Convergent and divergent signaling pathways in C3 rice and C4 foxtail millet crops in response to salt stress

Salt stress is a global constraint on agricultural production. Therefore, the development of salt tolerant plants has become a current research hotspot. While salt tolerance has evolved more frequently in C4 grass lineages, few studies have explored the molecular bases underlying salt stress tolerance in the C4 crop foxtail millet. In this study, we used a multi-pronged approach spanning the omics analyses of transcriptomes and physiological analysis of the C3 crop rice and the C4 model crop foxtail millet to investigate their responses to salt stress. The results revealed that compared to C3 rice, C4 foxtail millet has upregulated abscisic acid (ABA) and notably reduced CK biosynthesis and signaling transduction under salt stress. Salt stress in C3 rice plants triggered rapid downregulation of photosynthesis related genes, which was coupled with severely reduced net photosynthetic rates. In the salt-treated C3 rice and C4 foxtail millet, some stress responsive transcription factors (TFs), such as AP2/ERF, WRKY and MYB, underwent strong and distinct transcriptional changes. Based on a weighted gene co-expression network analysis (WGCNA), the AP2/ERF transcription factor Rice Starch Regulator1 SiRSR1 (Seita.3G044600) was identified as a key regulator of the salt stress response. To confirm its function, we generated OsRSR1-knockout lines using CRISPR/Cas9 genome editing in rice and its upstream repressor SimiR172a-overexpressing (172a-OE) transgenic plants in foxtail millet, which both showed increased salt tolerance. Overall, this study not only provides new insights into the convergent regulation of the salt stress responses of foxtail millet and rice, but it also sheds light on the divergent signaling networks between them in response to salt stress.