Exploring salt tolerance mechanisms using machine learning for transcriptomic insights: case study in Spartina alterniflora

Abstract

Salt stress poses a significant threat to global cereal crop production, emphasizing the need for a comprehensive understanding of salt tolerance mechanisms. Accurate functional annotations of differentially expressed genes are crucial for gaining insights into the salt tolerance mechanism. The challenge of predicting gene functions in under-studied species, especially when excluding infrequent GO terms, persists. Therefore, we proposed the use of NetGO 3.0, a machine learning-based annotation method that does not rely on homology information between species, to predict the functions of differentially expressed genes under salt stress. Spartina alterniflora, a halophyte with salt glands, exhibits remarkable salt tolerance, making it an excellent candidate for in-depth transcriptomic analysis. However, current research on the S. alterniflora transcriptome under salt stress is limited. In this study we used S. alterniflora as an example to investigate its transcriptional responses to various salt concentrations, with a focus on understanding its salt tolerance mechanisms. Transcriptomic analysis revealed substantial changes impacting key pathways, such as gene transcription, ion transport, and ROS metabolism. Notably, we identified a member of the SWEET gene family in S. alterniflora, SA_12G129900.m1, showing convergent selection with the rice ortholog SWEET15. Additionally, our genome-wide analyses explored alternative splicing responses to salt stress, providing insights into the parallel functions of alternative splicing and transcriptional regulation in enhancing salt tolerance in S. alterniflora. Surprisingly, there was minimal overlap between differentially expressed and differentially spliced genes following salt exposure. This innovative approach, combining transcriptomic analysis with machine learning-based annotation, avoids the reliance on homology information and facilitates the discovery of unknown gene functions, and is applicable across all sequenced species.

Acknowledgements

This work was financially supported by National Key R&D Program of China (2023ZD04073), the Nanfan special project, CAAS, Grant No. YBXM2304, and the Innovation Program of the Chinese Academy of Agricultural Sciences.

Author contributions

H.H.L. conceived the original idea, designed the experiments, and provided overall supervision and direction of the work. Z.P.H., S.K.C., K.H.H., and T.X.Y. performed the experiments and data analysis. J.J.F. and S.G. provided valuable advice for the experimental design and optimization. Z.P.H., S.K.C., and H.H.L. wrote the manuscript. All authors discussed and commented on the manuscript.

Data availability

All relevant data can be found within the paper and its supporting materials.

Conflict of interest

The authors declare no conflicts of interest.

Supplementary data

Supplementary data are available at Horticulture Research online.

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