Gene Set Enrichment Analysis Highlights ATP Hydrolysis and Membrane-Associated Pathways in Drought-Tolerant Potato Cultivars

Firat Kurt

doi:10.31015/2025.si.6

Gene Set Enrichment Analysis Highlights ATP Hydrolysis and Membrane-Associated Pathways in Drought-Tolerant Potato Cultivars

Abstract

This study investigated the molecular responses of drought-tolerant and drought-sensitive potato cultivars using Gene Set Enrichment Analysis (GSEA) on RNA-seq data. The main objective was to identify activated or suppressed biological pathways and functional gene groups under drought stress, providing insights into drought tolerance mechanisms. Principal Component Analysis (PCA) and heatmap analysis revealed distinct gene expression profiles between the drought-tolerant cultivar FB and the drought-sensitive cultivar Cardinal. GSEA identified statistically significant enrichment of the ATP hydrolysis activity (GO:0016887) term in the FB cultivar, suggesting enhanced energy metabolism under drought conditions. While other GO terms—such as those related to the plasma membrane (GO:0005886), transmembrane transport (GO:0055085), and intracellular membrane-bounded organelles (GO:0043231)—did not reach statistical significance, their positive normalized enrichment scores (NES) indicated a trend toward higher expression in FB. The observed upregulation of ATP hydrolysis activity suggests the critical role of energy-dependent processes, such as protein repair and ion transport, in drought tolerance. Additionally, the results showed the importance of maintaining plasma membrane integrity, regulating transmembrane transport for water conservation, and the involvement of intracellular organelles in adapting to drought stress.

Keywords

GSEA, Enrichment analysis, Potato, RNA-seq, Drought tolerance

References

Afgan, E., Baker, D., van den Beek, M., Blankenberg, D., Bouvier, D., Čech, M., Chilton, J., Clements, D., Coraor, N., Eberhard, C., Grüning, B., Guerler, A., Hillman-Jackson, J., von Kuster, G., Rasche, E., Soranzo, N., Turaga, N., Taylor, J., Nekrutenko, A., & Goecks, J. (2016). The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Research, 44(W1), W3–W10. https://doi.org/10.1093/nar/gkw343
Barra, M., Meneses, C., Riquelme, S., Pinto, M., Lagüe, M., Davidson, C., & Tai, H. H. (2019). Transcriptome profiles of contrasting potato (Solanum tuberosum L.) genotypes under water stress. Agronomy, 9(12), 848. https://doi.org/10.3390/agronomy9120848
Batut, B., Freeberg, M., Heydarian, M., Erxleben, A., Videm, P., Blank, C., Doyle, M., Soranzo, N., van Heusden, P., & Delisle, L. (2016). Reference-based RNA-Seq data analysis. Galaxy Training Materials, 1(1), 1. https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/ref-based/tutorial.html
Doyle, M., Phipson, B., & Dashnow, H. (2020). RNA-Seq reads to counts. Galaxy Training Materials. https://training.galaxyproject.org/training-material/
ElBasyoni, I., Saadalla, M., Baenziger, S., Bockelman, H., & Morsy, S. (2017). Cell membrane stability and association mapping for drought and heat tolerance in a worldwide wheat collection. Sustainability, 9(9), 1606. https://doi.org/10.3390/su9091606
Guo, X., Peng, C., Li, T., Huang, J., Song, H., Zhu, Q., & Wang, M. (2021). The effects of drought and re-watering on non-structural carbohydrates of Pinus tabulaeformis seedlings. Biology, 10(9), 915. https://doi.org/10.3390/biology10090915
Han, H., Lee, S., & Lee, I. (2019). Ngsea: Network-based gene set enrichment analysis for interpreting gene expression phenotypes with functional gene sets. Molecules and Cells, 42(8), 579–588. https://doi.org/10.14348/MOLCELLS.2019.0065
Hiltemann, S., Rasche, H., Gladman, S., Hotz, H. R., Larivière, D., Blankenberg, D., Jagtap, P. D., Wollmann, T., Bretaudeau, A., Goué, N., Griffin, T. J., Royaux, C., Le Bras, Y., Mehta, S., Syme, A., Coppens, F., Droesbeke, B., Soranzo, N., Bacon, W., … Batut, B. (2023). Galaxy training: A powerful framework for teaching! PLoS Computational Biology, 19(1), e1010752. https://doi.org/10.1371/journal.pcbi.1010752
Hong, Y., Zhang, W., & Wang, X. (2010). Phospholipase D and phosphatidic acid signalling in plant response to drought and salinity. Plant, Cell & Environment, 33(4), 627–635. https://doi.org/10.1111/j.1365-3040.2009.02087.x
Hotelling, H. (1933). Analysis of a complex of statistical variables into principal components. Journal of Educational Psychology, 24(6), 417–441. https://doi.org/10.1037/h0071325

Jarzyniak, K. M., & Jasiński, M. (2014). Membrane transporters and drought resistance: A complex issue. Frontiers in Plant Science, 5, 687. https://doi.org/10.3389/fpls.2014.00687
Jian, Y., Gao, C., Shang, Y., Qin, J., Duan, S., Bian, C., & Li, G. (2024). Metabolomic and transcriptomic analyses reveal MYB-related genes involved in drought resistance in grafted potatoes via the flavonoid pathway. Plant Stress, 14, 100665. https://doi.org/10.1016/j.stress.2024.100665
Johnson, S. C. (1967). Hierarchical clustering schemes. Psychometrika, 32(3), 241–254. https://doi.org/10.1007/BF02289588
Kawamoto, K., Masutomi, H., Matsumoto, Y., Akutsu, K., Momiki, R., & Ishihara, K. (2024). Drought response of tuber genes in processing potatoes (Solanum tuberosum L.) in Japan. Molecular Biology Reports, 51(1), 1020. https://doi.org/10.1007/s11033-024-09953-0
Kolde, R. (2019). pheatmap: Pretty heatmaps (R package version 1.0.12). CRAN. https://CRAN.R-project.org/package=pheatmap
Korotkevich, G., Sukhov, V., Budin, N., Shpak, B., Artyomov, M. N., & Sergushichev, A. (2016). Fast gene set enrichment analysis. bioRxiv, 060012. https://doi.org/10.1101/060012
Liu, N., Ni, Z., Zhang, H., Chen, Q., Gao, W., Cai, Y., Li, M., Sun, G., & Qu, Y. Y. (2018). The gene encoding subunit a of the vacuolar H+-ATPase from cotton plays an important role in conferring tolerance to water deficit. Frontiers in Plant Science, 9, 758. https://doi.org/10.3389/fpls.2018.00758
Luciński, R., & Adamiec, M. (2023). The role of plant proteases in the response of plants to abiotic stress factors. Frontiers in Plant Physiology, 14, 1330216. https://doi.org/10.3389/fphgy.2023.1330216
Maleki, F., Ovens, K., Hogan, D. J., & Kusalik, A. J. (2020). Gene set analysis: Challenges, opportunities, and future research. Frontiers in Genetics, 11, 654. https://doi.org/10.3389/fgene.2020.00654
Movahedi, A., Dzinyela, R., Aghaei-Dargiri, S., Alhassan, A. R., Yang, L., & Xu, C. (2023). Advanced study of drought-responsive protein pathways in plants. Agronomy, 13(3), 849. https://doi.org/10.3390/agronomy13030849
Pearson, K. (1901). On lines and planes of closest fit to systems of points in space. Philosophical Magazine, 2(11), 559–572. https://doi.org/10.1080/14786440109462720
Qin, T., Wang, Y., Pu, Z., Shi, N., Dormatey, R., Wang, H., & Sun, C. (2024). Comprehensive transcriptome and proteome analyses reveal the drought responsive gene network in potato roots. Plants, 13(11), 1530. https://doi.org/10.3390/plants13111530
Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., & Mesirov, J. P. (2005). Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences, 102(43), 15545–15550. https://doi.org/10.1073/pnas.0506580102
R Core Team. (2023). R: A language and environment for statistical computing. R Foundation for Statistical Computing. https://www.R-project.org/
Wang, M., Wang, L., Yu, X., Zhao, J., Tian, Z., Liu, X., Wang, G., Zhang, L., & Guo, X. (2023). Enhancing cold and drought tolerance in cotton: A protective role of SikCOR413PM1. BMC Plant Biology, 23(1), 74. https://doi.org/10.1186/s12870-023-04572-6
Wang, P., Wu, X., Li, N., Nie, H., Ma, Y., Wu, J., Zhang, Z., & Ma, Y. (2025). The StbHLH47 transcription factor negatively regulates drought tolerance in potato (Solanum tuberosum L.). BMC Plant Biology, 25(1), 10. https://doi.org/10.1186/s12870-024-06010-7
Yang, X., Lu, M., Wang, Y., Wang, Y., Liu, Z., & Chen, S. (2021). Response mechanism of plants to drought stress. Horticulturae, 7(3), 50. https://doi.org/10.3390/horticulturae7030050
Yi, J., Wang, L., Chen, Y., Li, C., & Gong, M. (2024). Potato E3 ubiquitin ligase StXERICO1 positively regulates drought resistance by enhancing ABA accumulation in potato and tobacco and interacts with the miRNA Novel-miR1730-3p and proteins StUBC and StTLP. Agronomy, 14(10), 2305. https://doi.org/10.3390/agronomy14102305

Details

Primary Language

English

Subjects

Plant Biotechnology in Agriculture

Journal Section

Research Article

Authors

Firat Kurt ^*
0000-0003-0172-1953
Türkiye

Early Pub Date

November 13, 2025

Publication Date

December 28, 2025

Submission Date

September 8, 2025

Acceptance Date

October 23, 2025

Published in Issue

Year 2025 Volume: 9 Number: Special

DOI

https://doi.org/10.31015/2025.si.6

IZ

https://izlik.org/JA69UP62XA

APA

Kurt, F. (2025). Gene Set Enrichment Analysis Highlights ATP Hydrolysis and Membrane-Associated Pathways in Drought-Tolerant Potato Cultivars. International Journal of Agriculture Environment and Food Sciences, 9(Special), 52-59. https://doi.org/10.31015/2025.si.6

AMA

1.Kurt F. Gene Set Enrichment Analysis Highlights ATP Hydrolysis and Membrane-Associated Pathways in Drought-Tolerant Potato Cultivars. int. j. agric. environ. food sci. 2025;9(Special):52-59. doi:10.31015/2025.si.6

Chicago

Kurt, Firat. 2025. “Gene Set Enrichment Analysis Highlights ATP Hydrolysis and Membrane-Associated Pathways in Drought-Tolerant Potato Cultivars”. International Journal of Agriculture Environment and Food Sciences 9 (Special): 52-59. https://doi.org/10.31015/2025.si.6.

EndNote

Kurt F (December 1, 2025) Gene Set Enrichment Analysis Highlights ATP Hydrolysis and Membrane-Associated Pathways in Drought-Tolerant Potato Cultivars. International Journal of Agriculture Environment and Food Sciences 9 Special 52–59.

IEEE

[1]F. Kurt, “Gene Set Enrichment Analysis Highlights ATP Hydrolysis and Membrane-Associated Pathways in Drought-Tolerant Potato Cultivars”, int. j. agric. environ. food sci., vol. 9, no. Special, pp. 52–59, Dec. 2025, doi: 10.31015/2025.si.6.

ISNAD

Kurt, Firat. “Gene Set Enrichment Analysis Highlights ATP Hydrolysis and Membrane-Associated Pathways in Drought-Tolerant Potato Cultivars”. International Journal of Agriculture Environment and Food Sciences 9/Special (December 1, 2025): 52-59. https://doi.org/10.31015/2025.si.6.

JAMA

1.Kurt F. Gene Set Enrichment Analysis Highlights ATP Hydrolysis and Membrane-Associated Pathways in Drought-Tolerant Potato Cultivars. int. j. agric. environ. food sci. 2025;9:52–59.

MLA

Kurt, Firat. “Gene Set Enrichment Analysis Highlights ATP Hydrolysis and Membrane-Associated Pathways in Drought-Tolerant Potato Cultivars”. International Journal of Agriculture Environment and Food Sciences, vol. 9, no. Special, Dec. 2025, pp. 52-59, doi:10.31015/2025.si.6.

Vancouver

1.Firat Kurt. Gene Set Enrichment Analysis Highlights ATP Hydrolysis and Membrane-Associated Pathways in Drought-Tolerant Potato Cultivars. int. j. agric. environ. food sci. 2025 Dec. 1;9(Special):52-9. doi:10.31015/2025.si.6

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Gene Set Enrichment Analysis Highlights ATP Hydrolysis and Membrane-Associated Pathways in Drought-Tolerant Potato Cultivars

Gene Set Enrichment Analysis Highlights ATP Hydrolysis and Membrane-Associated Pathways in Drought-Tolerant Potato Cultivars

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