Seed germination is a crucial stage in the life cycle of annuals in arid, saline regions and is particularly vulnerable to abiotic stresses. Peganum harmala, a valuable medicinal plant, has limited research on its seed germination response to different environmental stresses in the arid, saline regions of Central Asia. To investigate this, we studied the effects of various temperature regimes (ranging from 20/5 to 35/20 °C), light exposure (12 hours light/12 hours dark and continuous dark), seven levels of polyethylene glycol (PEG-6000) concentration (ranging from 0–30%), and four types of salinity (ranging from 0–600 mmol L⁻¹). Our findings show that photoperiod and temperature significantly influence germination. Optimal temperature range for seed germination was observed at 30/15 °C, with simulated critical and limit values of drought tolerance being highest (17.30% and 24.98%). However, higher temperatures (35/20 °C) and lower temperatures (20/5 °C) reduced the critical and limit values of drought tolerance. Additionally, the type and concentration of salinity had a significant effect on the seed germination, shoot, and root lengths of P. harmala. Regression analysis indicated that the critical values of NaCl, Na₂SO₄, NaHCO₃, and Na₂CO₃ tolerance during germination were 178 mmol L⁻¹, 101 mmol L⁻¹, 106 mmol L⁻¹, and 54 mmol L⁻¹, respectively. Salinity inhibition on seed germination followed the order: NaCl < NaHCO₃ < Na₂SO₄ < Na₂CO₃. Moreover, NaCl, Na₂SO₄, NaHCO₃, and Na₂CO₃ significantly inhibited the growth of P. harmala seedlings in both shoots and roots. Our study demonstrates the sensitivity of P. harmala to environmental factors such as light, temperature, drought, and salinity. The study provides valuable information on the germination ecology of P. harmala under diverse ecological scenarios, which can be useful in developing efficient propagation and utilization of this medicinal plant.

Dimorphic seeds from Suaeda aralocaspica exhibit different germination behaviors that are thought to be a bet-hedging strategy advantageous in harsh and unpredictable environments. To understand the molecular mechanisms of Suaeda aralocaspica dimorphic seed germination, we applied RNA sequencing and small RNA sequencing for samples collected at three germination stages. A total of 79,414 transcripts were assembled using Trinity, of which 57.67% were functionally annotated. KEGG enrichment unveiled that photosynthesis and flavonol biosynthesis pathways were activated earlier in brown seed compared with black seed. Gene expression analysis revealed that nine candidate unigenes in gibberellic acid and abscisic acid signal transduction and 23 unigenes in circadian rhythm-plant pathway showed distinct expression profiles to promote dimorphic seed germination. 194 conserved miRNAs comprising 40 families and 21 novel miRNAs belonging to 20 families in Suaeda aralocaspica were identified using miRDeep-P and Mfold. The expression of miRNAs in black seed was suppressed at imbibition stage. Among the identified miRNAs, 59 conserved and 13 novel miRNAs differentially expressed during seed germination. Of which, 43 conserved and nine novel miRNAs showed distinct expression patterns between black and brown seed. Using TAPIR, 208 unigenes were predicted as putative targets of 35 conserved miRNA families and 17 novel miRNA families. Among functionally annotated targets, genes participated in transcription regulation constituted the dominant category, followed by genes involved in signaling and stress response. Seven of the predicted targets were validated using 5′ rapid amplification of cDNA ends or real-time quantitative reverse transcription-PCR. Our results indicate that specific genes and miRNAs are regulated differently between black and brown seed during germination, which may contribute to the different germination behaviors of Suaeda aralocaspica dimorphic seeds in unpredictable variable environments. Our results lay a solid foundation for further studying the roles of candidate genes and miRNAs in Suaeda aralocaspica dimorphic seed germination.