Temporal transcriptome and WGCNA analysis unveils divergent drought response strategies in wild and cultivated Solanum varieties
Drought, exacerbated by climate change, threatens global food security, particularly impacting crop products, including tomatoes, which are economically essential but drought sensitive. This study explores drought responses in the wild-type Solanum pennellii (WT), known for drought tolerance, and cu...
Saved in:
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2025-07-01
|
| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2025.1572619/full |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850068790949183488 |
|---|---|
| author | Athira C. Rajeev Athira C. Rajeev Rajesh Raju Archana Pan |
| author_facet | Athira C. Rajeev Athira C. Rajeev Rajesh Raju Archana Pan |
| author_sort | Athira C. Rajeev |
| collection | DOAJ |
| description | Drought, exacerbated by climate change, threatens global food security, particularly impacting crop products, including tomatoes, which are economically essential but drought sensitive. This study explores drought responses in the wild-type Solanum pennellii (WT), known for drought tolerance, and cultivated Solanum lycopersicum (CT), through RNA-Seq analysis at three drought intervals (2 Weeks +5D, +8D, and +11D). Across these points, WT and CT showed 716 and 1459 differentially expressed genes (DEGs), respectively. Pathway enrichment revealed distinct metabolic adaptations: wild varieties prioritized arginine and proline metabolism early, shifting to cutin, suberin, and wax biosynthesis by day 11, while cultivated varieties emphasized steroid biosynthesis, secondary metabolite production, and photosynthesis-related pathways. Transcription factor analysis highlighted HB-HD-ZIP enrichment in wild varieties, contrasting with broader, less coordinated TF activation in cultivated varieties. WGCNA identified the blue module as significantly associated with prolonged drought in both species. Network analysis showed ribosomal pathways enriched in CT, while in WT, it was observed broader pathway enrichment, including secondary metabolites, carbon metabolism, and oxidative stress pathways. In WT unique hub genes were, sucrose synthase and malate synthase, suggesting specialized drought adaptation mechanisms. These findings highlight multifaceted drought resilience strategy of WT compared to growth-focused response of CT, offering a foundation for breeding drought-resistant tomato varieties critical for food security under climate pressures. |
| format | Article |
| id | doaj-art-9d6c5d3b13704e2cb214ff95fbf559a0 |
| institution | DOAJ |
| issn | 1664-462X |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj-art-9d6c5d3b13704e2cb214ff95fbf559a02025-08-20T02:47:58ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2025-07-011610.3389/fpls.2025.15726191572619Temporal transcriptome and WGCNA analysis unveils divergent drought response strategies in wild and cultivated Solanum varietiesAthira C. Rajeev0Athira C. Rajeev1Rajesh Raju2Archana Pan3Department of Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, IndiaCentre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore, IndiaCentre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore, IndiaDepartment of Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, IndiaDrought, exacerbated by climate change, threatens global food security, particularly impacting crop products, including tomatoes, which are economically essential but drought sensitive. This study explores drought responses in the wild-type Solanum pennellii (WT), known for drought tolerance, and cultivated Solanum lycopersicum (CT), through RNA-Seq analysis at three drought intervals (2 Weeks +5D, +8D, and +11D). Across these points, WT and CT showed 716 and 1459 differentially expressed genes (DEGs), respectively. Pathway enrichment revealed distinct metabolic adaptations: wild varieties prioritized arginine and proline metabolism early, shifting to cutin, suberin, and wax biosynthesis by day 11, while cultivated varieties emphasized steroid biosynthesis, secondary metabolite production, and photosynthesis-related pathways. Transcription factor analysis highlighted HB-HD-ZIP enrichment in wild varieties, contrasting with broader, less coordinated TF activation in cultivated varieties. WGCNA identified the blue module as significantly associated with prolonged drought in both species. Network analysis showed ribosomal pathways enriched in CT, while in WT, it was observed broader pathway enrichment, including secondary metabolites, carbon metabolism, and oxidative stress pathways. In WT unique hub genes were, sucrose synthase and malate synthase, suggesting specialized drought adaptation mechanisms. These findings highlight multifaceted drought resilience strategy of WT compared to growth-focused response of CT, offering a foundation for breeding drought-resistant tomato varieties critical for food security under climate pressures.https://www.frontiersin.org/articles/10.3389/fpls.2025.1572619/fullSolanumwildcultivateddroughttranscriptomeWGCNA |
| spellingShingle | Athira C. Rajeev Athira C. Rajeev Rajesh Raju Archana Pan Temporal transcriptome and WGCNA analysis unveils divergent drought response strategies in wild and cultivated Solanum varieties Frontiers in Plant Science Solanum wild cultivated drought transcriptome WGCNA |
| title | Temporal transcriptome and WGCNA analysis unveils divergent drought response strategies in wild and cultivated Solanum varieties |
| title_full | Temporal transcriptome and WGCNA analysis unveils divergent drought response strategies in wild and cultivated Solanum varieties |
| title_fullStr | Temporal transcriptome and WGCNA analysis unveils divergent drought response strategies in wild and cultivated Solanum varieties |
| title_full_unstemmed | Temporal transcriptome and WGCNA analysis unveils divergent drought response strategies in wild and cultivated Solanum varieties |
| title_short | Temporal transcriptome and WGCNA analysis unveils divergent drought response strategies in wild and cultivated Solanum varieties |
| title_sort | temporal transcriptome and wgcna analysis unveils divergent drought response strategies in wild and cultivated solanum varieties |
| topic | Solanum wild cultivated drought transcriptome WGCNA |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2025.1572619/full |
| work_keys_str_mv | AT athiracrajeev temporaltranscriptomeandwgcnaanalysisunveilsdivergentdroughtresponsestrategiesinwildandcultivatedsolanumvarieties AT athiracrajeev temporaltranscriptomeandwgcnaanalysisunveilsdivergentdroughtresponsestrategiesinwildandcultivatedsolanumvarieties AT rajeshraju temporaltranscriptomeandwgcnaanalysisunveilsdivergentdroughtresponsestrategiesinwildandcultivatedsolanumvarieties AT archanapan temporaltranscriptomeandwgcnaanalysisunveilsdivergentdroughtresponsestrategiesinwildandcultivatedsolanumvarieties |