Decoding seed vigor and longevity through functional genomics: molecular networks of DNA repair, proteostasis, antioxidant defense, and metabolic regulation

Seed vigor and longevity are polygenic traits that determine the performance of seeds during germination, storage, and the establishment of the seedling in different environments. During ageing, reactive oxygen species (ROS) cause damage to macromolecules and disrupt cellular homeostasis. Individual molecular, physiological, and environmental factors affecting seed quality have been extensively studied; however, the interactions between these factors and their contribution to seed vigor and longevity remain poorly understood. Here, we propose an integrated functional-genomics framework linking seed development and environmental history with transcriptional and phytohormonal networks, redox homeostasis, DNA repair, protein homeostasis, properties of the seed coat, protective carbohydrate metabolism, and secondary metabolism. We highlight the interplay between these processes in controlling cellular aging during storage and recovery upon imbibition and provide an overview of the genetic and epigenetic regulations involved. Particular attention is drawn to the opportunities offered by transcriptomic, proteomic, and metabolomic analyses, genome-wide association studies, reverse genetics, and CRISPR/Cas genome editing to decipher the function of regulators of seed vigor and longevity at multiple levels. We further discuss how destructive and non-destructive phenotyping can be combined with molecular profiling and predictive approaches to link variations at the molecular level with seed performance. We also identify gaps in current knowledge, including genotype and environment interactions, limitations of ageing models, the need for biomarker discovery, and possible trade-offs between seed longevity and vigor. This framework provides a conceptual basis for future research on deciphering the physiological and molecular regulators of seed storability and vigor and improving seed quality.