Dynamic transcriptome and metabolome analyses of two types of rice during the seed germination and young seedling growth stages

Abstract

Background: 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.

Results: 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.

Conclusions: 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.

Keywords: Germination; Metabolome; Rice; Seedling growth; Transcriptome.

Fig. 1

Germination and young seedling growth characteristic of 02428 and YZX. a Phenotypes of germination and growth of 02428 and YZX from 0 to 4 days. b Changes in seedling height of 02428 and YZX from 0 to 4 days. c Changes in root length of 02428 and YZX from 0 to 4 days

Fig. 2

Summary of changes in transcript and metabolite abundance in rice in response to germination and young seedling growth. a, b Summary of the number of significant changes in transcripts and metabolites between different time points. c, d Venn diagram of DEGs and DEMs between 02428 and YZX. e A total of 121 core metabolites accounted for the proportion of total metabolites. f The number and proportion of 121 core metabolites in various metabolites and their derivatives are detailed, and the black box represents the core metabolites. g Classification of 730 metabolites

Fig. 3

Identification of continuously differentially expressed genes and metabolites. a Venn diagram of DEGs during the three periods of 02428. b Venn diagram of DEGs during the three periods of YZX. c Venn diagram for 02428 and YZX based on continuously DEGs. d Heat maps of 14 continuously DEGs. Gene expression was standardized by the z-score method, with the yellow color representing high expression and the black color representing low expression. e, f, g and h The analyses of the contents of the corresponding metabolites

Fig. 4

MapMan metabolism overview maps showing differences in transcript levels during seed germination and young seedling growth of 02428. a 0 days v 2 days. b 2 days v 3 days. Log2 ratios for average transcript abundance were based on three replicates. The log₂-fold change color scale ranges from − 3.5 to 3.5, where blue represents downregulated transcripts, and red represents upregulated transcripts

Fig. 5

KEGG analyses for the DEGs (0 v 2 days, 2 v 3 days, and 3 v 4 days) in 02428 and YZX. Different colors show the values of FDR, and blanks indicate items that were not significantly enriched during this period

Fig. 6

The number of DEGs and the KEGG enrichment analysis of DEGs of 02428 and YZX at days 0, 2, 3, and 4. a Up- and downregulated genes detected between 02428 and YZX. b Venn diagram of DEGs between 02428 and YZX on days 2, 3 and 4. c KEGG enrichment analysis of DEGs of 02428 and YZX at days 0, 2, 3, and 4

Fig. 7

Changes in the AsA-GSH cycle-related genes and metabolites. a The AsA-GSH pathway model. Red arrows indicate upregulated expression, and blue indicates downregulated expression. b, c, d, e Four types of DEGs were significantly enriched on days 2, 3, and 4 and in the intersection set. f Heat map of the fold changes (02428 / YZX) of 9 NADPH oxidase genes in rice. Different colors show the value of the fold change, and blanks indicate that the differential expression of the gene was not significant during this period. g Changes in reduced glutathione (GSH) and oxidized glutathione (GSSG) content in 02428 and YZX. g Quantification of H₂O₂ content and the O₂⁻ production rate in 02428 and YZX for 0, 2, 3 and 4 days