Proteomic investigation reveals molecular mechanisms of plant height regulation in foxtail millet

Plant height is an essential characteristic of agronomic traits, and an ideal plant height is essential for high crop yield. Foxtail millet (Setaria italica) has been regarded as 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 our study. There were different degrees of the enrichment processes such as plant hormone signal transduction, the MAPK signaling pathway, and so on. 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 Hap1 and Hap2 in different materials. 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 are invaluable for molecular breeding efforts. The findings of this research help to elucidate the molecular mechanisms of plant height determination and preparation for crop variety innovation and breeding.