Single-cell resolution transcriptional atlases of aerial and subterranean pegs reveals auxin signaling associated with peg development in peanut

Pegging is a unique characteristic of peanut plants in which chasmogamous flowers are produced aerially that penetrate into the soil and develop 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. Here, we constructed a single-nucleus resolution transcriptomic atlas of both aerial and subterranean pegs comprising 50,903 individual cells and annotated nine major cell types using cell markers and in situ hybridization. Transcription factors (TFs) developmental differentiation trajectories and predicted interaction networks were identified during peg development. Combination of single-nucleus RNA-sequencing (snRNA-seq) and bulk RNA-seq in aerial and subterranean pegs highlighted the potential involvement of phytohormone signals in pegging. In addition, our findings suggest that auxin signal transduction pathways are crucial for gravity-regulated peg formation. This study provides new insights into the development of aerial and subterranean pegs in peanut at cell-type resolution, and could also serve as the basis for future investigation of the molecular mechanisms underlying cell maintenance and differentiation during pod formation.