UPGMA Cluster Analysis Research Articles

Genetic diversity assessment of Palestinian safflower (Carthamus tinctorius L.) utilizing DAMD molecular markers.

The current knowledge about Palestinian safflower landraces is relatively limited in terms of phenotypic and molecular characterization, however, the purpose of this investigation was to determine the amount of genetic diversity in eighteen local safflower landraces using seven DAMD markers. The banding patterns for each primer were scored and compiled into a data matrix. Subsequently, the data matrix was analyzed using UPGMA cluster analysis to identify distinct genetic groups among the landraces. In total, 88 DNA fragments were found, and there were an average of 12.6 loci per assay unit observed. Resolving Power (RP) revealed an average of 7.09 was determined, with the highest RP value at 13.3. The dendrogram obtained from DAMD data divided the landraces into three main clusters, denoted as I, II and III. The first cluster (I) consisted of one genotype (PTUK.SA16). The second cluster (II) consisted of two genotypes (PTUK.SA13 and PTUK.SA10). The third cluster (III) was later partitioned into two distinct sub-clusters, which are III.a and III.b. Sub-cluster III.a comprised seven genotypes (PTUK.SA4, PTUK.SA9, PTUK.SA8, PTUK.SA7, PTUK.SA6, PTUK.SA5 and PTUK.SA3). While Sub-cluster III.b consisted of eight genotypes (PTUK.SA15, PTUK.SA18, PTUK.SA17, PTUK.SA14, PTUK.SA12, PTUK.SA2, PTUK.SA11, and PTUK.SA1). This research assess the genetic diversity of Palestinian safflower landraces using PCR-based DAMD markers. The remarkable level of polymorphism detected using DAMD markers demonstrated their effectiveness in distinguishing between Palestinian safflower genotypes.

Assessment of Genomic Integrity of Vitex negundoL., An Important Indian Medicinal Plant, Using RAPD Markers

Vitex negundo is an Indian medicinal plant containing steroids, flavonoids, lignans and terpenoids that can be used as a precursor for commercial production. An efficient marker system such as Random Amplified Polymorphic DNA (RAPD) was used to assess the genetic integrity of V. negundo. The straightforward method RAPD can be used to evaluate genomic integrity because it uses a small amount of DNA for PCR amplification. Six out of thirteen RAPD primers generated 150 distinct bands, of which 31 were polymorphic, with an average of 5.16 polymorphic bands per primer. A maximum of up to 32 fragments were amplified, and an average of 25 per primer, and the amplicons varied in size between 100 and 2000bp. The percentage of polymorphism ranges from 12.9 to 22.5, with an average of 16.6. The PIC values ranged from 0.11 to 0.63 for RAPD primers. The study pointed out that RAPD markers evaluate the genetic fidelity in Vitex negundo. The UPGMA cluster analysis grouped all in vitro raised plantlets treated with different growth regulators such as BAP, DPU, TDZ, and mT. The principal component analysis also substantiates this clustering pattern. Thus, the phylogenetic relationship and a high genetic variation revealed in the present study could provide baseline data for the conservation and improvement of this plant in future. Also, the molecular marker identified in this study will be helpful in the authentication of this species to prevent adulteration in herbal medicine.

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

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

Morphological and molecular diversity analysis vis-a-vis phylogenetic correlation among pomegranate (Punica granatum L.) varieties

Abstract Identification of different pomegranate (Punica granatum L.) genotypes using morphological descriptors and further substantiated through molecular means is essential for a breeding program. Characterization using molecular markers has an advantage over its morphological counterpart due to its low expense, quick and reliable results, and the requirement of less sophisticated equipment. In this study, eight different pomegranate cultivars were characterized based on their morphological and molecular characters in sub-tropical regions between 2018 and 2019. Morphological experiments were conducted in a randomized block design replicated thrice for each cultivar, whereas RAPD markers were employed for molecular studies. Principal component analysis revealed significant morphological variation (79.61%) among the cultivars. A high level of polymorphism, similar to PCA, was observed with RAPD analysis (80.49%). Some discrepancies between morphological and molecular results were noted in UPGMA cluster analysis. However, eight primers (total = 41) distinctively separated the Bhagwa variety from others, with the maximum similarity coefficient value (ca. 0.54) and superior fruit quality distinguished in PCA analysis with the maximum mean Euclidean distance (ca. 16). Hence, RAPD markers could be used along with morphological markers for a quick screening of germplasms in further crop improvement programs.

First Report on Taxonomic Significance of Foliar Microanatomy of Lamiaceae Taxa from Pakistan; A Correct Tool for Taxa Authentication

The foliar epidermal, stomatal and trichome properties are frequently used as plant microscopic attributes from a taxonomic or ecological perspective. Among the angiosperm families, the Lamiaceae is one of the most taxonomically difficult, economically significant, and medicinally important families. To better understand the foliar microanatomy of Lamiaceae taxa obtained from Northern Pakistan, this study attempts to determine the variational and diagnostic features of 27 species that were analyzed using light microscopy (LM) and scanning electron microscopy (SEM). UPGMA cluster analysis, principal component analysis (PCA) and semantic differential chart (SDC) were used to characterize, visualize, and compare the leaf micromorphology across all species. Three different types of epidermal cell types were examined on both foliar surfaces i.e., irregular, hexagonal, and polygonal. Anticlinal wall pattern also shows variation. Anomocytic stomata is dominant in 8 studied species followed by paractic in 5 species, anisocytic in 4 species and diacytic in 2 species. The trichomes could be broadly classified into two groups, glandular trichomes (GTs) and non-glandular trichomes (NGTs). Lamiaceae has two types of glandular trichomes, small capitate and large peltate, which differ in size, structure, and distribution. In present research five distinct forms of non-glandular trichomes are unicellular, multicellular, stellate, branched, and unbranched trichomes. The results that characterized, illustrated, and contrasted the leaf anatomical characteristics of the Lamiaceae taxa can be better understood with the aid of statistical analysis. Future research will depend on these findings to improve the systematics of Lamiaceae taxa. These characteristics have a large taxonomic potential when considered as a whole.

Taxonomic identification of Nigerian Terminalia superba and Terminalia ivorensis Combretaceae) using AFLP molecular markers

Terminalia superba and T. ivorensis are difficult to identify with morphological markers. Molecular characterization is very effective to correct the delimitation of timber species, especially when the discriminatory power of morphological markers is weak. In this study, four amplified fragment length polymorphism (AFLP) marker combinations were used to determine the taxonomic relationship among a total of 33 accessions of the genus Terminalia, consisting of two species, Terminalia ivorensis (12 accessions) and T. superba (21). The primer combinations produced a total of 740 fragments out of which 619 (83.6%) were polymorphic. Among all the primer combinations used, E-ACT/M-CTC was the most informative, which generated 11 unique markers for clear identification of the two species. The average polymorphic information content (PIC) ranged from 0.24 (E-ACT/M-CAT) to 0.28 (E-ACT/M-CTC) while the resolving power (RP) varied from 40.73 (E-AAC/M-CTA) to 63.76 (E-ACT/M-CTC). The genetic difference between the two species was significant (PhiPT = 0.610, p<0.001). All 33 accessions were delimited by both the UPGMA cluster and principal component analysis. Based on the results, it was concluded that E-ACT/M-CTC is the best among the marker combinations used for molecular study of the two tree species and used significantly to distinguish them. STRUCTURE analysis identified two accessions of Terminalia superba with alleles derived from T. ivorensis as well as revealed five putative hybrid accessions, which requires further genetic investigation to substantiate the finding.

Genetic Diversity and Population Genetic Structure of Jatropha curcas L. Accessions from Different Provenances Revealed by Amplified Fragment-Length Polymorphism and Inter-Simple Sequence Repeat Markers

The genetic diversity and structure of 17 populations of J. curcas, including 92 accessions from different provenances (tropical and subtropical), were investigated and effectively evaluated using twelve inter-simple sequence repeats (ISSRs) and seven pairs of florescence-amplified fragment-length polymorphism (AFLP) primers. Genetic diversity, at the overall level among populations of J. curcas based on the ISSR markers, showed that the observed number of alleles (Na) was 1.593, the effective number of alleles (Ne) was 1.330, Nei’s gene diversity (H) was 0.200, Shannon’s information index (I) was 0.303, and the percentage of polymorphic loci was 59.29%, indicating moderate genetic diversity between and within the different populations of J. curcas. Based on the genetic diversity analysis of AFLP markers, there were 1.464 (Na) and 1.216 (Ne) alleles, Nei’s gene diversity (H) was 0.132, Shannon’s information index (I) was 0.204, and the percentage of polymorphic loci was 46.40%. The AMOVA analysis showed that this large variance was due to differences within the populations, with genetic distinctions and limited gene flow among those from varied regions. The 17 populations were clustered into five main groups via UPGMA clustering analysis based on Nei’s genetic distance, and the genetic relationships among the populations exhibited no significant correlations with geographical provenances. The genetic variation among Chinese populations of J. curcas distributed in dry-hot valley areas was remarkable, and the American germplasm presented with distinct genetic differentiation.

Analysis of the genetic diversity and population structure of Tilia amurensis from China using SSR markers: Implications for conservation

Tilia amurensis is a deciduous broad-leaved tree in the Malvaceae family. It is one of the second-class key protected wild plants in China. The evaluation of genetic polymorphisms of crucial protected species is necessary for conserving germplasm resources. In this study, 15 pairs of highly polymorphic SSR primers were used to analyse the genetic diversity of eight T. amurensis populations and the population structure of nine Tilia populations distributed in China. At the population level (Na = 6.050, Ne = 2.930, I = 1.123, HO = 0.485, HE = 0.523), there was a high level of genetic diversity. The AMOVA results showed that 12 % and 88 % of the total variation occurred among and within populations, respectively. The degree of genetic differentiation was moderate (FST = 0.124), and the level of gene flow was high (Nm = 1.763). The results of UPGMA cluster analysis, PCoA and structure analysis (ΔK = 2) revealed different degrees of gene introgression between the eight T. amurensis populations and Tilia japonica as the outgroup. These findings have important implications for formulating appropriate conservation strategies.

Genetic diversity evaluation of Luculia yunnanensis, a vulnerable species endemic to Yunnan, Southwestern China based on morphological traits and EST-SSR markers.

Luculia yunnanensis is a vulnerable species endemic to Yunnan Province, Southwestern China, which has high ornamental value. Its wild population has not been fully protected and utilized for a long time, which is not conducive to the long-term stable development of this species. Genetic diversity assessment is the basis and prerequisite for the conservation of rare species. In this study, 21 phenotypic traits and 17 highly polymorphic EST-SSR markers were used to analyze the genetic diversity and genetic structure of 164 individuals from six L. yunnanensis populations. The coefficient of variation of 21 phenotypic traits ranged from 11.76% to 52.58% (mean=21.72%), and the coefficient of variation of 18 traits was less than 30%. The average values of Ne, I, Ho and He were 1.710, 0.619, 0.384, and 0.352, respectively. The genetic diversity of LLO (Ho = 0.476 and He = 0.426) and LCM (Ho = 0.424 and He = 0.381) populations in Lushui County was highest. The GDX populations (Ho = 0.335 and He = 0.269) isolated by Gaoligong Mountain had the lowest genetic diversity. The AMOVA results showed that 13.04% of the genetic variation was among populations and 86.96% was within populations. The average phenotypic differentiation coefficient of phenotypic traits among populations was 18.69%. The results of phenotypic and genetic variation analysis were consistent, indicating that the most of variation exists within population. Genetic structure, UPGMA clustering and PCA analysis results showed that the populations of L. yunnanensis had obvious geographical divisions, and the populations distributed in the southern region and distributed in the northern region of the Nujiang River clustered into one group respectively. Combining the results of phenotypic and molecular markers, we recommend that give priority to the protection of LLO, LCM and GDX population, in order to ensure the sustainable utilization of L. yunnanensis germplasm resources.

Characterization of Lithuanian Tomato Varieties and Hybrids Using Phenotypic Traits and Molecular Markers.

The aim of this study was to evaluate phenotypic traits and genetic diversity of the 13 tomato (Solanum lycopersicum L.) varieties and 6 hybrids developed at the Institute of Horticulture Lithuanian Research Centre for Agriculture and Forestry (LRCAF IH). For the molecular characterisation, seven previously published microsatellite markers (SSR) were used. A24 and 26 alleles were detected in tomato varieties and hybrids, respectively. Based on the polymorphism information content (PIC) value, the most informative SSR primers for varieties were TMS52, TGS0007, LEMDDNa and Tom236-237, and the most informative SSR primers for hybrids were SSR248 and TMS52. In UPGMA cluster analysis, tomato varieties are grouped in some cases due to genetic relationships, as the same cluster cultivars 'Viltis' (the parent of cv. 'Laukiai') and 'Aušriai' (the progeny of cv. 'Jurgiai') are present. The grouping of all hybrids in the dendrogram is related to the parental forms, and it shows the usefulness of molecular markers for tomato breeding, as they can be used to trace the origin of hybrids and, eventually, varieties accurately. The knowledge about the genetic background of Lithuanian tomato cultivars will help plan targeted crosses in tomato breeding programs.

Microsatellite analysis of genetic diversity and population differentiation of Acanthopagrus schlegelii in China

The study utilized 9 self-selected polymorphic microsatellite loci to amplify and investigate the genetic diversity and differentiation of Acanthopagrus schlegelii populations in 10 wild populations along the Chinese coast. The values of Polymorphic Information Content (PIC) ranged from 0.4433 to 0.5804, with an average value of 0.5143. The average number of alleles per locus (A) ranged from 3.0000 to 3.4444, with a mean value of 3.2333 and an overall value of 3.6667. The average number of effective alleles per locus (Ae) ranged from 2.0130 to 2.6014, with a mean value of 2.2994 and an overall value of 2.8013. The observed heterozygosity (Ho) ranged from 0.4607 to 0.5789, with an average value of 0.5278 and an overall value of 0.5261. The expected heterozygosity (He) ranged from 0.4657 to 0.5967, with an average value of 0.5183 and an overall value of 0.6224. The results of genetic differentiation showed the genetic differentiation coefficient (Fst) was 0.1806, and the gene flow (Nm) was 1.1342. The UPGMA cluster analysis indicated significant genetic differentiation among A. schlegelii populations along the Chinese coast, with the populations being divided into two groups, namely the northern and southern populations. The genetic differentiation structure of the southern population was inconsistent with its geographical distribution. This study utilized microsatellite molecular markers to investigate the genetic diversity and genetic differentiation of 10 wild A. schlegelii populations along the coast of China. The research results indicate that the genetic diversity of the 10 wild A. schlegelii populations is at a moderate level, with evidence of north-south differentiation. This provides a scientific basis for the conservation, germplasm improvement, and aquaculture of A. schlegelii resources in China. It also offers background information for recent stock enhancement and release projects and their impact on the genetic resources of A. schlegelii.

Ethnobotanical study of medicinal plants used by Lao ethnic group in Central Laos

Results from an ethnobotanical study of medicinal plants used by Lao ethnic group between 2021 and 2023 identifying the medicinal plants use of 76 species 68 genera 43 families. The primary emphasis of the study was on the medicinal plants, we tested the differences between informant knowledge and informant age using linear regression. The most important medicinal plant species, including Blumea balsamifera, Chromolaena odorata, Smilax glabra, and Zingiber montanum (all with a Use Value of 1.00), were followed by Phyllanthus emblica (0.95) and Cucumis sativus (0.88). Remarkably, 65 plant species achieved the highest Fidelity Level with a 100% FL value. Within ailment categories, Respiratory system symptoms garnered the highest Informant Agreement Ratio value of 1.00. The Jaccard’s Similarity Index ranged from 0.0581 to 0.2690, with the highest JI observed between cultivated and market plants. The UPGMA cluster analysis indicated that wild plants exhibited lower similarity to the other areas. There were no significant differences in the number of plants known among different informants based on their age. In this research, we found that two plant species, Solanum lasiocarpum (used for nourishing the body) and Morinda coreia (employed in treating amenorrhea), have never been reported for their medicinal use before. These findings underscore the risk of traditional knowledge erosion, driven by the absence of written documentation and the influence of modern medical practices. The data obtained from this study is of immense value in formulating conservation strategies that can benefit both the Bolikhamxay province and the nation as a whole.

Genetic diversity in Pima (Gossypium barbadense L.) and advanced interspecific hybrids (Gossypium hirsutum x Gossypium barbadense) of cotton germplasm in Ethiopia

This study was conducted to assess the genetic diversity in Pima (Gossypium barbadense L.) and advanced interspecific hybrids (G. hirsutum L. x G. barbadense L.) of cotton germplasm in Ethiopia. A total of 26 germplasm were genotyped using 26 polymorphic simple sequence repeat (SSR) markers. A total of 165 polymorphic loci, with a range of 3 to 13 alleles and a mean of 6.35 per marker were detected. About 11% of total alleles were unique alleles in 11 germplasm. The gene diversity varied from 0.39 to 0. 89, while the heterozygosity was in the range of 0 to 1.00. Furthermore, the polymorphic information content of the markers varied from 0.37 (BNL1417) to 0.88 (BNL1672) with an average of 0.68. Among the complete panel of cotton germplasm used in this study, the pairwise genetic distance ranged from 0.08 to 0.94, with an overall mean of 0.61. The UPGMA cluster analysis grouped the Pima cotton germplasm into two cluster groups and the advanced interspecific hybrid cotton germplasm makes one cluster. Principal coordinate analysis indicates that the first three most informative principal coordinates explained 68.4% of the genetic variation. The result evidenced very low to high genetic dissimilarity and overall, a considerable genetic diversity among and within germplasm which could be used to further broaden the genetic base and to enlarge the number of available cotton germplasm.

Microsatellite marker-based analysis of the genetic diversity and population structure of three Arnebiae Radix in western China

Arnebiae Radix is an important medicinal and perennial herb found in Western China, particularly in the Xinjiang region. However, the assessment, utilization and conservation of Arnebiae Radix resources are still unexplored. In this study, we evaluated the genetic diversity of three Arnebiae Radix populations across 47 regions (Ae = 16, Ag = 16, Ad = 15) in Xinjiang, China, using inter-simple sequence repeat (ISSR) molecular markers. In total, 48 alleles were amplified by six pairs of primers screened with ISSR markers. The average number of effective alleles (Ne) was 1.5770. The percentage of interspecific genetic polymorphisms in A. guttata (Ag = 89.58 %) was greater than that in A. euchroma. and A. decumbens (Ae = Ad = 87.50 %). Intraspecific genetic polymorphisms, Bo Le (BL) population of A. euchroma exhibited the highest percentage of polymorphic bands (PPB% =58.33 %, Na = 1.313, Ne = 1.467, I = 0.0.366, H = 0.255), which indicated high genetic diversity. In contrast, the Tuo Li (TL) population of A. guttata had the lowest values for these parameters (PPB% =0.00 %, Na = 0.313, Ne = 1,000, I = 0.000, H = 0.000). The Arnebiae Radix germplasms were classified into two major groups (I and II) based on UPGMA cluster analysis (Fig. 8a) and principal coordinate analysis (PCOA). In addition, A. decumbens is placed in a separate category due to its high differentiation coefficient. The AMOVA and genetic differentiation coefficient results indicated that the genetic variation in Arnebiae Radix was predominantly due to intrapopulation differences (78 %). Additionally, the gene flow index (Nm) between populations was 2.4128, which further indicated that the genetic diversity of Arnebiae Radix was greater at the intrapopulation level. The destruction of the ecological environment leads to the continuous reduction and degradation of the genetic diversity of Arnebiae Radix germplasm resources. In this study, we used ISSR molecular markers to analyze the genetic diversity and relatedness of Arnebiae Radix, which revealed the genetic relationship of Arnebiae Radix germplasm resources at the molecular level and provided a scientific basis for future research on selecting and breeding good varieties, evaluating the quality of Arnebiae Radix, and conserving and utilizing its resources.

Comparative Analysis of Gut Bacterial Community Composition in Two Tropical Economic Sea Cucumbers under Different Seasons of Artificial Environment.

With the continuous rise of the sea cucumber aquaculture industry in China, the tropical sea cucumber aquaculture industry is also improving. However, research on the gut microorganisms of tropical sea cucumbers in captivity is scarce. In this study, high-throughput sequencing methods were used to analyze the gut microbial composition of Stichopus monotuberculatus and Holothuria scabra in the dry season and wet season of artificial environments. The results showed that 66 phyla were obtained in all samples, of which 59 phyla were obtained in the dry season, and 45 phyla were obtained in the wet season. The Tax4Fun analysis showed that certain gut bacterial communities affect the daily metabolism of two sea cucumber species and are involved in maintaining gut microecological balance in the gut of two sea cucumber species. In addition, compared with differences between species, PCoA and UPGMA clustering analysis showed the gut prokaryotes of the same sea cucumber species varied more in different seasons, indicating that the influence of environment was higher than the feeding choices of sea cucumbers under relatively closed conditions. These results revealed the gut bacterial community composition of S. monotuberculatus and H. scabra and the differences in gut bacterial structure between two sea cucumber species in different seasons were compared, which would provide the foundation for tropical sea cucumber aquaculture in the future.

Genetic variability and population divergence of Rhododendron platypodum Diels in China in the context of conservation

Genetic diversity in endangered species is of special significance in the face of escalating global climate change and alarming biodiversity declines. Rhododendron platypodum Diels, an endangered species endemic to China, is distinguished by its restricted geographical range. This study aimed to explore genetic diversity and differentiation among its populations, gathering samples from all four distribution sites: Jinfo Mountain (JFM), Zhaoyun Mountain (ZYM), Baima Mountain (BMM), and Mao’er Mountain (MEM). We employed 18 pairs of Simple Sequence Repeat (SSR) primers to ascertain the genetic diversity and structural characteristics of these samples and further utilized 19 phenotypic data points to corroborate the differentiation observed among the populations. These primers detected 52 alleles, with the average number of observed alleles (Na) being 2.89, the average number of effective alleles (Ne) being 2.12, the average observed heterozygosity (Ho) being 0.57, and the expected heterozygosity (He) being 0.50. This array of data demonstrates the efficacy of the primers in reflecting R. platypodum’s genetic diversity. SSR-based genetic analysis of the populations yielded Ho, He, and Shannon index (I) values ranging from 0.47 to 0.65, 0.36 to 0.46, and 0.53 to 0.69, respectively. Notably, the ZYM population emerged as the most genetically diverse. Further analysis, incorporating molecular variance, principal component analysis, UPGMA cluster analysis, and structure analysis, highlighted significant genetic differentiation between the Chongqing (BMM, JFM, ZYM) and Guangxi (MEM) populations. Morphological data analysis corroborated these findings. Additionally, marked genetic and morphological distinctions were evident among the three Chongqing populations (BMM, JFM, and ZYM). This suggests that, despite the observed regional differentiation, R. platypodum’s overall genetic diversity is relatively constrained compared to other species within the Rhododendron genus. Consequently, R. platypodum conservation hinges critically on preserving its genetic diversity and protecting its distinct populations.

Study on the characteristics of genetic diversity of different populations of Guizhou endemic plant Rhododendron pudingense based on microsatellite markers

BackgroundRhododendron pudingense, firstly discovered in Puding county of Guizhou province in 2020, have adapted to living in rocky fissure habitat, which has important ornamental and economic values. However, the genetic diversity and population structure of this species have been rarely described, which seriously affects the collection and protection of wild germplasm resources.ResultsIn the present study, 13 pairs of primers for polymorphic microsatellite were used to investigate the genetic diversity of 65 R. pudingense accessions from six different geographic populations. A total of 254 alleles (Na) were obtained with an average of 19.5 alleles per locus. The average values of polymorphic information content (PIC), observed heterozygosity (Ho), and expected heterozygosity (He) were 0.8826, 0.4501, and 0.8993, respectively, These results indicate that the microsatellite primers adopted demonstrate good polymorphism, and the R. pudingense exhibits a high level of genetic diversity at the species level. The average genetic differentiation coefficient (Fst) was 0.1325, suggested that moderate divergence occurred in R. pudingense populations. The average values of genetic differentiation coefficient and gene flow among populations were 0.1165 and 3.1281, respectively. The analysis of molecular variance (AMOVA) indicated that most of the population differences (88%) were attributed to within-population variation. The PCoA results are consistent with the findings of the UPGMA clustering analysis, supporting the conclusion that the six populations of R. pudingense can be clearly grouped into two separate clusters. Based on Mantel analysis, we speculate that the PD population may have migrated from WM-1 and WM-2. Therefore, it is advised to protect the natural habitat of R. pudingense in situ as much as possible, in order to maximize the preservation of its genetic diversity.ConclusionsThis is the first comprehensive analysis of genetic diversity and population structure of R. pudingense in Guizhou province. The research results revealed the high genetic diversity and moderate population diferentiation in this horticulture plant. This study provide a theoretical basis for the conservation of wild resources of the R. pudingense and lay the foundation for the breeding or cultivation of this new species.

Characters evolution of Encyclia (Laeliinae-Orchidaceae) reveals a complex pattern not phylogenetically determined: insights from macro- and micromorphology

Encyclia is the second-largest genus in the neotropical subtribe Laeliinae (Orchidaceae) and has more than 150 species, which are characterized by fairly consistent flower morphology. Its taxonomy and species boundaries, however, seem to be still under debate. In the present study, we first examined the lip micromorphology of 61 species of Encyclia sensu stricto. We correlated our results with external flower morphology and phylogenetic analyses performed on a combined dataset that included both nuclear (ITS, Xdh, PhyC) and plastid markers (ycf1, rpl32, and trnL-trnF). Phylogenetic reconstruction showed that Encyclia sensu stricto species form a coherent, monophyletic group. However, it is difficult to determine the relationships between the different groups within one larger clade. The groups all form distinct lineages that evolved from a common ancestor. The UPGMA cluster analysis for the seven qualitative micromorphological features clearly divides the genus into two main groups, the larger of which is further subdivided into two subgroups. None of these, however, overlap with any of the phylogeographic units distinguished in previously published papers or in presented article. It is worth noting that the groups resulting from the UPGMA analysis cannot be defined by macromorphological features. The pattern of similarities between species, taking into account both macro- and micromorphological features, is eminently mosaic in nature, and only a multifaceted approach can explain this enigmatic group.

Clinacanthus nutans genetic diversity and its association with anti-apoptotic, antioxidant, and anti-bacterial activities

Clinacanthus nutans (Burm. f.) Lindau has been extensively utilized in Thai folk medicine. However, there has been no prior exploration of its genetic diversity or its correlation with biological activity and phytochemical profiles. Herein, a total of 10 samples of C. nutans were collected from different geographic locations in different environments of Thailand, encompassing Northern, Northeastern, and Central regions. The genetic diversity study using sequence-related amplified polymorphism (SRAP) markers showed that all C. nutans samples were closely related, as indicated by UPGMA cluster analysis. When comparing the biological activities of C. nutans extracts, our findings demonstrated that those sourced from Northern Thailand exhibited the most potent activity in reducing lipopolysaccharide-inducing cell death, as accessed by cell viability assay. Furthermore, they showed remarkable antioxidant and antibacterial activities against Staphylococcus epidermidis, Staphylococcus aureus, Pseudomonas aeruginosa, and Escherichia coli. High-performance liquid chromatography (HPLC) analysis of phytochemical profiles revealed consistent chromatography peak patterns across all C. nutans extracts. However, they exhibited varying levels of phenolic contents, as judged by the Folin-Ciocalteu assay, which positively correlated with their observed activities. In conclusion, this study highlights the limited genetic variation within C. nutans population in Thailand. Furthermore, it underscores the association between the biological activity and the total phenolic contents which might be mainly impacted by environmental conditions.

Molecular Genetic Identification of Some Sweet Sorghum - Sorghum bicolor L. (Ankolib) Accessions – Sudan

This study is an attempt to identify some Sudanese Sweet Sorghum (Ankolib) [Sorghum bicolor (L.) Moench.] accessions using two types of DNA-based markers: RAPD and SSR. Seven (Ankolib) accessions were assayed, namely: Black Ankolib, Black White Ankolib, Dark Red Ankolib, Red Yellow Ankolib, White Ankolib, White Black Ankolib and Bengaga. All of the accessions were uniquely identified and fingerprinted. The levels of polymorphism among the accessions as revealed by (22) RAPD primers and (16) SSR primer pairs were (58%) and (76%) respectively, indicating that SSRs markers were highly polymorphic. The scored data of the two markers were analyzed using the Dice Coefficient to assess genetic relationships among the (7) (Ankolib) accessions. The results of the statistical analysis revealed that the accession Bengaga was distantly related to the other (6) accessions which all showed a close genetic similarity among them. UPGMA cluster analysis generated a dendrogram for each marker alone and for the combined data of the two markers. It was observed that in all of the dendrogram the accession Bengaga was found in a unique cluster thus indicating its uniqueness, since it is the only accession that has seeds that produce flour besides its juicy sweet stem.