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Transcriptome analysis during berry development provides insights into co-regulated and altered gene expression between a seeded wine grape variety and its seedless somatic variant.

Nwafor CC, Gribaudo I, Schneider A, Wehrens R, Grando MS, Costantini L - BMC Genomics (2014)

Bottom Line: However, the key genes underpinning molecular and cellular processes that play a significant role in seed development are not well characterized.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.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.

View Article: PubMed Central - PubMed

Affiliation: Fondazione Edmund Mach, Research and Innovation Centre, Via E, Mach 1-38010 San Michele all'Adige, Trento, Italy. laura.costantini@fmach.it.

ABSTRACT

Background: Seedless 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.

Results: The 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.

Conclusions: This 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.

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The eighteen relevant categories of triplets of significance. A red line indicates a significant up-regulation, a blue line a significant down-regulation, and a gray dashed line a non-significant difference between time points (the first position in the triplet corresponds to the shift from stage E-L 15 to E-L 27, the second position to the shift from stage E-L 27 to E-L 38 and the third position to the shift from stage E-L 15 to E-L 38). All DE genes for both the wild-type and the mutant formed 18 groups of differential expression patterns and the numbers of genes that fell within each group are shown in Table 3. Group 1 contains positively regulated genes along the whole time course; groups 2 and 3 consist of induced genes from stage E-L 15 to stage E-L 27, with no significant change afterwards; groups 4, 5 and 6 contain induced genes from stage E-L 15 to stage E-L 27, followed by a significant decrease in their expression; groups 7, 8 and 9 consist of stable genes from stage E-L 15 to stage E-L 27, with induced expression from stage E-L 15 or E-L 27 to stage E-L 38. Groups 10, 11 and 12 are made up of stable genes from stage E-L 15 to stage E-L 27 with reduced expression from stage E-L 15 or E-L 27 to stage E-L 38; groups 13, 14 and 15 contain repressed genes from stage E-L 15 to stage E-L 27, followed by a significant induction in their expression; groups 16 and 17 contain repressed genes from stage E-L 15 to stage E-L 27, with no significant subsequent change; group 18 contains negatively regulated genes along the whole time course.
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Fig1: The eighteen relevant categories of triplets of significance. A red line indicates a significant up-regulation, a blue line a significant down-regulation, and a gray dashed line a non-significant difference between time points (the first position in the triplet corresponds to the shift from stage E-L 15 to E-L 27, the second position to the shift from stage E-L 27 to E-L 38 and the third position to the shift from stage E-L 15 to E-L 38). All DE genes for both the wild-type and the mutant formed 18 groups of differential expression patterns and the numbers of genes that fell within each group are shown in Table 3. Group 1 contains positively regulated genes along the whole time course; groups 2 and 3 consist of induced genes from stage E-L 15 to stage E-L 27, with no significant change afterwards; groups 4, 5 and 6 contain induced genes from stage E-L 15 to stage E-L 27, followed by a significant decrease in their expression; groups 7, 8 and 9 consist of stable genes from stage E-L 15 to stage E-L 27, with induced expression from stage E-L 15 or E-L 27 to stage E-L 38. Groups 10, 11 and 12 are made up of stable genes from stage E-L 15 to stage E-L 27 with reduced expression from stage E-L 15 or E-L 27 to stage E-L 38; groups 13, 14 and 15 contain repressed genes from stage E-L 15 to stage E-L 27, followed by a significant induction in their expression; groups 16 and 17 contain repressed genes from stage E-L 15 to stage E-L 27, with no significant subsequent change; group 18 contains negatively regulated genes along the whole time course.

Mentions: An in-house R script was written to group DE genes with similar expression pattern based on the adjusted p-values. By indicating a significant up-regulation with “1”, a significant down-regulation with “-1” and a non-significant difference with “0”, the three comparisons between the developmental stages can be summarized with a triplet, e.g. “1, 0, 1”. This example indicates that there is a significant up-regulation going from the first to the second time point, no significant difference between the second and third time points, and a significant positive difference when comparing the first and last time points. Altogether, 27 different categories can be defined in this way, and 18 of these contain relevant patterns (for example the pattern “1, 1, −1” is impossible). These 18 groups are visualized in Figure 1. Each gene showing at least one significant difference between developmental stages was classified into one of these categories, for both the wild type and the mutant. The number of differentially expressed genes that fell to each pattern were compared between the wild-type and the mutant.Figure 1


Transcriptome analysis during berry development provides insights into co-regulated and altered gene expression between a seeded wine grape variety and its seedless somatic variant.

Nwafor CC, Gribaudo I, Schneider A, Wehrens R, Grando MS, Costantini L - BMC Genomics (2014)

The eighteen relevant categories of triplets of significance. A red line indicates a significant up-regulation, a blue line a significant down-regulation, and a gray dashed line a non-significant difference between time points (the first position in the triplet corresponds to the shift from stage E-L 15 to E-L 27, the second position to the shift from stage E-L 27 to E-L 38 and the third position to the shift from stage E-L 15 to E-L 38). All DE genes for both the wild-type and the mutant formed 18 groups of differential expression patterns and the numbers of genes that fell within each group are shown in Table 3. Group 1 contains positively regulated genes along the whole time course; groups 2 and 3 consist of induced genes from stage E-L 15 to stage E-L 27, with no significant change afterwards; groups 4, 5 and 6 contain induced genes from stage E-L 15 to stage E-L 27, followed by a significant decrease in their expression; groups 7, 8 and 9 consist of stable genes from stage E-L 15 to stage E-L 27, with induced expression from stage E-L 15 or E-L 27 to stage E-L 38. Groups 10, 11 and 12 are made up of stable genes from stage E-L 15 to stage E-L 27 with reduced expression from stage E-L 15 or E-L 27 to stage E-L 38; groups 13, 14 and 15 contain repressed genes from stage E-L 15 to stage E-L 27, followed by a significant induction in their expression; groups 16 and 17 contain repressed genes from stage E-L 15 to stage E-L 27, with no significant subsequent change; group 18 contains negatively regulated genes along the whole time course.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
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getmorefigures.php?uid=PMC4301461&req=5

Fig1: The eighteen relevant categories of triplets of significance. A red line indicates a significant up-regulation, a blue line a significant down-regulation, and a gray dashed line a non-significant difference between time points (the first position in the triplet corresponds to the shift from stage E-L 15 to E-L 27, the second position to the shift from stage E-L 27 to E-L 38 and the third position to the shift from stage E-L 15 to E-L 38). All DE genes for both the wild-type and the mutant formed 18 groups of differential expression patterns and the numbers of genes that fell within each group are shown in Table 3. Group 1 contains positively regulated genes along the whole time course; groups 2 and 3 consist of induced genes from stage E-L 15 to stage E-L 27, with no significant change afterwards; groups 4, 5 and 6 contain induced genes from stage E-L 15 to stage E-L 27, followed by a significant decrease in their expression; groups 7, 8 and 9 consist of stable genes from stage E-L 15 to stage E-L 27, with induced expression from stage E-L 15 or E-L 27 to stage E-L 38. Groups 10, 11 and 12 are made up of stable genes from stage E-L 15 to stage E-L 27 with reduced expression from stage E-L 15 or E-L 27 to stage E-L 38; groups 13, 14 and 15 contain repressed genes from stage E-L 15 to stage E-L 27, followed by a significant induction in their expression; groups 16 and 17 contain repressed genes from stage E-L 15 to stage E-L 27, with no significant subsequent change; group 18 contains negatively regulated genes along the whole time course.
Mentions: An in-house R script was written to group DE genes with similar expression pattern based on the adjusted p-values. By indicating a significant up-regulation with “1”, a significant down-regulation with “-1” and a non-significant difference with “0”, the three comparisons between the developmental stages can be summarized with a triplet, e.g. “1, 0, 1”. This example indicates that there is a significant up-regulation going from the first to the second time point, no significant difference between the second and third time points, and a significant positive difference when comparing the first and last time points. Altogether, 27 different categories can be defined in this way, and 18 of these contain relevant patterns (for example the pattern “1, 1, −1” is impossible). These 18 groups are visualized in Figure 1. Each gene showing at least one significant difference between developmental stages was classified into one of these categories, for both the wild type and the mutant. The number of differentially expressed genes that fell to each pattern were compared between the wild-type and the mutant.Figure 1

Bottom Line: However, the key genes underpinning molecular and cellular processes that play a significant role in seed development are not well characterized.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.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.

View Article: PubMed Central - PubMed

Affiliation: Fondazione Edmund Mach, Research and Innovation Centre, Via E, Mach 1-38010 San Michele all'Adige, Trento, Italy. laura.costantini@fmach.it.

ABSTRACT

Background: Seedless 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.

Results: The 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.

Conclusions: This 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.

Show MeSH