Genetic Regulation of Growth and Development of Woody Plants

In Fraxinus mandshurica Rupr. (F. mandshurica), the mature seeds exhibit a deep dormancy trait, and the seedlings are vulnerable to external environmental factors, such as low temperature and drought, leading to ecological dormancy. In order to investigate the role of FmDELLA in growth and development, the variation in FmDELLA transcriptional level, the endogenous hormone content in seed germination and bud dormancy release, and the effects of the month, organs, and exogenous hormones on FmDELLA were determined. The results showed that FmDELLA genes had a synergistic impact with the XERICO, PP2C, and DOG genes on regulating hypocotyl elongation during seed germination. Unlike growing buds, the dormant buds had much higher levels of FmDELLA transcripts. Still, these transcript levels were lowered by using 100 mg/L exogenous gibberellin acid (GA), which could promote bud dormancy release. Exogenous hormones regulated the transcription of FmDELLA, which primarily occurred in the stems, leaves, buds, and flowers and reached its lowest level in September. The transition from dormancy to germination for buds and seeds was related to increased GA, auxin, and cytokinin and decreased abscisic acid. In conclusion, our study revealed the role of FmDELLA in the seed germination and release of bud dormancy and provided a solid basis for F. mandshurica tissue culture and micropropagation. Full article

Environmental stresses can disrupt protein structure, resulting in unfolded or misfolded proteins, thereby triggering endoplasmic reticulum (ER) stress. The unfolded protein response (UPR), particularly as activated by Arabidopsis AtbZIP60 gene, is pivotal for counteracting ER stress and ensuring cell survival. The medicinal plant, Cyclocarya paliurus, known for its wealth of beneficial compounds, is threatened by environmental stresses, limiting the exploration of its therapeutic potential. In order to better exploit and utilize its value, it is necessary to understand the signal pathway of environmental stresses. Here, we identify a homolog of AtbZIP60 in C. paliurus, termed CpbZIP11, which can be upregulated by tunicamycin. The conserved double stem-loop structure in its mRNA is spliced under environmental stresses. This splicing event results in a novel CpbZIP11 mRNA variant, leading to the production of a nuclear-localized CpbZIP11 protein with transcriptional activation activity in yeast. We further delve into the study of evolutionary lineage and motif conservation of CpbZIP11 homologs across various plant groups. This research illuminates the stress adaptation mechanisms in C. paliurus and deepens our understanding of the bZIP evolution, which endows versatility for the understanding of this transcription factor. Full article

Cinnamomum migao H. W. Li is an evergreen woody plant that is only distributed in southwest China. The volatile oils from the fruits of C. migao have long been used as a special authentic medicinal herb by local ethnic minorities. Due to its low seed germination rate, destructive lumbering and low rates of artificial planting, C. migao is facing the danger of extinction. Therefore, it is urgent to exploit and protect this species using molecular biological technology, especially to target the genes involved in the biosynthesis of terpenoids in the volatile oil. However, the genomic data for this plant are not available. In this study, the transcriptome sequencing of C. migao was performed to obtain the key genes involved in terpenoid biosynthesis via a combination of full-length transcriptome and next-generation sequencing (NGS). More than 39.9 Gb of raw data was obtained and 515,929 circular consensus sequences (CCSs) were extracted. After clustering similar 472,858 full-length non-chimeric (FLNC) reads and correction with NGS data, 139,871 consensus isoforms were obtained. Meanwhile, 73,575 non-redundant transcripts were generated by removing redundant transcripts. Then, 70,427 isoforms were successfully annotated using public databases. Moreover, differentially expressed transcripts (DETs) in four different developmental stages of the C. migao fruit were analyzed and 5764 transcripts showed period-specific expression. Finally, 15 transcripts, 6 transcripts, and only 1 transcript were identified as being involved in the biosynthesis of sesquiterpenoids, diterpenoids, and monoterpenoids, respectively. This study provides a basis for future research in the gene mining, genetic breeding, and metabolic engineering of C. migao. Full article

Flavonoids are important secondary metabolites in plants, and their biosynthesis includes various enzymes. Although bamboo is a potential resource with abundant flavonoids, its flavonoids biosynthesis is still unclear. Based on the genome and transcriptome data of moso bamboo (Phyllostachys edulis), 24 late flavonoid biosynthesis genes (LFBGs) were identified. Further molecular characteristics analyses suggested they may have different biological functions in flavonoids biosynthesis. Sixteen differentially expressed genes were identified according to transcriptome data from different-height shoots, including five PeANSs, four PeANRs, three PeLARs, and PeDFR1. PeANR4 expressed continuously under drought stress was selected for further analysis. A co-expression network of PeANR4 and 27 differentially expressed transcription factors (DETFs) was constructed, and the regulatory relationship of four DETFs and PeANR4 was validated by Y1H assays. Furthermore, PeANR4 was ectopically expressed in Arabidopsis, and the transgenic lines had darker seed coat color and higher fresh, dry weight and proanthocyanidin (PA) content than the wild type and mutant. Moreover, the transgenic lines had higher germination rate and longer primary root than the wild type and mutant under osmotic and salt stress. These results provide a full understanding and lay a foundation for further functional studies on the LFBGs of bamboo. Full article

Bamboo is one of the essential ornamental plants that is widely used as a decorative landscape element in gardens. Phyllostachys violascens cv. Viridisulcata has a unique internode color phenotype with yellow culm and green sulcus, but their structural and development differences remain unknown. In the current study, we analyzed the histological analysis of internode cross-sections through SEM and microscopy. These results revealed that the vascular bundles distributed in the culm were organized in oblique rows and multiple lines. In contrast, the vascular bundles’ distribution in the sulcus was much more random. The distribution density, maximum length, and maximum width of vascular bundles were also differentiated between the sulcus and the culm. Further, the cell wall thickness of fiber cells in the culm was more than 30% thicker than the sulcus. The FT-IR analysis identified that the culm and sulcus had similar structural properties. The total lignin content measurement revealed that lignin accumulated more in the sulcus than in the culm. Additionally, we identified the lignin biosynthesis pathway genes, Pv4CL and PvC4H, which were differentially expressed between the culm and sulcus through transcriptomic data and qPCR analyses. In conclusion, our results identified that the vascular bundles’ structure differed between the culm and sulcus, and Pv4CL and PvC4H genes might play an essential role in their development. Full article

Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) is an important plantation tree species in China, and seed germination is a key step in forest tree cultivation. To reveal the gene expression network and molecular mechanisms in the germination of Chinese fir seeds, physiological indexes were measured and transcriptome and metabolome analyses were performed on Chinese fir seeds in four stages of germination (imbibition stage, preliminary stage, emergence stage, and germination stage). All six physiological indicators had significant differences at different developmental stages. In transcriptome and metabolome analysis, we identified a large number of differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs). Gene Ontology (GO) analysis showed a large number of DEGs associated with cell growth, and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that DEGs were significantly enriched in the flavonoid biosynthesis, phenylpropanoid biosynthesis, and plant hormone signal transduction pathways. The KEGG enrichment results of DAMs were similar to those of DEGs. The joint analysis of DEGs and DAMs indicated that flavonoid biosynthesis and phenylpropanoid biosynthesis were the key pathways of Chinese fir seed germination. Our study revealed a number of key genes and key metabolites, laying the foundation for further studies on the gene regulatory network of Chinese fir seed germination. Full article

Heat stress due to external heat sources such as fire is an ecological problem for plants. When forest plants suffer from fire, high temperatures cause an array of morphological, physiological, and biochemical changes, which affect growth and development. Michelia macclurei Dandy is an evergreen broad-leaved tree species with the characteristics of fast growth, strong adaptability, and good fire-resistance. Some studies have improved the understanding of how fire behavior affects physiology, function and mortality, but the extreme heat response genes and mechanisms need improved understanding. In this study, we conducted a fire experiment (slight and severe) and RNA-Seq in M. macclure. The de novo assembly obtained 104,052 unigenes, and 48.46% were annotated in at least one public database. Specifically, 4458 and 4810 differentially expressed genes (DEGs) were identified in slight and severe fire treatment groups, respectively. In two treatment groups, 612 unigenes were differentially expressed, which were enriched in ‘oxidoreductase activity’ in the molecular function (MF) category of Gene Ontology (GO) enrichment analysis, suggesting the core role of oxidoreductase activity in response to extremely high temperatures in M. macclurei. In KEGG enrichment analysis of DEGs, the ‘plant hormone signal transduction’ is overrepresented, suggesting that this process plays an important role during heat response in M. macclurei. In the pathways of cytokinine and salicylic acid, some vital DEGs were enriched, which were related to cell division, shoot initiation, and disease resistance, and the potential interactions during heat stress were discussed. Moreover, the DEGs linked to heat stress response were identified, including heat shock factors, stress enhanced protein, signal transduction, photosystem, and major transcription factors. The qRT-PCR examination of various tissues, expression dynamics, and treatments revealed that the genes coding for the heat shock protein HSF30, stress enhanced protein, and photosystem I reaction center subunit II exhibited particularities in leaf tissue. Genes coding for heat shock proteins displayed a distinct expression pattern between fire treatment and conventional heat stress, which could signify the distinctive function of HSPs and the mechanism of heat responses. Altogether, these may interact to respond to fire stress through alterations in cellular processes, signaling transduction, and the synthesis and degradation of response proteins in M. macclurei. The results of this study provide a crucial transcriptional profile influenced by heat stress in M. macclurei, and could be of great use to explore the fire prevention mechanisms of fire-resistant tree species. Full article

Camellia japonica is a woody flower with high ornamental and economic value used for landscaping and as a pot plant. Floral colors are among the most important ornamental traits of flower plants, particularly multicolored flowers. The C. japonica cultivar ‘Joy Kendrick’ has multicolored flowers; the corolla is pink with darker red stripes, but the molecular mechanism underlying this trait is unknown. Here, pigment analysis showed that there are more anthocyanins accumulate in red petal regions than in pink areas, which may be key to formation of red stripes. Furthermore, transcriptome analysis revealed that anthocyanin biosynthesis, modification, and transporter genes are highly expressed in red stripes, consistent with the observed anthocyanin accumulation. In addition, many plant hormone signal transduction genes, particularly auxin, may contribute to the regulation of red stripe formation. This study provides broad insights into pigment accumulation and the regulatory mechanisms underlying floral color formation in C. japonica, and lays a foundation for breeding new C. japonica varieties. Full article

Ilex dabieshanensis (K. Yao and M. B. Deng) is not only an important economic tree species, but also has the characteristics of evergreens in all seasons, as well as strong cold resistance. In order to understand the molecular mechanism of holly’s response to cold stress, we used transcriptome analysis to identify the main signaling pathways and key genes involved in cold stress. The result showed that 5750 differentially expressed genes (DEGs) were identified under different cold treatment times compared with the control (cold—0 h). The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of DEGs showed that seven phytohormone signal transduction were the most highly enriched, including abscisic acid (ABA), ethylene (ET), cytokinin (CK), auxin (IAA), gibberellin (GA), jasmonate (JA), and brassinosteroids (BR). In addition, proline metabolism, arginine metabolism, flavonoid biosynthesis, and anthocyanin biosynthesis were also implicated in response to cold stress. The weighted gene co-expression network analysis (WGCNA) showed that the genes in two modules were significantly up-regulated after 12 h and 24 h treatments, suggesting these two module genes may participate in the cold stress. The gene ontology (GO) results of the two module genes showed that calcium, scavenging reactive oxygen species, and nitric oxide might act as signaling molecules to regulate cold tolerance in holly. By calculating the connectivity and function prediction of genes in the two modules, five genes (evm.TU.CHR2.244, evm.TU.CHR1.1507, evm.TU.CHR1.1821, evm.TU.CHR2.89, and evm.TU.CHR2.210) were identified as the key hub genes of I. dabieshanensis response to cold stress. These results provided candidate genes and clues for further studies on the molecular genetic mechanism of cold stress in holly. Full article

The chestnut is widely cultivated fruit tree enriched with nutrients and has pleasant tasting fruit. The starch properties of kernels greatly influence the nutritional quality of chestnuts. Although various studies have examined the production and accumulation of starch in chestnuts, the transcription alteration linked with starch properties in the kernels has not yet been fully assessed. The present study was conducted to compare transcriptomic variation and starch profiling of three chestnut cultivars: “Garrone rosso” (eur), Castanea sativa Mill., native to Europe; “Dahongpao” (dhp) and “Jiandingyouli” (jdy), and Castanea mollissima Bl., native to China. The results revealed that “dhp” and “jdy” had higher amylose, amylopectin and total starch content than “eur”. Based on transcriptome data, we screened 63.17G clean bases, and detected numerous differentially expressed genes (DEGs) that were associated with starch and sucrose metabolism. Through the combined transcriptomic and starch profiling analysis showed that DEGs in “the starch and sucrose metabolism”, “bZIP transcriptional factors”, and “zinc finger protein” pathways were positively correlated with starch accumulation, genes encoding sucrose synthase (CMHBY215664 and CMHBY203813), USPase (CMHBY206855), and PGI (CMHBY200699) were found to participate in the biosynthesis, transport, and regulation of starch according to their expression patterns in chestnut kernels. Furthermore, genes encoding different transcription factors (ERF, bZIP, MYB, and WRKY) that potentially regulate the expression of genes involved in starch and sucrose metabolism were selected by coexpression analysis, which highlighted that most MYB and WRKY TF members were positively correlated with starch synthase (SS). qRT-PCR assay results of nine selected DEGs confirmed the accuracy of the RNA-Seq data. Our results provide insights into genetic resources for deciphering the molecular mechanisms of chestnut starch accumulation. Full article

Osmanthus fragrans Lour. is popular in landscaping and gardening in Asia. In recent years, growing attention has been given to evergreen tree flowering and adaptation. EARLY FLOWERING3 (ELF3) plays an essential role in plant flowering regulation and abiotic stress tolerance. However, there is very little known about how the ELF3 gene affects flowering time and salt tolerance in O. fragrans. To elucidate the potential role of the flowering-related gene ELF3 in responding to salt tolerance, a significantly upregulated gene OfELF3 was obtained by RNA sequencing (RNA-seq) after salt treatment in O. fragrans. Our results showed that OfELF3 is a nuclear protein, which did not have a transcriptional activation ability. OfELF3 accumulation was determined in different tissues and the differentiation process of floral buds by qRT–PCR, and the gene was also significantly induced by salt stress treatment. In addition, overexpression of OfELF3 accelerated the flowering time of transgenic Arabidopsis lines, and an increase in the expression of flowering integrators such as AtFT, AtSOC1, and AtAP1 was investigated. Moreover, OfELF3 overexpression significantly improved the salt tolerance of transgenic plants, seed germination and root length of transgenic plants and was superior to those of the wild type (WT) under NaCl treatment at 4 days post-germination and the 5-day-old seedling stage, respectively. Similarly, phenotype and physiological indexes (REL, MDA and soluble protein) of 3-week-old transgenic plants were superior to the WT plants as well. Together, our results suggest that OfELF3 is not only a positive regulator in the regulation of flowering but is also involved in the salt tolerance response in O. fragrans. Full article

Osmanthus fragrans is an evergreen shrub or tree of the Oleaceae family with a long history of cultivation in Asian countries and is one of the ten traditionally famous flowers in China, with important cultural and economic value. The unique floral color and fragrance of O. fragrans are formed by a variety of endogenous metabolites that distinguish it from other flowers and exhibit extraordinary ornamental value. However, many studies on the flower color and fragrance of this plant have been mainly based on bioactive extracts and physiological characteristics, leading to a notable lack of molecular machinery and systematic research. In this review, recent advances in bioactive ingredients associated with the underlying regulatory mechanisms, as well as the prospect for industrial utilization, are comprehensively presented and critically evaluated. In particular, the isolated components and essential genes required for flower color and fragrance are also well summarized, which will provide a scientific basis for molecular breeding for ornamental applications and facilitate the discovery of novel natural products for the future industrial development of O. fragrans. In prospect, we plan to use genetic research and high-throughput omics to analyze the genes related to the flower color and fragrance of O. fragrans, and at the same time, we will hybridize and breed excellent O. fragrans varieties that are resistant to low temperature. Full article