De novo sequencing of tree peony (Paeonia suffruticosa) transcriptome to identify critical genes involved in flowering and floral organ development

Flower morphology, flower color, flowering and floral fragrance in Paeonia L

Paeonia have diverse flower colors, rich flower types, varying bloom periods, and delightful fragrances, rendering them highly valuable for both ornamental and economic purposes in horticulture. Investigating the developmental mechanisms of morphology, flower color, flowering and floral fragrance in Paeonia holds significant value for enhancing their ornamental traits and conducting germplasm improvement. This review provides an overview of research progress on Paeonia flower morphology (including flower bud differentiation, classification, omics applications in shape studies, and functional genes regulating flower morphology), flower colors (omics applications in color research and functional genes regulating flower colors), bloom periods (flower bud dormancy, flowering time), and fragrances (preparation, analysis, components, and molecular biology research of flower fragrances) within the Paeonia. Additionally, it offers a comprehensive analysis of current research challenges and future directions.

Comparative Analysis Based on Physiological and Transcriptomic Data between Juvenile and Adult Tree Peony (Paeonia delavayi)

A long juvenile period limits the breeding process of many woody plants including tree peony. To investigate the physiological and transcriptomic differences between juvenile and adult plants of tree peony and to explore the key SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes, which are vital in age-dependent pathways, 1-year-old and 3-year-old Paeonia delavayi plants were used to compare the relevant physiological parameters and transcriptomic profiles of the leaves in two phases of plants. The results of the physiological parameters showed that the starch content in the leaves of adult plants remained unchanged and that the soluble sugar content significantly increased compared with those in the juvenile plants. In terms of plant hormones, the contents of cytokinin-like hormone (N6-isopentenyladenine (iP)) and jasmonic acid (JA) significantly decreased, whereas the contents of auxin (indole-3-acetic acid, IAA), abscisic acid (ABA), cytokinin-like hormone (N6-isopentenyladenenosine (iPR)), and ethylene precursor (1-aminocyclopropane-1-carboxylic acid, ACC) showed no statistic difference. Transcriptome sequencing results showed that there were 194 differentially expressed genes (DEGs) between juvenile and adult plants, including 171 up-regulated DEGs and 23 down-regulated DEGs. Circadian rhythm, plant hormone signal transduction, and sugar metabolism were closely related to the juvenile-to-adult transition in P. delavayi, involving a total of 12 DEGs. In addition, a total of 13 SPL genes were identified in the transcriptome data, but only PdSPL10 (c71307.graph_c0) was differentially expressed. It was further validated via qRT-PCR analysis, indicating that PdSPL10 might be a key gene regulating the process of juvenile-to-adult in P. delavayi. Based on the above results, a hypothetical transcriptional network regulating juvenile-to-adult transition and flowering in P. delavayi was proposed. These findings provide a reference for understanding the mechanism of juvenile-to-adult transition in tree peony.

Transcriptome Landscape Analyses of the Regulatory Network for Zygotic Embryo Development in Paeonia ostii

Paeonia ostii is a worldwide ornamental flower and an emerging oil crop. Zyotic embryogenesis is a critical process during seed development, and it can provide a basis for improving the efficiency of somatic embryogenesis (SE). In this study, transcriptome sequencing of embryo development was performed to investigate gene expression profiling in P. ostii and identified Differentially expressed genes (DEGs) related to transcription factors, plant hormones, and antioxidant enzymes. The results indicated that IAA (Indole-3-acetic acid), GA (Gibberellin), BR (Brassinosteroid) and ETH (Ethylene) were beneficial to early embryonic morphogenesis, while CTK (Cytokinin) and ABA (Abscisic Acid) promoted embryo morphogenesis and maturation. The antioxidant enzymes' activity was the highest in early embryos and an important participant in embryo formation. The high expression of the genes encoding fatty acid desaturase was beneficial to fast oil accumulation. Representative DEGs were selected and validated using qRT-PCR. Protein-protein interaction network (PPI) was predicted, and six central node proteins, including AUX1, PIN1, ARF6, LAX3, ABCB19, PIF3, and PIF4, were screened. Our results provided new insights into the formation of embryo development and even somatic embryo development in tree peonies.

Comparative transcriptome sequencing analysis to postulate the scheme of regulated leaf coloration in Perilla frutescens

Perilla as herb, ornamental, oil and edible plant is widely used in East Asia. Until now, the mechanism of regulated leaf coloration is still unclear. In this study, four different kinds of leaf colors were used to measure pigment contents and do transcriptome sequence to postulate the mechanism of leaf coloration. The measurements of chlorophyll, carotenoid, flavonoid, and anthocyanin showed that higher contents of all the aforementioned four pigments were in full purple leaf 'M357', and they may be determined front and back leaf color formation with purple. Meanwhile, the content of anthocyanin was controlled back leaf coloration. The chromatic aberration analysis and correlative analysis between different pigments and L*a*b* values analysis also suggested front and back leaf color change was correlated with the above four pigments. The genes involved in leaf coloration were identified through transcriptome sequence. The expression levels of chlorophyll synthesis and degradation related genes, carotenoid synthesis related genes and anthocyanin synthesis genes showed up-/down-regulated expression in different color leaves and were consistent of accumulation of these pigments. It was suggested that they were the candidate genes regulated perilla leaf color formation, and genes including F3'H, F3H, F3',5'H, DFR, and ANS are probably important for regulating both front and back leaf purple formation. Transcription factors involved in anthocyanin accumulation, and regulating leaf coloration were also identified. Finally, the probable scheme of regulated both full green and full purple leaf coloration and back leaf coloration was postulated.

Genome-wide association study of 23 flowering phenology traits and 4 floral agronomic traits in tree peony (Paeonia section Moutan DC.) reveals five genes known to regulate flowering time

Tree peony is a unique traditional flower in China, with large, fragrant, and colorful flowers. However, a relatively short and concentrated flowering period limits the applications and production of tree peony. A genome-wide association study (GWAS) was conducted to accelerate molecular breeding for the improvement of flowering phenology traits and ornamental phenotypes in tree peony. A diverse panel of 451 tree peony accessions was phenotyped for 23 flowering phenology traits and 4 floral agronomic traits over 3 years. Genotyping by sequencing (GBS) was used to obtain a large number of genome-wide single-nucleotide polymorphisms (SNPs) (107 050) for the panel genotypes, and 1047 candidate genes were identified by association mapping. Eighty-two related genes were observed during at least 2 years for flowering, and seven SNPs repeatedly identified for multiple flowering phenology traits over multiple years were highly significantly associated with five genes known to regulate flowering time. We validated the temporal expression profiles of these candidate genes and highlighted their possible roles in the regulation of flower bud differentiation and flowering time in tree peony. This study shows that GWAS based on GBS can be used to identify the genetic determinants of complex traits in tree peony. The results expand our understanding of flowering time control in perennial woody plants. Identification of markers closely related to these flowering phenology traits can be used in tree peony breeding programs for important agronomic traits.

Identification of differentially expressed miRNAs and their target genes in response to brassinolide treatment on flowering of tree peony (Paeonia ostii)

Tree peony is a famous flower plant in China, but the short and concentrated flowering period limits its ornamental value and economic value. Brassinolide (BR) plays an important role in plant growth and development including flowering. There have been a large number of reports on the molecular aspects of the flowering process, but the genetic mechanism that was responsible for miRNA-guided regulation of tree peony is almost unclear. In this study, the leaves of tree peony cultivar, 'Feng Dan', were sprayed with different concentrations of BR, and the obvious bloom delay was found at the treatment with BR 50 μg/L. The small RNA sequencing and transcriptome sequencing were performed on the petals of tree peony under an untreated control (CK) and the treatment with BR 50 μg/L during four consecutive flowering development stages. A total of 22 known miRNAs belonging to 12 families were identified and 84 novel miRNAs were predicted. Combined with transcriptome data, a total of 376 target genes were predicted for the 18 differentially expressed known miRNAs and 177 target genes were predicted for the 23 differentially expressed novel miRNAs. Additionally, the potential miRNAs and their target genes were identified, including miR156b targeting SPL, miR172a_4 targeting AP2 and four novel miRNAs targeting SPA1, and revealed that they might affect the flowering time in tree peony. Collectively, these results would provide a theoretical basis for further analysis of miRNA-guided regulation on flowering period in tree peony.

Integrated analysis of miRNAome transcriptome and degradome reveals miRNA-target modules governing floral florescence development and senescence across early- and late-flowering genotypes in tree peony

As a candidate national flower of China, tree peony has extremely high ornamental, medicinal and oil value. However, the short florescence and rarity of early-flowering and late-flowering varieties restrict further improvement of the economic value of tree peony. Specific miRNAs and their target genes engaged in tree peony floral florescence, development and senescence remain unknown. This report presents the integrated analysis of the miRNAome, transcriptome and degradome of tree peony petals collected from blooming, initial flowering, full blooming and decay stages in early-flowering variety Paeonia ostii 'Fengdan', an early-flowering mutant line of Paeonia ostii 'Fengdan' and late-flowering variety Paeonia suffruticosa 'Lianhe'. Transcriptome analysis revealed a transcript ('psu.G.00014095') which was annotated as a xyloglucan endotransglycosylase/hydrolase precursor XTH-25 and found to be differentially expressed across flower developmental stages in Paeonia ostii 'Fengdan' and Paeonia suffruticosa 'Lianhe'. The miRNA-mRNA modules were presented significant enrichment in various pathways such as plant hormone signal transduction, indole alkaloid biosynthesis, arachidonic acid metabolism, folate biosynthesis, fatty acid elongation, and the MAPK signaling pathway. Multiple miRNA-mRNA-TF modules demonstrated the potential functions of MYB-related, bHLH, Trihelix, NAC, GRAS and HD-ZIP TF families in floral florescence, development, and senescence of tree peony. Comparative spatio-temporal expression investigation of eight floral-favored miRNA-target modules suggested that transcript 'psu.T.00024044' and microRNA mtr-miR166g-5p are involved in the floral florescence, development and senescence associated agronomic traits of tree peony. The results might accelerate the understanding of the potential regulation mechanism in regards to floral florescence, development and abscission, and supply guidance for tree peony breeding of varieties with later and longer florescence characteristics.

The red/blue light ratios from light-emitting diodes affect growth and flower quality of Hippeastrum hybridum 'Red Lion'

Light quality strongly impacts the growth and flower quality of ornamental plants. The optimum light quality for the growth and flowering of Hippeastrum remains to be validated. In the present study, we investigated the effect of the red/blue light ratio of LEDs on the growth and flowering quality of H. hybrid 'Red Lion'. Two LEDs with red/blue light ratio of 1:9 (R₁₀B₉₀) and 9:1 (R₉₀B₁₀) were designed. LEDs of white light were the control. In the earlier vegetative and reproductive growth phase, R₉₀B₁₀ increased the biomass of the bulbs, leaves, and flowers. Compared with the control and R₁₀B₉₀ group, R₉₀B₁₀ LEDs delayed flowering by 2.30 d and 3.26 d, respectively. Based on chlorophyll contents, photosynthetic capacity, chlorophyll fluorescence parameters, and carbohydrate contents, the photosynthesis rate was higher in the R₁₀B₉₀ group. Optimal red and blue light intensity promoted the accumulation of carbohydrates and early flowering and prolonged the flowering period of H. hybrid. Microscopic analysis showed that stomatal density was high, and the number of chloroplasts was large in the R₁₀B₉₀ treatment group, which enhanced photosynthesis. Particularly, R₁₀B₉₀ promoted the expression of seven key genes related to chlorophyll synthesis. R₁₀B₉₀ also promoted early overexpression of the HpCOL gene that promotes early flowering. Thus, higher blue light and 10% red light intensities promote early and extended flowering, while higher red light and 10% blue light promote vegetative plant growth but delay flowering.

Characteristics of PoVIN3, a Key Gene of Vernalization Pathway, Affects Flowering Time

The tree peony (Paeonia section Moutan DC.) is the candidate flower in China, with abundant germplasm resources and high ornamental value. However, the short and concentrated flowering period severely restricted the improvement of the economic value of tree peonies. Based on the full-length transcriptome database of tree peonies, the PoVIN3 (GenBank ID: OP341879), involved in the flowering regulation of tree peonies were identified and cloned for the first time. The PoVIN3 was also characterized by bioinformatics methods, quantitative real-time PCR (qRT-PCR), and the establishment of a transgenic system. The expression levels of PoVIN3 in seven different petals developmental stages were the highest at the initial flowering stage of the variant cultivar of Paeonia ostii 'Fengdan,' the initial decay stage of the normal flowering Paeonia ostii 'Fengdan,' and the half opening stage of the late flowering Paeonia suffruticosa 'Lianhe.' Tissue-specific expression analysis showed that the relative expression levels of PoVIN3 were the highest in sepals of both normal flowering Paeonia ostii 'Fengdan' and the late flowering Paeonia suffruticosa 'Lianhe,' and the highest expression was in stamens of early flowering mutant Paeonia ostii 'Fengdan.' In addition, the flowering time of pCAMBIA2300-PoVIN3 transgenic plants was significantly earlier than that of the wild-type, indicating that PoVIN3 could promote plant flowering. The results provide a theoretical basis for exploring the role of PoVIN3 in the regulation of flowering in tree peonies.

From Floral Induction to Blooming: The Molecular Mysteries of Flowering in Woody Plants

Flowering is a pivotal developmental process in response to the environment and determines the start of a new life cycle in plants. Woody plants usually possess a long juvenile nonflowering phase followed by an adult phase with repeated flowering cycles. The molecular mechanism underlying flowering regulation in woody plants is believed to be much more complex than that in annual herbs. In this review, we briefly describe the successive but distinct flowering processes in perennial trees, namely the vegetative phase change, the floral transition, floral organogenesis, and final blooming, and summarize in detail the most recent advances in understanding how woody plants regulate flowering through dynamic gene expression. Notably, the florigen gene FLOWERING LOCUS T(FT) and its antagonistic gene TERMINAL FLOWER 1 (TFL1) seem to play a central role in various flowering transition events. Flower development in different taxa requires interactions between floral homeotic genes together with AGL6 conferring floral organ identity. Finally, we illustrate the issues and corresponding measures of flowering regulation investigation. It is of great benefit to the future study of flowering in perennial trees.

Nutrient Supply Is Essential for Shifting Tree Peony Reflowering Ahead in Autumn and Sugar Signaling Is Involved

The flowering time of tree peony is short and concentrated in spring, which limits the development of its industry. We previously achieved tree peony reflowering in autumn. Here, we further shifted its reflowering time ahead through proper gibberellin (GA) treatment plus nutrient supply. GA treatment alone initiated bud differentiation, but it aborted later, whereas GA plus nutrient (G + N) treatment completed the opening process 38 days before the control group. Through microstructural observation of bud differentiation and starch grains, we concluded that GA plays a triggering role in flowering induction, whereas the nutriment supply ensured the continuous developing for final opening, and both are necessary. We further determined the expression of five floral induction pathway genes and found that PsSOC1 and PsLFY probably played key integral roles in flowering induction and nutrient supply, respectively. Considering the GA signaling, PsGA2ox may be mainly involved in GA regulation, whereas PsGAI may regulate further flower formation after nutrient application. Furthermore, G + N treatment, but not GA alone, inhibited the expression of PsTPS1, a key restricting enzyme in sugar signaling, at the early stage, indicating that sugar signaling is also involved in this process; in addition, GA treatment induced high expression of PsSnRK1, a major nutrient insufficiency indicator, and the induction of PsHXK1, a rate-limiting enzyme for synthesis of sugar signaling substances, further confirmed the nutrient shortage. In short, besides GA application, exogenous nutrient supply is essential to shift tree peony reflowering ahead in autumn under current forcing culture technologies.

Transcriptome sequencing reveals terpene biosynthesis pathway genes accounting for volatile terpene of tree peony

Transcriptomic and volatile component analyses showed that high expression levels of genes from the terpenoid backbone biosynthesis pathway and the monoterpene metabolic pathway can strengthen the floral fragrance of tree peony. Floral fragrance is a crucial ornamental trait whose improvement is one of the primary objectives of tree peony breeding. So far, exploration of the floral fragrance of tree peony has focused on the identification of its volatile components, but the molecular mechanisms responsible for their formation remain unclear. Here, we identified 128 volatile components from the petals of tree peony and found that they consisted primarily of terpenes, alcohols, and esters. Based on the distribution pattern of these major fragrance components, 24 tree peony cultivars were classified into 4 types: grassy scent (ocimene), woody scent (longifolene), lily of the valley scent (linalool), and fruity scent (2-ethyl hexanol). We used RNA-seq to explore the mechanistic basis of terpenoid metabolism in tree peony petals with various scents. The expression levels of AACT, HMGR, PMK, DXS, DXR, HDS, HDR, and GGPS, which encode key enzymes of terpenoid backbone biosynthesis, were upregulated in 'Huangguan' (strong fragrance) compared to 'Fengdan' (faint fragrance). Moreover, the transcript abundance of LIS and MYS, two monoterpene synthase genes, was also enhanced in petals of 'Huangguan' compared to those of 'Fengdan'. Together, these results demonstrate that differences in the expression of genes from the monoterpene synthesis and terpenoid backbone pathways are associated with differences in the fragrance of tree peony. This research provides crucial genetic resources for fragrance improvement and also lays a foundation for further clarification of the mechanisms that underlie tree peony fragrance.

Molecular characterization and expression analysis of the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE gene family in Paeonia suffruticosa

A total of 16 PsSPL genes were identified in tree peony. PsSPLs potentially regulated flowering time, lateral bud and seed development, and the juvenile-to-adult phase transition. SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors are important for plant growth and development. Here, we report the identification of 16 full-length PsSPLs in tree peony (Peaonia suffruticosa Andr.) and 9 PsSPLs that have miR156 target sites. Phylogenetic analysis of the relationship of SPLs in P. suffruticosa and Arabidopsis suggested that they can be classified into six groups, and PsSPLs were highly correlated with Arabidopsis SPLs counterparts in the same group. Cis-element of promoter region analysis suggested that PsSPL genes play roles in physiological processes and developmental events. Expression analysis indicated that most PsSPL genes exhibited high expression levels in the tissues and organs examined here. The increasing expression levels of PsSPL1, PsSPL2, PsSPL8, PsSPL9, PsSPL12, and PsSPL16, and decreasing expression levels of PsSPL1A and PsSPL1B in buds over time suggested that they were probably regulated by the juvenile-to-adult phase transition. In addition, the expression profiles of PsSPL genes in different developmental buds and seeds suggested that PsSPL2, PsSPL3, PsSPL9, PsSPL10, PsSPL13, and PsSPL13A were important genes for regulating the flowering time of the tree peony; PsSPL2 and PsSPL8 might play a role in suppressing lateral bud development, and PsSPL2, PsSPL13, and PsSPL14 positively controlled grain size and number, and pod branching. These results provide a foundation for future functional analysis of PsSPL genes in tree peony growth and development.

Germplasm resources and genetic breeding of Paeonia: a systematic review

Members of the genus Paeonia, which consists of globally renowned ornamentals and traditional medicinal plants with a rich history spanning over 1500 years, are widely distributed throughout the Northern Hemisphere. Since 1900, over 2200 new horticultural Paeonia cultivars have been created by the discovery and breeding of wild species. However, information pertaining to Paeonia breeding is considerably fragmented, with fundamental gaps in knowledge, creating a bottleneck in effective breeding strategies. This review systematically introduces Paeonia germplasm resources, including wild species and cultivars, summarizes the breeding strategy and results of each Paeonia cultivar group, and focuses on recent progress in the isolation and functional characterization of structural and regulatory genes related to important horticultural traits. Perspectives pertaining to the resource protection and utilization, breeding and industrialization of Paeonia in the future are also briefly discussed.

Transcriptome profiling of the flowering transition in saffron (Crocus sativus L.)

Saffron, derived from the stigma of Crocus sativus, is not only a valuable traditional Chinese medicine but also the expensive spice and dye. Its yield and quality are seriously influenced by its flowering transition. However, the molecular regulatory mechanism of the flowering transition in C. sativus is still unknown. In this study, we performed morphological, physiological and transcriptomic analyses using apical bud samples from C. sativus during the floral transition process. Morphological results indicated that the flowering transition process could be divided into three stages: an undifferentiated period, the early flower bud differentiation period, and the late flower bud differentiation period. Sugar, gibberellin (GA₃), auxin (IAA) and zeatin (ZT) levels were steadily upregulated, while starch and abscisic acid (ABA) levels were gradually downregulated. Transcriptomic analysis showed that a total of 60 203 unigenes were identified, among which 19 490 were significantly differentially expressed. Of these, 165 unigenes were involved in flowering and were significantly enriched in the sugar metabolism, hormone signal transduction, cell cycle regulatory, photoperiod and autonomous pathways. Based on the above analysis, a hypothetical model for the regulatory networks of the saffron flowering transition was proposed. This study lays a theoretical basis for the genetic regulation of flowering in C. sativus.

Tree peony variegated flowers show a small insertion in the F3'H gene of the acyanic flower parts

BACKGROUND

The tree peony (Paeonia suffruticosa Andr.) cultivar 'Er Qiao' is appreciated for its unstable variegated flower coloration, with cyanic and acyanic flowers appearing on different branches of the same plant and occasionally in a single flower or petal. However, the variegation mechanism is still unclear.

RESULTS

In this study, we found significantly higher contents and more diverse sets of anthocyanins in the cyanic petals than in the acyanic petals. Comparative transcriptome analysis between the two flower types revealed 477 differentially expressed genes (DEGs). Quantitative real-time PCR results verified that the transcript levels of the flavonol synthase (FLS) gene were significantly increased in the acyanic petals. Furthermore, we found that a GCGGCG insertion at 246 bp in the flavonoid 3'-hydroxylase (F3'H) gene-coding region constitutes a duplication of the 241-245 bp section and was consistently found only in acyanic flowers. Sequence alignment of the F3'H gene from different plant species indicated that only the acyanic petals of 'Er Qiao' contained the GCGGCG insertion. The transformation of Arabidopsis tt7-1 lines demonstrated that the ectopic expression of F3'H-cyanic, but not F3'H-acyanic, could complement the colors in the hypocotyl and seed coat.

CONCLUSION

In summary, we found that an indel in F3'H and the upregulation of FLS drastically reduced the anthocyanin content in acyanic petals. Our results provide molecular candidates for a better understanding of the variegation mechanisms in tree peony.

Flowering in Persian walnut: patterns of gene expression during flower development

BACKGROUND

Flower development and sufficient fruit set are important parameters with respect to walnut yield. Knowledge about flowering genes of fruit trees can help to conduct better molecular breeding programs. Therefore, this study was carried out to investigate the expression pattern of some flowering genes (FT, SOC1, CAL, LFY and TFL1) in Persian walnut (cv. Chandler) during the growing season and winter dormancy.

RESULTS

The results showed that walnut flower induction and initiation in Shahmirzad, Iran occurred in early June and late September, respectively. After meeting chilling and heat requirement, flower differentiation and anthesis occurred in late-March and mid-April to early-May, respectively. Study of flowering gene expression showed that the expression of the FT gene increased in three stages including before breaking of bud dormancy, from late March to late April (coincided with flower differentiation and anthesis) and from late May to mid-June (coincided with flower induction). Like FT, the expression of SOC1 gene increased during flower induction and initiation (mid-May to early-August) as well as flower anthesis (mid-April to early-May). LFY and CAL genes as floral meristem identity genes are activated by FT and SOC1 genes. In contrast with flowering stimulus genes, TFL1 showed overexpression during winter dormancy which prevented flowering.

CONCLUSION

The expression of FT gene activated downstream floral meristem identity genes including SOC1, CAL and LFY which consequently led to release bud dormancy as well as flower anthesis and induction. Also, TFL1 as a flowering inhibitor gene in walnut showed overexpression during the bud dormancy. Chilling accumulation reduced TFL1 gene expression and increased the expression of flowering genes which ultimately led to overcome dormancy.

Transcriptome sequencing and identification of key callus browning-related genes from petiole callus of tree peony (Paeonia suffruticosa cv. Kao) cultured on media with three browning inhibitors

Tree peony (Paeonia suffruticosa Andrews) has ornamental, oil, and medicinal values, and demand in the markets for uniform tree peony seedlings is increasing. Micropropagation could quickly propagate uniform seedlings. However, the heavy browning phenomenon hinders large-scale development of uniform tree peony seedlings. In this paper, we measured the total phenolic compounds content, and sequenced the transcriptomes of tree peony 'Kao' petiole calluses cultured on media with three browning antagonist treatments and fresh petioles to identify the key genes involved in callus browning. Polyvinylpyrrolidone (PVP) treatment can reduce production of phenolic compounds and promote callus regeneration. A total of 218,957 unigenes were obtained from fresh petiole and three kinds of browning petiole calluses by transcriptome sequencing. The average sequence length of unigenes was 446 bp with an N50 of 493 bp. Functional annotation analysis revealed that 43,428, 45,357, 31,194, 30,019, and 21,357 unigenes were annotated using the NCBI-NR database, Swiss-Prot, KOG, GO, and KEGG, respectively. In total, 33 differentially expressed genes (DEGs) were identified as potentially associated with callus browning. Among these DEGs, 12 genes were predicted to participate in phenolic compounds biosynthesis, three genes were predicted to be involved in phenolic compounds oxidation, and six genes were predicted to participate in callus regeneration. Moreover, six transcription factors were observed to be differentially expressed in the fresh petiole and three treated petioles in tree peony. This study comprehensively identifies browning-related gene resources and will possibly help in deciphering the molecular mechanisms of callus browning of tree peony in the future.

Development of SSR markers in Paeonia based on De Novo transcriptomic assemblies

Peony is a famous ornamental and medicinal plant in China, and peony hybrid breeding is an important means of germplasm innovation. However, research on the genome of this species is limited, thereby hindering the genetic and breeding research on peony. In the present study, simple sequence repeat (SSR) locus analysis was performed on expressed sequence tags obtained by the transcriptome sequencing of Paeonia using Microsatellite software. Primers with polymorphism were obtained via polymerase chain reaction amplification and electrophoresis. As a result, a total of 86,195 unigenes were obtained by assembling the transcriptome data of Paeonia. Functional annotations were obtained in seven functional databases including 49,172 (Non-Redundant Protein Sequence Database: 57.05%), 38,352 (Nucleotide Sequence Database: 44.49%), 36,477 (Swiss Prot: 42.32%), 38,905 (Clusters of Orthologous Groups for Eukaryotic Complete Genomes: 45.14%), 37,993 (Kyoto Encyclopedia of Genes and Genomes: 44.08%), 26,832 (Gene Ontology: 31.13%) and 37,758 (Pfam: 43.81%) unigenes. Meanwhile, 21,998 SSR loci were distributed in 17,567 unigenes containing SSR sequences, and the SSR distribution frequency was 25.52%, with an average of one SSR sequence per 4.66 kb. Mononucleotide, dinucleotide, and trinucleotide were the main repeat types, accounting for 55.74%, 25.58%, and 13.21% of the total repeat times, respectively. Forty-five pairs of the 100 pairs of primers selected randomly could amplify clear polymorphic bands. The polymorphic primers of these 45 pairs were used to cluster and analyze 16 species of peony. The new SSR molecular markers can be useful for the study of genetic diversity and marker-assisted breeding of peony.

A New Insight into Flowering Regulation: Molecular Basis of Flowering Initiation in Magnolia × soulangeana 'Changchun'

Magnolia × soulangeana ‘Changchun’ are trees that bloom in spring and summer respectively after flower bud differentiation. Here, we use phenological and morphological observation and RNA-seq technology to study the molecular basis of flowering initiation in ‘Changchun’. During the process of flowering initiation in spring and summer, the growth of expanded flower buds increased significantly, and their shape was obviously enlarged, which indicated that flowering was initiated. A total of 168,120 expressed genes were identified in spring and summer dormant and expanded flower buds, of which 11,687 genes showed significantly differential expression between spring and summer dormant and expanded flower buds. These differentially expressed genes (DEGs) were mainly involved in plant hormone signal transduction, metabolic processes, cellular components, binding, and catalytic activity. Analysis of differential gene expression patterns revealed that gibberellin signaling, and some transcription factors were closely involved in the regulation of spring and summer flowering initiation in ‘Changchun’. A qRT-PCR (quantitative Real Time Polymerase Chain Reaction) analysis showed that BGISEQ-500 sequencing platform could truly reflect gene expression patterns. It also verified that GID1B (GIBBERELLIN INSENSITIVE DWARF1 B), GID1C, SPL8 (SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 8), and GASA (GIBBERELLIC ACID-STIMULATED ARABIDOPSIS) family genes were expressed at high levels, while the expression of SPY (SPINDLY) was low during spring and summer flowering initiation. Meanwhile, the up- and down-regulated expression of, respectively, AGL6 (AGAMOUS-LIKE 6) and DREB3 (DEHYDRATION-RESPONSIVE ELEMENT-BINDING PROTEIN 3), AG15, and CDF1 (CYCLIC DOF FACTOR 1) might also be involved in the specific regulation of spring and summer flowering initiation. Obviously, flowering initiation is an important stage of the flowering process in woody plants, involving the specific regulation of relevant genes and transcription factors. This study provides a new perspective for the regulation of the flowering process in perennial woody plants.