Combined Transcriptome and Proteome Analysis Reveals the Molecular Mechanism by Which ZmPDI Improves Salt Resistance in Rice (Oryza sativa)

As one of the most salt-tolerant grasses, characterizing salt-tolerance genes of Zoysia matrella [L.] Merr. not only broaden the theoretical information of salt tolerance, but also provide new salt-resistant genetic resources for crop breeding. The salt-inducible protein disulfide isomerase (ZmPDI) of Zoysia matrella [L.] Merr. was proved to enhance salt tolerance in homologous overexpression transgenic plants. In order to evaluate its potential application in crops, we conducted the salt tolerance evaluation in heterologous overexpression transgenic rice (OX-ZmPDI), Wild-type (WT) rice, and LOC_Os11g09280 (OsPDI, homologous gene of ZmPDI in rice) knock-out rice generated by CRISPR-Cas9 system (CR-OsPDI). Our findings revealed that OX-ZmPDI rice was higher and exhibited longer main root length, more proline (Pro) and malondialdehyde (MDA), and higher peroxidase (POD) activity than WT control after salt treatment, while CR-OsPDI resulted in contrary phenotypes. These results indicated that ZmPDI can significantly enhance the salt tolerance in rice, whereas loss-of-function of OsPDI reduces the salt tolerance. To further investigate these differences at the molecular level, we collected roots from OX-ZmPDI transgenic, CR-OsPDI transgenic, and wild-type (WT) plants at 0 and 24 h after salt treatment for RNA-seq and data-independent acquisition (DIA) proteome sequencing. Combined analysis of the transcriptome and proteome revealed that ZmPDI has the potential to enhance the salt tolerance of rice by modulating the expression of laccase-6, zingipain-2, WIP3, FKBP65, AKR4C10, GBSSII, Pho1, and TRXf1. Those results provided new information for the molecular regulation mechanism by which ZmPDI improves salt tolerance, and prove the potential of ZmPDI for application in crop breeding.