Transcriptome analysis revealed the regulation of gibberellin and the establishment of photosynthetic system promote rapid seed germination and early growth of seedling in pearl millet

BACKGROUND: Seed germination is the most important stage for the formation of a new plant. This process starts when the dry seed begins to absorb water and ends when the radicle protrudes. The germination rate of seed from different species varies. The rapid germination of seed from species that grow on marginal land allows seedlings to compete with surrounding species, which is also the guarantee of normal plant development and high yield. Pearl millet is an important cereal crop that is used worldwide, and it can also be used to extract bioethanol. Previous germination experiments have shown that pearl millet has a fast seed germination rate, but the molecular mechanisms behind pearl millet are unclear. Therefore, this study explored the expression patterns of genes involved in pearl millet growth from the germination of dry seed to the early growth stages. RESULTS: Through the germination test and the measurement of the seedling radicle length, we found that pearl millet seed germinated after 24 h of swelling of the dry seed. Using transcriptome sequencing, we characterized the gene expression patterns of dry seed, water imbibed seed, germ and radicle, and found more differentially expressed genes (DEGs) in radicle than germ. Further analysis showed that different genome clusters function specifically at different tissues and time periods. Weighted gene co-expression network analysis (WGCNA) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that many genes that positively regulate plant growth and development are highly enriched and expressed, especially the gibberellin signaling pathway, which can promote seed germination. We speculated that the activation of these key genes promotes the germination of pearl millet seed and the growth of seedlings. To verify this, we measured the content of gibberellin and found that the gibberellin content after seed imbibition rose sharply and remained at a high level. CONCLUSIONS: In this study, we identified the key genes that participated in the regulation of seed germination and seedling growth. The activation of key genes in these pathways may contribute to the rapid germination and growth of seed and seedlings in pearl millet. These results provided new insight into accelerating the germination rate and seedling growth of species with slow germination. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13068-021-01946-6.