Single-cell resolution transcriptional atlases of aerial and subterranean pegs reveals auxin signaling associated with peg development in peanut (<i>Arachis hypogaea</i> L.)

Peanut pegging is a unique characteristic in which flowers are produced aerially, penetrating the soil and developing into subterranean pods. However, the gene networks that regulate peg development in peanut remain largely unknown. To investigate the spatiotemporal regulation of gene regulatory networks during peg growth and development, a single-nucleus resolution transcriptomic atlas of both aerial and subterranean pegs comprising 50,903 individual cells was constructed, and nine major cell types were annotated using cell markers and <italic>in situ</italic> hybridization. Transcription factors (TFs), developmental differentiation trajectories, and predicted interaction networks were identified during peg development. A combination of single-nucleus RNA sequencing (snRNA-seq), and bulk RNA sequencing in aerial and subterranean pegs highlighted phytohormone signaling as a key driver of peg formation. In addition, the present findings suggest that auxin signal transduction pathways are crucial for gravity-regulated peg formation. This study advances our understanding of aerial and subterranean pegs development at cell-type resolution and provides a resource for exploring the molecular mechanisms underlying cell maintenance and differentiation during pod formation.