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Background To efficiently protect and exploit germplasm resources for marker development and breeding purposes, we must accurately depict the features of the tea populations. This study focuses on the Camellia sinensis ( C. sinensis ) population and aims to (i) identify single nucleotide polymorphisms (SNPs) on the genome level, (ii) investigate the genetic diversity and population structure, and (iii) characterize the linkage disequilibrium (LD) pattern to facilitate next genome-wide association mapping and marker-assisted selection. Results We collected 415 tea accessions from the Origin Center and analyzed the genetic diversity, population structure and LD pattern using the genotyping-by-sequencing (GBS) approach. A total of 79,016 high-quality SNPs were identified; the polymorphism information content (PIC) and genetic diversity (GD) based on these SNPs showed a higher level of genetic diversity in cultivated type than in wild type. The 415 accessions were clustered into three groups by STRUCTURE software and confirmed using principal component analyses (PCA)—wild type, cultivated type, and admixed wild type. However, unweighted pair group method with arithmetic mean (UPGMA) trees indicated the accessions should be grouped into more clusters. Further analyses identified four groups, the Pure Wild Type, Admixed Wild Type, ancient landraces and modern landraces using STRUCTURE, and the results were confirmed by PCA and UPGMA tree method. A higher level of genetic diversity was detected in ancient landraces and Admixed Wild Type than that in the Pure Wild Type and modern landraces. The highest differentiation was between the Pure Wild Type and modern landraces. A relatively fast LD decay with a short range (kb) was observed, and the LD decays of four inferred populations were different. Conclusions This study is, to our knowledge, the first population genetic analysis of tea germplasm from the Origin Center, Guizhou Plateau, using GBS. The LD pattern, population structure and genetic differentiation of the tea population revealed by our study will benefit further genetic studies, germplasm protection, and breeding.

Background Thaumatin-like proteins (TLPs) belong to the PR-5 family of the pathogenesis-related (PR) proteins, and have been widely reported in plants for their important role in resisting pathogenic bacteria. However, people know very little about the function it plays in helping tea plants resist tea blister blight. Results In the tea plant, a total of 43 CsTLPs were detected. According to the evolutionary tree analysis, these genes can be divided into 9 subfamilies. Through promoter analysis, a substantial quantity of elements associated with stress, hormone response, as well as growth and development were identified. The collinearity analysis indicates that the sequences of multiple CsTLPs genes have high homology in tea plants. The combination of transcriptome analysis and qRT-PCR demonstrated that the expression of CsTLP8 , CsTLP23 , CsTLP28 and CsTLP34 were significantly up-regulated after tea blister blight infection. In addition, we have verified the functionality of CsTLP8 . CsTLP8 is localized in cytoplasm, and has β-1,3-glucanase activity. Transient overexpression of CsTLP8 in tobacco can significantly increase POD and CAT activities and decrease hydrogen peroxide content. Conclusions The results will help to better understand the role of CsTLPs gene family in tea blister blight, and provide theoretical support for improving disease resistance of tea trees and breeding new varieties resistant to disease.

Background Tea is the most popular non-alcoholic health beverage in the world. The tea plant ( Camellia sinensis (L.) O. Kuntze) needs to undergo a cold acclimation process to enhance its freezing tolerance in winter. Changes that occur at the molecular level in response to low temperatures are poorly understood in tea plants. To elucidate the molecular mechanisms of cold acclimation, we employed RNA-Seq and digital gene expression (DGE) technologies to the study of genome-wide expression profiles during cold acclimation in tea plants. Results Using the Illumina sequencing platform, we obtained approximately 57.35 million RNA-Seq reads. These reads were assembled into 216,831 transcripts, with an average length of 356 bp and an N50 of 529 bp. In total, 1,770 differentially expressed transcripts were identified, of which 1,168 were up-regulated and 602 down-regulated. These include a group of cold sensor or signal transduction genes, cold-responsive transcription factor genes, plasma membrane stabilization related genes, osmosensing-responsive genes, and detoxification enzyme genes. DGE and quantitative RT-PCR analysis further confirmed the results from RNA-Seq analysis. Pathway analysis indicated that the “carbohydrate metabolism pathway” and the “calcium signaling pathway” might play a vital role in tea plants’ responses to cold stress. Conclusions Our study presents a global survey of transcriptome profiles of tea plants in response to low, non-freezing temperatures and yields insights into the molecular mechanisms of tea plants during the cold acclimation process. It could also serve as a valuable resource for relevant research on cold-tolerance and help to explore the cold-related genes in improving the understanding of low-temperature tolerance and plant-environment interactions.

Background Adventitious root (AR) formation is the key step for successful cutting propagation of tea plants ( Camellia sinensis L.). Studies showed that arbuscular mycorrhizal fungus (AMF) can promote the rooting ability, and auxin pathway in basal stem of cuttings was involved in this process. However, auxin and abscisic acid (another important regulator on AR formation) in the other parts of cuttings at different rooting stages responding to AMF inoculation are not well studied. Therefore, in this paper, contents, enzymes and genes related to these two plant hormones were comprehensively determined aiming to unveil how endogenous indole-3-acetic acid (IAA) and abscisic acid (ABA) involve in the AMF regulating AR development of tea cuttings. Results Inoculating with AMF significantly increased the proportion of cuttings at S2 stage (AR formation), which was more than twice as much as the control. And the total rooting rate in mycorrhizal treatment was also higher than that in the control with an increase of 8.66%. Enzyme activity assays showed that except for decreased polyphenol oxidase (PPO) activity at the S3 stage and peroxidase (POD) activity in middle stem of S3 stage, AMF inoculation increased activities of POD, PPO, superoxide dismutase (SOD) and catalase (CAT) to varying degrees in leaf, middle stem and basal stem of tea cuttings. After inoculation with AMF, the indoleacetic acid oxidase (IAAO) activity decreased to a certain extent in the first three stages of tea cuttings, which showed a trend of ‘low-high-low’ in the basal stem of all treatments. Besides, there was a significantly positive correlation between SOD activity and AR formation, especially for the proportion of cuttings at S2 and S3 stages. Higher IAA level and IAA/ABA ratio was found in basal stem of cuttings at S1 stage induced by AMF, which promoting the AR formation as revealed by correlation analysis. At the same time, AMF significantly elevated the level of IAA in leaf at S1 stage. By screening differentially expressed genes (DEGs) related to IAA and ABA pathways, together with redundant analysis, it was indicated that auxin biosynthesis and transport, as well as ABA transport and signal transduction, were involved in AMF regulating the rooting of tea cuttings. Conclusions Overall, both endogenous IAA and ABA played roles in the regulation of AR formation of tea cuttings by AMF inoculating, enriching the theoretical basis of AMF regulating rooting of cuttings and providing foundations for cutting propagation of tea plants.

Aims Phyllosphere microbes are closely linked to plant health and are important for the maintenance of host community stability. Tea plants ( Camellia sinensis ) can synthesize abundant secondary metabolites (SMs), however, it is unclear how they affect tea plant phyllosphere homeostasis. Methods We investigated the effects of secondary metabolites of two tea plant cultivars (Longjing43 and Zhongcha108) that have different levels of resistance to anthracnose on the composition, function, assembly and network of phyllosphere fungi. Results We found that the phyllosphere fungal compositions of Longjing43 and Zhongcha108 were distinct, with certain fungal pathogens significantly enriched in the susceptible cultivar Longjing43 (e.g., Fusarium ), which had a higher relative abundance of phytopathogenic functional groups. In addition, the phyllosphere fungal community assembly of the resistant cultivar Zhongcha108 with a higher habitat niche breadth was more influenced by stochastic processes. More importantly, the fungal network of Zhongcha108 exhibited higher complexity and stability, indicating a more resilient network structure. Random forest and partial least squares path models revealed that secondary metabolites, fungal community diversity, composition and function essentially determined network stability. (−)-Epigallocatechin-3-gallate (EGCG) and caffeine (CAF) were the most important predictors of phyllosphere fungal network stability in 2018 and 2019, respectively. Rare fungal taxa were particularly important in maintaining phyllosphere homeostasis. Conclusions Our study suggests that secondary metabolites may mediate phyllosphere fungal homeostasis in tea plants. These findings highlight the importance of secondary metabolites in shaping the phyllosphere fungal community and provide ideas for regulating plant resistance to pathogenic fungi.

Background Laccase (LAC) is the pivotal enzyme responsible for the polymerization of monolignols and stress responses in plants. However, the roles of LAC genes in plant development and tolerance to diverse stresses are still largely unknown, especially in tea plant ( Camellia sinensis ), one of the most economically important crops worldwide. Results In total, 51 CsLAC genes were identified, they were unevenly distributed on different chromosomes and classified into six groups based on phylogenetic analysis. The CsLAC gene family had diverse intron–exon patterns and a highly conserved motif distribution. Cis -acting elements in the promoter demonstrated that promoter regions of CsLACs encode various elements associated with light, phytohormones, development and stresses. Collinearity analysis identified some orthologous gene pairs in C. sinensis and many paralogous gene pairs among C. sinensis , Arabidopsis and Populus . Tissue-specific expression profiles revealed that the majority of CsLACs had high expression in roots and stems and some members had specific expression patterns in other tissues, and the expression patterns of six genes by qRT‒PCR were highly consistent with the transcriptome data. Most CsLACs showed significant variation in their expression level under abiotic (cold and drought) and biotic (insect and fungus) stresses via transcriptome data. Among them, CsLAC3 was localized in the plasma membrane and its expression level increased significantly at 13 d under gray blight treatment. We found that 12 CsLACs were predicted to be targets of cs-miR397a, and most CsLACs showed opposite expression patterns compared to cs-miR397a under gray blight infection. Additionally, 18 highly polymorphic SSR markers were developed, these markers can be widely used for diverse genetic studies of tea plants. Conclusions This study provides a comprehensive understanding of the classification, evolution, structure, tissue-specific profiles, and (a)biotic stress responses of CsLAC genes. It also provides valuable genetic resources for functional characterization towards enhancing tea plant tolerance to multiple (a)biotic stresses.

Background Nitrogen (N) plays an important role in the formation of tea quality-related compounds, like amino acids and flavor/aroma origin compounds. Lipids, which have been reported to be affected by N deficiency, are precursors to the generation of flavor/aroma origin compounds in tea plant. However, there is no literature about the lipid profiles of tea plant affected by N fertilization. Hence, we hypothesize that the biosynthesis of flavor-related compounds in tea was affected by N through its regulation of lipid metabolism. Results In this study, mature leaves and new shoots of tea plant grown under three N levels at the rates of 0, 285 and 474 kg/ha were applied for ultra-performance liquid chromatography-mass spectrometry (UPLC/MS) based lipidomic analysis. Totally, 178 lipid species were identified. The results showed that the composition of lipid compounds in mature leaves and new shoots varied dramatically, which was also affected by N levels. The higher content of the storage lipid TAG and higher carbon (C)/N ratio in mature leaves than that of new shoots in tea plants grown under low N level (0 kg/ha) suggested that tea plants could remobilize the C stored in TAG to maintain their C/N balance and help to improve the quality of tea. N fertilization resulted in a higher content of the compounds 36:6 MGDG and 36:6 DGDG. Since these compounds contain linolenic acid (18:3), a precursor to the formation of aroma origin compounds, we suggested their increase could contribute to the quality of tea. Conclusions Taken together, the present work indicated that appropriate application of N fertilizer could balance the lipid metabolism and the formation of flavor/aroma origin compounds, which help to improve the quality of tea. Moreover, excess N fertilization might deteriorate the aroma quality of made tea due to increases of precursors leading to grassy odor.

Background Intercropping, especially with legumes, as a productive and sustainable system, can promote plants growth and improves the soil quality than the sole crop, is an essential cultivation pattern in modern agricultural systems. However, the metabolic changes of secondary metabolites and the growth in tea plants during the processing of intercropping with soybean have not been fully analyzed. Results The secondary metabolomic of the tea plants were significant influence with intercropping soybean during the different growth stages. Especially in the profuse flowering stage of intercropping soybean, the biosynthesis of amino acids was significantly impacted, and the flavonoid biosynthesis, the flavone and flavonol biosynthesis also were changed. And the expression of metabolites associated with amino acids metabolism, particularly glutamate, glutamine, lysine and arginine were up-regulated, while the expression of the sucrose and D-Glucose-6P were down-regulated. Furthermore, the chlorophyll photosynthetic parameters and the photosynthetic activity of tea plants were higher in the tea plants-soybean intercropping system. Conclusions These results strengthen our understanding of the metabolic mechanisms in tea plant’s secondary metabolites under the tea plants-soybean intercropping system and demonstrate that the intercropping system of leguminous crops is greatly potential to improve tea quality. These may provide the basis for reducing the application of nitrogen fertilizer and improve the ecosystem in tea plantations.

Background The leaves of tea plants ( Camellia sinensis ) are used to produce tea, which is one of the most popular beverages consumed worldwide. The nutritional value and health benefits of tea are mainly related to three abundant characteristic metabolites; catechins, theanine and caffeine. Weighted gene co-expression network analysis (WGCNA) is a powerful system for investigating correlations between genes, identifying modules among highly correlated genes, and relating modules to phenotypic traits based on gene expression profiling. Currently, relatively little is known about the regulatory mechanisms and correlations between these three secondary metabolic pathways at the omics level in tea. Results In this study, levels of the three secondary metabolites in ten different tissues of tea plants were determined, 87,319 high-quality unigenes were assembled, and 55,607 differentially expressed genes (DEGs) were identified by pairwise comparison. The resultant co-expression network included 35 co-expression modules, of which 20 modules were significantly associated with the biosynthesis of catechins, theanine and caffeine. Furthermore, we identified several hub genes related to these three metabolic pathways, and analysed their regulatory relationships using RNA-Seq data. The results showed that these hub genes are regulated by genes involved in all three metabolic pathways, and they regulate the biosynthesis of all three metabolites. It is notable that light was identified as an important regulator for the biosynthesis of catechins. Conclusion Our integrated omics-level WGCNA analysis provides novel insights into the potential regulatory mechanisms of catechins, theanine and caffeine metabolism, and the identified hub genes provide an important reference for further research on the molecular biology of tea plants.

Background The new shoots of the albino tea cultivar ‘Anji Baicha’ are yellow or white at low temperatures and turn green as the environmental temperatures increase during the early spring. ‘Anji Baicha’ metabolite profiles exhibit considerable variability over three color and developmental stages, especially regarding the carotenoid, chlorophyll, and theanine concentrations. Previous studies focused on physiological characteristics, gene expression differences, and variations in metabolite abundances in albino tea plant leaves at specific growth stages. However, the molecular mechanisms regulating metabolite biosynthesis in various color and developmental stages in albino tea leaves have not been fully characterized. Results We used RNA-sequencing to analyze ‘Anji Baicha’ leaves at the yellow-green, albescent, and re-greening stages. The leaf transcriptomes differed considerably among the three stages. Functional classifications based on Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes enrichment analyses revealed that differentially expressed unigenes were mainly related to metabolic pathways, biosynthesis of secondary metabolites, phenylpropanoid biosynthesis, and carbon fixation in photosynthetic organisms. Chemical analyses revealed higher β-carotene and theanine levels, but lower chlorophyll a levels, in the albescent stage than in the green stage. Furthermore, unigenes involved in carotenoid, chlorophyll, and theanine biosyntheses were identified, and the expression patterns of the differentially expressed unigenes in these biosynthesis pathways were characterized. Through co-expression analyses, we identified the key genes in these pathways. These genes may be responsible for the metabolite biosynthesis differences among the different leaf color and developmental stages of ‘Anji Baicha’ tea plants. Conclusions Our study presents the results of transcriptomic and biochemical analyses of ‘Anji Baicha’ tea plants at various stages. The distinct transcriptome profiles for each color and developmental stage enabled us to identify changes to biosynthesis pathways and revealed the contributions of such variations to the albino phenotype of tea plants. Furthermore, comparisons of the transcriptomes and related metabolites helped clarify the molecular regulatory mechanisms underlying the secondary metabolic pathways in different stages.