Unveiling the development of cotton somatic embryos: Integrating spatial transcriptomics and metabolomics

Plant development necessitates a diverse array of cell types, metabolites, and intricate gene regulation patterns. Consequently, investigating the spatial localization of cells within tissues, the spatial expression of genes, and the distribution of both primary and secondary metabolites in plants is crucial. The process of somatic embryo development is vital for the genetic enhancement of cotton, yet it remains poorly understood. Moreover, there is currently a scarcity of available data resources on the spatial expression patterns of genes and metabolites in cotton somatic embryo cells. In this study, we employed 10 × Visium spatial transcriptomics (ST) technology and air flow-assisted desorption electrospray ionization mass spectrometry imaging (AFADESI-MSI) spatial metabolomics (SM) technology to establish sequencing libraries and metabolomes of upland cotton ( Gossypium hirsutum ) somatic embryos, specifically focusing on globular, torpedo, and cotyledonary embryos. Specifically, we have highlighted the spatially regulated gene networks and metabolite gradients critical to embryogenesis. For instance, the integrated analysis of ST and SM revealed that polyamines (putrescine, spermidine, and spermine) and their biosynthesis-related genes ( ADC , ODC , ARGAH1 , SPDSYN1 , and SPMS ) were highly expressed in globular embryos. These findings suggest that polyamines and their biosynthesis-related genes may play a pivotal role in the conversion of embryogenic callus into somatic embryos in cotton. In summary, we propose an integrated spatially resolved multiomics approach, which will aid in deciphering the complex regulatory networks involved in the development of cotton somatic embryos. • The 10 × Visium ST and AFADESI-MSI applied to cotton somatic embryos. • The integrated analysis of the metabolites and gene expression was performed. • The integrated analysis strategy can be applied to other tissues of cotton or other plant species.