Unweighted Pair-group Method With Arithmetic Averages Research Articles

Genetic Diversity Assessment of Cupressus gigantea W. C. Cheng & L. K. Fu Using Inter-Simple Sequence Repeat Technique

Cupressus gigantea W. C. Cheng & L. K. Fu is an endemic conifer tree species that is distributed widely along the northern portion of the deep gorge of the Yarlung Tsangbo River on the Tibetan Plateau. However, as a key plant species growing on the Tibetan plateau, C. gigantea has since become an endangered species due to habitat loss and degradation, overexploitation, and other factors. It has been listed as a first-grade national protected wild plant species in China. Accordingly, to conserve this plant species, we should obtain more information on its genetic structure. In this study, the genetic diversity and structure among 67 samples were evaluated by the inter-simple sequence repeat (ISSR) technique. Overall, 78 bands were produced with a molecular length of 200 bp to 3100 bp using 10 ISSR primers. The mean values for the average number of alleles (Na), effective number of alleles (Ne), Nei’s gene diversity (H), and Shannon’s information index (I) were 1.529, 1.348, 0.199, and 0.293, respectively. Additionally, the number of polymorphic loci (NPLs) and percentage of polymorphic loci (PPLs) averaged 41.25 and 52.90, respectively. Further, total variation among populations was 14.2%, while that within populations was 85.8%; accordingly, the within-population genetic differentiation was found to be significant (p < 0.001). These results demonstrated that a genetic structure model with K = 3 fitted the data best, which agreed with the unweighted pair group method with arithmetic average (UPGMA) cluster and the principal coordinate analysis (PCoA). These findings are beneficial for ensuring the development and genetic protection of C. gigantea populations in the future.

Determination of genetic diversity of two Lessonia species from the Atacama region using ISSR markers

Lessonia nigrescens and L. trabeculata are economically important kelp species in northern Chile. Despite their considerable value, the genetic diversity of these kelp has received limited attention in the Atacama region. This study aimed to analyze genetic diversity, establish genetic relationships, and identify diagnostic DNA markers in the Atacama region's L. nigrescens and L. trabeculata. Both species' Inter-sequence simple repeat (ISSR) band patterns showed high reproducibility and reliability. Among 17 ISSRs, 161 polymorphic bands were identified in Lessonia spp. Parameters, such as percentage polymorphism, number of alleles per locus, effective number of alleles, and Shannon information index, indicated that L. nigrescens had slightly higher genetic diversity than L. trabeculata. The Unweighted pair group method with arithmetic average (UPGMA) cluster analysis revealed two main clusters: one containing L. nigrescens and the other containing L. trabeculata. Additionally, four species diagnostic ISSR markers were identified for L. nigrescens and L. trabeculata. The ISSR markers proved valuable in detecting genetic diversity in L. nigrescens and L. trabeculata. This information is particularly important for marine management strategies and ensuring successful conservation.

Species Identification and Genetic Diversity Analysis of Medicinal Plants Aconitum pendulum Busch and Aconitum flavum Hand.-Mazz.

The classification system for the genus Aconitum is highly complex. It is also the subject of ongoing debate. Aconitum pendulum Busch and Aconitum flavum Hand.-Mazz. are perennial herbs of the genus Aconitum. Dried roots of these two plants are used in traditional Chinese medicine. In this study, morphological observations and ISSR molecular markers were employed to discriminate between A. flavum and A. pendulum, with the objective of gaining insights into the interspecies classification of Aconitum. The pubescence on the inflorescence of A. flavum was found to be appressed, while that on the inflorescence of A. pendulum was spread. UPGMA (unweighted pair-group method with arithmetic average) cluster analysis, PCoA (principal coordinates analysis), and Bayesian structural analysis divided the 199 individuals (99 individuals from DWM population and 100 individuals from QHL population) into two main branches, which is consistent with the observations of the morphology of pubescence on the inflorescence. These analyses indicated that A. flavum and A. pendulum are distinct species. No diagnostic bands were found between the two species. Two primer combinations (UBC808 and UBC853) were ultimately selected for species identification of A. flavum and A. pendulum. This study revealed high levels of genetic diversity in both A. flavum (He = 0.254, I = 0.395, PPB = 95.85%) and A. pendulum (He = 0.291, I = 0.445, PPB = 94.58%). We may say, therefore, that ISSR molecular markers are useful for distinguishing A. flavum and A. pendulum, and they are also suitable for revealing genetic diversity and population structure.

Application of SSR markers for assessment of genetic similarity and genotype identification in local winter wheat breeding program

Background. Simple sequence repeat (SSR) markers are widely used for genetic analysis in plant breeding, allowing for the investigation of genetic divergence and similarity of genotypes, identification of unique alleles and determination of levels of genetic diversity. Materials and Methods. Analysis of 42 wheat cultivars and lines from the bree­ding program of Poltava State Agrarian University was carried out using 11 SSR mar­kers located on different chromosomes. A set of 11 microsatellite single locus primer pairs was used in this study (Xgwm 11, Xgwm 44, Xgwm 46, Xgwm 135, Xgwm 174, Xgwm 186, Xgwm 194, Xgwm 219, Xgwm 312, Xgwm 372, Xgwm 389). Amplification of 11 loci was performed using the Kapa2G FastHotStart PCR Kit (Kapa Biosystems, Boston, USA). The mixture for PCR amplification contained 1.5 x Kapa2G buffer, 0.5 mM dNTP mix, 0.5 μM of each primer (Sigma-Aldrich), 1 unit of Kapa2G FastHotStart DNA Polymerase and 11.8 ng of template DNA in a volume of 25 μl. Fragment lengths were determined using GeneMapper 4.0 software (Applied Biosystems). Dendrogram was constructed using UPGMA (unweighted pair-group method with arithmetic average) in DarWin 6.0 software (Perrier and Jacquemoud-Collet 2006) for clustering analysis. Results and Discussion. The number of alleles detected per locus varied from 5 (Xgwm 11, Xgwm 135, Xgwm 219) to 12 (Xgwm 174). A total of 80 alleles were identified for the 11 loci studied. Among these, 25 unique alleles were found, each of which was present in only one genotype. The polimorphism information content (PIC) values ranged from 0.48 to 0.87. The markers Xgwm 174 (PIC = 0.87), Xgwm 389 (PIC = 0.84) and Xgwm 372 (PIC = 0.83) were the most polymorphic in our study. We obtained a distribution of cultivars and lines by genetic similarity into five clusters. Conclusion. The use of SSR markers made it possible to identify rare alleles within the varieties presented. The study of the genetic similarity of the presented geno­types showed their relationship according to their origin. It was shown that unique alleles tended to occur in certain local breeding genotypes. This study has shown that genotypes representing the local Ukrainian breeding program often have the same allelic variants and at the same time some genotypes have unique allelic variants. The results obtained from the study of 42 winter wheat genotypes based on 11 SSR markers showed that molecular markers can be very useful in assessing genetic similarity and identifying genotypes in the local breeding program.

Analyses of genetic diversity and population structure of endemic and endangered species Sideritis gulendamii (Lamiaceae) and implications for its conservation

AbstractSideritis gulendamii is a perennial, endangered plant endemic to Türkiye with narrow and fragmented populations encountered in gypsum and marl soil. This species is known as mountain tea and also has a significant potential for use for medicinal and aromatic purposes. Assessing the genetic diversity of this species holds significant importance in its conservation efforts due to its specific habitat requirements, small and isolated populations, and recent threats imposed on these populations. This study determined genetic diversity at the species and population levels using the inter simple sequence repeat (ISSR) fingerprinting method on 157 individuals from seven natural populations. We observed that the species-level genetic diversity is relatively high (H = 0.189, I = 0.298), but the population-level is low (H = 0.150, I = 0.231). The greater total genetic variation within populations was determined as 76% using the analysis of molecular variance (AMOVA). The obtained value of genetic differentiation (Gst = 0.208, Φpt = 0.24) among populations is considered to be at a moderate level, whereas gene flow appears to be high (Nm = 1.899). Supportive results were reached using the STRUCTURE cluster analysis, Unweighted Pair Group Method with Arithmetic Averages (UPGMA) dendrogram, and Principal Coordinate Analysis (PCoA). The positive correlation between the matrices of genetic distance and geographic distance is determined to be statistically significant, with values of r = 0.566 and p < 0.001 in the Mantel test. Some strategies were developed using the genetic variability pattern of this endangered species for its conservation.

SSR-marker Assisted Evaluation of Genetic Diversity in Greengram [Vigna radiata (L.) Wilcezk

Background: Assessing genetic diversity in greengram is a prerequisite for its genetic improvement for yield and quality. DNA markers such as simple sequence repeats (SSRs) have been preferred in this crop for the analysis of genetic diversity because SSR markers are locus-specific, widely dispersed throughout the genome, highly polymorphic due to variation in repeat units, highly informative because of co-dominant nature, high reproducibility and ease of assay by PCR (Polymerase chain reaction). The current study aimed to study the genetic diversity among the mutants of greengram at the molecular level using SSR markers. Methods: In this study, twenty-five SSR markers were used to analyze the genetic diversity amongst twenty mutant genotypes of greengram along with their parents. Genomic DNA was isolated from the leaves by using the standard CTAB DNA extraction method. Then DNA purification and PCR amplifications were carried out. The genetic variability and diversity among genotypes was examined by assessing the scoring of the amplified bands by SSR -PCR amplification. Result: Seventeen SSR primers generated 102 polymorphic bands with an average of the six polymorphic bands per primer. The number of alleles per locus ranged from four to nine. The size of amplification product varied for each primer and the range found to be 100bp to 2000bp. The mean polymorphic information content (PIC) value for SSR markers was found to be 0.6335. The value of Jaccard’s similarity coefficient had ranged from 0.07-0.70 with an average value of 0.38. The dendrogram constructed on SSR molecular markers data through the unweighted pair group method with arithmetic averages (UPGMA) method had enabled grouping of the genotypes into thirteen clusters. The results indicate the usefulness of SSR markers in the assessment of genetic variability and diversity among the mutant genotypes of greengram.

Assessing Genetic Diversity and Population Structure of Rice Genotypes using ISSR Markers

Background: The realm of genetic diversity within rice is immense and undermining it provides the opportunity to utilize them in rice improvement programs. Hence in our study, we aimed to undermine the genetic composition and structure of the selected rice accessions utilizing ISSR marker systems. Methods: ISSR analysis encompassed a set of thirty genotypes, comprising 16 cultivated varieties and 14 landraces. The screening was performed with a total of 49 ISSR primers. The consensus tree constructed from banding patterns generated by ISSR-PCR clustered 30 genotypes according to their respective genomes. The Sequential Agglomerative Hierarchical Non-overlapping (SAHN) clustering was employed with the Unweighted Pair Group Method with Arithmetic Averages (UPGMA) method. The grouping of the 30 accessions was carried out through data analysis using NTSYSpc 2.02. Result: Utilizing 49 ISSR markers, the cluster analysis produced three clusters. These clusters displayed pronounced separation and exhibited evident patterns. The Cluster I encompassed Bharathi, BG367-2, PTB33, ASD9, ASD16, ASD20, Rathu Heenati and Columbia-2. Notably, the largest cluster was Cluster II comprising 20 accessions, while Cluster III contained only Jeeraga Samba and Basmati 370. The study validates the efficacy of ISSR markers in detecting polymorphism within and among rice populations and/or species. The resulting DNA profiles hold potential for serving as diagnostic fingerprints of both cultivated and wild rice germplasm, aiding in comprehending evolutionary relationships.

Revealing genetic diversity of wild Phalaenopsis orchids in Thailand through Random Amplified Polymorphic DNA markers

Abstract. Kate-ngam S, Jantasuriyarat C, Lakote P, Promchot T, Chueakaew C. 2023. Revealing genetic diversity of wild Phalaenopsis orchids in Thailand through Random Amplified Polymorphic DNA markers. Biodiversitas 24: 5409-5417. Wild Phalaenopsis orchids are widely distributed in Thailand, especially along the banks of the Mekong River. The tremendous decrease in the population of these orchids is a matter of concern for maintaining and preventing genetic loss in the natural ecosystem. This study aimed to determine the genetic diversity of 50 wild Phalaenopsis accessions collected from the northeastern of Thailand using random amplified polymorphic DNA (RAPD) markers. The 204 polymorphic bands generated from 27 RAPD primers were employed for fingerprinting these orchid accessions. Dice’s similarity coefficients ranged from 0.43 to 0.98, with an average of 0.65. In general, a dendrogram constructed based on the unweighted pair group method with arithmetic average (UPGMA) grouped these wild Phalaenopsis accessions into two clusters, namely P. pulcherrima and P. ubonensis clusters. The UPGMA clustering pattern and principal component analysis (PCA) corresponded well with their morphological classification and ploidy level. Our results suggest that this wild Phalaenopsis orchid exhibits a moderate level of relatedness. This might be a consequence of habitat destruction and human over-exploitation which limit gene flow and cause genetic drift among populations. The present finding supports the urgent need for a systematic conservation effort of this orchid species in Thailand.

Detection of in silico SSR Markers Specific to Uzun and Kırmızı Cultivars in Pistachio

In the current paper, it was aimed to detect the SSR markers that can be used in the prevention of confusion that may occur in breeding or nurseries, and directly genetically separating Uzun and Kırmızı pistachio cultivars from other commercial cultivars. A total of genotypes of 16 Pistacia vera species, one P. atlantica, one P. eurycarpa and two P. terebinthus species were obtained from the farmer's orchard in Nizip district of Gaziantep province for genetic characterization. Genetic diversity and clustering analyzes were performed with UPGMA (Unweighted Pair Group Method with Arithmetic Average) and STRUCTURE 2.3.4 programs using the scored SSR loci. Genetic relationship and population structure of genotypes were defined using common and distinct polymorphic PCR fragments. Cultivar-specific markers to be used in identifying and distinguishing the genetic structure of Uzun and Kırmızı cultivars were carried out in the current research. CUPOhBa2127 marker has the highest allele number (Na=10). In addition, 11 out of 25 SSR markers were explained as cultivar-specific SSRs that can distinguish Uzun and Kırmızı cultivars. These markers can be used directly by breeders and geneticists without any preliminary screnning of the markers. A quite serious providence will be achieved in the cost and time that will occur with the preliminary analysis, and thus, the confusion that may occur in large scale orchard establishments or nurseries will be reduced to pretty low levels with DNA analysis.

Clonal aggregation of fluconazole-resistant Candida tropicalis isolated from sterile body fluid specimens from patients in Hefei, China.

Candida tropicalis, a human conditionally pathogenic yeast, is distributed globally, especially in Asia-Pacific. The increasing morbidity and azole resistance of C. tropicalis have made clinical treatment difficult. The correlation between clonality and antifungal susceptibility of clinical C. tropicalis isolates has been reported. To study the putative correlation in C. tropicalis isolated from normally sterile body fluid specimens and explore the distinct clonal complex (CC) in Hefei, 256 clinical C. tropicalis isolates were collected from four teaching hospitals during 2016-2019, of which 30 were fluconazole-resistant (FR). Genetic profiles of 63 isolates, including 30 FR isolates and 33 fluconazole-susceptible (FS) isolates, were characterized using multilocus sequence typing (MLST). Phylogenetic analysis of the data was conducted using UPGMA (unweighted pair group method with arithmetic averages) and the minimum spanning tree algorithm. MLST clonal complexes (CCs) were analyzed using the goeBURST package. Among 35 differentiated diploid sequence types (DSTs), 16 DSTs and 1 genotype were identified as novel. A total of 35 DSTs were assigned to five major CCs based on goeBURST analysis. CC1 (containing DST376, 505, 507, 1221, 1222, 1223, 1226, and 1229) accounted for 86.7% (26/30) of the FR isolates. However, the genetic relationships among the FS isolates were relatively decentralized. The local FR CC1 belongs to a large fluconazole non-susceptible CC8 in global isolates, of which the putative founder genotype was DST225. The putative correlation between MLST types and antifungal susceptibility of clinical C. tropicalis isolates in Hefei showed that DSTs are closely related to FR clones.

Morphology and SSR Markers-Based Genetic Diversity Analysis of Sesame (Sesamum indicum L.) Cultivars Released in China

Sesame is a highly valuable crop with significant global importance due to its nutritional and economic value. To better understand the genetic diversity of sesame genotypes at both molecular and morphological levels, a comprehensive study was conducted using 25 pairs of simple sequence repeat (SSR) primers and 56 biological traits in a collection of 183 sesame accessions, which comprised 101 Chinese cultivars, 62 landraces, and 20 exotic accessions. The analysis revealed a total of 166 SSR polymorphic bands, with an average of 6.64 bands per marker. The values of Shannon’s information index ranged from 0.2732 to 0.6497, indicating a moderate level of genetic diversity. The polymorphic information index ranged from 0.0859 to 0.6357, further supporting the presence of genetic variation. The average frequency of heterozygous genotypes was calculated as 0.34, suggesting a relatively narrow genetic diversity. The application of the unweighted pair group method with arithmetic averaging (UPGMA) clustering and principal component analysis allowed for the categorization of the 183 sesame accessions into three distinct groups. Furthermore, the genetic diversity coefficient of sesame germplasm is generally constrained, with no significant difference observed between the genetic diversity coefficient of Chinese cultivars and that of foreign resources. The results provide valuable data for various applications, including the breeding and promotion of new sesame cultivars in China, the protection of new variety rights, the inquiry and identification of DNA genetic information of cultivars, as well as the development and utilization of sesame germplasm resources both domestically and internationally.

ISSR Analysis to Detect Genetic Variation Among Some Lentil Genotypes in Syria

Lentil (Lens culinaris Medik) plays a significant role in human and animal nutrition. It is important to generate baseline information on genetic diversity of local and introduced lentil in Syria. Therefore, this study aimed to assess diversity and relationship among two local varieties and 35 introduced lentil lines from ICARDA using 20 Inter Simple Sequence Repeats (ISSR) primers.18 primers were able to amplify DNA bands with a total of 184 bands. Primers ISSR5, ISSR11, ISSR13, ISSR15 and ISSR16 presented 100% polymorphism percentage. The mean value of polymorphism percentage was 87.31%. ISSR primers could identify 19 unique bands in all genotypes, 12 of them were positive bands (present) and 7 were negative bands (absent). Primer ISSR11 was able to detect 3 positive unique bands in genotype Ln20. The UPGMA (unweighted pair group method with arithmetical averages) clustering based on ISSR data grouped 37 lentil genotypes into 6 clusters. The lowest genetic distance (0.20) was observed between (Ln15 and Ln16, Ln21 and Ln22, Ln27 and Ln28) which proves that they are closely related. While Ln24 presented the highest genetic distance (0.49) with both Ln18 and Idleb3 which refers to their genetic divergence.

Identification of Eight High Yielding Strains via Morpho-Molecular Characterization of Thirty-Three Wild Strains of Calocybe indica.

Calocybe indica, generally referred as milky mushroom, is one of the edible mushroom species suitable for cultivation in the tropical and sub-tropical regions of the world. However, lack of potential high yielding strains has limited its wider adaptability. To overcome this limitation, in this study, the germplasms of C. indica from different geographical regions of India were characterized based on their morphological, molecular and agronomical attributes. Internal transcribed spacers (ITS1 and ITS4)-based PCR amplification, sequencing and nucleotide analysis confirmed the identity of all the studied strains as C. indica. Further, evaluation of these strains for morphological and yield parameters led to the identification of eight high yielding strains in comparison to the control (DMRO-302). Moreover, genetic diversity analysis of these thirty-three strains was performed using ten sequence-related amplified polymorphism (SRAP) markers/combinations. The Unweighted Pair-group Method with Arithmetic Averages (UPGMA)-based phylogenetic analysis categorized the thirty-three strains along with the control into three clusters. Cluster I possesses the maximum number of strains. Among the high yielding strains, high antioxidant activity and phenol content was recorded in DMRO-54, while maximum protein content was observed in DMRO-202 and DMRO-299 as compared with the control strain. The outcome of this study will help the mushroom breeders and growers in commercializing C. indica.

Differential Detection of Alternaria alternata Haplotypes Isolated from Carya illinoinensis Using PCR-RFLP Analysis of Alt a1 Gene Region.

Alternaria black spot disease on pecan is caused by the opportunistic pathogen Alternaria alternata and poses a serious threat to the local South African and global pecan industry. Several diagnostic molecular marker applications have been established and used in the screening of various fungal diseases worldwide. The present study investigated the potential for polymorphism within samples of A. alternata isolates obtained from eight different geographical locations in South Africa. Pecan (Carya illinoinensis) leaves, shoots, and nuts-in-shuck with Alternaria black spot disease were sampled, and 222 A. alternata isolates were retrieved. For rapid screening to identify Alternaria black spot pathogens, polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of the Alternaria major allergen (Alt a1) gene region was used, followed by the digestion of the amplicons with HaeIII and HinfI endonucleases. The assay resulted in five (HaeIII) and two (HinfI) band patterns. Unique banding patterns from the two endonucleases showed the best profile and isolates were grouped into six clusters using a UPGMA (unweighted pair group method with arithmetic averages) distance matrix (Euclidean) dendrogram method on R-Studio. The analysis confirmed that the genetic diversity of A. alternata does not depend on host tissues or the pecan cultivation region. The grouping of selected isolates was confirmed by DNA sequence analysis. The Alt a1 phylogeny corroborated no speciation within the dendrogram groups and showed 98-100% bootstrap similarity. This study reports the first documented rapid and reliable technique for routine screening identification of pathogens causing Alternaria black spot in South Africa.

Phylogenetic Relationships and Diversity in Leymus (Poaceae, Triticeae) Based on Simple Sequence Repeats Markers

Aims: The objective of the study was to investigate: (1) the Ns genome donor and elucidate the origins of the Xm genome of Leymus; (2) evaluate the phylogenetic relationships among these species.
 Methodology: The CTAB (cetyltrimethylammonium bromide) procedure was used to extract total genomic DNA from fresh leaf tissue. A total of 150 pairs of SSR primers were tested to screen those produced polymorphic DNA bands to continue further analysis with Elymus species and 13 diploid perennial species as templates. The GS was used to construct a dendrogram via the unweighted pair group method with arithmetic average (UPGMA) and the SHAN (sequential, hierarchical, agglomerative, and nested clustering) routine in the NTSYS-pc program.
 Results: The primers WMC475, WMC11 and QWM213 showed more expansion efficiency in the research. There were significant diversity and polymorphism between Leymus and related diploid Triticeae species based on SSR makers. The largest GS coefficient values between Pse. stipifolia and Elymus hystrix indicates that the genetic distance is the closest and has a closer genetic relationship. In clade I, the Leymus species formed a very wellsupported into a small distinct group (Ia) first. Specifically, L. racemosus, L. salinus, L. secalinus and L. triticoides were clustered closely.
 Conclusion: Psathyrostachys juncea, Psa. huanshanica and Psa. fragilis (Ns genome) clustered together into clade I with Leymus species, which further illustrates Leymus that contains Ns genome is more closely related to Psathyrostachys. St genome and J genome did not participate in the origin of Leymus, and the genetic relationship and genetic distance of Leymus species are related to geographical distribution and environment.

Wing Morphometrics of Forensic Important Fly Species in Kelantan, Malaysia

This research discusses the possibility of determining the species and sex of necrophagous flies by examining their wing morphology. Fresh beef meat (500 g) was placed in both rural and urban areas of Kelantan, Malaysia, and third instar maggots were collected for rearing from the third to the seventh day. Adult flies were killed with chloroform and their species and sexual status were determined using standard procedures. After detaching their wings, the morphology was documented using a Leica MC 170HD digital camera attached to a Leica stereo microscope. Thirteen wing landmarks were chosen for geometric morphometric analysis. Principal Component Analysis (PCA), canonical variate analysis (CVA), centroid size variation, and the unweighted pair-group method with arithmetic averages (UPGMA) were used to analyse the wing morphology of Chyrsomya megacephala (Fabricius, 1794), Chrysomya rufifacies (Macquart, 1843), and Sarcophaga ruficornis (Fabricius, 1794) The results indicate that sex and fly species can be distinguished based on wing morphology, and that CVA is more effective at species differentiation than sex grouping using Malahanobis distances, with a P value of 0.0001. When comparing different species and sexes of the fly, CVA demonstrates distinct clustering. Identification of necrophagous fly wings is a useful alternative tool for fly classification.

Characterization and Application of EST-SSR Markers Developed from Transcriptome Sequences in Elymus breviaristatus (Poaceae: Triticeae).

Elymus L. is the largest genus in the Triticeae tribe. Most species in this genus are highly stress resistant, with excellent forage value. Elymus breviaristatus, a rare species endemic to the Qinghai-Tibet Plateau (QTP), is declining due to habitat fragmentation. However, genetic data for E. breviaristatus are limited, with expressed sequence tag (EST) markers being particularly rare, hampering genetic studies and protection measures. We obtained 9.06 Gb clean sequences from the transcriptome of E. breviaristatus, generating 171,522 unigenes, which were assembled and functionally annotated against five public databases. We identified 30,668 SSRs in the E. breviaristatus transcriptome, from which 103 EST-SSR primer pairs were randomly selected. Of these, 58 pairs of amplified products of the expected size, and 18 of the amplified products were polymorphic. Model-based Bayesian clustering, the unweighted pair group method with arithmetic average (UPGMA), and principal coordinate analysis (PCoA) of 179 wild E. breviaristatus in 12 populations using these EST-SSRs were generally consistent, grouping the 12 populations into two major clades. Analysis of molecular variance (AMOVA) found 70% of the genetic variation among the 12 populations and 30% within the populations, indicating a high level of genetic differentiation (or low gene exchange) among the 12 populations. The transferability of the 58 successful EST-SSR primers to 22 related hexaploid species was 86.2-98.3%. UPGMA analysis generally grouped species with similar genome types together. Here, we developed EST-SSR markers from the transcriptome of E. breviaristatus. The transferability of these markers was evaluated, and the genetic structure and diversity of E. breviaristatus were explored. Our results provide a basis for the conservation and management of this endangered species, and the obtained molecular markers represent valuable resources for the exploration of genetic relationships among species in the Elymus genus.

Variasi dan Analisis Fenetik Aksesi Kembang Sungsang (Gloriosa superba L.) di Daerah Istimewa Yogyakarta Berdasarkan Karakter Morfologi dan Anatomi

Kembang sungsang (Gloriosa superba L.) is a member of Colchicaceae family and distributed in tropical areas such as India, Malaysia, and Indonesia. G. superba has a high colchicine content, so it is widely used as a traditional medicine and biomutagen. The diverse habitats of G. superba have potential to create variations. The aims of this study were to determine the morphological, anatomical variations, and phenetic relationship of G. superba in Yogyakarta. A sample of 12 accessions was taken from 4 regencies in Yogyakarta: Bantul, Sleman, Kulon Progo, and Gunungkidul. Morphological characterization are tubers, stems, leaves, flowers, and fruit. Transversal section of leaves were prepared using paraffin embedding method to observe leaf structure and paradermal preparations to observe the leaf epidermis. The similarity index between OTUs is calculated using the Gower General Similarity Coefficient, clustering using UPGMA (Unweighted Pair Group Method with Arithmetic Averages) algorithm to form a dendrogram with MVSP (Multivariate Statistical Package) software. The results showed that the morphological variations of G. superba in Yogyakarta were large in terms of stem height, branching, number of leaves, leaf arrangement, leaf size, tuber shape, and tuber diameter. Leaf arrangement of G. superba population have 3 types: opposite, alternate, and mixed. Anatomical variations were large in terms of adaxial epidermal thickness, lamina thickness, midrib thickness, transport bundle size, stomatal size, and stomatal density. Based on the phenetic analysis, morphological characters are grouped into two clusters, while anatomical character into four clusters without pattern.

The assessment of genetic diversity and population structure of endemic Scutellaria yildirimlii (Lamiaceae) for conservation purposes

Scutellaria yildirimlii is an endangered perennial endemic species from Turkey and belongs to the family Lamiaceae, which has a high number of medicinal and aromatic plants. It is crucial to determine genetic diversity and population structure of this species for its conservation measures; therefore, 111 individuals from five natural populations of S. yildirimlii were investigated by using 15 inter simple sequence repeats (ISSR) primers. The percentage of polymorphic loci (PPL), Nei?s gene diversity (H), and Shannon?s information index (I) at the species and population-level were determined as 93.9%, 0.183, 0.292 and 56.5%, 0.158, 0.242, respectively. The analysis of molecular variance (AMOVA) showed that there is more genetic variation within populations (84%) than among populations (16%). Nei?s differentiation coefficient (GST = 0.144) was determined to be moderate, which was confirmed by the level of genetic differentiation among populations. Gene flow (Nm = 2.984) showed high genetic exchange among populations. Pairwise genetic distance values among populations ranged from 0.0219 to 0.0512. The Mantel test revealed a statistically significant positive correlation between genetic and geographical distance (r = 0.493, p < 0.001). The Unweighted Pair Group Method with Arithmetic Averages (UPGMA) dendrogram and Principal Coordinate Analysis (PCoA) showed similar results. STRUCTURE analysis (?K = 3) revealed that the K test yielded maximum peaks for 3 clusters. Based on the findings, measures for genetic conservation and management of this species were presented.

Assessment of craniometric sexual dimorphism and ontogenetic variation in invasive Rattus norvegicus and R. rattus from urban and peri-urban areas of Gauteng Province, South Africa

Abstract We evaluated craniometric sexual dimorphism and ontogenetic (age) variation in invasive Rattus norvegicus and R. rattus from urban and peri-urban areas of Gauteng Province, South Africa, using univariate and multivariate analyses. Two-way analysis of variance (ANOVA), percent contribution of the sum of squares (%SSQs) of each source of variation, principal components analysis (PCA) and unweighted pair-group method with arithmetic averages (UPGMA) cluster analysis showed no sexual dimorphism in both species, however in both species, significant age variation between five age classes based on maxillary molar toothrow cusp eruption and wear was found and the age classes were pooled into juveniles (i.e., individuals of tooth-wear class I), sub-adults (II–III), and adults (IV–V). Few variables showed statistically significant sex-age interaction. The largest %SSQs to the total variance were due to error (i.e., residual), suggesting that apart from sex, age, and their interaction, there were other components that are responsible for the variation. Our approach may be useful for partitioning the effect of sexual dimorphism and ontogenetic variation in other studies, such as our stable isotope analysis-based trophic ecological studies of Rattus species from urban and peri-urban areas of Gauteng Province, South Africa.