Transcriptome analysis reveals key genes in response to salinity stress during seed germination in Setaria italica

Abstract Salinity stress severely affects agricultural production. Seed germination is the most critical phase of plant life and is regulated by genetic and environmental factors. Setaria italica is an excellent model system for investigating the response to abiotic stresses. However, the key genes in response to salinity stress during seed germination in S. italica are largely unknown. Here, the transcriptional response of imbibed and radicle-protruded seeds to salinity stress revealed 4090 salinity responsive genes (SRGs) from the salt-tolerant cultivar Chigu 10 (CG) and salt-sensitive cultivar Fenghong 3 (FH) by RNA sequencing. Enrichment and expression pattern analysis indicated that the CG and FH cultivars exhibited specific similarities and preferences in the salinity stress response. Heatmap analysis suggested that S. italica seeds germinated under salinity stress required enhanced hormone regulation, more active primary metabolism and energy production, more cell wall modifications, and higher anticipation of autotrophic growth. Furthermore, functional validation experiments demonstrated that the SiDRM2 and SiKOR1 of SRGs significantly influenced seed germination under salinity stress. Collectively, our findings not only provide new insights into the regulatory mechanisms of seed germination under salinity stress, but also reveal promising gene resources to genetically improve the salt-tolerance capacity of S. italica and other crops.