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

Genomic DNA barcodes provide novel insights into species delimitation in the complex Camellia sect. Thea (Theaceae)

BACKGROUND

Species delimitation within Camellia sect. Thea is taxonomically challenging due to its complex evolutionary history. This study aims to utilize nuclear and chloroplast data as genomic DNA barcodes to delimit species within this economically important group of plants.

RESULTS

Whole genome sequencing (WGS) data were obtained for 98 accessions representing all but one species in C. sect. Thea. Based on 759 high-quality SCNs, 98 whole chloroplast genomes, and by using 2× coverage clean reads from WGS for Skmer analyses, we found that combining the findings from these three data sets resulted in nearly complete species delimitation and resolution of all interspecific relationships within C. sect. Thea. We also found support for the taxonomic elevation of two varieties (C. sinensis var. assamica and C. tachangensis var. remotiserrata) to species status (C. assamica and C. remotiserrata, respectively). Furthermore, we confirmed that C. formosensis represents a distinct species. Gene tree discordances, chloroplast-nuclear conflicts and complex network-like phylogenetic relationships were observed in C. sect. Thea.

CONCLUSION

Compared with the use of single parentally inherited chloroplast data sources, utilizing both uniparentally inherited chloroplast data and biparentally inherited nuclear data improved the species delimitation of taxa within C. sect. Thea. The intricate phylogenetic relationships observed are likely a result of widespread past hybridization and chloroplast capture events among species within this group, which may have blurred the species boundaries. Our novel approach to species delimitation within C. sect. Thea may serve as a blueprint for employing genomic DNA barcodes in other taxa with complex histories, and will significantly contribute to the conservation of cultivated tea plant species and their wild relatives.

Next-generation sequencing-based population genetics unravels the evolutionary history of Rhodomyrtus tomentosa in China

BACKGROUND

Rhodomyrtus tomentosa (Ait.) Hassk. is useful for its ornamental, medicinal, and ecological characteristics, and is considered a "Neglected and Underutilized Crop Species". However, our understanding of the geographic structure and evolutionary history of its wild populations is limited. To address this gap, we investigated genomic data from 284 samples of R. tomentosa from 28 wild populations in southern China.

RESULTS

The genetic diversity of populations in different regions revealed the similar trends using whole-genome and RAD-seq data, and Hainan Island having a higher genetic diversity than other regions. The 28 populations clustered into three distinct groups: (a) GROUP1 on the eastern mainland within Guangdong, Fujian, and Hunan Provinces; (b) GROUP2 on the western mainland within Guangxi and Yunnan Provinces; and (c) GROUP3 on Hainan Island. Mantel tests and redundancy analyses revealed population differentiation was affected by distance and environmental factors such as annual average radiation. Demographic history and gene flow analyses indicated the mainland populations and the Hainan Island populations diverged around 0.93 MYA, with gene flow primarily occurring from Hainan Island and the coastal regions (such as Zhanjiang in Guangdong and Fangchenggang in Guangxi) towards the mainland, reflecting an expansion trend within the species. PSMC' analyses indicated that the populations of the three groups underwent a bottleneck during the Pleistocene due to glacial-interglacial cycles and geological events. Niche analysis revealed that the ice ages caused habitat contraction for the species, and populations with higher genetic diversity are generally distributed in areas with more suitable habitats.

CONCLUSIONS

This study elucidates the current genetic distribution of the species within China and suggests that drastic Pleistocene climate change and geographical events caused population divergence and fluctuations in effective population size, shaping the current genetic distribution of R. tomentosa. These findings provide a theoretical basis for the genetic conservation and improvement of R. tomentosa.

Tea cultivation: facilitating soil organic carbon accumulation and altering soil bacterial community-Leishan County, Guizhou Province, Southwest China

Background

Camellia sinensis is an important cash crop in southwestern China, with soil organic carbon playing a vital role in soil fertility, and microorganisms contributing significantly to nutrient cycling, thus both of them influencing tea tree growth and development. However, existing studies primarily focus on soil organic carbon, neglecting carbon fractions, and the relationship between soil organic carbon fractions and microbial communities is unclear. Consequently, this study aims to clarify the impact of different tea planting durations on soil organic carbon fractions and microbial communities and identify the main factors influencing microbial communities. It provides a theoretical basis for soil quality evaluation in the study area and scientific guidance for tea plantation management, thus fostering the region's economic sustainability.

Methods

This study selected tea plantations with different tea planting durations of 3-5 years (Y5), 12-16 years (Y15), 18-22 years (Y20), 40-42 years (Y40), and 48-50 years (Y50), as research subjects and adjacent uncultivated forest without a history of tea planting (CK) served as controls. Soil organic carbon (SOC), particulate organic carbon (POC), easily oxidizable organic carbon (EOC), dissolved organic carbon (DOC), microbial biomass carbon (MBC), and bacterial diversity were measured in the 0-20 cm and 20-40 cm soil layers, respectively.

Results

Compared to the adjacent uncultivated forest (CK), the soil organic carbon (SOC), easily oxidizable carbon (EOC), particulate organic carbon (POC), and dissolved organic carbon (DOC) contents in a 40-year tea plantation significantly increased. Nonetheless, the microbial biomass carbon (MBC) content notably decreased. POC/SOC ratios rose with prolonged planting, signifying enhanced conversion of organic carbon into particulate forms. Bacterial community diversity peaked at 15 years and declined by 40 years post-planting and after tea planting dominated by Acidobacteriota, Chloroflexi, Proteobacteria, and Actinobacteriota in the tea garden. FAPROTAX analysis highlighted aerobic and anaerobic chemoheterotrophy, cellulolysis, and nitrogen fixation as key bacterial functions. POC and MBC significantly influenced bacterial community structure. In conclusion, tea plantation soil exhibited the highest organic carbon content at 40 years of tea planting, indicating strong carbon accumulation capacity. However, soil acidification in the tea plantation may affect changes in organic carbon and bacterial community. Therefore, in the tea planting process, it is necessary to improve the management system of tea plantations to ensure the maintenance of a good ecological environment in the tea plantation soil, thus achieving sustainable development of the tea industry in the region.

Genetic diversity and structure of Persicaria amphibia (Polygonaceae) in South Korea using genotyping by sequencing

BACKGROUND

Persicaria amphibia, a member of the Polygonaceae family, exists both aquatic and terrestrial forms. It is native to North America, Asia, Europe, and some parts of Africa.

OBJECTIVE

This study aimed to determine the genetic diversity within and among populations of P. amphibia and the distribution characteristics of each population to investigate insights into the genetic structure and conservation of P. amphibia.

METHODS

In this study, the genetic diversity and structure of 84 P. amphibia individuals from 7 populations in South Korea were analyzed using genotyping-by-sequencing (GBS). We used 2,469 single nucleotide polymorphisms (SNPs) to analyze genetic diversity, principal components, structure, and phylogeny.

RESULTS

Our results showed a mean observed heterozygosity and mean expected heterozygosity of 0.34409 and 0.34082, respectively. Genetic diversity analysis indicated that the variation among populations (60.08%) was greater than that within populations (39.92%). Fixation index values, principal components analysis, structure, and phylogeny analyses showed that the population in Gyodongdo, Ganghwa Island was highly different.

CONCLUSION

These results provide important insights for better understand the population history and genetic structure of P. amphibia.

Climatic factors, but not geographic distance, promote genetic structure and differentiation of Cleistogenes squarrosa (Trin.) Keng populations

Climate can shape plant genetic diversity and genetic structure, and genetic diversity and genetic structure can reflect the adaptation of plants to climate change. We used rbcl and trnL-trnF sequences to analyze the genetic diversity and genetic structure of C. squarrosa under the influence of different environmental factors in Inner Mongolia grassland. The results showed that the genetic diversity of this species was low. (The trnL-trnF sequences have higher genetic diversity than rbcl sequences.) C. squarrosa had low genetic diversity compared to other prairie plants, but had a more pronounced genetic structure. The haplotype network diagram of the combined sequences could be divided into two categories, and the results of the NJ, MP, and ML trees also showed that the haplotypes were divided into two branches. The results of genetic structure analysis showed that that the populations located in the desert steppe fall into exactly one cluster, and the populations located in the typical steppe fall into exactly another cluster. The neutrality tests were all negative and the mismatch distribution also showed a single peak across the population, suggesting that C. squarrosa had undergone population expansion and was well adapted to the local environment. The results of the mantel test showed that climate had a greater influence on the genetic distance of C. squarrosa, with annual precipitation having a higher influence than mean annual temperature. This study provided basic genetic information on the genetic structure of C. squarrosa and contributes to the study of genetic adaptation mechanisms in grassland plants.

Population genetic differentiation and structure of rare plant Anemone shikokiana based on genotyping-by-sequencing (GBS)

BACKGROUND

Anemone shikokiana (Makino) Makino is a perennial herb of the genus Anemone in the family Ranunculaceae. Endemic to the Shandong Peninsula in China and Shikoku Island in Japan, it is a rare and endangered plant with a narrow, disjunct distribution. It is threatened with extinction and is in urgent need of conservation. Evaluating the genetic diversity of species, revealing the population genetic structure and gene flow, and inferring the population history are of great importance for species conservation, especially for rare and endangered plants.

RESULTS

In our study, 73 samples from eight wild populations in China were sequenced by Super-GBS, yielding a total of 40.59 G clean reads and 52,231 SNPs. Based on the obtained SNP data set, we evaluated the population genetic diversity, genetic structure, and gene flow of A. shikokiana. A low level of genetic diversity was found (He = 0.1925, Ho = 0.1422). The neighbor-joining (NJ) tree, principal component analysis and ADMIXTURE analysis suggested that these 73 A. shikokiana could be considered as two groups. Pairwise genetic differentiation coefficients (Fst) indicated that genetic differentiation was lower between adjacent populations and higher between geographically separated populations. The gene flow between Kunyu Mountain and Lao Mountain was very low. However, neither of the two regions showed evidence of Isolation by Distance.

CONCLUSIONS

Here, we revealed the population genetic structure and gene flow of A. shikokiana from the Shandong Peninsula, China. This research provides valuable genetic resources for A. shikokiana and contributes to the scientific and effective conservation of the species.

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.

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.

Tea and Pleurotus ostreatus intercropping modulates structure of soil and root microbial communities

Intercropping with Pleurotus ostreatus has been demonstrated to increase the tea yield and alleviate soil acidification in tea gardens. However, the underlying mechanisms remain elusive. Here, high-throughput sequencing and Biolog Eco analysis were performed to identify changes in the community structure and abundance of soil microorganisms in the P. ostreatus intercropped tea garden at different seasons (April and September). The results showed that the soil microbial diversity of rhizosphere decreased in April, while rhizosphere and non-rhizosphere soil microbial diversity increased in September in the P. ostreatus intercropped tea garden. The diversity of tea tree root microorganisms increased in both periods. In addition, the number of fungi associated with organic matter decomposition and nutrient cycling, such as Penicillium, Trichoderma, and Trechispora, was significantly higher in the intercropped group than in the control group. Intercropping with P. ostreatus increased the levels of total nitrogen (TN), total phosphorus (TP), and available phosphorus (AP) in the soil. It also improved the content of secondary metabolites, such as tea catechins, and polysaccharides in tea buds. Microbial network analysis showed that Unclassified_o__Helotiales, and Devosia were positively correlated with soil TN and pH, while Lactobacillus, Acidothermus, and Monascus were positively correlated with flavone, AE, and catechins in tea trees. In conclusion, intercropping with P. ostreatus can improve the physical and chemical properties of soil and the composition and structure of microbial communities in tea gardens, which has significant potential for application in monoculture tea gardens with acidic soils.

Genome-wide association study, population structure, and genetic diversity of the tea plant in Guizhou Plateau

BACKGROUND

Guizhou Plateau, as one of the original centers of tea plant, has a profound multi-ethnic cultural heritage and abundant tea germplasm resources. However, the impact of indigenous community factors on the genetic diversity, population structure and geographical distribution of tea plant is still unclear.

RESULTS

Using the genotyping-by-sequencing (GBS) approach, we collected 415 tea plant accessions from the study sites, estimated genetic diversity, developed a core collection, and conducted a genome-wide association study (GWAS) based on 99,363 high-quality single-nucleotide polymorphisms (SNPs). A total of 415 tea accessions were clustered into six populations (GP01, GP02, GP03, GP04, GP05 and GP06), and the results showed that GP04 and GP05 had the highest and lowest genetic diversity (Pi = 0.214 and Pi = 0.145, respectively). Moreover, 136 tea accessions (33%) were selected to construct the core set that can represent the genetic diversity of the whole collection. By analyzing seven significant SNP markers associated with the traits such as the germination period of one bud and two leaves (OTL) and the germination period of one bud and three leaves (OtL), four candidate genes possibly related to OTL and OtL were identified.

CONCLUSIONS

This study revealed the impact of indigenous communities on the population structure of 415 tea accessions, indicating the importance of cultural practices for protection and utilization of tea plant genetic resources. Four potential candidate genes associated with the OTL and OtL of tea plant were also identified, which will facilitate genetic research, germplasm conservation, and breeding.

Analysis of the Genetic Diversity in Tea Plant Germplasm in Fujian Province Based on Restriction Site-Associated DNA Sequencing

Fujian province, an important tea-producing area in China, has abundant tea cultivars. To investigate the genetic relationships of tea plant cultivars in Fujian province and the characteristics of the tea plant varieties, a total of 70 tea cultivars from Fujian and other 12 provinces in China were subjected to restriction site-associated DNA sequencing (RAD-seq). A total of 60,258,975 single nucleotide polymorphism (SNP) sites were obtained. These 70 tea plant cultivars were divided into three groups based on analyzing the phylogenetic tree, principal component, and population structure. Selection pressure analysis indicated that nucleotide diversity was high in Southern China and genetically distinct from cultivars of Fujian tea plant cultivars, according to selection pressure analysis. The selected genes have significant enrichment in pathways associated with metabolism, photosynthesis, and respiration. There were ten characteristic volatiles screened by gas chromatography-mass spectrometry (GC-MS) coupled with multivariate statistical methods, among which the differences in the contents of methyl salicylate, 3-carene, cis-3-hexen-1-ol, (E)-4-hexen-1-ol, and 3-methylbutyraldehyde can be used as reference indicators of the geographical distribution of tea plants. Furthermore, a metabolome genome-wide association study (mGWAS) revealed that 438 candidate genes were related to the aroma metabolic pathway. Further analysis showed that 31 genes of all the selected genes were screened and revealed the reasons for the genetic differences in aroma among tea plant cultivars in Fujian and Southern China. These results reveal the genetic diversity in the Fujian tea plants as well as a theoretical basis for the conservation, development, and utilization of the Fujian highly aromatic tea plant cultivars.

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.