Single-nucleus multi-omics reveals the impact of drought stress on the development of soybean endosperm.

As a maternal nutrient-storage tissue in seeds, the endosperm is a drought-responsive compartment that influences seed development and crop yield through structural and compositional changes. However, the mechanisms that regulate these adaptive responses in soybean endosperm remain unclear owing to the complexity of this tissue. In this study, we performed single-nucleus multi-omics analysis across three key developmental stages of soybean seeds, generating a high-resolution map that identified 10 major cell types, as expected, and revealed that the endosperm is one of the main sites for drought response. Further sub-clustering delineated 12 distinct sub-populations representing five previously uncharacterized endosperm sub-cell types. Notably, the peripheral endosperm (PEN) showed the strongest drought response, with trajectory analysis revealing changes in PEN differentiation pathways and associated transcription factor (TF) networks under drought conditions. Moreover, analysis of cell-type-specific transcriptional regulatory networks demonstrated increased binding activity of drought-responsive TFs during stress. This study presents a single-nucleus atlas of drought-stressed soybean endosperm, offering molecular and cellular insights into drought tolerance mechanisms for soybean breeding.