Genetic diversity and domestication origin of tea plant Camellia taliensis (Theaceae) as revealed by microsatellite markers

Simple Sequence Repeat Marker-Based Genetic Diversity and Chemical Composition Analysis of Ancient Camellia sinensis in Jiulong County, Sichuan Province, China

BACKGROUND/OBJECTIVES

The ancient tea plant germplasm resources are rich in genetic diversity and provide an important basis for the genetic diversity in tea germplasm resources. To explore the genetic diversity of ancient tea plant germplasm resources in Jiulong County, Sichuan Province.

METHODS

59 ancient tea tree germplasm resources were analyzed using simple sequence repeat (SSR) molecular markers and chemical composition analysis.

RESULTS

The results showed that a total of 83 alleles were amplified by 23 pairs of SSR primers, with an average observed allele number (Na) of 3.6 and an effective allele number (Ne) of 2.335. The average Shannon information index (I) and the polymorphic information content (PIC) of the primers were 0.896 and 0.446, respectively. The results of the UPGMA cluster analysis showed that 59 ancient tea tree samples could be classified into five different subgroups. Based on the results of chemical composition analysis, two specific tea germplasm resources with high amino acid content, 10 excellent germplasm resources with tea polyphenol content over 20% and some other tea germplasm resources were identified.

CONCLUSIONS

This study reveals that Jiulong's ancient tea tree germplasm exhibits significant genetic diversity and includes valuable tea tree planting resources. These findings provide a foundational framework for the conservation, detailed exploration and sustainable utilization of these resources.

Insights into the Metabolite Profiles of Two Camellia (Theaceae) Species in Yunnan Province through Metabolomic and Transcriptomic Analysis

Tea (Camellia sinensis) falls into the family Theaceae, is a valuable commercial crop, and tea products made from its buds and young leaves are favored by consumers all over the world. The more common Thea plant is Camellia sinensis (C. sinensis), but its most important relative, Camellia taliensis (C. taliensis), is also utilized by locals in the area of cultivation to manufacture tea. In this investigation, C. taliensis (DL) and C. sinensis (QJZ) were characterized in terms of their agronomic traits, physicochemical indices, metabolomics, and transcriptomics. The leaf area of DL is larger than that of QJZ; the color of DL's buds and leaves is yellowish-green, while that of QJZ's is green. DL's buds and leaves are more densely velvety than those of QJZ. The HPLC results indicated that the physicochemical contents varied considerably between the two samples, with DL having greater concentrations of EGCG and GABA than QJZ, while QJZ had remarkably higher concentrations of C, CA, and EGC than DL. A total of 2269 metabolites and 362,190,414 genes were positively identified, with the number of DAMs and DEGs being 1001 and 34,026, respectively. The flavonoids, phenolic acids, and alkaloid metabolites were dramatically different between the two tea group plants. Bioinformatics profiling revealed that the DAMs and DEGs of the two tea group plants interacted with each other and were involved in metabolic pathways, including "biosynthesis of secondary metabolites", "biosynthesis of amino acids", "biosynthesis of cofactors", "phenylpropanoid biosynthesis", and "flavonoid biosynthesis". Overall, these results provide statistical support for germplasm conservation and production for both C. taliensis and C. sinensis.

Analysis of population structure and genetic diversity of Camellia tachangensis in Guizhou based on SNP markers

BACKGROUND

Camellia tachangensis F. C. Zhang is a five-compartment species in the ovary of tea group plants, which represents the original germline of early differentiation of some tea group plants.

METHODS AND RESULTS

In this study, we analyzed single-nucleotide polymorphisms (SNPs) at the genome level, constructed a phylogenetic tree, analyzed the genetic diversity, and further investigated the population structure of 100 C. tachangensis accessions using the genotyping-by-sequencing (GBS) method. A total of 91,959 high-quality SNPs were obtained. Population structure analysis showed that the 100 C. tachangensis accessions clustered into three groups: YQ-1 (Village Group), YQ-2 (Forest Group) and YQ-3 (Transition Group), which was further consistent with the results of phylogenetic analysis and principal component analyses (PCA). In addition, a comparative analysis of the genetic diversity among the three populations (Forest, Village, and Transition Groups) detected the highest genetic diversity in the Transition Group and the highest differentiation between Forest and Village Groups.

CONCLUSIONS

C. tachangensis plants growing in the forest had different genetic backgrounds from those growing in villages. This study provides a basis for the effective protection and utilization of C. tachangensis populations and lays a foundation for future C. tachangensis breeding.

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.

Genome-wide identification, characterization and primer designing of simple sequence repeats across Leguminosae family

Legumes are important clade of commercially important family Leguminosae that mainly include medicinal, flowering and edible plants. Although the genomic sequence of legumes is accessible, only the limited number of effective simple sequence repeat markers has been identified by prior research. Additional polymorphic simple sequence repeats marker discovery will aid in the genetics and breeding of legumes. In this study, 13 complete genome sequences were screened for the identification of chromosome-wise simple sequence repeats (SSRs) and 1,866,861 SSRs were identified. Based on the study, it was observed that the number of SSRs in non-coding region was more as compared to coding region and frequency of mononucleotides was highest followed by di-nucleotides while penta- and hexa-nucleotide repeats were least frequent one. The identified genome-wide SSRs and newly developed SSR markers, primers and their mapping will provide a powerful means for genetic researches across Leguminosae plants, including genetic diversity and evolutionary origin analysis, fingerprinting, QTL mapping and marker-assisted selection for breeding as well as comparative genomic analysis studies.

New Hydrolyzable Tannin with Potent Antioxidant and α-Glucosidase Inhibitory Activity from Black Tea Produced from Camellia taliensis

Camellia taliensis (W. W. Smith) Melchior, belonging to the genus Camellia sect. Thea., is mainly distributed from northern Myanmar to western and southwestern Yunnan province of China, and its leaves have been used to make various teas by the locals of its growing regions. The chemical constituents of C. taliensis are significantly related to those of cultivated tea plants, C. sinensis and C. sinensis var. assamica. The HPLC-ESI-MS analysis of black tea prepared from the leaves of C. taliensis showed a rich existence of polyphenols. Further comprehensive chemical study led to the separation and recognition of 32 compounds (1-32), including one new hydrolyzable tannin, 1-O-galloyl-4,6-tetrahydroxydibenzofurandicarboxyl-β-D-glucopyranose (1), and one new natural product (24). The known compounds referred to seven hydrolyzable tannins (2-8), 10 flavonols and glycosides (9-18), and 14 simple phenolics (19-32). Their structures were elucidated by comprehensive spectroscopic analyses. Among them, 20 compounds (2, 3, 6, 7, 8, 15, 17, 18, 20-22, 24-32) were isolated from black tea for the first time. Most isolates displayed obvious antioxidant activities on DPPH and ABTS⁺ assays, and the hydrolyzable tannins 1, 3-5, 7, and 8 exhibited stronger inhibitory activities on α-glycosidase than quercetin and acarbose (IC₅₀ = 5.75 and 223.30 μM, respectively), with IC₅₀ values ranging from 0.67 to 2.01 μM.

Population structure analysis to explore genetic diversity and geographical distribution characteristics of wild tea plant in Guizhou Plateau

BACKGROUND

Tea, the second largest consumer beverage in the world after water, is widely cultivated in tropical and subtropical areas. However, the effect of environmental factors on the distribution of wild tea plants is unclear.

RESULTS

A total of 159 wild tea plants were collected from different altitudes and geological types of the Guizhou Plateau. Using the genotyping-by-sequencing method, 98,241 high-quality single nucleotide polymorphisms were identified. Genetic diversity, population structure analysis, principal component analysis, phylogenetic analysis, and linkage disequilibrium were performed. The genetic diversity of the wild tea plant population from the Silicate Rock Classes of Camellia gymnogyna was higher than that from the Carbonate Rock Classes of Camellia tachangensis. In addition, the genetic diversity of wild tea plants from the second altitude gradient was significantly higher than that of wild tea plants from the third and first altitude gradients. Two inferred pure groups (GP01 and GP02) and one inferred admixture group (GP03) were identified by population structure analysis and were verified by principal component and phylogenetic analyses. The highest differentiation coefficients were determined for GP01 vs. GP02, while the lowest differentiation coefficients were determined for GP01 vs. GP03.

CONCLUSIONS

This study revealed the genetic diversity and geographical distribution characteristics of wild tea plants in the Guizhou Plateau. There are significant differences in genetic diversity and evolutionary direction between Camellia tachangensis with Carbonate Rock Classes at the first altitude gradient and Camellia gymnogyna with Silicate Rock Classes at the third altitude gradient. Geological environment, soil mineral element content, soil pH, and altitude markedly contributed to the genetic differentiation between Camellia tachangensis and Camellia gymnogyna.

Genome-wide characterization and development of SSR markers for genetic diversity analysis in northwestern Himalayas Walnut (Juglans regia L.)

In the present study, we designed and validated genome-wide polymorphic SSR markers (110 SSRs) by mining the walnut genome. A total of 198,924 SSR loci were identified. Among these, successful primers were designed for 162,594 (81.73%) SSR loci. Dinucleotides were the most predominant accounting for 88.40% (175,075) of total SSRs. The SSR frequency was 377.312 SSR/Mb and it showed a decreasing trend from dinucleotide to octanucleotide motifs. We identified 20 highly polymorphic SSR markers and used them to genotype 72 walnut accessions. Over all, we obtained 118 alleles that ranged from 2 to 12 with an average value of 5.9. The higher SSR PIC values indicate their robustness in discriminating walnut genotypes. Heat map, PCA, and population structure categorized 72 walnut genotypes into 2 distinct clusters. The genetic variation within population was higher than among population as inferred by analysis of molecular variance (AMOVA). For walnut improvement, it is necessary to have a large repository of SSRs with high discriminative power. The present study reports 150,000 SSRs, which is the largest SSR repository for this important nut crop. Scientific communities may use this repository for walnut improvement such as QTL mapping, genetic studies, linkage map construction, and marker-assisted selection.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03563-6.

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.

A DEK domain-containing protein GhDEK2D mediated Gossypium hirsutum enhanced resistance to Verticillium dahliae

DEK is associated with DNA replication and break repair, mRNA splicing, and transcriptional regulation, which had been studied in humans and mammals. The function of DEK in plants was poorly understood. In this study, GhDEK2D was identified in Gossypium hirsutum by genome-wide and post-translational modifications. GhDEK2D had been phosphorylated, acetylated and ubiquitylated under Verticillium dahliae (Vd) challenge. The GhDEK2D-silenced cotton decreased resistance against Vd. In GhDEK2D-silenced cotton plants, the reactive oxygen species was activated, the callose, xylogen, hypersensitive reaction (HR) and expression levels of defense-related genes were reduced. Homozygous overexpressing-GhDEK2D transgenic Arabidopsis lines were more resistant to Verticillium wilt (Vw). We propose that GhDEK2D was a potential molecular target for improving resistance to Vw in cotton.

Conservation of an Agrobacterium cT-DNA insert in Camellia section Thea reveals the ancient origin of tea plants from a genetically modified ancestor

Introduction

Many higher plants contain cellular T-DNA (cT-DNA) sequences from Agrobacterium and have been called "natural genetically modified organisms" (nGMOs). Among these natural transformants, the tea plant Camellia sinensis var. sinensis cv. Shuchazao contains a single 5.5 kb T-DNA fragment (CaTA) with three inactive T-DNA genes, with a 1 kb inverted repeat at the ends. Camellia plants are allogamous, so that each individual may contain two different CaTA alleles.

Methods

142 Camellia accessions, belonging to 10 of 11 species of the section Thea, were investigated for the presence of CaTA alleles.

Results discussion

All accessions were found to contain the CaTA insert, showing that section Thea derives from a single transformed ancestor. Allele phasing showed that 82 accessions each contained two different CaTA alleles, 60 others had a unique allele. A phylogenetic tree of these 225 alleles showed two separate groups, A and B, further divided into subgroups. Indel distribution corresponded in most cases with these groups. The alleles of the different Camellia species were distributed over groups A and B, and different species showed very similar CaTA alleles. This indicates that the species boundaries for section Thea may not be precise and require revision. The nucleotide divergence of the indirect CaTA repeats indicates that the cT-DNA insertion took place about 15 Mio years ago, before the emergence of section Thea. The CaTA structure of a C. fangchengensis accession has an exceptional structure. We present a working model for the origin and evolution of nGMO plants derived from allogamous transformants.

Whole-genome resequencing reveals the origin of tea in Lincang

Phylogeographic, population genetics and diversity analysis are crucial for local tea resource conservation and breeding programs. Lincang in Yunnan has been known as the possible place of domestication for tea worldwide, yet, its genetic makeup and unique Lincang origin are little understood. Here, we reported a large-scale whole-genome resequencing based population genomic analysis in eight main tea-producing areas of Lincang in Yunnan (1,350 accessions), and the first comprehensive map of tea genome variation in Lincang was constructed. Based on the population structure, tea sample in Lincang was divided into three subgroups, and inferred Xigui and Nahan Tea Mountain in Linxiang, Baiying Mountain Ancient Tea Garden in Yun, and Jinxiu Village of Xiaowan Town in Fengqing, which belong to the birthplace of the three subgroups, were all likely to be the origin center of Lincang tea. Meanwhile, the history population sizes analysis show that similar evolutionary patterns were observed for the three subgroups of Lincang. It also was observed that the hybrid among eight areas of Lincang was noticeable, resulting in insignificant genetic differentiation between geographical populations and low genetic diversity. The findings of this study clarified the genetic make-up and evolutionary traits of the local population of tea, which gave some insight into the development of Lincang tea.

Identification of low-molecular-weight color contributors of black tea infusion by metabolomics analysis based on UV-visible spectroscopy and mass spectrometry

Nine black tea samples with different color intensity were firstly determined by chromatic difference analyzer. The color characteristics were secondly quantitatively described by UV-visible spectroscopy. Thirdly, liquid chromatography tandem mass spectrometry (LC-MS) based metabolomics analysis was applied in low-molecular-weight compounds. Finally, the color contributors were identified by the correlation analysis of color, spectrometry and mass data. UV-visible based metabolomics analysis revealed that the wavelength at 380-520 nm (VIP > 1.50) was the critical absorbance band for distinguishing different color of BT infusions, while LC-MS based metabolomics analysis indicated that there were 48 main marker compounds responsible for the classification of different BT infusions. Correlation analysis results showed that the coefficients of theaflavins, thearubigins, theabrownins, flavonoid glycosides, and some hydroxycinnamoyl acids were > 0.7, which suggested they were main color contributors of BT infusion. The present study expanded a new vision on the color analysis of BT infusion.

Genetic Diversity and Genome Size Variability in the Russian Genebank Collection of Tea Plant [Camellia sinensis (L). O. Kuntze]

The tea collection of the FRC SSC RAS (Sochi, Maykop in Russia) represents one of the northernmost germplasm comprising a number of locally derived cultivars and ɣ-irradiation mutants. The latter are often characterized by larger genome size, which may lead to better adaptation to biotic and abiotic stress. Such genotypes may be a valuable genetic resource for better adaptability to extreme environmental conditions, which could enable tea cultivation outside global growing regions. Microsatellite markers are often the best choice for genetic diversity analysis in genebank collections. However, their use in polyploid species is questionable because simple sequence repeat (SSR) allele dosage cannot be readily determined. Therefore, the efficiency of SSR and start codon targeted (SCoT) markers was investigated using 43 selected cultivars from the Russian genebank collection derived from mutant breeding and clonal selection. Previously, the increase in genome size was confirmed in 18 mutants within this collection. Despite the presence of polyploid tea genotypes, our study revealed higher efficiency of SSR markers than SCoT markers. Subsequent SSR analysis of the 106 genotypes in the Russian genebank collection revealed three distinct genetic clusters after STRUCTURE analysis. Greater genetic variation was observed within genetic clusters than between clusters, indicating low genetic variation between collections. Nevertheless, the northernmost tea collection exhibited a greater genetic distance from the other two clusters than they did from each other. Close genetic relationships were found between many cultivars with particularly large leaves and mutant forms. Pearson's correlation analysis revealed a significant, moderate correlation between genome size and leaf area size. Our study shows that microsatellite fingerprinting is useful to estimate the genetic diversity and genetic background of tea germplasm in Russia despite polyploid tea accessions. Thus, the results of our study contribute to the development of future tea germplasm conservation strategies and modern tea breeding programs.

A first-generation haplotype map (HapMap-1) of tea (Camellia sinensis L. O. Kuntz)

MOTIVATION

Tea is a cross-pollinated woody perennial plant, which is why, application of conventional breeding is limited for its genetic improvement. However, lack of the genome-wide high-density SNP markers and genome-wide haplotype information has greatly hampered the utilization of tea genetic resources toward fast-track tea breeding programs. To address this challenge, we have generated a first-generation haplotype map of tea (Tea HapMap-1). Out-crossing and highly heterozygous nature of tea plants, make them more complicated for DNA-level variant discovery.

RESULTS

In this study, whole genome re-sequencing data of 369 tea genotypes were used to generate 2,334,564 biallelic SNPs and 1,447,985 InDels. Around 2928.04 million paired-end reads were used with an average mapping depth of ∼0.31× per accession. Identified polymorphic sites in this study will be useful in mapping the genomic regions responsible for important traits of tea. These resources lay the foundation for future research to understand the genetic diversity within tea germplasm and utilize genes that determine tea quality. This will further facilitate the understanding of tea genome evolution and tea metabolite pathways thus, offers an effective germplasm utilization for breeding the tea varieties.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Exploring the evolutionary characteristics between cultivated tea and its wild relatives using complete chloroplast genomes

Background

Cultivated tea is one of the most important economic and ecological trees distributed worldwide. Cultivated tea suffer from long-term targeted selection of traits and overexploitation of habitats by human beings, which may have changed its genetic structure. The chloroplast is an organelle with a conserved cyclic genomic structure, and it can help us better understand the evolutionary relationship of Camellia plants.

Results

We conducted comparative and evolutionary analyses on cultivated tea and wild tea, and we detected the evolutionary characteristics of cultivated tea. The chloroplast genome sizes of cultivated tea were slightly different, ranging from 157,025 to 157,100 bp. In addition, the cultivated species were more conserved than the wild species, in terms of the genome length, gene number, gene arrangement and GC content. However, comparing Camellia sinensis var. sinensis and Camellia sinensis var. assamica with their cultivars, the IR length variation was approximately 20 bp and 30 bp, respectively. The nucleotide diversity of 14 sequences in cultivated tea was higher than that in wild tea. Detailed analysis on the genomic variation and evolution of Camellia sinensis var. sinensis cultivars revealed 67 single nucleotide polymorphisms (SNPs), 46 insertions/deletions (indels), and 16 protein coding genes with nucleotide substitutions, while Camellia sinensis var. assamica cultivars revealed 4 indels. In cultivated tea, the most variable gene was ycf1. The largest number of nucleotide substitutions, five amino acids exhibited site-specific selection, and a 9 bp sequence insertion were found in the Camellia sinensis var. sinensis cultivars. In addition, phylogenetic relationship in the ycf1 tree suggested that the ycf1 gene has diverged in cultivated tea. Because C. sinensis var. sinensis and its cultivated species were not tightly clustered.

Conclusions

The cultivated species were more conserved than the wild species in terms of architecture and linear sequence order. The variation of the chloroplast genome in cultivated tea was mainly manifested in the nucleotide polymorphisms and sequence insertions. These results provided evidence regarding the influence of human activities on tea.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01800-1.

A functional molecular marker for detecting blister blight disease resistance in tea (Camellia sinensis L.)

Identification of an EST-SSR molecular marker associated with Blister blight, a common fungal disease of tea, facilitating marker-assisted selection, marking a milestone in tea molecular breeding. lister blight (BB) leaf disease of tea, caused by the fungus Exobasidium vexans, results in 25-30% crop loss annually. BB is presently controlled by Cu based fungicides, but genetic resistance is the most viable option in disease management. Tea is a naturally out-crossing, woody perennial necessitating a long time for completion of a breeding programme. Marker-assisted selection (MAS) is vital to expedite breeding programmes and also for better accuracy in gene identification. The aim of the current research was to derive marker-trait associations using an F₁ population segregating for BB. The population was genotyped at 11 expressed sequence tag simple sequence repeat loci followed by detecting the alleles by fragment analysis. The genotypic and phenotypic data were subjected to single-marker analysis resulting in the identification of EST-SSR073 as a diagnostic marker amplifying three alleles of the sizes, 168, 170 and 190 bp in F₁. Of them, alleles 190 and 168 bp were confirmed to concur BB resistance and susceptibility, respectively. The alleles were validated in a panel of 64 tea cultivars, resulting in the amplification of 12 alleles at EST-SSR073. The EST-SSR073 allele sequences matched with Camellia sinensis photosystem-I reaction center subunit-II. The marker EST-SSR073 can be effectively used in breeding tea against BB, recording a milestone in MAS in tea.

Accumulation of mutations in genes associated with sexual reproduction contributed to the domestication of a vegetatively propagated staple crop, enset

Enset (Ensete ventricosum (Welw.) Cheesman) is a drought tolerant, vegetatively propagated crop that was domesticated in Ethiopia. It is a staple food for more than 20 million people in Ethiopia. Despite its current importance and immense potential, enset is among the most genetically understudied and underexploited food crops. We collected 230 enset wild and cultivated accessions across the main enset producing regions in Ethiopia and applied amplified fragment length polymorphism (AFLP) and genotype by sequencing (GBS) analyses to these accessions. Wild and cultivated accessions were clearly separated from each other, with 89 genes found to harbour SNPs that separated wild from cultivated accessions. Among these, 17 genes are thought to be involved in flower initiation and seed development. Among cultivated accessions, differentiation was mostly associated with geographical location and with proximity to wild populations. Our results indicate that vegetative propagation of elite clones has favoured capacity for vegetative growth at the expense of capacity for sexual reproduction. This is consistent with previous reports that cultivated enset tends to produce non-viable seeds and flowers less frequently than wild enset.

Genome-wide identification of MADS-box gene family in sacred lotus (Nelumbo nucifera) identifies a SEPALLATA homolog gene involved in floral development

BACKGROUND

Sacred lotus (Nelumbo nucifera) is a vital perennial aquatic ornamental plant. Its flower shape determines the horticultural and ornamental values. However, the mechanisms underlying lotus flower development are still elusive. MADS-box transcription factors are crucial in various features of plant development, especially in floral organogenesis and specification. It is still unknown how the MADS-box transcription factors regulate the floral organogenesis in lotus.

RESULTS

To obtain a comprehensive insight into the functions of MADS-box genes in sacred lotus flower development, we systematically characterized members of this gene family based on the available genome information. A total of 44 MADS-box genes were identified, of which 16 type I and 28 type II genes were categorized based on the phylogenetic analysis. Furthermore, the structure of MADS-box genes and their expressional patterns were also systematically analyzed. Additionally, subcellular localization analysis showed that they are mainly localized in the nucleus, of which a SEPALLATA3 (SEP3) homolog NnMADS14 was proven to be involved in the floral organogenesis.

CONCLUSION

These results provide some fundamental information about the MADS-box gene family and their functions, which might be helpful in not only understanding the mechanisms of floral organogenesis but also breeding of high ornamental value cultivars in lotus.

Genetic diversity and population structure of Camellia huana (Theaceae), a limestone species with narrow geographic range, based on chloroplast DNA sequence and microsatellite markers

Camellia huana is an endangered species with a narrow distribution in limestone hills of northern Guangxi and southern Guizhou provinces, China. We used one chloroplast DNA (cpDNA) fragment and 12 pairs of microsatellite (simple sequence repeat; SSR) markers to assess the genetic diversity and structure of 12 C. huana populations. A total of 99 alleles were detected for 12 polymorphic loci, and eight haplotypes and nine polymorphic sites were detected within 5200 bp of cpDNA. C. huana populations showed a low level of genetic diversity (n = 8, Hd = 0.759, Pi = 0.00042 for cpDNA, N _A  = 3.931, H _E  = 0.466 for SSRs), but high genetic differentiation between populations (F _ST  = 0.2159 for SSRs, F _ST  = 0.9318 for cpDNA). This can be attributed to the narrow distribution and limestone habitat of C. huana. STRUCTURE analysis divided natural C. huana populations into two groups, consistent with their geographical distribution. Thus, we suggest that five natural C. huana populations should be split into two units to be managed effectively.

Population sequencing enhances understanding of tea plant evolution

Tea is an economically important plant characterized by a large genome, high heterozygosity, and high species diversity. In this study, we assemble a 3.26-Gb high-quality chromosome-scale genome for the 'Longjing 43' cultivar of Camellia sinensis var. sinensis. Genomic resequencing of 139 tea accessions from around the world is used to investigate the evolution and phylogenetic relationships of tea accessions. We find that hybridization has increased the heterozygosity and wide-ranging gene flow among tea populations with the spread of tea cultivation. Population genetic and transcriptomic analyses reveal that during domestication, selection for disease resistance and flavor in C. sinensis var. sinensis populations has been stronger than that in C. sinensis var. assamica populations. This study provides resources for marker-assisted breeding of tea and sets the foundation for further research on tea genetics and evolution.

Tea plant genomics: achievements, challenges and perspectives

Tea is among the world's most widely consumed non-alcoholic beverages and possesses enormous economic, health, and cultural values. It is produced from the cured leaves of tea plants, which are important evergreen crops globally cultivated in over 50 countries. Along with recent innovations and advances in biotechnologies, great progress in tea plant genomics and genetics has been achieved, which has facilitated our understanding of the molecular mechanisms of tea quality and the evolution of the tea plant genome. In this review, we briefly summarize the achievements of the past two decades, which primarily include diverse genome and transcriptome sequencing projects, gene discovery and regulation studies, investigation of the epigenetics and noncoding RNAs, origin and domestication, phylogenetics and germplasm utilization of tea plant as well as newly developed tools/platforms. We also present perspectives and possible challenges for future functional genomic studies that will contribute to the acceleration of breeding programs in tea plants.

Genetic diversity, linkage disequilibrium, and population structure analysis of the tea plant (Camellia sinensis) from an origin center, Guizhou plateau, using genome-wide SNPs developed by genotyping-by-sequencing

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.

Differences in chemical composition predictive of in vitro biological activity among commercially important cultivars of genus Camellia

Leaves of plants from the genus Camellia (CAM) are used to make tea; however, there are limited data that compares chemical composition and biological activity of CAM cultivars used to make six tea types. Fourteen CAM cultivars were analyzed by HPLC and UPLC-Q-TOF-MS/MS and biological activity was assessed in a cell growth assay. Tea bioactives and cell growth inhibition varied 2-4 fold. EGCG was the dominant catechin that predicted the magnitude of growth inhibition. However, pure EGCG did not fully account for inhibitory activity suggesting that it may serve as a chemical marker for bioefficacy. As an unbiased characterization of differences in chemical composition among CAM, individual metabolomes were determined and used to generate principle components (PC). PC's from the metabolome were complementary to those from targeted analyses of tea bioactives and were predictive of growth inhibition. This study provides a frame work for identifying CAM cultivars with beneficial traits.

Complete chloroplast genome of Camellia japonica genome structures, comparative and phylogenetic analysis

Camellia is an economically, ecologically and phylogenetically valuable genus in the family Theaceae. The frequent interspecific hybridization and polyploidization makes this genus phylogenetically and taxonomically under controversial and require detailed investigation. Chloroplast (cp) genome sequences have been used for cpDNA marker development and genetic diversity evaluation. Our research newly sequenced the chloroplast genome of Camellia japonica using Illumina HiSeq X Ten platform, and retrieved five other chloroplast genomes of Camellia previously published for comparative analyses, thereby shedding lights on a deeper understanding of the applicability of chloroplast information. The chloroplast genome sizes ranged in length from 156,607 to 157,166 bp, and their gene structure resembled those of other higher plants. There were four categories of SSRs detected in six Camellia cpDNA sequences, with the lengths ranging from 10 to 17bp. The Camellia species exhibited different evolutionary routes that lhbA and orf188, followed by orf42 and psbZ, were readily lost during evolution. Obvious codon preferences were also shown in almost all protein-coding cpDNA and amino acid sequences. Selection pressure analysis revealed the influence of different environmental pressures on different Camellia chloroplast genomes during long-term evolution. All Camellia species, except C. crapnelliana, presented the identical rate of amplification in the IR region. The datasets obtained from the chloroplast genomes are highly supportive in inferring the phylogenetic relationships of the Camellia taxa, indicating that chloroplast genome can be used for classifying interspecific relationships in this genus.

Conservation impacts of commercial cultivation of endangered and overharvested plants

Overharvesting is one of the greatest threats to species survival. Farming overharvested species is a conservation strategy that can meet growing market demand and conserve wild populations of the target species. This strategy is compatible with the international community's desire to uphold the right of local communities to use biological resources to support their livelihoods. However, studies investigating whether farming can alleviate poaching pressure have focused almost exclusively on animals. To address the shortfall in plant-focused studies, we compiled information on commercial cultivation of threatened plants to assess its conservation benefits. Because China's rising middle class has rapidly intensified demand for wildlife products, we searched the scientific literature published in Chinese (China National Knowledge Infrastructure and Baidu) and in English. We found 32 reports that contained data on 193 internationally or nationally threatened plant species that were under commercial cultivation. These reports showed that cultivations of 82% of the 193 species were sustained by collecting whole plants from the wild periodically or continuously. Although based on a small sample size, species that were maintained in cultivation only through artificial propagation or seeds collected in the wild were likely associated with a reported reduction in wild harvesting of whole plants. Even so, results of correlation analyses suggested that production system, scale, and when a species began being cultivated had little effect on conservation status of the species, either globally or in China. However, species brought into cultivation relatively recently and on a smaller scale were more likely to have undergone a reduction in collecting pressure. Farming of nonmedicinal plants was most problematic for species conservation because wild plants were laundered (i.e., sold as cultivated plants). For effective conservation, policy to guide cultivation operations based on the target species' biological characteristics, cultural significance, market demand, and conservation status is needed.

The western Mediterranean region provided the founder population of domesticated narrow-leafed lupin

This study revealed that the western Mediterranean provided the founder population for domesticated narrow-leafed lupin and that genetic diversity decreased significantly during narrow-leafed lupin domestication. The evolutionary history of plants during domestication profoundly shaped the genome structure and genetic diversity of today's crops. Advances in next-generation sequencing technologies allow unprecedented opportunities to understand genome evolution in minor crops, which constitute the majority of plant domestications. A diverse set of 231 wild and domesticated narrow-leafed lupin (Lupinus angustifolius L.) accessions were subjected to genotyping-by-sequencing using diversity arrays technology. Phylogenetic, genome-wide divergence and linkage disequilibrium analyses were applied to identify the founder population of domesticated narrow-leafed lupin and the genome-wide effect of domestication on its genome. We found wild western Mediterranean population as the founder of domesticated narrow-leafed lupin. Domestication was associated with an almost threefold reduction in genome diversity in domesticated accessions compared to their wild relatives. Selective sweep analysis identified no significant footprints of selection around domestication loci. A genome-wide association study identified single nucleotide polymorphism markers associated with pod dehiscence. This new understanding of the genomic consequences of narrow-leafed lupin domestication along with molecular marker tools developed here will assist plant breeders more effectively access wild genetic diversity for crop improvement.

Next Generation Sequencing-Based Molecular Marker Development: A Case Study in Betula Alnoides

Betula alnoides is a fast-growing valuable indigenous tree species with multiple uses in the tropical and warm subtropical regions in South-East Asia and southern China. It has been proved to be tetraploid in most parts of its distribution in China. In the present study, next generation sequencing (NGS) technology was applied to develop numerous SSR markers for B. alnoides, and 64,376 contig sequences of 106,452 clean reads containing 164,357 candidate SSR loci were obtained. Among the derived SSR repeats, mono-nucleotide was the main type (77.05%), followed by di- (10.18%), tetra- (6.12%), tri- (3.56%), penta- (2.14%) and hexa-nucleotide (0.95%). The short nucleotide sequence repeats accounted for 90.79%. Among the 291 repeat motifs, AG/CT (46.33%) and AT/AT (44.15%) were the most common di-nucleotide repeats, while AAT/ATT (48.98%) was the most common tri-nucleotide repeats. A total of 2549 primer sets were designed from the identified putative SSR regions of which 900 were randomly selected for evaluation of amplification successfulness and detection of polymorphism if amplified successfully. Three hundred and ten polymorphic markers were obtained through testing with 24 individuals from B. alnoides natural forest in Jingxi County, Guangxi, China. The number of alleles (NA) of each marker ranged from 2 to 19 with a mean of 5.14. The observed (HO) and expected (HE) heterozygosities varied from 0.04 to 1.00 and 0.04 to 0.92 with their means being 0.64 and 0.57, respectively. Shannon-Wiener diversity index (I) ranged from 0.10 to 2.68 with a mean of 1.12. Cross-species transferability was further examined for 96 pairs of SSR primers randomly selected, and it was found that 48.96⁻84.38% of the primer pairs could successfully amplify each of six related Betula species. The obtained SSR markers can be used to study population genetics and molecular marker assisted breeding, particularly genome-wide association study of these species in the future.

Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in Plants

Microsatellites, or simple sequence repeats (SSRs), are one of the most informative and multi-purpose genetic markers exploited in plant functional genomics. However, the discovery of SSRs and development using traditional methods are laborious, time-consuming, and costly. Recently, the availability of high-throughput sequencing technologies has enabled researchers to identify a substantial number of microsatellites at less cost and effort than traditional approaches. Illumina is a noteworthy transcriptome sequencing technology that is currently used in SSR marker development. Although 454 pyrosequencing datasets can be used for SSR development, this type of sequencing is no longer supported. This review aims to present an overview of the next generation sequencing, with a focus on the efficient use of de novo transcriptome sequencing (RNA-Seq) and related tools for mining and development of microsatellites in plants.

Domestication Origin and Breeding History of the Tea Plant (Camellia sinensis) in China and India Based on Nuclear Microsatellites and cpDNA Sequence Data

Although China and India are the two largest tea-producing countries, the domestication origin and breeding history of the tea plant in these two countries remain unclear. Our previous study suggested that the tea plant includes three distinct lineages (China type tea, Chinese Assam type tea and Indian Assam type tea), which were independently domesticated in China and India, respectively. To determine the origin and historical timeline of tea domestication in these two countries we used a combination of 23 nSSRs (402 samples) and three cpDNA regions (101 samples) to genotype domesticated tea plants and its wild relative. Based on a combination of demographic modeling, NewHybrids and Neighbour joining tree analyses, three independent domestication centers were found. In addition, two origins of Chinese Assam type tea were detected: Southern and Western Yunnan of China. Results from demographic modeling suggested that China type tea and Assam type tea first diverged 22,000 year ago during the last glacial maximum and subsequently split into the Chinese Assam type tea and Indian Assam type tea lineages 2770 year ago, corresponding well with the early record of tea usage in Yunnan, China. Furthermore, we found that the three tea types underwent different breeding histories where hybridization appears to have been the most important approach for tea cultivar breeding and improvements: a high proportion of the hybrid lineages were found to be F2 and BCs. Collectively, our results underscore the necessity for the conservation of Chinese Assam type tea germplasm and landraces as a valuable resource for future tea breeding.

Genetic diversity, population structure, and traditional culture of Camellia reticulata

Camellia reticulata is an arbor tree that has been cultivated in southwestern China by various sociolinguistic groups for esthetic purposes as well as to derive an edible seed oil. This study examined the influence of management, socio‐economic factors, and religion on the genetic diversity patterns of Camellia reticulata utilizing a combination of ethnobotanical and molecular genetic approaches. Semi‐structured interviews and key informant interviews were carried out with local communities in China's Yunnan Province. We collected plant material (n = 190 individuals) from five populations at study sites using single‐dose AFLP markers in order to access the genetic diversity within and between populations. A total of 387 DNA fragments were produced by four AFLP primer sets. All DNA fragments were found to be polymorphic (100%). A relatively high level of genetic diversity was revealed in C. reticulata samples at both the species (H_sp = 0.3397, I_sp = 0.5236) and population (percentage of polymorphic loci = 85.63%, H_pop = 0.2937, I_pop = 0.4421) levels. Findings further revealed a relatively high degree of genetic diversity within C. reticulata populations (Analysis of Molecular Variance = 96.31%). The higher genetic diversity within populations than among populations of C. reticulata from different geographies is likely due to the cultural and social influences associated with its long cultivation history for esthetic and culinary purposes by diverse sociolinguistic groups. This study highlights the influence of human management, socio‐economic factors, and other cultural variables on the genetic and morphological diversity of C. reticulata at a regional level. Findings emphasize the important role of traditional culture on the conservation and utilization of plant genetic diversity.

Indications for Three Independent Domestication Events for the Tea Plant (Camellia sinensis (L.) O. Kuntze) and New Insights into the Origin of Tea Germplasm in China and India Revealed by Nuclear Microsatellites

Background

Tea is the world’s most popular non-alcoholic beverage. China and India are known to be the largest tea producing countries and recognized as the centers for the domestication of the tea plant (Camellia sinensis (L.) O. Kuntze). However, molecular studies on the origin, domestication and relationships of the main teas, China type, Assam type and Cambod type are lacking.

Methodology/Principal Findings

Twenty-three nuclear microsatellite markers were used to investigate the genetic diversity, relatedness, and domestication history of cultivated tea in both China and India. Based on a total of 392 samples, high levels of genetic diversity were observed for all tea types in both countries. The cultivars clustered into three distinct genetic groups (i.e. China tea, Chinese Assam tea and Indian Assam tea) based on STRUCTURE, PCoA and UPGMA analyses with significant pairwise genetic differentiation, corresponding well with their geographical distribution. A high proportion (30%) of the studied tea samples were shown to possess genetic admixtures of different tea types suggesting a hybrid origin for these samples, including the Cambod type.

Conclusions

We demonstrate that Chinese Assam tea is a distinct genetic lineage from Indian Assam tea, and that China tea sampled from India was likely introduced from China directly. Our results further indicate that China type tea, Chinese Assam type tea and Indian Assam type tea are likely the result of three independent domestication events from three separate regions across China and India. Our findings have important implications for the conservation of genetic stocks, as well as future breeding programs.

Principles of Biomedical Agriculture Applied to the Plant Family Theaceae To Identify Novel Interventions for Cancer Prevention and Control

Plant materials from the family Theaceae have been used for over a thousand years as integral components within the food systems of many globally distributed cultures and to treat a variety of human ailments. These markedly different uses remain of considerable interest in the 21st century. This perspective draws heavily from the agricultural and biomedical literature published using plant materials from the genus Camellia. Our objective is to provide a rationale and framework for broadening the scope of investigation of genera and species within Theaceae beyond Camellia sinensis to accelerate the development of a new generation of Theaceae-based pharmaceuticals/nutraceuticals and the more general enhancement of the food supply with Theaceae-containing products that affect the development of chronic diseases such as cancer. This will require a concerted effort to systematically capitalize on the rapidly growing knowledge of germplasm resources within Theaceae using metabolomic profiling in combination with in vivo and in vitro approaches. The successful translation of this research into products that affect human health will be facilitated by recognition of the agronomic factors that are critical in making hot water infusions generically referred to as tea as well as food products containing ground leaf powders.

A Bird's-Eye View of Molecular Changes in Plant Gravitropism Using Omics Techniques

During evolution, plants have developed mechanisms to adapt to a variety of environmental stresses, including drought, high salinity, changes in carbon dioxide levels and pathogens. Central signaling hubs and pathways that are regulated in response to these stimuli have been identified. In contrast to these well studied environmental stimuli, changes in transcript, protein and metabolite levels in response to a gravitational stimulus are less well understood. Amyloplasts, localized in statocytes of the root tip, in mesophyll cells of coleoptiles and in the elongation zone of the growing internodes comprise statoliths in higher plants. Deviations of the statocytes with respect to the earthly gravity vector lead to a displacement of statoliths relative to the cell due to their inertia and thus to gravity perception. Downstream signaling events, including the conversion from the biophysical signal of sedimentation of distinct heavy mass to a biochemical signal, however, remain elusive. More recently, technical advances, including clinostats, drop towers, parabolic flights, satellites, and the International Space Station, allowed researchers to study the effect of altered gravity conditions - real and simulated micro- as well as hypergravity on plants. This allows for a unique opportunity to study plant responses to a purely anthropogenic stress for which no evolutionary program exists. Furthermore, the requirement for plants as food and oxygen sources during prolonged manned space explorations led to an increased interest in the identi-fication of genes involved in the adaptation of plants to microgravity. Transcriptomic, proteomic, phosphoproteomic, and metabolomic profiling strategies provide a sensitive high-throughput approach to identify biochemical alterations in response to changes with respect to the influence of the gravitational vector and thus the acting gravitational force on the transcript, protein and metabolite level. This review aims at summarizing recent experimental approaches and discusses major observations.

Genetic diversity and population structure of an important wild berry crop

The success of plant breeding in the coming years will be associated with access to new sources of variation, which will include landraces and wild relatives of crop species. In order to access the reservoir of favourable alleles within wild germplasm, knowledge about the genetic diversity and the population structure of wild species is needed. Bilberry (Vaccinium myrtillus) is one of the most important wild crops growing in the forests of Northern European countries, noted for its nutritional properties and its beneficial effects on human health. Assessment of the genetic diversity of wild bilberry germplasm is needed for efforts such as in situ conservation, on-farm management and development of plant breeding programmes. However, to date, only a few local (small-scale) genetic studies of this species have been performed. We therefore conducted a study of genetic variability within 32 individual samples collected from different locations in Iceland, Norway, Sweden, Finland and Germany, and analysed genetic diversity among geographic groups. Four selected inter-simple sequence repeat primers allowed the amplification of 127 polymorphic loci which, based on analysis of variance, made it possible to identify 85 % of the genetic diversity within studied bilberry populations, being in agreement with the mixed-mating system of bilberry. Significant correlations were obtained between geographic and genetic distances for the entire set of samples. The analyses also highlighted the presence of a north-south genetic gradient, which is in accordance with recent findings on phenotypic traits of bilberry.

Genome-Wide Identification of Genes Probably Relevant to the Uniqueness of Tea Plant (Camellia sinensis) and Its Cultivars

Tea (Camellia sinensis) is a popular beverage all over the world and a number of studies have focused on the genetic uniqueness of tea and its cultivars. However, molecular mechanisms underlying these phenomena are largely undefined. In this report, based on expression data available from public databases, we performed a series of analyses to identify genes probably relevant to the uniqueness of C. sinensis and two of its cultivars (LJ43 and ZH2). Evolutionary analyses showed that the evolutionary rates of genes involved in the pathways were not significantly different among C. sinensis, C. oleifera, and C. azalea. Interestingly, a number of gene families, including genes involved in the pathways synthesizing iconic secondary metabolites of tea plant, were significantly upregulated, expressed in C. sinensis (LJ43) when compared to C. azalea, and this may partially explain its higher content of flavonoid, theanine, and caffeine. Further investigation showed that nonsynonymous mutations may partially contribute to the differences between the two cultivars of C. sinensis, such as the chlorina and higher contents of amino acids in ZH2. Genes identified as candidates are probably relevant to the uniqueness of C. sinensis and its cultivars should be good candidates for subsequent functional analyses and marker-assisted breeding.

De novo assembly and transcriptome characterization: novel insights into catechins biosynthesis in Camellia sinensis

BACKGROUND

Tea is a popular natural non-alcoholic beverage consumed worldwide due to its bioactive ingredients, particularly catechins (flavan-3-ols). Catechins not only contribute to tea quality but also serve important functions in the anti-stress regulation of secondary metabolic pathways. However, the percentages of various catechins are different among tea plant [Camellia sinensis (L.) O. Kuntze] cultivars. This study aimed to elucidate the biosynthetic mechanism of catechins. Transcriptomes from leaf tissues of four tea plant cultivars, 'Yunnanshilixiang', 'Chawansanhao', 'Ruchengmaoyecha', and 'Anjibaicha', were sequenced using the high-throughput sequencing platform Illumina HiSeq™ 2000. De novo assemble were also performed. Catechins contents were measured through reversed-phase high-performance liquid chromatography (RP-HPLC), and the biosynthetic pathway was also surveyed.

RESULTS

We constructed a unified unigene database. A total of 146,342 pairs of putative orthologs from the four tea plant cultivars, 'Yunnanshilixiang', 'Chawansanhao', 'Ruchengmaoyecha', and 'Anjibaicha' were generated. Approximately 68,890 unigenes (47.1%) were aligned to the sequences of seven public databases with a cut-off E-value of 1E-5. A total of 217 differentially expressed genes were found through RPKM values, and 150 unigenes were assigned to the flavonoid biosynthetic pathway using the integrated function annotation. The (-)-EGC and (-)-EC contents were significantly lower and the (+)-GC and (+)-C contents were abnormally higher in 'Ruchengmaoyecha' than in 'Yunnanshilixiang', 'Chawansanhao', and 'Anjibaicha'. The proportion of catechins was confirmed by selecting critical genes (ANS, ANR, and LAR) for qRT-PCR analysis.

CONCLUSIONS

This study provided a global survey of transcriptomes from four tea plant cultivars and serves as an available resource of genetic diversity. The analyses of transcriptome profiles and physiological indicators not only identified the putative genes involved in the flavonoid biosynthetic pathway but also provided some novel insights for the mechanisms of catechins biosynthesis.

Varietal identification of tea (Camellia sinensis) using nanofluidic array of single nucleotide polymorphism (SNP) markers

Apart from water, tea is the world's most widely consumed beverage. Tea is produced in more than 50 countries with an annual production of approximately 4.7 million tons. The market segment for specialty tea has been expanding rapidly owing to increased demand, resulting in higher revenues and profits for tea growers and the industry. Accurate varietal identification is critically important to ensure traceability and authentication of premium tea products, which in turn contribute to on-farm conservation of tea genetic diversity. Using a set of single nucleotide polymorphism (SNP) markers developed from the expressed sequence tag (EST) database of Camilla senensis, we genotyped deoxyribonucleic acid (DNA) samples extracted from a diverse group of tea varieties, including both fresh and processed commercial loose-leaf teas. The validation led to the designation of 60 SNPs that unambiguously identified all 40 tested tea varieties with high statistical rigor (p<0.0001). Varietal authenticity and genetic relationships among the analyzed cultivars were further characterized by ordination and Bayesian clustering analysis. These SNP markers, in combination with a high-throughput genotyping protocol, effectively established and verified specific DNA fingerprints for all tested tea varieties. This method provides a powerful tool for variety authentication and quality control for the tea industry. It is also highly useful for the management of tea genetic resources and breeding, where accurate and efficient genotype identification is essential.