Time-Series Transcriptome Analysis Identifies LaMYB3R1d as a Novel Regulator of Cluster Root Growth in White Lupin

Under low-phosphorus (P) conditions, white lupin (Lupinus albus L.) develops cluster roots (CRs), characterized by dense clusters of determinate rootlets originating from a short region of the root axis. However, the molecular mechanisms controlling rootlet growth remain largely unclear. In this study, we conducted weighted gene co-expression network analysis (WGCNA) using publicly available time-course transcriptomes of developing CRs, which led to the identification of five stage-specific modules linked to sequential developmental and functional changes. Enrichment analysis of genes from modules associated with rootlet growth revealed significant overrepresentation of Gene Ontology (GO) terms, transcriptional factors (TFs), and cis-regulatory motifs related to cell cycle progression. Notably, we identified a novel TF, LaMYB3R1d, as a key regulator of rootlet growth. We demonstrated that LaMYB3R1d binds to the mitosis-specific activator (MSA) elements and activates the transcription of cell cycle genes, including LaCYCB1;4a and LaCYCB1;4b, thereby promoting rootlet growth. Together, these findings expand our understanding of the molecular control of CR development and provide new insights into the study of root adaptation to P deficiency.