BACKGROUND:Salt-alkali stress represents one of the most stressful events with deleterious consequences for plant growth and crop productivity. Despite studies focusing on the effects of salt-alkali stress on morphology and physiology, its molecular mechanisms remain unclear. Here, we employed RNA-sequencing (RNA-seq) to understand how Na2CO3 stress inhibits rice seedling growth.RESULTS:Na2CO3 stress significantly inhibited the growth of rice seedlings. Through RNA-seq, many differentially expressed genes (DEGs) were shown to be potentially involved in the rice seedling response to salt-alkali stress. After 1-day and 5-day treatments, RNA-seq identified 1780 and 2315 DEGs in the Na2CO3-treated versus -untreated rice seedling shoots, respectively. According to the gene ontology enrichment and the Kyoto Encylopedia of Genes and Genomes annotation of DEGs, the growth-inhibition processes associated with salt-alkali stress involve a myriad of molecular events, including biosynthesis and metabolism, enzyme activity, and binding, etc. CONCLUSION: Collectively, the transcriptome analyses in the present work revealed several potential key regulators of plant response to salt-alkali stress, and might pave a way to improve salt-alkali stress tolerance in rice.

Endophytes significantly improve salt-alkaline resistance of rice seedlings and promote their growth, but the definite mechanisms remain largely unknown. This study aimed to understand the molecular players behind the endophytic benefits for rice seedlings under salt-alkaline stress. RNA sequencing (RNA-seq) was performed on the roots and shoots of rice seedling (Oryza sativa L.) with/without endophytic infection under 10 mM Na2CO3-treatment. The differential expression genes (DEGs) resulting from endophytic infection were analyzed, and the functions of DEGs were annotated using gene ontology (GO) enrichment and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Results showed endophytic infection significantly promoted the growth of rice seedlings under salt-alkaline stress. Through RNA-seq, many genes were shown to be potentially involved in the endophytic benefits for rice seedlings. At one day of endophytic infection, RNA-seq identified 3469 DEGs in rice seedling roots and 572 DEGs in shoots, whereas five days of endophytic infection led to 297 and 257 DEGs in roots and shoots, respectively. According to the GO and KEGG annotation of DEGs, the growth-promotion processes correlating with the beneficial endophyte-rice interplay involve a multitude of molecular events, including biosynthesis, energy metabolism, enzyme activity, photosynthesis, ROS-scavenging system, and hormonal signaling, etc. Together, this work presents evidence of plant-microbe interaction that extends insights into the mechanisms underlying the endophyte-rice association.