Plant height is an essential characteristic of agronomic traits, and an ideal plant height is essential for achieving high crop yields. Foxtail millet (Setaria italica) has become a novel diploid C₄ model crop. The proteomic profiles of the internode, node, and leaf in two foxtail millet varieties with different heights, Ci846 and Yugu 18, were investigated at the jointing stage in this study. There were different degrees of enrichment in various processes, such as plant hormone signal transduction, the MAPK signaling pathway, and others. In particular, the proper content of auxin could activate downstream SiARFs-SiSAURs expression, which enhances the length of internodes. Haplotype analysis of SiSAUR-like revealed two differential haplotypes of associated plant height, Hap1 and Hap2. The molecular marker SiSAUR-like-FCM1-2 can effectively separate materials into Hap1 and Hap2. Two additional genes, designated SiGH3 and SiTCH4, were found to be associated with plant height regulation. In conclusion, this study not only uncovers the crucial role of auxin regulators in modulating plant height during the jointing stage but also provides molecular markers that will be invaluable for molecular breeding efforts. The findings of this research help to elucidate the molecular mechanisms of plant height determination that can be used for crop variety innovation and breeding.

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.