Spatial and Multiple Omics in Horticultural Plants: Advances and Prospects

Spatial and multi-omics technologies have revolutionized horticulture research, allowing seamless, high-resolution mapping of molecular and cellular landscapes in their original spatial contexts. By combining genomics, transcriptomics, proteomics, metabolomics, and epigenomics, spatial multi-omics uncovers the cellular heterogeneity and tissue arrangement of the processes of development, stress adaptation, and quality trait formation. When complemented with cutting-edge computational tools and machine learning, these multilayer datasets can accurately link genotype to phenotype, thus facilitating trait discovery and predictive breeding to a great extent. The ground-breaking technologies, such as spatial barcoding, multiplexed in situ sequencing, and imaging mass spectrometry, are continuously pushing the limit for the spatial resolution and throughput, thus making it possible to understand the spatio-temporal gene and metabolic network dynamics. Altogether, these integrative approaches lead to the advancement of sustainable crop improvement, the efficient use of phenotyping, and the solving of agroecological problems that are the main drivers of next-generation horticultural innovation.