Population sequencing enhances understanding of tea plant evolution

In-depth exploration of the genomic diversity in tea varieties based on a newly constructed pangenome of Camellia sinensis

Tea, one of the most widely consumed beverages globally, exhibits remarkable genomic diversity in its underlying flavour and health-related compounds. In this study, we present the construction and analysis of a tea pangenome comprising a total of 11 genomes, with a focus on three newly sequenced genomes comprising the purple-leaved assamica cultivar "Zijuan", the temperature-sensitive sinensis cultivar "Anjibaicha" and the wild accession "L618" whose assemblies exhibited excellent quality scores as they profited from latest sequencing technologies. Our analysis incorporates a detailed investigation of transposon complement across the tea pangenome, revealing shared patterns of transposon distribution among the studied genomes and improved transposon resolution with long read technologies, as shown by long terminal repeat (LTR) Assembly Index analysis. Furthermore, our study encompasses a gene-centric exploration of the pangenome, exploring the genomic landscape of the catechin pathway with our study, providing insights on copy number alterations and gene-centric variants, especially for Anthocyanidin synthases. We constructed a gene-centric pangenome by structurally and functionally annotating all available genomes using an identical pipeline, which both increased gene completeness and allowed for a high functional annotation rate. This improved and consistently annotated gene set will allow for a better comparison between tea genomes. We used this improved pangenome to capture the core and dispensable gene repertoire, elucidating the functional diversity present within the tea species. This pangenome resource might serve as a valuable resource for understanding the fundamental genetic basis of traits such as flavour, stress tolerance, and disease resistance, with implications for tea breeding programmes.

Metal tolerance protein CsMTP4 has dual functions in maintaining zinc homeostasis in tea plant

Plants have evolved a series of zinc (Zn) homeostasis mechanisms to cope with the fluctuating Zn in the environment. How Zn is taken up, translocated and tolerate by tea plant remains unknown. In this study, on the basis of RNA-Sequencing, we isolated a plasma membrane-localized Metal Tolerance Protein (MTP) family member CsMTP4 from Zn-deficient tea plant roots and investigated its role in regulation of Zn homeostasis in tea plant. Heterologous expression of CsMTP4 specifically enhanced the tolerance of transgenic yeast to Zn excess. Moreover, overexpression of CsMTP4 in tea plant hairy roots stimulated Zn uptake under Zn deficiency. In addition, CsMTP4 promoted the growth of transgenic Arabidopsis plants by translocating Zn from roots to shoots under Zn deficiency and conferred the tolerance to Zn excess by enhancing the efflux of Zn from root cells. Transcriptome analysis of the CsMTP4 transgenic Arabidopsis found that the expression of Zn metabolism-related genes were differentially regulated compared with wild-type plants when exposed to Zn deficiency and excess conditions. This study provides a mechanistic understanding of Zn uptake and translocation in plants and a new strategy to improve phytoremediation efficiency.

CsPAT1, a GRAS transcription factor, promotes lignin accumulation by antagonistic interacting with CsWRKY13 in tea plants

Lignin is an important component of plant cell walls and plays crucial roles in the essential agronomic traits of tea quality and tenderness. However, the molecular mechanisms underlying the regulation of lignin biosynthesis in tea plants remain unclear. CsWRKY13 acts as a negative regulator of lignin biosynthesis in tea plants. In this study, we identified a GRAS transcription factor, phytochrome A signal transduction 1 (CsPAT1), that interacts with CsWRKY13. Silencing CsPAT1 expression in tea plants and heterologous overexpression in Arabidopsis demonstrated that CsPAT1 positively regulates lignin accumulation. Further investigation revealed that CsWRKY13 directly binds to the promoters of CsPAL and CsC4H and suppresses transcription of CsPAL and CsC4H. CsPAT1 indirectly affects the promoter activities of CsPAL and CsC4H by interacting with CsWRKY13, thereby facilitating lignin biosynthesis in tea plants. Compared with the expression of CsWRKY13 alone, the co-expression of CsPAT1 and CsWRKY13 in Oryza sativa significantly increased lignin biosynthesis. Conversely, compared with the expression of CsPAT1 alone, the co-expression of CsPAT1 and CsWRKY13 in O. sativa significantly reduced lignin accumulation. These results demonstrated the antagonistic regulation of the lignin biosynthesis pathway by CsPAT1 and CsWRKY13. These findings improve our understanding of lignin biosynthesis mechanisms in tea plants and provide insights into the role of the GRAS transcription factor family in lignin accumulation.

New insights into evolution and functional diversification of Camellia sinensis LRR-RLKs

Leucine-rich repeat receptor-like kinases (LRR-RLKs) represent the largest subgroup of receptor-like kinases (RLKs) in plants. While some LRR-RLK members play a role in regulating various plant growth processes related to morphogenesis, disease resistance, and stress response, the functions of most LRR-RLK genes remain unclear. In this study, we identified 397 LRR-RLK genes from the genome of Camellia sinensis and categorized them into 16 subfamilies. Approximately 62% of CsLRR-RLK genes are situated in regions resulting from segmental duplications, suggesting that the expansion of CsLRR-RLK genes is due to segmental duplications. Analysis of gene expression patterns revealed differential expression of CsLRR-RLK genes across different tissues and in response to stress. Furthermore, we demonstrated that CssEMS1 localizes to the cell membrane and can complement Arabidopsis ems1 mutant. This study is the initial in-depth evolutionary examination of LRR-RLKs in tea and provides a basis for future investigations into their functionality.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-024-01458-1.

Genome-wide identification of tea plant (Camellia sinensis) BAHD acyltransferases reveals their role in response to herbivorous pests

BACKGROUND

BAHD acyltransferases are among the largest metabolic protein domain families in the genomes of terrestrial plants and play important roles in plant growth and development, aroma formation, and biotic and abiotic stress responses. Little is known about the BAHDs in the tea plant, a cash crop rich in secondary metabolites.

RESULTS

In this study, 112 BAHD genes (CsBAHD01-CsBAHD112) were identified from the tea plant genome, with 85% (98/112) unevenly distributed across the 15 chromosomes. The number of BAHD gene family members has significantly expanded from wild tea plants to the assamica type to the sinensis type. Phylogenetic analysis showed that they could be classified into seven subgroups. Promoter cis-acting element analysis revealed that they contain a large number of light, phytohormones, and stress-responsive elements. Many members displayed tissue-specific expression patterns. CsBAHD05 was expressed at more than 500-fold higher levels in purple tea leaves than in green tea leaves. The genes exhibiting the most significant response to MeJA treatment and feeding by herbivorous pests were primarily concentrated in subgroups 5 and 6. The expression of 23 members of these two subgroups at different time points after feeding by tea green leafhoppers and tea geometrids was examined via qPCR, and the results revealed that the expression of CsBAHD93, CsBAHD94 and CsBAHD95 was significantly induced after the tea plants were subjected to feeding by both pricking and chewing pests. Moreover, based on the transcriptome data for tea plants being fed on by these two pests, a transcriptional regulatory network of different transcription factor genes coexpressed with these 23 members was constructed.

CONCLUSIONS

Our study provides new insights into the role of BAHDs in the defense response of tea plants, and will facilitate in-depth studies of the molecular function of BAHDs in resistance to herbivorous pests.

Depicting the genetic and metabolic panorama of chemical diversity in the tea plant

As a frequently consumed beverage worldwide, tea is rich in naturally important bioactive metabolites. Combining genetic, metabolomic and biochemical methodologies, here, we present a comprehensive study to dissect the chemical diversity in tea plant. A total of 2837 metabolites were identified at high-resolution with 1098 of them being structurally annotated and 63 of them were structurally identified. Metabolite-based genome-wide association mapping identified 6199 and 7823 metabolic quantitative trait loci (mQTL) for 971 and 1254 compounds in young leaves (YL) and the third leaves (TL), respectively. The major mQTL (i.e., P < 1.05 × 10-5, and phenotypic variation explained (PVE) > 25%) were further interrogated. Through extensive annotation of the tea metabolome as well as network-based analysis, this study broadens the understanding of tea metabolism and lays a solid foundation for revealing the natural variations in the chemical composition of the tea plant. Interestingly, we found that galloylations, rather than hydroxylations or glycosylations, were the largest class of conversions within the tea metabolome. The prevalence of galloylations in tea is unusual, as hydroxylations and glycosylations are typically the most prominent conversions of plant specialized metabolism. The biosynthetic pathway of flavonoids, which are one of the most featured metabolites in tea plant, was further refined with the identified metabolites. And we demonstrated the further mining and interpretation of our GWAS results by verifying two identified mQTL (including functional candidate genes CsUGTa, CsUGTb, and CsCCoAOMT) and completing the flavonoid biosynthetic pathway of the tea plant.

The miR166 targets CsHDZ3 genes to negatively regulate drought tolerance in tea plant (Camellia sinensis)

Drought is the stressor with a significant adverse impact on the yield stability of tea plants. HD-ZIP III transcription factors (TFs) play important regulatory roles in plant growth, development, and stress responses. However, whether and how HD-ZIP III TFs are involved in drought response and tolerance in tea plants remains unclear. Here, we identified seven HD-ZIP III genes (CsHDZ3-1 to CsHDZ3-7) in tea plant genome. The evolutionary analysis demonstrated that CsHDZ3 members were subjected to purify selection. Subcellular localization analysis revealed that all seven CsHDZ3s located in the nucleus. Yeast self-activation and dual-luciferase reporter assays demonstrated that CsHDZ3-1 to CsHDZ3-4 have trans-activation ability whereas CsHDZ3-5 to CsHDZ3-7 served as transcriptional inhibitors. The qRT-PCR assay showed that all seven CsHDZ3 genes could respond to simulated natural drought stress and polyethylene glycol treatment. Further assays verified that all CsHDZ3 genes can be cleaved by csn-miR166. Overexpression of csn-miR166 inhibited the expression of seven CsHDZ3 genes and weakened drought tolerance of tea leaves. In contrast, suppression of csn-miR166 promoted the expression of seven CsHDZ3 genes and enhanced drought tolerance of tea leaves. These findings established the foundation for further understanding the mechanism of CsHDZ3-miR166 modules' participation in drought responses and tolerance.

Genetic analyses of ancient tea trees provide insights into the breeding history and dissemination of Chinese Assam tea (Camellia sinensis var. assamica)

Chinese Assam tea (Camellia sinensis var. assamica) is an important tea crop with a long history of cultivation in Yunnan, China. Despite its potential value as a genetic resource, its genetic diversity and domestication/breeding history remain unclear. To address this issue, we genotyped 469 ancient tea plant trees representing 26 C. sinensis var. assamica populations, plus two of its wild relatives (six and three populations of C. taliensis and C. crassicolumna, respectively) using 16 nuclear microsatellite loci. Results showed that Chinese Assam tea has a relatively high, but comparatively lower gene diversity (HS = 0.638) than the wild relative C. crassicolumna (HS = 0.658). Clustering in STRUCTURE indicated that Chinese Assam tea and its two wild relatives formed distinct genetic groups, with considerable interspecific introgression. The Chinese Assam tea accessions clustered into three gene pools, corresponding well with their geographic distribution. However, NewHybrids analysis indicated that 68.48% of ancient Chinese Assam tea plants from Xishuangbanna were genetic intermediates between the Puer and Lincang gene pools. In addition, 10% of the ancient Chinese Assam tea individuals were found to be hybrids between Chinese Assam tea and C. taliensis. Our results suggest that Chinese Assam tea was domesticated separately in three gene pools (Puer, Lincang and Xishuangbanna) in the Mekong River valley and that the hybrids were subsequently selected during the domestication process. Although the domestication history of Chinese Assam tea in southwestern Yunnan remains complex, our results will help to identify valuable genetic resources that may be useful in future tea breeding programs.

The MADS-box transcription factor CsAGL9 plays essential roles in seed setting in Camellia sinensis

The number of seed setting (NSS) is an important biological trait that affects tea propagation and yield. In this study, the NSS of an F1 tea population (n = 324) generated via a cross between 'Longjing 43' and 'Baihaozao' was investigated at two locations in two consecutive years. Quantitative trait locus (QTL) mapping of the NSS was performed, and 10 major QTLs were identified. In total, 318 genes were found in these 10 QTLs intervals, and 11 key candidate genes were preliminarily identified. Among them, the MADS-box transcription factor AGAMOUS LIKE 9 (CsAGL9, CSS0037962) located in the most stable QTL (qNSS2) was identified as a key gene affecting the NSS. CsAGL9 overexpression in Arabidopsis promoted early flowering and significantly decreased the length and number of pods and number of seeds per pod. Transcriptome analysis demonstrated that the auxin pathway, a key hormone pathway regulating plant reproduction, was highly affected in the transgenic lines. The auxin pathway was likewise the most prominent in the gene co-expression network study of CsAGL9 in tea plants. In summary, we identified CsAGL9 is essential for seed setting using QTL mapping integrated with RNA-seq, which shed a new light on the mechanism NSS of seed setting in tea plants.

Multi-Omics Research Accelerates the Clarification of the Formation Mechanism and the Influence of Leaf Color Variation in Tea (Camellia sinensis) Plants

Tea is a popular beverage with characteristic functional and flavor qualities, known to be rich in bioactive metabolites such as tea polyphenols and theanine. Recently, tea varieties with variations in leaf color have been widely used in agriculture production due to their potential advantages in terms of tea quality. Numerous studies have used genome, transcriptome, metabolome, proteome, and lipidome methods to uncover the causes of leaf color variations and investigate their impacts on the accumulation of crucial bioactive metabolites in tea plants. Through a comprehensive review of various omics investigations, we note that decreased expression levels of critical genes in the biosynthesis of chlorophyll and carotenoids, activated chlorophyll degradation, and an impaired photosynthetic chain function are related to the chlorina phenotype in tea plants. For purple-leaf tea, increased expression levels of late biosynthetic genes in the flavonoid synthesis pathway and anthocyanin transport genes are the major and common causes of purple coloration. We have also summarized the influence of leaf color variation on amino acid, polyphenol, and lipid contents and put forward possible causes of these metabolic changes. Finally, this review further proposes the research demands in this field in the future.

TPIA2: an updated tea plant information archive for Camellia genomics

The genus Camellia consists of about 200 species, which include many economically important species widely used for making tea, ornamental flowers and edible oil. Here, we present an updated tea plant information archive for Camellia genomics (TPIA2; http://tpia.teaplants.cn) by integrating more novel large-scale genomic, transcriptomic, metabolic and genetic variation datasets as well as a variety of useful tools. Specifically, TPIA2 hosts all currently available and well assembled 10 Camellia genomes and their comprehensive annotations from three major sections of Camellia. A collection of 15 million SNPs and 950 950 small indels from large-scale genome resequencing of 350 diverse tea accessions were newly incorporated, followed by the implementation of a novel 'Variation' module to facilitate data retrieval and analysis of the functionally annotated variome. Moreover, 116 Camellia transcriptomes were newly assembled and added, leading to a significant extension of expression profiles of Camellia genes to 13 developmental stages and eight abiotic/biotic treatments. An updated 'Expression' function has also been implemented to provide a comprehensive gene expression atlas for Camellia. Two novel analytic tools (e.g. Gene ID Convert and Population Genetic Analysis) were specifically designed to facilitate the data exchange and population genomics in Camellia. Collectively, TPIA2 provides diverse updated valuable genomic resources and powerful functions, and will continue to be an important gateway for functional genomics and population genetic studies in Camellia.

Expansion and contraction of lake basin shape the genetic structure of Sinocyclocheilus (Osteichthyes: Cypriniformes: Cyprinidae) populations in Central Yunnan, China

Geological events can strongly affect the genetic structures and differentiation of fish populations. Especially, as an endemic fish of the genus Sinocyclocheilus in the Yunnan-Guizhou Plateau, the effects of key geological events on the distributions and genetic structures remain poorly understood. Examining the phylogeographic patterns of Sinocyclocheilus fishes can be useful for elucidating the spatio-temporal dynamics of their population size, dispersal history and extent of geographical isolation, thereby providing a theoretical basis for their protection. Here, we used single nucleotide polymorphisms (SNP) method to investigate the phylogeographic patterns of Sinocyclocheilus fishes. Our analysis supports the endemicity of Sinocyclocheilus, but the samples of different regions of Sinocyclocheilus contain multiple ancestral components, which displayed more admixed and diversified genetic components, this may be due to the polymorphism of the ancestors themselves, or gene infiltration caused by hybridization between adjacent species of Sinocyclocheilus. We estimate that the most recent common ancestor (MRCA) of Sinocyclocheilus fish in the Central Yunnan Basin at approximately 3.75~3.11 Ma, and infer that the evolution of Sinocyclocheilus in the central Yunnan Basin is closely related to the formation of plateau lakes (around 4.0~0.02 Ma), and identifies the formation of Dianchi Lake and Fuxian Lake as key geological events shaping Sinocyclocheilus population structure. It is also the first time to prove that the altitude change has a great influence on the genetic variation among the populations of Sinocyclocheilus.

Changes in sensory characteristics, chemical composition and microbial succession during fermentation of ancient plants Pu-erh tea

"Ancient tea plants" are defined as tea trees > 100 years old, or with a trunk diameter > 25 cm; their leaves are manufactured to high - quality, valuable ancient plants pu-erh tea (APPT). In this study, a fermentation of APPT were developed, and outstanding sweetness of APPT infusion was observed. During fermentation, the content of soluble sugars, theabrownins (p < 0.05), as well as 41 metabolites were increased [Variable importance in projection (VIP) > 1.0; p < 0.05 and Fold-change (FC) FC > 2]; While relative levels of 72 metabolites were decreased (VIP > 1.0, p < 0.05 and FC < 0.5. Staphylococcus, Achromobacter, Sphingomonas, Thermomyces, Rasamsonia, Blastobotrys, Aspergillus and Cladosporium were identified as dominant genera, and their relative levels were correlated with contents of characteristic components (p < 0.05). Together, changes in sensory characteristics, chemical composition and microbial succession during APPT fermentation were investigated, and advanced the formation mechanism of its unique quality.

Analysis of the Genetic Diversity in Tea Plant Germplasm in Fujian Province Based on Restriction Site-Associated DNA Sequencing

Fujian province, an important tea-producing area in China, has abundant tea cultivars. To investigate the genetic relationships of tea plant cultivars in Fujian province and the characteristics of the tea plant varieties, a total of 70 tea cultivars from Fujian and other 12 provinces in China were subjected to restriction site-associated DNA sequencing (RAD-seq). A total of 60,258,975 single nucleotide polymorphism (SNP) sites were obtained. These 70 tea plant cultivars were divided into three groups based on analyzing the phylogenetic tree, principal component, and population structure. Selection pressure analysis indicated that nucleotide diversity was high in Southern China and genetically distinct from cultivars of Fujian tea plant cultivars, according to selection pressure analysis. The selected genes have significant enrichment in pathways associated with metabolism, photosynthesis, and respiration. There were ten characteristic volatiles screened by gas chromatography-mass spectrometry (GC-MS) coupled with multivariate statistical methods, among which the differences in the contents of methyl salicylate, 3-carene, cis-3-hexen-1-ol, (E)-4-hexen-1-ol, and 3-methylbutyraldehyde can be used as reference indicators of the geographical distribution of tea plants. Furthermore, a metabolome genome-wide association study (mGWAS) revealed that 438 candidate genes were related to the aroma metabolic pathway. Further analysis showed that 31 genes of all the selected genes were screened and revealed the reasons for the genetic differences in aroma among tea plant cultivars in Fujian and Southern China. These results reveal the genetic diversity in the Fujian tea plants as well as a theoretical basis for the conservation, development, and utilization of the Fujian highly aromatic tea plant cultivars.

Multiomics Analysis Reveals the Genetic Basis of Volatile Terpenoid Formation in Oolong Tea

Oolong tea has gained great popularity in China due to its pleasant floral and fruity aromas. Although numerous studies have investigated the aroma differences across various tea cultivars, the genetic mechanism is unclear. This study performed multiomics analysis of three varieties suitable for oolong tea and three others with different processing suitability. Our analysis revealed that oolong tea varieties contained higher levels of cadinane sesquiterpenoids. PanTFBS was developed to identify variants of transcription factor binding sites (TFBSs). We found that the CsDCS gene had two TFBS variants in the promoter sequence and a single nucleotide polymorphism (SNP) in the coding sequence. Integrating data on genetic variations, gene expression, and protein-binding sites indicated that CsDCS might be a pivotal gene involved in the biosynthesis of cadinane sesquiterpenoids. These findings advance our understanding of the genetic factors involved in the aroma formation of oolong tea and offer insights into the enhancement of tea aroma.

Transcriptomic and metabolomic analyses reveals keys genes and metabolic pathways in tea (Camellia sinensis) against six-spotted spider mite (Eotetranychus Sexmaculatus)

BACKGROUND

Six-spotted spider mite (Eotetranychus sexmaculatus) is one of the most damaging pests of tea (Camellia sinensis). E. sexmaculatus causes great economic loss and affects tea quality adversely. In response to pests, such as spider mites, tea plants have evolved resistance mechanisms, such as expression of defense-related genes and defense-related metabolites.

RESULTS

To evaluate the biochemical and molecular mechanisms of resistance in C. sinensis against spider mites, "Tianfu-5" (resistant to E. sexmaculatus) and "Fuding Dabai" (susceptible to E. sexmaculatus) were inoculated with spider mites. Transcriptomics and metabolomics based on RNA-Seq and liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) technology were used to analyze changes in gene expression and metabolite content, respectively. RNA-Seq data analysis revealed that 246 to 3,986 differentially expressed genes (DEGs) were identified in multiple compared groups, and these DEGs were significantly enriched in various pathways, such as phenylpropanoid and flavonoid biosynthesis, plant-pathogen interactions, MAPK signaling, and plant hormone signaling. Additionally, the metabolome data detected 2,220 metabolites, with 194 to 260 differentially abundant metabolites (DAMs) identified in multiple compared groups, including phenylalanine, lignin, salicylic acid, and jasmonic acid. The combined analysis of RNA-Seq and metabolomic data indicated that phenylpropanoid and flavonoid biosynthesis, MAPK signaling, and Ca2+-mediated PR-1 signaling pathways may contribute to spider mite resistance.

CONCLUSIONS

Our findings provide insights for identifying insect-induced genes and metabolites and form a basis for studies on mechanisms of host defense against spider mites in C. sinensis. The candidate genes and metabolites identified will be a valuable resource for tea breeding in response to biotic stress.

Pyrrolizidine Alkaloids in Tea (Camellia sinensis L.) from Weeds through Weed-Soil-Tea Transfer and Risk Assessment of Tea Intake

Pyrrolizidine alkaloids (PAs) have been detected in tea and can threaten human health. However, the specific source of PAs in tea is still unclear. Here, 88 dried tea products collected from six major tea-producing areas in Anhui Province, China, were analyzed. The detection frequency was 76%. The content of total PAs in dried tea was between 1.1 and 90.5 μg/kg, which was all below the MRL recommended by the European Union (150 μg/kg). In the Shexian tea garden, PAs in the weeds and weed rhizospheric soil around tea plants and the fresh tea leaves were analyzed. Intermedine (Im), intermedine-N-oxide (ImNO), and jacobine-N-oxide (JbNO) were transferred through the weed-to-soil-to-tea route into the fresh tea leaves; only Im and ImNO were detected in dried tea samples. Potential risk of the total PAs in the tea infusion was assessed according to the margin of exposure method, and it might be a low concern for public health.

Gene mining and genomics-assisted breeding empowered by the pangenome of tea plant Camellia sinensis

Tea is one of the world's oldest crops and is cultivated to produce beverages with various flavours. Despite advances in sequencing technologies, the genetic mechanisms underlying key agronomic traits of tea remain unclear. In this study, we present a high-quality pangenome of 22 elite cultivars, representing broad genetic diversity in the species. Our analysis reveals that a recent long terminal repeat burst contributed nearly 20% of gene copies, introducing functional genetic variants that affect phenotypes such as leaf colour. Our graphical pangenome improves the efficiency of genome-wide association studies and allows the identification of key genes controlling bud flush timing. We also identified strong correlations between allelic variants and flavour-related chemistries. These findings deepen our understanding of the genetic basis of tea quality and provide valuable genomic resources to facilitate its genomics-assisted breeding.

Integrative transcriptome and whole-genome bisulfite sequencing analyses of a temperature-sensitive albino tea plant cultivar

Green tea made from albino buds and leaves has a strong umami taste and aroma. The cultivar 'Zhonghuang 2' (ZH2, Camellia sinensis) is a natural mutant with young shoots that are yellow in spring and green or yellow-green in summer. However, the mechanism of leaf color change remains unclear. Here, we found that young shoots of ZH2 were yellow at low temperature (LT) and green at high temperature (HT), indicating that ZH2 is a temperature-sensitive cultivar. Transmission electron microscopy analysis showed that the grana in the chloroplasts of young shoots grown at LT were poorly stacked, which caused a lack of photoreactions and chlorophyll. RNA-seq results showed 1279 genes differentially expressed in the young shoots grown at LT compared with those at HT, including genes related to cytochrome synthesis, chloroplast development, photosynthesis, and DNA methylation. A whole-genome bisulfite sequencing assay revealed that the dynamics of DNA methylation levels in the CG, CHG, and CHH contexts decreased under LT, and the change was most obvious in the CHH context. Furthermore, 72 genes showed significant changes in both expression and DNA methylation levels, and most of them were related to cytochrome synthesis, chloroplast development, photosynthesis, transcription factors, and signaling pathways. These results demonstrate that DNA methylation is involved in the LT-regulated albino processes of ZH2. Changes in DNA methylation levels were associated with changes in gene expression levels, affecting the structure and function of chloroplasts, which may have a phenotypic impact on shoot and leaf color.

Uncovering the complex regulatory network of spring bud sprouting in tea plants: insights from metabolic, hormonal, and oxidative stress pathways

The sprouting process of tea buds is an essential determinant of tea quality and taste, thus profoundly impacting the tea industry. Buds spring sprouting is also a crucial biological process adapting to external environment for tea plants and regulated by complex transcriptional and metabolic networks. This study aimed to investigate the molecular basis of bud sprouting in tea plants firstly based on the comparisons of metabolic and transcriptional profiles of buds at different developmental stages. Results notably highlighted several essential processes involved in bud sprouting regulation, including the interaction of plant hormones, glucose metabolism, and reactive oxygen species scavenging. Particularly prior to bud sprouting, the accumulation of soluble sugar reserves and moderate oxidative stress may have served as crucial components facilitating the transition from dormancy to active growth in buds. Following the onset of sprouting, zeatin served as the central component in a multifaceted regulatory mechanism of plant hormones that activates a range of growth-related factors, ultimately leading to the promotion of bud growth. This process was accompanied by significant carbohydrate consumption. Moreover, related key genes and metabolites were further verified during the entire overwintering bud development or sprouting processes. A schematic diagram involving the regulatory mechanism of bud sprouting was ultimately proposed, which provides fundamental insights into the complex interactions involved in tea buds.

Global transcriptome analysis reveals fungal disease responsive core gene regulatory landscape in tea

Fungal infections are the inevitable limiting factor for productivity of tea. Transcriptome reprogramming recruits multiple regulatory pathways during pathogen infection. A comprehensive meta-analysis was performed utilizing previously reported, well-replicated transcriptomic datasets from seven fungal diseases of tea. The study identified a cumulative set of 18,517 differentially expressed genes (DEGs) in tea, implicated in several functional clusters, including the MAPK signaling pathway, transcriptional regulation, and the biosynthesis of phenylpropanoids. Gene set enrichment analyses under each pathogen stress elucidated that DEGs were involved in ethylene metabolism, secondary metabolism, receptor kinase activity, and various reactive oxygen species detoxification enzyme activities. Expressional fold change of combined datasets highlighting 2258 meta-DEGs shared a common transcriptomic response upon fungal stress in tea. Pervasive duplication events caused biotic stress-responsive core DEGs to appear in multiple copies throughout the tea genome. The co-expression network of meta-DEGs in multiple modules demonstrated the coordination of appropriate pathways, most of which involved cell wall organization. The functional coordination was controlled by a number of hub genes and miRNAs, leading to pathogenic resistance or susceptibility. This first-of-its-kind meta-analysis of host-pathogen interaction generated consensus candidate loci as molecular signatures, which can be associated with future resistance breeding programs in tea.

Transcriptome analysis revealed enrichment pathways and regulation of gene expression associated with somatic embryogenesis in Camellia sinensis

The high frequency, stable somatic embryo system of tea has still not been established due to the limitations of its own characteristics and therefore severely restricts the genetic research and breeding process of tea plants. In this study, the transcriptome was used to illustrate the mechanisms of gene expression regulation in the somatic embryogenesis of tea plants. The number of DEGs for the (IS intermediate stage)_PS (preliminary stage), ES (embryoid stage)_IS and ES_PS stages were 109, 2848 and 1697, respectively. The enrichment analysis showed that carbohydrate metabolic processes were considerably enriched at the ES_IS stage and performed a key role in somatic embryogenesis, while enhanced light capture in photosystem I could provide the material basis for carbohydrates. The pathway analysis showed that the enriched pathways in IS_PS process were far less than those in ES_IS or ES_PS, and the photosynthesis and photosynthetic antenna protein pathway of DEGs in ES_IS or ES_PS stage were notably enriched and up-regulated. The key photosynthesis and photosynthesis antenna protein pathways and the Lhcb1 gene were discovered in tea plants somatic embryogenesis. These results were of great significance to clarify the mechanism of somatic embryogenesis and the breeding research of tea plants.

Analysis of the effect of different withering methods on tea quality based on transcriptomics and metabolomics

Withering is very important to the quality of Wuyi rock tea. In this study, transcriptomics and metabolomics were used to analyze the effects of different withering methods on tea quality formation. The results showed that sunlight withering (SW) was most beneficial in increasing the gene expression of ubiquinone and other terpenoid-quinone biosynthesis (ko00130), pyruvate metabolism (ko00620), starch and sucrose metabolism (ko00500), and tryptophan metabolism (ko00380) pathways, and increasing the content of nucleotides and derivatives, terpenoids, organic acids and lipids, thus enhancing the mellowness, fresh and brisk taste and aroma of tea. Withering trough withering (WW) was most beneficial in increasing the gene expression of glutathione metabolism (ko00480), phenylpropanoid biosynthesis (ko00940) pathways, increasing the content of phenolic acids and flavonoids, thus enhancing tea bitterness. A comprehensive evaluation of the metabolite content and taste characteristics of tea leaves showed SW to be the best quality and charcoal fire withering (FW) to be the worst quality. This study provided an important basis for guiding the processing of Wuyi rock tea with different flavors.

The complete chloroplast genome and phylogenomic analysis of Camellia sinensis var. sinensis cultivar 'Liupao', a landrace from Guangxi, China

Liupao tea is one of the well-known Chinese tea brands and a famous local specialty in Wuzhou, Guangxi, China. However, the genetic background and phylogenetic relationship of the native resource plants of Liupao tea need study, especially at the genomic level. In this study, we reported the complete chloroplast (cp) genome sequence of Camellia sinensis var. sinensis cultivar 'Liupao' (LP, Liupao tea population) and inferred its phylogenetic relationship to other tea plant variants or cultivars. The cp genome had a total length of 157,097 bp and the overall GC content was 37.3%. The cp genome contained one LSC region (86,641 bp) and one SSC region (18,276 bp), which were separated by two IR regions (26,090 bp, respectively). Moreover, the cp genomes were composed of 130 genes, including 86 protein-coding genes, 36 tRNA genes, and eight rRNA genes. The phylogenetic analysis showed that LP was closely related to C. sinensis var. pabilimba cv. 'Lingyunbaihao'. This study will provide useful information for further investigating the genetic background, evolution, and breeding of LP as well as other tea cultivars and varieties.

Characterization of two O-methyltransferases involved in the biosynthesis of O-methylated catechins in tea plant

Tea is known for having a high catechin content, with the main component being (-)-epigallocatechin gallate (EGCG), which has significant bioactivities, including potential anti-cancer and anti-inflammatory activity. The poor intestinal stability and permeability of EGCG, however, undermine these health-improving benefits. O-methylated EGCG derivatives, found in a few tea cultivars in low levels, have attracted considerable interest due to their increased bioavailability. Here, we identify two O-methyltransferases from tea plant: CsFAOMT1 that has a specific O-methyltransferase activity on the 3''-position of EGCG to generate EGCG3''Me, and CsFAOMT2 that predominantly catalyzes the formation of EGCG4″Me. In different tea tissues and germplasms, the transcript levels of CsFAOMT1 and CsFAOMT2 are strongly correlated with the amounts of EGCG3''Me and EGCG4''Me, respectively. Furthermore, the crystal structures of CsFAOMT1 and CsFAOMT2 reveal the key residues necessary for 3''- and 4''-O-methylation. These findings may provide guidance for the future development of tea cultivars with high O-methylated catechin content.

Structural and Functional Analysis of the MADS-Box Genes Reveals Their Functions in Cold Stress Responses and Flower Development in Tea Plant (Camellia sinensis)

MADS-box genes comprise a large family of transcription factors that play crucial roles in all aspects of plant growth and development. However, no detailed information on the evolutionary relationship and functional characterization of MADS-box genes is currently available for some representative lineages, such as the Camellia plant. In this study, 136 MADS-box genes were detected from a reference genome of the tea plant (Camellia sinensis) by employing a 569 bp HMM (Hidden Markov Model) developed using nucleotide sequencing including 73 type I and 63 type II genes. An additional twenty-seven genes were identified, with five MIKC-type genes. Truncated and/or inaccurate gene models were manually verified and curated to improve their functional characterization. Subsequently, phylogenetic relationships, chromosome locations, conserved motifs, gene structures, and gene expression profiles were systematically investigated. Tea plant MIKC genes were divided into all 14 major eudicot subfamilies, and no gene was found in Mβ. The expansion of MADS-box genes in the tea plant was mainly contributed by WGD/fragment and tandem duplications. The expression profiles of tea plant MADS-box genes in different tissues and seasons were analyzed, revealing widespread evolutionary conservation and genetic redundancy. The expression profiles linked to cold stress treatments suggested the wide involvement of MADS-box genes from the tea plant in response to low temperatures. Moreover, a floral 'ABCE' model was proposed in the tea plant and proved to be both conserved and ancient. Our analyses offer a detailed overview of MADS-box genes in the tea plant, allowing us to hypothesize the potential functions of unknown genes and providing a foundation for further functional characterizations.

CsRVE1 promotes seasonal greening of albino Camellia sinensis cv. Huangkui by activating chlorophyll biosynthesis

Seasonal greening is a crucial survival strategy for albino tea cultivars, during which dysfunctional chloroplasts recover and chlorophyll biosynthesis increases in albino leaves. However, the regulatory mechanisms of seasonal greening in albino tea plants remain unclear. Here, we report that CsRVE1, a nuclear-located Myb-like transcription factor, can positively modulate the seasonal greening of albino Camellia sinensis cv. Huangkui leaves by activating the expression of genes involved in light harvesting and chlorophyll biosynthesis. The transcriptional expression of CsRVE1 increased during seasonal greening and was tightly correlated with increases in the expression of genes involved in light harvesting (CsLhcb) and chlorophyll biosynthesis (CsCHLH, CsHEMA1 and CsCAO). In vivo and in vitro molecular analyses showed that CsRVE1 can directly bind to the promoters of CsLhcb, CsCHLH and CsPORA, eventually leading to chlorophyll accumulation in tea leaves. Furthermore, transient suppression of CsRVE1 in tea leaves led to a decrease in target gene expression. In contrast, the overexpression of CsRVE1 in Arabidopsis led to chlorophyll increases and the activation of AtLhcb, AtPORA, AtCHLH, etc. These results identify CsRVE1 as an important promoter of seasonal greening that functions by regulating genes involved in chlorophyll biosynthesis in albino tea plants and shed new light on the regulatory mechanisms of leaf phenotypes in plants.

Application of Multi-Perspectives in Tea Breeding and the Main Directions

Tea plants are an economically important crop and conducting research on tea breeding contributes to enhancing the yield and quality of tea leaves as well as breeding traits that satisfy the requirements of the public. This study reviews the current status of tea plants germplasm resources and their utilization, which has provided genetic material for the application of multi-omics, including genomics and transcriptomics in breeding. Various molecular markers for breeding were designed based on multi-omics, and available approaches in the direction of high yield, quality and resistance in tea plants breeding are proposed. Additionally, future breeding of tea plants based on single-cellomics, pangenomics, plant-microbe interactions and epigenetics are proposed and provided as references. This study aims to provide inspiration and guidance for advancing the development of genetic breeding in tea plants, as well as providing implications for breeding research in other crops.

Traditional management of ancient Pu'er teagardens in Jingmai Mountains in Yunnan of China, a designated Globally Important Agricultural Heritage Systems site

BACKGROUND

Pu'er Traditional Tea Agroecosystem is one of the projects included in the United Nations' Globally Important Agricultural Heritage Systems (GIAHS) since 2012. Against the background of having rich biodiversity and a long history of tea culture, the ancient tea trees in Pu'er have experienced from wild-transition-cultivation for thousands of years, and the local people's knowledge about the management of ancient teagardens has not been rigorously recorded. For this reason, it is important to study and record the traditional management knowledge of Pu'er ancient teagardens and the influence on the formation of tea trees and communities. This study focuses on the traditional management knowledge of ancient teagardens in Jingmai Mountains, Pu'er, and monoculture teagardens (monoculture and intensively managed planting base for tea cultivation) were used as the control, through the community structure, composition and biodiversity of ancient teagardens to respond to the influence of traditional management, and this work with a view to providing a reference for further research on the stability and sustainable development of tea agroecosystem.

METHODS

From 2021 to 2022, information on traditional management of ancient teagardens was obtained through semi-structured interviews with 93 local people in the Jingmai Mountains area of Pu'er. Informed consent was obtained from each participant before conducting the interview process. The communities, tea trees and biodiversity of Jingmai Mountains ancient teagardens (JMATGs) and monoculture teagardens (MTGs) were examined through field surveys, measurements and biodiversity survey methods. The Shannon-Weiner (H), Pielou (E) and Margalef (M) indices were calculated for the biodiversity of the teagardens within the unit sample, using monoculture teagardens as a control.

RESULTS

The tea tree morphology, community structure and composition of Pu'er ancient teagardens are significantly different from those of monoculture teagardens, and the biodiversity is significantly higher than that of monoculture teagardens. The local people mainly manage the ancient tea trees mainly using several methods, including weeding (96.8%), pruning (48.4%) and pest control (33.3%). The pest control mainly relies on the removal of diseased branches. JMATGs annual gross output is approximately 6.5 times that of MTGs. The traditional management of ancient teagardens is through setting up forest isolation zones as protected areas, planting tea trees in the understory on the sunny side, keeping tea trees 1.5-7 m apart, as well as consciously protecting forest animals such as spiders, birds and bees, and reasonably rearing livestock in the teagardens.

CONCLUSIONS

This study shows that local people have rich traditional knowledge and experience in the management of ancient teagardens in Pu'er, and that this traditional management knowledge has impacted the growth of ancient tea trees, enriched the structure and composition of tea plantation communities and actively protected the biodiversity within ancient teagardens.

Transcriptome Analysis Reveals That Ascorbic Acid Treatment Enhances the Cold Tolerance of Tea Plants through Cell Wall Remodeling

Cold stress is a major environmental factor that adversely affects the growth and productivity of tea plants. Upon cold stress, tea plants accumulate multiple metabolites, including ascorbic acid. However, the role of ascorbic acid in the cold stress response of tea plants is not well understood. Here, we report that exogenous ascorbic acid treatment improves the cold tolerance of tea plants. We show that ascorbic acid treatment reduces lipid peroxidation and increases the Fv/Fm of tea plants under cold stress. Transcriptome analysis indicates that ascorbic acid treatment down-regulates the expression of ascorbic acid biosynthesis genes and ROS-scavenging-related genes, while modulating the expression of cell wall remodeling-related genes. Our findings suggest that ascorbic acid treatment negatively regulates the ROS-scavenging system to maintain ROS homeostasis in the cold stress response of tea plants and that ascorbic acid's protective role in minimizing the harmful effects of cold stress on tea plants may occur through cell wall remodeling. Ascorbic acid can be used as a potential agent to increase the cold tolerance of tea plants with no pesticide residual concerns in tea.

Genome-wide characterization of the U-box gene in Camellia sinensis and functional analysis in transgenic tobacco under abiotic stresses

Plants U-box genes are crucial for plant survival, and they extensively regulate plant growth, reproduction and development as well as coping with stress and other processes. In this study, we identified 92 CsU-box genes through genome-wide analysis in the tea plant (Camellia sinensis), all of them contained the conserved U-box domain and were divided into 5 groups, which supported by the further genes structure analysis. The expression profiles in eight tea plant tissues and under abiotic and hormone stresses were analyzed using the TPIA database. 7 CsU-box genes (CsU-box27/28/39/46/63/70/91) were selected to verify and analyze expression patterns under PEG-induced drought and heat stress in tea plant respectively, the qRT-PCR results showed consistent with transcriptome datasets; and the CsU-box39 were further heterologous expressed in tobacco to perform gene function analysis. Phenotypic analyses of overexpression transgenic tobacco seedlings and physiological experiments revealed that CsU-box39 positively regulated the plant response to drought stress. These results lay a solid foundation for studying the biological function of CsU-box, and will provide breeding strategy basis for tea plant breeders.

Genetic and morphological characterization of United States tea (Camellia sinensis): insights into crop history, breeding strategies, and regional adaptability

Multiple introductions of tea (Camellia sinensis) to the United States since the 1850s have resulted in US tea germplasm that are currently poorly characterized. To resolve questions concerning the relatedness and regional adaptability of US tea germplasm, 32 domestic individuals were evaluated using 10 InDel markers, and compared with a background population of 30 named and registered Chinese varieties of tea. The marker data were analyzed via a neighbor-joining cladistic tree derived from Nei's genetic distance, STRUCTURE, and Discriminant Analysis of Principal Components, which revealed four genetic groups. Nineteen individuals selected from the four groups were assessed for seven leaf traits, two floral descriptors, and leaf yield, to identify plants best adapted to Florida field conditions. Our analyses compared with available historical records led us to estimate the most likely provenance of some of the US individuals, to precisely identify tea plant material and to choose most diverse accessions for breeding tea improved for adaptability, yield and quality.

Phylogenomic analyses of Camellia support reticulate evolution among major clades

Camellia (Theaceae) is a morphologically highly diverse genus of flowering plants and includes many famous species with high economic value, and the phylogeny of this genus is not fully resolved. We used 95 transcriptomes from 87 Camellia species and identified 1481 low-copy genes to conduct a detailed analysis of the phylogeny of this genus according to various data-screening criteria. The results show that, very different from the two existing classification systems of Camellia, 87 species are grouped into 8 main clades and two independent species, and that all 8 clades except Clade 8 were strongly supported by almost all the coalescent or concatenated trees using different gene subsets. However, the relationships among these clades were weakly supported and different from analyses using different gene subsets; furthermore, they do not agree with the phylogeny from chloroplast genomes of Camellia. Additional analyses support reticulate evolution (probably resulting from introgression or hybridization) among some major Camellia lineages, providing explanation for extensive gene tree conflicts. Furthermore, we inferred that together with the formation of East Asian subtropical evergreen broad-leaved forests, Camellia underwent a radiative divergence of major clades at 23 ∼ 19 Ma in the late Miocene then had a subsequent species burst at 10 ∼ 5 Ma. Principal component and cluster analyses provides new insights into morphological changes underlying the evolution of Camellia and a reference to further clarify subgenus and sections of this genus. The comprehensive study here including a nuclear phylogeny and other analyses reveal the rapid evolutionary history of Camellia.

Effects of Different Donor Ages on the Growth of Cutting Seedlings Propagated from Ancient Platycladus orientalis

The effects of tree age on the growth of cutting seedlings propagated from ancient trees have been an important issue in plant breeding and cultivation. In order to understand seedling growth and stress resistance stability, phenotypic measurements, physiological assays, and high-throughput transcriptome sequencing were performed on sown seedlings propagated from 5-year-old donors and cutting seedlings propagated from 5-, 300-, and 700-year-old Platycladus orientalis donors. In this study, the growth of cutting seedlings propagated from ancient trees was significantly slower; the soluble sugar and chlorophyll contents gradually decreased with the increase in the age of donors, and the flavonoid and total phenolic contents of sown seedlings were higher than those of cutting seedlings. Enrichment analysis of differential genes showed that plant hormone signal transduction, the plant-pathogen interaction, and the flavone and flavonol biosynthesis pathways were significantly up-regulated with the increasing age of cutting seedlings propagated from 300- and 700-year-old donors. A total of 104,764 differentially expressed genes were calculated using weighted gene co-expression network analysis, and 8 gene modules were obtained. Further, 10 hub genes in the blue module were identified, which revealed that the expression levels of JAZ, FLS, RPM1/RPS3, CML, and RPS2 increased with the increase in tree age. The results demonstrated that the age of the donors seriously affected the growth of P. orientalis cutting seedlings and that cutting propagation can preserve the resistance of ancient trees. The results of this study provide important insights into the effects of age on asexually propagated seedlings, reveal potential molecular mechanisms, and contribute to an improvement in the level of breeding and conservation of ancient germplasm resources of P. orientalis trees.

Molecular markers in tea plant (Camellia sinensis): Applications to evolution, genetic identification, and molecular breeding

Tea plants have a long cultivation history in the world, and the beverage (tea) made from its leaves is well known in the world. Due to the characteristics of self-incompatibility, long-term natural and artificial hybridization, tea plants have a very complex genetic background, which make the classification of tea plants unclear. Molecular marker, one type of genetic markers, has the advantages of stable inheritance, large amount of information, and high reliability. The development of molecular marker has facilitated the understanding of complex tea germplasm resources. So far, molecular markers had played important roles in the study of the origin and evolution, the preservation and identification of tea germplasms, and the excellent cultivars breeding of tea plants. However, the information is scattered, making it difficult to understand the advance of molecular markers in tea plants. In this paper, we summarized the development process and types of molecular markers in tea plants. In addition, the application advance of these molecular markers in tea plants was reviewed. Perspectives of molecular markers in tea plants were also systematically provided and discussed. The elaboration of molecular markers in this paper should help us to renew understanding of its application in tea plants.

Characterization of the Difference between Day and Night Temperatures on the Growth, Photosynthesis, and Metabolite Accumulation of Tea Seedlings

Currently, the effects of the differences between day and night temperatures (DIFs) on tea plant are poorly understood. In order to investigate the influence of DIFs on the growth, photosynthesis, and metabolite accumulation of tea plants, the plants were cultivated under 5 °C (25/20 °C, light/dark), 10 °C (25/15 °C, light/dark), and 15 °C (25/10 °C, light/dark). The results showed that the growth rate of the new shoots decreased with an increase in the DIFs. There was a downward trend in the photosynthesis among the treatments, as evidenced by the lowest net photosynthetic rate and total chlorophyll at a DIF of 15 °C. In addition, the DIFs significantly affected the primary and secondary metabolites. In particular, the 10 °C DIF treatment contained the lowest levels of soluble sugars, tea polyphenols, and catechins but was abundant in caffeine and amino acids, along with high expression levels of theanine synthetase (TS3) and glutamate synthase (GOGAT). Furthermore, the transcriptome data revealed that the differentially expressed genes were enriched in valine, leucine, and isoleucine degradation, flavone/flavonol biosyntheses, flavonoid biosynthesis, etc. Therefore, we concluded that a DIF of 10 °C was suitable for the protected cultivation of tea plants in terms of the growth and the quality of a favorable flavor of tea, which provided a scientific basis for the protected cultivation of tea seedlings.

Tea plant (Camellia sinensis) lipid metabolism pathway modulated by tea field microbe (Colletotrichum camelliae) to promote disease

Tea is one of the most popular healthy and non-alcoholic beverages worldwide. Tea anthracnose is a disease in tea mature leaves and ultimately affects yield and quality. Colletotrichum camelliae is a dominant fungal pathogen in the tea field that infects tea plants in China. The pathogenic factors of fungus and the susceptible factors in the tea plant are not known. In this work, we performed molecular and genetic studies to observe a cerato-platanin protein CcCp1 from C. camelliae, which played a key role in fungal pathogenicity. △CcCp1 mutants lost fungal virulence and reduced the ability to produce conidia. Transcriptome and metabolome were then performed and analysed in tea-susceptible and tea-resistant cultivars, Longjing 43 and Zhongcha 108, upon C. camelliae wild-type CCA and △CcCp1 infection, respectively. The differentially expressed genes and the differentially accumulated metabolites in tea plants were clearly overrepresented such as linolenic acid and linoleic acid metabolism, glycerophospholipid metabolism, phenylalanine biosynthesis and metabolism, biosynthesis of flavonoid, flavone and flavonol etc. In particular, the accumulation of jasmonic acid was significantly increased in the susceptible cultivar Longjing 43 upon CCA infection, in the fungal CcCp1 protein dependent manner, suggesting the compound involved in regulating fungal infection. In addition, other metabolites in the glycerophospholipid and phenylalanine pathway were observed in the resistant cultivar Zhongcha 108 upon fungal treatment, suggesting their potential role in defense response. Taken together, this work indicated C. camelliae CcCp1 affected the tea plant lipid metabolism pathway to promote disease while the lost function of CcCp1 mutants altered the fungal virulence and plant response.

Ethnobotanical study on herbal tea drinks in Guangxi, China

BACKGROUND

Herbal tea drinks, different from classical Camellia beverages, are a wide variety of herbal drinks consumed for therapeutic purposes or health promotion. Herbal tea is widely consumed in Guangxi. However, the documentation on the plants for herbal tea and their related health benefits is still limited.

METHODS

An ethnobotanical survey was conducted in 52 villages and 21 traditional markets in Guangxi from 2016 to 2021. Semi-structured interviews, key informant interviews, and structured questionnaires were applied to obtain ethnobotanical information of herbal tea, in which 463 informants had participated. Relative frequency of citation (RFC) and cultural food significance index (CFSI) were used to evaluate the most culturally significant herbal tea plants, and informant consensus factor (ICF) was applied to assess the agreement among informants.

RESULTS

This study recorded 155 herbal tea species belonging to 49 families. The most commonly used parts included leaf (27.61%), whole plant (22.09%), branch and leaf (19.02%), and flower (13.50%). The most frequent preparation method of herbal tea was decoction. Herbal tea was very popular in Guangxi, attributing to its therapeutic value, special odor, and good taste. There are 41 health benefits classified into eight categories. Among them, clearing heat was the most medicinal effects. Local people had high consistency in tonic, removing cold and cough, improving blood circulation, and clearing heat away. Based on CFSI values of each species, the most culturally significant herbal tea species were Siraitia grosvenorii (Swingle) C. Jeffrey ex A. M. Lu & Zhi Y. Zhang, Plantago asiatica L., Gynostemma pentaphyllum (Thunb.) Makino, Zingiber officinale Roscoe, Pholidota chinensis Lindl., and Morus alba L.

CONCLUSION

Herbal tea is a valuable heritage that carries the local people's traditional knowledge, like health care and religious belief. The recorded herbal tea species in this study possess tremendous potential for local economic development in the future. Further research on efficacy evaluation and product development of herbal tea species is necessary.

The lineage-specific evolution of the oleosin family in Theaceae

Oleosins play essential roles in stabilization of lipid droplets (LDs) and seed oil production. However, evolution of this gene family has not been reported in Theaceae, a large plant family that contains many important tea and oil tea species. In this study, a total of 65 oleosin genes were identified in nine genome-sequenced Theaceae species. Among these genomes, the gene number of oleosin showed significant difference, with Camellia sinensis var. sinensis cv. Shuchazao and Camellia lanceoleosa displayed more oleosin numbers than other species. Phylogenetic analyses revealed that Theaceae oleosin genes were classified into three clades (U, SL, SH) respectively. Proteins within the same clade had similar gene structure and motif composition. Segmental duplication was the primary driving force for the evolution of oleosin genes in Shuchazao (SCZ), Huangdan (HD), C.lanceoleosa (Cla), and wild tea (DASZ). Synteny analysis showed that most oleosin genes displayed inter-species synteny among tea and oil tea species. Expression analysis demonstrated that oleosin genes were specifically expressed in seed and kernel of Huangdan (HD) and C.lanceoleosa. Moreover, expression divergence was observed in paralogous pairs and ∼1-2 oleosin genes in each clade have become activate. This study leads to a comprehensive understanding of evolution of oleosin family in Theaceae, and provides a rich resource to further address the functions of oleosin in tea and oil tea species.

Metabolic Variations among Three New Tea Varieties Cultivated in Shandong, China

Cultivar identification is a necessary step in tea breeding programs. Rapid identification methods would greatly improve these breeding processes. To preliminarily identify the three new Lucha tea varieties (LC6, LC7, and LC17) cultivated in Shandong, we measured their main agronomic characters and biochemical components. Then, we analyzed the metabolic profiles of these tea varieties and Fuding Dabaicha (FD) using a UPLC-ESI-MS/MS system. Their biochemical components indicated that the Lucha varieties had excellent varietal characteristics, with higher amino acid contents. Furthermore, secondary metabolism changed a lot in the Lucha tea varieties compared with that in the FD, with their accumulations of flavonoids and phenolic acids showing significant differences. These differential flavonoids were dominated by flavones and flavanone, flavonols, flavonoid carbonosides, and flavanols monomer. Flavanols especially, including epicatechin glucoside, epicatechin-3-(3″-O-methyl)gallate, epigallocatechin-3-O-(3,5-O-dimethyl)gallate, and epitheaflavic acid-3-O-Gallate, showed higher levels in the Lucha varieties. The phenolic acids containing caffeoyl groups showed higher levels in the Lucha varieties than those in the FD, while those containing galloyl groups showed a reverse pattern. Nitrogen metabolism, including amino acids, also showed obvious differences between the Lucha varieties and FD. The differential amino acids were mainly higher in the Lucha varieties, including 5-L-glutamyl-L-amino acid, N-monomethyl-L-arginine, and N-α-acetyl-L-ornithine. By using these approaches, we found that LC6, LC7, and LC17 were excellent varieties with a high yield and high quality for making green teas in Shandong.

Molecular regulation of immunity in tea plants

Tea, which is mainly produced using the young leaves and buds of tea plants (Camellia sinensis (L.) O. Kuntze), is one of the most common non-alcoholic beverages consumed in the world. The standard of tea mostly depends on the variety and quality of tea plants, which generally grow in subtropical areas, where the warm and humid conditions are also conducive to the occurrence of diseases. In fighting against pathogens, plants rely on their sophisticated innate immune systems which has been extensively studied in model plants. Many components involved in pathogen associated molecular patterns (PAMPs) triggered immunity (PTI) and effector triggered immunity (ETI) have been found. Nevertheless, the molecular regulating network against pathogens (e.g., Pseudopestalotiopsis sp., Colletotrichum sp. and Exobasidium vexans) causing widespread disease (such as grey blight disease, anthracnose, and blister blight) in tea plants is still unclear. With the recent release of the genome data of tea plants, numerous genes involved in tea plant immunity have been identified, and the molecular mechanisms behind tea plant immunity is being studied. Therefore, the recent achievements in identifying and cloning functional genes/gene families, in finding crucial components of tea immunity signaling pathways, and in understanding the role of secondary metabolites have been summarized and the opportunities and challenges in the future studies of tea immunity are highlighted in this review.

Understanding the Origin and Evolution of Tea (Camellia sinensis [L.]): Genomic Advances in Tea

Tea, which is processed by the tender shoots or leaves of tea plant (Camellia sinensis), is one of the most popular nonalcoholic beverages in the world and has numerous health benefits for humans. Along with new progress in biotechnologies, the refined chromosome-scale reference tea genomes have been achieved, which facilitates great promise for the understanding of fundamental genomic architecture and evolution of the tea plants. Here, we summarize recent achievements in genome sequencing in tea plants and review the new progress in origin and evolution of tea plants by population sequencing analysis. Understanding the genomic characterization of tea plants is import to improve tea quality and accelerate breeding in tea plants.

Genome-wide identification and characterization of PIN-FORMED (PIN) and PIN-LIKES (PILS) gene family reveals their role in adventitious root development in tea nodal cutting (Camellia Sinensis)

Auxin affects all aspects of plant growth and development, including morphogenesis and adaptive responses. Auxin transmembrane transport is promoted by PIN formation (PIN) and a structurally similar PIN-like (PILS) gene family, which jointly controls the directional transport of the auxin between plant cells, and the accumulation of intracellular auxin. At present, there is no study investigating the roles of CslPIN and CslPILS gene family in root development in the tea plant (Camellia sinensis). In this study, 8 CslPIN and 10 CslPILS genes were identified in the tea plant, and their evolutionary relationships, physical and chemical properties, conserved motifs, cis-acting elements, chromosome location, collinearity, and expression characteristics were analyzed. The mechanism of CslPIN and CslPILS in the formation of tea adventitious roots (ARs) was studied by the AR induction system. Through functional verification, the regulation of CslPIN3 gene on root growth and development of tea plant was studied by over-expression of CslPIN3 in Arabidopsis thaliana and in situ hybridization in Camellia sinensis. The results confirmed CslPIN3 was involved in the regulation of root growth and development as well as auxin accumulation. This study provides a better insight into the regulatory mechanism of CslPIN and CslPILS gene family on the formation of AR in tea plant.

Pectate Lyase Genes Abundantly Expressed During the Infection Regulate Morphological Development of Colletotrichum camelliae and CcPEL16 Is Required for Full Virulence to Tea Plants

Colletotrichum camelliae is the dominant species causing foliar diseases of tea plants (Camellia sinensis) in China. Transcriptome data and reverse transcription-quantitative PCR (qRT-PCR) analysis have demonstrated that the pectate lyase genes in C. camelliae (CcPELs) were significantly upregulated during infectious development on tea plants (cv. Longjing43). To further evaluate the biological functions of CcPELs, we established a polyethylene glycol (PEG)-mediated protoplast transformation system of C. camelliae and generated targeted deletion mutants of seven CcPELs. Phenotypic assays showed that the genes contribute to mycelial growth, conidiation, and appressorium development. The polypeptides encoded by each CcPEL gene contained a predicted N-terminal signal peptide, and a yeast invertase secretion assay suggested that each CcPEL protein could be secreted. Cell death-suppressive activity assays confirmed that all seven CcPELs did not suppress Bax-induced cell death in tobacco leaf cells. However, deletion of CcPEL16 significantly reduced necrotic lesions on tea leaves. Taken together, these results indicated that CcPELs play essential roles in regulating morphological development, and CcPEL16 is required for full virulence in C. camelliae. IMPORTANCE In this study, we first established a PEG-mediated protoplast transformation system of C. camelliae and used it to investigate the biological functions of seven pectate lyase genes (CcPELs) which were abundantly expressed during infection. The results provided insights into the contributions of pectate lyase to mycelial growth, conidial production, appressorium formation, and the pathogenicity of C. camelliae. We also confirmed the secretory function of CcPEL proteins and their role in suppressing Bax-induced cell death. Overall, this study provides an effective method for generating gene-deletion transformants in C. camelliae and broadens our understanding of pectate lyase in regulating morphological development and pathogenicity.

Transcriptome-based variations effectively untangling the intraspecific relationships and selection signals in Xinyang Maojian tea population

As one of the world's top three popular non-alcoholic beverages, tea is economically and culturally valuable. Xinyang Maojian, this elegant green tea, is one of the top ten famous tea in China and has gained prominence for thousands of years. However, the cultivation history of Xinyang Maojian tea population and selection signals of differentiation from the other major variety Camellia sinensis var. assamica (CSA) remain unclear. We newly generated 94 Camellia sinensis (C. sinensis) transcriptomes including 59 samples in the Xinyang area and 35 samples collected from 13 other major tea planting provinces in China. Comparing the very low resolution of phylogeny inferred from 1785 low-copy nuclear genes with 94 C. sinensis samples, we successfully resolved the phylogeny of C. sinensis samples by 99,115 high-quality SNPs from the coding region. The sources of tea planted in the Xinyang area were extensive and complex. Specifically, Shihe District and Gushi County were the two earliest tea planting areas in Xinyang, reflecting a long history of tea planting. Furthermore, we identified numerous selection sweeps during the differentiation of CSA and CSS and these positive selection genes are involved in many aspects such as regulation of secondary metabolites synthesis, amino acid metabolism, photosynthesis, etc. Numerous specific selective sweeps of modern cultivars were annotated with functions in various different aspects, indicating the CSS and CSA populations possibly underwent independent specific domestication processes. Our study indicated that transcriptome-based SNP-calling is an efficient and cost-effective method in untangling intraspecific phylogenetic relationships. This study provides a significant understanding of the cultivation history of the famous Chinese tea Xinyang Maojian and unravels the genetic basis of physiological and ecological differences between the two major tea subspecies.

Transcriptional Analysis of Tea Plants (Camellia sinensis) in Response to Salicylic Acid Treatment

Salicylic acid (SA) is an important plant hormone and signal required for establishing resistance to diverse pathogens and plant diseases. The abundant polyphenols in tea plants also defend plants from biotic and abiotic stresses. However, whether exogenous SA would increase the resistance of tea plants to adversity and the relationship between SA and polyphenols are still poorly understood. Here, we carried out SA treatment on tea seedlings and performed transcriptome sequencing. SA treatment inhibited the phenylpropanoid and flavonoid metabolic pathways but promoted the lignin metabolic pathways. The increased accumulation of lignin in tea leaves after treating with SA indicated that lignin might coordinate SA, enhance, and improve plant defense and disease resistance. Simultaneously, an SA-inducible flavonoid glucosyltransferase (CsUGT0554) specifically involved in 7-OH site glycosylation was characterized in vitro. These results provided valuable information about the effects of SA on tea seedlings and the molecular basis for SA-mediated immune responses.

The complete chloroplast genome sequence of Camellia sinensis var. sinensis cultivar 'FuDingDaBaiCha'

The complete chloroplast (cp) genome sequence of Camellia sinensis var. sinensis cultivar 'FuDingDaBaiCha' (FD), one of the key contributors to the history of tea breeding in China, was determined in this study. The cp genome of FD is 157,025 bp in length, including a large single-copy (LSC, 86,586 bp), a small single-copy (SSC, 18,277 bp), and a pair of inverted repeats (IRa and IRb, 26,081 bp). The overall GC content is 37.3%. A total of 137 genes were predicted, including 92 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis showed that FD was closely related to C. sinensis cv. 'AnHua', C. sinensis cv. 'QianCha 1', and C. sinensis cv. 'BanTianYao'. The determination of the complete cp genome sequence of FD provides a way for the subsequent study of the genetic background and phylogenetic relationships of different tea plant cultivars.

Topics and trends in fresh tea (Camellia sinensis) leaf research: A comprehensive bibliometric study

Tea plant (Camellia sinensis) is a widely cultivated cash crop and tea is a favorite functional food in the world. Fresh tea leaves (FTLs) play a critical role in bridging the two fields closely related to tea cultivation and tea processing, those are, tea plant biology and tea biochemistry. To provide a comprehensive overview of the development stages, authorship collaboration, research topics, and hotspots and their temporal evolution trends in the field of FTLs research, we conducted a bibliometric analysis, based on 971 publications on FTLs-related research published during 2001-2021 from Web of Science Core Collection. CiteSpace, R package Bibliometrix, and VOSviewer were employed in this research. The results revealed that the development history can be roughly divided into three stages, namely initial stage, slow development stage and rapid development stage. Journal of Agricultural & Food Chemistry published most articles in this field, while Frontiers in Plant Science held the highest total citations and h-index. The most influential country, institution, and author in this field was identified as China, the Chinese Academy of Agricultural Sciences, and Xiaochun Wan, respectively. FTLs-related research can be categorized into three main topics: the regulation mechanism of key genes, the metabolism and features of essential compounds, and tea plants' growth and stress responses. The most concerning hotspots are the application of advanced technologies, essential metabolites, leaf color variants, and effective cultivation treatments. There has been a shift from basic biochemical and enzymatic studies to studies of molecular mechanisms that depend on multi-omics technologies. We also discussed the future development in this field. This study provides a comprehensive summary of the research field, making it easier for researchers to be informed about its development history, status, and trends.

Development of SNP Markers for Original Analysis and Germplasm Identification in Camellia sinensis

Tea plants are widely grown all over the world because they are an important economic crop. The purity and authenticity of tea varieties are frequent problems in the conservation and promotion of germplasm resources in recent years, which has brought considerable inconvenience and uncertainty to the selection of parental lines for breeding and the research and cultivation of superior varieties. However, the development of core SNP markers can quickly and accurately identify the germplasm, which plays an important role in germplasm identification and the genetic relationship analysis of tea plants. In this study, based on 179,970 SNP loci from the whole genome of the tea plant, all of 142 cultivars were clearly divided into three groups: Assam type (CSA), Chinese type (CSS), and transitional type. Most CSA cultivars are from Yunnan Province, which confirms that Yunnan Province is the primary center of CSA origin and domestication. Most CSS cultivars are distributed in east China; therefore, we deduced that east China (mainly Zhejiang and Fujian provinces) is most likely the area of origin and domestication of CSS. Moreover, 45 core markers were screened using strict criteria to 179,970 SNP loci, and we analyzed 117 well-Known tea cultivars in China with 45 core SNP markers. The results were as follows: (1) In total, 117 tea cultivars were distinguished by eight markers, which were selected to construct the DNA fingerprint, and the remaining markers were used as standby markers for germplasm identification. (2) Ten pairs of parent and offspring relationships were confirmed or identified, and among them, seven pairs were well-established pedigree relationships; the other three pairs were newly identified. In this study, the east of China (mainly Zhejiang and Fujian provinces) is most likely the area of origin and domestication of CSS. The 45 core SNP markers were developed, which provide a scientific basis at the molecular level to identify the superior tea germplasm, undertake genetic relationship analysis, and benefit subsequent breeding work.

A Tea Plant (Camellia sinensis) FLOWERING LOCUS C-like Gene, CsFLC1, Is Correlated to Bud Dormancy and Triggers Early Flowering in Arabidopsis

Flowering and bud dormancy are crucial stages in the life cycle of perennial angiosperms in temperate climates. MADS-box family genes are involved in many plant growth and development processes. Here, we identified three MADS-box genes in tea plant belonging to the FLOWERING LOCUS C (CsFLC) family. We monitored CsFLC1 transcription throughout the year and found that CsFLC1 was expressed at a higher level during the winter bud dormancy and flowering phases. To clarify the function of CsFLC1, we developed transgenic Arabidopsis thaliana plants heterologously expressing 35S::CsFLC1. These lines bolted and bloomed earlier than the WT (Col-0), and the seed germination rate was inversely proportional to the increased CsFLC1 expression level. The RNA-seq of 35S::CsFLC1 transgenic Arabidopsis showed that many genes responding to ageing, flower development and leaf senescence were affected, and phytohormone-related pathways were especially enriched. According to the results of hormone content detection and RNA transcript level analysis, CsFLC1 controls flowering time possibly by regulating SOC1, AGL42, SEP3 and AP3 and hormone signaling, accumulation and metabolism. This is the first time a study has identified FLC-like genes and characterized CsFLC1 in tea plant. Our results suggest that CsFLC1 might play dual roles in flowering and winter bud dormancy and provide new insight into the molecular mechanisms of FLC in tea plants as well as other plant species.