Seed germination and young seedling growth are important agricultural traits for developing populations of both irrigated and directly seeded rice. Previous studies have focused on the identification of QTLs. However, there are few studies on the metabolome or transcriptome of germination and young seedling growth in rice. Here, an indica rice and a japonica rice were used as materials, and the transcripts and metabolites were detected during the germination and young seedling growth periods on a large scale by using RNA sequencing and a widely targeted metabolomics method, respectively. Fourteen shared transcripts and 15 shared metabolites that were continuously differentially expressed in the two materials were identified and may be essential for seed germination and young seedling growth. Enrichment analysis of differentially expressed genes in transcriptome expression profiles at different stages indicated that cell wall metabolism, lipid metabolism, nucleotide degradation, amino acid, etc., were enriched at 0–2 days, and most of the results are consistent with those of previous reports. Specifically, phenylpropanoid biosynthesis and glutathione metabolism were continuously enriched during the seed germination and young seedling growth stages. Next, KO enrichment analysis was conducted by using the differentially expressed genes of the two materials at 2, 3 and 4 days. Fourteen pathways were enriched. Additionally, 44 differentially expressed metabolites at 2, 3 and 4 days were identified. These metabolites may be responsible for the differences in germination and young seedling growth between the two materials. Further attention was focused on the ascorbate–glutathione pathway, and it was found that differences in ROS-scavenging abilities mediated by some APX, GPX and GST genes may be directly involved in mediating differences in the germination and young seedling growth speed of the two materials. In summary, these results may enhance the understanding of the overall mechanism of seed germination and young seedling growth, and the outcome of this study is expected to facilitate rice breeding for direct seeding.

中文翻译：

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两种类型水稻在种子萌发和幼苗生长阶段的动态转录组和代谢组学分析。

种子发芽和幼苗生长是灌溉水稻和直接播种水稻的重要农业特征。先前的研究集中在QTL的识别上。但是，关于水稻萌发和幼苗生长的代谢组或转录组的研究很少。在这里，以rice稻和粳稻为材料，分别通过RNA测序和广泛靶向的代谢组学方法，在发芽期和幼苗生长期间大规模检测转录本和代谢产物。鉴定了在两种材料中连续差异表达的14种共有转录本和15种共有代谢产物，它们可能对种子发芽和幼苗生长至关重要。转录组表达谱在不同阶段的差异表达基因的富集分析表明，细胞壁代谢，脂质代谢，核苷酸降解，氨基酸等在0–2天富集，大多数结果与以前的结果一致报告。具体而言，在种子萌发和幼苗生长阶段，苯丙烷类生物合成和谷胱甘肽代谢不断丰富。接下来，通过在2、3和4天使用两种材料的差异表达基因进行KO富集分析。丰富了十四种途径。此外，在第2、3和4天鉴定出44种差异表达的代谢产物。这些代谢物可能是两种物质之间发芽和幼苗生长的差异的原因。进一步的关注集中在抗坏血酸-谷胱甘肽途径上，并且发现由某些APX，GPX和GST基因介导的ROS清除能力的差异可能直接参与了介导这两种物质的发芽和幼苗生长速度的差异。 。总之，这些结果可以增进对种子萌发和幼苗生长的总体机制的理解，并且该研究的结果有望促进水稻育种的直接播种。