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Monoterpenes and sesquiterpenes are the most abundant volatiles in tea plants and have dual functions in aroma quality formation and defense responses in tea plants. Terpene synthases (TPS) are the key enzymes for the synthesis of terpenes in plants; however, the functions of most of them in tea plants are still unknown. In this study, six putative terpene biosynthesis gene clusters were identified from the tea plant genome. Then we cloned three new TPS-b subfamily genes, CsTPS08, CsTPS10 and CsTPS58. In vitro enzyme assays showed that CsTPS08 and CsTPS58 are two multiple-product terpene synthases, with the former synthesizing linalool as the main product, and β-myrcene, α-phellandrene, α-terpinolene, D-limonene, cis-β-ocimene, trans-β-ocimene and (4E,6Z)-allo-ocimene as minor products are also detected, while the latter catalyzing the formation of α-pinene and D-limonene using GPP as the substrate. No product of CsTPS10 was detected in the prokaryotic expression system, but geraniol production was detected when transiently expressed in tobacco leaves. CsTPS08 and CsTPS10 are two functional members of a monoterpene synthase gene cluster, which were significantly induced during both Ectropis oblique feeding and fresh leaf spreading treatments, suggesting that they have dual functions involved in tea plant pest defense and tea aroma quality regulation. In addition, the differences in their expression levels in different tea plant cultivars provide a possibility for the subsequent screening of tea plant resources with a specific aroma flavor. Our results deepen the understanding of terpenoid synthesis in tea plants.

Background Tea plants originated from the southwest of China. Guizhou is one of the origin center of tea plants, which is rich in tea plant germplasm resources. However, the distribution characteristics and transmission model of tea plant were still unclear. Results We collected 253 cultivated-type tea plant accessions from Guizhou plateau and analyzed the genetic diversity, PCA, phylogenetic, population structure, LD, and development of core collection using the genotyping-by-sequencing (GBS) approach. A total of 112,072 high-quality SNPs were identified, which was further used to analyze the genetic diversity and population structure. In this study, we found that the genetic diversity in cultivated-type tea accessions of PR Basin were significantly higher than that in cultivated-type tea accessions of YR Basin. Moreover, four groups, including three pure groups (CG-1, CG-2 and CG-3) and one admixture group (CG-4), were identified based on population structure analysis, which was verified by PAC and phylogenetic analysis. Our results showed that the highest GD and Fst values were found in CG-2 vs CG-3, followed by CG-1 vs CG-2 and CG-1 vs CG-3. The lowest GD and Fst values were detected in CG-4 vs CG-1, CG-4 vs CG-2, and CG-4 vs CG-3. Conclusions This study provided the evidence to confirm the contribution of PR and YR Basins and ancient hub road section to the transmission of cultivated-type tea accessions in Guizhou plateau. The genetic diversity, population structure and core collection revealed by our study will benefit further genetic studies, germplasm protection, and breeding.

Alternative splicing (AS) increases the diversity of transcripts and proteins through the selection of different splice sites and plays an important role in the growth, development and stress tolerance of plants. With the release of the reference genome of the tea plant (Camellia sinensis) and the development of transcriptome sequencing, researchers have reported the existence of AS in tea plants. However, there is a lack of a platform, centered on different RNA-seq datasets, that provides comprehensive information on AS.To facilitate access to information on AS and reveal the molecular function of AS in tea plants, we established the first comprehensive AS database for tea plants (TeaAS, http://www.teaas.cn/index.php). In this study, 3.96 Tb reads from 66 different RNA-seq datasets were collected to identify AS events. TeaAS supports four methods of retrieval of AS information based on gene ID, gene name, annotation (non-redundant/Kyoto encyclopedia of genes and genomes/gene ontology annotation or chromosomal location) and RNA-seq data. It integrates data pertaining to genome annotation, type of AS event, transcript sequence, and isoforms expression levels from 66 RNA-seq datasets. The AS events resulting from different environmental conditions and that occurring in varied tissue types, and the expression levels of specific transcripts can be clearly identified through this online database. Moreover, it also provides two useful tools, Basic Local Alignment Search Tool and Generic Genome Browser, for sequence alignment and visualization of gene structure.The features of the TeaAS database make it a comprehensive AS bioinformatics platform for researchers, as well as a reference for studying AS events in woody crops. It could also be helpful for revealing the novel biological functions of AS in gene regulation in tea plants.

Spreading is an indispensable process in the aroma formation of premium green tea. In this study, volatile metabolomics and transcriptomics were performed for three tea plant cultivars to investigate the mechanism of changes occurring in volatile compounds during green tea spreading. The content of primary aroma compounds significantly increased after spreading, the Wickremasinghe-Yamanishi ratio decreased and the Owuor’s flavor index increased with the extension of spreading time, and the degree of aroma production was genotype-dependent. Volatile terpenes and fatty acid-derived volatiles were the principal aroma volatiles that accumulated during the spreading of green tea, and the trends of their changes were consistent with the expression pattern of related synthesis pathway genes, indicating that they were primarily derived from de novo synthesis rather than glycoside hydrolysis. Two co-expression networks that were highly correlated with variations in the volatile component contents during the spreading process were identified via WGCNA. Our results provide insights into spreading that can be considered to improve the quality of green tea.

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. Electronic supplementary material The online version of this article (10.1186/s12870-019-1917-5) contains supplementary material, which is available to authorized users.

SABATH methyltransferases convent plant small-molecule metabolites into volatile methyl esters, which play important roles in many biological processes and defense reactions in plants. In this study, a total of 32 SABATH genes were identified in the Camellia sinensis var. sinensis (CSS) genome, which were renamed CsSABATH1 to CsSABATH32. Genome location annotation suggested that tandem duplication was responsible for the expansion of SABATH genes in tea plant. Multiple sequence alignment and phylogenetic analysis showed that the CsSABATHs could be classified into three groups (I, II and III), which were also supported by gene structures and conserved motifs analysis. Group II contained only two CsSABATH proteins, which were closely related to PtIAMT, AtIAMT and OsIAMT. The group III SABATH genes of tea plant exhibited expansion on the CSS genome compared with Camellia sinensis var. assamica (CSA) genome. Based on RNA-seq data, the CsSABATHs exhibited tissue-specific expression patterns, and the members with high expression in buds and young leaves were also obviously upregulated after MeJA treatment. The expression of many transcription factors was significantly correlated with that of different members of the CsSABATH gene family, suggesting a potential regulatory relationship between them. Quantitative real-time PCR (qPCR) expression analysis showed that CsSABATHs could respond to exogenous JA, SA and MeSA treatments in tea plants. RNA-seq data analysis and qPCR validation suggested that CsSABATH8, 11, 16, 25, 29 and 32 might play a special role in plant defense against insect herbivory. These results provide references for evolutionary studies of the plant SABATH family and the exploration of the potential roles of CsSABATHs in tea plant defense responses.

Figure S1. Graphical method allowing the detection of the number of groups using ∆K inferred population structure of the 263 Pure Cultivation Type. Figure S2. Inferred population structure of the 263Pure Cultivation Type using STRUCTURE software. Bar plot of individual ancestry proportions for the genetic clusters inferred using STRUCTURE (K = 2) and the reduced dataset. Individual ancestry proportions (q values) are sorted within each cluster. Admixture model, independent frequencies, 30,000 burn-in iterations, 100,000 Markov Chain Monte Carlo iterations were used for this analysis. Ancient landraces (GP03–1) and modern landraces (GP03–2) are shown in yellow and green, respectively. Figure S3.. Four inferred populations of the 415tea accessions using STRUCTURE (K = 3). GP01 are shown in red, GP02 are shown in red and blue, GP03–1 are shown in blue, and GP03–2 are shown in green. (PDF 207 kb)

Geographic distribution of tea accessions analyzed in the current study according to the collection. (A) The geographical position of Guizhou province in China. (B) Agriculture climate regionalization map for tea plant growth in Guizhou Plateau [35]. Ia: Area with a very suitable climate for tea plant growth in North of Guizhou; Ib: Area with a very suitable climate for tea plants growth in East of Guizhou; Ic: Area with a very suitable climate for tea plants growth in South of Guizhou; II: Area with a suitable climate for tea plant growth in Center of Guizhou; III: Area with a minor suitable climate for tea plant growth in West of Guizhou; IV: Area with an unsuitable climate for tea plants growth in West of Guizhou. (PDF 157 kb)

Actin-depolymerizing factors (ADFs) are the members of actin-binding proteins, which play pivotal roles in various cellular processes in plant cells. In this study, we isolated an ADF gene ZmADF3 from the kernels of a popcorn inbred N04. This gene had a 417 bp open reading frame (ORF) which encoded for 139 amino acids. Phylogenetic analysis showed that ZmADF3 had a high sequence identity with TaADF3 and OsADF4. Quantitative real-time PCR and western blotting showed that ZmADF3 expressed variously according to tissues and developmental stages during kernel development both in RNA and in protein levels. A 1738 bp promoter for ZmADF3 was obtained and the cis-acting regulatory elements were predicted. Furthermore, yeast two-hybrid screening revealed that ZmADF3 interacted with glyceradehyde-3-phosphate dehydrogenase (GAPDH). Heterologous overexpression of ZmADF3 showed an increase in seed size in transgenic Arabidopsis plants mainly through the increase in cell size. In addition, the positive regulation of seed size genes SHB1 and IKU1 were up-regulated while the negative regulators AP2 and ARF2 were down-regulated in the transgenic lines. Our results showed that ZmADF3 might play important roles in kernel development in maize. However, further research should be done to thoroughly explore the mechanism of ZmADF3 in playing these functions.

Favorable agronomic traits are important to improve productivity of popcorn. In this study, a recombinant inbred line (RIL) population consisting of 258 lines was evaluated to identify quantitative trait loci (QTLs) for nine agronomic traits (plant height, ear height, top height (plant height subtracted ear height), top height/plant height, number of leaves above the top ear, leaf area, stalk diameter, number of tassel branches and the length of tassel) under three environments. Meta-analysis was conducted then to integrate QTLs identified across three generations (RIL, F2:3 and BC2F2) developed from the same crosses. In total, 179 QTLs and 36 meta-QTLs (mQTL) were identified. The percentage of phenotypic variation (R2) explained by any single QTL varied from 3.86 to 28.4%, and 24 QTLs with contributions over 15%. Nine common QTLs located in the same or similar chromosome regions were detected across three generations. Five meta-QTLs were identified including QTLs in three independent studies. Seven important mQTLs were composed of 11–26 QTLs for 4–7 traits, respectively. Only 11 mQTLs were commonly identified in the same or similar chromosome regions across agronomic traits, popping characteristics (popping fold, popping volume and popping rate) and grain yield components (ear weight per plant, grain weight per plant, 100-grain weight, ear length, kernel number per row, ear diameter, row number per ear and kernel ratio) by meta-QTL analysis. In conclusion, we identified a list of QTLs, some of which with much higher contributions to agronomic traits should be valuable for further study in improving both popping characteristics and grain yield components in popcorn.

An accurate depiction of the genetic relationship, the development of core collection, and genome-wide association analysis (GWAS) are key for the effective exploitation and utilization of genetic resources. Here, genotyping-by-sequencing (GBS) was used to characterize 415 tea accessions mostly collected from the Guizhou region in China. A total of 30,282 high-quality SNPs was used to estimate the genetic relationships, develop core collections, and perform GWAS. We suggest 198 and 148 accessions to represent the core set and mini-core set, which consist of 47% and 37% of the whole collection, respectively, and contain 93–95% of the total SNPs. Furthermore, the frequencies of all alleles and genotypes in the whole set were very well retained in the core set and mini-core set. The 415 accessions were clustered into 14 groups and the core and the mini-core collections contain accessions from each group, species, cultivation status and growth habit. By analyzing the significant SNP markers associated with multiple traits, nine SNPs were found to be significantly associated with four leaf size traits, namely MLL, MLW, MLA and MLSI (P

The ethylene response factor (ERF) plays a key role in the transcriptional regulation of plant growth, development, and response to various environmental perturbations. Study of ERF transcription factors, especially those in cultivated crops, could facilitate their molecular genetic modification. In this study, an ERF1 gene, designated as ZmERF1, which was found to be localized in the nucleus, was isolated from popcorn (Zea mays L.). Further analysis showed that the ZmERF1 proteins could bind to the GCC box motif and act as a transcriptional activator. A clear picture of ZmERF1 expression pattern showed that ZmERF1 expression varies during different development stages of endosperm. Furthermore, its expression could be highly induced by salinity, osmotic and heat stress, suggesting that the gene is involved in stress signaling pathways in maize. Therefore, ZmERF1 could play important role in abiotic stress tolerance and endosperm development in maize.

The formation and development of maize kernel is a complex dynamic physiological and biochemical process that involves the temporal and spatial expression of many proteins and the regulation of metabolic pathways. In this study, the protein profiles of the endosperm and pericarp at three important developmental stages were analyzed by isobaric tags for relative and absolute quantification (iTRAQ) labeling coupled with LC-MS/MS in popcorn inbred N04. Comparative quantitative proteomic analyses among developmental stages and between tissues were performed, and the protein networks were integrated. A total of 6,876 proteins were identified, of which 1,396 were nonredundant. Specific proteins and different expression patterns were observed across developmental stages and tissues. The functional annotation of the identified proteins revealed the importance of metabolic and cellular processes, and binding and catalytic activities for the development of the tissues. The whole, endosperm-specific and pericarp-specific protein networks integrated 125, 9 and 77 proteins, respectively, which were involved in 54 KEGG pathways and reflected their complex metabolic interactions. Confirmation for the iTRAQ endosperm proteins by two-dimensional gel electrophoresis showed that 44.44% proteins were commonly found. However, the concordance between mRNA level and the protein abundance varied across different proteins, stages, tissues and inbred lines, according to the gene cloning and expression analyses of four relevant proteins with important functions and different expression levels. But the result by western blot showed their same expression tendency for the four proteins as by iTRAQ. These results could provide new insights into the developmental mechanisms of endosperm and pericarp, and grain formation in maize.

ADP-ribosylation factors (ARFs) are small GTP-binding proteins that regulate a wide variety of cell functions. Previously, we isolated a new ARF, ZmArf2, from maize (Zea mays). Sequence and expression characteristics indicated that ZmArf2 might play a critical role in the early stages of endosperm development. In this study, we investigated ZmArf2 function by analysis of its GTP-binding activity and subcellular localization. We also over-expressed ZmArf2 in Arabidopsis and measured organ and cell size and counted cell numbers. The expression levels of five organ size-associated genes were also determined in 35S::ZmArf2 transgenic and wild-type plants. Results showed that the recombinant ZmArf2 protein purified from Escherichia coli exhibited GTP-binding activity. Subcellular localization revealed that ZmArf2 was localized in the cytoplasm and plasma membrane. ZmArf2 over-expression in Arabidopsis showed that 35S::ZmArf2 transgenic plants were taller and had larger leaves and seeds compared to wild-type plants, which resulted from cell expansions, not an increase in cell numbers. In addition, three cell expansion-related genes, AtEXP3, AtEXP5 and AtEXP10, were upregulated in 35S::ZmArf2 transgenic lines, while the expression levels of AtGIF1 and AtGRF5, were unchanged. Collectively, our studies suggest that ZmArf2 has an active GTP-binding function, and plays a crucial role in growth and development in Arabidopsis through cell expansion mediated by cell expansion genes.

Grain water relations were closely correlated with matter accumulation during grain development. In this study, QTL mapping for Grain Water Content (GWC) at four stages after pollination and Grain Dehydration Rate (GDR) during six intervals were done using 258 Recombinant Inbred Lines (RIL). Meta-QTL (mQTL) was revealed by meta-analysis using Bio Mercator for both traits herein and together with seven traits related with grain matter accumulation in our previous research. Among 40 QTL detected for GWC and 35 QTL for GDR, 45 QTL were stage/period specific. QTL on chromosome 5 could be considered as full-stage QTL. Eight of 11 mQTL included QTL for both traits. Grain matter traits were positively correlated with GWC, but negatively correlated with GDR in most cases. Low coincidences in QTL position and opposite allelic effects for two kinds of traits suggested that their simultaneous improvement might be realized. Selection for low grain moisture could be focused on QTL at bins 1.07- 1.08, 2.08, 4.03-4.04 and 5.03-5.04, while it should be followed to QTL at bins 7.02-7.03, 1.03-1.04 and 10.05-10.06 for high grain weight. However, this should be proved through practical selection, and the related marker intervals needed to be narrowed down in further research.