Unweighted Pair Group Method Analysis Research Articles

Molecular genotyping of sweet potato (Ipomoea batatas L. Lam) accessions using microsatellites

The experiment was conducted to ascertain the level of genetic diversity in sweet potato accessions using microsatellites. Thirty sweet potato accessions obtained from the International Potato Center (CIP), Kumasi, Ghana, Mozambique, and local germplasm of the National Root Crops Research Institute (NRCRI), Umudike, Abia State, Nigeria, as well as sweet potato vines from local farmers' fields in Jos, Plateau State, and Bauchi State, Nigeria, were analyzed for genetic diversity using five microsatellite markers. The results showed that the polymorphic SSR loci revealed diverse relationship among the sweet potato cultivars, which was grouped into four major clusters by unweighted pair group method analysis (UPGMA) method. Cluster analysis showed a Jaccard co-efficient ranging from 0.0 to 3.0 indicating high genetic diversity. The primers detected a total of 18 alleles and the number of alleles per locus was 4 for IBR-19, IBR-286, IBR-297 and 3 for IBR-16 and IBR-242 with an average of 3.67 alleles per locus. The polymorphic information content (PIC) of the markers varied from 0.35 to 0.72 with an average of 0.497. Marker IBR-19 revealed the highest PIC of 0.72, while marker IBR-297 had the lowest PIC of 0.35. Observed heterozygosity ranged from 0.32 to 0.89 with a mean of 0.675 across the five SSR loci. The results from the Analysis of molecular variance (AMOVA) which was used to quantify the diversity level and genetic relationship among the thirty sweet potato accessions indicated that a high diversity was mostly distributed within the populations for sweet potato accessions (75.12%) and (15.67%) among the populations.

Intra-Discrete Typing Unit TcV Genetic Variability of Trypanosoma cruzi in Chronic Chagas' Disease Bolivian Immigrant Patients in Barcelona, Spain.

Background: Trypanosoma cruzi has a high rate of biological and genetic variability, and its population structure is divided into seven distinct genetic groups (TcI-TcVI and Tcbat). Due to immigration, Chagas disease (ChD), caused by T. cruzi, has become a serious global health problem including in Europe. Therefore, the aim of this study was to evaluate the existence of genetic variability within discrete typing unit (DTU) TcV of T. cruzi in Bolivian patients with chronic ChD residing in Barcelona, Spain.Methods: The DNA was extracted from the peripheral blood of 27 patients infected with T. cruzi DTU TcV and the fragments of the genetic material were amplificated through the low stringency single primer-polymerase chain reaction (LSSP-PCR). The data generated after amplification were submitted to bioinformatics analysis.Results: Of the 27 patients evaluated in the study, 8/27 (29.6%) were male and 19/27 (70.4%) female, 17/27 (62.9%) were previously classified with the indeterminate clinical form of Chagas disease and 10/27 (37.1%) with Chagas cardiomyopathy. The LSSP-PCR detected 432 band fragments from 80 to 1,500 bp. The unweighted pair-group method analysis and principal coordinated analysis data demonstrated the existence of three distinct genetic groups with moderate-high rates of intraspecific genetic variability/diversity that had shared parasite's alleles in patients with the indeterminate and cardiomyopathy forms of ChD.Conclusions: This study demonstrated the existence of a moderate to high rate of intra-DTU TcV variability in T. cruzi. Certain alleles of the parasite were associated with the absence of clinical manifestations in patients harboring the indeterminate form of ChD. These results support the need to search for increasingly specific targets in the genome of T. cruzi to be correlated with its main biological properties and clinical features in patients with chronic ChD.

Agro-morphological characteristics and genetic diversity of glutinous rice (Oryza sativa) landraces in north Vietnam

The genetic relationship analysis of local glutinous rice is very important for genetic management, conservation and new varietal selection. The experiment was conducted during 2018-19 at Dien Bien district, Dien Bien province, Vietnam to assess the agro-morphological characteristics and genetic diversity of 42 accessions of glutinous rice landraces. Results showed that the varieties have relatively diverse growth times, are largely middle-day group, and mainly medium-to-high plant height with weight of 1000 grains from medium to high majority. In addition, Polymorphic Information Content (PIC) was calculated by using 35 polymorphic SSR markers. Then a cluster analysis of rice collection was performed from the similarity matrix using the Unweighted Pair- Group Method Analysis (UPGMA). The results investigated a total of 106 alleles with an average of 3.03 per locus. PIC values ranged from 0.08 to 0.84, with an average of 0.5. The genetic similarity coefficient of 42 studied rice landraces ranged from 0.63 to 0.97. Based on UPGMA for molecular data using NTSYS-pc 2.1, 42 glutinous rice landraces were divided into 7 groups with genetic differences which could possibly lay a foundation for the development of glutinous rice varieties in Vietnam.

Development of EST-SSR Markers Linked to Flowering Candidate Genes in Elymus sibiricus L. Based on RNA Sequencing.

Elymus sibiricus L. is an important cold-season grass with excellent cold and drought tolerance, good palatability, and nutrition. Flowering time is a key trait that affects forage and seed yield. Development of EST-SSR (expressed sequence tag simple sequence repeat) markers based on flowering genes contributes to the improvement of flowering traits. In the study, we detected 155 candidate genes related to flowering traits from 10,591 unigenes via transcriptome sequencing in early- and late-flowering genotypes. These candidate genes were mainly involved in the photoperiodic pathway, vernalization pathway, central integrator, and gibberellin pathway. A total of 125 candidate gene-based EST-SSRs were developed. Further, 15 polymorphic EST-SSRs closely associated to 13 candidate genes were used for genetic diversity and population structure analysis among 20 E. sibiricus accessions, including two contrasting panels (early-flowering and late-flowering). Among them, primer 28366, designed from heading date 3a (HD3a), effectively distinguished early- and late-flowering genotypes using a specifically amplified band of 175 bp. The polymorphic information content (PIC) value ranged from 0.12 to 0.48, with an average of 0.25. The unweighted pair group method analysis (UPGMA) cluster and structure analysis showed that the 20 E. sibiricus genotypes with similar flowering times tended to group together. These newly developed EST-SSR markers have the potential to be used for molecular markers assisted selection and germplasm evaluation of flowering traits in E. sibiricus.

Evaluation of genetic diversity and construction of DNA fingerprinting in Polygonatum Mill. based on EST-SSR and SRAP molecular markers.

Polygonatum sibiricum is widely consumed as a traditional Chinese herb and edible plant in China. Despite its nutritional and medical values, research on Polygonatum Mill. has been scarce, particularly as far as its genetic diversity is concerned. In this study, fourteen expressed sequence tag-derived simple sequence repeat (EST-SSR) and seven sequence-related amplified polymorphism (SRAP) markers were used to evaluate the genetic diversity in fifty Polygonatum Mill. accessions. The EST-SSRs and SRAPs produced 173 (90.58%) and 113 (93.39%) polymorphic bands, respectively. Unweighted Pair-Group Method Analysis (UPGMA) based on the combined data matrices of EST-SSRs and SRAPs divided the fifty Polygonatum Mill. accessions into fourteen groups. In addition, accessions of P. cyrtonema Hua obtained from Anhui and Zhejiang provinces were clustered according to their geographic origin. Furthermore, some accessions were gathered together based on species, such as P. kingianum Coll. et Hemsl, P. punctatum Royle ex Kunth, P. odoratum (Mill.) Druce, and P. sibiricum Red., and bootstrap analysis for clustering fully supported the grouping of the accessions. The Analysis of Molecular Variance (AMOVA) results revealed higher variation within populations (95%) rather than among populations (5%), indicating that Polygonatum Mill. has a low genetic differentiation between populations, and Principal Coordinate Analysis (PCoA) greatly supported the results of cluster analysis and AMOVA analysis. Finally, five markers which could produce abundant and stable bands were used to construct DNA fingerprinting database of Polygonatum Mill.. Our results demonstrated the utility of both EST-SSR and SRAP markers to successfully evaluate and identify Polygonatum Mill..

Multivariate analysis of quantitative characters variability in Ethiopian barley (Hordeum vulgare L.) landrace: Based on regions and altitude

Barley (Hordeum vulgare L.) is Ethiopia’s most important highland cereal crop and widely growing in most part of the country. Based on high levels of genetic and phenotypic diversity, the country is considered as center of diversity for barley. Assessments of the amount of genetic variation within and among populations are crucial for effective and efficient genetic improvement of the crop. Hence, this study was conducted to assess the diversity of barley landraces collected from various altitudes and regions of Ethiopia. A total of 585 barley landraces and 10 checks were evaluated using augmented randomized complete block design consisting of six blocks. All the 585 landraces were planted in un-replicated plots and the 10 checks were replicated six times (ones in each block) to estimate an error variance. Data on 13 quantitative characters were subjected to calculation of descriptive statistics, ANOVA and multivariate analysis (Unweighted Pair Group Method Analysis (UPGMA) cluster analysis and principal component analysis). There were significant differences (ANOVA, P<0.01) among landraces for plant height, 1000-seed weight, number of seeds per spike, days to heading and days to maturity. All the genotypes were grouped into five clusters where 74.02% of the accessions (433) fall in cluster I, IV and V. Early matured accessions were grouped in cluster I, while late matured, high yielding and tall accessions were clustered in cluster IV. The highest intra-cluster distance was 23.12 for cluster III whereas the highest inter-cluster distance was 57.37 between cluster IV and V. The first three principal components contributed 51.76% of the total variations observed among the genotypes. Principal component one (PC1) alone had contributed 22.56% of the total variations mainly due to plant height, 1000-seed weight, grain yield and peduncle length in their respective order. Principal component two (PC2) contributed 18.94% of the total variations mainly through spike density, number of kernels per spike, spike weight and days to maturity in their descending order. Principal component three (PC3) had contributed 10.94% of the total variations through total number of tillers per plant, number of seed-bearing tillers, days to 90% maturity and days to 50% heading. Altitude of the original landrace collection sites also significantly impacted the various quantitative characteristics studied. Regional differentiations were also evident among the landrace collections. These results reveal the existence of significant agro-morphological variations among the landraces included in this study. Based on the characters considered and populations evaluated, the marked diversity observed among the barley landraces in Ethiopia could be utilized in future crop improvement for various agronomically important traits. The information generated complements the robust barley breeding program of competitive, stable and climate-resilient varieties of end users’ preferences in different agro-ecologies of Ethiopia.

Molecular identification of mung bean accessions (Vigna radiata L.) from Northeast China using capillary electrophoresis with fluorescence‐labeled SSR markers

AbstractThe purpose of this study was to construct the DNA fingerprinting and query system with which to identify mung bean varieties from Northeast China. Eight primer pairs for fluorescent‐labeled simple sequence repeat markers with high polymorphism and a strong discrimination ability were used to detect 151 mung bean varieties from Northeast China. A total of 59 bands were detected, ranging from 4 to 11 with an average of 7.4. An unweighted pair group method analysis was used to cluster the mung bean varieties into five separate groups according to their genetic characteristics, which were consistent with the results of principal component analysis. Unique identification cards and barcodes with which each variety can be identified were established according to fingerprinting. A query system was also established which can provide the information and genetic relationships among some indefinite variety and mung bean varieties from Northeast China. This research will significantly assist in identification, traceability management, protection of origin, and intellectual property rights. It will also provide essential technical support for revealing the level of genetic diversity for breeding and germplasm innovation of mung bean varieties in Northeast China.

Genotyping of Leptospira interrogans isolates from Mexican patients.

ABSTRACTThe aim of this study was genotypically characterize Leptospira sp. clinical isolates from Mexico which were previously identified as Leptospira interrogans serovar Pomona (POM) by phenotypic methods. The Random Amplified Polymorphic DNA (RAPD) method was used for DNA amplification with five oligonucleotides. A dendrogram was constructed using the Unweighted Pair Group Method Analysis (UPGMA). During the genotypic characterization, the studied isolates constituted a group which was associated with the reference strain L. interrogans serovar Pomona. The Minimum Spanning Networks (MST) analysis revealed the same cluster between Mexican isolates and the reference strain POM. Clinical isolates identified as L. interrogans serovar POM have a clonal reproduction type, suggesting that this clone is distributed in different regions of Mexico.

Intestinal microbiome and its potential functions in bighead carp (Aristichthys nobilis) under different feeding strategies.

Bighead carps (Aristichthys nobilis) were divided into four groups with different feeding strategies: group A, nature live food only (fertiliser only, 200 g urea + 160 g ethylamine phosphate + 250 g Huangjintai bio-fertiliser); group B, nature live food + 1/2 formulated feed; group C, nature live food + formulated feed; and group D, formulated feed only. The intestinal microbiomes of the different groups were compared through the Illumina MiSeq sequencing of the bacterial 16S rRNA gene. The specific growth rate (SGR), survival and blood biochemical factors of the fish were also investigated. Results showed that feeding treatment influenced the intestinal communities in the fish. In specific, more bacterial phyla dominated in groups A and B (phyla Bacteroidetes, Fusobacteria, Firmicutes and Proteobacteria in group A, phyla Proteobacteria and Fusobacteria in group B) than in groups C and D (phylum Proteobacteria). The diversity was also lower in groups C and D than in groups A and B. Unweighted pair-group method analysis revealed a clear difference in intestinal microbiota among the different feeding treatments. No difference in survival rate was found among the treatment groups, but the SGR was significantly higher (P < 0.01) in groups B, C and D than in group A. Functional analysis showed that the intestinal bacteria correlated with fish glucose metabolism in group A but with lipid metabolic activity in groups B, C and D. In summary, the intestinal microbiomes and their potential functions vary in bighead carp under different feeding treatments. This study provides new insights into the gut microbiomes of filter-feeding and formulated diet-fed fish.

Development and application of polymorphic microsatellite markers in Saxifraga genus

In order to develop genomic-SSR markers for species of Saxifraga genus, a mixed plant genomic DNA sample was sequenced based on high-throughput Illumina MiSeq platform. According to genomic sequencing data, SSR loci were identified with MISA software, and then primers were designed with Primer 3 software. A total of 120 pairs of primers were randomly synthesized and amplified in genomic DNA of a few plant samples. Those primers who have yielded polymorphic bands and were considered easy to amplify were identified. After that, transferability of these primers was evaluated, and phylogenetic relationship of 25 species of Saxifraga genus was analyzed with UPGMA (unweighted pair group method analysis). In our results, 587 256 sequences containing SSRs were identified from a total of 1 881 979 combined read pairs obtained in genomic sequencing. Primers were designated to amplify SSRs containing two to six nucleotide repeat units, screened in a small portion of species. Finally, 17 pairs of primers which have produced abundant of polymorphic bands with little problem were amplified in 25 species of Saxifraga genus. A total of 2 687 polymorphic bands were obtained, the average polymorphic rate was 158 bands per pairs of primers. The transferability rate was ranging from 88.0% to 100% across 25 species of Saxifraga. In phylogenetic analysis, the clustering of 25 species based on 17 pairs of SSR primers was different from morphological classification. Our analysis has provided molecular data for genetic relationship of Saxifraga genus, and the transferable and polymorphic SSRs have provided information for genetic diversity research.

Morphological phylogeny among 15 accessions of bamboos growing in Kokrajhar district of the Bodoland Territorial Area Districts, Assam

Bamboo is nature’s wonderful gift historically associated with the rural population of the Bodoland Territorial Area Districts. However, indiscriminate use of the resource and the ambiguity in the identification of bamboos in the absence of flowering characters pose a potential risk to the bamboo germplasm. Therefore, we considered revising the taxonomic positions and phylogenetic relationships among 15 tropical bamboo species using 35 key morphological descriptors (MD) to assess the reliability of vegetative characters in identifying species. The phylogenetic tree constructed from the similarity matrix, derived from an unweighted pair group method of analysis (UPGMA) of the 35 MDs, marginally deviated from the conventional taxonomic positions of the bamboo species. While the two varieties, one forma of Bambusa vulgaris (var. Vittata, var. Vulgaris, fo. Waminii) and two species of the genus Dendrocalamus (D. giganteus and D. hamiltonii) clustered together in a single clade, and D. strictus was distantly placed from their congeners. This discrepancy with the conventional classification might have ensued since only vegetative characters such as culm anatomy, culm sheath, leaf, and leaf sheath were considered in the present study. While the phylogenetic relationship among the 15 tropical bamboos (computed from exhaustive MDs) grossly corroborate the conventional taxonomic grouping, a molecular-marker-based multidisciplinary approach should resolve the remaining conflicts in bamboo identification.

Genome Survey Sequencing of Luffa Cylindrica L. and Microsatellite High Resolution Melting (SSR-HRM) Analysis for Genetic Relationship of Luffa Genotypes.

Luffa cylindrica (L.) Roem. is an economically important vegetable crop in China. However, the genomic information on this species is currently unknown. In this study, for the first time, a genome survey of L. cylindrica was carried out using next-generation sequencing (NGS) technology. In total, 43.40 Gb sequence data of L. cylindrica, about 54.94× coverage of the estimated genome size of 789.97 Mb, were obtained from HiSeq 2500 sequencing, in which the guanine plus cytosine (GC) content was calculated to be 37.90%. The heterozygosity of genome sequences was only 0.24%. In total, 1,913,731 contigs (>200 bp) with 525 bp N50 length and 1,410,117 scaffolds (>200 bp) with 885.01 Mb total length were obtained. From the initial assembled L. cylindrica genome, 431,234 microsatellites (SSRs) (≥5 repeats) were identified. The motif types of SSR repeats included 62.88% di-nucleotide, 31.03% tri-nucleotide, 4.59% tetra-nucleotide, 0.96% penta-nucleotide and 0.54% hexa-nucleotide. Eighty genomic SSR markers were developed, and 51/80 primers could be used in both “Zheda 23” and “Zheda 83”. Nineteen SSRs were used to investigate the genetic diversity among 32 accessions through SSR-HRM analysis. The unweighted pair group method analysis (UPGMA) dendrogram tree was built by calculating the SSR-HRM raw data. SSR-HRM could be effectively used for genotype relationship analysis of Luffa species.

Phylogenetic relationships of fluorescent Pseudomonad isolates associated with bacterial canker of stone fruit trees in Kurdistan province, Iran

Bacterial canker is one of the most important diseases of stone fruit trees in various locations of Kurdistan province, Iran. Genetic diversity and evolutionary relationships among 20 fluorescent pseudomonads isolated from stone fruit trees with symptoms similar to bacterial canker were investigated using a polyphasic approach by means of phenotypic characterizations, repetitive PCR using the REP and ERIC primers and multilocus sequence typing (MLST) of four housekeeping genes (gapA, rpoD, gyrB and gltA). The pathogenicity of strains was carried out under greenhouse conditions. Twelve strains produced an expected amplified DNA fragment of about 752-bp which indicated the presence of the syrB gene. Based on MLST, these strains belonged to P. syringae species complex and included in the genomospecies 1, phylogroup 2b and 2d. Phylogenetic analysis of the other eight fluorescent pseudomonad strains by using gyrB and rpoD sequences allowed the identification of strains into P. fluorescens, P. putida and P. lutea groups. Unweighted pair group method analysis (UPGMA) of genomic fingerprints obtained by rep-PCR revealed 17 different patterns which grouped P. syringae strains into three clusters clearly separated from other fluorescent pseudomonads. MLST confirmed the genetic variability among strains obtained by rep-PCR. Grouping identified of P. syringae strains by both rep-PCR and MLST was related to geographic locations of strains.

Genetic diversity of isolates of foodborne Listeria monocytogenes by RAPD-PCR

In this study, randomly amplified polymorphic DNA-PCR (RAPD-PCR) was employed to investigate the genetic diversity of 308 wild isolates of Listeria monocytogenes. These isolates were taken from 1288 samples isolated from six food sources obtained within the Baoding and Shijiazhuang areas of Hebei province, China. Genetic distant coefficient analysis of the band profiles was carried out using unweighted pair-group method analysis (UPGMA) and cluster analysis. The oligomer RP1 was used as a primer to type 308 isolates of foodborne L. monocytogenes and 228 different RAPD-PCR fingerprinting patterns were obtained. The clustering analysis showed that the 308 isolates of L. monocytogenes could be grouped into six genetic clusters. Among them, Clusters I and II were the dominant species from this region. Also, many differences between genetic clusters from different foods, sampling times, and regions were found. The differences in RAPD-PCR fingerprinting patterns obtained from the six food types sampled indicate that the L. monocytogenes subtypes isolated were genetically diverse.

The characterisation of Vitis vinifera ’Refošk’ with AFLP and SSR molecular markers and ampelographic traits

The genetic diversity and ampelographic variability of autochthonous red wine cultivar ‘Refošk’ (Vitis vinifera L.) grown in Slovenia were evaluated with AFLP molecular markers and OIV descriptors, respectively. SSR molecular markers were employed to confirm cultivar identity of analysed samples. Eight AFLP primer combinations, one was monomorphic, produced 16 polymorphic markers in 41 out of 113 samples, what classified samples into monomorphic and polymorphic group. Dendrogram constructed with simple matching coefficient and unweighted pair-group method analysis presented genetic diversity within polymorphic group. Refošk biotypes from monomorphic and polymorphic groups were evaluated with 22 OIV descriptors related to bunch, berry and must, but on the basis of ampelographic characterization samples were not differentiated among two major groups obtained with AFLP analysis. Results of genetic analysis indicated that ‘Refošk’ originated from closely related plants that are phenotypically very similar. With regard to low observed genetic diversity more attention should be dedicated to the selection in order to conserve remaining genetic diversity.

Morpho-Genetic Study and Detection of Boron Toxicity Tolerance of Wild Wheat Genotypes

&lt;p&gt;The occurrence of boron toxicity becomes a major constraint in cereal production in the world, thus cause significant yield loss particularly in wheat, one of the most susceptible crops to boron toxicity. Development of tolerant variety is now of utmost importance since agronomic management of soil boron is becoming ineffective to mitigate the toxicity. Due to narrow genetic base of the existing wheat cultivars, genetic variation for this character was poorly reported. The present study was devoted to identify such variation by using two different genetic background of wheat including &lt;em&gt;Aegilops&lt;/em&gt; and &lt;em&gt;Triticum&lt;/em&gt;, which could be readily used in wheat breeding program. Morphological and genetic screening revealed that two species &lt;em&gt;Ae. longissima &lt;/em&gt;and &lt;em&gt;Ae. sharonensis&lt;/em&gt; expressed tolerance against boron toxicity. The molecular marker analysis such as unweighted pair group method and principal coordinate analysis confirmed these two species&lt;em&gt; &lt;/em&gt;to be more tolerant to excessive boron with higher root length. Their derivatives genotypes TL-09 and TL-17 were found to explained considerable tolerance to boron. On other hand, among the SSR markers used, Xgwm192 was the most robust in identifying boron tolerance polymorphism. The diversity and variability observed in this work could open new avenue in developing B toxicity tolerant wheat variety.&lt;/p&gt;

Genetic variation and geographic differentiation among populations of the nonmigratory agricultural pest Oedaleus infernalis (Orthoptera: Acridoidea) in China.

The nonmigratory grasshopper Oedaleus infernalis Saussure (Orthoptera : Acridoidea) is an agricultural pest to crops and forage grasses over a wide natural geographical distribution in China. The genetic diversity and genetic variation among 10 geographically separated populations of O. infernalis was assessed using polymerase chain reaction-based molecular markers, including the intersimple sequence repeat and mitochondrial cytochrome oxidase sequences. A high level of genetic diversity was detected among these populations from the intersimple sequence repeat (H: 0.2628, I: 0.4129, Hs: 0.2130) and cytochrome oxidase analyses (Hd: 0.653). There was no obvious geographical structure based on an unweighted pair group method analysis and median-joining network. The values of FST, θII, and Gst estimated in this study are low, and the gene flow is high (Nm > 4). Analysis of the molecular variance suggested that most of the genetic variation occurs within populations, whereas only a small variation takes place between populations. No significant correlation was found between the genetic distance and geographical distance. Overall, our results suggest that the geographical distance plays an unimpeded role in the gene flow among O. infernalis populations.

Genetic diversity in intraspecific hybrid populations of Eucommia ulmoides Oliver evaluated from ISSR and SRAP molecular marker analysis.

Eucommia ulmoides Oliver, the only extant species of Eucommiaceae, is a second-category state-protected endangered plant in China. Evaluation of genetic diversity among some intraspecific hybrid populations of E. ulmoides Oliver is vital for breeding programs and further conservation of this rare species. We studied the genetic diversity of 130 accessions from 13 E. ulmoides intraspecific hybrid populations using inter-simple sequence related (ISSR) and sequence-related amplified polymorphism (SRAP) markers. Of the 100 ISSR primers and 100 SRAP primer combinations screened, eight ISSRs and eight SRAPs were used to evaluate the level of polymorphism and discriminating capacity. A total number of 65 bands were amplified using eight ISSR primers, in which 50 bands (76.9%) were polymorphic, with an average of 8.1 polymorphic fragments per primer. Alternatively, another 244 bands were observed using eight SRAP primer combinations, and 163 (66.8%) of them were polymorphic, with an average of 30.5 polymorphic fragments per primer. The unweighted pair-group method (UPGMA) analysis showed that these 13 populations could be classified into three groups by the ISSR marker and two groups by the SRAP marker. Principal coordinate analysis using SRAP was completely identical to the UPGMA-based clustering, although this was partly confirmed by the results of UPGMA cluster analysis using the ISSR marker. This study provides insights into the genetic background of E. ulmoides intraspecific hybrids. The progenies of the variations "Huazhong-3", "big fruit", "Yanci", and "smooth bark" present high genetic diversity and offer great potential for E. ulmoides breeding and conservation.

Interactions of human galectins with Trypanosoma cruzi: binding profile correlate with genetic clustering of lineages.

We report here the specific interaction between several members of the human galectin family with the three developmental stages of several genetic lineages of the protozoan parasite Trypanosoma cruzi. We provide data of specific and differential binding of human galectin (gal)-1, -3, -4, -7 and -8 to 14 strains of T. cruzi that belong to the six genetic lineages representing the genetic diversity of the parasite. It is shown that galectins preferentially bind forms present in the host, trypomastigotes and amastigotes, compared with the non-infective epimastigote present on the intestinal tract of the vector, reflecting the changes on glycosylation that occur during the metacyclogenesis and amastigogenesis process. Also, it is evidenced that galectin binding to the parasites promotes binding to the host cells and higher infection rates. In addition, evidence is provided indicating that the intracellular amastigotes may take over the cytosolic pool of some galectins when released to the extracellular medium. Finally, by applying unweighted pair group method analysis to the galectin-binding profile to either cell-derived trypomastigotes or amastigotes, we show that the differential-binding profile by the host galectins to the six lineages resembles the clustering based in genetic data. Therefore, the differential-binding profile for the six lineages could have implications in the immunopathology of Chagas' disease, affecting the complex network of immune responses on which galectins mediate, thus providing linkage clues to the notion that different lineages may be related to different clinical forms of the disease.

Assessment of genetic diversity and distribution of endophytic fungal communities of Alternaria solani isolates associated with the dominant Karanja plants in Sanganer Region of Rajasthan

Higher plants are ubiquitously colonized with fungal endophytes that often lack readily detectable structures. Current study examines the distribution of endophytic fungal communities within Karanja plants and diversity of novel fungal endophyte Alternaria solani isolates collected from different locations of Sanganer region of Rajasthan. Results confirmed that A. solani is a major fungal endophyte consortium associated with Karanja plants. PCR Amplified fragments using random amplified polymorphic DNA (RAPD) primers were subjected to unweighted pair group method analysis (UPGMA), which clearly distinguished twelve ecologically diverse A. solani isolates. A total of 58 RAPD loci were amplified, out of which 35 (60.34%) were polymorphic and 23 were monomorphic (39.66%) in nature. These polymorphic loci were identified with an average of 2.92 bands per primer. The efficacy of RAPD markers proved as an efficient marker system with respect to detection of polymorphism and number of loci scored and can be used for the identification of a particular isolates, thereby defining core collections and strengthening their exploitation in acquiring novel products produced by them.