Application of RNA sequencing to understand the benefits of endophytes in the salt-alkaline resistance of rice seedlings

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.