Function Identification of MdTIR1 in Apple Root Growth Benefited from the Predicted MdPPI Network

Protein-protein interaction (PPI) network analysis is an effective method to identify key proteins during plant development, especially in species for which basic molecular research is lacking, such as apple (Malus domestica). Here, an MdPPI network containing 30 806 PPIs was inferred in apple and its quality and reliability were rigorously verified. Subsequently, a root-growth subnetwork was extracted to screen for critical proteins in root growth. Because hormone-related proteins occupied the largest proportion of critical proteins, a hormone-related sub-subnetwork was further extracted from the root-growth subnetwork. Among these proteins, auxin-relatedM. domesticaTRANSPORT INHIBITOR RESISTANT 1 (MdTIR1) served as the central, high-degree node, implying that this protein exerts essential roles in root growth. Furthermore, transgenic apple roots overexpressing anMdTIR1transgene displayed increased primary root elongation. Expression analysis showed that MdTIR1 significantly upregulated auxin-responsive genes in apple roots, indicating that it mediates root growth in an auxin-dependent manner. Further experimental validation revealed that MdTIR1 interacted with and accelerated the degradation of MdIAA28, MdIAA43, and MdIAA46. Thus, MdTIR1-mediated degradation of MdIAAs is critical in auxin signal transduction and root growth regulation in apple. Moreover, our network analysis and high-degree node screening provide a novel research technique for more generally characterizing molecular mechanisms.