High-throughput yeast screening and transcriptomic integration identify salt-tolerance genes in Spartina alterniflora

Identifying genes that confer salt tolerance is essential for understanding the mechanisms underpinning salt tolerance in plants. Spartina alterniflora , a halophyte with exceptional salt and flooding tolerance and strong reproduction and dispersal capabilities, presents valuable potential for crop improvement and stress tolerance research. Here, we constructed a stress-induced yeast cDNA library and employed high-throughput screening under salt stress to identify 1,279 distinct genes. Gene ontology analysis revealed significant enrichment in transcription-related complexes, and these genes were predominantly enriched in categories related to salt stress responses. Transcriptome analysis identified 12,669 differentially expressed genes, and these genes were predominantly enriched in categories related to salt stress responses. By integrating transcriptome data across varying NaCl concentrations with knowledge of the S. alterniflora genome, we screened and identified two key genes: SA_26G130100.m1 , encoding a Multidrug and toxic compound extrusion (MATE) protein, and SA_04G199900.m1 , a novel protein with unknown function. Both genes exhibited significant expression changes under salt stress. Structural predictions revealed that the MATE transporter SA_26G130100.m1 possesses a compact substrate-binding cavity with unique residue composition, suggesting an evolutionary adaptation for efficient ion transport under salinity. Additionally, a genome-wide analysis of the S. alterniflora gene family encoding MATEs revealed that most members are root-expressed and salt-induced, implying a possible role in mitigating the effects of salt stress. This study provides a robust, highly efficient platform for the large-scale screening and identification of S. alterniflora genes conferring abiotic stress tolerance and offers a valuable genetic resource for advancing salt tolerance breeding programs. • A total of 1279 specific genes from Spartina alterniflora were identified under salt stress using a stress-induced yeast cDNA library and high-throughput screening. • The specific genes are significantly enriched in transcription-related complexes and categories associated with salt stress responses. • Two key salt-responsive genes, SA_26G130100.m1 and SA_04G199900.m1 , were identified by integrating transcriptome and stress-induced yeast cDNA library. • Most of the SaMATE genes are root-expressed and salt-induced.