Comparative proteomic analysis of seed germination in five crop species

Seed germination is a critical process in the plant life cycle, regulated through complex molecular processes. Although proteomic studies have elucidated germination mechanisms in individual species, cross-species comparisons remain limited. Here, we performed a systematic comparative proteomic analysis of five crop species across distinct germination stages. We identified 538 orthogroups conserved across five species, along with several species-specific orthogroups, which participate in stress-response pathways, early responses to abscisic acid, and the subsequent mobilization of storage reserves. However, the expression patterns of these proteins differ between monocots and dicots. Several species-specific proteins and pathways have also been identified, such as lipid metabolism in Glycine max, Sesamum indicum Yuzhi No.10 (YZ10), and Setaria italica; nitrogen metabolism in Triticum aestivum Jimai 22 (JM22); and the pentose phosphate pathway in Triticum aestivum JM22 and Bainong 207 (BN207). Proteins involved in glutathione metabolism were identified in all species, including members of the glutathione S-transferase family. Heat shock proteins, nonspecific lipid transfer proteins, peroxidases, and late embryogenesis abundant proteins constitute the largest proportion of stress-related proteins, indicating their importance in maintaining protein homeostasis, antioxidant defense, and pathogen resistance during seed germination. However, their expression patterns differ across species. For example, compared with the wheat variety BN207, JM22 contains more LEA proteins. LEA proteins in JM22 are expressed throughout the entire germination process, whereas in BN207 their abundance declines more rapidly. These findings not only provide insights into germination characteristics across species but also offer guidance for enhancing seed vigor and breeding strategies.