Unweighted Pair-group Method With Arithmetic Averages Research Articles

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.

Simple Sequence Repeat (SSR)-Based Genetic Diversity in Interspecific Plumcot-Type (Prunus salicina × Prunus armeniaca) Hybrids.

The main objective of many fruit-breeding programs around the world is the release of new cultivars from interspecific hybridizations between species of the Prunus genus. Plum × apricot (Prunus salicina Lindl. × Prunus armeniaca L.) are the most widespread interspecific hybrids, which include plumcots, pluots, and apriums. In this work, 115 accessions of interspecific hybrids from different origins and 27 reference genotypes of apricot and other diploid plum species were analyzed using eight simple sequence repeat (SSR) markers to assess the population structure and current genetic diversity. A total of 149 alleles were obtained, with an average of 19 alleles per locus. The overall polymorphic information content (PIC) mean value of SSR markers was 0.81, indicating a high degree of polymorphism of the SSR. The genetic analysis revealed 141 unique genotypes and two synonyms. The unweighted pair group method with arithmetic averages (UPGMA) dendrogram and the population structure with five groups inferred through the discriminant analysis of principal components (DAPC) revealed a clear genetic differentiation between apricot genotypes and the rest of the accessions since the interspecific hybrids clustered with the Japanese plum genotypes. Repeated backcrosses between interspecific hybrids with plum genotypes could be the cause of the higher genetic proximity of the hybrids with respect to plum than with apricot genotypes. This corresponds to the fruit morphology and agronomic behavior observed in most interspecific hybrids, which also resemble plums more than apricots.

Phylogenetic Analysis of Ryegrass (Lolium rigidum) Populations and the Proliferation of ALS Resistance in Saudi Arabia

Morphological and simple sequence repeat (SSR) approaches were used to determine the genetic diversity of 29 ryegrass (Lolium rigidum) genotypes belonging to eight populations collected from several regions in Saudi Arabia. In this study, 50 in Silico-developed SSR markers derived from genomic and expressed sequence tag (EST) microsatellites were examined. Analysis of variance showed highly significant differences in all studied traits. Cluster analysis based on the morphological data of the 29 Lolium genotypes and using PAST (paleontological statistics) software was performed. According to the results, clustering was based mostly on genotype location. The sensitive genotypes for herbicide were clustered in one group. In addition, using EST-SSR markers, we observed the existence of a considerable number of genetic variations among Lolium genotypes. From these markers, only 31 produced reasonable amplification products. The results showed that 23 SSR markers revealed that 74.19% were polymorphic. The number of alleles detected per primer ranged from one to five in the primer LTC SSR1. The tested primers amplified 1434 bands across eight populations, with an average of 46.26 bands per primer. The polymorphism information content (PIC) values ranged from 0.11 to 0.76 for the primers LT EST-SSR5 and LTC SSR1. The unweighted pair group method with arithmetic average (UPGMA) clustering of the 29 genotypes representing eight populations was based essentially on their locations and herbicide-tolerance levels. Most of the populations formed into four clusters, together representing genotypes. Moreover, the tolerant populations were distinguished from the sensitive ones. The relationship between the genetic diversity and geographical source of Lolium rigidum populations of Saudi Arabia was revealed through this study. The results showed that the efficiency of developed SSR markers are transferable across species. They have been helpful to assess the genetic diversity of the ryegrass population as this could be applied to differentiate between tolerant and sensitive populations of ryegrass.

Determination of Genetic Diversity and Similarity among Methicillin Resistant Staphylococcus aureus strains by RAPD-PCR

Purpose: The aim of this study was to determine the genetic diversity and genetic similarity of Methicillin Resistant S.aureus (MRSA) strains isolated from clinical samples. Material and Methods: Thirty-two MRSA strains were identified by conventional methods. Methicillin resistance of strains were determined by PCR using the mecA gene primers. These strains were genetically typed by RAPD PCR using primers OLP-11 and OLP-13. Bionumerics V7.5 (Applied Maths) program was used for analysis and dendograms were generated by unweighted pair group method with arithmetic averages (UPGMA). Results: All strains were confirmed as MRSA by PCR. Many different bands from 400 bp to 1000 bp were detected by RAPD PCR and five clusters (1-5) with OLP-11 and four clusters (1-4) were formed with OLP-13. In RAPD PCR performed with OLP-11 and OLP-13 primers, 80% (cluster 3-5) and 86% (cluster 1-4) similarities were found, respectively. MRSA strains isolated from wound samples were found to be more genetically similar to each other, with at least one in each cluster. Conclusion: RAPD PCR was found to be an effective method for the evaluation of genetic similarity and genetic diversity of MRSA strains.

Assessment of phylogenetic diversity and relationships among &lt;i&gt;Grewia tenax&lt;/i&gt; population in Sudan using RAPD and ISSR molecular markers

&lt;abstract&gt; &lt;p&gt;This research is conducted to study the genetic diversity of the genus &lt;italic&gt;Grewia tenax&lt;/italic&gt; in Sudan. This plant has a common vernacular Sudanese Arabic name: “Gudeim”. It is mainly cultivated in North Darfur and Western Sudan. Common uses of &lt;italic&gt;Grewia&lt;/italic&gt; species were overviewed in areas of nutrition, folk medicine and famine food. The genetic variation and genetic relationships among &lt;italic&gt;Grewia spp&lt;/italic&gt; populations from different regions were efficiently determined using RAPD and ISSR markers.&lt;/p&gt; &lt;p&gt;The results of genetic analysis were statistically analyzed by STATISTCA and GenALEx 6.5 software. The results of molecular variance revealed that 74% of total genetic diversity was due to within populations variations as opposed to 26% due to variations between populations unweighted pair- group method with arithmetic average (UPGMA) were constructed for and RAPD + ISSR. The UPGMA results showed variability of &lt;italic&gt;Grewia&lt;/italic&gt; genotypes.&lt;/p&gt; &lt;p&gt;It was concluded that both the marker systems RAPD and ISSR combination can be effectively used in determination of genetic relationships among &lt;italic&gt;Grewia tenax&lt;/italic&gt; genotypes.&lt;/p&gt; &lt;/abstract&gt;

Morphological and molecular characterization of banana clones growing in Turkey

This study was conducted to estimate genetic relationships among banana clones growing in Turkey via some morphological parameters and two molecular marker systems. In terms of yield parameters such as bunch weight, hand number, fruit weight, and total fruit number, Grand Nain (GN) clone came to the forefront with the highest values. It was followed by Azman (AZ), Dwarf Cavendish (DC), and Erdemli Yerli (EY) clones, respectively. To see the variation between clones more clearly, 24 RAPD (Random Amplified Polymorphic DNA) primers and 48 SRAP (Sequence Related Amplified Polymorphism) primer combinations were used in molecular analysis. The total number of amplified bands was 194, and 142 of them were polymorphic for RAPD analysis. The total and polymorphic bands per primer ranged from 0 to 14. A total of 272 bands were obtained from SRAP analysis, of which 154 were polymorphic. The total number of bands per primer varied between 0 and 11, and the number of polymorphic bands varied between 0 and 10. According to the dendrogram formed by unweighted pair group method with arithmetic averages (UPGMA) analysis, clones were collected in two main groups. In all evaluation methods, EY was completely separated from the other clones. GN, DC, and AZ were gathered on a single branch in the dendrogram. As a result of the SRAP assessment, DC and GN were the closest related clones. Contrary to the SRAP results, GN and AZ were identified as the most genetically related clones in morphological and RAPD assessments. This study showed that morphological and molecular characterization could be useful to assess the relationship among banana clones.

Genetic Diversity among Some Walnut (Juglans regia L.) Genotypes by SSR Markers

The food needs for increasing population, climatic changes, urbanization and industrialization, along with the destruction of forests, are the main challenges of modern life. Therefore, it is very important to evaluate plant genetic resources in order to cope with these problems. Therefore, in this study, a set of ninety-one walnut (Juglans regia L.) accessions from Central Anatolia region, composed of seventy-four accessions and eight commercial cultivars from Turkey, and nine international reference cultivars, was analyzed using 45 SSR (Simple Sequence Repeats) markers to reveal the genetic diversity. SSR analysis identified 390 alleles for 91 accessions. The number of alleles per locus ranged from 3 to 19 alleles with a mean value of 9 alleles per locus. Genetic dissimilarity coefficients ranged from 0.03 to 0.68. The highest number of alleles was obtained from CUJRA212 locus (Na = 19). The values of polymorphism information content (PIC) ranged from 0.42 (JRHR222528) to 0.86 (CUJRA212) with a mean PIC value of 0.68. Genetic distances were estimated according to the UPGMA (Unweighted Pair Group Method with Arithmetic Average), Principal Coordinates (PCoA), and the Structure-based clustering. The UPGMA and Structure clustering of the accessions depicted five major clusters supporting the PCoA results. The dendrogram revealed the similarities and dissimilarities among the accessions by identifying five major clusters. Based on this study, SSR analyses indicate that Yozgat province has an important genetic diversity pool and rich genetic variance of walnuts.

Application of inter-SINE amplified polymorphism (ISAP) markers for genotyping of Cucumis melo accessions and its transferability in Coleus spp

Abstract. Sormin SYM, Purwantoro A, Setiawan AB, Teo CH. 2021. Application of inter-SINE amplified polymorphism (ISAP) markers for genotyping of Cucumis melo accessions and its transferability in Coleus spp. Biodiversitas 22: 2918-2929. An unambiguous characterization of melon (Cucumis melo L.) accessions based on their morphological traits is often laborious and affected by environment when compared with molecular marker genotyping. Short interspersed nuclear elements (SINEs) are highly abundant non-autonomous and non-coding retrotransposons that are widely scattered over all chromosomes of eukaryotes. They can serve as a good molecular marker for routine genotyping in plant breeding and marker-assisted selection. This study aimed to apply inter-SINE amplified polymorphism (ISAP) markers for genotyping of Cucumis melo accessions and its transferability in Coleus spp. Twenty-one C. melo accessions, one C. metuliferus E. Mey. ex Naudin, and 15 accessions of Coleus spp. were used for ISAP marker development. A copy of cucumber-specific long interspersed nuclear element (LINE) and multiple copies of melon-specific SINE were identified and isolated. ISAP primers were designed from the highly conserved region of the SINEs and LINE. The melon and cucumber-specific ISAP markers showed a higher degree of polymorphism (87.5%-100%) than potato ISAP markers (60%-100%) in all the tested melon accessions. The unweighted pair group method with arithmetic average (UPGMA) dendrogram generated from polymorphic ISAP bands clearly distinguish the Cucumis melo accessions from their distantly related wild species C. metuliferus. The transferable nature of Cucumis ISAP marker system was demonstrated in Coleus species, where the marker differentiates the tested accessions.

Morphological and anatomical characters variation of Indigofera accessions from Java, Indonesia

Abstract. Muzzazinah, Suratman, Nurmiyati, Ariani SRD. 2021. Morphological and anatomical characters variation of Indigofera accessions from Java, Indonesia. Biodiversitas 22: 2104-2116. The objective of this research was to evaluate morphological and anatomical character variation of Indigofera accessions from Java, Indonesia. A total of 15 accessions from three species of Indigofera were collected from centers of Batik manufacturing in Java located in the following locations: West Java (Pangandaran), Yogyakarta (Bantul, Kulonprogo), Central Java (Sragen, Sukoharjo, Karanganyar) and East Java (Tuban). There were 14 tested morphological characters based on measurement of vegetative and generative organs. Anatomical characters were observed from paradermal sections and there were 12 tested characters. Analysis of variance was performed for observed morphological and anatomical characters data in order to test the significance of variation among accessions using SPSS software. The characters' mean values then were used to perform principal component analysis and cluster analysis using PAST software. A cluster analysis was conducted by applying an Unweighted Pair Group Method with Arithmetic Averages (UPGMA) in order to group the accessions based on morphological and anatomical character similarity. The analysis of variance for the evaluated morphological and anatomical characters revealed highly significant differences among accessions for all of the tested characters suggesting that there was a high degree of phenotypic diversity among Indigofera accessions. Principal component analysis indicated that the first 2 components accounted for 90.72 % and 88.96 % of the total variation for morphological and anatomical data sets, respectively. Cluster analysis using morphological characters data revealed three main clusters. Four main clusters were then highlighted in cluster analysis of the anatomical character data. The grouping of the accession into clusters showed that there was no correlation between ecological habitat origin and the character diversity expressed among Indigofera accession. However, accessions that came from the same species had the tendency to cluster together.

Genetic Diversity and Relationships of Terebinth (Pistacia terebinthus L.) Genotypes Growing Wild in Turkey

Genetic diversity and relationships of 54 wild-grown terebinths (Pistacia terebinthus L.) were determined using 40 SSR (simple sequence repeat) markers (38 in silico polymorphic SSR markers and 2 SSR markers). In silico polymorphic SSR analysis, 430 alleles were identified. The number of alleles per locus ranged from 3 to 25 with a mean value of 11 alleles per locus. The values of polymorphism information content (PIC) ranged from 0.34 (CUPOhBa4344) to 0.91 (CUPSiBa4072) with a mean PIC value of 0.68. Genetic distances were estimated according to the UPGMA (Unweighted Pair Group Method with Arithmetic Average), the Structure, and Principal Coordinates (PCoA) based clustering. The structure analysis and UPGMA clustering of the genotypes depicted two major clusters. PCoA results supported cluster analysis results. The dendrogram revealed two major clusters. Forty-two samples were obtained from the Kazankaya canyon and 12 samples from the Karanlıkdere region. The two regions are 130 km apart from each other but in a dendrogram, we did not find geographical isolation. The results proved the efficiency of SSRs for genetic diversity analysis in the terebinth. Based on the results, SSRs can be applied as a trustworthy tool for the evaluation of genetic diversity in terebinth genotypes. Molecular analysis on the terebinth genotypes in this study will promote the germplasm collection and the selection of the populations in future studies on terebinths for genetic mapping, genetic diversity, germplasm characterization, and rootstock breeding.

Diversity assessment of indigenous and exotic Diaporthe species associated with various crops using ISSR, URP and SRAP markers

Genetic diversity among the isolates representing five Diaporthe (syn: Phomopsis) species isolated from seeds of various crops representing both exotic as well as indigenous collections from India was analyzed using molecular markers, viz., inter-simple sequence repeats (ISSR), universal rice primers (URP) and sequence-related amplified polymorphism (SRAP). The isolates of Diaporthe showed differences among themselves by clustering distinctly which otherwise could not be distinguished with morphological characterization. The total number of polymorphic alleles was 323 with a range of 0.1–3.4 kb in ISSR, 293 with a range of 0.08–3.4 kb in URP and 293 with a range of 0.08–3.4 kb in SRAP. Genetic diversity determining parameters like polymorphic information content, expected heterozygosity, Shannon’s information index, effective multiplex ratio, and marker index was highest in URP markers. Unweighted pair group method with arithmetic average (UPGMA) analysis clustered the isolates into 2 major groups at 61% genetic similarity during combined analysis using these three sets of markers. Among molecular markers, URP markers showed superiority in detecting genetic diversity by differentiating both domestic and exotic isolates representing various species of Diaporthe. Exotic isolates of D. phaseolorum collected from jatropha showed the highest similarity whereas, indigenous isolates of D. phaseolorum isolated from soybean showed the highest level of variation. The isolates did not correspond to agro-ecological regions and the crop origin. This will be helpful in developing species-specific primers for detection of Diaporthe species.

Genetic Diversity of Castor Bean (Ricinus communis L.) Revealed by ISSR and RAPD Markers

Castor (Ricinus communis L.), known as castor oil plant or castor bean, is a non-edible oilseed crop. In the present study, the genetic diversity among 54 samples (3 wild and 51 cultivated) collected worldwide was evaluated using inter-simple sequence repeats (ISSRs) and random amplified polymorphic DNA (RAPD) markers. A total of 9 ISSR primers produced 83 high-resolution bands with 61 (74.53%) as polymorphic. The percentage of polymorphic bands per primer and the genetic similarity coefficient ranged from 54.55% (UBC-836) to 100% (UBC-808) and from 0.74 to 0.96, respectively. A total of 11 out of 20 RAPD primers amplified unique polymorphic products with an average percentage of polymorphic bands of 60.98% (56 polymorphic bands out of a total of 90 bands obtained). The percentage of polymorphic bands per primer ranged from 25% (OPA-02 and B7) to 90.91% (B21) with the genetic similarity coefficient ranging from 0.73 to 0.98. The unweighted pair group method with arithmetic averages (UPGMA) dendrogram using two molecular markers divided 54 castor genotypes into three groups. Furthermore, based on morphological data, all 54 castor varieties were grouped into three main clusters. The genetic diversity analysis based on two molecular makers showed that most varieties from China were closely related to each other with three varieties (GUANGDONGwild, ZHEJIANGWild, and HANNANWild) belonging to a wild group separated from most of the cultivated castor samples from China, India, France, and Jordan. These results suggested that the cultivated castor contains a narrow genetic base. Accordingly, we recommend that wild castor genetic resources be introduced for breeding novel castor varieties. Furthermore, the Vietnam, Malaysia, Indonesia, and Nigeria accessions were clustered into the same group. The results of principal coordinate analysis (PCoA) and UPGMA cluster analysis were consistent with each other. The findings of this study are important for future breeding studies of castor.

Understanding the genetic diversity and population structure of Dendrobium chrysotoxum Lindl.-An endangered medicinal orchid and implication for its conservation

Genetic variation study in 11 populations of D. chrysotoxum was conducted using 20 different inter-simple sequence repeats (ISSR) and 9 start codon targeted (SCoT) primers. Out of 199 bands produced by ISSR markers, 196 bands were polymorphic, resulting in high polymorphism (98.49%). SCoT markers, however, produced 111 polymorphic fragments generating 100% polymorphism. The Nei's genetic diversity at the species level (H = 0.184±0.11 for ISSR; H = 0.236±0.12 for SCoT) was higher than the average value at the population level (H = 0.160±0.15 for ISSR; H = 0.174±0.15 for SCoT). Low genetic differentiation among the populations (Gst = 0.1566 for ISSR; Gst = 0.2677 for SCoT) was observed due to high estimate of gene flow (Nm = 2.6938 for ISSR; Nm = 1.3678 for SCoT). Mantel test revealed a non-significant correlation between the genetic and geographical distance (r = -0.62; p = 0.86 for ISSR; r = -0.68; p = 0.82 for SCoT). Two-dimensional principal coordinate analysis (PCoA) determined the contribution of the first two principal components to the total genetic variation for combined ISSR and SCoT data at 13.71%. The distribution of individuals in the PCoA plot was in accordance with the unweighted pair group method with arithmetic averages (UPGMA) cluster analysis. Bayesian model-based STRUCTURE determined three (K = 3) gene pools for both ISSR and SCoT markers with a high degree of admixture in the populations. GENELAND further assigned the 11 different populations into 7 genetic clusters. Based on the genetic information obtained from the present investigation, we recommended different conservation strategies suited for effectively managing the endangered orchid. To the best of our knowledge, this is the first report of estimating the genetic diversity and population genetic structure of D. chrysotoxum in Manipur, a north-eastern state of India bordering Myanmar.

Morphological characterization and assessment of genetic diversity of natural Moroccan populations of Capparis spinosa

Capparis spinosa is one of the most important species in the genus Capparis owing to its ecological, medicinal and economic values. It spread in the North of Africa and grows naturally in Morocco. In this work, we evaluate the inter-variation, in eight natural Moroccan populations of Capparis spp. from the Fez-Meknes region in north-central Morocco, at the morphological and genetic level. Genetic variation of this species was assessed using Inter-Simple Sequence Repeats (ISSR) markers. The morphological traits submitted to canonical discriminant analysis enabled separation of eight populations of C. spinosa. The AMOVA results revealed that the genetic variation among the populations (13%) was revealed to be significantly less pronounced than that observed within the some populations (87%). The STRUCTURE analysis and cluster analysis assumed from the Unweighted Pair Group Method with Arithmetic Averages (UPGMA) highlighted three groups within the ISSR data. Our results suggested the presence of hybrid forms of C. spinosa in north-central Morocco. The raised levels of genetic variation revealed within the Moroccan Capparis population by ISSR markers indicate that an appropriate conservation program will allow capturing the majority of genetic diversity found within this species to help ensure its long-term breeding success.

Molecular Diversity and Genetic Relatedness of Candida albicans Isolates from Birds in Hungary

The molecular epidemiology of Candida albicans infections in animals has been rarely studied. In this study, multilocus sequence typing was used to characterise the genetic diversity and population structure of 24 avian origin C. albicans isolates collected from different birds with candidiasis and compared to human isolates. Fourteen diploid sequence types (DSTs) including six new DSTs were determined. Cluster analysis revealed that isolates grouped into 8 clades. Bird isolates mainly belonged to minor clades and Clade 15 with DST 172 was the most common (11 isolates; 45.8%). The remaining isolates were clustered into Clade 7 (5 isolates; 20.8%), Clade 10 (4 isolates; 16.6%), Clade 8 (2 isolates; 8.3%), Clade 4 (1 isolate; 4.2%) and Clade 16 (1 isolate; 4.2%). Unweighted pair group method with arithmetic averages (UPGMA) and eBURST analyses showed that the genetic construction of avian origin C. albicans population is fairly diverse. Although species-specific lineages were not found, some degree of separation in the evolution of bird and human strains could be observed.

Molecular Characterization of Alternaria porri (Ellis) Cif., The Causal Agent of Purple Blotch Disease of Onion, With the Help of Simple Sequence Repeat Markers

Purple blotch disease of onion, caused by Alternaria porri (Ellis) Cif., causes extensive damage to the bulb and seed crops. The present study was aimed to assess the morpho-cultural variations and genetic diversity in 14 isolates of A. porri by simple sequence repeat (SSR) markers (selected on the basis of polymorphism pattern). Most isolates showed white fluffy colony growth and yellow to light orange pigmentation with circular, irregular and smooth margin along with clear-cut zonation. During the study period, 36 loci were obtained and the average expected gene diversity was found in the range of 0.0531-0.3707. Shan cluster analysis and unweighted pair-group method with arithmetic averages (UPGMA) analysis revealed that the isolates ‘A.p.B4’ and ‘A.p.B1' had maximum similarity coefficient (0.9166667), while isolates ‘A.p.B12’ and ‘A.p.B13’ had distant similarity coefficient (0.6111111). The SSR primers D.N.alt4 (200-720 bp) and D.N.alt10 (300-600 bp) represented unique bands for all isolates which were used for the identification of isolates. The polymorphic information content (PIC) value for primer D.N.alt-4 and D.N.alt-10 was 0.0, with maximum and minimum PIC value for D.N.alt14 (0.2978) and D.N.alt-5 (0.0495), respectively, thus represented the discriminatory power of a locus. The study revealed that the nine SSR markers tested were helpful in the isolation and molecular characterization of A. porri on the basis of polymorphism or genetic diversity.