Analyses of single nucleotide polymorphisms identified by ddRAD-seq reveal genetic structure of tea germplasm and Japanese landraces for tea breeding

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

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

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.

Genome-wide SNPs of vegetable leafminer, Liriomyza sativae: Insights into the recent Australian invasion

Liriomyza sativae, the vegetable leafminer, is an important agricultural pest originally from the Americas, which has now colonized all continents except Antarctica. In 2015, L. sativae arrived on the Australian mainland and established on the Cape York Peninsula in the northeast of the country near the Torres Strait, which provides a possible pathway for pests to enter Australia and evade biosecurity efforts. Here, we assessed genetic variation in L. sativae based on genome-wide single nucleotide polymorphisms (SNPs) generated by double digest restriction-site-associated DNA sequencing (ddRAD-seq), aiming to uncover the potential origin(s) of this pest in Australia and contribute to reconstructing its global invasion history. Our fineRADstructure results and principal component analysis suggest Australian mainland populations were genetically close to populations from the Torres Strait, whereas populations from Asia, Africa, and Papua New Guinea (PNG) were more distantly related. Hawaiian populations were genetically distinct from all other populations of L. sativae included in our study. Admixture analyses further revealed that L. sativae from the Torres Strait may have genetic variation originating from multiple sources including Indonesia and PNG, and which has now spread to the Australian mainland. The L. sativae lineages from Asia and Africa appear closely related. Isolation-by-distance (IBD) was found at a broad global scale, but not within small regions, suggesting that human-mediated factors likely contribute to the local spread of this pest. Overall, our findings suggest that an exotic Liriomyza pest invaded Australia through the Indo-Papuan conduit, highlighting the importance of biosecurity programs aimed at restricting the movement of pests and diseases through this corridor.

Genetic diversity and structure of Rhododendron meddianum, a plant species with extremely small populations

Rhododendron meddianum is a critically endangered species with important ornamental value and is also a plant species with extremely small populations. In this study, we used double digest restriction-site-associated DNA sequencing (ddRAD) technology to assess the genetic diversity, genetic structure and demographic history of the three extant populations of R. meddianum. Analysis of SNPs indicated that R. meddianum populations have a high genetic diversity (π = 0.0772 ± 0.0024, H _E  = 0.0742 ± 0.002). Both F _ST values (0.1582-0.2388) and AMOVA showed a moderate genetic differentiation among the R. meddianum populations. Meanwhile, STRUCTURE, PCoA and NJ trees indicated that the R. meddianum samples were clustered into three distinct genetic groups. Using the stairway plot, we found that R. meddianum underwent a population bottleneck about 70,000 years ago. Furthermore, demographic models of R. meddianum and its relative, Rhododendron cyanocarpum, revealed that these species diverged about 3.05 (2.21-5.03) million years ago. This divergence may have been caused by environmental changes that occurred after the late Pliocene, e.g., the Asian winter monsoon intensified, leading to a drier climate. Based on these findings, we recommend that R. meddianum be conserved through in situ, ex situ approaches and that its seeds be collected for germplasm.

Tissue-Dependent Variation Profiles of Tea Quality-Related Metabolites in New Shoots of Tea Accessions

Several metabolites define tea quality in new tea shoots composed of leaf and stem. To improve tea quality for breeding, it is important to understand the tissue-dependent genetic mechanisms and metabolic network responsible for the profile of tea quality-related metabolites. We analyzed the volatiles and specialized metabolites as the tea quality-related metabolites in leaves and stems of new shoots in 30 tea accessions to understand the tissue variation and network between tea quality-related metabolites. Our results provided the tissue-dependent variation network in the tea quality-related metabolites, including volatiles in new leaves and stems in tea accessions. Each volatile content in tea accessions showed the coefficient of variation ranging from 58.7 to 221.9% and 54.2 to 318.3% in new leaves and new stems, respectively. The accumulation pattern of tea quality-related metabolites in new leaves and stems varied depending on the accession. When comparing tea genetic populations, the profile of tea quality-related metabolites of new leaves, but not new stems, was the key to distinguishing tea genetic populations by chemical indicators. We described the network between tea quality-related metabolites, especially the dense network in new leaves. These results also will provide the key information for metabolic engineering and the selection of breeding materials in tea plants based on the tea quality-related metabolites and aid in understanding their molecular mechanisms and network of metabolic variation.

Genome-wide SNP discovery from Darjeeling tea cultivars - their functional impacts and application toward population structure and trait associations

Genotyping by sequencing and identification of functionally relevant nucleotide variations in crop accessions are the key steps to unravel genetic control of desirable traits. Elite cultivars of Darjeeling tea were undergone SNP genotyping by double-digest restriction-site associated DNA sequencing method. This study reports a set of 54,206 high-quality SNP markers discovered from ~10.4 GB sequence data, encompassing 15 chromosomes of the reference tea genome. Genetic relatedness among the accessions conforms to the analyses of Bayesian clustering, UPGMA, and PCoA methods. Genomic positions of the discovered SNPs and their putative effect on annotated genes designated a thoughtful understanding of their functional aspects in tea system biology. A group of 95 genes was identified to be affected by high impact variants. Genome-wide association analyses of 21 agronomic and biochemical phenotypes resulted in trait-linked polymorphic loci with strong confidence (p < 0.05 and 0.001).

Genomic predictions and genome-wide association studies based on RAD-seq of quality-related metabolites for the genomics-assisted breeding of tea plants

Effectively using genomic information greatly accelerates conventional breeding and applying it to long-lived crops promotes the conversion to genomic breeding. Because tea plants are bred using conventional methods, we evaluated the potential of genomic predictions (GPs) and genome-wide association studies (GWASs) for the genetic breeding of tea quality-related metabolites using genome-wide single nucleotide polymorphisms (SNPs) detected from restriction site-associated DNA sequencing of 150 tea accessions. The present GP, based on genome-wide SNPs, and six models produced moderate prediction accuracy values (r) for the levels of most catechins, represented by ( -)-epigallocatechin gallate (r = 0.32-0.41) and caffeine (r = 0.44-0.51), but low r values for free amino acids and chlorophylls. Integrated analysis of GWAS and GP detected potential candidate genes for each metabolite using 80-160 top-ranked SNPs that resulted in the maximum cumulative prediction value. Applying GPs and GWASs to tea accession traits will contribute to genomics-assisted tea breeding.

Exploring plant metabolic genomics: chemical diversity, metabolic complexity in the biosynthesis and transport of specialized metabolites with the tea plant as a model

The diversity and complexity of secondary metabolites in tea plants contribute substantially to the popularity of tea, by determining tea flavors and their numerous health benefits. The most significant characteristics of tea plants are that they concentrate the complex plant secondary metabolites into one leaf: flavonoids, alkaloids, theanine, volatiles, and saponins. Many fundamental questions regarding tea plant secondary metabolism remain unanswered. This includes how tea plants accumulate high levels of monomeric galloylated catechins, unlike the polymerized flavan-3-ols in most other plants, as well as how they are evolved to selectively synthesize theanine and caffeine, and how tea plants properly transport and store these cytotoxic products and then reuse them in defense. Tea plants coordinate many metabolic pathways that simultaneously take place in young tea leaves in response to both developmental and environmental cues. With the available genome sequences of tea plants and high-throughput metabolomic tools as great platforms, it is of particular interest to launch metabolic genomics studies using tea plants as a model system. Plant metabolic genomics are to investigate all aspects of plant secondary metabolism at the genetic, genome, and molecular levels. This includes plant domestication and adaptation, divergence and convergence of secondary metaboloic pathways. The biosynthesis, transport, storage, and transcriptional regulation mechanisms of all metabolites are of core interest in the plant as a whole. This review highlights relevant contexts of metabolic genomics, outstanding questions, and strategies for answering them, with aim to guide future research for genetic improvement of nutrition quality for healthier plant foods.

Screening Tea Cultivars for Novel Climates: Plant Growth and Leaf Quality of Camellia sinensis Cultivars Grown in Mississippi, United States

The United States (U.S.) consumed over 80 billion servings of tea, approximately 3.8 billion gallons, in the year of 2018. With the vast majority of tea demand being met by importation, the United States became the third largest tea importer worldwide after Russia and Pakistan. As demand for domestically produced tea increases and growers expressing increasing interest in growing and producing tea, tea production became an emerging industry in the United States. Compared to major tea producing countries with centuries of growing history, tea production in the United States is limited and requires research support in many aspect of tea production including selecting suitable cultivars adapted to local climatic conditions. This study evaluated nine tea cultivars, including 'BL1,' 'BL2,' 'Black Sea,' 'Christine's Choice,' 'Dave's Fave,' 'Large Leaf,' 'Small Leaf,' 'Sochi,' and 'var. assamica,' for plant growth, leaf morphological characteristics, cold tolerance, and leaf biochemical compositions when grown in Mississippi United States with a subtropical climate. The nine tested cultivars had varying plant growth indices (PGI) and varying degrees of cold tolerance to freezing temperatures in winter, but resumed healthy growth the following spring. 'BL2' showed the highest PGI of 104.53 cm by February 2019, which might be helpful toward suppressing weed and early establishment of tea plantation. The nine cultivars also showed varying leaf characteristics in terms of leaf length, width, area, fresh and dry weights, and new shoot weight. There existed a diversity in leaf biochemical composition including soluble solids, carbohydrates, total polyphenols (TP), free amino acids (AA), L-theanine and caffeine among the nine cultivars and among different harvesting seasons of spring, summer, and fall within a certain cultivar. The nine cultivars in this study generally grow well in local environment. All tea samples collected from nine cultivars and three seasons were considered suitable for green tea processing with low TP/AA ratios ranging from 1.72 to 3.71 in this study.