Integrative genetic and hormonal coordination of endocarp/stone development in drupe fruit

The hardened endocarp/stone is a defining feature of drupe fruits and is essential for seed protection, yet it poses significant challenges for fruit processing. Stone development is not an isolated process; rather, it is closely coordinated with seed and fruit growth through complex hormonal and genetic signaling networks. This review synthesizes advances in elucidating how these networks guide the developmental trajectory from early cellular specification in the ovary to lignification and programmed cell death (PCD). Following fertilization, a conserved transcriptional cascade is initiated in which embryo-derived signals activate MADS-box and other regulatory factors to determine endocarp fate. Subsequent upregulation of additional transcription factors/genes, such as NAC, MYB, PODs, LACs, and others, drives cell division and specialization, ultimately leading to activation of the phenylpropanoid pathway and the biosynthesis and deposition of lignin in endocarp cells, which is central to stone hardening. As fruit ripens, the lignified tissue undergoes PCD, forming a rigid protective structure. This developmental process is highly coordinated, and disruptions-whether genetic, hormonal, or environmental-can produce phenotypes such as split-pit, incomplete lignification, or altered stone thickness. Despite research progress, the spatial and temporal regulation of genes and their associated biochemical pathways during development remains poorly understood. The mechanisms by which metabolic and hormonal fluxes in the endocarp are directed from embryonic tissues to stony precursor cells, and how these processes contribute to differential lignification between endocarp and mesocarp tissues, require further investigation. This can be achieved through the integration of pangenomics, single-cell spatial transcriptomics, and precision gene editing.