Combined QTL mapping, GWAS and transcriptomic analysis revealed a candidate gene associated with the timing of spring bud flush in tea plant (Camellia sinensis).
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ABSTRACT:
SUBMITTER: Liu Y
PROVIDER: S-EPMC10483171 | biostudies-literature | 2023 Sep
REPOSITORIES: biostudies-literature
Publications
Combined QTL mapping, GWAS and transcriptomic analysis revealed a candidate gene associated with the timing of spring bud flush in tea plant (<i>Camellia sinensis</i>).
Liu Yujie Y Chen Si S Jiang Chenkai C Liu Haoran H Wang Junyu J He Weizhong W Moon Doogyung D Chen Jiedan J Chen Liang L Ma Jianqiang J
Horticulture research 20230726 9
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Project description:BackgroundAP2/ERF transcription factors (AP2/ERFs) are important regulators of plant physiological and biochemical metabolism. Evidence suggests that AP2/ERFs may be involved in the regulation of bud break in woody perennials. Green tea is economically vital in China, and its production value is significantly affected by the time of spring bud break of tea plant. However, the relationship between AP2/ERFs in tea plant and spring bud break remains largely unknown.ResultsA total of 178 AP2/ERF genes (CsAP2/ERFs) were identified in the genome of tea plant. Based on the phylogenetic analysis, these genes could be classified into five subfamilies. The analysis of gene duplication events demonstrated that whole genome duplication (WGD) or segmental duplication was the primary way of CsAP2/ERFs amplification. According to the result of the Ka/Ks value calculation, purification selection dominated the evolution of CsAP2/ERFs. Furthermore, gene composition and structure analyses of CsAP2/ERFs indicated that different subfamilies contained a variety of gene structures and conserved motifs, potentially resulting in functional differences among five subfamilies. The promoters of CsAP2/ERFs also contained various signal-sensing elements, such as abscisic acid responsive elements, light responsive elements and low temperature responsive elements. The evidence presented here offers a theoretical foundation for the diverse functions of CsAP2/ERFs. Additionally, the expressions of CsAP2/ERFs during spring bud break of tea plant were analyzed by RNA-seq and grouped into clusters A-F according to their expression patterns. The gene expression changes in clusters A and B were more synchronized with the spring bud break of tea plant. Moreover, several potential correlation genes, such as D-type cyclin genes, were screened out through weighted correlation network analysis (WGCNA). Temperature and light treatment experiments individually identified nine candidate CsAP2/ERFs that may be related to the spring bud break of tea plant.ConclusionsThis study provides new evidence for role of the CsAP2/ERFs in the spring bud break of tea plant, establishes a theoretical foundation for analyzing the molecular mechanism of the spring bud break of tea plant, and contributes to the improvement of tea cultivars.
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Project description:In this study, a unique tea cultivar ‘Anxi kucha’ was discovered for the first time, which is rich in both secondary metabolites. In the targeted data, theacrine (17.44 mg/g) was detected only in the ‘Anxi kucha’ tea plant in the test materials. The content of EGCG3"Me in ‘Anxi kucha’ (11.25mg/g), ‘Tieguanyin’ (5.32mg/g) and ‘Fudingdabaicha’ (0.93mg/g) showed high, medium and low changes. Through proteomics and transcriptomics, it was identified that the key pathways for the synthesis of theacrine and EGCG3"Me were the purine metabolism pathway and the flavonoid biosynthesis pathway, respectively. Combined proteome-transcriptome-metabolome analysis showed that SAMS3, APRT1, IMPDH, and TCS1 were the main enzymes promoting theacrine synthesis; CHI1, CHI2, FLS2 and LAR1 were the main enzymes that promote the synthesis of EGCG3"Me. The results of transcription factor analysis showed that MYB4 and bHLH74 had positive regulatory effects on the synthesis of theacrine and EGCG3"Me. Theacrine and EGCG3"Me are both bitter compounds. This study provides a valuable material rich in theacrine and EGCG3"Me, which provides a material basis for further development and utilization in the field of tea health food and a theoretical basis for studying the functional components of tea.
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Project description:The timing of bud flush (TBF) in the spring is one of the most important agronomic traits of tea plants (Camellia sinensis). In this study, we designed an open-pollination breeding program using 'Emei Wenchun' (EW, a clonal tea cultivar with extra-early TBF) as a female parent. A half-sib population (n = 388) was selected for genotyping using specific-locus amplified fragment sequencing. The results enabled the identification of paternity for 294 (75.8%) of the offspring, including 11 (2.8%) from EW selfing and 217 (55.9%) assigned to a common father, 'Chuanmu 217' (CM). The putative EW × CM full-sib population was used to construct a linkage map. The map has 4244 markers distributed in 15 linkage groups, with an average marker distance of 0.34 cM. A high degree of collinearity between the linkage map and physical map was observed. Sprouting index, a trait closely related to TBF, was recorded for the offspring population in 2020 and 2021. The trait had moderate variation, with coefficients of variation of 18.5 and 17.6% in 2020 and 2021, respectively. Quantitative trait locus (QTL) mapping that was performed using the linkage map identified two major QTLs and three minor QTLs related to the sprouting index. These QTLs are distributed on Chr3, Chr4, Chr5, Chr9, and Chr14 of the reference genome. A total of 1960 predicted genes were found within the confidence intervals of QTLs, and 22 key candidate genes that underlie these QTLs were preliminarily screened. These results are important for breeding and understanding the genetic base of the TBF trait of tea plants.
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Project description:Theanine, a unique and the most abundant non-proteinogenic amino acid in tea plants, endows tea infusion with the umami taste and anti-stress effects. Its content in tea correlates highly with green tea quality. Theanine content in new shoots of tea plants is high in mid-spring and greatly decreases in late spring. However, how the decrease is regulated is largely unknown. In a genetic screening, we observed that a yeast mutant, glutamate dehydrolase 2 (gdh2), was hypersensitive to 40 mM theanine and accumulated more theanine. This result implied a role of CsGDH2s in theanine accumulation in tea plants. Therefore, we identified the two homologs of GDH2, CsGDH2.1 and CsGDH2.2, in tea plants. Yeast complementation assay showed that the expression of CsGDH2.1 in yeast gdh2 mutant rescued the theanine hypersensitivity and hyperaccumulation of this mutant. Subcellular localization and tissue-specific expression showed CsGDH2.1 localized in the mitochondria and highly expressed in young tissues. Importantly, CsGDH2.1 expression was low in early spring, and increased significantly in late spring, in the new shoots of tea plants. These results all support the idea that CsGDH2.1 regulates theanine accumulation in the new shoots. Moreover, the in vitro enzyme assay showed that CsGDH2.1 had glutamate catabolic activity, and knockdown of CsGDH2.1 expression increased glutamate and theanine accumulation in the new shoots of tea plants. These findings suggested that CsGDH2.1-mediated glutamate catabolism negatively regulates theanine accumulation in the new shoots in late spring, and provides a functional gene for improving late-spring green tea quality.
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Project description:Tea leaf-color mutants have attracted increasing attention due to their accumulation of quality-related biochemical components. However, there is limited understanding of the molecular mechanisms behind leaf-color bud mutation in tea plants. In this study, a chlorina tea shoot (HY) and a green tea shoot (LY) from the same tea plant were investigated using transcriptome and biochemical analyses. The results showed that the chlorophyll a, chlorophyll b, and total chlorophyll contents in the HY were significantly lower than the LY's, which might have been caused by the activation of several genes related to chlorophyll degradation, such as SGR and CLH. The down-regulation of the CHS, DFR, and ANS involved in flavonoid biosynthesis might result in the reduction in catechins, and the up-regulated GDHA and GS2 might bring about the accumulation of glutamate in HY. RT-qPCR assays of nine DEGs confirmed the RNA-seq results. Collectively, these findings provide insights into the molecular mechanism of the chlorophyll deficient-induced metabolic change in tea plants.
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Project description:Winter dormancy is an important biological feature for tea plant to survive cold winters, and it also affects the economic output of tea plant, one of the few woody plants in the world whose leaves are harvested and one of the few non-conifer evergreen species with characterized dormancies. To discover the bud dormancy regulation mechanism of tea plant in winter, we analyzed the global gene expression profiles of axillary buds at the paradormancy, endodormancy, ecodormancy, and bud flush stages by RNA-Seq analysis. In total, 16,125 differentially expressed genes (DEGs) were identified among the different measured conditions. Gene set enrichment analysis was performed on the DEGs identified from each dormancy transition. Enriched gene ontology terms, gene sets and transcription factors were mainly associated with epigenetic mechanisms, phytohormone signaling pathways, and callose-related cellular communication regulation. Furthermore, differentially expressed transcription factors as well as chromatin- and phytohormone-associated genes were identified. GI-, CAL-, SVP-, PHYB-, SFR6-, LHY-, ZTL-, PIF4/6-, ABI4-, EIN3-, ETR1-, CCA1-, PIN3-, CDK-, and CO-related gene sets were enriched. Based on sequence homology analysis, we summarized the key genes with significant expression differences in poplar and tea plant. The major molecular pathways involved in tea plant dormancy regulation are consistent with those of poplar to a certain extent; however, the gene expression patterns varied. This study provides the global transcriptome profiles of overwintering buds at different dormancy stages and is meaningful for improving the understanding of bud dormancy in tea plant.
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Project description:Tea (Camellia sinensis (L.) O. Kuntze) is an important non-alcoholic commercial beverage crop. Tea tree is a perennial plant, and winter dormancy is its part of biological adaptation to environmental changes. We recently discovered a novel tea tree cultivar that can generate tender shoots in winter, but the regulatory mechanism of this ever-growing tender shoot development in winter is not clear. In this study, we conducted a proteomic analysis for identification of key genes and proteins differentially expressed between the winter and spring tender shoots, to explore the putative regulatory mechanisms and physiological basis of its ever-growing character during winter.
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Project description:The tea plant (Camellia sinensis) presents an excellent system to study evolution and diversification of the numerous classes, types and variable contents of specialized metabolites. Here, we investigate the relationship among C. sinensis phylogenetic groups and specialized metabolites using transcriptomic and metabolomic data on the fresh leaves collected from 136 representative tea accessions in China. We obtain 925,854 high-quality single-nucleotide polymorphisms (SNPs) enabling the refined grouping of the sampled tea accessions into five major clades. Untargeted metabolomic analyses detect 129 and 199 annotated metabolites that are differentially accumulated in different tea groups in positive and negative ionization modes, respectively. Each phylogenetic group contains signature metabolites. In particular, CSA tea accessions are featured with high accumulation of diverse classes of flavonoid compounds, such as flavanols, flavonol mono-/di-glycosides, proanthocyanidin dimers, and phenolic acids. Our results provide insights into the genetic and metabolite diversity and are useful for accelerated tea plant breeding.
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Project description:To unravel the molecular mechanism of defense against blister blight (BB) disease caused by an obligate biotrophic fungus, Exobasidium vexans, transcriptome of BB interaction with resistance and susceptible tea genotypes was analysed through RNA-seq using Illumina GAIIx at four different stages during ~20-day disease cycle. Approximately 69 million high quality reads were assembled de novo, yielding 37,790 unique transcripts with more than 55% being functionally annotated. Differentially expressed, 149 defense related transcripts/genes, namely defense related enzymes, resistance genes, multidrug resistant transporters, transcription factors, retrotransposons, metacaspases and chaperons were observed in RG, suggesting their role in defending against BB. Being present in the major hub, putative master regulators among these candidates were identified from predetermined protein-protein interaction network of Arabidopsis thaliana. Further, confirmation of abundant expression of well-known RPM1, RPS2 and RPP13 in quantitative Real Time PCR indicates salicylic acid and jasmonic acid, possibly induce synthesis of antimicrobial compounds, required to overcome the virulence of E. vexans. Compendiously, the current study provides a comprehensive gene expression and insights into the molecular mechanism of tea defense against BB to serve as a resource for unravelling the possible regulatory mechanism of immunity against various biotic stresses in tea and other crops.
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