Transcriptome analysis of fenugreek under mixed saline-alkali stress

Soil salinization and alkalization are major constraints to global crop production. Fenugreek (Trigonella foenum-graecum L.) is considered a potential salt-alkali-tolerant crop; however, the molecular mechanisms underlying its tolerance remain poorly understood.

Four fenugreek provenances were evaluated under saline-alkali stress at the seedling stage. Growth and physiological traits were measured to assess stress tolerance. Based on these results, the most tolerant provenance was selected for transcriptome analysis. Saline-alkali treatments of 0 (control), 100 mmol/L (moderate stress), and 200 mmol/L (severe stress) were applied according to preliminary physiological experiments to induce measurable but non-lethal stress responses suitable for transcriptomic investigation.

The tolerance of the four provenances followed the order: Qinghai > Anhui > Yunnan > Gansu, with the Qinghai provenance showing the strongest tolerance. Transcriptome sequencing generated 47,757 unigenes, of which 27,300 were successfully annotated. A total of 2,041 differentially expressed genes (DEGs) were identified among treatments. Functional enrichment analysis indicated that these DEGs were mainly involved in metabolic processes, stress responses, and key pathways such as flavonoid biosynthesis, plant hormone signal transduction, and starch and sucrose metabolism. In addition, 24 transcription factors associated with abiotic stress were identified, primarily belonging to the AP2/ERF, bHLH, MYB, and NAC families. The reliability of the RNA-Seq results was confirmed by qRT-PCR analysis of nine selected DEGs using β-actin as the reference gene.

These findings provide new insights into the molecular mechanisms underlying saline-alkali tolerance in fenugreek and offer valuable genetic resources for the breeding of stress-tolerant cultivars.