Transcriptome and metabolome analyses revealing the potential mechanism of seed germination in Polygonatum cyrtonema

Hormonomics profiles revealed the mechanisms of cold stratification in breaking the dormancy during seed germination and emergence process of Polygonatum sibiricum Red

Polygonatum sibiricum Red, known as Huangjing in Chinese, is a perennial plant valued in traditional Chinese medicine and is a nutritional food ingredient. With increasing market demand outpacing wild resource availability, cultivation has become essential for sustainable production. However, the cultivation of P. sibiricum is challenged by the double dormancy characteristics of seeds, which include embryo and physiological dormancy. This affected the germination of seeds and the establishment of seedlings. This study investigates the role of plant hormones in breaking seed dormancy and regulating germination and emergence in P. sibiricum. We found that cold stratification at 4°C for over 70 d significantly alleviates seed dormancy, associated with changes in endogenous hormone levels. Auxin, gibberellin, abscisic acid, cytokinin, salicylic acid, jasmonic acid, and ethylene were identified as key players in these processes. Exogenous applications of GA3 and 2-coumarate (2-hydroxycinnamic acid) significantly enhanced seed germination, while 6-BA and GA3 promoted corm growth and development. In conclusion, our research provides insights into the hormonal regulation of seed dormancy and germination in P. sibiricum, offering valuable strategies for improving cultivation practices. Further studies are needed to explore the specific mechanisms of hormone interactions and to develop optimized germination and seedling establishment strategies for this medicinally important plant.

Transcriptome and metabolite conjoint analysis reveals the seed dormancy release process of perilla

Seed dormancy is a common physiological phenomenon during storage which has a great impact on timely germination of seeds. An in-depth analysis of the physiological and molecular mechanisms of perilla seed dormancy release is of great significance for cultivating high-vigor perilla varieties. We used gibberellin A3-soaked seeds (GA), natural dormancy-release seeds (CK) and water-soaked seeds (WA) to study the changes in the transcriptome and metabolome of dormancy release. The germination test revealed that the optimum concentration of gibberellin A3 for releasing dormancy from perilla seeds was 200 mg/L. The results revealed that plant hormone signal transduction, starch and sucrose metabolism and citric acid cycle were significantly enriched metabolic pathways closely related to seed dormancy release. Perilla seeds release their dormancy by enhancing the expression of GID1, PIF3, SnRK2, IAA, ARR-A, GH3, MKK4_5, otsB, GN1_2_3, glgC, WAXY, inhibiting the expression of DELLA, PP2C, glga, bglX, and GN4, and regulating the content of gibberellin A4, abscisic acid, auxin, sucrose, maltose, trehalose, and α-D-glucose 1-phosphate. Auxin plays an important role in breaking perilla seed dormancy and promoting seed germination. The energy required for breaking seed dormancy and germination of perilla seeds is mainly provided through sucrose metabolism. Citric acid cycle (TCA cycle) is the main energy supply transformation pathway for seed germination.

Comparative transcriptome analysis provides novel insights into the seed germination of Panax japonicus, an endangered species in China

Panax japonicus, an endangered species in China, is usually used as a traditional medicine with functions of hemostasis, pain relief, and detoxify. However, the seeds of P. japonicus are hard to germinate in natural conditions, and the molecular events and systematic changes occurring in seed germination are still largely unknown. In this study, we compared the seeds in different germination stages in terms of morphological features, antioxidant enzyme activities, and transcriptomics. The results indicated that sand storage at 25℃ for 120 d effectively released the seed dormancy of P. japonicus and promoted the seed germination. Moreover, sand storage treatment increased the antioxidant capacity of P. japonicus seeds through increasing the activities of SOD, POD, and CAT. The RNA-seq identified 28,908 differentially expressed genes (DEGs) between different germination stages, of which 1697 DEGs significantly changed throughout the whole germination process. Functional annotations showed that the seed germination of P. japonicus was mainly regulated by the DEGs related to pathways of ROS-scavenging metabolism, plant hormonal signal transduction, starch and sucrose metabolism, energy supply (glycolysis, pyruvate metabolism, and oxidative phosphorylation), and phenylpropanoid biosynthesis, as well as the transcription factors such as bHLHs, MYBs, WRKYs, and bZIPs. This study provides a foundation for unveiling molecular mechanisms underlying the seed germination and is beneficial for accelerating the development of P. japonicus industry.

Enhanced CO2 Coordinates the Spatial Recruitment of Diazotrophs in Rice Via Root Development

Understanding the reciprocal interaction between root development and coadapted beneficial microbes in response to elevated CO2 (eCO2) will facilitate the identification of nutrient-efficient cultivars for sustainable agriculture. Here, systematic morphological, anatomical, chemical and gene expression assays performed under low-nitrogen conditions revealed that eCO2 drove the development of the endodermal barrier with respect to L-/S-shaped lateral roots (LRs) in rice. Next, we applied metabolome and endodermal-cell-specific RNA sequencing and showed that rice adapts to eCO2 by spatially recruiting diazotrophs via flavonoid secretion in L-shaped LRs. Using the rice Casparian strip mutant Oscasp1-1, we confirmed that reduced lignin deposition selectively recruits the diazotrophic family of Oxalobacteraceae to confer tolerance to low nitrogen availability.

Decoding the Transcriptomics of Oil Palm Seed Germination

Seed dormancy and germination are critical factors affecting oil palm production efficiency. The typical dormancy-breaking process involves dry heat treatment (38-40 °C for 40-60 days) followed by germination at 30-32 °C. To understand the molecular mechanisms behind this process and improve germination rates and speed, we conducted transcriptome analysis at three stages: pre-incubation, 45-day incubation at 40 °C, and 14-day germination at 32 °C. Our findings, supported by qRT-PCR and DEGs analysis, identified four key stages: ABA degradation, energy mobilization, starch mobilization, and cell elongation and division. ABA pathway genes (SnRK2, PYR/PYL) were active during dormancy release, while GAE and GPI were upregulated after heat treatment, indicating increased energy metabolism and structural changes. During germination, genes involved in starch/sucrose metabolism (SPS, TPP, SS, MGAM) and cell wall biosynthesis (GAUT1, PE, GAE) supported embryo expansion, with BAM, PGM, GlgB fueling early growth. Auxin (TIR1, AUX/IAA, ARF), brassinosteroid (BRI1, BSK, BIN2, CYCD3), ethylene (ETR, CTR1), and jasmonic acid (JAR1, COI1) pathway genes regulated cell growth and stress response, promoting seedling development. Though gibberellins were not crucial for this oil palm variety, gene expression varied between varieties. This study provides information on oil palm seed germination that could be applied to other oil palm species, particularly in terms of incubation times and chemical treatments.

Catechin promotes the germination of Pistacia chinensis seeds via GA biosynthesis

BACKGROUND AND AIMS

Chinese pistachio (Pistacia chinensis), an important horticultural plant species, holds great ornamental value with beautiful leaves and fruits. Seedling propagation of this tree species is restricted by its erratic seed germination; however, the germination mechanism is ambiguous. The aim of this study was to determine the germination mechanism from a novel perspective based on the multi-omics data.

METHODS

The multi-omics technique combined with hormone content measurement was applied to seed germination of Chinese pistachio.

KEY RESULTS

Due to its great accumulation during seed germination, catechin stood out from the identified metabolites in a broadly targeted metabolomic analysis. Exogenous catechin at 10 mg L-1 significantly improved the germination of Chinese pistachio seeds. An interesting result of hormone analysis was that the improving effect of catechin could be attributed to an increase in gibberellic acid 3 (GA3) content rather than a decrease in abscisic acid (ABA) content before germination. Treatments with paclobutrazol (PAC, a GA biosynthesis inhibitor) and PAC + catechin also showed that the promoting effect of catechin on seed germination depends on GA biosynthesis. Transcriptome analysis and qRT‒PCR further revealed that catechin induced the expression of PcGA20ox5 to activate GA biosynthesis. Several transcription factors were induced by catechin and GA treatments, such as TCP, bZIP and C3H, which may play an important regulatory role in GA biosynthesis in a catechin-mediated way.

CONCLUSIONS

Catechin promotes seed germination via GA biosynthesis in Chinese pistachios. This study proposes a novel mechanism by which catechin promotes seed germination via the GA pathway, which provides new insight into a comprehensive understanding of seed dormancy and germination.

Comparative transcriptome analysis reveals the potential mechanism of GA3-induced dormancy release in Suaeda glauca black seeds

Suaeda glauca Bunge produces dimorphic seeds on the same plant, with brown seeds displaying non-dormant characteristics and black seeds exhibiting intermediate physiological dormancy traits. Previous studies have shown that black seeds have a very low germination rate under natural conditions, but exogenous GA3 effectively enhanced the germination rate of black seeds. However, the physiological and molecular mechanisms underlying the effects of GA3 on S. glauca black seeds are still unclear. In this study, transcriptomic profiles of seeds at different germination stages with and without GA3 treatment were analyzed and compared, and the TTF, H2O2, O2 -, starch, and soluble sugar contents of the corresponding seed samples were determined. The results indicated that exogenous GA3 treatment significantly increased seed vigor, H2O2, and O2 - contents but decreased starch and soluble sugar contents of S. glauca black seeds during seed dormancy release. RNA-seq results showed that a total of 1136 DEGs were identified in three comparison groups and were involved mainly in plant hormone signal transduction, diterpenoid biosynthesis, flavonoid biosynthesis, phenylpropanoid biosynthesis, and carbohydrate metabolism pathway. Among them, the DEGs related to diterpenoid biosynthesis (SgGA3ox1, SgKAO and SgGA2ox8) and ABA signal transduction (SgPP2Cs) could play important roles during seed dormancy release. Most genes involved in phenylpropanoid biosynthesis were activated under GA3 treatment conditions, especially many SgPER genes encoding peroxidase. In addition, exogenous GA3 treatment also significantly enhanced the expression of genes involved in flavonoid synthesis, which might be beneficial to seed dormancy release. In accordance with the decline in starch and soluble sugar contents, 15 genes involved in carbohydrate metabolism were significantly up-regulated during GA3-induced dormancy release, such as SgBAM, SgHXK2, and SgAGLU, etc. In a word, exogenous GA3 effectively increased the germination rate and seed vigor of S. glauca black seeds by mediating the metabolic process or signal transduction of plant hormones, phenylpropanoid and flavonoid biosynthesis, and carbohydrate metabolism processes. Our results provide novel insights into the transcriptional regulation mechanism of exogenous GA3 on the dormancy release of S. glauca black seeds. The candidate genes identified in this study may be further studied and used to enrich our knowledge of seed dormancy and germination.

Integrated Metabolomics and Transcriptomics Analysis of Flavonoid Biosynthesis Pathway in Polygonatum cyrtonema Hua

Flavonoids, a class of phenolic compounds, are one of the main functional components and have a wide range of molecular structures and biological activities in Polygonatum. A few of them, including homoisoflavonoids, chalcones, isoflavones, and flavones, were identified in Polygonatum and displayed a wide range of powerful biological activities, such as anti-cancer, anti-viral, and blood sugar regulation. However, few studies have systematically been published on the flavonoid biosynthesis pathway in Polygonatum cyrtonema Hua. Therefore, in the present study, a combined transcriptome and metabolome analysis was performed on the leaf, stem, rhizome, and root tissues of P. cyrtonema to uncover the synthesis pathway of flavonoids and to identify key regulatory genes. Flavonoid-targeted metabolomics detected a total of 65 active substances from four different tissues, among which 49 substances were first study to identify in Polygonatum, and 38 substances were flavonoids. A total of 19 differentially accumulated metabolites (DAMs) (five flavonols, three flavones, two dihydrochalcones, two flavanones, one flavanol, five phenylpropanoids, and one coumarin) were finally screened by KEGG enrichment analysis. Transcriptome analysis indicated that a total of 222 unigenes encoding 28 enzymes were annotated into three flavonoid biosynthesis pathways, which were "phenylpropanoid biosynthesis", "flavonoid biosynthesis", and "flavone and flavonol biosynthesis". The combined analysis of the metabolome and transcriptome revealed that 37 differentially expressed genes (DEGs) encoding 11 enzymes (C4H, PAL, 4CL, CHS, CHI, F3H, DFR, LAR, ANR, FNS, FLS) and 19 DAMs were more likely to be regulated in the flavonoid biosynthesis pathway. The expression of 11 DEGs was validated by qRT-PCR, resulting in good agreement with the RNA-Seq. Our studies provide a theoretical basis for further elucidating the flavonoid biosynthesis pathway in Polygonatum.

Chromosome-level genome assembly provides insights into the genome evolution and functional importance of the phenylpropanoid-flavonoid pathway in Thymus mongolicus

BACKGROUND

Thymus mongolicus (family Lamiaceae) is a Thyme subshrub with strong aroma and remarkable environmental adaptability. Limited genomic information limits the use of this plant.

RESULTS

Chromosome-level 605.2 Mb genome of T. mongolicus was generated, with 96.28% anchored to 12 pseudochromosomes. The repetitive sequences were dominant, accounting for 70.98%, and 32,593 protein-coding genes were predicted. Synteny analysis revealed that Lamiaceae species generally underwent two rounds of whole genome duplication; moreover, species-specific genome duplication was identified. A recent LTR retrotransposon burst and tandem duplication might play important roles in the formation of the Thymus genome. Using comparative genomic analysis, phylogenetic tree of seven Lamiaceae species was constructed, which revealed that Thyme plants evolved recently in the family. Under the phylogenetic framework, we performed functional enrichment analysis of the genes on nodes that contained the most gene duplication events (> 50% support) and of relevant significant expanded gene families. These genes were highly associated with environmental adaptation and biosynthesis of secondary metabolites. Combined transcriptome and metabolome analyses revealed that Peroxidases, Hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferases, and 4-coumarate-CoA ligases genes were the essential regulators of the phenylpropanoid-flavonoid pathway. Their catalytic products (e.g., apigenin, naringenin chalcone, and several apigenin-related compounds) might be responsible for the environmental tolerance and aromatic properties of T. mongolicus.

CONCLUSION

This study enhanced the understanding of the genomic evolution of T. mongolicus, enabling further exploration of its unique traits and applications, and contributed to the understanding of Lamiaceae genomics and evolutionary biology.

Integrated transcriptomic and metabolomic analyses elucidate the mechanism of flavonoid biosynthesis in the regulation of mulberry seed germination under salt stress

Seed propagation is the main method of mulberry expansion in China, an important economic forest species. However, seed germination is the most sensitive stage to various abiotic stresses, especially salinity stress. To reveal the molecular regulatory mechanism of mulberry seed germination under salt stress, flavonoid metabolomics and transcriptomics analyses were performed on mulberry seeds germinated under 50 and 100 mmol/L NaCl stress. Analysis of the flavonoid metabolome revealed that a total of 145 differential flavonoid metabolites (DFMs) were classified into 9 groups, 40 flavonols, 32 flavones, 16 chalcones and 14 flavanones. Among them, 61.4% (89) of the DFMs accumulated continuously with increasing salt concentration, reaching the highest level at a 100 mmol/L salt concentration; these DFMs included quercetin-3-O-glucoside (isoquercitrin), kaempferol (3,5,7,4'-tetrahydroxyflavone), quercetin-7-O-glucoside, taxifolin (dihydroquercetin) and apigenin (4',5,7-trihydroxyflavone), indicating that these flavonoids may be key metabolites involved in the response to salt stress. Transcriptional analysis identified a total of 3055 differentially expressed genes (DEGs), most of which were enriched in flavonoid biosynthesis (ko00941), phenylpropanoid biosynthesis (ko00940) and biosynthesis of secondary metabolites (ko01110). Combined analysis of flavonoid metabolomic and transcriptomic data indicated that phenylalanine ammonia-lyase (PAL), 4-coumarate-CoA ligase (4CL), chalcone synthase (CHS), flavonol synthase (FLS), bifunctional dihydroflavonol 4-reductase/flavanone 4-reductase (DFR) and anthocyanidin reductase (ANR) were the key genes involved in flavonoid accumulation during mulberry seed germination under 50 and 100 mmol/L NaCl stress. In addition, three transcription factors, MYB, bHLH and NAC, were involved in the regulation of flavonoid accumulation under salt stress. The results of quantitative real-time PCR (qRT‒PCR) validation showed that the expression levels of 11 DEGs, including 7 genes involved in flavonoid biosynthesis, under different salt concentrations were consistent with the transcriptomic data, and parallel reaction monitoring (PRM) results showed that the expression levels of 6 key enzymes (proteins) involved in flavonoid synthesis were consistent with the accumulation of flavonoids. This study provides a new perspective for investigating the regulatory role of flavonoid biosynthesis in the regulation of mulberry seed germination under salt stress at different concentrations.

Transcriptome Analysis Reveals the Molecular Mechanisms of BR Negative Regulatory Factor StBIN2 Maintaining Tuber Dormancy

Potato is an important food crop. After harvest, these tubers will undergo a period of dormancy. Brassinosteroids (BRs) are a new class of plant hormones that regulate plant growth and seed germination. In this study, 500 nM of BR was able to break the dormancy of tubers. Additionally, exogenous BR also upregulated BR signal transduction genes, except for StBIN2. StBIN2 is a negative regulator of BR, but its specific role in tuber dormancy remains unclear. Transgenic methods were used to regulate the expression level of StBIN2 in tubers. It was demonstrated that the overexpression of StBIN2 significantly prolonged tuber dormancy while silencing StBIN2 led to premature sprouting. To further investigate the effect of StBIN2 on tuber dormancy, RNA-Seq was used to analyze the differentially expressed genes in OE-StBIN2, RNAi-StBIN2, and WT tubers. The results showed that StBIN2 upregulated the expression of ABA signal transduction genes but inhibited the expression of lignin synthesis key genes. Meanwhile, it was also found that StBIN2 physically interacted with StSnRK2.2 and StCCJ9. These results indicate that StBIN2 maintains tuber dormancy by mediating ABA signal transduction and lignin synthesis. The findings of this study will help us better understand the molecular mechanisms underlying potato tuber dormancy and provide theoretical support for the development of new varieties using related genes.

In order to lower the antinutritional activity of serine protease inhibitors, we need to understand their role in seed development

Proteases, including serine proteases, are involved in the entire life cycle of plants. Proteases are controlled by protease inhibitors (PI) to limit any uncontrolled or harmful protease activity. The role of PIs in biotic and abiotic stress tolerance is well documented, however their role in various other plant processes has not been fully elucidated. Seed development is one such area that lack detailed work on the function of PIs despite the fact that this is a key process in the life cycle of the plant. Serine protease inhibitors (SPI) such as the Bowman-Birk inhibitors and Kunitz-type inhibitors, are abundant in legume seeds and act as antinutrients in humans and animals. Their role in seed development is not fully understood and present an interesting research target. Whether lowering the levels and activity of PIs, in order to lower the anti-nutrient levels in seed will affect the development of viable seed, remains an important question. Studies on the function of SPI in seed development are therefore required. In this Perspective paper, we provide an overview on the current knowledge of seed storage proteins, their degradation as well as on the serine protease-SPI system in seeds and what is known about the consequences when this system is modified. We discuss areas that require investigation. This includes the identification of seed specific SPIs; screening of germplasms, to identify plants with low seed inhibitor content, establishing serine protease-SPI ratios and lastly a focus on molecular techniques that can be used to modify seed SPI activity.

Fusarium solani infection disrupts metabolism during the germination of roselle (Hibiscus sabdariffa L.) seeds

Fungal infections adversely influence the production and quality of seeds. Previously, Fusarium solani was reported as the causal agent of roselle (Hibiscus sabdariffa L.) seed rot. This study was designed to evaluate the effect of F. solani infection on the germination, biochemical composition, energy reserves, and antioxidant activity of roselle seeds because there is currently a lack of information on the relationship between seed metabolism and infection with F. solani. The results showed that roselle seeds infected with F. solani exhibited a ca. 55% reduction in overall germination. Additionally, the fungal infection decreased antioxidant activity, total phenolic content, protein, sugar (sucrose, fructose, and glucose), and some amino acid (glutamine, serine, and arginine) contents. In contrast, some metabolites were more abundant in infected seeds, including alanine (2.1-fold) and some fatty acids (palmitic acid and heptadecanoic acid by 1.1- and 1.4-fold, respectively). The infection-associated changes in fatty acid profile resulted in the ratio of unsaturated/saturated fatty acids being 2.1-fold higher in infected seeds. Therefore, our results reveal that F. solani infection remarkably altered the biochemical composition of roselle seeds, which may have contributed to the loss of germination and quality of roselle seeds.

Metabolomics and transcriptomics strategies to reveal the mechanism of diversity of maize kernel color and quality

BACKGROUND

Maize has many kernel colors, from white to dark black. However, research on the color and nutritional quality of the different varieties is limited. The color of the maize grain is an important characteristic. Colored maize is rich in nutrients, which have received attention for their role in diet-related chronic diseases and have different degrees of anti-stress protection for animal and human health.

METHODS

A comprehensive metabolome (LC-MS/MS) and transcriptome analysis was performed in this study to compare different colored maize varieties from the perspective of multiple recombination in order to study the nutritional value of maize with different colors and the molecular mechanism of color formation.

RESULTS

Maize kernels with diverse colors contain different types of health-promoting compounds, highlighting that different maize varieties can be used as functional foods according to human needs. Among them, red-purple and purple-black maize contain more flavonoids than white and yellow kernels. Purple-black kernels have a high content of amino acids and nucleotides, while red-purple kernels significantly accumulate sugar alcohols and lipids.

CONCLUSION

Our study can provide insights for improving people's diets and provide a theoretical basis for the study of food structure for chronic diseases.

Multi-Omics Analysis Reveals the Resistance Mechanism and the Pathogens Causing Root Rot of Coptis chinensis

Coptis chinensis is a traditional Chinese medicinal herb used for more than 2,000 years. Root rot in C. chinensis can cause brown discoloration (necrosis) in the fibrous roots and rhizomes, leading to plants wilting and dying. However, little information exists about the resistance mechanism and the potential pathogens of the root rot of C. chinensis plants. As a result, in order to investigate the relationship between the underlying molecular processes and the pathogenesis of root rot, transcriptome and microbiome analyses were performed on healthy and diseased C. chinensis rhizomes. This study found that root rot can lead to the significant reduction of medicinal components of Coptis, including thaliotrine, columbamine, epiberberin, coptisine, palmatine chloride, and berberine, affecting its efficacy quality. In the present study, Diaporthe eres, Fusarium avenaceum, and Fusarium solani were identified as the main pathogens causing root rot in C. chinensis. At the same time, the genes in phenylpropanoid biosynthesis, plant hormone signal transduction, plant-pathogen interaction, and alkaloid synthesis pathways were involved in the regulation of root rot resistance and medicinal component synthesis. In addition, harmful pathogens (D. eres, F. avenaceum and F. solani) also induce the expression of related genes in C. chinensis root tissues to reduce active medicinal ingredients. These results provide insights into the root rot tolerance study and pave the way for process disease resistance breeding and quality production of C. chinensis. IMPORTANCE Root rot disease significantly reduces the medicinal quality of Coptis chinensis. In the present study, results found that the C. chinensis fibrous and taproot have different tactics in response to rot pathogen infection. Diaporthe eres, Fusarium avenaceum, and Fusarium solani were isolated and identified to cause different degrees of C. chinensis root rot. These results are helpful for researchers to further explore the mechanism of resistance to rhizoma Coptis root rot.

Integrating Transcriptomics and Hormones Dynamics Reveal Seed Germination and Emergence Process in Polygonatum cyrtonema Hua

Polygonatum cyrtonema Hua is a traditional Chinese herb propagated using rhizomes, and excessive demand for seedlings and quality deterioration caused by rhizome propagation has highlighted that seed propagation may be an ideal solution to address these issues. However, the molecular mechanisms involved in P. cyrtonema Hua seed germination and emergence stages are not well understood. Therefore, in the present study, we performed transcriptomics combined with hormone dynamics during different seed germination stages, and 54,178 unigenes with an average length of 1390.38 bp (N50 = 1847 bp) were generated. Significant transcriptomic changes were related to plant hormone signal transduction and the starch and carbohydrate pathways. Genes related to ABA(abscisic acid), IAA(Indole acetic acid), and JA(Jasmonic acid) signaling, were downregulated, whereas genes related to ethylene, BR(brassinolide), CTK(Cytokinin), and SA(salicylic acid) biosynthesis and signaling were activated during the germination process. Interestingly, GA biosynthesis- and signaling-related genes were induced during the germination stage but decreased in the emergence stage. In addition, seed germination significantly upregulated the expression of genes associated with starch and sucrose metabolism. Notably, raffinose biosynthesis-related genes were induced, especially during the emergence stage. In total, 1171 transcription factor (TF) genes were found to be differentially expressed. Our results provide new insights into the mechanisms underlying P. cyrtonema Hua seed germination and emergence processes and further research for molecular breeding.

Transcriptome and Metabolome Analysis Reveal the Flavonoid Biosynthesis Mechanism of Abelmoschus manihot L. at Different Anthesis Stages

Abelmoschus manihot L. (HSK) is a rare and endangered species in the wild that grows on the cliffs of deep mountains. As a natural plant, the chemical composition of HSK is relatively complex, which mainly includes flavonoids, organic acids, polysaccharides, and various trace elements with good effects of clearing away heat, anti-inflammatory, analgesic, and calming nerves, and inhibiting tumor cells. In this experiment, different developmental stages of HSK flowers were used for optimization of the flavonoid extraction and determining method. The antioxidant activities, flavonoid accumulation pattern, and synthesis regulatory network were analyzed using biochemistry, RNA-seq, and UPLC-MS/MS. The total content of flavonoids, vitexin rhamnoside, hyperoside, and rutin in HSK flowers at T3 stage (flower wilting) was significantly higher than in T2 (full flowering) and T1 (bud) stages. Compared with T1 and T2, the antioxidant capacity of the T3 flower alcohol extract was also the strongest, including the total reducing ability, DPPH clearance, OH clearance, O^2- clearance, and total antioxidant capacity. A total of 156 flavonoids and 47,179 unigenes were detected by UPLC-MS/MS and RNA-Seq, respectively. The candidate genes and key metabolites involved in flavonoid biosynthesis were identified and the regulatory networks were also analyzed in this study. qRT-PCR test further proved that the gene expression level was consistent with the results of RNA sequence data. The relationship between the gene expression and flavonoid accumulation network provides a theoretical basis for the mining and regulation of functional genes related to the flavonoid biosynthesis and metabolism in Abelmoschus manihot L.

Combined analysis of multi-omics reveals the potential mechanism of flower color and aroma formation in Macadamia integrifolia

INTRODUCTION

Macadamia integrifolia Maiden & Betche is a domesticated high-value nut crop. The development of nut flower affects the fruit setting rate, yield and quality of nuts. Therefore, in this experiment, two varieties with different flower color, flowering time, flowering quantity and nut yield (single fruit weight) were selected as the research objects.

METHODS

Transcriptome (RNA-Seq) and metabolome (LC-MS/MS, GC-MS) analyses were performed to study the regulatory mechanisms of nut flower development, color and aroma.

RESULTS

The results indicated that plant hormone signal transduction, starch sucrose metabolism, phenylpropanoid metabolism, flavonoid biosynthesis, and anthocyanin biosynthesis pathways were related to nut flower development and flower color formation. In the early stage of flowering, most of the differentially expressed genes (DEGs) are involved in the IAA signal transduction pathway, while in the later stage, the brassinolide signal pathway is mainly involved. In starch and sugar metabolism, DEGs are mainly involved in regulating and hydrolyzing stored starch into small molecular sugars in flower tissues. In the phenylpropanoid biosynthesis pathway, DEGs are mainly related to the color and aroma (volatile organic compounds, VOCs) formation of nut flowers. Four color formation metabolites (anthocyanins) in nut flowers were found by LC-MS/MS detection. In addition, the VOCs showed no significant difference between red nut flowers (R) and white nut flowers (W), which was mainly reflected in the aroma formation stage (flowering time). And 12 common differentially accumulation metabolites (DAMs) were detected by GC-MS and LC-MS/MS. At the same time, the DEGs, AAT, LOX and PAL genes, were also identified to regulate key metabolite synthesis during nut flower development. These genes were further verified by qRT-PCR.

CONCLUSION

Our results provide insights to clarify the molecular mechanism of color and aroma formation during M. integrifolia flower development that pave the way for nut quality and yield breeding.

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.

Transcriptomics and metabolomics changes triggered by exogenous 6-benzylaminopurine in relieving epicotyl dormancy of Polygonatum cyrtonema Hua seeds

Polygonatum cyrtonema Hua is one of the most useful herbs in traditional Chinese medicine and widely used in medicinal and edible perennial plant. However, the seeds have the characteristics of epicotyl dormancy. In this study, the molecular basis for relieving epicotyl dormancy of P. cyrtonema seeds under exogenous 6-benzylaminopurine (6-BA) treatment was revealed for the first time through transcriptome and metabolomics analysis. We determined the elongation of epicotyl buds as a critical period for dormancy release and found that the content of trans-zeatin, proline, auxin and gibberellin was higher, while flavonoids and arginine were lower in the treatment group. Transcriptome analysis showed that there were significant differences in gene expression in related pathways, and the expression patterns were highly consistent with the change of metabolites in corresponding pathways. Co-expression analysis showed that cytokinin dehydrogenase of P. cyrtonema (PcCKXs) and pelargonidin in flavonoid biosynthesis, as well as L-proline, L-ornithine, and L-citrulline in arginine and proline metabolism form network modules, indicating that they have related regulatory roles. Above all, our findings provide new insight into the exogenous 6-BA relieving epicotyl dormancy of P. cyrtonema seeds.

Metabolome profiling of stratified seeds provides insight into the regulation of dormancy in Davidia involucrata

Dove tree (Davidia involucrata), a tertiary vestige species, is well-adapted to cool conditions. Dormancy in D. involucrata seed lasts for an extremely long period of time, typically between 3 and 4 years, and this characteristic makes the species an excellent model for studying the mechanisms of seed dormancy. The molecular mechanisms governing germination control in D. involucrata are still unknown. Seed stratification have been reported to enhance germination in recalcitrant seeds. We performed a widely targeted metabolome profiling to identify metabolites and associated pathways in D. involucrata seeds from six different moist sand stratification durations (0-30 months) using the ultra-high-performance liquid chromatography-Q Exactive Orbitrap-Mass spectrometry. There was an increasing germination rate with prolonged stratification durations (12-30 months). Furthermore, we detected 10,008 metabolites in the stratified seeds. We also detected 48 differentially accumulated metabolites (DAMs) between all stratification periods in the seeds, with 10 highly conserved metabolites. Most of the differentially accumulated metabolites between unstratified and stratified seeds were enriched in purine metabolism, pyrimidine metabolism, flavone and flavonol biosynthesis, phenylpropanoid biosynthesis, and arginine biosynthesis pathways. Key phytohormones, abscisic acid, indole-3 acetic acid, and sinapic acid were differentially accumulated in the seeds and are predicted to regulate dormancy in D. involucrata. We have provided extensive metabolic information useful for future works on dove tree germination study.

Quantitative Trait Locus Mapping Combined with RNA Sequencing Reveals the Molecular Basis of Seed Germination in Oilseed Rape

Rapid and uniform seed germination improves mechanized oilseed rape production in modern agricultural cultivation practices. However, the molecular basis of seed germination is still unclear in Brassica napus. A population of recombined inbred lines of B. napus from a cross between the lower germination rate variety ‘APL01’ and the higher germination rate variety ‘Holly’ was used to study the genetics of seed germination using quantitative trait locus (QTL) mapping. A total of five QTLs for germination energy (GE) and six QTLs for germination percentage (GP) were detected across three seed lots, respectively. In addition, six epistatic interactions between the QTLs for GE and nine epistatic interactions between the QTLs for GP were detected. qGE.C3 for GE and qGP.C3 for GP were co-mapped to the 28.5–30.5 cM interval on C3, which was considered to be a novel major QTL regulating seed germination. Transcriptome analysis revealed that the differences in sugar, protein, lipid, amino acid, and DNA metabolism and the TCA cycle, electron transfer, and signal transduction potentially determined the higher germination rate of ‘Holly’ seeds. These results contribute to our knowledge about the molecular basis of seed germination in rapeseed.