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| Status |
Public on Apr 14, 2024 |
| Title |
Investigating the phenotypic plasticity of two red grapevine varieties: an integrated study of transcriptome and environmentome by WGCNA |
| Organism |
Vitis vinifera |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Grapevine (Vitis spp., family Vitaceae) is characterized by a marked phenotypic plasticity and its ability to withstand various environmental conditions depends on the activation of highly coordinated responses, resulting from the interaction among genotypes (G) and environmental factors (E). Understanding genotype by environment (GxE) interplays is highly complex and challenging, and often the outcome of the genetic responses to field performance is not straightforward also due to the difficulties to reach a precise definition of the E component in field studies. In this work, the transcriptome of commercially ripe berries of Cabernet sauvignon and Aglianico genotypes grown in open-field at three different sites of central-southern Italy (Campania, Molise and Sicily) was analyzed by RNAseq. These transcriptomic data were integrated with a comprehensive set of climatic indices, forming an “environmentome”, through Weighted Gene Co-expression Network Analysis (WGCNA). A total of 11,887 differentially expressed genes (DEGs) have been retrieved, most of them found in the Aglianico genotype, suggesting that Aglianico transcriptome is largely influenced by the environment. Furthermore, the comparisons involving the Sicilian site exhibited the highest number of DEGs for both genotypes. WGCNA suggested that most of the climatic data (such as daily maximum air temperature, relative humidity, air pressure, dew point, hours of sun radiation) significantly correlated with “lightcyan1” module. Among these eingengenes, the low expression of ACA10 cation transporter is suggested to be indirectly related to the low anthocyanin content in Cabernet sauvignon in Campania, thus confirming WGCNA as powerful approach to identify gene of high biological interest. Similarly, transcriptome was also correlated with quality trait, such as total soluble solids and polyphenol content, leading to the discovery of hub genes that might function as markers of wine quality.
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| Overall design |
In order to explored the gene-environment (GxE) interactions of two red grape varieties, samples of fully ripe berries of Aglianico and Cabernet Sauvignon varieties grown in open-field conditions at three different sites in southern Italy (Sicily, Molise and Campania) were collected.
We then performed RNAseq and gene expression analysis considering three biological replicates for each sample above described
Differential expression analysis of each variety in the trhee sites was performed
WGCNA was applied to correlate the RNAseq results with several climatic parameters, as well as and with quality traits including total soluble solid, anthocyanin and polyphenol content.
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| Contributor(s) |
Sicilia A, Villano C, Aversano R, Di Serio E, Nicolosi E, Ferlito F, Lo Piero AR |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Mar 15, 2024 |
| Last update date |
Apr 14, 2024 |
| Contact name |
Angela Roberta Lo Piero |
| E-mail(s) |
rlopiero@unict.it
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| Phone |
+39-0957580238
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| Organization name |
University of Catania
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| Department |
Di3A
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| Lab |
Plant genetics
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| Street address |
Via S. Sofia 98
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| City |
Catania |
| State/province |
CT |
| ZIP/Postal code |
95123 |
| Country |
Italy |
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| Platforms (1) |
| GPL18740 |
Illumina HiSeq 2000 (Vitis vinifera) |
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| Samples (18)
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| GSM8148764 |
Grape berry. Aglianico genotype, Campania site rep1 |
| GSM8148765 |
Grape berry. Aglianico genotype, Campania site rep2 |
| GSM8148766 |
Grape berry. Aglianico genotype, Campania site rep3 |
| GSM8148767 |
Grape berry. Aglianico genotype, Molise site rep1 |
| GSM8148768 |
Grape berry. Aglianico genotype, Molise site rep2 |
| GSM8148769 |
Grape berry. Aglianico genotype, Molise site rep3 |
| GSM8148770 |
Grape berry. Aglianico genotype, Sicily site rep1 |
| GSM8148771 |
Grape berry. Aglianico genotype, Sicily site rep2 |
| GSM8148772 |
Grape berry. Aglianico genotype, Sicily site rep3 |
| GSM8148773 |
Grape berry. Cabernet sauvignon genotype, Campania site rep1 |
| GSM8148774 |
Grape berry. Cabernet sauvignon genotype, Campania site rep2 |
| GSM8148775 |
Grape berry. Cabernet sauvignon genotype, Campania site rep3 |
| GSM8148776 |
Grape berry. Cabernet sauvignon genotype, Molise site rep1 |
| GSM8148777 |
Grape berry. Cabernet sauvignon genotype, Molise site rep2 |
| GSM8148778 |
Grape berry. Cabernet sauvignon genotype, Molise site rep3 |
| GSM8148779 |
Grape berry. Cabernet sauvignon genotype, Sicily site rep1 |
| GSM8148780 |
Grape berry. Cabernet sauvignon genotype, Sicily site rep2 |
| GSM8148781 |
Grape berry. Cabernet sauvignon genotype, Sicily site rep3 |
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| Relations |
| BioProject |
PRJNA1088419 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE261685_Unigene.fasta.gz |
35.6 Mb |
(ftp)(http) |
FASTA |
| GSE261685_raw_counts.txt.gz |
1.8 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
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