Analysis Of Genetic Relationships Research Articles

Genetic Variability, Population Structure, and Relatedness Analysis of Meagre Stocks as an Informative Basis for New Breeding Schemes

This study evaluates the genetic diversity of different meagre broodstocks sampled in Greece. A multiplex of twelve microsatellite markers was used to genotype 946 fish from eleven stocks and batches used for broodstock selection, and the genetic data was used to calculate genetic population parameters as well as to investigate the genetic differentiation between stocks. The results from a relatedness analysis were used as the guiding lines for a fine-tuned and overall evaluation of the genetic distance between stocks, and the choice of candidate breeders from some of them. The approach implemented in this study uses well-established population genetics methods to evaluate the selection of breeder candidates in aquaculture commercial conditions utilizing a descriptive genetic data set based on microsatellite analyses, and to outline an efficient methodology for establishing the basis of new breeding schemes.

805. Outbreak of Ralstonia pickettii Bacteremia Caused by Contaminated Hydromorphone in a Universitary Hospital in Bogota, Colombia

Background Ralstonia pickettii are aerobic non fermenter gram negative bacilli isolated in water and soil. It is related to nosocomial infection outbreaks and considered an opportunistic pathogen. There have been outbreaks reports due to contaminated water systems and sterile drug solutions which mainly occurs during manufacturing. We present the report of an outbreak of R. pickettii bacteremia secondary to a contamination of hydromorphone vials.MethodsIn February 2021 an outbreak of R. pickettii bacteremia was identified. All isolates were from blood cultures with slow growth, thus indicating the culturing of liquid inputs, intravenous administration solutions and commonly used drugs among patients including hydromorphone. Mass spectrometry (MALDI-TOF) was used for the identification and automated microdilution to determine sensitivity to antimicrobials of the isolates and clonality analysis of genetic relationships was carried out using the DICE coefficient, UPGMA algorithm ResultsDuring the outbreak, 19 patients with R. pickettii bacteremia were identified The global attack rate was 1,9%. 11/19 (58%) were women and 13/19 (68%) of the isolations were from inward patients and 6/19 (32%) were from intensive care unit. Factors that could contribute to the appearance of the outbreak were underlying pathology, 2 patients with a diagnosis of diabetes mellitus, 10 patients with a diagnosis of arterial hypertension, 5 patients with obesity, 6 patients with heart disease, additionally 7 patients with a diagnosis of SARS COV 2 and 6 patients with the use of corticosteroids. The global attack rate was 1,9% and mortality was 31.5% (6 patients). R. pickettii was identified from two batches of hydromorphone by MALDI-TOF and the clonality study concluded that the isolates analyzed, were clonal with a 100% similarity. The associated mortality rate was 5/29 (26.3%). ConclusionWe confirmed an outbreak of R. pickettii due to the contamination of two hydromorphone badges in Colombia. It is crucial to acknowledge the importance of infection control and surveillance during the COVID-19 pandemic as well as maintaining adequate quality control of medication production in order to avoid presenting this kind of outbreaks. Disclosures Sandra Liliana. Valderrama-Beltrán, MD, MSc, Biotoscana (Speaker’s Bureau)MSD (Grant/Research Support, Scientific Research Study Investigator, Research Grant or Support, Speaker’s Bureau)Pfiezer (Speaker’s Bureau)

Genetic diversity and relationship analyses of the Korea native black goat line using microsatellite markers

Genetic diversity and relationship analyses of the Korea native black goat line using microsatellite markers

Development of a standardized multiplex SSR kit for genotyping both goats and sheep

In this technical note, we report the development of a reliable standardized protocol based on the multiplex SSR-PCR approach for genotyping the two small ruminant species, goats and sheep. The method is based on PCR conditions optimization allowing 12 informative microsatellites (SSR) markers to be co-amplified in two multiplex sets of 6 SSR markers, followed by a co-migration into one run onto a genetic analyzer. The performance of the assay was tested on a total of 207 goats and 197 sheep, originating from different breeds and localities sampled mainly in Benin, but also to lesser extent in Belgium. The optimized assay showed that the 12 selected markers were suited to amplify all the loci distributed between the two species with valuable genetic information, specific-species allelic patterns and similar polymorphism information content. The validated loci were polymorphic with high allele numbers for the two species, ranging from 6 to 21 for goats and 7 to 15 for sheep, with average 10.58 alleles per locus for goats and 11.33 for sheep, respectively. The Polymorphic Information Content (PIC) of selected markers averaged a value of 0.712 for goats and 0.751 for sheep. The differentiation of SSR alleles at an intraspecific resolution level allowed different heterotic groups to be detected, such as geographical or breeding groups. The newly developed genotyping kit could be successfully applied in diverse genetic variability studies and relatedness analyses, as well as for population structure assessment, parentage determination and traceability concerns, within and among sheep and goat species.

Genetic Variation Among Three Zea Mays L Cultivars In Iraq

Maize is a very fertile and widely environmental grown crop and it globally cultivated. The purpose of our research was to determine genetic variation among three Zea mays L. cultivars (Al maha, Drachma and Talar F-1). The primer ITS1 and ITS4 used as a molecular marker in a conventional Polymerase Chain Reaction (PCR) with a 290 bp ampli- fication outcome. The nucleotide sequences of amplification products were analyzed, sequence alignment was significantly revealed which confirming Zea mays diagnosis. Furthermore, analysis of genetic relationship revealed a neighboring relationship between Talar F-1 and Almaha cultivars(93),whereas phylogeny schematic diagram clearly showed presence of Drachma cultivar in other cluster(77).

Phenotypic and genetic characterization of “Aglione della Valdichiana”: Population structure and genetic relationship analysis of a white gentle giant

“Aglione della Valdichiana” (Allium ampeloprasum var. holmense) is a landrace of Great Headed Garlic (GHG), an historical and healthy vegetable that has been recently rediscovered and registered in the National and Regional catalog of local varieties. It is grown in small fields in a region between Tuscany and Umbria, Italy, and due to its high market value, it is at risk of commercial frauds. The morphological traits and molecular profile of 9 local populations were evaluated together with 36 accessions of leek, garlic, wild relatives and other GHGs of different geographic origins and used as controls. The 39 morphological descriptors were able to distinguish the 9 accessions from leek and garlic, but unable to distinguish among them. The 549 AFLP (Amplified Fragment Length Polymorphism) amplicons obtained from nine primer combinations were able to clearly distinguish Aglione accessions from all the others, both by UPGMA (Unweighted Pair Group Method with Arithmetic mean) clustering and by STRUCTURE analysis, and this is due to several private AFLP bands, most from M+AGC/E+CTG primer combination. Despite its vegetative propagation, the within accession variability of Aglione is higher than expected and most likely due to somatic mutations. The genetic relationships are discussed, including the closer relationship found between Aglione and garlic vs. Aglione and leek.

Genetic and phenotypic analysis of the causal relationship between aging and COVID-19

BackgroundEpidemiological studies revealed that the elderly and those with comorbidities are most affected by COVID-19, but it is important to investigate shared genetic mechanisms between COVID-19 risk and aging.MethodsWe conducted a multi-instrument Mendelian Randomization analysis of multiple lifespan-related traits and COVID-19. Aging clock models were applied to the subjects with different COVID-19 conditions in the UK-Biobank cohort. We performed a bivariate genomic scan for age-related COVID-19 and Mendelian Randomization analysis of 389 immune cell traits to investigate their effect on lifespan and COVID-19 risk.ResultsWe show that the genetic variation that supports longer life is significantly associated with the lower risk of COVID-19 infection and hospitalization. The odds ratio is 0.31 (P = 9.7 × 10−6) and 0.46 (P = 3.3 × 10−4), respectively, per additional 10 years of life. We detect an association between biological age acceleration and future incidence and severity of COVID-19 infection. Genetic profiling of age-related COVID-19 infection indicates key contributions of Notch signaling and immune system development. We reveal a negative correlation between the effects of immune cell traits on lifespan and COVID-19 risk. We find that lower B-cell CD19 levels are indicative of an increased risk of COVID-19 and decreased life expectancy, which is further validated by COVID-19 clinical data.ConclusionsOur analysis suggests that the factors that accelerate aging lead to an increased COVID-19 risk and point to the importance of Notch signaling and B cells in both. Interventions that target these factors to reduce biological age may reduce the risk of COVID-19.

Genetic characterization of Carbapenem-Resistant\xa0Escherichia coli\xa0from China, 2015\u20132017

BackgroundThe molecular characteristics of carbapenem-resistant Escherichia coli (CREco) remain unclear.MethodsWe conducted a multi-center bacterial resistance monitoring project from 2015 to 2017.The minimum inhibitory concentrations ofCREco were determined bybroth microdilution method. The genome sequencing of CREcoisolates was performed, and single-nucleotide polymorphism (SNP) was analyzed.ResultsA total of 144CREcoisolatescollected from 10 cities in China were involved in this study. ST167 (n = 43) is the most popular type, followed by ST410(n = 14), ST131(n = 9). There were 102 (70.83%) CREco isolates that produced various NDMs, including NDM-1 (n = 16), NDM-4(n = 1), NDM-5(n = 79), NDM-6(n = 2) and NDM-9(n = 4). In addition, 15 isolates produced KPC-2, three isolates wereIMP-4 positive, and three isolates produced OXA-48. Genetic relatedness and phylogenetic analysis showed that isolates with the same ST had a high degree of homology. Some STs (including ST167, ST410, ST131, ST46, ST405 and ST617) exhibited a trend of outbreak.ConclusionsThe majority of CREco belonged to ST167, followed by ST410 and ST131, and most of them carried various NDM-coding genes. The spread of high-risk clones of CREco has occurred in different regions of China.

Breeding Strategy Shapes the Composition of Bacterial Communities in Female Nile Tilapia Reared in a Recirculating Aquaculture System.

In industrial animal production, breeding strategies are essential to produce offspring of better quality and vitality. It is also known that host microbiome has a bearing on its health. Here, we report for the first time the influence of crossbreeding strategy, inbreeding or outbreeding, on the buccal and intestinal bacterial communities in female Nile tilapia (Oreochromis niloticus). Crossbreeding was performed within a family and between different fish families to obtain the inbred and outbred study groups, respectively. The genetic relationship and structure analysis revealed significant genetic differentiation between the inbred and outbred groups. We also employed a 16S rRNA gene sequencing technique to understand the significant differences between the diversities of the bacterial communities of the inbred and outbred groups. The core microbiota composition in the mouth and the intestine was not affected by the crossbreeding strategy but their abundance varied between the two groups. Furthermore, opportunistic bacteria were abundant in the buccal cavity and intestine of the outbred group, whereas beneficial bacteria were abundant in the intestine of the inbred group. The present study indicates that crossbreeding can influence the abundance of beneficial bacteria, core microbiome and the inter-individual variation in the microbiome.

RecA gene genetic diversity and its regulatory element analysis: The case of Vibrio cholerae

In conventional systems, indicator organisms are used to monitor drinking water quality which is unspecific in detecting pathogens. On the contrary, molecular techniques play vital role in these aspects by providing precise genetic information about particular pathogen of interest via proper biomarkers. The aim of this study was to undertake genetic relatedness and promoter region analysis for V. cholerae strains based on recA gene sequences which were retrieved from NCBI. Sequences homologous were ensured using BLASTn from RefSeq sequence in the NCBI using V. cholerae serotype O1 strain N16961 as a reference. Accordingly, considering only complete and coding sequences with query coverage of greater than 90% and E-value of less than 5%, a total of 109 sequences were recovered from NCBI. The genetic diversity analysis was carried out using MEGA X. The analysis revealed more than 99% sequence similarity among V. cholerae strains. From promoter regions analyses, five motifs shared by all (100%) of the promoter input sequences were identified. Using TOMTOM web application, motif_1was compared to a known prokaryotes' transcription factor database to search for its similarity with known regulatory motifs and was shown to serve as abundant binding site for helix-turn-helix (HTH) transcription factor gene family to regulate expression of V. cholerae recA genes. Furthermore, our analysis revealed that the V. cholerae recA gene promoter regions are CpG islands rich. In conclusion, all V. cholerae strains shared a very high degree of recA gene sequence similarity apart from other vibrios, which indicates that these non-virulent strains may be the remnant of pathogenic strains with the loss of toxin encoding genes.

Analysis of genetic diversity and relationships of Perilla frutescens using novel EST-SSR markers derived from transcriptome between wild-type and mutant Perilla.

Perilla frutescens (Lamiaceae) is distributed in East Asia and is classified into var. frutescens and crispa. P. frutescens is multipurpose crop for human health because of a variety of secondary metabolites such as phenolic compound and essential oil. However, a lack of genetic information has hindered the development and utilization of Perilla genotypes. This study was performed to develop expressed sequence tag-simple sequence repeat (EST-SSR) markers from P. frutescens var. crispa (wild type) and Antisperill (a mutant cultivar) and used them to assess the genetic diversity of, and relationships among, 94 P. frutescens genotypes. We obtained 65Gb of sequence data comprising 632,970 transcripts by de novo RNA-sequencing. Of the 14,780 common SSRs, 102 polymorphic EST-SSRs were selected using in silico polymerase chain reaction (PCR). Overall, successful amplification from 58 EST-SSRs markers revealed remarkable genetic diversity and relationships among 94 P. frutescens genotypes. In total, 268 alleles were identified, with an average of 4.62 alleles per locus (range 2-11 alleles/locus). The average polymorphism information content (PIC) value was 0.50 (range 0.04-0.86). In phylogenetic and population structure analyses, the genotypes formed two major groups: Group I (var. crispa) and Group II (var. frutescens). This results suggest that 58 novel EST-SSR markers derived from wild-type cultivar (var. crispa) and its mutant cultivar (Antisperill) have potential uses for population genetics and recombinant inbred line mapping analyses, which will provide comprehensive insights into the genetic diversity and relationship of P. frutescens.

A new mutation in mgrb mediating polymyxin resistance in Klebsiella variicola

Polymyxin resistance is a public health concern – present in humans, animals and the environment – caused by chromosomal-encoding or plasmid-encoding mechanisms. Chromosomal alterations in MgrB are frequently detected in Klebsiella spp., but not yet reported and characterised in Klebsiella variicola (K. variicola). This study performed microbiological and genomic characterisation of three polymyxin-resistant K. variicola isolates (M14, M15 and M50) recovered from the microbiota of migratory birds in Brazil.The isolates were submitted to SpeI-PFGE, broth microdilution and whole genome sequencing using Illumina MiSeq for analysis of genetic relatedness, sequence typing and detection of antimicrobial-resistance genes. K. variicola isolates belonged to two clones, and susceptibility tests showed resistance only for polymyxins. Sequences of chromosomal two-component systems (PmrAB, PhoPQ, RstAB, CrrAB) and MgrB were evaluated by blastN and blastP against a polymyxin-susceptible K. variicola (A58243), and mutations with biological effect were checked by the PROVEAN tool. K. variicola isolates belonged to two clones, and susceptibility tests showed resistance for polymyxins. In M14 and M15, phoQ deleterious mutations (D90N, I122S and G385S) were identified, while an mgrB variant containing a single deletion (C deletion on position 93) leading to the production of a non-functional protein was detected in M50. mgrB complementation studies showed restoration of polymyxin susceptibility (64 to ≤ 0.25 mg/L) as a wild-type mgrB was inserted into the mgrB-deficient M50.This study confirmed the role of a non-functional mgrB variant in conferring polymyxin resistance, stressing the role of this regulator in K. variicola and drawing attention to novel polymyxin resistance mechanisms emerging in wildlife.

Genetic Diversity, Structure and Effective Population Size of Old-Growth vs. Second-Growth Populations of Keystone and Long-Lived Conifer, Eastern White Pine (Pinus strobus): Conservation Value and Climate Adaptation Potential.

Whether old-growth (OG) forests have higher genetic diversity and effective population size, consequently higher conservation value and climate adaptive potential than second-growth (SG) forests, remain an unresolved issue. We have tested the hypothesis that old-growth forest tree populations have higher genetic diversity, effective population size (NE), climate adaptive potential and conservation value and lower genetic differentiation than second-growth forest tree populations, employing a keystone and long-lived conifer, eastern white pine (EWP; Pinus strobus). Genetic diversity and population structure of old-growth and second-growth populations of eastern white pine (EWP) were examined using microsatellites of the nuclear and chloroplast genomes and single nucleotide polymorphisms (SNPs) in candidate nuclear genes putatively involved in adaptive responses to climate and underlying multilocus genetic architecture of local adaptation to climate in EWP. Old-growth and second-growth EWP populations had statistically similar genetic diversity, inbreeding coefficient and inter-population genetic differentiation based on nuclear microsatellites (nSSRs) and SNPs. However, old-growth populations had significantly higher chloroplast microsatellites (cpSSRs) haploid diversity than second-growth populations. Old-growth EWP populations had significantly higher coalescence-based historical long-term NE than second-growth EWP populations, but the linkage disequilibrium (LD)-based contemporary NE estimates were statistically similar between the old-growth and second-growth EWP populations. Analyses of population genetic structure and inter-population genetic relationships revealed some genetic constitution differences between the old-growth and second-growth EWP populations. Overall, our results suggest that old-growth and second-growth EWP populations have similar genetic resource conservation value. Because old-growth and second-growth EWP populations have similar levels of genetic diversity in genes putatively involved in adaptive responses to climate, old-growth, and second-growth populations may have similar adaptive potential under climate change. Our results could potentially be generalized across most of the boreal and temperate conifer forest trees. Our study contributes to address a long-standing issue, advances research field and knowledge about conservation and ecological and climate adaptation of forest trees.

AFLP analysis of Genetic diversity and Phylogenetic relationships of Vigna radiata (L) Wilczek

Among the important pulse-yielding plants Vigna radiata is important. In the Indian subcontinent, it is an essential source of dietary protein particularly in the vegetarian population. It contains abundant nutrients with biological activities. Soaked seeds are eaten as a good source of protein and mature seeds are cooked or can be sprouted for human consumption. Mung beans and its sprouts contain chemical constituents like flavonoids, phenolic acids, organic acids, amino acids, carbohydrates, and lipids. It is related to different biological activities like antioxidant, antimicrobial, antitumor, anti-inflammatory, anti-diabetic, and antihypertensive effects, etc. The seeds are a traditional source of cures for paralysis, rheumatism, coughs, fevers, and liver ailments. As a green manure or cover crop, the plant can be grown, enriching the soil with the nitrogen formed on its roots. The powerful Amplified Fragment Length Polymorphism (AFLP) is a molecular marker used for a variety of applications like assessing genetic diversity within species or among closely related species, inferring population-level phylogenies, generating genetic maps, and determining the relatedness among cultivars. AFLP has become extremely beneficial in the study of taxa including bacteria, fungi, and plants, where much is still unknown about the genomic makeup of various organisms. A study was made to assess the genetic diversity and phylogenetic relationships of a set of five varieties of Vigna radiata (L) Wilczek using the AFLP technique. Five different varieties of Vigna radiata viz. B1, TARM 2, PDM 84, TM 99, and TM 98 were subjected to AFLP analysis. A total of 471 fragments were scored across all the 12 AFLP primer sets used and the results were used to plot a dendrogram. It was observed that these five varieties formed three distinct groups among which the aromatic B1 variety formed a distinct group.

Epidemiology of resistance of carbapenemase-producing Klebsiella pneumoniae to ceftazidime-avibactam in a Chinese hospital.

Aims Klebsiella pneumoniae has been reported to develop increased antibiotic resistance. Ceftazidime‐avibactam (CZA) is a novel antibiotic with activity against serine‐lactamase. Here, we investigated the sensitivity of carbapenem‐resistant K. pneumoniae (CRKP) to CZA and the mechanisms of drug resistance in our hospital.Methods and ResultsPatient characteristics were obtained from medical records. K. pneumoniae and its antibiotic susceptibility were determined using the Vitek‐2 Compact instrument. The antibiotic resistance genes KPC, NDM, OXA‐48, VIM, IMP, CIM, SPM, TMB, SMB, SIM, AIM and DIM were detected using real‐time PCR. Multilocus sequence typing was used for genetic RELATEDNESS analysis. In total, 121 CRKP strains were isolated from patients in the intensive care unit (51·2%), senior ward (12·4%) and neurosurgery department (10%). With an average age of 72·5 years, most patients were in care for respiratory (34·7%), brain (20·7%), digestive tract (13·2%) and cardiovascular (8·3%) diseases. Specimens were predominantly obtained from sputum (39·67%), urine (29·75%) and blood (6·61%).ConclusionOf 23 CZA‐resistant CRKP strains (19·01%), ST11 being the most common at 56·52%, 11 NDM‐1‐positive (47·83%) and four NDM‐5‐positive (17·39%) strains were detected.Significance and Impact of the StudyOur study indicates that CZA resistance occurs in ~19·01% CRKP strains and that bla NDM‐1 and bla NDM‐5 might be critical for resistance.

De Novo SNP Discovery and Genotyping of Iranian Pimpinella Species Using ddRAD Sequencing

The species of Pimpinella, one of the largest genera of the family Apiaceae, are traditionally cultivated for medicinal purposes. In this study, high-throughput double digest restriction-site associated DNA sequencing technology (ddRAD-seq) was used to identify single nucleotide polymorphisms (SNPs) in eight Pimpinella species from Iran. After double-digestion with the enzymes HpyCH4IV and HinfI, a total of 334,702,966 paired-end reads were de novo assembled into 1,270,791 loci with an average of 28.8 reads per locus. After stringent filtering, 2440 high-quality SNPs were identified for downstream analysis. Analysis of genetic relationships and population structure, based on these retained SNPs, indicated the presence of three major groups. Gene ontology and pathway analysis were determined by using comparison SNP-associated flanking sequences with a public non-redundant database. Due to the lack of genomic resources in this genus, our present study is the first report to provide high-quality SNPs in Pimpinella based on a de novo analysis pipeline using ddRAD-seq. This data will enhance the molecular knowledge of the genus Pimpinella and will provide an important source of information for breeders and the research community to enhance breeding programs and support the management of Pimpinella genomic resources.

Detection and phylogenetic analysis of deformed wing virus (DWV) in honey bees, Apis mellifera L. and parasitic mite, Varroa destructor Anderson and Trueman (Acari: Varroidae)

Deformed wing virus is one of the most common viral infections in honeybee populations around the world. In this study, a total of 30 apiaries located in different geographical regions of Hamedan, Iran were analyzed for the presence of deformed wing virus on capped larvae and workers of the honeybee, Apis mellifera (Hym: Apidae), as well as the parasitic mite, Varroa destructor (Acari: Varroidae), using reverse-transcription PCR. Two target sequences within the putative VP1, VP4, and VP2 structural-protein genes and the RNA helicase enzyme gene, were selected for amplification and sequencing. According to the results, 36.6% of apiaries were found to be infected with deformed wing virus, including 8, 0, and 3 positive samples on capped larvae and workers, and Varroa mites, respectively. Four strains of the virus obtained from honeybees and mites were selected for analysis of genetic diversity and phylogenetic relationships with other sequences deposited in GenBank. The results showed a high degree of similarity between the virus strains in honeybee and Varroa mite. The phylogenetic results highlight the higher suitability of non-structural in comparison with structural proteins for genetic diversity and phylogenetic studies of deformed wing virus strains.

ANALYSIS OF GENETIC DIVERSITY OF PALM OIL PLANT (Elaeis guineensis Jacq.) PALM OIL RESEARCH CENTER (PPKS) BASED ON PRIMARY SSR (Simple Sequence Repeats)

The background of this research was to obtain information of genetic diversity within and among populations of E. guineensis using SSR markers. This research was conduted in Biology Molecular Laboratory, Indonesian Oil Palm Research Institute, Marihat, Pematangsiantar, North Sumatra from March 2016 to January 2017. A total of 100 palm oil samples used in this research, including 20 samples from the populations of E. guineensis TR01S, including 20 samples from the populations of E. guineensis BJ022S, including 20 samples from the populations of E. guineensis BJ42S, including 20 samples from the populations of E. guineensis BO52S, and including 20 samples from the populations of E. guineensis MA19S. Calculation and Desciptive analysis in this research using software GeneMarker® version 2.40, software DARwin version 6.0.13 and Microsoft Excel 2007. Research shows that the number of banding patterns detected 104 The banding patterns WITH range 8-9 per primary banding pattern, and the size of the banding patterns ranging from 101 bp -328 bp. mEgCIR2569 primary is the most widely primer to amplify DNA and the average of the percentage of polymorphism in the primer being used by 71%. Analysis dendogram 100 samples All 3 hearts big group of Jatropha genetic WITH BETWEEN Yang ranged from 0.03 to 1.00 Based on the findings of the analysis of genetic relationships WITH Matrix Method using differences Simple Matching Value factorial analysis (PCoA) declared WITH axis I and axis II ON 12 primary SSR of 20.3%. mEgCIR2569 primary is the most widely primer to amplify DNA and the average of the percentage of polymorphism in the primer being used by 71%. Analysis dendogram 100 samples All 3 hearts big group of Jatropha genetic WITH BETWEEN Yang ranged from 0.03 to 1.00 Based on the findings of the analysis of genetic relationships WITH Matrix Method using differences Simple Matching Value factorial analysis (PCoA) declared WITH axis I and axis II ON 12 primary SSR of 20.3%. mEgCIR2569 primary is the most widely primer to amplify DNA and the average of the percentage of polymorphism in the primer being used by 71%. Analysis dendogram 100 samples All 3 hearts big group of Jatropha genetic WITH BETWEEN Yang ranged from 0.03 to 1.00 Based on the findings of the analysis of genetic relationships WITH Matrix Method using differences Simple Matching Value factorial analysis (PCoA) declared WITH axis I and axis II ON 12 primary SSR of 20.3%.

Genetic relationship analysis of Dendrobium anosmum Lindl. var. semialba based on the chloroplast matK and rbcL genes

Dendrobium anosmum Lindl. var. semialba has variants of flower shapes. Currently, it has high economic value and is favored on the market. In this study, the genetic relationship of Dendrobium anosmum Lindl. var. semialba species was determined based on the analysis of chloroplast matK, rbcL gene sequences. The matK and rbcL genes of twelve species were amplified and their DNA sequenced. These DNA sequences were compared, calculated genetic distance and constructed phylogenetic tree. The results showed that 100% of samples were amplified and sequenced successfully. The analysis of matK sequences showed that 12 species had very high genetic similarity with the low genetic distance of 0 - 0.001; the nucleotide sequences were almost unchanged except for one variable nucleotide position in TB1 and TB1 was in a separate branch of the phylogenetic tree. The analysis of rbcL sequences showed that all species had a low genetic distance of 0 - 0.012 and had 7 mutant positions in nucleotide sequences of TB1 and TB5. These species were in a separate branch of the phylogenetic tree while the other species were grouped in the other branch of the phylogenetic tree. The study provided a reliable molecular database of the Dendrobium anosmum Lindl. var. semialba for identification, classification, biodiversity assessment and conservation of genetic resources.

Genetic diversity and genetic relatedness in Plasmodium falciparum parasite population in individuals with uncomplicated malaria based on microsatellite typing in Eastern and Western regions of Uganda, 2019\u20132020

BackgroundGenetic diversity and parasite relatedness are essential parameters for assessing impact of interventions and understanding transmission dynamics of malaria parasites, however data on its status in Plasmodium falciparum populations in Uganda is limited. Microsatellite markers and DNA sequencing were used to determine diversity and molecular characterization of P. falciparum parasite populations in Uganda.MethodsA total of 147 P. falciparum genomic DNA samples collected from cross-sectional surveys in symptomatic individuals of 2–10 years were characterized by genotyping of seven highly polymorphic neutral microsatellite markers (n = 85) and genetic sequencing of the Histidine Rich Protein 2 (pfhrp2) gene (n = 62). ArcGIS was used to map the geographical distribution of isolates while statistical testing was done using Student's t-test or Wilcoxon's rank-sum test and Fisher’s exact test as appropriate at P ≤ 0.05.ResultsOverall, 75.5% (95% CI 61.1–85.8) and 24.5% (95% CI14.2–38.9) of parasites examined were of multiclonal (mixed genotype) and single clone infections, respectively. Multiclonal infections occurred more frequently in the Eastern region 73.7% (95% CI 48.8–89.1), P < 0.05. Overall, multiplicity of infection (MOI) was 1.9 (95% CI 1.7–2.1), P = 0.01 that was similar between age groups (1.8 vs 1.9), P = 0.60 and regions (1.9 vs 1.8), P = 0.43 for the < 5 and ≥ 5 years and Eastern and Western regions, respectively. Genomic sequencing of the pfhrp2 exon2 revealed a high level of genetic diversity reflected in 96.8% (60/62) unique sequence types. Repeat type AHHAAAHHATD and HRP2 sequence Type C were more frequent in RDT−/PCR + samples (1.9% vs 1.5%) and (13% vs 8%), P < 0.05 respectively. Genetic relatedness analysis revealed small clusters of gene deleted parasites in Uganda, but no clustering with Eritrean parasites.ConclusionHigh level of genetic diversity of P. falciparum parasites reflected in the frequency of multiclonal infections, multiplicity of infection and variability of the pfhrp2 gene observed in this study is consistent with the high malaria transmission intensity in these settings. Parasite genetic analysis suggested spontaneous emergence and clonal expansion of pfhrp2 deleted parasites that require close monitoring to inform national malaria diagnosis and case management policies.