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

Spatially resolved transcriptomic analysis of the germinating barley grain

Seeds are a vital source of calories for humans and a unique stage in the life cycle of flowering plants. During seed germination, the embryo undergoes major developmental transitions to become a seedling. Studying gene expression in individual seed cell types has been challenging due to the lack of spatial information or low throughput of existing methods. To overcome these limitations, a spatial transcriptomics workflow was developed for germinating barley grain. This approach enabled high-throughput analysis of spatial gene expression, revealing specific spatial expression patterns of various functional gene categories at a sub-tissue level. This study revealed over 14 000 genes differentially regulated during the first 24 h after imbibition. Individual genes, such as the aquaporin gene family, starch degradation, cell wall modification, transport processes, ribosomal proteins and transcription factors, were found to have specific spatial expression patterns over time. Using spatial autocorrelation algorithms, we identified auxin transport genes that had increasingly focused expression within subdomains of the embryo over time, suggesting their role in establishing the embryo axis. Overall, our study provides an unprecedented spatially resolved cellular map for barley germination and identifies specific functional genomics targets to better understand cellular restricted processes during germination. The data can be viewed at https://spatial.latrobe.edu.au/.

Integrated transcriptome, proteome and metabolome analyses revealed secondary metabolites and auxiliary carbohydrate metabolism augmenting drought tolerance in rice

Drought is one of the major consequences of climate change and a serious threat to rice production. Drought stress activates interactions among genes, proteins and metabolites at the molecular level. A comparative multi-omics analysis of drought-tolerant and drought-sensitive rice cultivars can decipher the molecular mechanisms involved in drought tolerance/response. Here, we characterized the global-level transcriptome, proteome, and metabolome profiles, and performed integrated analyses thereof in a drought-sensitive (IR64) and a drought-tolerant (Nagina 22) rice cultivar under control and drought-stress conditions. The transcriptional dynamics and its integration with proteome analysis revealed the role of transporters in regulation of drought stress. The proteome response illustrated the contribution of translational machinery to drought tolerance in N22. The metabolite profiling revealed that aromatic amino acids and soluble sugars contribute majorly to drought tolerance in rice. The integrated transcriptome, proteome and metabolome analysis performed using statistical and knowledge-based methods revealed the preference for auxiliary carbohydrate metabolism through glycolysis and pentose phosphate pathway contributed to drought tolerance in N22. In addition, L-phenylalanine and the genes/proteins responsible for its biosynthesis were also found to contribute to drought tolerance in N22. In conclusion, our study provided mechanistic insights into the drought response/adaptation mechanism and is expected to facilitate engineering of drought tolerance in rice.

Analysis of Hormone Regulation on Seed Germination of Coix Based on Muli-Omics Analysis

Seed germination is an important stage of growth and reproduction and plays an important role in the life cycle of spermatophyte. It is co-determined by both genetic and environmental factors, and plant hormone regulation may be a highly conservative mechanism. Coix lachryrma-jobi (coix) is a grain with balanced nutrition for medicine and food and has substantial production value. It is an important part of agricultural production, and the efficiency of seed germination after sowing is a key link. In this study, coix species "small white shell Xingren" was used as the experimental material, and changes in gene expression levels and metabolite enrichment in seeds were identified by transcriptome and metabonomic analysis before and after seed germination. A total of 599 metabolites, including those from amino acid metabolism, sugar metabolism, and fatty acid metabolism, were significantly increased in germinating coix. Simultaneously, 10,929 differentially expressed genes (DEGs) were identified, and functional clusters of genes were also significantly clustered in hormone-signaling and glucose and fatty acid metabolism. In addition, this study found that a considerable number of hormone-signaling genes were significantly up-regulated during seed germination, activating multiple metabolic processes. The results of our conjoint analysis of multi omics showed that glucose and fatty acid metabolism played an important role in seed germination under hormone regulation.

Transcriptome Analysis of Rice Embryo and Endosperm during Seed Germination

Seed germination is a complex, multistage developmental process that is an important step in plant development. In this study, RNA-Seq was conducted in the embryo and endosperm of unshelled germinating rice seeds. A total of 14,391 differentially expressed genes (DEGs) were identified between the dry seeds and the germinating seeds. Of these DEGs, 7109 were identified in both the embryo and endosperm, 3953 were embryo specific, and 3329 were endosperm specific. The embryo-specific DEGs were enriched in the plant-hormone signal-transduction pathway, while the endosperm-specific DEGs were enriched in phenylalanine, tyrosine, and tryptophan biosynthesis. We categorized these DEGs into early-, intermediate-, and late-stage genes, as well as consistently responsive genes, which can be enriched in various pathways related to seed germination. Transcription-factor (TF) analysis showed that 643 TFs from 48 families were differentially expressed during seed germination. Moreover, 12 unfolded protein response (UPR) pathway genes were induced by seed germination, and the knockout of OsBiP2 resulted in reduced germination rates compared to the wild type. This study enhances our understanding of gene responses in the embryo and endosperm during seed germination and provides insight into the effects of UPR on seed germination in rice.

Transcriptome and metabolome analyses reveal novel insights into the seed germination of Michelia chapensis, an endangered species in China

Michelia chapensis Dandy, a well-known medicinal woody plant endemic to China, is endangered and seriously constricted by seed dormancy-induced low-regeneration in natural conditions. Cold stratification can effectively reduce seed dormancy and promote the seed germination of M. chapensis. However, the molecular events and systematic changes that occurred during seed germination in M. chapensis remain largely unknown. In this study, we carried out transcriptomic and metabolomic analyses to elucidate the potential molecular mechanisms underlying seed germination in M. chapensis under cold stratification. The results showed that the embryo cells became bigger and looser with increasing stratification time. Moreover, the endosperm appeared reduced due to the consumption of nutrients. Seventeen phytohormones were examined by the metabolome targeted for hormones. Compared with the ES (no stratification), the levels of indole-3-acetic acid (IAA) and gibberellin A₃ (GA₃) were increased in the MS (stratification for 45 days), while the abscisic acid (ABA) was downregulated in both MS and LS (stratification for 90 days). The transcriptome profiling identified 24975 differentially expressed genes (DEGs) in the seeds during germination. The seed germination of M. chapensis was mainly regulated by the biological pathways of plant hormone signal transduction, energy supply, secondary metabolite biosynthesis, photosynthesis-related metabolism, and transcriptional regulation. This study reveals the biological evidence of seed germination at the transcriptional level and provides a foundation for unraveling molecular mechanisms regulating the seed germination of M. chapensis.

Transcriptome and DNA Methylome Analysis of Two Contrasting Rice Genotypes under Salt Stress during Germination

With climate change and labor shortages, direct-seeding rice cultivation is becoming popular worldwide, especially in Asia. Salinity stress negatively affects rice seed germination in the direct-seeding process, and the cultivation of suitable direct-seeding rice varieties under salinity stress is necessary. However, little is known about the underlying mechanism of salt responses during seed germination under salt stress. To investigate the salt tolerance mechanism at the seed germination stage, two contrasting rice genotypes differing in salt tolerance, namely, FL478 (salt-tolerant) and IR29 (salt-sensitive), were used in this study. We observed, that compared to IR29, FL478 appeared to be more tolerant to salt stress with a higher germination rate. GD1 (germination defective 1), which was involved in seed germination by regulating alpha-amylase, was upregulated significantly in the salt-sensitive IR29 strain under salt stress during germination. Transcriptomic data showed that salt-responsive genes tended to be up/downregulated in IR29 but not in FL478. Furthermore, we investigated the epigenetic changes in FL478 and IR29 during germination under saline treatment using whole genome bisulfite DNA sequencing (BS-seq) technology. BS-seq data showed that the global CHH methylation level increased dramatically under salinity stress in both strains, and the hyper CHH differentially methylated regions (DMRs) were predominantly located within the transposable elements regions. Compared with FL478, differentially expressed genes with DMRs in IR29 were mainly related to gene ontology terms such as response to water deprivation, response to salt stress, seed germination, and response to hydrogen peroxide pathways. These results may provide valuable insights into the genetic and epigenetic basis of salt tolerance at the seed germination stage, which is important for direct-seeding rice breeding.

Comparative Metabolomic Studies of Siberian Wildrye (Elymus sibiricus L.): A New Look at the Mechanism of Plant Drought Resistance

Drought is one of the most important factors affecting plant growth and production due to ongoing global climate change. Elymus sibiricus has been widely applied for ecological restoration and reseeding of degraded grassland in the Qinghai-Tibetan Plateau (QTP) because of its strong adaptability to barren, salted, and drought soils. To explore the mechanism of drought resistance in E. sibiricus, drought-tolerant and drought-sensitive genotypes of E. sibiricus were used in metabolomic studies under simulated long-term and short-term drought stress. A total of 1091 metabolites were detected, among which, 27 DMs were considered to be the key metabolites for drought resistance of E. sibiricus in weighted gene co-expression network analysis (WGCNA). Ten metabolites, including 3-amino-2-methylpropanoic acid, coniferin, R-aminobutyrate, and so on, and 12 metabolites, including L-Proline, L-histidine, N-acetylglycine, and so on, showed differential accumulation patterns under short-term and long-term drought stress, respectively, and thus, could be used as biomarkers for drought-tolerant and drought-sensitive E. sibiricus. In addition, different metabolic accumulation patterns and different drought response mechanisms were also found in drought-tolerant and drought-sensitive genotypes of E. sibiricus. Finally, we constructed metabolic pathways and metabolic patterns for the two genotypes. This metabolomic study on the drought stress response of E. sibiricus can provide resources and a reference for the breeding of new drought-tolerant cultivars of E. sibiricus.

Combined transcriptome and metabolome reveal glutathione metabolism plays a critical role in resistance to salinity in rice landraces HD961

Rice (Oryza sativa) is one of the most important food crops around the world, which is sensitive to salt stress, especially in the seedling and booting stage. HD961 is a salt-tolerant rice landrace that grows along coastal beaches and has disease and insect pest resistance, salt tolerance, and vigorous growth characteristics. We performed a combined transcriptome and metabolome analysis to clarify salinity resistance mechanisms in cultivar HD961, which has adapted to salinity soil at the early seedling stage. The results showed that the growth and antioxidant capacity of HD961 were stronger than 9311 under salt stress (SS). Transcriptomic analysis showed that a total of 6,145, 3,309, 1,819, and 1,296 differentially expressed genes (DEGs) were identified in the groups of TH60 (control group vs. 60 mM group of HD961 for transcriptome), TH120 (control group vs. 120 mM group of HD961 for transcriptome), T60 (control group vs. 60 mM group of 9311 for transcriptome), and T120 (control group vs. 120 mM group of 9311 for transcriptome), respectively. Starch and sucrose metabolism and phenylpropanoid biosynthesis were shared in the four treatment groups based on a KEGG enrichment analysis of DEGs. In addition, alpha-linolenic acid metabolism, plant hormone signal transduction, plant-pathogen interaction, and fatty acid elongation were specific and significantly different in HD961. A total of 92, 158, 151, and 179 significantly regulated metabolites (SRMs) responded to SS in MH60 (control group vs. 60 mM group of HD961 for metabolome), MH120 (control group vs. 120 mM group of HD961 for metabolome), M60 (control group vs. 60 mM group of 9311 for metabolome), and M120 (control group vs. 120 mM group of 9311 for metabolome), respectively. The KEGG analysis showed that eight common metabolic pathways were identified in the four treatment groups, of which biosynthesis of amino acids was the most significant. Three specific metabolic pathways were identified in the HD961, including glutathione metabolism, ascorbate and aldarate metabolism, and pantothenate and CoA biosynthesis. Integrative analysis between the transcriptome and metabolome showed that glutathione metabolism was specific and significantly affected under SS in HD961. A total of seven SRMs and 48 DEGs and four SRMs and 15 DEGs were identified in the glutathione metabolism pathway in HD961 and 9311, respectively. The Pearson correlation analysis showed a significant correlation between reduced glutathione and 16 genes (12 upregulated and four downregulated genes), suggesting these genes could be candidates as salt-tolerance regulation genes. Collectively, our data show that glutathione metabolism plays a critical role in response to SS in rice. Moreover, the stronger regulative ability of related common genes and metabolites might contribute to salt resistance in HD961.

Bruceine D may affect the phenylpropanoid biosynthesis by acting on ADTs thus inhibiting Bidens pilosa L. seed germination

Bruceine D is a natural quassinoid, which was successfully isolated in our research group from the residue of Brucea javanica (L.) seeds. Our previous research showed that Bruceine D prevented Bidens pilosa L. seed germination by suppressing the activity of key enzymes and the expression levels of key genes involved in the phenylpropanoid biosynthesis pathway. In this study, integrated analyses of non-targeted metabolomic and transcriptomic were performed. A total of 356 different accumulated metabolites (DAMs) were identified, and KEGG pathway analyses revealed that most of these DAMs were involved in phenylpropanoid biosynthesis. The decreased expression of ADTs and content of L-phenylalanine implicates that Bruceine D may suppress the downstream phenylpropanoid biosynthesis pathway by disrupting primary metabolism, that is, the phenylalanine biosynthesis pathway, thus inhibiting the final products, resulting in the interruption of B. pilosa seed germination. These results suggest that Bruceine D may inhibit the B. pilosa seed germination by suppressing phenylpropanoid biosynthesis through acting on ADTs.

Integrative Analysis of the Transcriptome and Metabolome Reveals Genes Involved in Phenylpropanoid and Flavonoid Biosynthesis in the Trapa bispinosa Roxb

BACKGROUND

Trapa bispinosa Roxb. is grown worldwide as an important aquatic cash crop. Current research on Trapa bispinosa primarily focuses on the separation and identification of active ingredients, as well as the inhibitory effect on tumors; however, research on the molecular mechanism of secondary metabolite accumulation is rather limited. Consequently, an integrative analysis of transcriptome and metabolome is required to identify the key metabolic pathways, and key genes, and to explain the molecular mechanism of Trapa bispinosa.

RESULTS

The biosynthesis pathways of phenolics in Trapa bispinosa were examined through transcriptome and metabolome analyses. Transcriptome analysis yielded 42.76 million clean reads representing 81,417 unigenes with an average length of 1,752 bp. KEGG pathway analysis revealed that 1,623 unigenes, including 88 candidate unigenes related to phenolics biosynthesis, were up-regulated in Trapa bispinosa shell (FR) when compared to leaves (LF), root (RT), and stem (ST). The FR vs. LF group had the highest number of specific genes involved in phenylpropanoid, flavonoid, flavone, and flavonol biosynthesis pathways compared to all other comparison groups. In addition, RNA sequencing revealed 18,709 SSRs spanning 14,820 unigenes and 4,387 unigenes encoding transcription factors. Metabolome analysis identified 793 metabolites, including 136 flavonoids and 31 phenylpropane compounds. In the FR group compared to the LF group, there were 202 differentially accumulated metabolites (DAMs). The combined transcriptome and metabolome analyses indicated a significant correlation between 1,050 differentially expressed genes (DEGs) and 62 DAMs. This view proposes a schematic of flavonoid biosynthesis in the FR vs. LF group, providing evidence for the differences in genes and metabolites between FR and LF.

CONCLUSION

In this study, through de novo transcriptome assembly and metabolome analysis, several DEGs and DAMs were identified, which were subsequently used to build flavonoid biosynthesis pathways and a correlation network. The findings pave the way for future research into the molecular mechanisms and functional characterization of Trapa bispinosa candidate genes for phenolics biosynthesis.

QTL mapping and candidate gene analysis of low temperature germination in rice (Oryza sativa L.) using a genome wide association study

Low temperature germination (LTG) is a key agronomic trait in rice (Oryza sativa L.). However, the genetic basis of natural variation for LTG is largely unknown. Here, a genome-wide association study (GWAS) was performed using 276 accessions from the 3,000 Rice Genomes (3K-RG) project with 497 k single nucleotide polymorphisms (SNPs) to uncover potential genes for LTG in rice. In total, 37 quantitative trait loci (QTLs) from the 6th day (D6) to the 10th day (D10) were detected in the full population, overlapping with 12 previously reported QTLs for LTG. One novel QTL, namely qLTG1-2, was found stably on D7 in both 2019 and 2020. Based on two germination-specific transcriptome datasets, 13 seed-expressed genes were isolated within a 200 kb interval of qLTG1-2. Combining with haplotype analysis, a functional uncharacterized gene, LOC_Os01g23580, and a seed germination-associated gene, LOC_Os01g23620 (OsSar1a), as promising candidate genes, both of which were significantly differentially expressed between high and low LTG accessions. Collectively, the candidate genes with favorable alleles may be useful for the future characterization of the LTG mechanism and the improvement of the LTG trait in rice breeding.

Transcriptomics View over the Germination Landscape in Biofortified Rice

Hidden hunger, or micronutrient deficiency, is a worldwide problem. Several approaches are employed to alleviate its effects (e.g., promoting diet diversity, use of dietary supplements, chemical fortification of processed food), and among these, biofortification is considered as one of the most cost-effective and highly sustainable. Rice is one of the best targets for biofortification since it is a staple food for almost half of the world’s population as a high-energy source but with low nutritional value. Multiple biofortified rice lines have been produced during the past decades, while few studies also reported modifications in germination behavior (in terms of enhanced or decreased germination percentage or speed). It is important to underline that rapid, uniform germination, and seedling establishment are essential prerequisites for crop productivity. Combining the two traits, biofortified, highly-nutritious seeds with improved germination behavior can be envisaged as a highly-desired target for rice breeding. To this purpose, information gathered from transcriptomics studies can reveal useful insights to unveil the molecular players governing both traits. The present review aims to provide an overview of transcriptomics studies applied at the crossroad between biofortification and seed germination, pointing out potential candidates for trait pyramiding.

Comparative Metabolomics Reveals Two Metabolic Modules Affecting Seed Germination in Rice (Oryza sativa)

The process of seed germination is crucial not only for the completion of the plant life cycle but also for agricultural production and food chemistry; however, the underlying metabolic regulation mechanism involved in this process is still far from being clearly revealed. In this study, one indica variety (Zhenshan 97, with rapid germination) and one japonica variety (Nipponbare, with slow germination) in rice were used for in-depth analysis of the metabolome at different germination stages (0, 3, 6, 9, 12, 24, 36, and 48 h after imbibition, HAI) and exploration of key metabolites/metabolic pathways. In total, 380 annotated metabolites were analyzed by using a high-performance liquid chromatography (HPLC)-based targeted method combined with a nontargeted metabolic profiling method. By using bioinformatics and statistical methods, the dynamic changes in metabolites during germination in the two varieties were compared. Through correlation analysis, coefficient of variation analysis and differential accumulation analysis, 74 candidate metabolites that may be closely related to seed germination were finally screened. Among these candidates, 29 members belong to the ornithine–asparagine–polyamine module and the shikimic acid–tyrosine–tryptamine–phenylalanine–flavonoid module. As the core member of the second module, shikimic acid’s function in the promotion of seed germination was confirmed by exogenous treatment. These results told that nitrogen flow and antioxidation/defense responses are potentially crucial for germinating seeds and seedlings. It deepens our understanding of the metabolic regulation mechanism of seed germination and points out the direction for our future research.

Integrating GWAS and transcriptomics to identify genes involved in seed dormancy in rice

Several QTLs and genes responsible for seed dormancy were detected and SNP candidates were shown to cause changes in seed germination. Seed dormancy is a key agricultural trait to prevent pre-harvest sprouting in crop plants such as rice (Oryza sativa L.), wheat (Triticum aestivum), and barley (Hordeum vulgare L.). However, our knowledge of seed dormancy is hampered by the complexities of studying a trait that changes over time after seed harvest, and is complicated by interactions between phytohormones, seed coat components and the environment. Here, we have conducted a genome-wide association study using a panel of 311 natural accessions of cultivated rice, examining a total of 519,158 single nucleotide polymorphisms (SNPs). Eight quantitative trait loci (QTLs) were found to associate with seed dormancy in the whole panel and five in the Japonica and Indica subpanel; expression of candidate genes within 100 kb of each QTL was examined in two published, germination-specific transcriptomic datasets. Ten candidate genes, differentially expressed within the first four days post-imbibition, were identified. Five of these genes had previously been associated with awn length, heading date, yield, and spikelet length phenotypes. Two candidates were validated using Quantitative Reverse Transcription (qRT)-PCR. In addition, previously identified genes involved in hormone signaling during germination were found to be differentially expressed between a japonica and an indica line; SNPs in the promoter of Os9BGlu33 were associated with germination index, with qRT-PCR validation. Collectively, our results are useful for future characterization of seed dormancy mechanism and crop improvement, and suggest haplotypes for further analysis that may be of use to boost PHS resistance in rice.

Dynamic Transcriptomic and Metabolomic Analyses of Madhuca pasquieri (Dubard) H. J. Lam During the Post-germination Stages

The wild population of Madhuca pasquieri (Dubard) H. J. Lam is currently dwindling; its understory seedlings are rare, and there is a lack of molecular studies, which impedes the conservation of this species. This study exploited second-generation sequencing and widely targeted metabolomics analysis to uncover the dynamic changes in differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) in five post-germination stages of M. pasquieri whole organism. Notably, the weighted gene co-expression network analysis (WGCNA), transcriptome, and metabolome association analyses all indicated significant enrichment of the flavonoid biosynthesis pathway in stage 4 (two-leaf), and an upregulation of the genes encoding flavonol biosynthesis in this stage. In stage 5 (nine-leaf), the flavonols were significantly accumulated, indicating that the changes in metabolites were driven at the transcript level. According to the significant changes in gene expression encoding auxin transport carriers and their correlation with flavonols during stage 5, the flavonols were speculated to have a direct inhibitory effect on the expression of PIN4 encoding gene, which may inhibit the process of polar auxin transport. The results provided important insights into the molecular network relationships between the transcription and metabolism of this rare and endangered species during the post-germination stages and explained the reasons for the slow growth of its seedlings at the molecular level.

Regulatory Network of Preharvest Sprouting Resistance Revealed by Integrative Analysis of mRNA, Noncoding RNA, and DNA Methylation in Wheat

Preharvest sprouting (PHS) of grain occurs universally and sharply decreases grain quality and yield, but the mechanism remains unclear. MingXian169, a breeding inducer wheat for stripe rust, is widely used in the Huanghuai wheat-producing region, China. In this study, we found that MingXian169 could be considered an ideal material for PHS research because of its high PHS resistance. To further analyze the network of PHS, transcriptome sequencing of mRNA, noncoding RNA (ncRNA), and DNA methylome data were used to comparison germination seeds (GS) and dormant seeds (DS); 3027, 1516, and 22 genes and 95 103 methylation regions were identified as differentially expressed mRNA, DE-microRNAs (DE-miRNA), DE-long noncoding RNAs (DE-lncRNA), and differentially methylated regions (DMRs). Pathway enrichment tests highlighted plant hormone biosynthesis and signal transduction, glutathione-ascorbate metabolism, and starch and sucrose metabolism processes related to PHS mechanisms. Further analysis demonstrated that long noncoding RNA, miRNA, and DNA methylation played critical roles in transcriptional regulation of critical pathways during PHS by modifying and interacting with target genes. Quantitative real-time polymerase chain reaction (PCR) analyses of mRNA and miRNA confirmed the sequencing results. In the phytohormone content assay, abscisic acid (ABA) and jasmonic acid (JA) increased significantly in DS, and GA19 increased in GS. The ascorbate peroxidase (APX), monodehydroascorbate reductase (MDHAR), and β-d-glucosidase (BGLU) enzyme activities and the substance content of glutathione and sucrose were significantly higher in GS than in DS, implying that they were responsible for increasing PHS in MingXian169. Our results provide new insights into wheat PHS resistance at mRNA, ncRNA, and DNA methylation levels, with suggestions for crop breeding and production.