Transcriptome Analysis of Carbohydrate Metabolism Genes and Molecular Regulation of Sucrose Transport Gene LoSUT on the Flowering Process of Developing Oriental Hybrid Lily 'Sorbonne' Bulb

Nitric Oxide Pre-Treatment Advances Bulblet Dormancy Release by Mediating Metabolic Changes in Lilium

The lily is a globally popular cut flower, and managing dormancy in lily bulblets is essential for continuous, year-round production. While nitric oxide (NO) has been shown to influence seed dormancy and germination, its role in dormancy release in lilies was previously unconfirmed. In this study, we investigated the effects of NO on dormancy release in lily bulblets using SNP and c-PTIO. Results showed that SNP treatment promoted dormancy release, while c-PTIO inhibited it. Measurement of endogenous NO levels in the bulbs, along with enzyme activities of NOS-like and NR and gene expression levels of LoNOS-IP and LoNR, confirmed that NO plays a role in promoting dormancy release in lilies. To further elucidate the physiological mechanisms involved, we analyzed H2O2 levels, antioxidant enzyme activities, endogenous hormone levels, and carbohydrate metabolism in the bulbs. Findings demonstrated that NO facilitated dormancy release by increasing H2O2, gibberellins (GAs), indole-3-acetic acid (IAA), zeatin riboside (ZR), reducing sugars, and by accelerating the metabolism of abscisic acid (ABA) and starch. This study provides a foundation for deeper investigation into the mechanisms underlying dormancy release in lily bulbs.

Integrative Analysis of Metabolome and Transcriptome Provides Insights into the Mechanism of Flower Induction in Pineapple (Ananas comosus (L.) Merr.) by Ethephon

Exogenous ethylene is commonly utilized to initiate flower induction in pineapple (Ananas comosus (L.) Merr.). However, the molecular mechanisms and metabolic changes involved are not well understood. In this study, we explored the genetic network and metabolic shifts in the 'Comte de Paris' pineapple variety during ethylene-induced flowering. This was achieved through an integrative analysis of metabolome and transcriptome profiles at vegetative shoot apexes (0 d after ethephon treatment named BL_0d), the stage of bract primordia (8 d after ethephon treatment named BL_8d), stage of flower primordia (18 d after ethephon treatment named BL_18d), and the stage of stopped floret differentiation (34 d after ethephon treatment named BL_34d). We isolated and identified 804 metabolites in the pineapple shoot apex and inflorescence, categorized into 24 classes. Notably, 29, 31, and 46 metabolites showed significant changes from BL_0d to BL_8d, BL_8d to BL_18d, and BL_18d to BL_34d, respectively. A marked decrease in indole was observed, suggesting its role as a characteristic metabolite during flower induction. Transcriptomic analysis revealed 956, 1768, and 4483 differentially expressed genes (DEGs) for BL_0d vs. BL_8d, BL_8d vs. BL_18d, and BL_18d vs. BL_34d, respectively. These DEGs were significantly enriched in carbohydrate metabolism and hormone signaling pathways, indicating their potential involvement in flower induction. Integrating metabolomic and transcriptomic data, we identified several candidate genes, such as Agamous-Like9 (AGL9), Ethylene Insensitive 3-like (ETIL3), Apetala2 (AP2), AP2-like ethylene-responsive transcription factor ANT (ANT), and Sucrose synthase 2 (SS2), that play potentially crucial roles in ethylene-induced flower induction in pineapple. We also established a regulatory network for pineapple flower induction, correlating metabolites and DEGs, based on the Arabidopsis thaliana pathway as a reference. Overall, our findings offer a deeper understanding of the metabolomic and molecular mechanisms driving pineapple flowering.

Transcriptomic and Hormone Analyses Provide Insight into the Regulation of Axillary Bud Outgrowth of Eucommia ulmoides Oliver

An essential indicator of Eucommia ulmoides Oliver (E. ulmoides) is the axillary bud; the growth and developmental capacity of axillary buds could be used to efficiently determine the structural integrity of branches and plant regeneration. We obtained axillary buds in different positions on the stem, including upper buds (CK), tip buds (T1), and bottom buds (T2), which provided optimal materials for the study of complicated regulatory networks that control bud germination. This study used transcriptomes to analyze the levels of gene expression in three different types of buds, and the results showed that 12,131 differentially expressed genes (DEGs) were discovered via the pairwise comparison of transcriptome data gathered from CK to T2, while the majority of DEGs (44.38%) were mainly found between CK and T1. These DEGs were closely related to plant hormone signal transduction and the amino acid biosynthesis pathway. We also determined changes in endogenous hormone contents during the process of bud germination. Interestingly, except for indole-3-acetic acid (IAA) content, which showed a significant upward trend (p < 0.05) in tip buds on day 4 compared with day 0, the other hormones showed no significant change during the process of germination. Then, the expression patterns of genes involved in IAA biosynthesis and signaling were examined through transcriptome analysis. Furthermore, the expression levels of genes related to IAA biosynthesis and signal transduction were upregulated in tip buds. Particularly, the expression of the IAA degradation gene Gretchen Hagen 3 (GH3.1) was downregulated on day 4, which may support the concept that endogenous IAA promotes bud germination. Based on these data, we propose that IAA synthesis and signal transduction lead to morphological changes in tip buds during the germination process. On this basis, suggestions to improve the efficiency of the production and application of E. ulmoides are put forward to provide guidance for future research.

LoSWEET14, a Sugar Transporter in Lily, Is Regulated by Transcription Factor LoABF2 to Participate in the ABA Signaling Pathway and Enhance Tolerance to Multiple Abiotic Stresses in Tobacco

Sugar transport and distribution plays an important role in lily bulb development and resistance to abiotic stresses. In this study, a member of the Sugar Will Eventually be Exported Transporters (SWEET) gene family, LoSWEET14, from Oriental hybrid lily 'Sorbonne' was identified. LoSWEET14 encodes a protein of 278 amino acids and is capable of transporting sucrose and some types of hexoses. The transcript level of the LoSWEET14 gene was significantly increased under various stress conditions including drought, cold, salt stresses, and abscisic acid (ABA) treatment. Overexpression of LoSWEET14 in tobacco (Nicotiana tabacum) showed that the transgenic lines had larger leaves, accumulated more soluble sugars, and were more resistant to drought, cold, and salt stresses, while becoming more sensitive to ABA compared with wild-type lines. Promoter analysis revealed that multiple stress-related cis-acting elements were found in the promoter of LoSWEET14. According to the distribution of cis-acting elements, different lengths of 5'-deletion fragments were constructed and the LoSWEET14-pro3(-540 bp) was found to be able to drive GUS gene expression in response to abiotic stresses and ABA treatment. Furthermore, a yeast one hybrid (Y1H) assay proved that the AREB/ABF (ABRE-binding protein/ABRE-binding factor) from lilies (LoABF2) could bind to the promoter of LoSWEET14. These findings indicated that LoSWEET14 is induced by LoABF2 to participate in the ABA signaling pathway to promote soluble sugar accumulation in response to multiple abiotic stresses.

Identification of Differentially Expressed Genes Related to Floral Bud Differentiation and Flowering Time in Three Populations of Lycoris radiata

The transition from vegetative to reproductive growth is important for controlling the flowering of Lycoris radiata. However, the genetic control of this complex developmental process remains unclear. In this study, 18 shoot apical meristem (SAM) samples were collected from early-, mid- and late-flowering populations during floral bud differentiation. The histological analysis of paraffin sections showed that the floral bud differentiation could be divided into six stages; the differentiation time of the early group was earlier than that of the middle and late groups, and the late group was the latest. In different populations, some important differential genes affecting the flowering time were identified by transcriptome profiles of floral bud differentiation samples. Weighted gene co-expression network analysis (WGCNA) was performed to enrich the gene co-expression modules of diverse flowering time populations (FT) and floral bud differentiation stages (ST). In the MEyellow module, five core hub genes were identified, including CO14, GI, SPL8, SPL9, and SPL15. The correlation network of hub genes showed that they interact with SPLs, AP2, hormone response factors (auxin, gibberellin, ethylene, and abscisic acid), and several transcription factors (MADS-box transcription factor, bHLH, MYB, and NAC3). It suggests the important role of these genes and the complex molecular mechanism of floral bud differentiation and flowering time in L. radiata. These results can preliminarily explain the molecular mechanism of floral bud differentiation and provide new candidate genes for the flowering regulation of Lycoris.

Characterization of Phytohormones and Transcriptomic Profiling of the Female and Male Inflorescence Development in Manchurian Walnut (Juglans mandshurica Maxim.)

Flowers are imperative reproductive organs and play a key role in the propagation of offspring, along with the generation of several metabolic products in flowering plants. In Juglans mandshurica, the number and development of flowers directly affect the fruit yield and subsequently its commercial value. However, owing to the lack of genetic information, there are few studies on the reproductive biology of Juglans mandshurica, and the molecular regulatory mechanisms underlying the development of female and male inflorescence remain unclear. In this study, phytohormones and transcriptomic sequencing analyses at the three stages of female and male inflorescence growth were performed to understand the regulatory functions underlying flower development. Gibberellin is the most dominant phytohormone that regulates flower development. In total, 14,579 and 7188 differentially expressed genes were identified after analyzing the development of male and female flowers, respectively, wherein, 3241 were commonly expressed. Enrichment analysis for significantly enriched pathways suggested the roles of MAPK signaling, phytohormone signal transduction, and sugar metabolism. Genes involved in floral organ transition and flowering were obtained and analyzed; these mainly belonged to the M-type MADS-box gene family. Three flowering-related genes (SOC1/AGL20, ANT, and SVP) strongly interacted with transcription factors in the co-expression network. Two key CO genes (CO3 and CO1) were identified in the photoperiod pathway. We also identified two GA20xs genes, one SVP gene, and five AGL genes (AGL8, AGL9, AGL15, AGL19, and AGL42) that contributed to flower development. The findings are expected to provide a genetic basis for the studies on the regulatory networks and reproductive biology in inflorescence development for J. mandshurica.

Carbon fluxes and environmental interactions during legume development, with a specific focus on Pisum sativum

Grain legumes are major food crops cultivated worldwide for their seeds with high nutritional content. To answer the growing concern about food safety and protein autonomy, legume cultivation must increase in the coming years. In parallel, current agricultural practices are facing environmental challenges, including global temperature increase and more frequent and severe episodes of drought stress. Crop yield directly relies on carbon allocation and is particularly affected by these global changes. We review the current knowledge on source-sink relationships and carbon resource allocation at all developmental stages, from germination to vegetative growth and seed production in grain legumes, focusing on pea (Pisum sativum). We also discuss how these source-sink relationships and carbon fluxes are influenced by biotic and abiotic factors. Major agronomic traits, including seed yield and quality, are particularly impacted by drought, temperatures, salinity, waterlogging, or pathogens and can be improved through the promotion of beneficial soil microorganisms or through optimized plant carbon resource allocation. Altogether, our review highlights the need for a better understanding of the cellular and molecular mechanisms regulating carbon fluxes from source leaves to sink organs, roots, and seeds. These advancements will further improve our understanding of yield stability and stress tolerance and contribute to the selection of climate-resilient crops.

Expression Patterns of Sugar Transporter Genes in the Allocation of Assimilates and Abiotic Stress in Lily

During the growth cycle of lilies, assimilates undergo a process of accumulation, consumption and reaccumulation in bulbs and are transported and allocated between aboveground and underground organs and tissues. The sink-source relationship changes with the allocation of assimilates, affecting the vegetative growth and morphological establishment of lilies. In this study, the carbohydrate contents in different tissues of five critical stages during lily development were measured to observe the assimilates allocation. The results showed bulbs acted as the main source to provide energy before the budding stage (S3); after the flowering stage (S4), bulbs began to accumulate assimilates as a sink organ again. During the period when the plant height was 30cm with leaf-spread (S2), leaves mainly accumulated assimilates from bulbs through the symplastic pathway, while when leaves were fully expanded, it transformed to export carbohydrates. At the S4 stage, flowers became a new active sink with assimilates influx. To further understand the allocation of assimilates, 16 genes related to sugar transport and metabolism (ST genes) were identified and categorized into different subfamilies based on the phylogenetic analysis, and their protein physicochemical properties were also predicted. Tissue-specific analysis showed that most of the genes were highly expressed in stems and petals, and it was mainly the MST (monosaccharide transporter) genes that were obviously expressed in petals during the S4 stage, suggesting that they may be associated with the accumulation of carbohydrates in flowers and thus affect flower development process. LoSWEET14 (the Sugar will eventually be exported transporters) was significantly correlated with starch in scales and with soluble sugar in leaves. Sugar transporters LoHXT6 and LoSUT1 were significantly correlated with soluble sugar and sucrose in leaves, suggesting that these genes may play key roles in the accumulation and transportation of assimilates in lilies. In addition, we analyzed the expression patterns of ST genes under different abiotic stresses, and the results showed that all genes were significantly upregulated. This study lays a solid foundation for further research on molecular mechanism of sink-source change and response to abiotic stresses in lilies.

Changes of starch and sucrose content and related gene expression during the growth and development of Lanzhou lily bulb

As the main forms of carbohydrates, starch and sucrose play a vital role in the balance and coordination of various carbohydrates. Lanzhou lily is the most popular edible lily in China, mainly distributed in the central region of Gansu. To clarify the relationship between carbohydrate metabolism and bulb development of Lanzhou lily, so as to provide a basis for the promotion of the growth and development in Lanzhou lily and its important economic value, we studied lily bulbs in the squaring stage, flowering stage, half withering stage and withering stage. The plant height, fresh weight of mother and daughter bulbs continued to increase during the whole growth period and fresh weight of stem and leaf began to decrease in the half withering stage. The content of starch, sucrose and total soluble sugar in the lily mother bulb accumulated mostly in the flowering, withering and half withering stages, respectively. Starch, sucrose and total soluble sugar accumulated in the daughter bulb with the highest concentration during the withering stage. In the transcription level, sucrose synthase (SuSy1) and sucrose invertase (INV2) expressed the highest in squaring stage, and the expression was significantly higher in the mother bulb than in the daughter bulb. In flowering stage, the expression levels of soluble starch synthase (SSS1), starch-branching enzyme (SBE) and adenosine diphosphate-glucose pyrophosphorylase (AGP1) genes were higher in the mother bulb than in the daughter bulb. Altogether, our results indicate that starch and sucrose are important for the bulb growth and development of Lanzhou lily.

Global identification of long non-coding RNAs involved in the induction of spinach flowering

Background

Spinach is a beneficial annual vegetable species and sensitive to the bolting or early flowering, which causes a large reduction in quality and productivity. Indeed, bolting is an event induced by the coordinated effects of various environmental factors and endogenous genetic components. Although some key flowering responsive genes have been identified in spinach, non-coding RNA molecules like long non-coding RNAs (lncRNAs) were not investigated yet. Herein, we used bioinformatic approaches to analyze the transcriptome datasets from two different accessions Viroflay and Kashan at two vegetative and reproductive stages to reveal novel lncRNAs and the construction of the lncRNA-mRNA co-expression network. Additionally, correlations among gene expression modules and phenotypic traits were investigated; day to flowering was chosen as our interesting trait.

Results

In the present study, we identified a total of 1141 lncRNAs, of which 111 were differentially expressed between vegetative and reproductive stages. The GO and KEGG analyses carried out on the cis target gene of lncRNAs showed that the lncRNAs play an important role in the regulation of flowering spinach. Network analysis pinpointed several well-known flowering-related genes such as ELF, COL1, FLT, and FPF1 and also some putative TFs like MYB, WRKY, GATA, and MADS-box that are important regulators of flowering in spinach and could be potential targets for lncRNAs.

Conclusions

This study is the first report on identifying bolting and flowering-related lncRNAs based on transcriptome sequencing in spinach, which provides a useful resource for future functional genomics studies, genes expression researches, evaluating genes regulatory networks and molecular breeding programs in the regulation of the genetic mechanisms related to bolting in spinach.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07989-1.

Antagonism between abscisic acid and gibberellin regulates starch synthesis and corm development in Gladiolus hybridus

Understanding corm development in flower bulbs is of importance for securing the quality of cut flowers and propagation of commercial stocks. Gladiolus is one of the most popular bulb plants worldwide. Its corm development is characterized by starch accumulation. Previous research has shown that phytohormones (especially gibberellin (GA)) are involved in tuber development. However, the relationship between abscisic acid (ABA)/GA and starch during corm development remains unclear. To gain deeper insights into the biological process of corm development, we performed a detailed anatomical characterization of different stages of corm development and analyzed phytohormone levels. Our study showed that corm development is linked to hormones (ABA and GA) and carbohydrates (sucrose and starch). Exogenous hormone treatment and silencing of endogenous hormone biosynthesis genes indicated that ABA positively regulates corm development, while GA acts as an antagonist of ABA function. A sucrose synthase gene (GhSUS2) was shown to be involved in the antagonism between ABA and GA. GhSUS2 was upregulated by ABA and downregulated by GA. The increase in the transcript level of GhSUS2 coincided with the development of corm/cormels. Silencing of GhSUS2 repressed corm development and starch accumulation. In conclusion, we propose that GhSUS2, an essential enzyme in sucrose degradation, is differentially regulated by ABA and GA and controls corm development in Gladiolus.

Short Time-Series Expression Transcriptome Data Reveal the Gene Expression Patterns of Dairy Cow Mammary Gland as Milk Yield Decreased Process

The existing research on dairy cow mammary gland genes is extensive, but there have been few reports about dynamic changes in dairy cow mammary gland genes as milk yield decrease. For the first time, transcriptome analysis based on short time-series expression miner (STEM) and histological observations were performed using the Holstein dairy cow mammary gland to explore gene expression patterns in this process of decrease (at peak, mid-, and late lactation). Histological observations suggested that the number of mammary acinous cells at peak/mid-lactation was significantly higher than that at mid-/late lactation, and the lipid droplets area secreted by dairy cows was almost unaltered across the three stages of lactation (p > 0.05). Totals of 882 and 1439 genes were differentially expressed at mid- and late lactation, respectively, compared to peak lactation. Function analysis showed that differentially expressed genes (DEGs) were mainly related to apoptosis and energy metabolism (fold change ≥ 2 or fold change ≤ 0.5, p-value ≤ 0.05). Transcriptome analysis based on STEM identified 16 profiles of differential gene expression patterns, including 5 significant profiles (false discovery rate, FDR ≤ 0.05). Function analysis revealed DEGs involved in milk fat synthesis were downregulated in Profile 0 and DEGs in Profile 12 associated with protein synthesis. These findings provide a foundation for future studies on the molecular mechanisms underlying mammary gland development in dairy cows.

Change in Sucrose Cleavage Pattern and Rapid Starch Accumulation Govern Lily Shoot-to-Bulblet Transition in vitro

In bulb crops, bulbing is a key progress in micropropagation and is the feature that most distinguishes bulbous crops from other plants. Generally, bulbing involves a shoot-to-bulblet transition; however, the underlying mechanism remains elusive. We explored this process by tracking the shoot-to-bulblet transition under different culture conditions. Rapid starch accumulation occurred at 15 days after transplanting (DAT) in the bulblet-inducing treatments as confirmed via histological observations and the significant elevation of starch synthesis related-gene transcription, including LohAGPS, LohAGPL, LohGBSS, LohSS, and LohSBE. However, for shoots that did not transition to bulblets and maintained the shoot status, much higher soluble sugars were detected. Interestingly, we observed a clear shift from invertase-catalyzed to sucrose synthase-catalyzed sucrose cleavage pattern based on the differential expression of LohCWIN and LohSuSy during the key transition stage (prior to and after bulbing at 0-15 DAT). Shoots that transitioned into bulblets showed significantly higher LohSuSy expression, especially LohSuSy4 expression, than shoots that did not transition. A symplastic phloem unloading pathway at the bulblet emergence stage (15 DAT) was verified via the 6(5)-carboxyfluorescein diacetate fluorescent tracer. We propose that starch is the fundamental compound in the shoot-to-bulblet transition and that starch synthesis is likely triggered by the switch from apoplastic to symplastic sucrose unloading, which may be related to sucrose depletion. Furthermore, this study is the first to provide a complete inventory of the genes involved in starch metabolism based on our transcriptome data. Two of these genes, LohAGPS1.2b and LohSSIIId, were verified by rapid amplification of cDNA ends cloning, and these data will provide additional support for Lilium research since whole genome is currently lacking.