80% of them were commonly expressed in the two lines. Differential gene expression analysis revealed a total of 1075 differentially expressed genes (DE) in the pairwise comparison of developmental stages, which included DE genes specific to the wild-type background, DE genes specific to the mutant background and DE genes commonly shared in both backgrounds. The analysis of differential expression patterns and functional category enrichment of wild-type and mutant DE genes highlighted significant coordination and enrichment of pollen and ovule developmental pathways. The expression of some selected DE genes was further confirmed by real-time RT-PCR analysis.ConclusionsThis study represents the most comprehensive attempt to characterize the genetic bases of seed formation in grapevine. With a high throughput method, we have shown that a seeded wine grape and its seedless somatic variant are similar in several biological processes. Nevertheless, we could identify an inventory of genes with altered expression in the mutant compared to the wild-type, which may be responsible for the seedless phenotype. The genes located within known genomic regions regulating seed content may be used for the development of molecular tools to assist table grape breeding. Therefore the data reported here have provided a rich genomic resource for practical use and functional characterization of the genes that potentially underpin seedlessness in grapevine.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-1030) contains supplementary material, which is available to authorized users.
Highlights
Seedless grapes are greatly appreciated for fresh and dry fruit consumption
In the wild-type and the mutant 23,640 and 23,072 genes were expressed in all three developmental stages, respectively (Figure 2). While it is not surprising the comparable number of genes shared by the three developmental stages in each clone, it is interesting to note that fewer genes were expressed at each developmental stage: 586, 430 and 421 genes at stages E-L 15, E-L 27 and E-L 38 in the wild-type (Figure 2A) and 802, 337 and 351 genes at respective stages in the mutant (Figure 2B), which further highlights a reduction in gene expression in the mutant compared to the wild-type after fertilization
This has in turn allowed a comprehensive description of distinguishing transcriptional events in the two lines, based on the analysis of differentially expressed genes, gene patterns and enriched functional categories
Summary
Parthenocarpy and stenospermocarpy have been described as the main phenomena responsible for seedlessness in Vitis vinifera. Over the past decade there has been a sustained increase in the world production of table grapes, which reached 22.3 million tons [1]. This is largely due to consumer demand for seedless grape for fresh and dry fruit consumption. Vitis vinifera L. is considered a good model for the study of seed development in fruit crops. The major events that take place in grapevine normal seed development, parthenocarpy and stenospermocarpy are shown schematically in [4] and are described in detail by [5,6]
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