Analysis of genetic population structure and diversity in Mallotus oblongifolius using ISSR and SRAP markers

The Variability of Phytophthora infestans Isolates Collected from Estonian Islands in the Baltic Sea

Knowledge of a pathogen's genetic variability and population structure is of great importance to effective disease management. In this study, 193 isolates of Phytophthora infestans collected from three Estonian islands were characterized over 3 years using simple sequence repeat (SSR) marker data complemented by information on their mating type and resistance to metalaxyl. In combination with SSR marker data from samples in the neighboring Pskov region of Northwest Russia, the impact of regional and landscape structure on the level of genetic exchange was also examined. Among the 111 P. infestans isolates from Estonian islands, 49 alleles were detected among 12 SSR loci, and 59 SSR multilocus genotypes were found, of which 64% were unique. The genetic variation was higher among years than that among islands, as revealed by the analysis of molecular variance. The frequency of metalaxyl-resistant isolates increased from 9% in 2012 to 30% in 2014, and metalaxyl resistance was most frequent among A1 isolates. The test for isolation by distance among the studied regions was not significant, and coupled with the absence of genetic differentiation, the result revealed gene flow and the absence of local adaptation. The data are consistent with a sexual population in which diversity is driven by an annual germination of soilborne oospores. The absence of shared genotypes over the years has important implications when it comes to the management of diseases. Such population diversity can make it difficult to predict the nature of the outbreak in the coming year as the genetic makeup is different for each year.

Clustering Analysis of Natural D-borneol Resource Plants Based on Simple Sequence Repeat (SSR) Markers, Leaf Morphology, and Chemical Composition

D-borneol is a double-loop monoterpene with a wide use in the pharmaceutical, food, and cosmetics industries. Natural D-borneol can be extracted from branches and leaves of D-borneol resource plants. With the widespread use of natural D-borneol, the identification of D-borneol resource plants and the protection of germplasm resources have become the focus of research. In this study, plant leaf morphology, chemical composition, and simple sequence repeat (SSR) molecular marker analysis were used to analyze and cluster 5 species of D-borneol resource plants and their closely related species. It was found that all three analysis methods could distinguish and cluster these D-borneol resource plants to some degree. The result of SSR analysis using capillary electrophoresis was the best, and it could distinguish Mei Pian tree from Yin Xiang as well as Longnao Zhang from An Zhang. The correlation analysis between SSR similarity matrix and leaf morphology analysis and between SSR similarity matrix and chemical composition similarity matrix revealed that they both had significant correlations (P < 0.0001) and the correlation (r = 0.588) between SSR and leaf morphology was a little higher than that (r = 0.519) between SSR and chemical composition. This indicated that the environment had a greater impact on the chemical composition than on leaf morphology. The research findings will offer efficient techniques to cluster natural D-borneol resource plants and establish a theoretical basis for their future development and utilization.

The impact of non-environmental factors on the chemical variation of Radix Scrophulariae

Radix Scrophulariae is a commonly used Chinese herb derived from the dried root of Scrophularia ningpoesis Hemsl. (S. ningpoensis). It is difficult to accurately estimate the dosage of Chinese medicinal materials used in the prescription because of the chemical variation caused by various factors. To analyze the non-environmental factors affecting the chemical variation of Radix Scrophulariae, we planted nine different cultivated varieties of S. ningpoensis in the same plantation. Based on sequence-related amplified polymorphism (SRAP), simple sequence repeats (SSR) markers and high-performance liquid chromatography (HPLC) analysis, we found that the materials from the cultivated varieties could be divided into two groups, the Zhejiang group, and the southwest China group. The genetic distance based on molecular data between the two groups was above 0.3882, and the Euclidean distance based on chemical data between the two groups was above 5.312. The correlation analysis between the genetic distance matrix based on SRAP and the Euclidean distance matrix based on 18 HPLC peaks of the whole underground part revealed that the genetic differentiation and chemical variation were positively related, r = 0.7196 (p < 0.05). The genetic background, different part of the roots and the different development of the roots are the three non-environmental factors causing the chemical variation. The coefficient of variation (C.V) of chemical composition of Radix Scrophulariae with different genetic background reached to 93.62 %, the C.V of the chemical composition of Radix Scrophulariae derived from the same variety reached to 64.21 %, the C.V of the chemical composition of Radix Scrophulariae derived from the middle part of the roots of S. ningpoensis from the same variety reached to 45.55 %. The C.V of chemical composition of Radix Scrophulairae produced in the same plantation could be controlled to 38.43 % by using the same variety of roots with the approximate mass derived from the middle part of the roots under 20 g. Our findings provided insights to decrease the chemical variation of Chinese medicinal materials by controlling non-environmental factors.

Aroma Difference Analysis of Partridge Tea (Mallotus oblongifolius) with Different Drying Treatments Based on HS-SPME-GC-MS Technique

Partridge tea has high medicinal value due to its rich content of terpenoids, phenols, flavonoids, and other related bioactive components. In order to study the best drying method for partridge tea, four treatments, including outdoor sun drying (OD), indoor shade drying (ID), hot-air drying (HAD), and low-temperature freeze-drying (LTD), were performed. The results showed that the OD and HAD treatments favored the retention of the red color of their products, while the ID and LTD treatments were more favorable for the retention of the green color. The HS-SPME-GC-MS results showed that a total of 82 compounds were identified in the four drying treatments of partridge tea, and the most abundant compounds were terpenoids (88.34-89.92%). The HAD-treated tea had the highest terpenoid content (89.92%) and high levels of flavor compounds typical of partridge tea (52.28%). OPLS-DA and PCA showed that α-copaene, β-bourbonene, caryophyllene, α-guaiene, and δ-cadinene could be considered candidate marker compounds for judging the aroma quality of partridge tea with different drying treatments. This study will not only provide a basis for processing and flavor quality control but also for spice and seasoning product development in partridge tea.

Morphological and molecular diversity in mid-late and late maturity genotypes of cauliflower

Genetic diversity is the prerequisite for the success of crop improvement programmes. Keeping in view, the current investigation was undertaken to assess the agro-morphological and molecular diversity involving 36 diverse mid-late and late cauliflower genotypes following α-RBD design during winter season 2021-22. Six morphological descriptors predicted as polymorphic using Shannon diversity index with maximum for leaf margin (0.94). The genotypes grouped into nine clusters based on D2 analysis with four as monogenotypic and gross plant weight (32.38%) revealed maximum contribution towards the genetic diversity. Molecular diversity analysis revealed 2-7 alleles among 36 polymorphic simple sequence repeats (SSR) with average of 4.22. Primer BoESSR492 (0.77) showed maximum polymorphic information content (PIC) with mean of 0.58. SSR analysis revealed two clusters each with two subclusters with a composite pattern of genotype distribution. STRUCTURE analysis showed homogenous mixture with least amount of gene pool introgression within the genotypes. Thus, based on morphological and molecular studies, the diverse genotypes namely, DPCaCMS-1, DPCaf-W4, DPCaf-US, DPCaf-W131W, DPCaf-S121, DPCaf-18, DPCaf-13, DPCaf-29 and DPCaf-CMS5 can be utilized in hybridization to isolate potential transgressive segregants to broaden the genetic base of cauliflower or involve them to exploit heterosis.

The mechanism leading to color differences between purple-red and green partridge tea leaves

BACKGROUND

Partridge tea (Mallotus oblongifolius) is used as an important beverage and medical plant in Hainan province of China. Although some information about the morphology, cytology, and genetics of partridge tea has been reported in the literature, knowledge about this plant is still very limited. The leaves are the most important part for every tea plant, with a major role in nutrition and other functions. The leaves of different cultivars of partridge tea are different in colors and functions. The molecular mechanism of color formation of partridge tea leaf is still unclear. We reveal the molecular mechanism of the color difference between purple-red and green partridge tea leaves through metabolome and transcriptome analysis.

RESULTS

We identified 665 compounds in the two partridge tea cultivars through metabolome analysis. Among these compounds, the content of 324 differed between the two cultivars. We also annotated 50 042 unigenes in the two cultivars by transcriptome analysis; 9665 unigenes were expressed differently between the two cultivars. Using an integrated analysis of the metabolome and transcriptome data, we found that the compounds and genes involved in anthocyanin biosynthesis were up-regulated in the purple-red leaves, compared with the green leaves.

CONCLUSION

Our results showed that the anthocyanin biosynthesis pathway genes were up-regulated, which resulted in the up-regulation of the anthocyanin, making the leaf color purple-red. Our study reveals the molecular mechanism of the color difference between purple-red and green partridge tea, and lays a foundation for the genetic breeding of partridge tea genetic and the utilization of its volatile components. © 2022 Society of Chemical Industry.

Genetic variation of Amaranthus retroflexus L. and Chenopodium album L. (Amaranthaceae) suggests multiple independent introductions into Iran

Amaranthus retroflexus L. and Chenopodium album L. (Amaranthaceae) are weedy plants that cause severe ecological and economic damage. In this study, we collected DNA from three different countries and assessed genetic diversity using inter-simple sequence repeat (ISSR) markers. Our analysis shows both weed species have low genetic diversity within a population and high genetic diversity among populations, as well as a low value of gene flow among the populations. UPGMA clustering and principal coordinate analysis indicate four distinct groups for A. retroflexus L. and C. album L. exist. We detected significant isolation-by-distance for A. retroflexus L. and no significant correlation for C.album L. These conclusions are based data from 13 ISSR primers where the average percentage of polymorphism produced was 98.46% for A. retroflexus L. and 74.81% for C. album L.These data suggest that each population was independently introduced to the location from which it was sampled and these noxious weeds come armed with considerable genetic variability giving them the opportunity to manifest myriad traits that could be used to avoid management practices. Our results, albeit not definitive about this issue, do not support the native status of C. album L. in Iran.

Exploring the genetic makeup and population structure among Capsicum accessions for crop improvement and breeding curriculum insights

Background

Capsicum or chilli is an important crop in India which exhibits immense structural and genetic variations reflecting their intra- and inter-specific relationships. The aim of this study was to establish relationships amongst 54 Capsicum accessions through analysis of genetic and population structure using ISSR markers.

Results

Out of 19, successful DNA amplifications were shown by 7 ISSR primers and a total of 80 bands were identified ranging between 8 and 14 with an average of 11.43 bands/primer. A significant degree of polymorphic information content (PIC), discriminating power (DP), resolving power (RP), effective multiplex ratio (EMR), and marker index (MI) were identified as 0.39, 0.70, 6.40, 5.88, and 2.30, respectively, using ISSR markers in chillies. The cross-transferability ranged from 8.0 to 72.15% with an average of 52.63% among chillies. Amongst genetic information, grand mean values were 0.264, 0.180, 0.376, 0.296, and 0.180, which correspond to Shannon’s information index (I), expected heterozygosity (He), Nei’s gene diversity, total diversity among species (Ht), diversity within species (Hs), respectively. Further, the coefficients of gene differentiation (Gst) and gene flow (Nm) were 0.393 and 0.773, representing higher genetic variation among the population which was confirmed by analysis of molecular variance (AMOVA).

Conclusion

ISSR markers represented a potent system for the estimation of relationships or variation studies and generated information useful for planning crop management and improvement strategies in chilli breeding.

Authentication of Geographical Origin in Hainan Partridge Tea (Mallotus obongifolius) by Stable Isotope and Targeted Metabolomics Combined with Chemometrics

Partridge tea (Mallotus oblongifolius (Miq.) Müll.Arg.) is a local characteristic tea in Hainan, the southernmost province of China, and the quality of partridge tea may be affected by the producing areas. In this study, stable isotope and targeted metabolomics combined chemometrics were used as potential tools for analyzing and identifying partridge tea from different origins. Elemental analysis-stable isotope ratio mass spectrometer and liquid chromatography-tandem mass spectrometrywas used to analyze the characteristics of C/N/O/H stable isotopes and 54 chemical components, including polyphenols and alkaloids in partridge tea samples from four regions in Hainan (Wanning, Wenchang, Sanya and Baoting). The results showed that there were significant differences in the stable isotope ratios and polyphenol and alkaloid contents of partridge tea from different origins, and both could accurately classify partridge tea from different origins. The correct separation and clustering of the samples were observed by principal component analysis and the cross-validated Q² values by orthogonal partial least squares discriminant analysis (OPLS-DA) were 0.949 (based on stable isotope) and 0.974 (based on polyphenol and alkaloid), respectively. Potential significance indicators for origin identification were screened out by OPLS-DA and random forest algorithm, including three stable isotopes (δ¹³C, δ D, and δ¹⁸O) and four polyphenols (luteolin, protocatechuic acid, astragalin, and naringenin). This study can provide a preliminary guide for the origin identification of Hainan partridge tea.

Uncovering the genetic diversity of yams (Dioscorea spp.) in China by combining phenotypic trait and molecular marker analyses

Yam is an important edible tuber and root plant worldwide; China as one of the native places of yams has many diverse local resources. The goal of this study was to clarify the genetic diversity of the commonly cultivated yam landraces and the genetic relationship between the main yam species in China. In this study, 26 phenotypic traits of 112 yam accessions from 21 provinces in China were evaluated, and 24 simple sequence repeat (SSR) and 29 sequence-related amplified polymorphism (SRAP) markers were used for the genetic diversity analysis. Phenotypic traits revealed that Dioscorea opposita had the highest genetic diversity, followed by D. alata, D. persimilis, D. fordii, and D. esculenta. Among the 26 phenotypic traits, the Shannon diversity indexes of leaf shape, petiole color, and stem color were high, and the range in the variation of tuber-related traits in the underground part was higher than that in the aboveground part. All accessions were divided into six groups by phenotypic trait clustering, which was also supported by principal component analysis (PCA). Molecular marker analysis showed that SSR and SRAP markers had good amplification effects and could effectively and accurately evaluate the genetic variation of yam. The unweighted pair-group method with arithmetic means analysis based on SSR-SRAP marker data showed that the 112 accessions were also divided into six groups, similar to the phenotypic trait results. The results of PCA and population structure analysis based on SSR-SRAP data also produced similar results. In addition, the analysis of the origin and genetic relationship of yam indicated that the species D. opposita may have originated from China. These results demonstrate the genetic diversity and distinctness among the widely cultivated species of Chinese yam and provide a theoretical reference for the classification, breeding, germplasm innovation, utilization, and variety protection of Chinese yam resources.

Assessment of genetic diversity in Amomum tsao-ko Crevost & Lemarié, an important medicine food homologous crop from Southwest China using SRAP and ISSR markers

Amomum tsao-ko Crevost & Lemarié is an important crop that has been widely used in traditional Chinese medicine and daily diets for a long time. In this study, the genetic diversity and relationships of eight cultivated populations of A. tsao-ko grown in Southwest China were examined using sequence-related amplified polymorphism (SRAP) and inter-simple sequence repeat (ISSR) markers. The results showed that 139 (99.29%) of 140 and 185 (99.46%) of 186 bands were polymorphic by SRAP and ISSR primers amplification, respectively. The polymorphic information content of detected bands were 0.270 (SRAP) and 0.232 (ISSR), respectively. The average Nei's gene diversity (H = 0.217) and Shannon's information index (I = 0.348) at the species level generated by SRAP primer were higher than those by ISSR analysis (H = 0.158, I = 0.272). Genetic differentiation coefficients and molecular variance analysis (AMOVA) indicated that the genetic variance of A. tsao-ko mainly occurred within populations rather than among populations. The high genetic identity among populations was revealed by SRAP (0.937) and ISSR (0.963). Using UPGMA cluster analysis, principal coordinate analysis, and population structure analysis, the accessions were categorized into two major groups. Overall, results obtained here will be useful for A. tsao-ko germplasm characterization, conservation, and utilization.

Complete plastome sequence of Nephelium topengii (Merr.) H. S. Lo (Sapindaceae): an endemic species in Hainan

Nephelium topengii is an evergreen tree of the Sapindaceae family, which can be used as timber. Here, we report and characterize the complete plastome of N. topengii. The complete plastome is 162,944 bp in length and contains the typical structure and gene content of angiosperm plastome, including two inverted repeat (IR) regions of 30,092 bp, a large single-copy (LSC) region of 85,909 bp and a small single-copy (SSC) region of 16,851bp. The plastome contains 130 genes, consisting of 80 unique protein-coding genes, 30 unique tRNA gene, 4 unique rRNA genes (5S rRNA, 4.5S rRNA, 23S rRNA and 16S rRNA). The overall A/T content in the plastome of N. topengii is 62.30%. The complete plastome sequence of N. topengii will provide a useful resource for the conservation genetics of this species as well as for phylogenetic studies in Sapindaceae.

Complete plastome sequence of Flueggea virosa (Roxburgh ex Willdenow) Voigt (Phyllanthaceae): a medicinal plant

Flueggea virosa is a tropical plant of the Phyllanthaceae family, which has high medicinal value. Here, we report and characterize the complete plastome of F. virosa. The complete plastome is 154,961 bp in length and contains the typical structure and gene content of angiosperm plastome, including two inverted repeat (IR) regions of 27,575 bp, a large single-copy (LSC) region of 83,397 bp and a small single-copy (SSC) region of 16,414 bp. The plastome contains 130 genes, consisting of 80 unique protein-coding genes, 30 unique tRNA gene, 4 unique rRNA genes (5S rRNA, 4.5S rRNA, 23S rRNA and 16S rRNA). The overall A/T content in the plastome of F. virosa is 63.10%. The complete plastome sequence of F. virosa will provide a useful resource for the conservation genetics of this species as well as for phylogenetic studies in Phyllanthaceae.

Temperature-Mediated Plasticity Regulates the Adaptation of Phytophthora infestans to Azoxystrobin Fungicide

Fungicide is one of the main approaches used in agriculture to manage plant diseases for food production, but their effectiveness can be reduced due to the evolution of plant pathogens. Understanding the genetics and evolutionary processes responsible for the development of fungicide resistance is a key to food production and social sustainability. In this study, we used a common garden experiment to examine the source of genetic variation, natural selection, and temperature contributing to the development of azoxystrobin resistance in Phytophthora infestans and infer sustainable ways of plant disease management in future. We found that plasticity contributed to ~40% of phenotypic variation in azoxystrobin sensitivity while heritability accounted for 16%. Further analysis indicated that overall population differentiation in azoxystrobin sensitivity (QST) was significantly greater than the overall population differentiation in simple sequence repeat (SSR) marker (FST), and the P. infestans isolates demonstrated higher level of azoxystrobin sensitivity at the higher experimental temperature. These results suggest that changes in target gene expression, enzymatic activity, or metabolic rate of P. infestans play a more important role in the adaptation of the pathogen to azoxystrobin resistance than that of mutations in target genes. The development of azoxystrobin resistance in P. infestans is likely driven by diversifying selection for local adaptation, and elevated temperature associated with global warming in the future may increase the effectiveness of using azoxystrobin to manage P. infestans. The sustainable approaches for increasing disease control effectiveness and minimizing the erosion of the fungicide efficacy are proposed.

Complete plastome sequence of Mallotus peltatus (Geiseler) Müll. Arg. (Euphorbiaceae): A beverage and medicinal plant in Hainan, China

Mallotus peltatus is a tropical plant of the Euphorbiaceae family, which could be used as a beverage and medicine in Hainan, China. Here, we report and characterize the complete plastome of M. peltatus. The complete plastome is 163,304 bp in length and contains a typical structure and gene content of angiosperm plastome, including two inverted repeat (IR) regions of 27,112 bp, a large single-copy (LSC) region of 89,886 bp and a small single-copy (SSC) region of 18,840 bp. The plastome contains 131 genes, consisting of 78 unique protein-coding genes, 30 unique tRNA gene, four unique rRNA genes (5S rRNA, 4.5S rRNA, 23S rRNA and 16S rRNA), and eight pseudogenes. The overall A/T content in the plastome of M. peltatus is 64.02%. The complete plastome sequence of M. peltatus will provide a useful resource for the conservation genetics of this species as well as for phylogenetic studies in Euphorbiaceae.

Genetic Diversity and Population Divergence of a Rare, Endemic Grass (Elymus breviaristatus) in the Southeastern Qinghai-Tibetan Plateau

Elymus breviaristatus is a grass species only distributed in the southeast of Qinghai-Tibetan Plateau (QTP), which has suffered from serious habitat fragmentation. Therefore, understanding patterns of genetic diversity within and among natural E. breviaristatus populations could provide insight for future conservation strategies. In this study, sequence-related amplified polymorphism markers were employed to investigate the genetic diversity and hierarchical structure of seven E. breviaristatus populations from QTP, China. Multiple measures of genetic diversity indicated that there is low to moderate genetic variation within E. breviaristatus populations, consistent with its presumed mating system. In spite of its rarity, E. breviaristatus presented high genetic diversity that was equivalent to or even higher than that of widespread species. Bayesian clustering approaches, along with clustering analysis and principal coordinate analysis partitioned the studied populations of E. breviaristatus into five genetic clusters. Differentiation coefficients (Fst, GST, etc.) and AMOVA analysis revealed considerable genetic divergence among different populations. BARRIER analyses indicated that there were two potential barriers to gene flow among the E. breviaristatus populations. Despite these patterns of differentiation, genetic distances between populations were independent of geographic distances (r = 0.2197, p = 0.2534), indicating little isolation by distance. Moreover, despite detecting a common outlier by two methods, bioclimatic factors (altitude, annual mean temperature, and annual mean precipitation) were not related to diversity parameters, indicating little evidence for isolation caused by the environment. These patterns of diversity within and between populations are used to propose a conservation strategy for E. breviaristatus.