Pollen diversity, viability and floral structure of some Musa genotypes

African Journals Online (AJOL)

Prof. Ogunji

Pollen diversity, viability and floral structure of some Musa genotypes ... at the Faculty of Agriculture & Natural Resources Management farm, Ebonyi State University,. Abakaliki. ..... Roots, tuber, plantains and bananas in human nutrition. Rome,.

Genotypic and phenotypic diversity of Alicyclobacillus acidocaldarius isolates.

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Félix-Valenzuela, L; Guardiola-Avila, I; Burgara-Estrella, A; Ibarra-Zavala, M; Mata-Haro, V

2015-10-01

The fruit juice industry recognizes Alicyclobacillus as a major quality control target micro-organism. In this study, we analysed 19 bacterial isolates to identify Alicyclobacillus species by polymerase chain reaction (PCR) and sequencing analyses. Phenotypic and genomic diversity among isolates were investigated by API 50CHB system and ERIC-PCR (enterobacterial repetitive intergenic consensus-PCR) respectively. All bacterial isolates were identified as Alicyclobacillus acidocaldarius, and almost all showed identical DNA sequences according to their 16S rRNA (rDNA) gene partial sequences. Only few carbohydrates were fermented by A. acidocaldarius isolates, and there was little variability in the biochemical profile. Genotypic fingerprinting of the A. acidocaldarius isolates showed high diversity, and clusters by ERIC-PCR were distinct to those obtained from the 16S rRNA gene phylogenetic tree. There was no correlation between phenotypic and genotypic variability in the A. acidocaldarius isolates analysed in this study. Detection of Alicyclobacillus strains is imperative in fruit concentrates and juices due to the production of guaiacol. Identification of the genera originates rejection of the product by processing industry. However, not all the Alicyclobacillus species are deteriorative and hence the importance to differentiate among them. In this study, partial 16S ribosomal RNA sequence alignment allowed the differentiation of species. In addition, ERIC-PCR was introduced for the genotypic characterization of Alicyclobacillus, as an alternative for differentiation among isolates from the same species. © 2015 The Society for Applied Microbiology.

Analysis of genotype diversity and evolution of Dengue virus serotype 2 using complete genomes

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Vaishali P. Waman

2016-08-01

Full Text Available Background Dengue is one of the most common arboviral diseases prevalent worldwide and is caused by Dengue viruses (genus Flavivirus, family Flaviviridae. There are four serotypes of Dengue Virus (DENV-1 to DENV-4, each of which is further subdivided into distinct genotypes. DENV-2 is frequently associated with severe dengue infections and epidemics. DENV-2 consists of six genotypes such as Asian/American, Asian I, Asian II, Cosmopolitan, American and sylvatic. Comparative genomic study was carried out to infer population structure of DENV-2 and to analyze the role of evolutionary and spatiotemporal factors in emergence of diversifying lineages. Methods Complete genome sequences of 990 strains of DENV-2 were analyzed using Bayesian-based population genetics and phylogenetic approaches to infer genetically distinct lineages. The role of spatiotemporal factors, genetic recombination and selection pressure in the evolution of DENV-2 is examined using the sequence-based bioinformatics approaches. Results DENV-2 genetic structure is complex and consists of fifteen subpopulations/lineages. The Asian/American genotype is observed to be diversified into seven lineages. The Asian I, Cosmopolitan and sylvatic genotypes were found to be subdivided into two lineages, each. The populations of American and Asian II genotypes were observed to be homogeneous. Significant evidence of episodic positive selection was observed in all the genes, except NS4A. Positive selection operational on a few codons in envelope gene confers antigenic and lineage diversity in the American strains of Asian/American genotype. Selection on codons of non-structural genes was observed to impact diversification of lineages in Asian I, cosmopolitan and sylvatic genotypes. Evidence of intra/inter-genotype recombination was obtained and the uncertainty in classification of recombinant strains was resolved using the population genetics approach. Discussion Complete genome-based analysis

AFLP analysis of Genetic Diversity Among Different Jatropha curcas L. Genotypes from Africa and Ecuador

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Konan, NO.

2018-01-01

Full Text Available Six populations amounting to a total number of seventy genotypes of Jatropha curcas L. originating from Africa (Senegal, Mali, Burkina Faso and Madagascar and Ecuador were investigated for genetic diversity using two AFLP primer combinations. The results revealed a high genetic diversity in the populations studied. The population with greatest genetic diversity was Madagascar (He = 0.2638 and I = 0.4066 and the least diverse was Senegal-Tamba (He = 0.1962 and I = 0.3079. AMOVA (analysis of molecular variance detected the highest proportion of variation within populations (81% of the total molecular variation. This may be attributed to the high level of allogamy observed in this species. The Nei's standard unbiased genetic distance (D between the populations ranged from 0.010 (Senegal-Tamba and Burkina Faso to 0.131 (Mali and Ecuador; the average was 0.063. Analysis of the genetic relationships among the 6 populations using both neighbor-joining cluster analysis and principal component analysis (PCoA showed five clusters with globally, groupings of i most of Burkina Faso and Senegal-Tamba genotypes, ii most of Mali and Senegal-Diobass genotypes , iii most of Madagascar and Ecuador genotypes, and iv some mixings of genotypes with different origins. Considering the distance existing between the different origins there are prospects to develop F1 hybrids. The greatest heterosis might be expected from crossing involving genotypes of cluster I and cluster V which group the more distant genotypes. Such crossing schemes might produce greater success in the production of genetic variability and might maximize the exploitation of heterosis and segregation.

Genetic Diversity and Population Structure of F3:6 Nebraska Winter Wheat Genotypes Using Genotyping-By-Sequencing.

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Eltaher, Shamseldeen; Sallam, Ahmed; Belamkar, Vikas; Emara, Hamdy A; Nower, Ahmed A; Salem, Khaled F M; Poland, Jesse; Baenziger, Peter S

2018-01-01

The availability of information on the genetic diversity and population structure in wheat ( Triticum aestivum L.) breeding lines will help wheat breeders to better use their genetic resources and manage genetic variation in their breeding program. The recent advances in sequencing technology provide the opportunity to identify tens or hundreds of thousands of single nucleotide polymorphism (SNPs) in large genome species (e.g., wheat). These SNPs can be utilized for understanding genetic diversity and performing genome wide association studies (GWAS) for complex traits. In this study, the genetic diversity and population structure were investigated in a set of 230 genotypes (F 3:6 ) derived from various crosses as a prerequisite for GWAS and genomic selection. Genotyping-by-sequencing provided 25,566 high-quality SNPs. The polymorphism information content (PIC) across chromosomes ranged from 0.09 to 0.37 with an average of 0.23. The distribution of SNPs markers on the 21 chromosomes ranged from 319 on chromosome 3D to 2,370 on chromosome 3B. The analysis of population structure revealed three subpopulations (G1, G2, and G3). Analysis of molecular variance identified 8% variance among and 92% within subpopulations. Of the three subpopulations, G2 had the highest level of genetic diversity based on three genetic diversity indices: Shannon's information index ( I ) = 0.494, diversity index ( h ) = 0.328 and unbiased diversity index (uh) = 0.331, while G3 had lowest level of genetic diversity ( I = 0.348, h = 0.226 and uh = 0.236). This high genetic diversity identified among the subpopulations can be used to develop new wheat cultivars.

Genetic diversity of maize genotypes on the basis of morpho ...

African Journals Online (AJOL)

Genetic diversity of maize genotypes on the basis of morpho-physiological and simple sequence repeat (SSR) markers. Ashish Kumar, Arunita Rakshit, Naresh K Mangilipelli, Y Varalaxmi, T Vijayalakshmi, Jainender M Vanaja, SK Yadav, B Venkateswarlu, M Maheswari ...

Genotypic and phenotypic diversity does not affect productivity and drought response in competitive stands of Trifolium repens

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Heidrun eHuber

2016-03-01

Full Text Available Clonal plants can form dense canopies in which plants of different genetic origin are competing for the uptake of essential resources. The competitive relationships among these clones are likely to be affected by extreme environmental conditions, such as prolonged drought spells, which are predicted to occur more frequently due to global climate change. This, in turn, may alter characteristics of the ecological system and its associated functioning.We hypothesized that the relative success of individual clones will depend on the size of the ramets as ramets with larger leaves and longer petioles (large ramets were predicted to have a competitive advantage in terms of increased light interception over smaller-sized ramets. Under drier conditions the relative performances of genotypes were expected to change leading to a change in genotype ranking. We also hypothesized that increased genotypic and phenotypic diversity will increase stand performance and resistance to drought. These hypotheses and the mechanisms responsible for shifts in competitive relationships were investigated by subjecting genotypes of the important pasture legume Trifolium repens to competition with either genetically identical clones, genetically different but similarly sized clones, or genetically as well as morphologically different clones under well-watered and dry conditions.Competitive relationships were affected by ramet size with large genotypes outperforming small genotypes in diverse stands in terms of biomass production. However, large genotypes also produced relatively fewer ramets than small genotypes and could not benefit in terms of clonal reproduction from competing with smaller genotypes, indicating that evolutionary shifts in genotype composition will depend on whether ramet size or ramet number is under selection. In contrast to our hypotheses, diversity did not increase stand performance under different selection regimes and genotype ranking was hardly

Genotypic and Phenotypic Diversity Does Not Affect Productivity and Drought Response in Competitive Stands of Trifolium repens.

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Huber, Heidrun; During, Heinjo J; Bruine de Bruin, Fabienne; Vermeulen, Peter J; Anten, Niels P R

2016-01-01

Clonal plants can form dense canopies in which plants of different genetic origin are competing for the uptake of essential resources. The competitive relationships among these clones are likely to be affected by extreme environmental conditions, such as prolonged drought spells, which are predicted to occur more frequently due to global climate change. This, in turn, may alter characteristics of the ecological system and its associated functioning. We hypothesized that the relative success of individual clones will depend on the size of the ramets as ramets with larger leaves and longer petioles (large ramets) were predicted to have a competitive advantage in terms of increased light interception over smaller-sized ramets. Under drier conditions the relative performances of genotypes were expected to change leading to a change in genotype ranking. We also hypothesized that increased genotypic and phenotypic diversity will increase stand performance and resistance to drought. These hypotheses and the mechanisms responsible for shifts in competitive relationships were investigated by subjecting genotypes of the important pasture legume Trifolium repens to competition with either genetically identical clones, genetically different but similarly sized clones, or genetically as well as morphologically different clones under well-watered and dry conditions. Competitive relationships were affected by ramet size with large genotypes outperforming small genotypes in diverse stands in terms of biomass production. However, large genotypes also produced relatively fewer ramets than small genotypes and could not benefit in terms of clonal reproduction from competing with smaller genotypes, indicating that evolutionary shifts in genotype composition will depend on whether ramet size or ramet number is under selection. In contrast to our hypotheses, diversity did not increase stand performance under different selection regimes and genotype ranking was hardly affected by soil

Emergence of new genotype and diversity of Theileria orientalis parasites from bovines in India.

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George, Neena; Bhandari, Vasundhra; Reddy, D Peddi; Sharma, Paresh

2015-12-01

Bovine theileriosis is a serious threat to livestock worldwide. Uncertainty around species prevalence, antigenic diversity and genotypes of strains make it difficult to assess the impact of this parasite and to provide necessary treatment. We aimed to characterize genotypic diversity, phylogeny and prevalence of Theileria orientalis parasites from the states of Telangana and Andhra Pradesh, India by collecting bovine blood samples from the major districts of the two states. Bioinformatic analysis identified antigenic diversity among the prevalent parasite strains using major piroplasm surface protein (MPSP) gene. Our study revealed a prevalence rate of 4.8% (n=41/862) of T. orientalis parasites in bovine animals and a new genotype of T. orientalis parasite which was not previously reported in India. The emergence of these new genotypes could be an explanation for the frequent outbreaks of bovine theileriosis. Further, whole genome sequencing of T. orientalis strains will help to elucidate the genetic factors relevant for transmissibility and virulence as well as vaccine and new drug development. Copyright © 2015 Elsevier B.V. All rights reserved.

Genotypic and phenotypic diversity in populations of plant-probiotic Pseudomonas spp. colonizing roots

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Picard, Christine; Bosco, Marco

2008-01-01

Several soil microorganisms colonizing roots are known to naturally promote the health of plants by controlling a range of plant pathogens, including bacteria, fungi, and nematodes. The use of theses antagonistic microorganisms, recently named plant-probiotics, to control plant-pathogenic fungi is receiving increasing attention, as they may represent a sustainable alternative to chemical pesticides. Many years of research on plant-probiotic microorganisms (PPM) have indicated that fluorescent pseudomonads producing antimicrobial compounds are largely involved in the suppression of the most widespread soilborne pathogens. Phenotype and genotype analysis of plant-probiotic fluorescent pseudomonads (PFP) have shown considerable genetic variation among these types of strains. Such variability plays an important role in the rhizosphere competence and the biocontrol ability of PFP strains. Understanding the mechanisms by which genotypic and phenotypic diversity occurs in natural populations of PFP could be exploited to choose those agricultural practices which best exploit the indigenous PFP populations, or to isolate new plant-probiotic strains for using them as inoculants. A number of different methods have been used to study diversity within PFP populations. Because different resolutions of the existing microbial diversity can be revealed depending on the approach used, this review first describes the most important methods used for the assessment of fluorescent Pseudomonas diversity. Then, we focus on recent data relating how differences in genotypic and phenotypic diversity within PFP communities can be attributed to geographic location, climate, soil type, soil management regime, and interactions with other soil microorganisms and host plants. It becomes evident that plant-related parameters exert the strongest influence on the genotypic and phenotypic variations in PFP populations.

Mycobacterium tuberculosis Isolates from Single Outpatient Clinic in Panama City Exhibit Wide Genetic Diversity

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Sambrano, Dilcia; Correa, Ricardo; Almengor, Pedro; Domínguez, Amada; Vega, Silvio; Goodridge, Amador

2014-01-01

Understanding Mycobacterium tuberculosis biodiversity and transmission is significant for tuberculosis control. This short report aimed to determine the genetic diversity of M. tuberculosis isolates from an outpatient clinic in Panama City. A total of 62 M. tuberculosis isolates were genotyped by 12 loci mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU-VNTR) and Spoligotyping. Forty-five (72.6%) of the isolates showed unique MIRU-VNTR genotypes, and 13 (21%) of the isolates were grouped into four clusters. Four isolates showed polyclonal MIRU-VNTR genotypes. The MIRU-VNTR Hunter-Gaston discriminatory index reached 0.988. The Spoligotyping analysis revealed 16 M. tuberculosis families, including Latin American-Mediterranean, Harlem, and Beijing. These findings suggest a wide genetic diversity of M. tuberculosis isolates at one outpatient clinic. A detailed molecular epidemiology survey is now warranted, especially following second massive immigration for local Panama Canal expansion activities. PMID:24865686

Assessment of RAPD Markers to Analyse the Genetic Diversity among Sunflower (Helianthus annuus L. Genotypes

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Ali Raza

2018-02-01

Full Text Available Genetic diversity estimation among different species is an important tool for genetic improvement to maximize the yield, desirable quality, wider adaptation, pest and insect resistance that ultimately boosting traditional plant breeding methods. The most efficient way of diversity estimation is application of molecular markers. In this study, twenty random amplified polymorphic DNA (RAPD primers were utilized to estimate the genetic diversity between ten sunflower genotypes. Overall 227 bands were amplified by 20 primers with an average of 11.35 bands per primer. RAPD data showed 86.34% polymorophic bands and 13.65% of monomorophic bands. Genetic similarity was ranged from 50.22% to 87.22%. The lowest similarity (50.22% was observed between FH-352 and FH-359 and the maximum similarity 87.22% was observed between A-23 and G-46. Polymorphic information content (PIC values were varying from 0.05 to 0.12 with a mean of 0.09. Cluster analysis based on RAPD results displayed two major distinct groups 1 and 2. Group-2 contains FH-352 which was the most diverse genotype, while group-1 consists of few sub groups with all other genotypes. Ample diversity was found in all the genotypes. Present study reveals novel information about sunflower genome which can be used in future studies for sunflower improvement.

Appraisal of genetic diversity of different peach cultivars and genotypes through rapd markers

International Nuclear Information System (INIS)

Bakht, J.; Jamal, N.; Shafi, M

2012-01-01

The present study was amid to investigate the genetic diversity of twenty peach cultivars and genotypes by RAPD primers at the Institute of Biotechnology and Genetic Engineering, KPK Agricultural University Peshawar. The result indicated that fifteen primers (GLCO9, GLC20, GLA20, GLA13, GLB10, GLB20, GLB06, GLB19, GLA19, GLB19, GLD16, GLB15, GLA15, GLB12, GLB11) gave genetic distance among the peach cultivars and genotypes under study by PCR amplification. Average genetic diversity (estimated as genetic distance) ranged between 12 and 58%. The molecular size of most of the bands were from 150 bp to 1000 bp. Based on dendrogram analysis, Khyber 1 and Khyber 2 was grouped in cluster A, and Tex-A6-69 and BY-8-135 in cluster B, Candan and 6A were most closely related cultivars and genotypes among the 20 peach cultivars and genotypes while Lering, Flam crest, Tex x-9, early grand and Floradaking were distinctly grouped when compared with the rest of population. (author)

Mixed genotype transmission bodies and virions contribute to the maintenance of diversity in an insect virus

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Clavijo, Gabriel; Williams, Trevor; Muñoz, Delia; Caballero, Primitivo; López-Ferber, Miguel

2010-01-01

An insect nucleopolyhedrovirus naturally survives as a mixture of at least nine genotypes. Infection by multiple genotypes results in the production of virus occlusion bodies (OBs) with greater pathogenicity than those of any genotype alone. We tested the hypothesis that each OB contains a genotypically diverse population of virions. Few insects died following inoculation with an experimental two-genotype mixture at a dose of one OB per insect, but a high proportion of multiple infections were observed (50%), which differed significantly from the frequencies predicted by a non-associated transmission model in which genotypes are segregated into distinct OBs. By contrast, insects that consumed multiple OBs experienced higher mortality and infection frequencies did not differ significantly from those of the non-associated model. Inoculation with genotypically complex wild-type OBs indicated that genotypes tend to be transmitted in association, rather than as independent entities, irrespective of dose. To examine the hypothesis that virions may themselves be genotypically heterogeneous, cell culture plaques derived from individual virions were analysed to reveal that one-third of virions was of mixed genotype, irrespective of the genotypic composition of the OBs. We conclude that co-occlusion of genotypically distinct virions in each OB is an adaptive mechanism that favours the maintenance of virus diversity during insect-to-insect transmission. PMID:19939845

Genotypic diversity and clonal structure of Erigeron annuus (Asteraceae in Lithuania

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Tunaitienė, Virginija

2014-02-01

Full Text Available This study was conducted to assess the clonal structure and genetic diversity of alien herbaceous plant species Erigeron annuus. The global warming and changes in agriculture practice in the past few decades were favourable for the expansion of this species in Lithuania. We used RAPD and ISSR assays to assess genetic variation within and among 29 populations of E. annuus. A total of 278 molecular markers were revealed. Our study detected reduced level of genetic diversity of invasive populations of E. annuus. Significant differences in DNA polymorphism among populations of E. annuus were also found. Some populations of this species are composed of genetically identical plants, while others were polymorphic. Clonal diversity of study populations ranged from 0.083 to 0.4 for both DNA marker systems. The Simpsons diversity index values ranged from 0.0 to 0.636. The average number of genotypes per population established using both assays was about 1.7. Out of 328 E. annuus individuals only 16 showed unique RAPD and 14 unique ISSR banding patterns. The remaining plants were clones of different size. The most common genotype of E. annuus identified in our study was represented by predominate in nine populations.

Yersinia enterocolitica of porcine origin: carriage of virulence genes and genotypic diversity.

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Tadesse, Daniel A; Bahnson, Peter B; Funk, Julie A; Morrow, W E Morgan; Abley, Melanie J; Ponte, Valeria A; Thakur, Siddhartha; Wittum, Thomas; DeGraves, Fred J; Rajala-Schultz, Paivi J; Gebreyes, Wondwossen A

2013-01-01

Yersinia enterocolitica is an important foodborne pathogen, and pigs are recognized as a major reservoir and potential source of pathogenic strains to humans. A total of 172 Y. enterocolitica recovered from conventional and antimicrobial-free pig production systems from different geographic regions (North Carolina, Ohio, Michigan, Wisconsin, and Iowa) were investigated to determine their pathogenic significance to humans. Phenotypic and genotypic diversity of the isolates was assessed using antibiogram, serogrouping, and amplified fragment length polymorphism (AFLP). Carriage of chromosomal and plasmid-borne virulence genes were investigated using polymerase chain reaction. A total of 12 antimicrobial resistance patterns were identified. More than two-thirds (67.4%) of Y. enterocolitica were pan-susceptible, and 27.9% were resistant against β-lactams. The most predominant serogroup was O:3 (43%), followed by O:5 (25.6%) and O:9 (4.1%). Twenty-two of 172 (12.8%) isolates were found to carry Yersinia adhesion A (yadA), a virulence gene encoded on the Yersinia virulence plasmid. Sixty-nine (40.1%) isolates were found to carry ail gene. The ystA and ystB genes were detected in 77% and 26.2% of the strains, respectively. AFLP genotyping of isolates showed wide genotypic diversity and were grouped into nine clades with an overall genotypic similarity of 66.8-99.3%. AFLP analysis revealed that isolates from the same production system showed clonal relatedness, while more than one genotype of Y. enterocolitica circulates within a farm.

DNA landmarks for genetic relatedness and diversity assessment in Pakistani wheat genotypes using RAPD markers

International Nuclear Information System (INIS)

Siddiqui, M.F.; Iqbal, S.; Naz, N.; Khan, S.; Erum, S.

2010-01-01

DNA profiles from 10 Pakistani wheat genotypes were evaluated for diversity assessment based on RAPD markers. A total of 79 DNA fragments were generated by 10 RAPD primers, with an average of 7.9 bands primer-1. Of these, 64 fragments (81%) were polymorphic among 10 genotypes. Genetic diversity was evaluated via UPGMA cluster analysis by constructing dendrogram, which were used for the calculation of similarity coefficients between these genotypes. The greatest similarity (95%) was observed between PR-94 and PR-95, whereas PR-96 with PR-90 showed the lowest similarity (60%). Adoption of this technology would be useful to the plant protection regulatory systems, especially for plant variety identification and registration of new plant varieties, breeding programs and protection purposes. (author)

DNA landmarks for genetic relatedness and diversity assessment in Pakistani wheat genotypes using RAPD markers

Energy Technology Data Exchange (ETDEWEB)

Siddiqui, M F; Iqbal, S; Naz, N; Khan, S [Federal Seed Certification and Registration Dept., Islamabad (Pakistan); Erum, S [National Agricultural Research Centre, Islamabad (Pakistan). Plant Genetic Resources Inst.

2010-04-15

DNA profiles from 10 Pakistani wheat genotypes were evaluated for diversity assessment based on RAPD markers. A total of 79 DNA fragments were generated by 10 RAPD primers, with an average of 7.9 bands primer-1. Of these, 64 fragments (81%) were polymorphic among 10 genotypes. Genetic diversity was evaluated via UPGMA cluster analysis by constructing dendrogram, which were used for the calculation of similarity coefficients between these genotypes. The greatest similarity (95%) was observed between PR-94 and PR-95, whereas PR-96 with PR-90 showed the lowest similarity (60%). Adoption of this technology would be useful to the plant protection regulatory systems, especially for plant variety identification and registration of new plant varieties, breeding programs and protection purposes. (author)

Molecular characterization and genetic diversity of different genotypes of Oryza sativa and Oryza glaberrima

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Caijin Chen

2017-11-01

Conclusions: Genetic diversity studies revealed that 50 rice types were clustered into different subpopulations whereas three genotypes were admixtures. Molecular fingerprinting and 10 specific markers were obtained to identify the 53 rice genotypes. These results can facilitate the potential utilization of sibling species in rice breeding and molecular classification of O. sativa and O. glaberrima germplasms.

Genetic diversity in South African maize ( Zea mays L.) genotypes as ...

African Journals Online (AJOL)

One thousand and forty three (1043) maize genotypes including white and yellow maize inbred lines as well as hybrids from the public germplasm collection were characterized with 80 microsatellite markers distributed throughout the genome. A total of 1874 alleles were amplified and used in the genetic diversity analysis.

Global phylogeography and genetic diversity of the zoonotic tapeworm Echinococcus granulosus sensu stricto genotype G1.

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Kinkar, Liina; Laurimäe, Teivi; Acosta-Jamett, Gerardo; Andresiuk, Vanessa; Balkaya, Ibrahim; Casulli, Adriano; Gasser, Robin B; van der Giessen, Joke; González, Luis Miguel; Haag, Karen L; Zait, Houria; Irshadullah, Malik; Jabbar, Abdul; Jenkins, David J; Kia, Eshrat Beigom; Manfredi, Maria Teresa; Mirhendi, Hossein; M'rad, Selim; Rostami-Nejad, Mohammad; Oudni-M'rad, Myriam; Pierangeli, Nora Beatriz; Ponce-Gordo, Francisco; Rehbein, Steffen; Sharbatkhori, Mitra; Simsek, Sami; Soriano, Silvia Viviana; Sprong, Hein; Šnábel, Viliam; Umhang, Gérald; Varcasia, Antonio; Saarma, Urmas

2018-05-19

Echinococcus granulosus sensu stricto (s.s.) is the major cause of human cystic echinococcosis worldwide and is listed among the most severe parasitic diseases of humans. To date, numerous studies have investigated the genetic diversity and population structure of E. granulosus s.s. in various geographic regions. However, there has been no global study. Recently, using mitochondrial DNA, it was shown that E. granulosus s.s. G1 and G3 are distinct genotypes, but a larger dataset is required to confirm the distinction of these genotypes. The objectives of this study were to: (i) investigate the distinction of genotypes G1 and G3 using a large global dataset; and (ii) analyse the genetic diversity and phylogeography of genotype G1 on a global scale using near-complete mitogenome sequences. For this study, 222 globally distributed E. granulosus s.s. samples were used, of which 212 belonged to genotype G1 and 10 to G3. Using a total sequence length of 11,682 bp, we inferred phylogenetic networks for three datasets: E. granulosus s.s. (n = 222), G1 (n = 212) and human G1 samples (n = 41). In addition, the Bayesian phylogenetic and phylogeographic analyses were performed. The latter yielded several strongly supported diffusion routes of genotype G1 originating from Turkey, Tunisia and Argentina. We conclude that: (i) using a considerably larger dataset than employed previously, E. granulosus s.s. G1 and G3 are indeed distinct mitochondrial genotypes; (ii) the genetic diversity of E. granulosus s.s. G1 is high globally, with lower values in South America; and (iii) the complex phylogeographic patterns emerging from the phylogenetic and geographic analyses suggest that the current distribution of genotype G1 has been shaped by intensive animal trade. Copyright © 2018 Australian Society for Parasitology. Published by Elsevier Ltd. All rights reserved.

Toxoplasma gondii seroprevalence and genotype diversity in select wildlife species from the southeastern United States

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Richard W. Gerhold

2017-10-01

Full Text Available Abstract Background Toxoplasma gondii is a widespread protozoan parasite that infects humans and other animals. Previous studies indicate some genotypes of T. gondii are more frequently isolated in wildlife than agricultural animals, suggesting a wild/feral animal diversity model. To determine seroprevalence and genetic diversity of T. gondii in southeastern US wildlife, we collected sera from 471 wild animals, including 453 mammals and 18 birds, between 2011 and 2014. These serum samples were assayed for T. gondii infection using the modified agglutination test (MAT. Heart or tongue tissues from 66 seropositive animals were bioassayed in mice and 19 isolates were obtained. The isolated parasites were genotyped by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP method employing 10 genetic markers. Results One hundred and ninety-six of 471 samples (41.6% had a titer ≥1:32 and were considered positive for T. gondii infection. Of 453 mammals, 195 (43% were seropositive, whereas only one (5.6% of 18 birds was seropositive. The seroprevalence in mammals was significantly higher than in the birds. Mammalian hosts with adequate samples size (≥ 20 comprised white-tailed deer (n = 241, feral hogs (n = 100, raccoons (n = 34 and coyotes (n = 22, with seroprevalences of 41.0%, 51.0%, 50.0% and 72.7%, respectively. Coyotes had significantly higher seroprevalence than the white-tailed deer. Genotyping revealed five distinct genotypes, including the ToxoDB PCR-RFLP genotype #5 (a.k.a type 12 for 15 isolates, genotype #3 (a.k.a. type II for 1 isolate, and genotypes #154, #167 and #216, each for 1 isolate. The results showed moderate to high infection rates of T. gondii in white-tailed deer, feral hogs, raccoons and coyotes. Genotyping results indicated limited genetic diversity and a dominance of genotype #5, which has been reported as a major type in wildlife in North America. Conclusions We conclude that T. gondii

Geographically diverse Australian isolates of Melissococcus pluton exhibit minimal genotypic diversity by restriction endonuclease analysis.

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Djordjevic, S P; Smith, L A; Forbes, W A; Hornitzky, M A

1999-04-15

Melissococcus pluton, the causative agent of European foulbrood is an economically significant disease of honey bees (Apis mellifera) across most regions of the world and is prevalent throughout most states of Australia. 49 Isolates of M. pluton recovered from diseased colonies or honey samples in New South Wales, Queensland, South Australia, Tasmania and Victoria were compared using SDS-PAGE, Western immunoblotting and restriction endonuclease analyses. DNA profiles of all 49 geographically diverse isolates showed remarkably similar AluI profiles although four isolates (one each from Queensland, South Australia, New South Wales and Victoria) displayed minor profile variations compared to AluI patterns of all other isolates. DNA from a subset of the 49 Australian and three isolates from the United Kingdom were digested separately with the restriction endonucleases CfoI, RsaI and DraI. Restriction endonuclease fragment patterns generated using these enzymes were also similar although minor variations were noted. SDS-PAGE of whole cell proteins from 13 of the 49 isolates from different states of Australia, including the four isolates which displayed minor profile variations (AluI) produced indistinguishable patterns. Major immunoreactive proteins of approximate molecular masses of 21, 24, 28, 30, 36, 40, 44, 56, 60, 71, 79 and 95 kDa were observed in immunoblots of whole cell lysates of 22 of the 49 isolates and reacted with rabbit hyperimmune antibodies raised against M. pluton whole cells. Neither SDS-PAGE or immunoblotting was capable of distinguishing differences between geographically diverse isolates of M. pluton. Collectively these data confirm that Australian isolates of M. pluton are genetically homogeneous and that this species may be clonal. Plasmid DNA was not detected in whole cell DNA profiles of any isolate resolved using agarose gel electrophoresis.

Genotypic diversity of Coxiella burnetii in the 2007-2010 Q fever outbreak episodes in The Netherlands

NARCIS (Netherlands)

Tilburg, Jeroen J. H. C.; Rossen, John W. A.; van Hannen, Erik J.; Melchers, Willem J. G.; Hermans, Mirjam H. A.; van de Bovenkamp, Jeroen; Roest, Hendrik Jan I. J.; de Bruin, Arnout; Nabuurs-Franssen, Marrigje H.; Horrevorts, Alphons M.; Klaassen, Corne H. W.

The genotypic diversity of Coxiella burnetii in clinical samples obtained from the Dutch Q fever outbreak episodes of 2007-2010 was determined by using a 6-locus variable-number tandem repeat analysis panel. The results are consistent with the introduction of one founder genotype that is gradually

Genotypic Diversity of Escherichia coli in the Water and Soil of Tropical Watersheds in Hawaii ▿

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Goto, Dustin K.; Yan, Tao

2011-01-01

High levels of Escherichia coli were frequently detected in tropical soils in Hawaii, which present important environmental sources of E. coli to water bodies. This study systematically examined E. coli isolates from water and soil of several watersheds in Hawaii and observed high overall genotypic diversity (35.5% unique genotypes). In the Manoa watershed, fewer than 9.3% of the observed E. coli genotypes in water and 6.6% in soil were shared between different sampling sites, suggesting the lack of dominant fecal sources in the watershed. High temporal variability of E. coli genotypes in soil was also observed, which suggests a dynamic E. coli population corresponding with the frequently observed high concentrations in tropical soils. When E. coli genotypes detected from the same sampling events were compared, limited sharing between the soil and water samples was observed in the majority of comparisons (73.5%). However, several comparisons reported up to 33.3% overlap of E. coli genotypes between soil and water, illustrating the potential for soil-water interactions under favorable environmental conditions. In addition, genotype accumulation curves for E. coli from water and soil indicated that the sampling efforts in the Manoa watershed could not exhaust the overall genotypic diversity. Comparisons of E. coli genotypes from other watersheds on Oahu, Hawaii, identified no apparent grouping according to sampling locations. The results of the present study demonstrate the complexity of using E. coli as a fecal indicator bacterium in tropical watersheds and highlight the need to differentiate environmental sources of E. coli from fecal sources in water quality monitoring. PMID:21515724

Genotypic and phenotypic diversity of Bacillus spp. isolated from steel plant waste

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Chartone-Souza Edmar

2008-10-01

Full Text Available Abstract Background Molecular studies of Bacillus diversity in various environments have been reported. However, there have been few investigations concerning Bacillus in steel plant environments. In this study, genotypic and phenotypic diversity and phylogenetic relationships among 40 bacterial isolates recovered from steel plant waste were investigated using classical and molecular methods. Results 16S rDNA partial sequencing assigned all the isolates to the Bacillus genus, with close genetic relatedness to the Bacillus subtilis and Bacillus cereus groups, and to the species Bacillus sphaericus. tDNA-intergenic spacer length polymorphisms and the 16S–23S intergenic transcribed spacer region failed to identify the isolates at the species level. Genomic diversity was investigated by molecular typing with rep (repetitive sequence based PCR using the primer sets ERIC2 (enterobacterial repetitive intergenic consensus, (GTG5, and BOXAIR. Genotypic fingerprinting of the isolates reflected high intraspecies and interspecies diversity. Clustering of the isolates using ERIC-PCR fingerprinting was similar to that obtained from the 16S rRNA gene phylogenetic tree, indicating the potential of the former technique as a simple and useful tool for examining relationships among unknown Bacillus spp. Physiological, biochemical and heavy metal susceptibility profiles also indicated considerable phenotypic diversity. Among the heavy metal compounds tested Zn, Pb and Cu were least toxic to the bacterial isolates, whereas Ag inhibited all isolates at 0.001 mM. Conclusion Isolates with identical 16S rRNA gene sequences had different genomic fingerprints and differed considerably in their physiological capabilities, so the high levels of phenotypic diversity found in this study are likely to have ecological relevance.

Porphyromonas gingivalis Fim-A genotype distribution among Colombians

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Jaramillo, Adriana; Parra, Beatriz; Botero, Javier Enrique; Contreras, Adolfo

2015-01-01

Introduction: Porphyromonas gingivalis is associated with periodontitis and exhibit a wide array of virulence factors, including fimbriae which is encoded by the FimA gene representing six known genotypes. Objetive: To identify FimA genotypes of P. gingivalis in subjects from Cali-Colombia, including the co-infection with Aggregatibacter actinomycetemcomitans, Treponema denticola, and Tannerella forsythia. Methods: Subgingival samples were collected from 151 people exhibiting diverse periodontal condition. The occurrence of P. gingivalis, FimA genotypes and other bacteria was determined by PCR. Results: P. gingivalis was positive in 85 patients. Genotype FimA II was more prevalent without reach significant differences among study groups (54.3%), FimA IV was also prevalent in gingivitis (13.0%). A high correlation (p= 0.000) was found among P. gingivalis, T. denticola, and T. forsythia co-infection. The FimA II genotype correlated with concomitant detection of T. denticola and T. forsythia. Conclusions: Porphyromonas gingivalis was high even in the healthy group at the study population. A trend toward a greater frequency of FimA II genotype in patients with moderate and severe periodontitis was determined. The FimA II genotype was also associated with increased pocket depth, greater loss of attachment level, and patients co-infected with T. denticola and T. forsythia. PMID:26600627

Diversity among Modern Tomato Genotypes at Different Levels in Fresh-Market Breeding

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Krishna Bhattarai

2018-01-01

Full Text Available Cultivated tomato has been in existence for about 400 years and breeding activities have been conducted for only eight decades. However, more than 10,000 tomato cultivars have already been developed. Ninety-one tomato genotypes were characterized for twenty-one morphological traits using developmental, vegetative, and fruit traits. Correlation, principal component, and cluster analysis between the traits were carried out. Higher correlations between fruit traits including fruit shape, fruit size, and fruit types were observed. These correlations indicate that specific fruit types require specific traits like branched inflorescence and a greater number of fruits per inflorescence are beneficial only for smaller fruit sizes like cherry and grape tomatoes. Contrastingly, traits like determinate growth habit and fruit maturity are preferred in all fruit types of tomato for better cultivation practices and longer production duration and hence showed lower correlations. Principal component analysis clustered tomato genotypes into three main clusters with multiple subgroups. Similar tomato genotypes were placed into one or more clusters confirming the results from correlation analysis. Involvement of private breeding programs in cultivar development has increased the competition on introgression of novel and desired traits across new cultivars. Understanding the diversity present in modern cultivars and potential traits identification in related wild species can enhance tomato diversity and improve quality and production.

Diversity and genetic stability in banana genotypes in a breeding program using inter simple sequence repeats (ISSR) markers.

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Silva, A V C; Nascimento, A L S; Vitória, M F; Rabbani, A R C; Soares, A N R; Lédo, A S

2017-02-23

Banana (Musa spp) is a fruit species frequently cultivated and consumed worldwide. Molecular markers are important for estimating genetic diversity in germplasm and between genotypes in breeding programs. The objective of this study was to analyze the genetic diversity of 21 banana genotypes (FHIA 23, PA42-44, Maçã, Pacovan Ken, Bucaneiro, YB42-47, Grand Naine, Tropical, FHIA 18, PA94-01, YB42-17, Enxerto, Japira, Pacovã, Prata-Anã, Maravilha, PV79-34, Caipira, Princesa, Garantida, and Thap Maeo), by using inter-simple sequence repeat (ISSR) markers. Material was generated from the banana breeding program of Embrapa Cassava & Fruits and evaluated at Embrapa Coastal Tablelands. The 12 primers used in this study generated 97.5% polymorphism. Four clusters were identified among the different genotypes studied, and the sum of the first two principal components was 48.91%. From the Unweighted Pair Group Method using Arithmetic averages (UPGMA) dendrogram, it was possible to identify two main clusters and subclusters. Two genotypes (Garantida and Thap Maeo) remained isolated from the others, both in the UPGMA clustering and in the principal cordinate analysis (PCoA). Using ISSR markers, we could analyze the genetic diversity of the studied material and state that these markers were efficient at detecting sufficient polymorphism to estimate the genetic variability in banana genotypes.

Genetic diversity within and among two-spotted spider mite resistant and susceptible common bean genotypes

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Zeinab YOUSEFI

2017-12-01

Full Text Available Two-spotted spider mite (Tetranychus urticae C. L. Koch, 1836, is one of the most destructive herbivores of common bean. Very little is known about the diversity among resistant sources in this crop. The present study was conducted to characterize 22 resistant and susceptible common bean genotypes by 8 Simple Sequence Repeats (SSRs and 8 Random Amplified Polymorphic DNA (RAPD markers. These SSR and RAPD primers produced 100 % and 81.8 % polymorphic bands. Based on RAPD fingerprints and SSR profiles, pairwise genetic similarity ranged from 0.0 to 0.857 and from 0.125 to 1, respectively. The resistant and susceptible common bean accessions were grouped together in the dendrograms generated from RAPD and SSR clustering analyses. The results indicate that RAPD and SSR analysis could be successfully used for the estimation of genetic diversity among genotypes. SSR markers could group genotypes according to their resistibility and susceptibility to the spotted spider mite but RAPD could not. Therefore, the SSR markers can facilitate the development of resistant common bean cultivars through breeding programs against T. urticae.

Genetic Diversity and Selective Pressure in Hepatitis C Virus Genotypes 1-6: Significance for Direct-Acting Antiviral Treatment and Drug Resistance.

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Cuypers, Lize; Li, Guangdi; Libin, Pieter; Piampongsant, Supinya; Vandamme, Anne-Mieke; Theys, Kristof

2015-09-16

Treatment with pan-genotypic direct-acting antivirals, targeting different viral proteins, is the best option for clearing hepatitis C virus (HCV) infection in chronically infected patients. However, the diversity of the HCV genome is a major obstacle for the development of antiviral drugs, vaccines, and genotyping assays. In this large-scale analysis, genome-wide diversity and selective pressure was mapped, focusing on positions important for treatment, drug resistance, and resistance testing. A dataset of 1415 full-genome sequences, including genotypes 1-6 from the Los Alamos database, was analyzed. In 44% of all full-genome positions, the consensus amino acid was different for at least one genotype. Focusing on positions sharing the same consensus amino acid in all genotypes revealed that only 15% was defined as pan-genotypic highly conserved (≥99% amino acid identity) and an additional 24% as pan-genotypic conserved (≥95%). Despite its large genetic diversity, across all genotypes, codon positions were rarely identified to be positively selected (0.23%-0.46%) and predominantly found to be under negative selective pressure, suggesting mainly neutral evolution. For NS3, NS5A, and NS5B, respectively, 40% (6/15), 33% (3/9), and 14% (2/14) of the resistance-related positions harbored as consensus the amino acid variant related to resistance, potentially impeding treatment. For example, the NS3 variant 80K, conferring resistance to simeprevir used for treatment of HCV1 infected patients, was present in 39.3% of the HCV1a strains and 0.25% of HCV1b strains. Both NS5A variants 28M and 30S, known to be associated with resistance to the pan-genotypic drug daclatasvir, were found in a significant proportion of HCV4 strains (10.7%). NS5B variant 556G, known to confer resistance to non-nucleoside inhibitor dasabuvir, was observed in 8.4% of the HCV1b strains. Given the large HCV genetic diversity, sequencing efforts for resistance testing purposes may need to be

Genotype Diversity and Distribution of Orientia tsutsugamushi Causing Scrub Typhus in Thailand

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2011-07-01

Society for Microbiology. All Rights Reserved. Genotype Diversity and Distribution of Orientia tsutsugamushi Causing Scrub Typhus in Thailand" Toon...2011 Scrub typhus , caused by antigenically disparate isolates of Orientia tsutsugamushi, is a widely distributed mite-borne human disease in the Asia...evaluation of scrub typhus - specific diagnostic assays and vaccines. Using indirect immunoHuorescence assays (IF A) and PCR assays, 0. tsutsugamushi

Identification of genetically diverse genotypes for photoperiod insensitivity in soybean using RAPD markers.

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Singh, R K; Bhatia, V S; Yadav, Sanjeev; Athale, Rashmi; Lakshmi, N; Guruprasad, K N; Chauhan, G S

2008-10-01

Most of the Indian soybean varieties were found to be highly sensitive to photoperiod, which limits their cultivation in only localized area. Identification of genetically diverse source of photoperiod insensitive would help to broaden the genetic base for this trait. Present study was undertaken with RAPD markers for genetic diversity estimation in 44 accessions of soybean differing in response to photoperiod sensitivity. The selected twenty-five RAPD primers produced a total of 199 amplicons, which generated 89.9 % polymorphism. The number of amplification products ranged from 2 to 13 for different primers. The polymorphism information content ranged from 0.0 for monomorphic loci to 0.5 with an average of 0.289. Genetic diversity between pairs of genotypes was 37.7% with a range of 3.9 to 71.6%. UPGMA cluster analysis placed all the accessions of soybean into four major clusters. No discernable geographical patterns were observed in clustering however; the smaller groups corresponded well with pedigree. Mantel's test (r = 0.915) indicates very good fit for clustering pattern. Two genotypes, MACS 330 and 111/2/1939 made a very divergent group from other accessions of soybean and highly photoperiod insensitive that may be potential source for broadening the genetic base of soybean for this trait.

Study of Genetic Diversity of Some Persian walnut Genotypes in Mashhad Commercial Orchards by using ISSR Marker

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Shadi Attar

2018-02-01

Full Text Available Introduction: Persian walnut (Juglans regia L., belonging to the Juglandaceae family, has its natural origin in the mountainous regions of central Asia and especially northern forests of Iran. Most walnut genotypes are seedling and sexually reproduced. Conducting studies on the genetic structure of these genotypes to identify, select and maintain their genetic resources is important. Identifying and collecting local varieties of fruit trees is considered as the first step on the path of breeding programs and lack of information regarding plants genetic characteristics causes the breeding work to be done slowly. Various methods have been used for studying genetic diversity and determining the genetic relationship between European and Asian varieties of walnut and identifying commercial walnut varieties, among which we can mention: Morphologic indices, Alozyme, Isozym, RFLP, RAPD, AFLP and ISSR markers. ISSR molecular marker was used in order to investigate genetic diversity of some genotypes of Persian walnut (Juglans regia L. in Mashhad orchards. . Materials and methods: To begin with, about 56 walnut trees from 4 orchards in Mashhad (Esteghlal (1, Golestan (2, Alandasht (3 and Emam Reza (4 were selected and tagged from 2014 to 2016. In the spring of 2014 with the beginning of trees growth and opening of leaves, a number of leaves from each genotype were collected. After DNA extraction, the quality of samples by agarose gel (1 percentage and electrophoresis method and quantity of them via spectrophotometer device at 260 and 280 nm wavelengths were determined. First, 24 primers of ISSR marker were prepared and after initial evaluation on 5 random genotypes, 9 primers with high polymorphism and repeatability were selected for further investigation. For PCR reaction, Amplicon kit (code 180 301, made in Denmark was used. Gel electrophoresis images of primers that produced polymorphic bands with suitable resolution were analyzed manually. After

Genotyping and genetic diversity of Arcobacter butzleri by amplified fragment length polymorphism (AFLP) analysis

DEFF Research Database (Denmark)

On, Stephen L.W.; Atabay, H.I.; Amisu, K.O.

2004-01-01

Aims: To investigate the potential of amplified fragment length polymorphism (AFLP) profiling for genotyping Arcobacter butzleri and to obtain further data on the genetic diversity of this organism. Methods and Results: Seventy-three isolates of Danish, British, Turkish, Swedish, Nigerian and Nor...

The Chado Natural Diversity module: a new generic database schema for large-scale phenotyping and genotyping data.

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Jung, Sook; Menda, Naama; Redmond, Seth; Buels, Robert M; Friesen, Maren; Bendana, Yuri; Sanderson, Lacey-Anne; Lapp, Hilmar; Lee, Taein; MacCallum, Bob; Bett, Kirstin E; Cain, Scott; Clements, Dave; Mueller, Lukas A; Main, Dorrie

2011-01-01

Linking phenotypic with genotypic diversity has become a major requirement for basic and applied genome-centric biological research. To meet this need, a comprehensive database backend for efficiently storing, querying and analyzing large experimental data sets is necessary. Chado, a generic, modular, community-based database schema is widely used in the biological community to store information associated with genome sequence data. To meet the need to also accommodate large-scale phenotyping and genotyping projects, a new Chado module called Natural Diversity has been developed. The module strictly adheres to the Chado remit of being generic and ontology driven. The flexibility of the new module is demonstrated in its capacity to store any type of experiment that either uses or generates specimens or stock organisms. Experiments may be grouped or structured hierarchically, whereas any kind of biological entity can be stored as the observed unit, from a specimen to be used in genotyping or phenotyping experiments, to a group of species collected in the field that will undergo further lab analysis. We describe details of the Natural Diversity module, including the design approach, the relational schema and use cases implemented in several databases.

Evaluation of Genetic Diversity of Iris Genotypes (Iris spp Using ISSR

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seyedeh zeinab attari

2017-02-01

Full Text Available Introduction: Some of Iris species are growing in different parts of the Iran as wild species. Iris species have important medicinal and horticultural properties. Understanding of the genetic variation within and between populations is essential for the establishment of effective and efficient methods for conservation of the plants. Genetic variation studies are fundamental for the management and conservation of this species. The use of molecular markers is a powerful tool in the genetic study of populations. The use of DNA marker, such as AFLP, SSR, RAPD and ISSR represents an alternative method in detection of polymorphism. ISSRs are highly variable, require less investment in time, money and labor than other methods. ISSR can generate higher percentages of polymorphic loci than other PCR methods. These can serve as an efficient tool for phylogenetic studies. ISSRs had reported that used in studies of cultivated species to produce genetic linkage maps and to determine the relatedness of lines of agriculturally important species. ISSR analysis involves the PCR amplification of regions between adjacent, inversely oriented microsatellites, using a single simple sequence repeat (SSR motifs (dinucleotide, trinucleotide, tetranucleotide or penta nucleotides. Therefore, little is known about the genetic variability of the Iranian Iris ssp .The objectives of this study were to evaluate genetic diversity among genotypes using ISSR markers and the degree of polymorphism generated from ISSR technique as a pre-requisite for their applicability to population genetics studies in Iris ssp. Materials and Methods: To evaluate genetic variations in some wild Iris genotypes, Iris kopetdaghensis ،Iris songarica and Iris fosteriana were collected from some parts of Khorasan province. Genomic DNA was extracted from young leaves following the cetyltrimethylammonium bromide (CTAB procedure. Extracted DNA concentration was quantified by using the spectrophotometer

Genetic diversity analysis among male and female Jojoba genotypes employing gene targeted molecular markers, start codon targeted (SCoT) polymorphism and CAAT box-derived polymorphism (CBDP) markers.

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Heikrujam, Monika; Kumar, Jatin; Agrawal, Veena

2015-09-01

To detect genetic variations among different Simmondsia chinensis genotypes, two gene targeted markers, start codon targeted (SCoT) polymorphism and CAAT box-derived polymorphism (CBDP) were employed in terms of their informativeness and efficiency in analyzing genetic relationships among different genotypes. A total of 15 SCoT and 17 CBDP primers detected genetic polymorphism among 39 Jojoba genotypes (22 females and 17 males). Comparatively, CBDP markers proved to be more effective than SCoT markers in terms of percentage polymorphism as the former detecting an average of 53.4% and the latter as 49.4%. The Polymorphic information content (PIC) value and marker index (MI) of CBPD were 0.43 and 1.10, respectively which were higher than those of SCoT where the respective values of PIC and MI were 0.38 and 1.09. While comparing male and female genotype populations, the former showed higher variation in respect of polymorphic percentage and PIC, MI and Rp values over female populations. Nei's diversity (h) and Shannon index (I) were calculated for each genotype and found that the genotype "MS F" (in both markers) was highly diverse and genotypes "Q104 F" (SCoT) and "82-18 F" (CBDP) were least diverse among the female genotype populations. Among male genotypes, "32 M" (CBDP) and "MS M" (SCoT) revealed highest h and I values while "58-5 M" (both markers) was the least diverse. Jaccard's similarity co-efficient of SCoT markers ranged from 0.733 to 0.922 in female genotypes and 0.941 to 0.746 in male genotype population. Likewise, CBDP data analysis also revealed similarity ranging from 0.751 to 0.958 within female genotypes and 0.754 to 0.976 within male genotype populations thereby, indicating genetically diverse Jojoba population. Employing the NTSYS (Numerical taxonomy and multivariate analysis system) Version 2.1 software, both the markers generated dendrograms which revealed that all the Jojoba genotypes were clustered into two major groups, one group consisting of

Genetic diversity and distribution of Mycobacterium tuberculosis genotypes in Limpopo, South Africa.

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Maguga-Phasha, N T C; Munyai, N S; Mashinya, F; Makgatho, M E; Mbajiorgu, E F

2017-12-12

Tuberculosis remains a major health problem and knowledge of the diversity of Mycobacterium tuberculosis strains in specific geographical regions can contribute to the control of the disease. This study describes the genetic profile of M. tuberculosis in five districts of Limpopo Province. A total 487 isolates were collected from the National Health Laboratory Services from all regions/districts of Limpopo Province. Only 215 isolates were confirmed to be M. tuberculosis by Bactec Mycobacterium Growth Indicator Tube 960® and Rhodamine-Auramine staining. Isolates were subcultured on Löwenstein-Jensen medium agar slants to validate purity. They were spoligotyped and data analysed using the international spoligotyping database 4 (SpolDB4). Of the 215 isolates, 134 (62.3%) were genotyped into 21 genotype families while 81 (37.7%) were orphans. The 81 orphans were further subjected to resolution employing SpolDB3/RIM. Overall, the study revealed a high diversity of strains of 32 predominantly the non-Beijing lineages: the LAM- LAM3 (9.8%), LAM9 (4.7%) and LAM11- ZWE (3.3%), the T-T1(15.0%), T2 (0.9%), T2-T3 (1.4%), the CAS-CAS1-Delhi 5 (1.9%) and CAS1-KILI (1.4%) the MANU2 (1.4%), U (0.5%), X-X1(1.4%), X3 (1.9%), S (9.8%), CAS (1.4%), LAM7(0.9%), T3(0.5%), LAM8(4.7%), T4(1.4%), X2(0.4%), AI5(1.9%), LAM1(0.5%), FAMILY33 (1.9%), EAI4(1.4%), M. microti (1.9%). The Beijing and Beijing-like families were (14.9%) and (0.9%), respectively. A total of 28(13%) clusters and 77(36%) unique cases were identified. Beijing strain (SIT 1) formed the biggest cluster constituting 14%, followed by LAM3 (SIT 33), T1 (SIT 53) and LAM4 (SIT 811) with 7%, 5.1% and 2.8%, respectively. The Beijing family was the only genotype found in all the five districts and was predominant in Mopani (18.8%), Sekhukhune (23.7%) and Vhembe (23.3%). Dominant genotypes in Capricorn and Waterberg were LAM3 (11.9%) and T1 (13.3%), respectively. A wide diversity of lineages was demonstrated at district level. A

Characteristics of spring wheat genotypes exhibiting high resistance to FHB in terms of their resistance to other fungal diseases

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Danuta Kurasiak-Popowska

2016-09-01

Full Text Available The field experiment was carried out in 2010–2012 at the Dłoń Agricultural Research Station, the Poznań University of Life Sciences, Poland. The study was designed to evaluate the degree of infection by powdery mildew, brown rust, and septoria leaf blotch in 61 spring wheat genotypes differing in their resistance to Fusarium ssp. The vast majority of spring wheat genotypes in the collection of gene resources in the USA defined as resistant to Fusarium ssp. confirmed their resistance under Polish climatic conditions. The B .graminis infection rate of genotypes that are considered to be resistant to Fusarium head blight was high. The resistance ranged from 7 for Sumai 3 (PL2 up to 8.8 for Ning 8331 (in a 9-point scale. Most of the genotypes (56.5% were infected by Puccinia recondita at a level of 1–3 (in a 9-point scale. The genotypes of Sumai 3 exhibited high resistance to septoria leaf blotch, amounting to 1–2 in a 9-point scale; the resistance of Frontana ranged from 1 to 3.5, while the genotypes of Ning were infected by Mycosphaerella graminicola at 5–6.

Microsatellite genotyping and genome-wide single nucleotide polymorphism-based indices of Plasmodium falciparum diversity within clinical infections.

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Murray, Lee; Mobegi, Victor A; Duffy, Craig W; Assefa, Samuel A; Kwiatkowski, Dominic P; Laman, Eugene; Loua, Kovana M; Conway, David J

2016-05-12

In regions where malaria is endemic, individuals are often infected with multiple distinct parasite genotypes, a situation that may impact on evolution of parasite virulence and drug resistance. Most approaches to studying genotypic diversity have involved analysis of a modest number of polymorphic loci, although whole genome sequencing enables a broader characterisation of samples. PCR-based microsatellite typing of a panel of ten loci was performed on Plasmodium falciparum in 95 clinical isolates from a highly endemic area in the Republic of Guinea, to characterize within-isolate genetic diversity. Separately, single nucleotide polymorphism (SNP) data from genome-wide short-read sequences of the same samples were used to derive within-isolate fixation indices (F ws), an inverse measure of diversity within each isolate compared to overall local genetic diversity. The latter indices were compared with the microsatellite results, and also with indices derived by randomly sampling modest numbers of SNPs. As expected, the number of microsatellite loci with more than one allele in each isolate was highly significantly inversely correlated with the genome-wide F ws fixation index (r = -0.88, P 10 % had high correlation (r > 0.90) with the index derived using all SNPs. Different types of data give highly correlated indices of within-infection diversity, although PCR-based analysis detects low-level minority genotypes not apparent in bulk sequence analysis. When whole-genome data are not obtainable, quantitative assay of ten or more SNPs can yield a reasonably accurate estimate of the within-infection fixation index (F ws).

Genetic Diversity Assessment and Identification of New Sour Cherry Genotypes Using Intersimple Sequence Repeat Markers

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Roghayeh Najafzadeh

2014-01-01

Full Text Available Iran is one of the chief origins of subgenus Cerasus germplasm. In this study, the genetic variation of new Iranian sour cherries (which had such superior growth characteristics and fruit quality as to be considered for the introduction of new cultivars was investigated and identified using 23 intersimple sequence repeat (ISSR markers. Results indicated a high level of polymorphism of the genotypes based on these markers. According to these results, primers tested in this study specially ISSR-4, ISSR-6, ISSR-13, ISSR-14, ISSR-16, and ISSR-19 produced good and various levels of amplifications which can be effectively used in genetic studies of the sour cherry. The genetic similarity among genotypes showed a high diversity among the genotypes. Cluster analysis separated improved cultivars from promising Iranian genotypes, and the PCoA supported the cluster analysis results. Since the Iranian genotypes were superior to the improved cultivars and were separated from them in most groups, these genotypes can be considered as distinct genotypes for further evaluations in the framework of breeding programs and new cultivar identification in cherries. Results also confirmed that ISSR is a reliable DNA marker that can be used for exact genetic studies and in sour cherry breeding programs.

High Prevalence and Genotypic Diversity of the Human Papillomavirus in Amazonian Women, Brazil

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Danielle Albuquerque Pires Rocha

2013-01-01

Full Text Available The aim of this study was to determine the prevalence of human papillomavirus (HPV in a women population living within the state of Amazonas, Brazil, and to determine the viral genotypes found. The study included 361 sexually active women over 18 years of age. We performed the Pap test and the molecular diagnosis for HPV DNA using polymerase chain reaction (PCR. The amplicons obtained were sequenced in automatic sequencer for genotyping. The presence of HPV DNA was found in 29.1% (105 of the women. Only 321 women presented satisfactory slides for cytological diagnosis, 97.9% (314 had normal cytology (negative for cancer, and 2.1% (7 had abnormal cytology (4 ASCUS, 1 LSIL, and 2 HSIL. The types more frequently found were HPV 16 (58.1% and HPV 58 (20.0%. Additionally, we found more 13 types of HPV. Compared with previous studies in Brazil, our data confirmed a high prevalence and genotypic diversity of HPV in Brazilian women.

High-throughput genotyping for species identification and diversity assessment in germplasm collections.

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Mason, Annaliese S; Zhang, Jing; Tollenaere, Reece; Vasquez Teuber, Paula; Dalton-Morgan, Jessica; Hu, Liyong; Yan, Guijun; Edwards, David; Redden, Robert; Batley, Jacqueline

2015-09-01

Germplasm collections provide an extremely valuable resource for breeders and researchers. However, misclassification of accessions by species often hinders the effective use of these collections. We propose that use of high-throughput genotyping tools can provide a fast, efficient and cost-effective way of confirming species in germplasm collections, as well as providing valuable genetic diversity data. We genotyped 180 Brassicaceae samples sourced from the Australian Grains Genebank across the recently released Illumina Infinium Brassica 60K SNP array. Of these, 76 were provided on the basis of suspected misclassification and another 104 were sourced independently from the germplasm collection. Presence of the A- and C-genomes combined with principle components analysis clearly separated Brassica rapa, B. oleracea, B. napus, B. carinata and B. juncea samples into distinct species groups. Several lines were further validated using chromosome counts. Overall, 18% of samples (32/180) were misclassified on the basis of species. Within these 180 samples, 23/76 (30%) supplied on the basis of suspected misclassification were misclassified, and 9/105 (9%) of the samples randomly sourced from the Australian Grains Genebank were misclassified. Surprisingly, several individuals were also found to be the product of interspecific hybridization events. The SNP (single nucleotide polymorphism) array proved effective at confirming species, and provided useful information related to genetic diversity. As similar genomic resources become available for different crops, high-throughput molecular genotyping will offer an efficient and cost-effective method to screen germplasm collections worldwide, facilitating more effective use of these valuable resources by breeders and researchers. © 2015 John Wiley & Sons Ltd.

Generalist dinoflagellate endosymbionts and host genotype diversity detected from mesophotic (67-100 m depths coral Leptoseris

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Kahng Samuel E

2009-09-01

Full Text Available Abstract Background Mesophotic corals (light-dependent corals in the deepest half of the photic zone at depths of 30 - 150 m provide a unique opportunity to study the limits of the interactions between corals and endosymbiotic dinoflagellates in the genus Symbiodinium. We sampled Leptoseris spp. in Hawaii via manned submersibles across a depth range of 67 - 100 m. Both the host and Symbiodinium communities were genotyped, using a non-coding region of the mitochondrial ND5 intron (NAD5 and the nuclear ribosomal internal transcribed spacer region 2 (ITS2, respectively. Results Coral colonies harbored endosymbiotic communities dominated by previously identified shallow water Symbiodinium ITS2 types (C1_ AF333515, C1c_ AY239364, C27_ AY239379, and C1b_ AY239363 and exhibited genetic variability at mitochondrial NAD5. Conclusion This is one of the first studies to examine genetic diversity in corals and their endosymbiotic dinoflagellates sampled at the limits of the depth and light gradients for hermatypic corals. The results reveal that these corals associate with generalist endosymbiont types commonly found in shallow water corals and implies that the composition of the Symbiodinium community (based on ITS2 alone is not responsible for the dominance and broad depth distribution of Leptoseris spp. The level of genetic diversity detected in the coral NAD5 suggests that there is undescribed taxonomic diversity in the genus Leptoseris from Hawaii.

Prevalence of single nucleotide polymorphism among 27 diverse alfalfa genotypes as assessed by transcriptome sequencing

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Li Xuehui

2012-10-01

Full Text Available Abstract Background Alfalfa, a perennial, outcrossing species, is a widely planted forage legume producing highly nutritious biomass. Currently, improvement of cultivated alfalfa mainly relies on recurrent phenotypic selection. Marker assisted breeding strategies can enhance alfalfa improvement efforts, particularly if many genome-wide markers are available. Transcriptome sequencing enables efficient high-throughput discovery of single nucleotide polymorphism (SNP markers for a complex polyploid species. Result The transcriptomes of 27 alfalfa genotypes, including elite breeding genotypes, parents of mapping populations, and unimproved wild genotypes, were sequenced using an Illumina Genome Analyzer IIx. De novo assembly of quality-filtered 72-bp reads generated 25,183 contigs with a total length of 26.8 Mbp and an average length of 1,065 bp, with an average read depth of 55.9-fold for each genotype. Overall, 21,954 (87.2% of the 25,183 contigs represented 14,878 unique protein accessions. Gene ontology (GO analysis suggested that a broad diversity of genes was represented in the resulting sequences. The realignment of individual reads to the contigs enabled the detection of 872,384 SNPs and 31,760 InDels. High resolution melting (HRM analysis was used to validate 91% of 192 putative SNPs identified by sequencing. Both allelic variants at about 95% of SNP sites identified among five wild, unimproved genotypes are still present in cultivated alfalfa, and all four US breeding programs also contain a high proportion of these SNPs. Thus, little evidence exists among this dataset for loss of significant DNA sequence diversity from either domestication or breeding of alfalfa. Structure analysis indicated that individuals from the subspecies falcata, the diploid subspecies caerulea, and the tetraploid subspecies sativa (cultivated tetraploid alfalfa were clearly separated. Conclusion We used transcriptome sequencing to discover large numbers of SNPs

Are Tree Species Diversity and Genotypic Diversity Effects on Insect Herbivores Mediated by Ants?

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María José Campos-Navarrete

Full Text Available Plant diversity can influence predators and omnivores and such effects may in turn influence herbivores and plants. However, evidence for these ecological feedbacks is rare. We evaluated if the effects of tree species (SD and genotypic diversity (GD on the abundance of different guilds of insect herbivores associated with big-leaf mahogany (Swietenia macrophylla were contingent upon the protective effects of ants tending extra-floral nectaries of this species. This study was conducted within a larger experiment consisting of mahogany monocultures and species polycultures of four species and -within each of these two plot types- mahogany was represented by either one or four maternal families. We selected 24 plots spanning these treatment combinations, 10 mahogany plants/plot, and within each plot experimentally reduced ant abundance on half of the selected plants, and surveyed ant and herbivore abundance. There were positive effects of SD on generalist leaf-chewers and sap-feeders, but for the latter group this effect depended on the ant reduction treatment: SD positively influenced sap-feeders under ambient ant abundance but had no effect when ant abundance was reduced; at the same time, ants had negative effects on sap feeders in monoculture but no effect in polyculture. In contrast, SD did not influence specialist stem-borers or leaf-miners and this effect was not contingent upon ant reduction. Finally, GD did not influence any of the herbivore guilds studied, and such effects did not depend on the ant treatment. Overall, we show that tree species diversity influenced interactions between a focal plant species (mahogany and ants, and that such effects in turn mediated plant diversity effects on some (sap-feeders but not all the herbivores guilds studied. Our results suggest that the observed patterns are dependent on the combined effects of herbivore identity, diet breadth, and the source of plant diversity.

Assessment of Genetic Diversity and Structure of Large Garlic (Allium sativum Germplasm Bank, by Diversity Arrays Technology “Genotyping-by-Sequencing” Platform (DArTseq

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Leticia A. Egea

2017-07-01

Full Text Available Garlic (Allium sativum is used worldwide in cooking and industry, including pharmacology/medicine and cosmetics, for its interesting properties. Identifying redundancies in germplasm blanks to generate core collections is a major concern, mostly in large stocks, in order to reduce space and maintenance costs. Yet, similar appearance and phenotypic plasticity of garlic varieties hinder their morphological classification. Molecular studies are challenging, due to the large and expected complex genome of this species, with asexual reproduction. Classical molecular markers, like isozymes, RAPD, SSR, or AFLP, are not convenient to generate germplasm core-collections for this species. The recent emergence of high-throughput genotyping-by-sequencing (GBS approaches, like DArTseq, allow to overcome such limitations to characterize and protect genetic diversity. Therefore, such technology was used in this work to: (i assess genetic diversity and structure of a large garlic-germplasm bank (417 accessions; (ii create a core collection; (iii relate genotype to agronomical features; and (iv describe a cost-effective method to manage genetic diversity in garlic-germplasm banks. Hierarchical-cluster analysis, principal-coordinates analysis and STRUCTURE showed general consistency, generating three main garlic-groups, mostly determined by variety and geographical origin. In addition, high-resolution genotyping identified 286 unique and 131 redundant accessions, used to select a reduced size germplasm-bank core collection. This demonstrates that DArTseq is a cost-effective method to analyze species with large and expected complex genomes, like garlic. To the best of our knowledge, this is the first report of high-throughput genotyping of a large garlic germplasm. This is particularly interesting for garlic adaptation and improvement, to fight biotic and abiotic stresses, in the current context of climate change and global warming.

Genotypic diversity of root and shoot characteristics of

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ali ganjali

2009-06-01

Full Text Available Root and shoot characteristics of chickpea (Cicer arietinum L. genotypes are believed to be important in drought tolerance. There is a little information about the response of genotypes root growth in hydroponics and greenhouse culture, also the relationships between root size and drought tolerance. This study was conducted to observe whether genotypes differ in root size, and to see that root size is associated with drought tolerance during early vegetative growth. We found significant differences (p0.01 in root dry weight, total root length, tap root length, root area, leaf dry weight, leaf area and shoot biomass per plant among 30 genotypes of chickpea grown in hydroponics culture for three weeks. Each of these parameters correlated with all others, positively. Among 30 genotypes, 10 genotypes with different root sizes were selected and were grown in a greenhouse in sand culture experiment under drought stress (FC %30 for three weeks. There were not linear or non-linear significant correlations between root characters in hydroponics and greenhouse environments. It seems that environmental factors are dominant on genetic factors in seedling stage and so, the expression of genotypics potential for root growth characteristics of genotypes are different in hydroponic and greenhouse conditions. In this study, the selection of genotypes with vigorous roots system in hydroponic condition did not lead to genotypes with the same root characters in greenhouse environment. The genotype×drought interactions for root characters of chickpea seedlings in 30 days were not significant (p

High diversity of vacA and cagA Helicobacter pylori genotypes in patients with and without gastric cancer.

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Yolanda López-Vidal

Full Text Available BACKGROUND: Helicobacter pylori is associated with chronic gastritis, peptic ulcers, and gastric cancer. The aim of this study was to assess the topographical distribution of H. pylori in the stomach as well as the vacA and cagA genotypes in patients with and without gastric cancer. METHODOLOGY/PRINCIPAL FINDINGS: Three gastric biopsies, from predetermined regions, were evaluated in 16 patients with gastric cancer and 14 patients with dyspeptic symptoms. From cancer patients, additional biopsy specimens were obtained from tumor centers and margins; among these samples, the presence of H. pylori vacA and cagA genotypes was evaluated. Positive H. pylori was 38% and 26% in biopsies obtained from the gastric cancer and non-cancer groups, respectively (p = 0.008, and 36% in tumor sites. In cancer patients, we found a preferential distribution of H. pylori in the fundus and corpus, whereas, in the non-cancer group, the distribution was uniform (p = 0.003. A majority of the biopsies were simultaneously cagA gene-positive and -negative. The fundus and corpus demonstrated a higher positivity rate for the cagA gene in the non-cancer group (p = 0.036. A mixture of cagA gene sizes was also significantly more frequent in this group (p = 0.003. Ninety-two percent of all the subjects showed more than one vacA gene genotype; s1b and m1 vacA genotypes were predominantly found in the gastric cancer group. The highest vacA-genotype signal-sequence diversity was found in the corpus and 5 cm from tumor margins. CONCLUSION/SIGNIFICANCE: High H. pylori colonization diversity, along with the cagA gene, was found predominantly in the fundus and corpus of patients with gastric cancer. The genotype diversity observed across systematic whole-organ and tumor sampling was remarkable. We find that there is insufficient evidence to support the association of one isolate with a specific disease, due to the multistrain nature of H. pylori infection shown in this work.

A robust, simple genotyping-by-sequencing (GBS approach for high diversity species.

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Robert J Elshire

Full Text Available Advances in next generation technologies have driven the costs of DNA sequencing down to the point that genotyping-by-sequencing (GBS is now feasible for high diversity, large genome species. Here, we report a procedure for constructing GBS libraries based on reducing genome complexity with restriction enzymes (REs. This approach is simple, quick, extremely specific, highly reproducible, and may reach important regions of the genome that are inaccessible to sequence capture approaches. By using methylation-sensitive REs, repetitive regions of genomes can be avoided and lower copy regions targeted with two to three fold higher efficiency. This tremendously simplifies computationally challenging alignment problems in species with high levels of genetic diversity. The GBS procedure is demonstrated with maize (IBM and barley (Oregon Wolfe Barley recombinant inbred populations where roughly 200,000 and 25,000 sequence tags were mapped, respectively. An advantage in species like barley that lack a complete genome sequence is that a reference map need only be developed around the restriction sites, and this can be done in the process of sample genotyping. In such cases, the consensus of the read clusters across the sequence tagged sites becomes the reference. Alternatively, for kinship analyses in the absence of a reference genome, the sequence tags can simply be treated as dominant markers. Future application of GBS to breeding, conservation, and global species and population surveys may allow plant breeders to conduct genomic selection on a novel germplasm or species without first having to develop any prior molecular tools, or conservation biologists to determine population structure without prior knowledge of the genome or diversity in the species.

Phylogenetic diversity and genotypical complexity of H9N2 influenza A viruses revealed by genomic sequence analysis.

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Guoying Dong

Full Text Available H9N2 influenza A viruses have become established worldwide in terrestrial poultry and wild birds, and are occasionally transmitted to mammals including humans and pigs. To comprehensively elucidate the genetic and evolutionary characteristics of H9N2 influenza viruses, we performed a large-scale sequence analysis of 571 viral genomes from the NCBI Influenza Virus Resource Database, representing the spectrum of H9N2 influenza viruses isolated from 1966 to 2009. Our study provides a panoramic framework for better understanding the genesis and evolution of H9N2 influenza viruses, and for describing the history of H9N2 viruses circulating in diverse hosts. Panorama phylogenetic analysis of the eight viral gene segments revealed the complexity and diversity of H9N2 influenza viruses. The 571 H9N2 viral genomes were classified into 74 separate lineages, which had marked host and geographical differences in phylogeny. Panorama genotypical analysis also revealed that H9N2 viruses include at least 98 genotypes, which were further divided according to their HA lineages into seven series (A-G. Phylogenetic analysis of the internal genes showed that H9N2 viruses are closely related to H3, H4, H5, H7, H10, and H14 subtype influenza viruses. Our results indicate that H9N2 viruses have undergone extensive reassortments to generate multiple reassortants and genotypes, suggesting that the continued circulation of multiple genotypical H9N2 viruses throughout the world in diverse hosts has the potential to cause future influenza outbreaks in poultry and epidemics in humans. We propose a nomenclature system for identifying and unifying all lineages and genotypes of H9N2 influenza viruses in order to facilitate international communication on the evolution, ecology and epidemiology of H9N2 influenza viruses.

Characterization of diverse soybean genotypes using 14 carbon for organic acid exudation under phosphorus stress and its relationship with phosphorus acquisition efficiency

International Nuclear Information System (INIS)

Vengavasi, Krishnapriya; Pandey, Renu

2017-01-01

To characterise the physiological aspects influencing organic acid exudation under low phosphorus (P) stress, experiment was conducted to screen a diverse soybean panel (comprising 116 genotypes) for total carbon exudation employing shoot labelling with 14 CO 2 technique. Among the traits measured at seedling stage, total carbon ( 14 C) exudation, P uptake and total dry weight contributed to the maximum genotypic variability in soybean. The proportion of organic acids (including oxalate, citrate, succinate and fumarate) was the highest among root-exuded compounds induced by low P stress in soybean. Improved root length, surface area and volume coupled with higher activity of enzymes in TCA cycle contributed to enhanced organic acid exudation under low P. Efficient soybean genotypes (EC-232019 and G-2344) exhibited superior growth and P acquisition efficiency under low soil P availability attributed to its higher root exudation potential aiding in mining fixed soil P. To understand the molecular mechanism differentially regulating root exudation potential in contrasting genotypes (EC-232019 and EC-113396), root proteome analysis at low P stress was carried out. Among the total proteins visualised by 2D-gel electrophoresis, 105 genotypes (32%) were differentially expressed between sufficient and low P levels. A total of 44 (14%) proteins were down-regulated by more than two-fold while 61 (15%) proteins were up-regulated by more than two-fold at low P. The differential proteins were involved in a myriad of functions including organic acid accumulation, carbohydrate, protein and lipid metabolism under low P stress. Characterisation of 17 proteins with unknown function indicated the role of novel genes under low P stress. The identified genotypes have potential to be used as donors in crop improvement programs to develop high-yielding P-efficient cultivars which may be an asset to low-input sustainable agriculture. (author)

Low genetic diversity of bovine Mycobacterium avium subspecies paratuberculosis isolates detected by MIRU-VNTR genotyping.

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de Kruijf, Marcel; Lesniak, Olga N; Yearsley, Dermot; Ramovic, Elvira; Coffey, Aidan; O'Mahony, Jim

2017-05-01

Mycobacterial interspersed repetitive unit and variable number tandem repeat (MIRU-VNTR) has been developed as a simple, rapid and cost efficient molecular typing method to differentiate Mycobacterium avium subspecies paratuberculosis (MAP) isolates. The aim of this study was to determine the genomic diversity of MAP across the Republic of Ireland by utilising the MIRU-VNTR typing method on a large collection of MAP isolates. A total of 114 MAP isolates originated from 53 herds across 19 counties in the Republic of Ireland were genotyped based on eight established MIRU-VNTR loci. Four INMV groups were observed during this study. INMV 1 was found in 67 MAP isolates (58.8%) and INMV 2 was observed in 45 isolates (39.4%). INMV 3 and INMV 116 recorded only one isolate each (0.9%). The unique INMV 116 group has never been reported among herds thus far and the molecular pattern of the MAP isolate classified in INMV 116 showed a difference at the MIRU-VNTR X3 locus compared to the other three INMV groups observed. INMV 1, INMV 2 and INMV 3 are observed frequently in Europe and comprised 99.1% of the total MAP isolates characterised in this study, indicating that MAP exhibited low level of genetic diversity across the Republic of Ireland using the MIRU-VNTR method. By the implementation of SNP analysis or MLSSR as an additional typing method, MAP genetic diversity would increase. INMV 3 is unique to Ireland and whereas INMV 116 has never been previously reported among herds by MIRU-VNTR typing. Copyright © 2017 Elsevier B.V. All rights reserved.

Large scale phenotyping and data analysis of pepper genotypes in the EU-SPICY project

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Dieleman, J.A.; Magán, J.J.; Wubs, A.M.; Palloix, A.; Lenk, S.; Glasbey, C.; Eeuwijk, van F.A.

2012-01-01

In breeding the best genotypes for diverse conditions, ideally the breeder should test all his crossings under all these conditions. Especially with complex physiological traits like yield, which exhibit large variation, this would require many expensive and large field trials. The EU project “Smart

Impact of enumeration method on diversity of Escherichia coli genotypes isolated from surface water.

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Martin, E C; Gentry, T J

2016-11-01

There are numerous regulatory-approved Escherichia coli enumeration methods, but it is not known whether differences in media composition and incubation conditions impact the diversity of E. coli populations detected by these methods. A study was conducted to determine if three standard water quality assessments, Colilert ® , USEPA Method 1603, (modified mTEC) and USEPA Method 1604 (MI), detect different populations of E. coli. Samples were collected from six watersheds and analysed using the three enumeration approaches followed by E. coli isolation and genotyping. Results indicated that the three methods generally produced similar enumeration data across the sites, although there were some differences on a site-by-site basis. The Colilert ® method consistently generated the least diverse collection of E. coli genotypes as compared to modified mTEC and MI, with those two methods being roughly equal to each other. Although the three media assessed in this study were designed to enumerate E. coli, the differences in the media composition, incubation temperature, and growth platform appear to have a strong selective influence on the populations of E. coli isolated. This study suggests that standardized methods of enumeration and isolation may be warranted if researchers intend to obtain individual E. coli isolates for further characterization. This study characterized the impact of three USEPA-approved Escherichia coli enumeration methods on observed E. coli population diversity in surface water samples. Results indicated that these methods produced similar E. coli enumeration data but were more variable in the diversity of E. coli genotypes observed. Although the three methods enumerate the same species, differences in media composition, growth platform, and incubation temperature likely contribute to the selection of different cultivable populations of E. coli, and thus caution should be used when implementing these methods interchangeably for

The genotypic diversity and lipase production of some thermophilic bacilli from different genera

OpenAIRE

Koc, Melih; Cokmus, Cumhur; Cihan, Arzu Coleri

2015-01-01

Abstract Thermophilic 32 isolates and 20 reference bacilli were subjected to Rep-PCR and ITS-PCR fingerprinting for determination of their genotypic diversity, before screening lipase activities. By these methods, all the isolates and references could easily be differentiated up to subspecies level from each other. In screening assay, 11 isolates and 7 references were found to be lipase producing. Their extracellular lipase activities were measured quantitatively by incubating in both tributy...

First insight into the genotypic diversity of clinical Mycobacterium tuberculosis isolates from Gansu Province, China.

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Jie Liu

Full Text Available BACKGROUND: Investigations of Mycobacterium tuberculosis genetic diversity in China have indicated a significant regional distribution. The aim of this study was to characterize the genotypes of clinical M. tuberculosis isolates obtained from Gansu, which has a special geographic location in China. METHODOLOGY/PRINCIPAL FINDINGS: A total of 467 clinical M. tuberculosis strains isolated in Gansu Province were genotyped by 15-locus mycobacterial interspersed repetitive units-variable number tandem repeats (MIRU-VNTR and spoligotyping. The results showed that 445 isolates belonged to six known spoligotype lineages, whereas 22 isolates were unknown. The Beijing genotype was the most prevalent (87.58%, n = 409, while the shared type 1 was the dominant genotype (80.94%, n = 378. The second most common lineage was the T lineage, with 25 isolates (5.35%, followed by the H lineage with 5 isolates (1.07%, the MANU family (0.64%, 3 isolates, the U family (0.43%, 2 isolates and the CAS lineage with 1 isolate (0.21%. By using the VNTR15China method, we observed 15 groups and 228 genotypes among the 467 isolates. We found no association between the five larger groups (including the Beijing genotype and sex, age, or treatment status, and there was no noticeable difference in the group analysis in different areas. In the present study, seven of the 15 MIRU-VNTR loci were highly or moderately discriminative according to their Hunter-Gaston discriminatory index. CONCLUSIONS/SIGNIFICANCE: The Beijing genotype is the predominant genotype in Gansu province. We confirm that VNTR15China is suitable for typing Beijing strains in China and that it has a better discriminatory power than spoligotyping. Therefore, the use of both methods is the most suitable for genotyping analysis of M. tuberculosis.

Loss of heterozygosity drives clonal diversity of Phytophthora capsici in China.

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Jian Hu

Full Text Available Phytophthora capsici causes significant loss to pepper (Capsicum annum in China and our goal was to develop single nucleotide polymorphism (SNP markers for P. capsici and characterize genetic diversity nationwide. Eighteen isolates of P. capsici from locations worldwide were re-sequenced and candidate nuclear and mitochondrial SNPs identified. From 2006 to 2012, 276 isolates of P. capsici were recovered from 136 locations in 27 provinces and genotyped using 45 nuclear and 2 mitochondrial SNPs. There were two main mitochondrial haplotypes and 95 multi-locus genotypes (MLGs identified. Genetic diversity was geographically structured with a high level of genotypic diversity in the north and on Hainan Island in the south, suggesting outcrossing contributes to diversity in these areas. The remaining areas of China are dominated by four clonal lineages that share mitochondrial haplotypes, are almost exclusively the A1 or A2 mating type and appear to exhibit extensive diversity based on loss of heterozygosity (LOH. Analysis of SNPs directly from infected peppers confirmed LOH in field populations. One clonal lineage is dominant throughout much of the country. The overall implications for long-lived genetically diverse clonal lineages amidst a widely dispersed sexual population are discussed.

Improved resolution of reef-coral endosymbiont (Symbiodinium species diversity, ecology, and evolution through psbA non-coding region genotyping.

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Todd C LaJeunesse

Full Text Available Ribosomal DNA sequence data abounds from numerous studies on the dinoflagellate endosymbionts of corals, and yet the multi-copy nature and intragenomic variability of rRNA genes and spacers confound interpretations of symbiont diversity and ecology. Making consistent sense of extensive sequence variation in a meaningful ecological and evolutionary context would benefit from the application of additional genetic markers. Sequences of the non-coding region of the plastid psbA minicircle (psbA(ncr were used to independently examine symbiont genotypic and species diversity found within and between colonies of Hawaiian reef corals in the genus Montipora. A single psbA(ncr haplotype was recovered in most samples through direct sequencing (~80-90% and members of the same internal transcribed spacer region 2 (ITS2 type were phylogenetically differentiated from other ITS2 types by substantial psbA(ncr sequence divergence. The repeated sequencing of bacterially-cloned fragments of psbA(ncr from samples and clonal cultures often recovered a single numerically common haplotype accompanied by rare, highly-similar, sequence variants. When sequence artifacts of cloning and intragenomic variation are factored out, these data indicate that most colonies harbored one dominant Symbiodinium genotype. The cloning and sequencing of ITS2 DNA amplified from these same samples recovered numerically abundant variants (that are diagnostic of distinct Symbiodinium lineages, but also generated a large amount of sequences comprising PCR/cloning artifacts combined with ancestral and/or rare variants that, if incorporated into phylogenetic reconstructions, confound how small sequence differences are interpreted. Finally, psbA(ncr sequence data from a broad sampling of Symbiodinium diversity obtained from various corals throughout the Indo-Pacific were concordant with ITS lineage membership (defined by denaturing gradient gel electrophoresis screening, yet exhibited

Cluster-distinguishing genotypic and phenotypic diversity of carbapenem-resistant Gram-negative bacteria in solid-organ transplantation patients: a comparative study.

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Karampatakis, Theodoros; Geladari, Anastasia; Politi, Lida; Antachopoulos, Charalampos; Iosifidis, Elias; Tsiatsiou, Olga; Karyoti, Aggeliki; Papanikolaou, Vasileios; Tsakris, Athanassios; Roilides, Emmanuel

2017-07-31

Solid-organ transplant recipients may display high rates of colonization and/or infection by multidrug-resistant bacteria. We analysed and compared the phenotypic and genotypic diversity of carbapenem-resistant (CR) strains of Klebsiella pneumoniae, Pseudomonas aeruginosa and Acinetobacter baumannii isolated from patients in the Solid Organ Transplantation department of our hospital. Between March 2012 and August 2013, 56 CR strains from various biological fluids underwent antimicrobial susceptibility testing with VITEK 2, molecular analysis by PCR amplification and genotypic analysis with pulsed-field gel electrophoresis (PFGE). They were clustered according to antimicrobial drug susceptibility and genotypic profiles. Diversity analyses were performed by calculating Simpson's diversity index and applying computed rarefaction curves.Results/Key findings. Among K. pneumoniae, KP-producers predominated (57.1 %). VIM and OXA-23 carbapenemases prevailed among P. aeruginosa and A. baumannii (89.4 and 88.9 %, respectively). KPC-producing K. pneumoniae and OXA-23 A. baumannii were assigned in single PFGE pulsotypes. VIM-producing P. aeruginosa generated multiple pulsotypes. CR K. pneumoniae strains displayed phenotypic diversity in tigecycline, colistin (CS), amikacin (AMK), gentamicin (GEN) and co-trimoxazole (SXT) (16 clusters); P. aeruginosa displayed phenotypic diversity in cefepime (FEP), ceftazidime, aztreonam, piperacillin, piperacillin-tazobactam, AMK, GEN and CS (9 clusters); and A. baumannii displayed phenotypic diversity in AMK, GEN, SXT, FEP, tobramycin and rifampicin (8 clusters). The Simpson diversity indices for the interpretative phenotype and PFGE analysis were 0.89 and 0.6, respectively, for K. pneumoniae strains (P<0.001); 0.77 and 0.6 for P. aeruginosa (P=0.22); and 0.86 and 0.19 for A. baumannii (P=0.004). The presence of different antimicrobial susceptibility profiles does not preclude the possibility that two CR K. pneumoniae or A. baumannii

DNA fingerprinting and diversity analysis in Aus genotypes using microsatellite markers

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MD. MONIRUL ISLAM

2015-08-01

Full Text Available DNA fingerprinting and genetic diversity of 94 Aus (6 BRRI released Aus variety and 88 local Aus landraces genotypes were carried out to protect the Aus landraces from biopiracy. A total of 91 microsatellite markers were tested for screening the genotypes. Among 91 amplified products, 56% have polymorphic bands giving 195 alleles. The number of alleles per locus ranged from four (RM25 and RM147 to twenty seven (RM519, where average allele number was 9.76. The Polymorphism Information Contents (PIC lied between 0.455 (RM5 to 0.934 (RM519. Most robust marker was found RM519 since it provided the highest PIC value (0.934. Pair-wise genetic dissimilarity co-efficient showed the lowest genetic dissimilarity was found BRRI dhan42 and BRRI dhan43 and the highest genetic dissimilarity was found local landraces each other. Here it is shown that most Aus landraces is recognized to have broad genetic base. Thus it is recommended to use these landraces for future breeding program or include new and untouched local landraces to incorporate new genes and broaden genetic base.

Genetic diversity in soybean genotypes using phenotypic characters and enzymatic markers.

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Zambiazzi, E V; Bruzi, A T; Sales, A P; Borges, I M M; Guilherme, S R; Zuffo, A M; Lima, J G; Ribeiro, F O; Mendes, A E S; Godinho, S H M; Carvalho, M L M

2017-09-21

The objective of this study was to evaluate the genetic diversity of soybean cultivars by adopting phenotypic traits and enzymatic markers, the relative contribution of agronomic traits to diversity, as well as diversity between the level of technology used in soybean cultivars and genetic breeding programs in which cultivars were inserted. The experiments were conducted on the field at the Center for Scientific and Technological Development in crop-livestock production and the Electrophoresis Laboratory of Lavras Federal University. The agronomic traits adopted were grain yield, plant height, first legume insertion, plant lodging, the mass of one thousand seeds, and days for complete maturation, in which the Euclidean distance, grouped by Tocher and UPGMA criteria, was obtained. After electrophorese gels for enzymatic systems, dehydrogenase alcohol, esterase, superoxide dismutase, and peroxidase were performed. The genetic similarity estimative was also obtained between genotypes by the Jaccard coefficient with subsequent grouping by the UPGMA method. The formation of two groups was shown using phenotypic characters in the genetic diversity study and individually discriminating the cultivar 97R73 RR. The character with the greatest contribution to the genetic divergence was grain yield with contribution higher than 90.0%. To obtain six different groups, individually discriminating the cultivars CG 8166 RR, FPS Jupiter RR, and BRS MG 780 RR, enzymatic markers were used. Cultivars carrying the RR technology presented more divergence than conventional cultivars and IPRO cultivars.

Phylogenetic studies reveal existence of multiple lineages of a single genotype of DENV-1 (genotype III in India during 1956–2007

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Bhattacharya D

2009-01-01

Full Text Available Abstract Background Dengue virus type 1 (DENV-1 have been mostly circulating silently with dominant serotypes DENV-2 and DENV-3 in India. However recent times have marked an increase in DENV-1 circulation in yearly outbreaks. Many studies have not been carried out on this virus type, leaving a lacunae pertaining to the circulating genotypes, since its earliest report in India. In the present study, we sequenced CprM gene junction of 13 DENV-1 isolated from Delhi and Gwalior (North India between 2001–2007 and one 1956 Vellore isolate as reference. For comparison, we retrieved 11 other Indian and 70 global reference sequences from NCBI database, making sure that Indian and global isolates from all decades are available for comparative analysis. Results The region was found to be AT rich with no insertion or deletion. Majority of the nucleotide substitutions were silent, except 3 non-conservative amino acid changes (I → T, A → T and L → S at amino acid positions 59,114 and 155 respectively in the Indian DENV-1 sequences, sequenced in this study. Except two 1997–98 Delhi isolates, which group in genotype I; all other Indian isolates group in genotype III. All Indian genotype III DENV-1 exhibited diversity among them, giving rise to at least 4 distinct lineages (India 1–4 showing proximity to isolates from diverse geographic locations. Conclusion The extensive phylogenetic analysis revealed consistent existence of multiple lineages of DENV-1 genotype III during the last 5 decades in India.

Assessment of genetic diversity, population structure and relationships in Indian and non-Indian genotypes of finger millet (Eleusine coracana (L.) Gaertn) using genomic SSR markers.

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Ramakrishnan, M; Antony Ceasar, S; Duraipandiyan, V; Al-Dhabi, N A; Ignacimuthu, S

2016-01-01

We evaluated the genetic variation and population structure in Indian and non-Indian genotypes of finger millet using 87 genomic SSR primers. The 128 finger millet genotypes were collected and genomic DNA was isolated. Eighty-seven genomic SSR primers with 60-70 % GC contents were used for PCR analysis of 128 finger millet genotypes. The PCR products were separated and visualized on a 6 % polyacrylamide gel followed by silver staining. The data were used to estimate major allele frequency using Power Marker v3.0. Dendrograms were constructed based on the Jaccard's similarity coefficient. Statistical fitness and population structure analyses were performed to find the genetic diversity. The mean major allele frequency was 0.92; the means of polymorphic alleles were 2.13 per primer and 1.45 per genotype; the average polymorphism was 59.94 % per primer and average PIC value was 0.44 per primer. Indian genotypes produced an additional 0.21 allele than non-Indian genotypes. Gene diversity was in the range from 0.02 to 0.35. The average heterozygosity was 0.11, close to 100 % homozygosity. The highest inbreeding coefficient was observed with SSR marker UGEP67. The Jaccard's similarity coefficient value ranged from 0.011 to 0.836. The highest similarity value was 0.836 between genotypes DPI009-04 and GPU-45. Indian genotypes were placed in Eleusine coracana major cluster (EcMC) 1 along with 6 non-Indian genotypes. AMOVA showed that molecular variance in genotypes from various geographical regions was 4 %; among populations it was 3 % and within populations it was 93 %. PCA scatter plot analysis showed that GPU-28, GPU-45 and DPI009-04 were closely dispersed in first component axis. In structural analysis, the genotypes were divided into three subpopulations (SP1, SP2 and SP3). All the three subpopulations had an admixture of alleles and no pure line was observed. These analyses confirmed that all the genotypes were genetically diverse and had been grouped based on

Genotyping-by-Sequencing Analysis for Determining Population Structure of Finger Millet Germplasm of Diverse Origins

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Anil Kumar

2016-07-01

Full Text Available Finger millet [ (L. Gaertn.] is grown mainly by subsistence farmers in arid and semiarid regions of the world. To broaden its genetic base and to boost its production, it is of paramount importance to characterize and genotype the diverse gene pool of this important food and nutritional security crop. However, as a result of nonavailability of the genome sequence of finger millet, the progress could not be made in realizing the molecular basis of unique qualities of the crop. In the present investigation, attempts have been made to characterize the genetically diverse collection of 113 finger millet accessions through whole-genome genotyping-by-sequencing (GBS, which resulted in a genome-wide set of 23,000 single-nucleotide polymorphisms (SNPs segregating across the entire collection and several thousand SNPs segregating within every accession. A model-based population structure analysis reveals the presence of three subpopulations among the finger millet accessions, which are in parallel with the results of phylogenetic analysis. The observed population structure is consistent with the hypothesis that finger millet was domesticated first in Africa, and from there it was introduced to India some 3000 yr ago. A total of 1128 gene ontology (GO terms were assigned to SNP-carrying genes for three main categories: biological process, cellular component, and molecular function. Facilitated access to high-throughput genotyping and sequencing technologies are likely to improve the breeding process in developing countries, and as such, this data will be very useful to breeders who are working for the genetic improvement of finger millet.

Genotyping-by-Sequencing Analysis for Determining Population Structure of Finger Millet Germplasm of Diverse Origins.

Science.gov (United States)

Kumar, Anil; Sharma, Divya; Tiwari, Apoorv; Jaiswal, J P; Singh, N K; Sood, Salej

2016-07-01

Finger millet [ (L.) Gaertn.] is grown mainly by subsistence farmers in arid and semiarid regions of the world. To broaden its genetic base and to boost its production, it is of paramount importance to characterize and genotype the diverse gene pool of this important food and nutritional security crop. However, as a result of nonavailability of the genome sequence of finger millet, the progress could not be made in realizing the molecular basis of unique qualities of the crop. In the present investigation, attempts have been made to characterize the genetically diverse collection of 113 finger millet accessions through whole-genome genotyping-by-sequencing (GBS), which resulted in a genome-wide set of 23,000 single-nucleotide polymorphisms (SNPs) segregating across the entire collection and several thousand SNPs segregating within every accession. A model-based population structure analysis reveals the presence of three subpopulations among the finger millet accessions, which are in parallel with the results of phylogenetic analysis. The observed population structure is consistent with the hypothesis that finger millet was domesticated first in Africa, and from there it was introduced to India some 3000 yr ago. A total of 1128 gene ontology (GO) terms were assigned to SNP-carrying genes for three main categories: biological process, cellular component, and molecular function. Facilitated access to high-throughput genotyping and sequencing technologies are likely to improve the breeding process in developing countries, and as such, this data will be very useful to breeders who are working for the genetic improvement of finger millet. Copyright © 2016 Crop Science Society of America.

Genotypic Diversity Is Associated with Clinical Outcome and Phenotype in Cryptococcal Meningitis across Southern Africa.

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Mathew A Beale

Full Text Available Cryptococcal meningitis is a major cause of mortality throughout the developing world, yet little is known about the genetic markers underlying Cryptococcal virulence and patient outcome. We studied a cohort of 230 Cryptococcus neoformans (Cn isolates from HIV-positive South African clinical trial patients with detailed clinical follow-up using multi-locus sequence typing and in vitro phenotypic virulence assays, correlating these data with clinical and fungal markers of disease in the patient. South African Cn displayed high levels of genetic diversity and locus variability compared to globally distributed types, and we identified 50 sequence types grouped within the main molecular types VNI, VNII and VNB, with 72% of isolates typed into one of seven 'high frequency' sequence types. Spatial analysis of patients' cryptococcal genotype was not shown to be clustered geographically, which might argue against recent local acquisition and in favour of reactivation of latent infection. Through comparison of MLST genotyping data with clinical parameters, we found a relationship between genetic lineage and clinical outcome, with patients infected with the VNB lineage having significantly worse survival (n=8, HR 3.35, CI 1.51-7.20, p=0.003, and this was maintained even after adjustment for known prognostic indicators and treatment regimen. Comparison of fungal genotype with in vitro phenotype (phagocytosis, laccase activity and CSF survival performed on a subset of 89 isolates revealed evidence of lineage-associated virulence phenotype, with the VNII lineage displaying increased laccase activity (p=0.001 and ex vivo CSF survival (p=0.0001. These findings show that Cryptococcus neoformans is a phenotypically heterogeneous pathogen, and that lineage plays an important role in cryptococcal virulence during human infection. Furthermore, a detailed understanding of the genetic diversity in Southern Africa will support further investigation into how genetic

GENETIC DIVERSITY OF S3 MAIZE GENOTYPES RESISTANT TO DOWNY MILDEW BASED ON SSR MARKERS

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Amran Muis

2016-02-01

Full Text Available The compulsory requirement for releasing new high yielding maize varieties is resistance to downy mildew. The study aimed to determine the level of homozygosity, genetic diversity, and  genetic distance of 30 S3 genotypes of maize. Number of primers to be used were 30 polymorphic SSR loci which are distributed over the entire maize genomes. The S3 genotypes used were resistant to downy mildew with homozygosity level of >80%, genetic distance between the test and tester strains >0.7, and anthesis silking interval (ASI between inbred lines and tester lines was maximum 3 days. The results showed that 30 SSR primers used were spread evenly across the maize genomes which were manifested in the representation of SSR loci on each chromosome of a total of 10 chromosomes. The levels of polymorphism ranged from 0.13 to 0.78, an average of 0.51, and the number of alleles ranged from 2 to 8 alleles per SSR locus, an average of 4 alleles per SSR locus. The size of nucleotides in each locus also varied from 70 to 553 bp. Cophenetic correlation value (r at 0.67 indicated that the Unweighted Pair-Group Method Using Arithmetic Averages (UPGMA was less reliable for differentiating genotypes in five groups. Of the total of 30 genotypes analyzed, 17 genotypes had homozygosity level of >80% so it can be included in the hybrid assembly program.

HBV genotypic variability in Cuba.

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Carmen L Loureiro

Full Text Available The genetic diversity of HBV in human population is often a reflection of its genetic admixture. The aim of this study was to explore the genotypic diversity of HBV in Cuba. The S genomic region of Cuban HBV isolates was sequenced and for selected isolates the complete genome or precore-core sequence was analyzed. The most frequent genotype was A (167/250, 67%, mainly A2 (149, 60% but also A1 and one A4. A total of 77 isolates were classified as genotype D (31%, with co-circulation of several subgenotypes (56 D4, 2 D1, 5 D2, 7 D3/6 and 7 D7. Three isolates belonged to genotype E, two to H and one to B3. Complete genome sequence analysis of selected isolates confirmed the phylogenetic analysis performed with the S region. Mutations or polymorphisms in precore region were more common among genotype D compared to genotype A isolates. The HBV genotypic distribution in this Caribbean island correlates with the Y lineage genetic background of the population, where a European and African origin prevails. HBV genotypes E, B3 and H isolates might represent more recent introductions.

HBV Genotypic Variability in Cuba

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Loureiro, Carmen L.; Aguilar, Julio C.; Aguiar, Jorge; Muzio, Verena; Pentón, Eduardo; Garcia, Daymir; Guillen, Gerardo; Pujol, Flor H.

2015-01-01

The genetic diversity of HBV in human population is often a reflection of its genetic admixture. The aim of this study was to explore the genotypic diversity of HBV in Cuba. The S genomic region of Cuban HBV isolates was sequenced and for selected isolates the complete genome or precore-core sequence was analyzed. The most frequent genotype was A (167/250, 67%), mainly A2 (149, 60%) but also A1 and one A4. A total of 77 isolates were classified as genotype D (31%), with co-circulation of several subgenotypes (56 D4, 2 D1, 5 D2, 7 D3/6 and 7 D7). Three isolates belonged to genotype E, two to H and one to B3. Complete genome sequence analysis of selected isolates confirmed the phylogenetic analysis performed with the S region. Mutations or polymorphisms in precore region were more common among genotype D compared to genotype A isolates. The HBV genotypic distribution in this Caribbean island correlates with the Y lineage genetic background of the population, where a European and African origin prevails. HBV genotypes E, B3 and H isolates might represent more recent introductions. PMID:25742179

Exploiting genotypic diversity of 2,4-Diacetylphloroglucinol-producing Pseudomonas spp.: characterization of superior root-colonizing P. fluorescens strain Q8r1-96

NARCIS (Netherlands)

Raaijmakers, J.M.; Weller, D.M.

2001-01-01

The genotypic diversity that occurs in natural populations of antagonistic microorganisms provides an enormous resource for improving biological control of plant diseases. In this study, we determined the diversity of indigenous 2,4-diacetylphloroglucinol (DAPG)-producing Pseudomonas spp. occurring

Evaluation of genetic diversity among soybean (Glycine max) genotypes using univariate and multivariate analysis.

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Oliveira, M M; Sousa, L B; Reis, M C; Silva Junior, E G; Cardoso, D B O; Hamawaki, O T; Nogueira, A P O

2017-05-31

The genetic diversity study has paramount importance in breeding programs; hence, it allows selection and choice of the parental genetic divergence, which have the agronomic traits desired by the breeder. This study aimed to characterize the genetic divergence between 24 soybean genotypes through their agronomic traits, using multivariate clustering methods to select the potential genitors for the promising hybrid combinations. Six agronomic traits evaluated were number of days to flowering and maturity, plant height at flowering and maturity, insertion height of the first pod, and yield. The genetic divergence evaluated by multivariate analysis that esteemed first the Mahalanobis' generalized distance (D 2 ), then the clustering using Tocher's optimization methods, and then the unweighted pair group method with arithmetic average (UPGMA). Tocher's optimization method and the UPGMA agreed with the groups' constitution between each other, the formation of eight distinct groups according Tocher's method and seven distinct groups using UPGMA. The trait number of days for flowering (45.66%) was the most efficient to explain dissimilarity between genotypes, and must be one of the main traits considered by the breeder in the moment of genitors choice in soybean-breeding programs. The genetic variability allowed the identification of dissimilar genotypes and with superior performances. The hybridizations UFU 18 x UFUS CARAJÁS, UFU 15 x UFU 13, and UFU 13 x UFUS CARAJÁS are promising to obtain superior segregating populations, which enable the development of more productive genotypes.

Genetic diversity among Juglans regia L. genotypes assessed by morphological traits and microsatellite markers

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Mahmoodi, R.; Rahmani, F.; Rezaee, R.

2013-06-01

In this study, genetic diversity was assayed among 16 accessions and five cultivars of Persian walnut (Juglans regia L.) using morphological traits and nine simple sequence repeat (SSR) markers. Samples were collected from Agriculture Research Center of Urmia city (North West Iran). Study on important morphological traits revealed genetic similarity of -0.6 to 0.99 based on CORR coefficient. The microsatellite marker system produced 34 alleles in range of 160-290 bp. The minimum (2) and maximum (7) number of alleles were obtained from WGA71 and WGA202 genetic loci, respectively. The mean number of alleles per locus was 4.25. Jaccards similarity coefficient ranged from 0.13 to 0.76. The results of this paper indicate high diversity among these genotypes which could be used for breeding management. (Author) 28 refs.

High degree of genetic diversity among genotypes of the forage grass Brachiaria ruziziensis (Poaceae) detected with ISSR markers.

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Azevedo, A L S; Costa, P P; Machado, M A; de Paula, C M P; Sobrinho, F S

2011-11-17

The grasses of the genus Brachiaria account for 80% of the cultivated pastures in Brazil. Despite its importance for livestock production, little information is available for breeding purposes. Embrapa has a population of B. ruziziensis from different regions of Brazil, representing most of existing variability. This population was used to initiate an improvement program based on recurrent selection. In order to assist the genetic improvement program, we estimated the molecular variability among 93 genotypes of Embrapa's collection using ISSR (inter-simple sequence repeat) markers. DNA was extracted from the leaves. Twelve ISSR primers generated 89 polymorphic bands in the 93 genotypes. The number of bands identified by each primer ranged from two to 13, with a mean of 7.41. Cluster analysis revealed a clearly distinct group, containing most of the B. ruziziensis genotypes apart from the outgroup genotypes. Genetic similarity coefficients ranged from 0.0 to 0.95, with a mean of 0.50 and analysis of molecular variance indicated higher variation within (73.43%) than among species (26.57%). We conclude that there is a high genetic diversity among these B. ruziziensis genotypes, which could be explored by breeding programs.

ToxGen: an improved reference database for the identification of type B-trichothecene genotypes in Fusarium.

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Kulik, Tomasz; Abarenkov, Kessy; Buśko, Maciej; Bilska, Katarzyna; van Diepeningen, Anne D; Ostrowska-Kołodziejczak, Anna; Krawczyk, Katarzyna; Brankovics, Balázs; Stenglein, Sebastian; Sawicki, Jakub; Perkowski, Juliusz

2017-01-01

Type B trichothecenes, which pose a serious hazard to consumer health, occur worldwide in grains. These mycotoxins are produced mainly by three different trichothecene genotypes/chemotypes: 3ADON (3-acetyldeoxynivalenol), 15ADON (15-acetyldeoxynivalenol) and NIV (nivalenol), named after these three major mycotoxin compounds. Correct identification of these genotypes is elementary for all studies relating to population surveys, fungal ecology and mycotoxicology. Trichothecene producers exhibit enormous strain-dependent chemical diversity, which may result in variation in levels of the genotype's determining toxin and in the production of low to high amounts of atypical compounds. New high-throughput DNA-sequencing technologies promise to boost the diagnostics of mycotoxin genotypes. However, this requires a reference database containing a satisfactory taxonomic sampling of sequences showing high correlation to actually produced chemotypes. We believe that one of the most pressing current challenges of such a database is the linking of molecular identification with chemical diversity of the strains, as well as other metadata. In this study, we use the Tri12 gene involved in mycotoxin biosynthesis for identification of Tri genotypes through sequence comparison. Tri12 sequences from a range of geographically diverse fungal strains comprising 22 Fusarium species were stored in the ToxGen database, which covers descriptive and up-to-date annotations such as indication on Tri genotype and chemotype of the strains, chemical diversity, information on trichothecene-inducing host, substrate or media, geographical locality, and most recent taxonomic affiliations. The present initiative bridges the gap between the demands of comprehensive studies on trichothecene producers and the existing nucleotide sequence databases, which lack toxicological and other auxiliary data. We invite researchers working in the fields of fungal taxonomy, epidemiology and mycotoxicology to join the

Characteristics of Streptococcus mutans genotypes and dental caries in children

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Cheon, Kyounga; Moser, Stephen A.; Wiener, Howard W.; Whiddon, Jennifer; Momeni, Stephanie S.; Ruby, John D.; Cutter, Gary R.; Childers, Noel K.

2013-01-01

This longitudinal cohort study evaluated the diversity, commonality, and stability of Streptococcus mutans genotypes associated with dental caries history. Sixty-seven 5 and 6 yr-old children, considered being at high caries risk, had plaque collected from baseline through 36 months for S. mutans isolation and genotyping with repetitive extragenic palindromic-PCR (4,392 total isolates). Decayed, missing, filled surfaces (dmfs/DMFS) for each child were recorded at baseline. At baseline, 18 distinct genotypes were found among 911 S. mutans isolates from 67 children (diversity) and 13 genotypes were shared by at least 2 children (commonality). The number of genotypes per individual was positively associated with the proportion of decayed surfaces (p-ds) at baseline. Twenty-four of the 39 children who were available at follow-up visits maintained a predominant genotype for the follow-up periods (stability) and was negatively associated with p-ds. The observed diversity, commonality, and stability of S. mutans genotypes represent a pattern of dental caries epidemiology in this high caries risk community, which suggest fewer decayed surfaces are significantly associated with lower diversity and stability of S. mutans genotypes. PMID:23659236

Multi-locus genotypes of Enterocytozoon bieneusi in captive Asiatic black bears in southwestern China: High genetic diversity, broad host range, and zoonotic potential.

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Deng, Lei; Li, Wei; Zhong, Zhijun; Gong, Chao; Cao, Xuefeng; Song, Yuan; Wang, Wuyou; Huang, Xiangming; Liu, Xuehan; Hu, Yanchun; Fu, Hualin; He, Min; Wang, Ya; Zhang, Yue; Wu, Kongju; Peng, Guangneng

2017-01-01

Enterocytozoon bieneusi is an obligate eukaryotic intracellular parasite that infects a wide variety of vertebrate and invertebrate hosts. Although considerable research has been conducted on this organism, relatively little information is available on the occurrence of E. bieneusi in captive Asiatic black bears. The present study was performed to determine the prevalence, genetic diversity, and zoonotic potential of E. bieneusi in captive Asiatic black bears in zoos in southwestern China. Fecal specimens from Asiatic black bears in four zoos, located in four different cities, were collected and analyzed for the prevalence of E. bieneusi. The average prevalence of E. bieneusi was 27.4% (29/106), with the highest prevalence in Guiyang Zoo (36.4%, 16/44). Altogether, five genotypes of E. bieneusi were identified among the 29 E. bieneusi-positive samples, including three known genotypes (CHB1, SC02, and horse2) and two novel genotypes named ABB1 and ABB2. Multi-locus sequence typing using three microsatellites (MS1, MS3, and MS7) and one minisatellite (MS4) revealed V, III, V, and IV genotypes at these four loci, respectively. Phylogenetic analysis showed that the genotypes SC02 and ABB2 were clustered into group 1 of zoonotic potential, the genotypes CHB1 and ABB1 were clustered into a new group, and the genotype horse2 was clustered into group 6 of unclear zoonotic potential. In conclusion, this study identified two novel E. bieneusi genotypes in captive Asiatic black bears, and used microsatellite and minisatellite markers to reveal E. bieneusi genetic diversity. Moreover, our findings show that genotypes SC02 (identified in humans) and ABB2 belong to group 1 with zoonotic potential, suggesting the risk of transmission of E. bieneusi from Asiatic black bears to humans and other animals.

Multi-locus genotypes of Enterocytozoon bieneusi in captive Asiatic black bears in southwestern China: High genetic diversity, broad host range, and zoonotic potential.

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Lei Deng

Full Text Available Enterocytozoon bieneusi is an obligate eukaryotic intracellular parasite that infects a wide variety of vertebrate and invertebrate hosts. Although considerable research has been conducted on this organism, relatively little information is available on the occurrence of E. bieneusi in captive Asiatic black bears. The present study was performed to determine the prevalence, genetic diversity, and zoonotic potential of E. bieneusi in captive Asiatic black bears in zoos in southwestern China. Fecal specimens from Asiatic black bears in four zoos, located in four different cities, were collected and analyzed for the prevalence of E. bieneusi. The average prevalence of E. bieneusi was 27.4% (29/106, with the highest prevalence in Guiyang Zoo (36.4%, 16/44. Altogether, five genotypes of E. bieneusi were identified among the 29 E. bieneusi-positive samples, including three known genotypes (CHB1, SC02, and horse2 and two novel genotypes named ABB1 and ABB2. Multi-locus sequence typing using three microsatellites (MS1, MS3, and MS7 and one minisatellite (MS4 revealed V, III, V, and IV genotypes at these four loci, respectively. Phylogenetic analysis showed that the genotypes SC02 and ABB2 were clustered into group 1 of zoonotic potential, the genotypes CHB1 and ABB1 were clustered into a new group, and the genotype horse2 was clustered into group 6 of unclear zoonotic potential. In conclusion, this study identified two novel E. bieneusi genotypes in captive Asiatic black bears, and used microsatellite and minisatellite markers to reveal E. bieneusi genetic diversity. Moreover, our findings show that genotypes SC02 (identified in humans and ABB2 belong to group 1 with zoonotic potential, suggesting the risk of transmission of E. bieneusi from Asiatic black bears to humans and other animals.

Genotypic Diversity of Phytophthora cinnamomi and P. plurivora in Maryland's Nurseries and Mid-Atlantic Forests.

Science.gov (United States)

Beaulieu, Justine; Ford, Blaine; Balci, Yilmaz

2017-06-01

Genetic diversity of two Phytophthora spp.-P. cinnamomi (102 isolates), commonly encountered in Maryland nurseries and forests in the Mid-Atlantic United States, and P. plurivora (186 isolates), a species common in nurseries-was characterized using amplified fragment length polymorphism. Expected heterozygosity and other indices suggested a lower level of diversity among P. cinnamomi than P. plurivora isolates. Hierarchical clustering showed P. cinnamomi isolates separated into four clusters, and two of the largest clusters were closely related, containing 80% of the isolates. In contrast, P. plurivora isolates separated into six clusters, one of which included approximately 40% of the isolates. P. plurivora isolates recovered from the environment (e.g., soil and water) were genotypically more diverse than those found causing lesions. For both species, isolate origin (forest versus nursery or among nurseries) was a significant factor of heterozygosity. Clonal groups existed within P. cinnamomi and P. plurivora and included isolates from both forest and nurseries, suggesting that a pathway from nurseries to forests or vice versa exists.

Genotypic diversity of european Phytophthora ramorum isolates based on SSR analysis

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Kris Van Poucke; Annelies Vercauteren; Martine Maes; Sabine Werres; Kurt Heungens

2013-01-01

in Scotland were genotyped using seven microsatellite markers as described by Vercauteren et al. (2010). Thirty multilocus genotypes were identified within the Scottish population, with 51 percent of the isolates belonging to the main European genotype EU1MG1 and 13 unique detected genotypes. Ten of those genotypes were site specific, often represented by...

Genotypic diversity and mixed infection in newborn disease and hearing loss in congenital cytomegalovirus infection.

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Pati, Sunil K; Pinninti, Swetha; Novak, Zdenek; Chowdhury, Nazma; Patro, Raj K; Fowler, Karen; Ross, Shannon; Boppana, Suresh

2013-10-01

Congenital cytomegalovirus (cCMV) is a common congenital infection and a leading nongenetic cause of sensorineural hearing loss (SNHL). CMV exhibits extensive genetic variability, and infection with multiple CMV strains (mixed infection) was shown to be common in congenital CMV. The role of mixed infections in disease and outcome remains to be defined. Genotyping of envelope glycoproteins, UL55 (gB), UL73 (gN) and UL75 (gH), was performed on saliva specimens of 79 infants from the ongoing CMV and Hearing Multicenter Screening (CHIMES) Study and on blood and urine specimens of 52 infants who participated in natural history studies at the University of Alabama at Birmingham. Genotyping of UL144 and US28 was also performed in the CHIMES cohort. The association of individual genotypes and mixed infection with clinical findings at birth and SNHL was examined. Thirty-seven of 131 infants (28%) were symptomatic at birth and 26 (20%) had SNHL at birth. All known genotypes of UL55, UL75, UL73 and US28 were represented, and no particular genotype was associated with symptomatic infection or SNHL. UL144 subtype C was more common in symptomatic infants but not associated with SNHL. Mixed infection was observed in 59 infants (45%) and not associated with symptoms (P = 0.43) or SNHL at birth (P = 0.82). In the cohort of 52 infants with long-term hearing outcome, mixed infection at birth was not predictive of SNHL. Mixed infection is common in infants with congenital CMV but is neither associated with symptomatic infection nor associated with SNHL.

Genotypic variations in the accumulation of Cd, Cu, Pb and Zn exhibited by six commonly grown vegetables

International Nuclear Information System (INIS)

Alexander, P.D.; Alloway, B.J.; Dourado, A.M.

2006-01-01

Metal contaminants in garden and allotment soils could possibly affect human health through a variety of pathways. This study focused on the potential pathway of consumption of vegetables grown on contaminated soil. Five cultivars each of six common vegetables were grown in a control and in a soil spiked with Cd, Cu, Pb and Zn. Highly significant differences in metal content were evident between cultivars of a number of vegetables for several of the contaminants. Carrot and pea cultivars exhibited significant differences in accumulated concentrations of Cd and Cu with carrot cultivars also exhibiting significant differences in Zn. Distinctive differences were also identified when comparing one vegetable to another, legumes (Leguminosae) tending to be low accumulators, root vegetables (Umbelliferae and Liliaceae) tending to be moderate accumulators and leafy vegetables (Compositae and Chenopodiaceae) being high accumulators. - Genotypic differences between cultivars of vegetable species can be important in determining the extent of accumulation of metals from contaminated soil

Genetic diversity of popcorn genotypes using molecular analysis.

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Resh, F S; Scapim, C A; Mangolin, C A; Machado, M F P S; do Amaral, A T; Ramos, H C C; Vivas, M

2015-08-19

In this study, we analyzed dominant molecular markers to estimate the genetic divergence of 26 popcorn genotypes and evaluate whether using various dissimilarity coefficients with these dominant markers influences the results of cluster analysis. Fifteen random amplification of polymorphic DNA primers produced 157 amplified fragments, of which 65 were monomorphic and 92 were polymorphic. To calculate the genetic distances among the 26 genotypes, the complements of the Jaccard, Dice, and Rogers and Tanimoto similarity coefficients were used. A matrix of Dij values (dissimilarity matrix) was constructed, from which the genetic distances among genotypes were represented in a more simplified manner as a dendrogram generated using the unweighted pair-group method with arithmetic average. Clusters determined by molecular analysis generally did not group material from the same parental origin together. The largest genetic distance was between varieties 17 (UNB-2) and 18 (PA-091). In the identification of genotypes with the smallest genetic distance, the 3 coefficients showed no agreement. The 3 dissimilarity coefficients showed no major differences among their grouping patterns because agreement in determining the genotypes with large, medium, and small genetic distances was high. The largest genetic distances were observed for the Rogers and Tanimoto dissimilarity coefficient (0.74), followed by the Jaccard coefficient (0.65) and the Dice coefficient (0.48). The 3 coefficients showed similar estimations for the cophenetic correlation coefficient. Correlations among the matrices generated using the 3 coefficients were positive and had high magnitudes, reflecting strong agreement among the results obtained using the 3 evaluated dissimilarity coefficients.

Variation of meat quality traits among five genotypes of chicken.

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Tang, H; Gong, Y Z; Wu, C X; Jiang, J; Wang, Y; Li, K

2009-10-01

The main objective of this study was to examine the diversity of meat quality traits among 5 chicken genotypes. The genotypes included 2 Chinese native breeds (Wenchang,WCH, and Xianju), 1 commercial broiler line (Avian, AV), 1 commercial layer line (Hy-Line Brown, HLB), and 1 Chinese commercial broiler line (Lingnanhuang, LNH) synthesized by exotic and native breeds, which were slaughtered at their market ages: 16, 7, 16, and 8 wk, respectively. The effects of genotype, muscle type, and sex on meat quality traits were examined. Birds from slow-growing genotypes (WCH, Xianju, and HLB) exhibited higher shear value, inosine-5'-monophosphate concentration, lower cook loss, and more fat than those from fast-growing genotypes (AV and LNH). Chickens from WCH possessed the lowest expressible moisture, cook loss, and the highest lipid (%) among the 3 slow-growing genotypes. The HLB birds were intermediate in expressible moisture and cook loss and lowest in lipid among all genotypes. The LNH cross birds were similar to AV broilers in most meat quality parameters, although they had a lower shear force value and higher fat content than AV broilers. Breast muscle had higher expressible moisture, shear force, protein (%), inosine-5'-monophosphate content, lower cook loss, and lipid (%) than leg muscle. Muscles from male chickens had higher expressible moisture than those from the females. Variability of meat quality characteristics is mainly related to genotype and muscle type differences.

The genotypic diversity and lipase production of some thermophilic bacilli from different genera

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Melih Koc

2015-12-01

Full Text Available Abstract Thermophilic 32 isolates and 20 reference bacilli were subjected to Rep-PCR and ITS-PCR fingerprinting for determination of their genotypic diversity, before screening lipase activities. By these methods, all the isolates and references could easily be differentiated up to subspecies level from each other. In screening assay, 11 isolates and 7 references were found to be lipase producing. Their extracellular lipase activities were measured quantitatively by incubating in both tributyrin and olive oil broths at 60 °C and pH 7.0. During the 24, 48 and 72-h period of incubation, the changes in the lipase activities, culture absorbance, wet weight of biomass and pH were all measured. The activity was determined by using pNPB in 50 mM phosphate buffer at pH 7.0 at 60 °C. The lipase production of the isolates in olive oil broths varied between 0.008 and 0.052, whereas these values were found to be 0.002-0.019 (U/mL in the case of tyributyrin. For comparison, an index was established by dividing the lipase activities to cell biomass (U/mg. The maximum thermostable lipase production was achieved by the isolates F84a, F84b, and G. thermodenitrificans DSM 465T (0.009, 0.008 and 0.008 U/mg within olive oil broth, whereas G. stearothermophilus A113 displayed the highest lipase activity than its type strain in tyributyrin. Therefore, as some of these isolates displayed higher activities in comparison to references, new lipase producing bacilli were determined by presenting their genotypic diversity with DNA fingerprinting techniques.

Genetic Diversity Among Historical Olive (Olea europaea L.) Genotypes from Southern Anatolia Based on SSR Markers.

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Sakar, Ebru; Unver, Hulya; Ercisli, Sezai

2016-12-01

Olive (Olea europaea) is an ancient and important crop in both olive oil production and table use. It is important to identify the genetic diversity of olive genetic resources for cultivar development and evaluation of olive germplasm. In the study, 14 microsatellite markers (UDO4, UDO8, UDO9, UDO11, UDO12, UDO22, UDO24, UDO26, UDO28, DCA9, DCA11, DCA13, DCA15, and DCA18) were used to assess the genetic variation on 76 olive (Olea europaea L.) genotypes from Mardin province together with 6 well-known Turkish and 4 well-known foreign reference cultivars. All microsatellite markers showed polymorphism and the number of alleles varied between 9 and 22, with an average of 14.57. The most informative loci were DCA 11 (22 alleles) and DCA 9 (21 alleles). Dendrogram based on genetic distances was constructed for the 86 olive genotypes/cultivars, which revealed the existence of different clusters. The high genetic similarity was evident between Bakırkire2 and Zinnar5 (0.74) genotypes, while the most genetically divergent genotypes were Gürmeşe5 and Yedikardeşler2 (0.19). It was concluded that there was abundant SSR polymorphism in olive germplasm in southern Anatolia in Turkey and could be important for future breeding activities.

Genotyping of ancient Mycobacterium tuberculosis strains reveals historic genetic diversity.

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Müller, Romy; Roberts, Charlotte A; Brown, Terence A

2014-04-22

The evolutionary history of the Mycobacterium tuberculosis complex (MTBC) has previously been studied by analysis of sequence diversity in extant strains, but not addressed by direct examination of strain genotypes in archaeological remains. Here, we use ancient DNA sequencing to type 11 single nucleotide polymorphisms and two large sequence polymorphisms in the MTBC strains present in 10 archaeological samples from skeletons from Britain and Europe dating to the second-nineteenth centuries AD. The results enable us to assign the strains to groupings and lineages recognized in the extant MTBC. We show that at least during the eighteenth-nineteenth centuries AD, strains of M. tuberculosis belonging to different genetic groups were present in Britain at the same time, possibly even at a single location, and we present evidence for a mixed infection in at least one individual. Our study shows that ancient DNA typing applied to multiple samples can provide sufficiently detailed information to contribute to both archaeological and evolutionary knowledge of the history of tuberculosis.

Genetic Diversity and Geographic Population Structure of Bovine Neospora caninum Determined by Microsatellite Genotyping Analysis

Science.gov (United States)

Regidor-Cerrillo, Javier; Díez-Fuertes, Francisco; García-Culebras, Alicia; Moore, Dadín P.; González-Warleta, Marta; Cuevas, Carmen; Schares, Gereon; Katzer, Frank; Pedraza-Díaz, Susana; Mezo, Mercedes; Ortega-Mora, Luis M.

2013-01-01

The cyst-forming protozoan parasite Neospora caninum is one of the main causes of bovine abortion worldwide and is of great economic importance in the cattle industry. Recent studies have revealed extensive genetic variation among N . caninum isolates based on microsatellite sequences (MSs). MSs may be suitable molecular markers for inferring the diversity of parasite populations, molecular epidemiology and the basis for phenotypic variations in N . caninum , which have been poorly defined. In this study, we evaluated nine MS markers using a panel of 11 N . caninum -derived reference isolates from around the world and 96 N . caninum bovine clinical samples and one ovine clinical sample collected from four countries on two continents, including Spain, Argentina, Germany and Scotland, over a 10-year period. These markers were used as molecular tools to investigate the genetic diversity, geographic distribution and population structure of N . caninum . Multilocus microsatellite genotyping based on 7 loci demonstrated high levels of genetic diversity in the samples from all of the different countries, with 96 microsatellite multilocus genotypes (MLGs) identified from 108 N . caninum samples. Geographic sub-structuring was present in the country populations according to pairwise F ST. Principal component analysis (PCA) and Neighbor Joining tree topologies also suggested MLG segregation partially associated with geographical origin. An analysis of the MLG relationships, using eBURST, confirmed that the close genetic relationship observed between the Spanish and Argentinean populations may be the result of parasite migration (i.e., the introduction of novel MLGs from Spain to South America) due to cattle movement. The eBURST relationships also revealed genetically different clusters associated with the abortion. The presence of linkage disequilibrium, the co-existence of specific MLGs to individual farms and eBURST MLG relationships suggest a predominant clonal

ToxGen: an improved reference database for the identification of type B-trichothecene genotypes in Fusarium

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Tomasz Kulik

2017-02-01

Full Text Available Type B trichothecenes, which pose a serious hazard to consumer health, occur worldwide in grains. These mycotoxins are produced mainly by three different trichothecene genotypes/chemotypes: 3ADON (3-acetyldeoxynivalenol, 15ADON (15-acetyldeoxynivalenol and NIV (nivalenol, named after these three major mycotoxin compounds. Correct identification of these genotypes is elementary for all studies relating to population surveys, fungal ecology and mycotoxicology. Trichothecene producers exhibit enormous strain-dependent chemical diversity, which may result in variation in levels of the genotype’s determining toxin and in the production of low to high amounts of atypical compounds. New high-throughput DNA-sequencing technologies promise to boost the diagnostics of mycotoxin genotypes. However, this requires a reference database containing a satisfactory taxonomic sampling of sequences showing high correlation to actually produced chemotypes. We believe that one of the most pressing current challenges of such a database is the linking of molecular identification with chemical diversity of the strains, as well as other metadata. In this study, we use the Tri12 gene involved in mycotoxin biosynthesis for identification of Tri genotypes through sequence comparison. Tri12 sequences from a range of geographically diverse fungal strains comprising 22 Fusarium species were stored in the ToxGen database, which covers descriptive and up-to-date annotations such as indication on Tri genotype and chemotype of the strains, chemical diversity, information on trichothecene-inducing host, substrate or media, geographical locality, and most recent taxonomic affiliations. The present initiative bridges the gap between the demands of comprehensive studies on trichothecene producers and the existing nucleotide sequence databases, which lack toxicological and other auxiliary data. We invite researchers working in the fields of fungal taxonomy, epidemiology and

Welcome to the neighbourhood: interspecific genotype by genotype interactions in Solidago influence above- and belowground biomass and associated communities.

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Genung, Mark A; Bailey, Joseph K; Schweitzer, Jennifer A

2012-01-01

Intra- and interspecific plant-plant interactions are fundamental to patterns of community assembly and to the mixture effects observed in biodiversity studies. Although much research has been conducted at the species level, very little is understood about how genetic variation within and among interacting species may drive these processes. Using clones of both Solidago altissima and Solidago gigantea, we found that genotypic variation in a plant's neighbours affected both above- and belowground plant traits, and that genotype by genotype interactions between neighbouring plants impacted associated pollinator communities. The traits for which focal plant genotypic variation explained the most variation varied by plant species, whereas neighbour genotypic variation explained the most variation in coarse root biomass. Our results provide new insight into genotypic and species diversity effects in plant-neighbour interactions, the extended consequences of diversity effects, and the potential for evolution in response to competitive or to facilitative plant-neighbour interactions. © 2011 Blackwell Publishing Ltd/CNRS.

Genotypic and Phenotypic Diversity of Cryptococcus gattii VGII Clinical Isolates and Its Impact on Virulence

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Vanessa A. Barcellos

2018-02-01

Full Text Available The Cryptococcus gattii species complex harbors the main etiological agents of cryptococcosis in immunocompetent patients. C. gattii molecular type VGII predominates in the north and northeastern regions of Brazil, leading to high morbidity and mortality rates. C. gattii VGII isolates have a strong clinical relevance and phenotypic variations. These phenotypic variations among C. gattii species complex isolates suggest that some strains are more virulent than others, but little information is available related to the pathogenic properties of those strains. In this study, we analyzed some virulence determinants of C. gattii VGII strains (CG01, CG02, and CG03 isolated from patients in the state of Piauí, Brazil. The C. gattii R265 VGIIa strain, which was isolated from the Vancouver outbreak, differed from C. gattii CG01, CG02 and CG03 isolates (also classified as VGII when analyzed the capsular dimensions, melanin production, urease activity, as well as the glucuronoxylomannan (GXM secretion. Those differences directly reflected in their virulence potential. In addition, CG02 displayed higher virulence compared to R265 (VGIIa strain in a cryptococcal murine model of infection. Lastly, we examined the genotypic diversity of these strains through Multilocus Sequence Type (MLST and one new subtype was described for the CG02 isolate. This study confirms the presence and the phenotypic and genotypic diversity of highly virulent strains in the Northeast region of Brazil.

The genetic diversity of hepatitis A genotype I in Bulgaria.

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Cella, Eleonora; Golkocheva-Markova, Elitsa N; Trandeva-Bankova, Diljana; Gregori, Giulia; Bruni, Roberto; Taffon, Stefania; Equestre, Michele; Costantino, Angela; Spoto, Silvia; Curtis, Melissa; Ciccaglione, Anna Rita; Ciccozzi, Massimo; Angeletti, Silvia

2018-01-01

The purpose of this study was to analyze sequences of hepatitis A virus (HAV) Ia and Ib genotypes from Bulgarian patients to investigate the molecular epidemiology of HAV genotype I during the years 2012 to 2014. Around 105 serum samples were collected by the Department of Virology of the National Center of Infectious and Parasitic Diseases in Bulgaria. The sequenced region encompassed the VP1/2A region of HAV genome. The sequences obtained from the samples were 103. For the phylogenetic analyses, 5 datasets were built to investigate the viral gene in/out flow among distinct HAV subpopulations in different geographic areas and to build a Bayesian dated tree, Bayesian phylogenetic and migration pattern analyses were performed. HAV Ib Bulgarian sequences mostly grouped into a single clade. This indicates that the Bulgarian epidemic is partially compartmentalized. It originated from a limited number of viruses and then spread through fecal-oral local transmission. HAV Ia Bulgarian sequences were intermixed with European sequences, suggesting that an Ia epidemic is not restricted to Bulgaria but can affect other European countries. The time-scaled phylogeny reconstruction showed the root of the tree dating in 2008 for genotype Ib and in 1999 for genotype Ia with a second epidemic entrance in 2003. The Bayesian skyline plot for genotype Ib showed a slow but continuous growth, sustained by fecal-oral route transmission. For genotype Ia, there was an exponential growth followed by a plateau, which suggests better infection control. Bidirectional viral flow for Ib genotype, involving different Bulgarian areas, was observed, whereas a unidirectional flow from Sofia to Ihtiman for genotype Ia was highlighted, suggesting the fecal-oral transmission route for Ia. Copyright © 2017 The Authors. Published by Wolters Kluwer Health, Inc. All rights reserved.

Morphological and Biochemical Characteristics of Fruits of Different Cornelian Cherry (Cornus mas L. Genotypes from Spontaneous Flora

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Felicia-Constantina CORNESCU

2017-12-01

Full Text Available The current study was carried out on six local cornelian cherry (Cornus mas L. genotypes, grown in Turceni town (Gorj county and Baita village (Hunedoara county, in Romania. Several morphological and biochemical characteristics of cultivars were determined. Fruit weight and fruit flesh ratio of the analyzed genotypes ranged from 1.33 to 2.31 g and 61.53 to 78.58% respectively. Soluble solid contents were determined, the lowest noted as 10% and the highest as 25.5%. Results have shown that there was a high diversity in cornelian cherry populations within different ecological areas. Differences were exhibited in terms of fruit size and biochemical characteristics. The results of the study are useful for attempting to select superior genotypes of cornelian cherry for culture.

Genetic History of Hepatitis C Virus in Venezuela: High Diversity and Long Time of Evolution of HCV Genotype 2

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Sulbarán, Maria Z.; Di Lello, Federico A.; Sulbarán, Yoneira; Cosson, Clarisa; Loureiro, Carmen L.; Rangel, Héctor R.; Cantaloube, Jean F.; Campos, Rodolfo H.; Moratorio, Gonzalo; Cristina, Juan; Pujol, Flor H.

2010-01-01

Background The subtype diversity of the hepatitis C virus (HCV) genotypes is unknown in Venezuela. Methodology/Principal Findings Partial sequencing of the NS5B region was performed in 310 isolates circulating in patients from 1995 to 2007. In the samples collected between 2005 and 2007, HCV genotype 1 (G1) was the most common genotype (63%), composed as expected of mainly G1a and G1b. G2 was the second most common genotype (33%), being G2a almost absent and G2j the most frequent subtype. Sequence analysis of the core region confirmed the subtype assignment performed within the NS5b region in 63 isolates. The complete genome sequence of G2j was obtained. G2j has been described in France, Canada and Burkina Fasso, but it was not found in Martinique, where several subtypes of G2 circulate in the general population. Bayesian coalescence analysis indicated a most recent common ancestor (MRCA) of G2j around 1785, before the introduction of G1b (1869) and G1a (1922). While HCV G1a and G1b experienced a growth reduction since 1990, coincident with the time when blood testing was implemented in Venezuela, HCV G2j did not seem to reach growth equilibrium during this period. Conclusions/Significance Assuming the introduction of G2j from Africa during the slave trade, the high frequency of G2j found in Venezuela could suggest: 1- the introduction of African ethnic groups different from the ones introduced to Martinique or 2- the occurrence of a founder effect. This study represents an in-depth analysis of the subtype diversity of HCV in Venezuela, which is still unexplored in the Americas and deserves further studies. PMID:21179440

Genetic history of hepatitis C virus in Venezuela: high diversity and long time of evolution of HCV genotype 2.

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Maria Z Sulbarán

Full Text Available BACKGROUND: The subtype diversity of the hepatitis C virus (HCV genotypes is unknown in Venezuela. METHODOLOGY/PRINCIPAL FINDINGS: Partial sequencing of the NS5B region was performed in 310 isolates circulating in patients from 1995 to 2007. In the samples collected between 2005 and 2007, HCV genotype 1 (G1 was the most common genotype (63%, composed as expected of mainly G1a and G1b. G2 was the second most common genotype (33%, being G2a almost absent and G2j the most frequent subtype. Sequence analysis of the core region confirmed the subtype assignment performed within the NS5b region in 63 isolates. The complete genome sequence of G2j was obtained. G2j has been described in France, Canada and Burkina Fasso, but it was not found in Martinique, where several subtypes of G2 circulate in the general population. Bayesian coalescence analysis indicated a most recent common ancestor (MRCA of G2j around 1785, before the introduction of G1b (1869 and G1a (1922. While HCV G1a and G1b experienced a growth reduction since 1990, coincident with the time when blood testing was implemented in Venezuela, HCV G2j did not seem to reach growth equilibrium during this period. CONCLUSIONS/SIGNIFICANCE: Assuming the introduction of G2j from Africa during the slave trade, the high frequency of G2j found in Venezuela could suggest: 1- the introduction of African ethnic groups different from the ones introduced to Martinique or 2- the occurrence of a founder effect. This study represents an in-depth analysis of the subtype diversity of HCV in Venezuela, which is still unexplored in the Americas and deserves further studies.

Evaluation of genetic diversity amongst Descurainia sophia L. genotypes by inter-simple sequence repeat (ISSR) marker.

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Saki, Sahar; Bagheri, Hedayat; Deljou, Ali; Zeinalabedini, Mehrshad

2016-01-01

Descurainia sophia is a valuable medicinal plant in family of Brassicaceae. To determine the range of diversity amongst D. sophia in Iran, 32 naturally distributed plants belonging to six natural populations of the Iranian plateau were investigated by inter-simple sequence repeat (ISSR) markers. The average percentage of polymorphism produced by 12 ISSR primers was 86 %. The PIC values for primers ranged from 0.22 to 0.40 and Rp values ranged between 6.5 and 19.9. The relative genetic diversity of the populations was not high (Gst =0.32). However, the value of gene flow revealed by the ISSR marker was high (Nm = 1.03). UPGMA clustering method based on Jaccard similarity coefficient grouped the genotypes into two major clusters. Graph results from Neighbor-Net Network generated after a 1000 bootstrap test using Jaccard coefficient, and STRUCTURE analysis confirmed the UPGMA clustering. The first three PCAs represented 57.31 % of the total variation. The high levels of genetic diversity were observed within populations, which is useful in breeding and conservation programs. ISSR is found to be an eligible marker to study genetic diversity of D. sophia.

Highly efficient infectious cell culture of three hepatitis C virus genotype 2b strains and sensitivity to lead protease, nonstructural protein 5A, and polymerase inhibitors

DEFF Research Database (Denmark)

Ramirez, Santseharay; Li, Yi-Ping; Jensen, Sanne B

2014-01-01

UNLABELLED: Hepatitis C virus (HCV) is a genetically diverse virus with multiple genotypes exhibiting remarkable differences, particularly in drug susceptibility. Drug and vaccine development will benefit from high-titer HCV cultures mimicking the complete viral life cycle, but such systems only ...

Invasion Dynamics and Genotypic Diversity of Cogongrass (Imperata cylindrica) at the Point of Introduction in the Southeastern United States

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Ludovic J. A. Capo-chichi; Wilson H. Faircloth; A. G. Williamson; Michael G. Patterson; James H. Miller; Edzard van Santen

2008-01-01

Nine sites of cogongrass were included in a study of genotypic dimity and spread dynamics at the point of introduction and its adjacent areas in the southern United States. Clones evaluated with two primer pairs yielded a total of 137 amplified fragment length polymorphism (AFLP) hi of which 102 (74.4%) were polymorphic. Genetic diversity was measured as the percentage...

Genetic diversity analysis of cyanogenic potential (CNp) of root among improved genotypes of cassava using simple sequence repeat markers.

Science.gov (United States)

Moyib, O K; Mkumbira, J; Odunola, O A; Dixon, A G

2012-12-01

Cyanogenic potential (CNp) of cassava constitutes a serious problem for over 500 million people who rely on the crop as their main source of calories. Genetic diversity is a key to successful crop improvement for breeding new improved variability for target traits. Forty-three improved genotypes of cassava developed by International Institute of Tropical Agriculture (ITA), Ibadan, were characterized for CNp trait using 35 Simple Sequence.Repeat (SSR) markers. Essential colorimetry picric test was used for evaluation of CNp on a color scale of 1 to 14. The CNp scores obtained ranged from 3 to 9, with a mean score of 5.48 (+/- 0.09) based on Statistical Analysis System (SAS) package. TMS M98/ 0068 (4.0 +/- 0.25) was identified as the best genotype with low CNp while TMS M98/0028 (7.75 +/- 0.25) was the worst. The 43 genotypes were assigned into 7 phenotypic groups based on rank-sum analysis in SAS. Dissimilarity analysis representatives for windows generated a phylogenetic tree with 5 clusters which represented hybridizing groups. Each of the clusters (except 4) contained low CNp genotypes that could be used for improving the high CNp genotypes in the same or near cluster. The scatter plot of the genotypes showed that there was little or no demarcation for phenotypic CNp groupings in the molecular groupings. The result of this study demonstrated that SSR markers are powerful tools for the assessment of genetic variability, and proper identification and selection of parents for genetic improvement of low CNp trait among the IITA cassava collection.

Genotypic Diversity of Staphylococcus aureus α-Hemolysin Gene (hla and Its Association with Clonal Background: Implications for Vaccine Development.

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Meng Xiao

Full Text Available The α-hemolysin, encoded by the hla gene, is a major virulence factor in S. aureus infections. Changes in key amino acid residues of α-hemolysin can result in reduction, or even loss, of toxicity. The aim of this study was to investigate the diversity of the hla gene sequence and the relationship of hla variants to the clonal background of S. aureus isolates. A total of 47 clinical isolates from China were used in this study, supplemented with in silico analysis of 318 well-characterized whole genome sequences from globally distributed isolates. A total of 28 hla genotypes were found, including three unique to isolates from China, 20 found only in the global genomes and five found in both. The hla genotype generally correlated with the clonal background, particularly the multilocus sequence type, but was not related to geographic origin, host source or methicillin-resistance phenotype. In addition, the hla gene showed greater diversity than the seven loci utilized in the MLST scheme for S. aureus. Our investigation has provided genetic data which may be useful for future studies of toxicity, immunogenicity and vaccine development.

Decoding noises in HIV computational genotyping.

Science.gov (United States)

Jia, MingRui; Shaw, Timothy; Zhang, Xing; Liu, Dong; Shen, Ye; Ezeamama, Amara E; Yang, Chunfu; Zhang, Ming

2017-11-01

Lack of a consistent and reliable genotyping system can critically impede HIV genomic research on pathogenesis, fitness, virulence, drug resistance, and genomic-based healthcare and treatment. At present, mis-genotyping, i.e., background noises in molecular genotyping, and its impact on epidemic surveillance is unknown. For the first time, we present a comprehensive assessment of HIV genotyping quality. HIV sequence data were retrieved from worldwide published records, and subjected to a systematic genotyping assessment pipeline. Results showed that mis-genotyped cases occurred at 4.6% globally, with some regional and high-risk population heterogeneities. Results also revealed a consistent mis-genotyping pattern in gp120 in all studied populations except the group of men who have sex with men. Our study also suggests novel virus diversities in the mis-genotyped cases. Finally, this study reemphasizes the importance of implementing a standardized genotyping pipeline to avoid genotyping disparity and to advance our understanding of virus evolution in various epidemiological settings. Copyright © 2017 Elsevier Inc. All rights reserved.

Genotypic diversity of multidrug-, quinolone- and extensively drug-resistant Mycobacterium tuberculosis isolates in Thailand.

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Disratthakit, Areeya; Meada, Shinji; Prammananan, Therdsak; Thaipisuttikul, Iyarit; Doi, Norio; Chaiprasert, Angkana

2015-06-01

Drug-resistant tuberculosis (TB), which includes multidrug-resistant (MDR-TB), quinolone-resistant (QR-TB) and extensively drug-resistant tuberculosis (XDR-TB), is a serious threat to TB control. We aimed to characterize the genotypic diversity of drug-resistant TB clinical isolates collected in Thailand to establish whether the emergence of drug-resistant TB is attributable to transmitted resistance or acquired resistance. We constructed the first molecular phylogeny of MDR-TB (n=95), QR-TB (n=69) and XDR-TB (n=28) in Thailand based on spoligotyping and proposed 24-locus multilocus variable-number of tandem repeat analysis (MLVA). Clustering analysis was performed using the unweighted pair group method with arithmetic mean. Spoligotyping identified the Beijing strain (SIT1) as the most predominant genotype (n=139; 72.4%). The discriminatory power of 0.9235 Hunter-Gaston Discriminatory Index (HGDI) with the 15-locus variable-number tandem repeats of mycobacterial interspersed repetitive units typing was improved to a 0.9574 HGDI with proposed 24-locus MLVA, thereby resulting in the subdivision of a large cluster of Beijing strains (SIT1) into 17 subclusters. We identified the spread of drug-resistant TB clones caused by three different MLVA types in the Beijing strain (SIT1) and a specific clone of XDR-TB caused by a rare genotype, the Manu-ancestor strain (SIT523). Overall, 49.5% of all isolates were clustered. These findings suggest that a remarkable transmission of drug-resistant TB occurred in Thailand. The remaining 50% of drug-resistant TB isolates were unique genotypes, which may have arisen from the individual acquisition of drug resistance. Our results suggest that transmitted and acquired resistance have played an equal role in the emergence of drug-resistant TB. Further characterization of whole genome sequences of clonal strains could help to elucidate the mycobacterial genetic factors relevant for drug resistance, transmissibility and virulence

Comparative ultrastructure of fruit plastids in three genetically diverse genotypes of apple (Malus × domestica Borkh.) during development

Science.gov (United States)

Schaeffer, Scott M.; Christian, Ryan; Castro-Velasquez, Nohely; Hyden, Brennan; Lynch-Holm, Valerie

2017-01-01

Plastids are the defining organelle for a plant cell and are critical for myriad metabolic functions. The role of leaf plastid, chloroplast, is extensively documented; however, fruit plastids—chromoplasts—are poorly understood, especially in the context of the diverse metabolic processes operating in these diverse plant organs. Recently, in a comparative study of the predicted plastid-targeted proteomes across seven plant species, we reported that each plant species is predicted to harbor a unique set of plastid-targeted proteins. However, the temporal and developmental context of these processes remains unknown. In this study, an ultrastructural analysis approach was used to characterize fruit plastids in the epidermal and collenchymal cell layers at 11 developmental timepoints in three genotypes of apple (Malus × domestica Borkh.): chlorophyll-predominant ‘Granny Smith’, carotenoid-predominant ‘Golden Delicious’, and anthocyanin-predominant ‘Top Red Delicious’. Plastids transitioned from a proplastid-like plastid to a chromoplast-like plastid in epidermis cells, while in the collenchyma cells, they transitioned from a chloroplast-like plastid to a chloro-chromo-amyloplast plastid. Plastids in the collenchyma cells of the three genotypes demonstrated a diverse array of structures and features. This study enabled the identification of discrete developmental stages during which specific functions are most likely being performed by the plastids as indicated by accumulation of plastoglobuli, starch granules, and other sub-organeller structures. Information regarding the metabolically active developmental stages is expected to facilitate biologically relevant omics studies to unravel the complex biochemistry of plastids in perennial non-model systems. PMID:28698906

Heterogeneous recombination among Hepatitis B virus genotypes.

Science.gov (United States)

Castelhano, Nadine; Araujo, Natalia M; Arenas, Miguel

2017-10-01

The rapid evolution of Hepatitis B virus (HBV) through both evolutionary forces, mutation and recombination, allows this virus to generate a large variety of adapted variants at both intra and inter-host levels. It can, for instance, generate drug resistance or the diverse viral genotypes that currently exist in the HBV epidemics. Concerning the latter, it is known that recombination played a major role in the emergence and genetic diversification of novel genotypes. In this regard, the quantification of viral recombination in each genotype can provide relevant information to devise expectations about the evolutionary trends of the epidemic. Here we measured the amount of this evolutionary force by estimating global and local recombination rates in >4700 HBV complete genome sequences corresponding to nine (A to I) HBV genotypes. Counterintuitively, we found that genotype E presents extremely high levels of recombination, followed by genotypes B and C. On the other hand, genotype G presents the lowest level, where recombination is almost negligible. We discuss these findings in the light of known characteristics of these genotypes. Additionally, we present a phylogenetic network to depict the evolutionary history of the studied HBV genotypes. This network clearly classified all genotypes into specific groups and indicated that diverse pairs of genotypes are derived from a common ancestor (i.e., C-I, D-E and, F-H) although still the origin of this virus presented large uncertainty. Altogether we conclude that the amount of observed recombination is heterogeneous among HBV genotypes and that this heterogeneity can influence on the future expansion of the epidemic. Copyright © 2017 Elsevier B.V. All rights reserved.

Lactobacillus buchneri genotyping on the basis of clustered regularly interspaced short palindromic repeat (CRISPR) locus diversity.

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Briner, Alexandra E; Barrangou, Rodolphe

2014-02-01

Clustered regularly interspaced short palindromic repeats (CRISPR) in combination with associated sequences (cas) constitute the CRISPR-Cas immune system, which uptakes DNA from invasive genetic elements as novel "spacers" that provide a genetic record of immunization events. We investigated the potential of CRISPR-based genotyping of Lactobacillus buchneri, a species relevant for commercial silage, bioethanol, and vegetable fermentations. Upon investigating the occurrence and diversity of CRISPR-Cas systems in Lactobacillus buchneri genomes, we observed a ubiquitous occurrence of CRISPR arrays containing a 36-nucleotide (nt) type II-A CRISPR locus adjacent to four cas genes, including the universal cas1 and cas2 genes and the type II signature gene cas9. Comparative analysis of CRISPR spacer content in 26 L. buchneri pickle fermentation isolates associated with spoilage revealed 10 unique locus genotypes that contained between 9 and 29 variable spacers. We observed a set of conserved spacers at the ancestral end, reflecting a common origin, as well as leader-end polymorphisms, reflecting recent divergence. Some of these spacers showed perfect identity with phage sequences, and many spacers showed homology to Lactobacillus plasmid sequences. Following a comparative analysis of sequences immediately flanking protospacers that matched CRISPR spacers, we identified a novel putative protospacer-adjacent motif (PAM), 5'-AAAA-3'. Overall, these findings suggest that type II-A CRISPR-Cas systems are valuable for genotyping of L. buchneri.

SSR based genetic diversity of pigmented and aromatic rice (Oryza sativa L.) genotypes of the western Himalayan region of India.

Science.gov (United States)

Ashraf, Humaira; Husaini, Amjad M; Ashraf Bhat, M; Parray, G A; Khan, Salim; Ganai, Nazir A

2016-10-01

A set of 24 of SSR markers were used to estimate the genetic diversity in 16 rice genotypes found in Western Himalayas of Kashmir and Himachal Pradesh, India. The level of polymorphism among the genotypes of rice was evaluated from the number of alleles and PIC value for each of the 24 SSR loci. A total of 68 alleles were detected across the 16 genotypes through the use of these 24 SSR markers The number of alleles per locus generated varied from 2 (RM 338, RM 452, RM 171) to 6 (RM 585, RM 249, RM 481, RM 162). The PIC values varied from 0.36 (RM 1) to 0.86 (RM 249) with an average of 0.62 per locus. Based on information generated, the genotypes got separated in six different clusters. Cluster 1 comprised of 4 genotypes viz; Zag 1, Zag 13, Pusa sugandh 3, and Zag 14, separated from each other at a similarity value of 0.40. Cluster second comprised of 3 landraces viz; Zag 2. Zag 4 and Zag10 separated from each other at a similarity value of 0.45. Cluster third comprised of 3 genotypes viz; Grey rice, Mushk budji and Kamad separated from each other at a similarity value of 0.46. Cluster fourth had 2 landraces viz; Kawa kreed and Loual anzul, and was not sub clustered. Fifth cluster had 3 genotypes viz; Zag 12, Purple rice and Jhelum separated from each other at a similarity value of 0.28. Cluster 6 comprised of a single popular variety i.e. Shalimar rice 1 with independent lineage.

Genetic and DNA methylation changes in cotton (Gossypium genotypes and tissues.

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Kenji Osabe

Full Text Available In plants, epigenetic regulation is important in normal development and in modulating some agronomic traits. The potential contribution of DNA methylation mediated gene regulation to phenotypic diversity and development in cotton was investigated between cotton genotypes and various tissues. DNA methylation diversity, genetic diversity, and changes in methylation context were investigated using methylation-sensitive amplified polymorphism (MSAP assays including a methylation insensitive enzyme (BsiSI, and the total DNA methylation level was measured by high-performance liquid chromatography (HPLC. DNA methylation diversity was greater than the genetic diversity in the selected cotton genotypes and significantly different levels of DNA methylation were identified between tissues, including fibre. The higher DNA methylation diversity (CHG methylation being more diverse than CG methylation in cotton genotypes suggest epigenetic regulation may be important for cotton, and the change in DNA methylation between fibre and other tissues hints that some genes may be epigenetically regulated for fibre development. The novel approach using BsiSI allowed direct comparison between genetic and epigenetic diversity, and also measured CC methylation level that cannot be detected by conventional MSAP.

Genetic and DNA methylation changes in cotton (Gossypium) genotypes and tissues.

Science.gov (United States)

Osabe, Kenji; Clement, Jenny D; Bedon, Frank; Pettolino, Filomena A; Ziolkowski, Lisa; Llewellyn, Danny J; Finnegan, E Jean; Wilson, Iain W

2014-01-01

In plants, epigenetic regulation is important in normal development and in modulating some agronomic traits. The potential contribution of DNA methylation mediated gene regulation to phenotypic diversity and development in cotton was investigated between cotton genotypes and various tissues. DNA methylation diversity, genetic diversity, and changes in methylation context were investigated using methylation-sensitive amplified polymorphism (MSAP) assays including a methylation insensitive enzyme (BsiSI), and the total DNA methylation level was measured by high-performance liquid chromatography (HPLC). DNA methylation diversity was greater than the genetic diversity in the selected cotton genotypes and significantly different levels of DNA methylation were identified between tissues, including fibre. The higher DNA methylation diversity (CHG methylation being more diverse than CG methylation) in cotton genotypes suggest epigenetic regulation may be important for cotton, and the change in DNA methylation between fibre and other tissues hints that some genes may be epigenetically regulated for fibre development. The novel approach using BsiSI allowed direct comparison between genetic and epigenetic diversity, and also measured CC methylation level that cannot be detected by conventional MSAP.

Genetic diversity enhances the resistance of a seagrass ecosystem to disturbance

OpenAIRE

Hughes, A. R.; Stachowicz, John J

2004-01-01

Motivated by recent global reductions in biodiversity, empirical and theoretical research suggests that more species-rich systems exhibit enhanced productivity, nutrient cycling, or resistance to disturbance or invasion relative to systems with fewer species. In contrast, few data are available to assess the potential ecosystem-level importance of genetic diversity within species known to play a major functional role. Using a manipulative field experiment, we show that increasing genotypic di...

Comparative genotyping of Clostridium thermocellum strains isolated from biogas plants: genetic markers and characterization of cellulolytic potential.

Science.gov (United States)

Koeck, Daniela E; Zverlov, Vladimir V; Liebl, Wolfgang; Schwarz, Wolfgang H

2014-07-01

Clostridium thermocellum is among the most prevalent of known anaerobic cellulolytic bacteria. In this study, genetic and phenotypic variations among C. thermocellum strains isolated from different biogas plants were determined and different genotyping methods were evaluated on these isolates. At least two C. thermocellum strains were isolated independently from each of nine different biogas plants via enrichment on cellulose. Various DNA-based genotyping methods such as ribotyping, RAPD (Random Amplified Polymorphic DNA) and VNTR (Variable Number of Tandem Repeats) were applied to these isolates. One novel approach - the amplification of unknown target sequences between copies of a previously discovered Random Inserted Mobile Element (RIME) - was also tested. The genotyping method with the highest discriminatory power was found to be the amplification of the sequences between the insertion elements, where isolates from each biogas plant yielded a different band pattern. Cellulolytic potentials, optimal growth conditions and substrate spectra of all isolates were characterized to help identify phenotypic variations. Irrespective of the genotyping method used, the isolates from each individual biogas plant always exhibited identical patterns. This is suggestive of a single C. thermocellum strain exhibiting dominance in each biogas plant. The genotypic groups reflect the results of the physiological characterization of the isolates like substrate diversity and cellulase activity. Conversely, strains isolated across a range of biogas plants differed in their genotyping results and physiological properties. Both strains isolated from one biogas plant had the best specific cellulose-degrading properties and might therefore achieve superior substrate utilization yields in biogas fermenters. Copyright © 2014 Elsevier GmbH. All rights reserved.

Molecular diversity in irregular or refugee immigrant patients with HBV-genotype-E infection living in the metropolitan area of Naples.

Science.gov (United States)

Sagnelli, Caterina; Ciccozzi, Massimo; Coppola, Nicola; Minichini, Carmine; Lo Presti, Alessandra; Starace, Mario; Alessio, Loredana; Macera, Margherita; Cella, Eleonora; Gualdieri, Luciano; Caprio, Nunzio; Pasquale, Giuseppe; Sagnelli, Evangelista

2017-06-01

In a recent testing in the metropolitan area of Naples, Italy, on 945 irregular immigrants or refugees, 87 HBsAg chronic carriers were identified, 53 of whom were infected by HBV-genotype E. The aim of the present study was to identify the genetic diversity of HBV-genotype E in these 53 immigrants. The 53 immigrant patients with HBV-genotype-E infection were born in Africa, central or eastern Asia, eastern Europe or Latin America. These patients had been seen for a clinical consultation at one of the four first-level units from January 2012 to 2013. The first dataset contained 53 HBV-S gene isolates plus 128 genotype/subgenotype specific reference sequences downloaded from the National Center for Biotechnology Information. The second dataset, comprising the 53 HBV-S gene isolates, previously classified as HBV-genotype E, was used to perform the time-scaled phylogeny reconstruction using a Bayesian approach. Phylogenetic analysis showed that all 53 HBV-S isolates belonged to HBV-genotype E. Bayes factor analysis showed that the relaxed clock exponential growth model fitted the data significantly better than the other models. The time-scaled Bayesian phylogenetic tree of the second dataset showed that the root of the tree dated back to the year 1990 (95% HPD:1984-2000). Four statistically supported clusters were identified. Cluster A dated back to 2012 (95% HPD:1997-2012); cluster B dated back to 2008 (95% HPD:2001-2015); cluster C to 2006 (95% HPD:1999-2013); cluster D to 2004 (95% HPD:1998-2011). This study disclosed the genetic evolution and phylogenesis in a group of HBV-genotype-E-infected immigrants. J. Med. Virol. 89:1015-1024, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Genotypic diversity of stress response in Lactobacillus plantarum, Lactobacillus paraplantarum and Lactobacillus pentosus.

Science.gov (United States)

Ricciardi, Annamaria; Parente, Eugenio; Guidone, Angela; Ianniello, Rocco Gerardo; Zotta, Teresa; Abu Sayem, S M; Varcamonti, Mario

2012-07-02

Lactobacillus plantarum, Lactobacillus pentosus and Lactobacillus paraplantarum are three closely related species which are widespread in food and non-food environments, and are important as starter bacteria or probiotics. In order to evaluate the phenotypic diversity of stress tolerance in the L. plantarum group and the ability to mount an adaptive heat shock response, the survival of exponential and stationary phase and of heat adapted exponential phase cells of six L. plantarum subsp. plantarum, one L. plantarum subsp. argentoratensis, one L. pentosus and two L. paraplantarum strains selected in a previous work upon exposure to oxidative, heat, detergent, starvation and acid stresses was compared to that of the L. plantarum WCFS1 strain. Furthermore, to evaluate the genotypic diversity in stress response genes, ten genes (encoding for chaperones DnaK, GroES and GroEL, regulators CtsR, HrcA and CcpA, ATPases/proteases ClpL, ClpP, ClpX and protease FtsH) were amplified using primers derived from the WCFS1 genome sequence and submitted to restriction with one or two endonucleases. The results were compared by univariate and multivariate statistical methods. In addition, the amplicons for hrcA and ctsR were sequenced and compared by multiple sequence alignment and polymorphism analysis. Although there was evidence of a generalized stress response in the stationary phase, with increase of oxidative, heat, and, to a lesser extent, starvation stress tolerance, and for adaptive heat stress response, with increased tolerance to heat, acid and detergent, different growth phases and adaptation patterns were found. Principal component analysis showed that while heat, acid and detergent stresses respond similarly to growth phase and adaptation, tolerance to oxidative and starvation stresses implies completely unrelated mechanisms. A dendrogram obtained using the data from multilocus restriction typing (MLRT) of stress response genes clearly separated two groups of L

Performance of chickpea genotypes under Swat valley conditions

International Nuclear Information System (INIS)

Khan, A.; Rahim, M.; Ahmad, F.; Ali, A.

2004-01-01

Twenty-two genetically diverse chickpeas genotypes were studied for their physiological efficiency to select the most desirable genotype/genotypes for breeding program on chickpea. Genotype 'CM7-1' was found physiologically efficient stain with maximum harvest index (37.33%) followed by genotype 'CM1571-1-A' with harvest index of 35.73%. Genotype '90206' produced maximum biological yield (7463 kg ha/sup -1/) followed by genotypes 'CM31-1' and 'E-2034' with biological yield of 7352 and 7167 kg ha/sup -1/, respectively. Harvest index and economic yield showed significant positive correlation value of (r=+0.595), while negative correlation value of (r = -0.435) was observed between harvest index and biological yield. (author)

Exploiting genotypic diversity of 2,4-diacetylphloroglucinol-producing Pseudomonas spp.: characterization of superior root-colonizing P. fluorescens strain Q8r1-96.

Science.gov (United States)

Raaijmakers, J M; Weller, D M

2001-06-01

The genotypic diversity that occurs in natural populations of antagonistic microorganisms provides an enormous resource for improving biological control of plant diseases. In this study, we determined the diversity of indigenous 2,4-diacetylphloroglucinol (DAPG)-producing Pseudomonas spp. occurring on roots of wheat grown in a soil naturally suppressive to take-all disease of wheat. Among 101 isolates, 16 different groups were identified by random amplified polymorphic DNA (RAPD) analysis. One RAPD group made up 50% of the total population of DAPG-producing Pseudomonas spp. Both short- and long-term studies indicated that this dominant genotype, exemplified by P. fluorescens Q8r1-96, is highly adapted to the wheat rhizosphere. Q8r1-96 requires a much lower dose (only 10 to 100 CFU seed(-1) or soil(-1)) to establish high rhizosphere population densities (10(7) CFU g of root(-1)) than Q2-87 and 1M1-96, two genotypically different, DAPG-producing P. fluorescens strains. Q8r1-96 maintained a rhizosphere population density of approximately 10(5) CFU g of root(-1) after eight successive growth cycles of wheat in three different, raw virgin soils, whereas populations of Q2-87 and 1M1-96 dropped relatively quickly after five cycles and were not detectable after seven cycles. In short-term studies, strains Q8r1-96, Q2-87, and 1M1-96 did not differ in their ability to suppress take-all. After eight successive growth cycles, however, Q8r1-96 still provided control of take-all to the same level as obtained in the take-all suppressive soil, whereas Q2-87 and 1M1-96 gave no control anymore. Biochemical analyses indicated that the superior rhizosphere competence of Q8r1-96 is not related to in situ DAPG production levels. We postulate that certain rhizobacterial genotypes have evolved a preference for colonization of specific crops. By exploiting diversity of antagonistic rhizobacteria that share a common trait, biological control can be improved significantly.

Existence of various human parvovirus B19 genotypes in Chinese plasma pools: genotype 1, genotype 3, putative intergenotypic recombinant variants and new genotypes.

Science.gov (United States)

Jia, Junting; Ma, Yuyuan; Zhao, Xiong; Huangfu, Chaoji; Zhong, Yadi; Fang, Chi; Fan, Rui; Lv, Maomin; Zhang, Jingang

2016-09-17

Human parvovirus B19 (B19V) is a frequent contaminant of blood and plasma-derived medicinal products. Three distinct genotypes of B19V have been identified. The distribution of the three B19V genotypes has been investigated in various regions or countries. However, in China, data on the existence of different B19V genotypes are limited. One hundred and eighteen B19V-DNA positive source plasma pool samples collected from three Chinese blood products manufacturers were analyzed. The subgenomic NS1/VP1u region junction of B19V was amplified by nested PCR. These amplified products were then cloned and subsequently sequenced. For genotyping, their phylogenetic inferences were constructed based on the NS1/VP1-unique region. Then putative recombination events were analyzed and identified. Phylogenetic analysis of 118 B19V sequences attributed 61.86 % to genotype 1a, 10.17 % to genotype 1b, and 17.80 % to genotype 3b. All the genotype 3b sequences obtained in this study grouped as a specific, closely related cluster with B19V strain D91.1. Four 1a/3b recombinants and 5 new atypical B19V variants with no recombination events were identified. There were at least 3 subtypes (1a, 1b and 3b) of B19V circulating in China. Furthermore, putative B19V 1a/3b recombinants and unclassified strains were identified as well. Such recombinant and unclassified strains may contribute to the genetic diversity of B19V and consequently complicate the B19V infection diagnosis and NAT screening. Further studies will be required to elucidate the biological significance of the recombinant and unclassified strains.

High genotypic diversity of the reef-building coral Porites lobata (Scleractinia: Poritidae in Isla del Coco National Park, Costa Rica

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Jennifer N. Boulay

2012-11-01

Full Text Available The isolated Isla del Coco experiences periodic, extreme disturbances which devastate coral reefs surrounding the island. Scleractinian corals build the physical structure of the reef therefore ecosystem recovery relies on coral species recovery. Coral recruits can be of sexual or asexual origin, and the relative success of the two recruit types influences the speed and spread of recovery processes. Here we focus on the massive coral, Porites lobata, because it is the main reef-builder around Isla del Coco to describe the relative contribution of asexual and sexual recruits to population maintenance. P. lobata samples were collected using a spatially explicit random sampling design in three plots at Isla del Coco: Punta Ulloa (n=17, Bahía Weston (n=20 and Punta María (n=20 and samples were genotyped with 11 microsatellite markers. Additional sampling was conducted at three “coastal” sites near the Costa Rican mainland (Isla del Caño Biological Reserve: Caño1 (n=8, Caño2 (n=10, Caño5 (n=11 to compare the contributions of asexual and sexual recruits at Isla del Coco sites to coastal sites. Isla del Coco sites were characterized by small colony size (>60% of colonies <0.5m2 and high sexual reproduction. Sites were either mostly or entirely sexual,consisting of only unique genotypes (N G/N= 0.90-1.00; G O/G E=0.83-1.00; D=0.99-1.00. Although there were no significant differences in genetic diversity (number of alleles per locus, number of private alleles or colony size between Isla del Coco and the coastal sites, the coastal sites exhibited a greater range of genotypic diversity from moderately asexual (N G/N=0.5; G O/G E=0.36; D=0.8 to purely sexual (N G/N=1.0; G O/G E=1.0; D=1.0. The mode of asexual reproduction in P. lobata is likely fragmentation of adult colonies rather than asexual larval production because ramets of P. lobata occurred close together and asexually produced larvae have not been reported in gonochoric broadcast

Phenotypic Diversity of Sickle Cell Disease in Patients with a Double Heterozygosity for Hb S and Hb D-Punjab.

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Torres, Lidiane S; Okumura, Jéssika V; Belini-Júnior, Édis; Oliveira, Renan G; Nascimento, Patrícia P; Silva, Danilo G H; Lobo, Clarisse L C; Oliani, Sonia M; Bonini-Domingos, Claudia R

2016-09-01

Phenotypic heterogeneity for sickle cell disease is associated to several genetic factors such as genotype for sickle cell disease, β-globin gene cluster haplotypes and Hb F levels. The coinheritance of Hb S (HBB: c.20A > T) and Hb D-Punjab (HBB: c.364G > C) results in a double heterozygosity, which constitutes one of the genotypic causes of sickle cell disease. This study aimed to assess the phenotypic diversity of sickle cell disease presented by carriers of the Hb S/Hb D-Punjab genotype and the Bantu [- + - - - -] haplotype. We evaluated medical records from 12 patients with sickle cell disease whose Hb S/Hb D-Punjab genotype and Bantu haplotype were confirmed by molecular analysis. Hb S and Hb D-Punjab levels were quantified by chromatographic analysis. Mean concentrations of Hb S and Hb D-Punjab were 44.8 ± 2.3% and 43.3 ± 1.8%, respectively. Painful crises were present in eight (66.7%) patients evaluated, representing the most common clinical event. Acute chest syndrome (ACS) was the second most prevalent manifestation, occurring in two individuals (16.7%). Three patients were asymptomatic, while another two exhibited greater diversity of severe clinical manifestations. Medical records here analyzed reported a significant clinical diversity in sickle cell disease ranging from the absence of symptoms to wide phenotypic variety. The sickle cell disease genotype, Bantu haplotype and hemoglobin (Hb) levels did not influence the clinical diversity. Thus, we concluded that the phenotypic variation in sickle cell disease was present within a specific genotype for disease regardless of the β-globin gene cluster haplotypes.

Salt and genotype impact on plant physiology and root proteome variations in tomato.

Science.gov (United States)

Manaa, Arafet; Ben Ahmed, Hela; Valot, Benoît; Bouchet, Jean-Paul; Aschi-Smiti, Samira; Causse, Mathilde; Faurobert, Mireille

2011-05-01

To evaluate the genotypic variation of salt stress response in tomato, physiological analyses and a proteomic approach have been conducted in parallel on four contrasting tomato genotypes. After a 14 d period of salt stress in hydroponic conditions, the genotypes exhibited different responses in terms of plant growth, particularly root growth, foliar accumulation of Na(+), and foliar K/Na ratio. As a whole, Levovil appeared to be the most tolerant genotype while Cervil was the most sensitive one. Roma and Supermarmande exhibited intermediary behaviours. Among the 1300 protein spots reproducibly detected by two-dimensional electrophoresis, 90 exhibited significant abundance variations between samples and were submitted to mass spectrometry for identification. A common set of proteins (nine spots), up- or down-regulated by salt-stress whatever the genotype, was detected. But the impact of the tomato genotype on the proteome variations was much higher than the salt effect: 33 spots that were not variable with salt stress varied with the genotype. The remaining number of variable spots (48) exhibited combined effects of the genotype and the salt factors, putatively linked to the degrees of genotype tolerance. The carbon metabolism and energy-related proteins were mainly up-regulated by salt stress and exhibited most-tolerant versus most-sensitive abundance variations. Unexpectedly, some antioxidant and defence proteins were also down-regulated, while some proteins putatively involved in osmoprotectant synthesis and cell wall reinforcement were up-regulated by salt stress mainly in tolerant genotypes. The results showed the effect of 14 d stress on the tomato root proteome and underlined significant genotype differences, suggesting the importance of making use of genetic variability.

Genetic Diversity of the Hepatitis B Virus Strains in Cuba: Absence of West-African Genotypes despite the Transatlantic Slave Trade

Science.gov (United States)

Rodríguez Lay, Licel A.; Corredor, Marité B.; Villalba, Maria C.; Frómeta, Susel S.; Wong, Meilin S.; Valdes, Lidunka; Samada, Marcia; Sausy, Aurélie; Hübschen, Judith M.; Muller, Claude P.

2015-01-01

Cuba is an HBsAg low-prevalence country with a high coverage of anti-hepatitis B vaccine. Its population is essentially the result of the population mix of Spanish descendants and former African slaves. Information about genetic characteristics of hepatitis B virus (HBV) strains circulating in the country is scarce. The HBV genotypes/subgenotypes, serotypes, mixed infections, and S gene mutations of 172 Cuban HBsAg and HBV-DNA positive patients were determined by direct sequencing and phylogenetic analysis. Phylogenetic analysis of HBV S gene sequences showed a predominance of genotype A (92.4%), subgenotype A2 (84.9%) and A1 (7.6%). Genotype D (7.0%) and subgenotype C1 (0.6%) were also detected but typical (sub)genotypes of contemporary West-Africa (E, A3) were conspicuously absent. All genotype A, D, and C strains exhibited sequence characteristics of the adw2, ayw2, and adrq serotypes, respectively. Thirty-three (19.1%) patients showed single, double, or multiple point mutations inside the Major Hydrophilic domain associated with vaccine escape; eighteen (10.5%) patients had mutations in the T-cell epitope (amino acids 28-51), and there were another 111 point mutations downstream of the S gene. One patient had an HBV A1/A2 mixed infection. This first genetic study of Cuban HBV viruses revealed only strains that were interspersed with strains from particularly Europe, America, and Asia. The absence of genotype E supports previous hypotheses about an only recent introduction of this genotype into the general population in Africa. The presence of well-known vaccine escape (3.5%) and viral resistance mutants (2.9%) warrants strain surveillance to guide vaccination and treatment strategies. PMID:25978398

MIRU-VNTR genotype diversity and indications of homoplasy in M. avium strains isolated from humans and slaughter pigs in Latvia.

Science.gov (United States)

Kalvisa, Adrija; Tsirogiannis, Constantinos; Silamikelis, Ivars; Skenders, Girts; Broka, Lonija; Zirnitis, Agris; Jansone, Inta; Ranka, Renate

2016-09-01

Diseases which are caused by non-tuberculous mycobacteria (NTM) are an increasing problem in the developed countries. In Latvia, one of the most clinically important members of NTM is Mycobacterium avium (M. avium), an opportunistic pathogen which has been isolated from several lung disease patients and tissue samples of slaughter pigs. This study was designed to characterize the genetic diversity of the M. avium isolates in Latvia and to compare the distribution of genotypic patterns among humans and pigs. Eleven (Hall and Salipante, 2010) clinical M. avium samples, isolated from patients of Center of Tuberculosis and Lung Diseases (years 2003-2010), and 32 isolates from pig necrotic mesenterial lymph nodes in different regions (years 2003-2007) were analyzed. The majority (42 of 43) of samples were identified as M. avium subsp. hominissuis; one porcine isolate belonged to M. avium subsp. avium. MIRU-VNTR genotyping revealed 13 distinct genotypes, among which nine genotype patterns, including M. avium subsp. avium isolate, were newly identified. IS1245 RFLP fingerprinting of 25 M. avium subsp. hominissuis samples yielded 17 different IS1245 RFLP patterns, allowing an efficient discrimination of isolates. Clusters of identical RFLP profiles were observed within host species, geographical locations and time frame of several years. Additional in silico analysis on simulated MIRU-VNTR genotype population datasets showed that the MIRU-VNTR pattern similarity could partly arise due to probabilistic increase of acquiring homoplasy among subpopulations, thus the similar MIRU-VNTR profiles of M. avium strains even in close geographical proximity should be interpreted with caution. Copyright © 2016 Elsevier B.V. All rights reserved.

Genetic similarity of soybean genotypes revealed by seed protein

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Nikolić Ana

2005-01-01

Full Text Available More accurate and complete descriptions of genotypes could help determinate future breeding strategies and facilitate introgression of new genotypes in current soybean genetic pool. The objective of this study was to characterize 20 soybean genotypes from the Maize Research Institute "Zemun Polje" collection, which have good agronomic performances, high yield, lodging and drought resistance, and low shuttering by seed proteins as biochemical markers. Seed proteins were isolated and separated by PAA electrophoresis. On the basis of the presence/absence of protein fractions coefficients of similarity were calculated as Dice and Roger and Tanamoto coefficient between pairs of genotypes. The similarity matrix was submitted for hierarchical cluster analysis of un weighted pair group using arithmetic average (UPGMA method and necessary computation were performed using NTSYS-pc program. Protein seed analysis confirmed low level of genetic diversity in soybean. The highest genetic similarity was between genotypes P9272 and Kador. According to obtained results, soybean genotypes were assigned in two larger groups and coefficients of similarity showed similar results. Because of the lack of pedigree data for analyzed genotypes, correspondence with marker data could not be determined. In plant with a narrow genetic base in their gene pool, such as soybean, protein markers may not be sufficient for characterization and study of genetic diversity.

Genotypic and phenotypic diversity of Ralstonia pickettii and Ralstonia insidiosa isolates from clinical and environmental sources including High-purity Water.

LENUS (Irish Health Repository)

Ryan, Michael P

2011-08-30

Abstract Background Ralstonia pickettii is a nosocomial infectious agent and a significant industrial contaminant. It has been found in many different environments including clinical situations, soil and industrial High Purity Water. This study compares the phenotypic and genotypic diversity of a selection of strains of Ralstonia collected from a variety of sources. Results Ralstonia isolates (fifty-nine) from clinical, industrial and environmental origins were compared genotypically using i) Species-specific-PCR, ii) PCR and sequencing of the 16S-23S rRNA Interspatial region (ISR) iii) the fliC gene genes, iv) RAPD and BOX-PCR and v) phenotypically using biochemical testing. The species specific-PCR identified fifteen out of fifty-nine designated R. pickettii isolates as actually being the closely related species R. insidiosa. PCR-ribotyping of the 16S-23S rRNA ISR indicated few major differences between the isolates. Analysis of all isolates demonstrated different banding patterns for both the RAPD and BOX primers however these were found not to vary significantly. Conclusions R. pickettii species isolated from wide geographic and environmental sources appear to be reasonably homogenous based on genotypic and phenotypic characteristics. R. insidiosa can at present only be distinguished from R. pickettii using species specific PCR. R. pickettii and R. insidiosa isolates do not differ significantly phenotypically or genotypically based on environmental or geographical origin.

Diverse Genotypes of Yersinia pestis Caused Plague in Madagascar in 2007.

Science.gov (United States)

Riehm, Julia M; Projahn, Michaela; Vogler, Amy J; Rajerison, Minoaerisoa; Andersen, Genevieve; Hall, Carina M; Zimmermann, Thomas; Soanandrasana, Rahelinirina; Andrianaivoarimanana, Voahangy; Straubinger, Reinhard K; Nottingham, Roxanne; Keim, Paul; Wagner, David M; Scholz, Holger C

2015-06-01

Yersinia pestis is the causative agent of human plague and is endemic in various African, Asian and American countries. In Madagascar, the disease represents a significant public health problem with hundreds of human cases a year. Unfortunately, poor infrastructure makes outbreak investigations challenging. DNA was extracted directly from 93 clinical samples from patients with a clinical diagnosis of plague in Madagascar in 2007. The extracted DNAs were then genotyped using three molecular genotyping methods, including, single nucleotide polymorphism (SNP) typing, multi-locus variable-number tandem repeat analysis (MLVA), and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) analysis. These methods provided increasing resolution, respectively. The results of these analyses revealed that, in 2007, ten molecular groups, two newly described here and eight previously identified, were responsible for causing human plague in geographically distinct areas of Madagascar. Plague in Madagascar is caused by numerous distinct types of Y. pestis. Genotyping method choice should be based upon the discriminatory power needed, expense, and available data for any desired comparisons. We conclude that genotyping should be a standard tool used in epidemiological investigations of plague outbreaks.

Genotype dependant callogenic and morphogenic response of lycopersicon esculentum hybrids

International Nuclear Information System (INIS)

Jatoi, S.A.; Sajid, G.M.; Ahmad, S.; Anwar, R.; Munir, M.

2002-01-01

Leaf explants from field grown F1 hybrids of Lycopersicon esculentum, namely Bornia and Royesta were cultured on MS media containing 5 x 5 diallelic combinations of IAA and Kin at 0, 4, 8, 12 and 16 micro M/l each. Callogenesis, root and shoot regeneration potential of these hybrids were compared on these hormonal regimes. Royesta exhibited better callogenesis response (85%) than Bornia (72%). However, callogenesis on a given hormonal regime was genotype dependant. Root and shoot regeneration was better in case of Bornia than in Royesta. Hybrid Bornia produced shoots much more frequently (6-14%) on many diverse hormonal regimes than Royesta which produced shoots only rarely (5%) on a single hormonal regime. (author)

Genetic diversity among some productive genotypes of tomato ...

African Journals Online (AJOL)

HP

2015-06-03

Jun 3, 2015 ... weight, cluster VIII had highest number of locules per fruit, fruit yield per plant and yield per hectare and cluster XVII was .... Cluster means for yield and quality contributing characters of 60 genotypes of tomato. Cluster lycopene β- ..... Sharma JP, Singh AK, Satesh K, Sanjeev K. (2009). Identification of.

Evaluation of wheat genotypes for salinity tolerance using physiological indices as screening tool

International Nuclear Information System (INIS)

Zafar, S.; Niaz, M.; Kausar, A.

2015-01-01

Salinity is a major threat to world food security, to ensure future food needs of an increasing world population, development of salt tolerant crop varieties are necessary. Effective screening techniques for salinity tolerance would be beneficial in developing high yielding and salt tolerant wheat varieties. In the present study, an attempt for rapid screening of wheat genotypes for salt tolerance was made. Twenty wheat genotypes were evaluated for salinity tolerance under laboratory/green-house conditions using different physiological indices like germination stress tolerance index (GSI), shoot length stress tolerance index (SLSI), root length stress tolerance index (RLSI) , shoot dry biomass stress tolerance index (SDSI). The data was pooled together to different multivariate techniques including correlation and cluster analysis to assess the diversity for salt tolerance in wheat genotypes. Highly significant and positive correlations were found between GSI, SDWSI and RDWSI. Cluster analysis classified 20 genotypes into three divergent groups. The members of first cluster (Abadgharr, Bhakkar-2000, Chakwal-86, Kiran-95, LU-26-S, Margalla-99, Marvi Pak-81, Sarsabaz) exhibited adequate degree of salt tolerance on the basis of various physiological stress tolerance indices, whereas, cluster-2 included genotypes (Bhattai, Pasban-90, Shafaq-2006, Soghat-90) with medium level of salt tolerance and cluster-3 consisted of wheat genotypes (Inqilab-91, Iqbal-2000, Kohistan-97, PARI-73, Punjab-90, Sehar-2006 and Uqab-6) with lower level of salt tolerance and did not perform upto the mark. On the basis of results and scores obtained, indicated that physiological indices can be used as a selection tool for salinity tolerance in wheat. (author)

The influence of 5-HTTLPR transporter genotype on amygdala-subgenual anterior cingulate cortex connectivity in autism spectrum disorder

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Francisco Velasquez

2017-04-01

Full Text Available Social deficits in autism spectrum disorder (ASD are linked to amygdala functioning and functional connection between the amygdala and subgenual anterior cingulate cortex (sACC is involved in the modulation of amygdala activity. Impairments in behavioral symptoms and amygdala activation and connectivity with the sACC seem to vary by serotonin transporter-linked polymorphic region (5-HTTLPR variant genotype in diverse populations. The current preliminary investigation examines whether amygdala-sACC connectivity differs by 5-HTTLPR genotype and relates to social functioning in ASD. A sample of 108 children and adolescents (44 ASD completed an fMRI face-processing task. Youth with ASD and low expressing 5-HTTLPR genotypes showed significantly greater connectivity than youth with ASD and higher expressing genotypes as well as typically developing (TD individuals with both low and higher expressing genotypes, in the comparison of happy vs. baseline faces and happy vs. neutral faces. Moreover, individuals with ASD and higher expressing genotypes exhibit a negative relationship between amygdala-sACC connectivity and social dysfunction. Altered amygdala-sACC coupling based on 5-HTTLPR genotype may help explain some of the heterogeneity in neural and social function observed in ASD. This is the first ASD study to combine genetic polymorphism analyses and functional connectivity in the context of a social task.

Genetic diversity among 16 genotypes of Coffea arabica in the Brazilian cerrado.

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Machado, C M S; Pimentel, N S; Golynsk, A; Ferreira, A; Vieira, H D; Partelli, F L

2017-09-21

For the selection of coffee plants that have favorable characteristics, it is necessary to evaluate variables related to production. Knowledge of the genetic divergence of arabica coffee is of extreme importance, as this knowledge can be associated with plant breeding programs in order to combine genetic divergence with good productive performance. The objective of this study was to evaluate the genetic divergence among 16 genotypes of Coffea arabica with the purpose of identifying the most dissimilar genotypes for the establishment of breeding programs and adaptation to the Brazilian cerrado. The genetic divergence was evaluated using multivariate procedures, the analysis of the average grouping unweighted pair group method with arithmetic mean (UPGMA) and main components in 2013 and 2014. Eight characters were evaluated in an experiment conducted in Morrinhos, Goiás. The presence of genetic divergence among the 16 C. arabica genotypes under cerrado conditions was recorded. The formation of UPGMA groups for the evaluated characteristics was pertinent due to the number of genotypes. The first three major components accounted for 81.77% of the total variance. The genotype H-419-3-4-4-13(C-241) of low size was the most divergent, followed by Catucaí 2 SL and Catiguá MG2, according to the main components.

Genotype-by-environment interactions leads to variable selection on life-history strategy in Common Evening Primrose (Oenothera biennis).

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Johnson, M T J

2007-01-01

Monocarpic plant species, where reproduction is fatal, frequently exhibit variation in the length of their prereproductive period prior to flowering. If this life-history variation in flowering strategy has a genetic basis, genotype-by-environment interactions (G x E) may maintain phenotypic diversity in flowering strategy. The native monocarpic plant Common Evening Primrose (Oenothera biennis L., Onagraceae) exhibits phenotypic variation for annual vs. biennial flowering strategies. I tested whether there was a genetic basis to variation in flowering strategy in O. biennis, and whether environmental variation causes G x E that imposes variable selection on flowering strategy. In a field experiment, I randomized more than 900 plants from 14 clonal families (genotypes) into five distinct habitats that represented a natural productivity gradient. G x E strongly affected the lifetime fruit production of O. biennis, with the rank-order in relative fitness of genotypes changing substantially between habitats. I detected genetic variation in annual vs. biennial strategies in most habitats, as well as a G x E effect on flowering strategy. This variation in flowering strategy was correlated with genetic variation in relative fitness, and phenotypic and genotypic selection analyses revealed that environmental variation resulted in variable directional selection on annual vs. biennial strategies. Specifically, a biennial strategy was favoured in moderately productive environments, whereas an annual strategy was favoured in low-productivity environments. These results highlight the importance of variable selection for the maintenance of genetic variation in the life-history strategy of a monocarpic plant.

Genomic diversity among drug sensitive and multidrug resistant isolates of Mycobacterium tuberculosis with identical DNA fingerprints.

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Stefan Niemann

2009-10-01

Full Text Available Mycobacterium tuberculosis complex (MTBC, the causative agent of tuberculosis (TB, is characterized by low sequence diversity making this bacterium one of the classical examples of a genetically monomorphic pathogen. Because of this limited DNA sequence variation, routine genotyping of clinical MTBC isolates for epidemiological purposes relies on highly discriminatory DNA fingerprinting methods based on mobile and repetitive genetic elements. According to the standard view, isolates exhibiting the same fingerprinting pattern are considered direct progeny of the same bacterial clone, and most likely reflect ongoing transmission or disease relapse within individual patients.Here we further investigated this assumption and used massively parallel whole-genome sequencing to compare one drug-susceptible (K-1 and one multidrug resistant (MDR isolate (K-2 of a rapidly spreading M. tuberculosis Beijing genotype clone from a high incidence region (Karakalpakstan, Uzbekistan. Both isolates shared the same IS6110 RFLP pattern and the same allele at 23 out of 24 MIRU-VNTR loci. We generated 23.9 million (K-1 and 33.0 million (K-2 paired 50 bp purity filtered reads corresponding to a mean coverage of 483.5 fold and 656.1 fold respectively. Compared with the laboratory strain H37Rv both Beijing isolates shared 1,209 SNPs. The two Beijing isolates differed by 130 SNPs and one large deletion. The susceptible isolate had 55 specific SNPs, while the MDR variant had 75 specific SNPs, including the five known resistance-conferring mutations.Our results suggest that M. tuberculosis isolates exhibiting identical DNA fingerprinting patterns can harbour substantial genomic diversity. Because this heterogeneity is not captured by traditional genotyping of MTBC, some aspects of the transmission dynamics of tuberculosis could be missed or misinterpreted. Furthermore, a valid differentiation between disease relapse and exogenous reinfection might be impossible using

Genomic diversity among drug sensitive and multidrug resistant isolates of Mycobacterium tuberculosis with identical DNA fingerprints.

Science.gov (United States)

Niemann, Stefan; Köser, Claudio U; Gagneux, Sebastien; Plinke, Claudia; Homolka, Susanne; Bignell, Helen; Carter, Richard J; Cheetham, R Keira; Cox, Anthony; Gormley, Niall A; Kokko-Gonzales, Paula; Murray, Lisa J; Rigatti, Roberto; Smith, Vincent P; Arends, Felix P M; Cox, Helen S; Smith, Geoff; Archer, John A C

2009-10-12

Mycobacterium tuberculosis complex (MTBC), the causative agent of tuberculosis (TB), is characterized by low sequence diversity making this bacterium one of the classical examples of a genetically monomorphic pathogen. Because of this limited DNA sequence variation, routine genotyping of clinical MTBC isolates for epidemiological purposes relies on highly discriminatory DNA fingerprinting methods based on mobile and repetitive genetic elements. According to the standard view, isolates exhibiting the same fingerprinting pattern are considered direct progeny of the same bacterial clone, and most likely reflect ongoing transmission or disease relapse within individual patients. Here we further investigated this assumption and used massively parallel whole-genome sequencing to compare one drug-susceptible (K-1) and one multidrug resistant (MDR) isolate (K-2) of a rapidly spreading M. tuberculosis Beijing genotype clone from a high incidence region (Karakalpakstan, Uzbekistan). Both isolates shared the same IS6110 RFLP pattern and the same allele at 23 out of 24 MIRU-VNTR loci. We generated 23.9 million (K-1) and 33.0 million (K-2) paired 50 bp purity filtered reads corresponding to a mean coverage of 483.5 fold and 656.1 fold respectively. Compared with the laboratory strain H37Rv both Beijing isolates shared 1,209 SNPs. The two Beijing isolates differed by 130 SNPs and one large deletion. The susceptible isolate had 55 specific SNPs, while the MDR variant had 75 specific SNPs, including the five known resistance-conferring mutations. Our results suggest that M. tuberculosis isolates exhibiting identical DNA fingerprinting patterns can harbour substantial genomic diversity. Because this heterogeneity is not captured by traditional genotyping of MTBC, some aspects of the transmission dynamics of tuberculosis could be missed or misinterpreted. Furthermore, a valid differentiation between disease relapse and exogenous reinfection might be impossible using standard

Hepatitis B virus genotypes circulating in Brazil: molecular characterization of genotype F isolates

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Virgolino Helaine A

2007-11-01

Full Text Available Abstract Background Hepatitis B virus (HBV isolates have been classified in eight genotypes, A to H, which exhibit distinct geographical distributions. Genotypes A, D and F are predominant in Brazil, a country formed by a miscegenated population, where the proportion of individuals from Caucasian, Amerindian and African origins varies by region. Genotype F, which is the most divergent, is considered indigenous to the Americas. A systematic molecular characterization of HBV isolates from different parts of the world would be invaluable in establishing HBV evolutionary origins and dispersion patterns. A large-scale study is needed to map the region-by-region distribution of the HBV genotypes in Brazil. Results Genotyping by PCR-RFLP of 303 HBV isolates from HBsAg-positive blood donors showed that at least two of the three genotypes, A, D, and F, co-circulate in each of the five geographic regions of Brazil. No other genotypes were identified. Overall, genotype A was most prevalent (48.5%, and most of these isolates were classified as subgenotype A1 (138/153; 90.2%. Genotype D was the most common genotype in the South (84.2% and Central (47.6% regions. The prevalence of genotype F was low (13% countrywide. Nucleotide sequencing of the S gene and a phylogenetic analysis of 32 HBV genotype F isolates showed that a great majority (28/32; 87.5% belonged to subgenotype F2, cluster II. The deduced serotype of 31 of 32 F isolates was adw4. The remaining isolate showed a leucine-to-isoleucine substitution at position 127. Conclusion The presence of genotypes A, D and F, and the absence of other genotypes in a large cohort of HBV infected individuals may reflect the ethnic origins of the Brazilian population. The high prevalence of isolates from subgenotype A1 (of African origin indicates that the African influx during the colonial slavery period had a major impact on the circulation of HBV genotype A currently found in Brazil. Although most genotype F

Genetic diversity of Toxoplasma gondii isolates in Egyptian feral cats reveals new genotypes.

Science.gov (United States)

Al-Kappany, Y M; Rajendran, C; Abu-Elwafa, S A; Hilali, M; Su, C; Dubey, J P

2010-12-01

Cats are important in the epidemiology of Toxoplasma gondii because they are the only hosts that excrete environmentally resistant oocysts in feces. In the present study, 115 viable T. gondii isolates from tissues of cats from Egypt were genotyped using 10 PCR-restriction fragment length polymorphism markers (SAG1, SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1, and Apico) and DNA from tachyzoites. Seven genotypes were recognized including the clonal Type II, Type III (2 genotypes), and 4 atypical genotypes. Ninety percent (103 of 115) of isolates were clonal, i.e., Type II (n  =  61) and Type III (n  =  42) strains. Of the 61 Type II strains, all had the Type II alleles at all loci, except for 2 strains that had allele I at Apico. Eight isolates were divided into 4 atypical genotypes. One of these genotypes (with 4 isolates) was previously reported in dogs from Sri Lanka and in sand cats from the United Arab Emirates. Four isolates had mixed infections. These results revealed a strong clonal population structure with the dominance of clonal Type II and III lineages of T. gondii in feral cats from Egypt.

Probing genetic diversity to characterize red rot resistance in sugarcane

Energy Technology Data Exchange (ETDEWEB)

Mumtaz, A S; Dure-e-Nayab,; Iqbal, M J; Shinwari, Z.K., E-mail: asmumtaz@qau.edu.pk

2011-10-15

Genetic diversity was assessed in a set of twelve sugarcane genotypes using Random Amplified Polymorphic DNA (RAPD). A total of thirty-two oligo-primers were employed, sixteen of them revealed amplification at 149 loci, out of which 136 were polymorphic. The genotype SPSG-26 showed the highest number of polymorphic loci, followed by CSSG-668 and HSF-242. Pairwise genetic similarity ranged from 67.2% to 83.3%. The UPGMA cluster analysis resolved most of the accessions in two groups. The clustering pattern did not place all resistant varieties in one or related group which depict diverse resistance source in the present set of sugarcane varieties. Ten primers revealed genotype specific bands among which four primers (K07, H02, K10 and F01) produced multiple genotype specific bands that aid genotype identification especially those with red rot resistance. The present study not only provided information on the genetic diversity among the genotypes but also revealed the potential of RAPD-PCR markers for genotype identification and therefore could be utilized in marker assisted selection for red rot resistance in sugarcane. (author)

Genotype-specific responses to light stress in eelgrass Zostera marina, a marine foundation plant

DEFF Research Database (Denmark)

Salo, Tiina Elina; Reusch, Thorsten B. H.

2015-01-01

, and their performance during light limitation and 4 wk of recovery was compared to non-shaded controls. In addition to growth and biomass, we investigated storage carbohydrates and quantified the expression of genes involved in carbohydrate metabolism, photosynthesis and control of oxidative stress. Plants showed......Within mono-specific meadows of clonal plants, genotypic diversity may functionally replace species diversity. Little is known about the variability in performance and plasticity of different genotypes towards anthropogenically induced stressors. In this field experiment we compared light......-limitation stress responses and recovery of different eelgrass Zostera marina genotypes to assess the variability in phenotypic plasticity and gene expression between different genotypes. Replicated monoculture plots of 4 genotypes were subjected to a simulated turbidity period of 4 wk using shading screens...

The population genetics of Pseudomonas aeruginosa isolates from different patient populations exhibits high-level host specificity.

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Rosa van Mansfeld

Full Text Available OBJECTIVE: To determine whether highly prevalent P. aeruginosa sequence types (ST in Dutch cystic fibrosis (CF patients are specifically linked to CF patients we investigated the population structure of P. aeruginosa from different clinical backgrounds. We first selected the optimal genotyping method by comparing pulsed-field gel electrophoresis (PFGE, multilocus sequence typing (MLST and multilocus variable number tandem-repeat analysis (MLVA. METHODS: Selected P. aeruginosa isolates (n = 60 were genotyped with PFGE, MLST and MLVA to determine the diversity index (DI and congruence (adjusted Rand and Wallace coefficients. Subsequently, isolates from patients admitted to two different ICUs (n = 205, from CF patients (n = 100 and from non-ICU, non-CF patients (n = 58, of which 19 were community acquired were genotyped with MLVA to determine distribution of genotypes and genetic diversity. RESULTS: Congruence between the typing methods was >79% and DIs were similar and all >0.963. Based on costs, ease, speed and possibilities to compare results between labs an adapted MLVA scheme called MLVA9-Utrecht was selected as the preferred typing method. In 363 clinical isolates 252 different MLVA types (MTs were identified, indicating a highly diverse population (DI  = 0.995; CI  = 0.993-0.997. DI levels were similarly high in the diverse clinical sources (all >0.981 and only eight genotypes were shared. MTs were highly specific (>80% for the different patient populations, even for similar patient groups (ICU patients in two distinct geographic regions, with only three of 142 ICU genotypes detected in both ICUs. The two major CF clones were unique to CF patients. CONCLUSION: The population structure of P. aeruginosa isolates is highly diverse and population specific without evidence for a core lineage in which major CF, hospital or community clones co-cluster. The two genotypes highly prevalent among Dutch CF patients appeared unique to CF patients

Comparative ultrastructure of fruit plastids in three genetically diverse genotypes of apple (Malus × domestica Borkh.) during development.

Science.gov (United States)

Schaeffer, Scott M; Christian, Ryan; Castro-Velasquez, Nohely; Hyden, Brennan; Lynch-Holm, Valerie; Dhingra, Amit

2017-10-01

Comparative ultrastructural developmental time-course analysis has identified discrete stages at which the fruit plastids undergo structural and consequently functional transitions to facilitate subsequent development-guided understanding of the complex plastid biology. Plastids are the defining organelle for a plant cell and are critical for myriad metabolic functions. The role of leaf plastid, chloroplast, is extensively documented; however, fruit plastids-chromoplasts-are poorly understood, especially in the context of the diverse metabolic processes operating in these diverse plant organs. Recently, in a comparative study of the predicted plastid-targeted proteomes across seven plant species, we reported that each plant species is predicted to harbor a unique set of plastid-targeted proteins. However, the temporal and developmental context of these processes remains unknown. In this study, an ultrastructural analysis approach was used to characterize fruit plastids in the epidermal and collenchymal cell layers at 11 developmental timepoints in three genotypes of apple (Malus × domestica Borkh.): chlorophyll-predominant 'Granny Smith', carotenoid-predominant 'Golden Delicious', and anthocyanin-predominant 'Top Red Delicious'. Plastids transitioned from a proplastid-like plastid to a chromoplast-like plastid in epidermis cells, while in the collenchyma cells, they transitioned from a chloroplast-like plastid to a chloro-chromo-amyloplast plastid. Plastids in the collenchyma cells of the three genotypes demonstrated a diverse array of structures and features. This study enabled the identification of discrete developmental stages during which specific functions are most likely being performed by the plastids as indicated by accumulation of plastoglobuli, starch granules, and other sub-organeller structures. Information regarding the metabolically active developmental stages is expected to facilitate biologically relevant omics studies to unravel the complex

Diversity of dengue virus-3 genotype III in Jeddah, Saudi Arabia.

Science.gov (United States)

Hashem, Anwar M; Sohrab, Sayed S; El-Kafrawy, Sherif A; Abd-Alla, Adly M M; El-Ela, Saeid Abo; Abujamel, Turki S; Hassan, Ahmed M; Farraj, Suha A; Othman, Noura A; Charrel, Remi N; Azhar, Esam I

2018-07-01

Dengue is the most important arboviral disease in tropical and subtropical countries. Dispersal of the vector and an increase in migratory flow between countries have led to large epidemics and severe clinical outcomes. Over the past 20 years, dengue epidemics have become more wide-spread and frequent. Previous studies have shown that dengue is endemic in Jeddah, Makkah and Al-Madinah in western Saudi Arabia as well as in Jazan region in the southern part of the country. The four serotypes of dengue virus (DENV) have been reported from western Saudi Arabia. It has been suggested that pilgrims could play a significant and unique role in DENV-1 and DENV-2 introduction into Saudi Arabia, especially in the cities of Jeddah, Makkah and Al-Madinah during Hajj and Umrah seasons. However, only limited data on DENV-3 in Saudi Arabia are available. All available DENV-3 sequences published and unpublished from Saudi Arabia and other countries were retrieved from Genbank and gene sequence repository and phylogenetically analyzed to examine the diversity of DENV-3 into the city of Jeddah. Based on the analysis of the envelope gene and non-structural 1 (E/NS1) junction sequences, we show that there were at least four independent introductions of DENV-3, all from genotype III into Jeddah. The first introduction was most probably before 1997 as Saudi virus isolates from 1997 formed a cluster without any close relationship to other globally circulating isolates, suggesting their local circulation from previous introduction events. Two introductions were most probably in 2004 with isolates closely-related to isolates from Africa and India (Asia), in addition to another introduction in 2014 with isolates clustering with those from Singapore (Asia). Our data shows that only genotype III isolates of DENV-3 are circulating in Jeddah and highlights the potential role of pilgrims in DENV-3 importation into western Saudi Arabia and subsequent exportation to their home countries during Hajj

Functional diversity exhibits a diverse relationship with area, even a decreasing one

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Karadimou, Elpida K.; Kallimanis, Athanasios S.; Tsiripidis, Ioannis; Dimopoulos, Panayotis

2016-01-01

The relationship between species richness and area is one of the few well-established laws in ecology, and one might expect a similar relationship with functional diversity (FD). However, only a few studies investigate the relationship between trait-based FD and area, the Functional Diversity - Area Relationship (FDAR). To examine FDAR, we constructed the species accumulation curve and the corresponding FD curve. We used plant diversity data from nested plots (1–128 m2), recorded on the Volcanic islands of Santorini Archipelagos, Greece. Six multidimensional FD indices were calculated using 26 traits. We identified a typology of FDARs depending on the facet of FD analyzed: (A) strongly positive for indices quantifying the range of functional traits in the community, (B) negative correlation for indices quantifying the evenness in the distribution of abundance in the trait space, (C) no clear pattern for indices reflecting the functional similarity of species and (D) idiosyncratic patterns with area for functional divergence. As area increases, the range of traits observed in the community increases, but the abundance of traits does not increase proportionally and some traits become dominant, implying a reliance on some functions that may be located in either the center or the periphery of the trait space. PMID:27752086

Evolution and Diversity in Human Herpes Simplex Virus Genomes

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Gatherer, Derek; Ochoa, Alejandro; Greenbaum, Benjamin; Dolan, Aidan; Bowden, Rory J.; Enquist, Lynn W.; Legendre, Matthieu; Davison, Andrew J.

2014-01-01

Herpes simplex virus 1 (HSV-1) causes a chronic, lifelong infection in >60% of adults. Multiple recent vaccine trials have failed, with viral diversity likely contributing to these failures. To understand HSV-1 diversity better, we comprehensively compared 20 newly sequenced viral genomes from China, Japan, Kenya, and South Korea with six previously sequenced genomes from the United States, Europe, and Japan. In this diverse collection of passaged strains, we found that one-fifth of the newly sequenced members share a gene deletion and one-third exhibit homopolymeric frameshift mutations (HFMs). Individual strains exhibit genotypic and potential phenotypic variation via HFMs, deletions, short sequence repeats, and single-nucleotide polymorphisms, although the protein sequence identity between strains exceeds 90% on average. In the first genome-scale analysis of positive selection in HSV-1, we found signs of selection in specific proteins and residues, including the fusion protein glycoprotein H. We also confirmed previous results suggesting that recombination has occurred with high frequency throughout the HSV-1 genome. Despite this, the HSV-1 strains analyzed clustered by geographic origin during whole-genome distance analysis. These data shed light on likely routes of HSV-1 adaptation to changing environments and will aid in the selection of vaccine antigens that are invariant worldwide. PMID:24227835

Phenotypic diversity of basic characteristics of genotypes from the Serbia onion collection

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Gvozdanović-Varga Jelica

2013-01-01

Full Text Available The onion is a widely distributed vegetable crop, which takes an important place in the vegetable production in Serbia. The traditional planting method is the one from sets. Old cultivars and populations and, in recent years, foreign cultivars are grown. The large variety of genotypes, including both domestic populations and cultivars, comprises the significant gene pool of this region. The onion collection of the Institute of Field and Vegetable Crops in Novi Sad is based on the populations and cultivars from the territory of the former Yugoslavia. This paper reviews 30 onion genotypes on the basic IPGRI descriptors (ANNEX I. Variability of the reviewed characteristics was determined by PC analysis. High variability values have been established for bulb skin color, bulb flesh color, bulb hearting and bulb skin thickness. The genotypes varied in bulb skin color as well as in bulb flesh color from white to dark violet. These two characteristics had the largest impact on clustering, with a single genotype being heterogeneous exactly for these two characteristics. [Projekat Ministarstva nauke Republike Srbije, br. TR 31030

Warfarin Pharmacogenomics in Diverse Populations.

Science.gov (United States)

Kaye, Justin B; Schultz, Lauren E; Steiner, Heidi E; Kittles, Rick A; Cavallari, Larisa H; Karnes, Jason H

2017-09-01

Genotype-guided warfarin dosing algorithms are a rational approach to optimize warfarin dosing and potentially reduce adverse drug events. Diverse populations, such as African Americans and Latinos, have greater variability in warfarin dose requirements and are at greater risk for experiencing warfarin-related adverse events compared with individuals of European ancestry. Although these data suggest that patients of diverse populations may benefit from improved warfarin dose estimation, the vast majority of literature on genotype-guided warfarin dosing, including data from prospective randomized trials, is in populations of European ancestry. Despite differing frequencies of variants by race/ethnicity, most evidence in diverse populations evaluates variants that are most common in populations of European ancestry. Algorithms that do not include variants important across race/ethnic groups are unlikely to benefit diverse populations. In some race/ethnic groups, development of race-specific or admixture-based algorithms may facilitate improved genotype-guided warfarin dosing algorithms above and beyond that seen in individuals of European ancestry. These observations should be considered in the interpretation of literature evaluating the clinical utility of genotype-guided warfarin dosing. Careful consideration of race/ethnicity and additional evidence focused on improving warfarin dosing algorithms across race/ethnic groups will be necessary for successful clinical implementation of warfarin pharmacogenomics. The evidence for warfarin pharmacogenomics has a broad significance for pharmacogenomic testing, emphasizing the consideration of race/ethnicity in discovery of gene-drug pairs and development of clinical recommendations for pharmacogenetic testing. © 2017 Pharmacotherapy Publications, Inc.

Genetic Diversity of Plasmodium falciparum Field Isolates in Central Sudan Inferred by PCR Genotyping of Merozoite Surface Protein 1 and 2.

Science.gov (United States)

Hamid, Muzamil M Abdel; Mohammed, Sara B; El Hassan, Ibrahim M

2013-02-01

Characterization of Plasmodium falciparum diversity is commonly achieved by amplification of the polymorphic regions of the merozoite surface proteins 1 (MSP1) and 2 (MSP2) genes. The present study aimed to determine the allelic variants distribution of MSP1 and MSP2 and multiplicity of infection in P. falciparum field isolates from Kosti, central Sudan, an area characterized by seasonal malaria transmission. Total 121 samples (N = 121) were collected during a cross-sectional survey between March and April 2003. DNA was extracted and MSP1 and MSP2 polymorphic loci were genotyped. The total number of alleles identified in MSP1 block 2 was 11, while 16 alleles were observed in MSP2 block 3. In MSP1, RO33 was found to be the predominant allelic type, carried alone or in combination with MAD20 and K1 types, whereas FC27 family was the most prevalent in MSP2. Sixty two percent of isolates had multiple genotypes and the overall mean multiplicity of infection was 1.93 (CI 95% 1.66-2.20). Age correlated with parasite density (P = 0.017). In addition, a positive correlation was observed between parasite densities and the number of alleles (P = 0.022). Genetic diversity in P. falciparum field isolates in central Sudan was high and consisted of multiple clones.

Characterizing bread wheat genotypes of Pakistani origin for grain zinc biofortification potential.

Science.gov (United States)

Rehman, Abdul; Farooq, Muhammad; Nawaz, Ahmad; Al-Sadi, Abdullah M; Al-Hashmi, Khalid S; Nadeem, Faisal; Ullah, Aman

2018-03-15

Zinc (Zn) is essential for all life forms and its deficiency is a major issue of malnutrition in humans. This study was carried out to characterize 28 wheat genotypes of Pakistani origin for grain zinc biofortification potential, genetic diversity and relatedness. There was low genetic differentiation among the tested genotypes. However, they differed greatly in yield-related traits, grain mineral (Zn, calcium (Ca) and protein) concentrations and Zn bioavailability. Zinc application increased the concentration of Zn in wheat grain (32.1%), embryo (19.8%), aleurone (47%) and endosperm (23.7%), with an increase in bioavailable Zn (22.2%) and a reduction in phytate concentration (6.8%). Application of Zn also enhanced grain protein and Ca concentrations. Among wheat genotypes, Blue Silver had the highest concentration of Zn in grain, embryo, aleurone and endosperm, with high bioavailable Zn, while Kohinoor-83 had low phytate concentration. Wheat genotypes of Pakistan are genetically less diverse owing to continuous focus on the development of high-yielding varieties only. Therefore genetically diverse wheat genotypes with high endospermic Zn concentration and better grain yield should be used in breeding programs approaches, aiming at improving Zn bioavailability. © 2018 Society of Chemical Industry. © 2018 Society of Chemical Industry.

Genotyping of Coxiella burnetii from domestic ruminants in northern Spain

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Astobiza Ianire

2012-12-01

Full Text Available Abstract Background Information on the genotypic diversity of Coxiella burnetii isolates from infected domestic ruminants in Spain is limited. The aim of this study was to identify the C. burnetii genotypes infecting livestock in Northern Spain and compare them to other European genotypes. A commercial real-time PCR targeting the IS1111a insertion element was used to detect the presence of C. burnetii DNA in domestic ruminants from Spain. Genotypes were determined by a 6-loci Multiple Locus Variable number tandem repeat analysis (MLVA panel and Multispacer Sequence Typing (MST. Results A total of 45 samples from 4 goat herds (placentas, N = 4, 12 dairy cattle herds (vaginal mucus, individual milk, bulk tank milk, aerosols, N = 20 and 5 sheep flocks (placenta, vaginal swabs, faeces, air samples, dust, N = 21 were included in the study. Samples from goats and sheep were obtained from herds which had suffered abortions suspected to be caused by C. burnetii, whereas cattle samples were obtained from animals with reproductive problems compatible with C. burnetii infection, or consisted of bulk tank milk (BTM samples from a Q fever surveillance programme. C. burnetii genotypes identified in ruminants from Spain were compared to those detected in other countries. Three MLVA genotypes were found in 4 goat farms, 7 MLVA genotypes were identified in 12 cattle herds and 4 MLVA genotypes were identified in 5 sheep flocks. Clustering of the MLVA genotypes using the minimum spanning tree method showed a high degree of genetic similarity between most MLVA genotypes. Overall 11 different MLVA genotypes were obtained corresponding to 4 different MST genotypes: MST genotype 13, identified in goat, sheep and cattle from Spain; MST genotype 18, only identified in goats; and, MST genotypes 8 and 20, identified in small ruminants and cattle, respectively. All these genotypes had been previously identified in animal and human clinical samples from several

Structural characterization of alkaline hydrogen peroxide pretreated grasses exhibiting diverse lignin phenotypes

Science.gov (United States)

2012-01-01

Background For cellulosic biofuels processes, suitable characterization of the lignin remaining within the cell wall and correlation of quantified properties of lignin to cell wall polysaccharide enzymatic deconstruction is underrepresented in the literature. This is particularly true for grasses which represent a number of promising bioenergy feedstocks where quantification of grass lignins is particularly problematic due to the high fraction of p-hydroxycinnamates. The main focus of this work is to use grasses with a diverse range of lignin properties, and applying multiple lignin characterization platforms, attempt to correlate the differences in these lignin properties to the susceptibility to alkaline hydrogen peroxide (AHP) pretreatment and subsequent enzymatic deconstruction. Results We were able to determine that the enzymatic hydrolysis of cellulose to to glucose (i.e. digestibility) of four grasses with relatively diverse lignin phenotypes could be correlated to total lignin content and the content of p-hydroxycinnamates, while S/G ratios did not appear to contribute to the enzymatic digestibility or delignification. The lignins of the brown midrib corn stovers tested were significantly more condensed than a typical commercial corn stover and a significant finding was that pretreatment with alkaline hydrogen peroxide increases the fraction of lignins involved in condensed linkages from 88–95% to ~99% for all the corn stovers tested, which is much more than has been reported in the literature for other pretreatments. This indicates significant scission of β-O-4 bonds by pretreatment and/or induction of lignin condensation reactions. The S/G ratios in grasses determined by analytical pyrolysis are significantly lower than values obtained using either thioacidolysis or 2DHSQC NMR due to presumed interference by ferulates. Conclusions It was found that grass cell wall polysaccharide hydrolysis by cellulolytic enzymes for grasses exhibiting a diversity of

Structural characterization of alkaline hydrogen peroxide pretreated grasses exhibiting diverse lignin phenotypes

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Li Muyang

2012-06-01

exhibiting a diversity of lignin structures and compositions could be linked to quantifiable changes in the composition of the cell wall and properties of the lignin including apparent content of the p-hydroxycinnamates while the limitations of S/G estimation in grasses is highlighted.

Protein landmarks for diversity assessment in wheat genotypes

African Journals Online (AJOL)

jai ganesha

2013-07-17

Jul 17, 2013 ... of genetic diversity in wheat has been on differences in morphological and ... glutenins, are the main components of gluten, which is the main contributor to the .... However, there was no within variety diversity observed as a ...

DQ High genotypic diversity among methicillin-resistant Staphylococcus pseudintermedius isolated from canine infections in Denmark

DEFF Research Database (Denmark)

Damborg, Peter; Moodley, Arshnee; Aalbaek, Bent

2016-01-01

genotypic diversity and antimicrobial resistance of clinical MRSP isolates obtained from dogs, including dogs sampled on multiple occasions, in Denmark over a six-year period. For that purpose a total of 46 clinical MRSP isolates obtained from 36 dogs between 2009 and 2014 were subjected to antimicrobial...... susceptibility testing, multilocus-sequence typing (MLST) and SCCmec typing. Results: Twenty-three sequence types were identified with ST71, mostly associated with SCCmec II-III, as the most common occurring in 13 dogs. Among the remaining 33 isolates, 19 belonged to clonal complex (CC) 258 comprising ST258...... resistant and almost all CC258 isolates being susceptible. Sixteen of the 19 CC258 isolates had oxacillin MICs of 0.5 g/L, whereas MICs for CC71 isolates were consistently above 4 g/L. Four of five dogs representing multiple isolates had distinct STs on different sampling events. Conclusions: The overall...

Phosphorus use efficiency in pima cotton (Gossypium barbadense L. genotypes

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Elcio Santos

2015-06-01

Full Text Available In the Brazilian Cerrado, P deficiency restricts cotton production, which requires large amounts of phosphate fertilizer. To improve the yield of cotton crops, genotypes with high P use efficiency must be identified and used. The present study evaluated P uptake and use efficiency of different Gossypium barbadense L. genotypes grown in the Cerrado. The experiment was carried out in a greenhouse with a completely randomized design, 15 x 2 factorial treatment structure (15 genotypes x 2 P levels, and four replicates. The genotypes were MT 69, MT 70, MT 87, MT 91, MT 92, MT 94, MT 101, MT 102, MT 103, MT 105, MT 106, MT 110, MT 112, MT 124, and MT 125; P levels were sufficient (1000 mg pot-1, PS treatment or deficient (PD treatment. Dry matter (DM and P levels were determined in cotton plant parts and used to calculate plant P content and use efficiency. In general, DM and P content were higher in the PS than in the PD treatment, with the exception of root DM and total DM in some genotypes. Genotypes also differed in terms of P uptake and use capacity. In the PS treatment, genotypes MT 92 and MT 102 had the highest response to phosphate fertilization. Genotype MT 69 exhibited the most efficient P uptake in the PD treatment. Genotype MT 124 showed the best shoot physiological efficiency, apparent recovery efficiency, and utilization efficiency, whereas MT 110 exhibited the highest root physiological efficiency.

Diversity of genotypes in CTX-M-producing Klebsiella pneumoniae isolated in different hospitals in Brazil

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Thiago Pavoni Gomes Chagas

Full Text Available OBJECTIVE: The present study was undertaken to characterize CTX-M ESBL-producing Klebsiella pneumoniae collected from hospitals in different cities of Brazil. MATERIAL AND METHODS: Eighty-five K. pneumoniae strains isolated from hospitalized patients in six different hospitals of three cities of Brazil were analyzed. ESBL production was confirmed by the standard double-disk synergy test and the Etest®. The MIC50 and MIC90 for ESBL-producing isolates were determined by the Etest® method. The antimicrobial susceptibilities of bacterial isolates were determined using the agar diffusion method according to the CLSI. Screening for blaTEM, blaSHV, blaCTX-M genes and class 1 integron was performed by PCR amplification. To determine the genomic diversity of CTX-M-producers, isolates were analyzed by macrorestriction profile analysis following PFGE. RESULTS AND DISCUSSION: Seventy-one K. pneumoniae isolates were ESBL-producing. PCR and sequencing experiments detected 38 CTX-M-producing K. pneumoniae belonged to groups CTX-M 1, CTX-M 2, CTX-M 8 and CTX-M 9. The association of different types ESBL (CTX-M, SHV and TEM was frequent. All K. pneumoniae isolates carried class 1 integron. PFGE analysis revealed thirty-one clonal types among CTX-M-producing isolates. The data presented herein illustrate the diversity of genotypes of CTX-M producing K. pneumoniae among Brazilians hospitals.

Relationship between Trypanosoma brucei rhodesiense genetic diversity and clinical spectrum among sleeping sickness patients in Uganda.

Science.gov (United States)

Kato, Charles D; Mugasa, Claire M; Nanteza, Ann; Matovu, Enock; Alibu, Vincent P

2017-10-27

Human African trypanosomiasis (HAT) due to Trypanosoma brucei rhodesiense in East and southern Africa is reported to be clinically diverse. We tested the hypothesis that this clinical diversity is associated with a variation in trypanosome genotypes. Trypanosome DNA isolated from HAT patients was genotyped using 7 microsatellite markers directly from blood spotted FTA cards following a whole genome amplification. All markers were polymorphic and identified 17 multi-locus genotypes with 56% of the isolates having replicate genotypes. We did not observe any significant clustering between isolates and bootstrap values across major tree nodes were insignificant. When genotypes were compared among patients with varying clinical presentation or outcome, replicate genotypes were observed at both extremes showing no significant association between genetic diversity and clinical outcome. Our study shows that T. b. rhodesiense isolates are homogeneous within a focus and that observed clinical diversity may not be associated with parasite genetic diversity. Other factors like host genetics and environmental factors might be involved in determining clinical diversity. Our study may be important in designing appropriate control measures that target the parasite.

Assessment of Genetic Variation and Population Structure of Diverse Rice Genotypes Adapted to Lowland and Upland Ecologies in Africa Using SNPs

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Marie Noelle Ndjiondjop

2018-04-01

Full Text Available Using interspecific crosses involving Oryza glaberrima Steud. as donor and O. sativa L. as recurrent parents, rice breeders at the Africa Rice Center developed several ‘New Rice for Africa (NERICA’ improved varieties. A smaller number of interspecific and intraspecific varieties have also been released as ‘Advanced Rice for Africa (ARICA’. The objective of the present study was to investigate the genetic variation, relatedness, and population structure of 330 widely used rice genotypes in Africa using DArTseq-based single nucleotide polymorphisms (SNPs. A sample of 11 ARICAs, 85 NERICAs, 62 O. sativa spp. japonica, and 172 O. sativa spp. indica genotypes were genotyped with 27,560 SNPs using diversity array technology (DArT-based sequencing (DArTseq platform. Nearly 66% of the SNPs were polymorphic, of which 15,020 SNPs were mapped to the 12 rice chromosomes. Genetic distance between pairs of genotypes that belong to indica, japonica, ARICA, and NERICA varied from 0.016 to 0.623, from 0.020 to 0.692, from 0.075 to 0.763, and from 0.014 to 0.644, respectively. The proportion of pairs of genotypes with genetic distance > 0.400 was the largest within NERICAs (35.1% of the pairs followed by ARICAs (18.2%, japonica (17.4%, and indica (5.6%. We found one pair of japonica, 11 pairs of indica, and 35 pairs of NERICA genotypes differing by <2% of the total scored alleles, which was due to 26 pairs of genotypes with identical pedigrees. Cluster analysis, principal component analysis, and the model-based population structure analysis all revealed two distinct groups corresponding to the lowland (primarily indica and lowland NERICAs and upland (japonica and upland NERICAs growing ecologies. Most of the interspecific lowland NERICAs formed a sub-group, likely caused by differences in the O. glaberrima genome as compared with the indica genotypes. Analysis of molecular variance revealed very great genetic differentiation (FST = 0.688 between the

Assessment of Genetic Variation and Population Structure of Diverse Rice Genotypes Adapted to Lowland and Upland Ecologies in Africa Using SNPs.

Science.gov (United States)

Ndjiondjop, Marie Noelle; Semagn, Kassa; Sow, Mounirou; Manneh, Baboucarr; Gouda, Arnaud C; Kpeki, Sèdjro B; Pegalepo, Esther; Wambugu, Peterson; Sié, Moussa; Warburton, Marilyn L

2018-01-01

Using interspecific crosses involving Oryza glaberrima Steud. as donor and O. sativa L. as recurrent parents, rice breeders at the Africa Rice Center developed several 'New Rice for Africa (NERICA)' improved varieties. A smaller number of interspecific and intraspecific varieties have also been released as 'Advanced Rice for Africa (ARICA)'. The objective of the present study was to investigate the genetic variation, relatedness, and population structure of 330 widely used rice genotypes in Africa using DArTseq-based single nucleotide polymorphisms (SNPs). A sample of 11 ARICAs, 85 NERICAs, 62 O. sativa spp. japonica , and 172 O. sativa spp. indica genotypes were genotyped with 27,560 SNPs using diversity array technology (DArT)-based sequencing (DArTseq) platform. Nearly 66% of the SNPs were polymorphic, of which 15,020 SNPs were mapped to the 12 rice chromosomes. Genetic distance between pairs of genotypes that belong to indica, japonica, ARICA, and NERICA varied from 0.016 to 0.623, from 0.020 to 0.692, from 0.075 to 0.763, and from 0.014 to 0.644, respectively. The proportion of pairs of genotypes with genetic distance > 0.400 was the largest within NERICAs (35.1% of the pairs) followed by ARICAs (18.2%), japonica (17.4%), and indica (5.6%). We found one pair of japonica, 11 pairs of indica, and 35 pairs of NERICA genotypes differing by <2% of the total scored alleles, which was due to 26 pairs of genotypes with identical pedigrees. Cluster analysis, principal component analysis, and the model-based population structure analysis all revealed two distinct groups corresponding to the lowland (primarily indica and lowland NERICAs) and upland (japonica and upland NERICAs) growing ecologies. Most of the interspecific lowland NERICAs formed a sub-group, likely caused by differences in the O. glaberrima genome as compared with the indica genotypes. Analysis of molecular variance revealed very great genetic differentiation ( F ST = 0.688) between the lowland and upland

Cloning of the unculturable parasite Pasteuria ramosa and its Daphnia host reveals extreme genotype-genotype interactions.

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Luijckx, Pepijn; Ben-Ami, Frida; Mouton, Laurence; Du Pasquier, Louis; Ebert, Dieter

2011-02-01

The degree of specificity in host-parasite interactions has important implications for ecology and evolution. Unfortunately, specificity can be difficult to determine when parasites cannot be cultured. In such cases, studies often use isolates of unknown genetic composition, which may lead to an underestimation of specificity. We obtained the first clones of the unculturable bacterium Pasteuria ramosa, a parasite of Daphnia magna. Clonal genotypes of the parasite exhibited much more specific interactions with host genotypes than previous studies using isolates. Clones of P. ramosa infected fewer D. magna genotypes than isolates and host clones were either fully susceptible or fully resistant to the parasite. Our finding enhances our understanding of the evolution of virulence and coevolutionary dynamics in this system. We recommend caution when using P. ramosa isolates as the presence of multiple genotypes may influence the outcome and interpretation of some experiments. © 2010 Blackwell Publishing Ltd/CNRS.

Analysis of the genetic diversity of four rabbit genotypes using ...

African Journals Online (AJOL)

Dr.Ola

2013-05-15

May 15, 2013 ... consumption and low cost, it has been widely utilized in genetics analysis in ... isozyme variation among the selected individuals within each rabbit genotype. ... with different embryo survival (Bolet and Theau-Clement, 1994).

Determination of genetic diversity among some almond accessions

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Pinar Hasan

2015-01-01

Full Text Available More recently the use of different molecular markers in fruit species to determine particularly genetic diversity, genetic relationships and cultivar identification has been gained more importance. In the study, 13 randomly amplified polimorfic DNA (RAPD and 4 inter-simple sequence repeat (ISSR markers were used to evaluate genetic relationships among 95 almong accessions (26 foreign cultivars and 69 national cultivars and selections. The all plant material found in Almond Germplasm Repository in Gaziantep, Turkey. Both RAPD and ISSR markers distinguished the almond cultivars and selections in various levels. 17 RAPD and ISSR markers yielded a total of 73 scorable bands, which 51 are polymorphic. The two marker system exhibited variation with regard to average band sizes and polymorphism ratio. The average polymorphism was higher in ISSR (88% compared to RAPD (74%. RAPD and ISSR marker systems were found to be useful for determining genetic diversity among almong genotypes and cultivars. Combining of two dendrograms obtained through these markers show different clustering of 96 almond specimens without geographical isolation. These results supported that almonds in Turkey indicated considerable genetic diversity.

Developmental plasticity: re-conceiving the genotype.

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Sultan, Sonia E

2017-10-06

In recent decades, the phenotype of an organism (i.e. its traits and behaviour) has been studied as the outcome of a developmental 'programme' coded in its genotype. This deterministic view is implicit in the Modern Synthesis approach to adaptive evolution as a sorting process among genetic variants. Studies of developmental pathways have revealed that genotypes are in fact differently expressed depending on environmental conditions. Accordingly, the genotype can be understood as a repertoire of potential developmental outcomes or norm of reaction. Reconceiving the genotype as an environmental response repertoire rather than a fixed developmental programme leads to three critical evolutionary insights. First, plastic responses to specific conditions often comprise functionally appropriate trait adjustments, resulting in an individual-level, developmental mode of adaptive variation. Second, because genotypes are differently expressed depending on the environment, the genetic diversity available to natural selection is itself environmentally contingent. Finally, environmental influences on development can extend across multiple generations via cytoplasmic and epigenetic factors transmitted to progeny individuals, altering their responses to their own, immediate environmental conditions and, in some cases, leading to inherited but non-genetic adaptations. Together, these insights suggest a more nuanced understanding of the genotype and its evolutionary role, as well as a shift in research focus to investigating the complex developmental interactions among genotypes, environments and previous environments.

Genotyping of Brucella species using clade specific SNPs

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Foster Jeffrey T

2012-06-01

Full Text Available Abstract Background Brucellosis is a worldwide disease of mammals caused by Alphaproteobacteria in the genus Brucella. The genus is genetically monomorphic, requiring extensive genotyping to differentiate isolates. We utilized two different genotyping strategies to characterize isolates. First, we developed a microarray-based assay based on 1000 single nucleotide polymorphisms (SNPs that were identified from whole genome comparisons of two B. abortus isolates , one B. melitensis, and one B. suis. We then genotyped a diverse collection of 85 Brucella strains at these SNP loci and generated a phylogenetic tree of relationships. Second, we developed a selective primer-extension assay system using capillary electrophoresis that targeted 17 high value SNPs across 8 major branches of the phylogeny and determined their genotypes in a large collection ( n = 340 of diverse isolates. Results Our 1000 SNP microarray readily distinguished B. abortus, B. melitensis, and B. suis, differentiating B. melitensis and B. suis into two clades each. Brucella abortus was divided into four major clades. Our capillary-based SNP genotyping confirmed all major branches from the microarray assay and assigned all samples to defined lineages. Isolates from these lineages and closely related isolates, among the most commonly encountered lineages worldwide, can now be quickly and easily identified and genetically characterized. Conclusions We have identified clade-specific SNPs in Brucella that can be used for rapid assignment into major groups below the species level in the three main Brucella species. Our assays represent SNP genotyping approaches that can reliably determine the evolutionary relationships of bacterial isolates without the need for whole genome sequencing of all isolates.

Epidemic Spread of Symbiotic and Non-Symbiotic Bradyrhizobium Genotypes Across California.

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Hollowell, A C; Regus, J U; Gano, K A; Bantay, R; Centeno, D; Pham, J; Lyu, J Y; Moore, D; Bernardo, A; Lopez, G; Patil, A; Patel, S; Lii, Y; Sachs, J L

2016-04-01

The patterns and drivers of bacterial strain dominance remain poorly understood in natural populations. Here, we cultured 1292 Bradyrhizobium isolates from symbiotic root nodules and the soil root interface of the host plant Acmispon strigosus across a >840-km transect in California. To investigate epidemiology and the potential role of accessory loci as epidemic drivers, isolates were genotyped at two chromosomal loci and were assayed for presence or absence of accessory "symbiosis island" loci that encode capacity to form nodules on hosts. We found that Bradyrhizobium populations were very diverse but dominated by few haplotypes-with a single "epidemic" haplotype constituting nearly 30 % of collected isolates and spreading nearly statewide. In many Bradyrhizobium lineages, we inferred presence and absence of the symbiosis island suggesting recurrent evolutionary gain and or loss of symbiotic capacity. We did not find statistical phylogenetic evidence that the symbiosis island acquisition promotes strain dominance and both symbiotic and non-symbiotic strains exhibited population dominance and spatial spread. Our dataset reveals that a strikingly few Bradyrhizobium genotypes can rapidly spread to dominate a landscape and suggests that these epidemics are not driven by the acquisition of accessory loci as occurs in key human pathogens.

Prospects of castor (Ricinus communis L.) genotypes for biodiesel production in India

International Nuclear Information System (INIS)

Lavanya, C.; Murthy, I.Y.L.N.; Nagaraj, G.; Mukta, N.

2012-01-01

The search for suitable non-edible oilseed crops for production of biodiesel has led to exploration of the potential of castor, hitherto an export oriented commercial oilseed crop in India. In this context, a study was conducted to identify high yielding castor genotypes ideal for biodiesel production. The material evaluated included seed of 15 castor genotypes grown in rainfed conditions of Alfisols at Hyderabad, India. Variability for palmitic, stearic, oleic, linoleic fatty acids was recorded. Ricinoleic acid, the predominant mono unsaturated fatty acid varied among castor genotypes from 86.7 to 92.1%. Correlation coeffecients between fatty acid profile and biodiesel traits were computed. Genotypes 48-1 and DCH-200 exhibited high O/L ratio, low Iodine value (IV) and high cetane number (CN) which indicates higher stability, longer shelf life, quick ignition and greater combustion quality. Genotype DPC-9 exhibited potential as a female parent for development of biodiesel suitable hybrid. -- Highlights: ► Evaluated 15 castor genotypes for fatty acid profile. ► Computed biodiesel related traits like saponification number, iodine value and cetane number. ► Ricinoleic acid, the predominant mono unsaturated fatty acid ranged from 86.7 to 92.1%. ► Variety 48-1 and hybrid DCH-200 exhibited high O/L ratio, low iodine value (IV) and high cetane number (CN).

Pollen diversity, viability and floral structure of some Musa genotypes

African Journals Online (AJOL)

Prof. Ogunji

This is related to sterility due to triploidy, variation in genome size and structure ... Pollen grains are structures that house the male gametophytes generation of .... the mean value for all the genotypes was recorded for PITA 14, an 11TA hybrid.

Geographical distribution of Toxoplasma gondii genotypes in Asia: A link with neighboring continents.

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Chaichan, P; Mercier, A; Galal, L; Mahittikorn, A; Ariey, F; Morand, S; Boumédiène, F; Udonsom, R; Hamidovic, A; Murat, J B; Sukthana, Y; Dardé, M L

2017-09-01

Defining the pattern of genetic diversity of Toxoplasma gondii is important to understand its worldwide distribution. During the last decades, a large number of studies have been published on Toxoplasma genotypes circulating in Europe, in North and South America. Two continents are still largely unexplored, Africa and, to a less extent, Asia. In this last continent, an increasing number of publications reported genotypes circulating in diverse provinces of China, but very few data are available for other Asian countries. After a systematic database search, 47 papers related to T. gondii genotypes in Asia were analyzed. Genetic characterization of DNA was performed by microsatellite markers, or more usually by a multiplex PCR using 11 PCR-RFLP markers, allowing data comparison to draw a first global picture of the population structure of this parasite throughout Asia. Overall, 390 isolates or DNA extracts were completely typed by PCR-RFLP and/or microsatellite marker methods, revealing 36 different PCR-RFLP or equivalent microsatellite genotypes: 15 genotypes identified by a ToxoDB number and 21 atypical or unique genotypes. The most common genotype found in Asia is the genotype ToxoDB#9 (Chinese 1). The clonal types I, II and II variant, and III were also commonly found in Asia. The geographical distribution of these genotypes across Asia may reflect either a continuum with Europe for the western part of Asia (presence of Type II), or the circulation of strains through animal migration or human activities between Africa and the Southwestern part of Asia (Africa 1 genotype in Turkey or ToxoDB#20 both I Sri-Lanka and in Ethiopia or Egypt). Although there are some indications of a genetic population structure in Southeast Asian countries different from the rest of Asia, more studies in this tropical part of Asia will be necessary for a region which represent as well as Africa one of the missing links of the T. gondii genetic diversity. Copyright © 2017 Elsevier B

Genomic Diversity and Evolution of the Lyssaviruses

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Delmas, Olivier; Holmes, Edward C.; Talbi, Chiraz; Larrous, Florence; Dacheux, Laurent; Bouchier, Christiane; Bourhy, Hervé

2008-01-01

Lyssaviruses are RNA viruses with single-strand, negative-sense genomes responsible for rabies-like diseases in mammals. To date, genomic and evolutionary studies have most often utilized partial genome sequences, particularly of the nucleoprotein and glycoprotein genes, with little consideration of genome-scale evolution. Herein, we report the first genomic and evolutionary analysis using complete genome sequences of all recognised lyssavirus genotypes, including 14 new complete genomes of field isolates from 6 genotypes and one genotype that is completely sequenced for the first time. In doing so we significantly increase the extent of genome sequence data available for these important viruses. Our analysis of these genome sequence data reveals that all lyssaviruses have the same genomic organization. A phylogenetic analysis reveals strong geographical structuring, with the greatest genetic diversity in Africa, and an independent origin for the two known genotypes that infect European bats. We also suggest that multiple genotypes may exist within the diversity of viruses currently classified as ‘Lagos Bat’. In sum, we show that rigorous phylogenetic techniques based on full length genome sequence provide the best discriminatory power for genotype classification within the lyssaviruses. PMID:18446239

Genomic diversity and evolution of the lyssaviruses.

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Olivier Delmas

2008-04-01

Full Text Available Lyssaviruses are RNA viruses with single-strand, negative-sense genomes responsible for rabies-like diseases in mammals. To date, genomic and evolutionary studies have most often utilized partial genome sequences, particularly of the nucleoprotein and glycoprotein genes, with little consideration of genome-scale evolution. Herein, we report the first genomic and evolutionary analysis using complete genome sequences of all recognised lyssavirus genotypes, including 14 new complete genomes of field isolates from 6 genotypes and one genotype that is completely sequenced for the first time. In doing so we significantly increase the extent of genome sequence data available for these important viruses. Our analysis of these genome sequence data reveals that all lyssaviruses have the same genomic organization. A phylogenetic analysis reveals strong geographical structuring, with the greatest genetic diversity in Africa, and an independent origin for the two known genotypes that infect European bats. We also suggest that multiple genotypes may exist within the diversity of viruses currently classified as 'Lagos Bat'. In sum, we show that rigorous phylogenetic techniques based on full length genome sequence provide the best discriminatory power for genotype classification within the lyssaviruses.

Diversification of Orientia tsutsugamushi genotypes by intragenic recombination and their potential expansion in endemic areas.

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Gwanghun Kim

2017-03-01

Full Text Available Scrub typhus is a mite-borne febrile disease caused by O. tsutsugamushi infection. Recently, emergence of scrub typhus has attracted considerable attention in several endemic countries in Asia and the western Pacific. In addition, the antigenic diversity of the intracellular pathogen has been a serious obstacle for developing effective diagnostics and vaccine.To understand the evolutionary pathway of genotypic diversification of O. tsutsugamushi and the environmental factors associated with the epidemiological features of scrub typhus, we analyzed sequence data, including spatiotemporal information, of the tsa56 gene encoding a major outer membrane protein responsible for antigenic variation. A total of 324 tsa56 sequences covering more than 85% of its open reading frame were analyzed and classified into 17 genotypes based on phylogenetic relationship. Extensive sequence analysis of tsa56 genes using diverse informatics tools revealed multiple intragenic recombination events, as well as a substantially higher mutation rate than other house-keeping genes. This suggests that genetic diversification occurred via frequent point mutations and subsequent genetic recombination. Interestingly, more diverse bacterial genotypes and dominant vector species prevail in Taiwan compared to other endemic regions. Furthermore, the co-presence of identical and sub-identical clones of tsa56 gene in geographically distant areas implies potential spread of O. tsutsugamushi genotypes.Fluctuation and diversification of vector species harboring O. tsutsugamushi in local endemic areas may facilitate genetic recombination among diverse genotypes. Therefore, careful monitoring of dominant vector species, as well as the prevalence of O. tsutsugamushi genotypes may be advisable to enable proper anticipation of epidemiological changes of scrub typhus.

NS5A Sequence Heterogeneity and Mechanisms of Daclatasvir Resistance in Hepatitis C Virus Genotype 4 Infection.

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Zhou, Nannan; Hernandez, Dennis; Ueland, Joseph; Yang, Xiaoyan; Yu, Fei; Sims, Karen; Yin, Philip D; McPhee, Fiona

2016-01-15

Daclatasvir is an NS5A inhibitor approved for treatment of infection due to hepatitis C virus (HCV) genotypes (GTs) 1-4. To support daclatasvir use in HCV genotype 4 infection, we examined a diverse genotype 4-infected population for HCV genotype 4 subtype prevalence, NS5A polymorphisms at residues associated with daclatasvir resistance (positions 28, 30, 31, or 93), and their effects on daclatasvir activity in vitro and clinically. We performed phylogenetic analysis of genotype 4 NS5A sequences from 186 clinical trial patients and 43 sequences from the European HCV database, and susceptibility analyses of NS5A polymorphisms and patient-derived NS5A sequences by using genotype 4 NS5A hybrid genotype 2a replicons. The clinical trial patients represented 14 genotype 4 subtypes; most prevalent were genotype 4a (55%) and genotype 4d (27%). Daclatasvir 50% effective concentrations for 10 patient-derived NS5A sequences representing diverse phylogenetic clusters were ≤0.080 nM. Most baseline sequences had ≥1 NS5A polymorphism at residues associated with daclatasvir resistance; however, only 3 patients (1.6%) had polymorphisms conferring ≥1000-fold daclatasvir resistance in vitro. Among 46 patients enrolled in daclatasvir trials, all 20 with baseline resistance polymorphisms achieved a sustained virologic response. Circulating genotype 4 subtypes are genetically diverse. Polymorphisms conferring high-level daclatasvir resistance in vitro are uncommon before therapy, and clinical data suggest that genotype 4 subtype and baseline polymorphisms have minimal impact on responses to daclatasvir-containing regimens. © The Author 2015. Published by Oxford University Press for the Infectious Diseases Society of America.

Genetic diversity for grain Zn concentration in finger millet genotypes: Potential for improving human Zn nutrition

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Ramegowda Yamunarani

2016-06-01

Full Text Available Nearly half of the world population suffers from micronutrient malnutrition, particularly Zn deficiency. It is important to understand genetic variation for uptake and translocation behaviors of Zn in relevant crop species to increase Zn concentration in edible parts. In the present study, genetic variation in grain Zn concentration of 319 finger millet genotypes was assessed. Large genetic variation was found among the genotypes, with concentrations ranging from 10 to 86 μg g− 1 grain. Uptake and translocation studies with Zn/65Zn application in 12 selected low-Zn genotypes showed wide variation in root uptake and shoot translocation, with genotypes GEC331 and GEC164 showing greater uptake and translocation. Genotypes GEC164 and GEC543 showed increased grain Zn concentration. Genotypes GEC331 and GEC164 also showed improved yield under Zn treatment. Appreciable variation in grain Zn concentration among finger millet genotypes found in this study offers opportunities to improve Zn nutrition through breeding.

Micropropagation of six Paulownia genotypes through tissue culture

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Lydia Shtereva

2014-12-01

Full Text Available We investigated the effect of genotype and culture medium on the in vitro germination and development of plantlets from seeds of 6 different Paulownia genotypes (P. tomentosa, hybrid lines P. tomentosa P. fortunei (Mega, Ganter and Caroline, P. elongata and hybrid line P. elongata P. fortunei. Nodal and shoot tip explants were used for micropropagation of Paulownia genotypes by manipulating plant growth regulators. The highest germination percentage for all genotypes was obtained for seeds inoculated on medium supplemented with 50 mg*L GA3 (MSG2. On Thidiazuron containing media, the explants of hybrid line P. elongata P. fortunei exhibited the highest frequency of axillary shoot proliferation following by P. tomentosa P. fortunei. The results are discussed with the perspective of applying an improved protocol for in vitro seed germination and plantlet formation in several economically valuable Paulownia genotypes.

Morphophysiology, Phenotypic and Molecular Diversity of Auxin-induced Passiflora mucronata Lam. (Passifloraceae).

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França, Juliany M; Venial, Lucimara R; Costa, Eloá B; Schmildt, Edilson R; Schmildt, Omar; Bernardes, Paula M; Tatagiba, Sandro D; Lopes, José C; Ferreira, Marcia F S; Alexandre, Rodrigo S

2018-01-01

Genetic diversity allows identification of potential intraspecific genotypes in the genus Passiflora. The objective of this study was to examine the morphological and genetic diversity of auxin-induced Passiflora mucronata. The experiments were arranged in a complete randomized block design, with a 9 x 2 factorial arrangement (nine genotypes x presence and absence of auxin, indole-3-butyric acid (IBA)), with four replicates of 16 cuttings. The rooting and vegetative growth responses were variable. Genotype 5 was more responsive in the absence of IBA and genotypes 3, 8 and 9 were more responsive in the presence of IBA. Auxin increased rooting rate and percentage, reducing the average time of root protrusion in eight days. IBA also contributed to increase photosynthesis and dry root and shoot mass in 55.55 and 44.44% of the genotypes, respectively. The highest relative contribution to phenotypic diversity in the absence of auxin was rate (38.75%) and percentage (20.27%) of rooting, whereas in the presence of auxin was stomatal conductance (23.19%) and root dry mass (20.91%). Similarity was found for phenotypic and molecular divergence in the presence of IBA, in which genotypes 1 and 6; genotypes 5, 8 and 9; and genotype 3 were clustered in distinct groups.

Estimation of genetic diversity in rice ( Oryza sativa L. ) genotypes ...

African Journals Online (AJOL)

Thirty rice genotypes comprising land races, pure lines, somaclones, breeding lines and varieties specifically adapted to costal saline environments were characterized by SSR markers and morphological characters in this study. Out of 35 primers of SSR markers, 28 were found to be polymorphic. The PIC value ranged ...

Widespread recombination, reassortment, and transmission of unbalanced compound viral genotypes in natural arenavirus infections.

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Mark D Stenglein

2015-05-01

Full Text Available Arenaviruses are one of the largest families of human hemorrhagic fever viruses and are known to infect both mammals and snakes. Arenaviruses package a large (L and small (S genome segment in their virions. For segmented RNA viruses like these, novel genotypes can be generated through mutation, recombination, and reassortment. Although it is believed that an ancient recombination event led to the emergence of a new lineage of mammalian arenaviruses, neither recombination nor reassortment has been definitively documented in natural arenavirus infections. Here, we used metagenomic sequencing to survey the viral diversity present in captive arenavirus-infected snakes. From 48 infected animals, we determined the complete or near complete sequence of 210 genome segments that grouped into 23 L and 11 S genotypes. The majority of snakes were multiply infected, with up to 4 distinct S and 11 distinct L segment genotypes in individual animals. This S/L imbalance was typical: in all cases intrahost L segment genotypes outnumbered S genotypes, and a particular S segment genotype dominated in individual animals and at a population level. We corroborated sequencing results by qRT-PCR and virus isolation, and isolates replicated as ensembles in culture. Numerous instances of recombination and reassortment were detected, including recombinant segments with unusual organizations featuring 2 intergenic regions and superfluous content, which were capable of stable replication and transmission despite their atypical structures. Overall, this represents intrahost diversity of an extent and form that goes well beyond what has been observed for arenaviruses or for viruses in general. This diversity can be plausibly attributed to the captive intermingling of sub-clinically infected wild-caught snakes. Thus, beyond providing a unique opportunity to study arenavirus evolution and adaptation, these findings allow the investigation of unintended anthropogenic impacts on

Methods of developing core collections based on the predicted genotypic value of rice ( Oryza sativa L.).

Science.gov (United States)

Li, C T; Shi, C H; Wu, J G; Xu, H M; Zhang, H Z; Ren, Y L

2004-04-01

The selection of an appropriate sampling strategy and a clustering method is important in the construction of core collections based on predicted genotypic values in order to retain the greatest degree of genetic diversity of the initial collection. In this study, methods of developing rice core collections were evaluated based on the predicted genotypic values for 992 rice varieties with 13 quantitative traits. The genotypic values of the traits were predicted by the adjusted unbiased prediction (AUP) method. Based on the predicted genotypic values, Mahalanobis distances were calculated and employed to measure the genetic similarities among the rice varieties. Six hierarchical clustering methods, including the single linkage, median linkage, centroid, unweighted pair-group average, weighted pair-group average and flexible-beta methods, were combined with random, preferred and deviation sampling to develop 18 core collections of rice germplasm. The results show that the deviation sampling strategy in combination with the unweighted pair-group average method of hierarchical clustering retains the greatest degree of genetic diversities of the initial collection. The core collections sampled using predicted genotypic values had more genetic diversity than those based on phenotypic values.

Assessment of genetic diversity in indigenous turmeric (Curcuma longa) germplasm from India using molecular markers.

Science.gov (United States)

Verma, Sushma; Singh, Shweta; Sharma, Suresh; Tewari, S K; Roy, R K; Goel, A K; Rana, T S

2015-04-01

Curcuma longa L., commonly known as turmeric, is one of the economically and medicinally important plant species. It is predominantly cultivated in the tropical and sub tropical countries. India is the largest producer, and exporter of turmeric in the world, followed by China, Indonesia, Bangladesh and Thailand. In the present study, Directed Amplification of Minisatellite DNA (DAMD) and Inter Simple Sequence Repeats (ISSR), methods were used to estimate the genetic variability in indigenous turmeric germplasm. Cumulative data analysis for DAMD (15) and ISSR (13) markers resulted into 478 fragments, out of which 392 fragments were polymorphic, revealing 82 % polymorphism across the turmeric genotypes. Wide range of pairwise genetic distances (0.03-0.59) across the genotypes revealed that these genotypes are genetically quite diverse. The UPGMA dendrogram generated using cumulative data showed significant relationships amongst the genotypes. All 29 genotypes studied grouped into two clusters irrespective of their geographical affiliations with 100 % bootstrap value except few genotypes, suggesting considerable diversity amongst the genotypes. These results suggested that the current collection of turmeric genotypes preserve the vast majority of natural variations. The results further demonstrate the efficiency and reliability of DAMD and ISSR markers in determining the genetic diversity and relationships among the indigenous turmeric germplasm. DAMD and ISSR profiling have identified diverse turmeric genotypes, which could be further utilized in various genetic improvement programmes including conventional as well as marker assisted breeding towards development of new and desirable turmeric genotypes.

First Insight into a Nationwide Genotypic Diversity of Mycobacterium tuberculosis among Previously Treated Pulmonary Tuberculosis Cases in Benin, West Africa.

Science.gov (United States)

Affolabi, Dissou; Sanoussi, N'Dira; Codo, Sergio; Sogbo, Fréderic; Wachinou, Prudence; Massou, Faridath; Kehinde, Aderemi; Anagonou, Séverin

2017-01-01

Molecular studies on tuberculosis (TB) are rare in low-resource countries like Benin, where data on molecular study on previously treated TB cases is unavailable. From January to December 2014, all smear- and culture-positive previously treated pulmonary TB patients from all TB clinics were systematically recruited. Drug susceptibility testing and spoligotyping were performed on all isolates. Of the 100 patients recruited, 71 (71.0%) were relapse cases and 24 (24.0%) were failure cases, while 5 (5.0%) were default cases. Resistance rate to any first-line drug was 40.0%, while 12.0% of strains were multidrug-resistant (MDR) and no strain was extensively drug-resistant (XDR). A total of 40 distinct spoligotypes were found to be corresponding to a genotypic diversity of 40.0%. ST61 was the most predominant spoligotype with prevalence of 33.0%. In all, 31 single spoligotypes and nine clusters were observed with 2 to 33 strains per cluster giving a clustering rate of 69.0%. Euro-American (Lineage 4) was the most prevalent lineage (74.0%) and Lineage 2 was associated with resistance to streptomycin. This first insight into genetic diversity of previously treated pulmonary TB patients in Benin showed a relatively high genetic diversity of Mycobacterium tuberculosis .

First Insight into a Nationwide Genotypic Diversity of Mycobacterium tuberculosis among Previously Treated Pulmonary Tuberculosis Cases in Benin, West Africa

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Dissou Affolabi

2017-01-01

Full Text Available Background. Molecular studies on tuberculosis (TB are rare in low-resource countries like Benin, where data on molecular study on previously treated TB cases is unavailable. Materials and Methods. From January to December 2014, all smear- and culture-positive previously treated pulmonary TB patients from all TB clinics were systematically recruited. Drug susceptibility testing and spoligotyping were performed on all isolates. Results. Of the 100 patients recruited, 71 (71.0% were relapse cases and 24 (24.0% were failure cases, while 5 (5.0% were default cases. Resistance rate to any first-line drug was 40.0%, while 12.0% of strains were multidrug-resistant (MDR and no strain was extensively drug-resistant (XDR. A total of 40 distinct spoligotypes were found to be corresponding to a genotypic diversity of 40.0%. ST61 was the most predominant spoligotype with prevalence of 33.0%. In all, 31 single spoligotypes and nine clusters were observed with 2 to 33 strains per cluster giving a clustering rate of 69.0%. Euro-American (Lineage 4 was the most prevalent lineage (74.0% and Lineage 2 was associated with resistance to streptomycin. Conclusion. This first insight into genetic diversity of previously treated pulmonary TB patients in Benin showed a relatively high genetic diversity of Mycobacterium tuberculosis.

Genetic diversity in some Turkish pepper (Capsicum annuum L ...

African Journals Online (AJOL)

STORAGESEVER

2009-09-15

Sep 15, 2009 ... RFLP, RAPD, AFLP, and micro-satellites have been beneficial by being ... List of pepper genotypes used in the experiment. Genotype. Type. Source. Classification of ..... Artificial selection might decrease the genetic diversity ...

Genetic variation of european maize genotypes (zea mays l. Detected using ssr markers

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Martin Vivodík

2017-01-01

Full Text Available The SSR molecular markers were used to assess genetic diversity in 40 old European maize genotypes. Ten SSR primers revealed a total of 65 alleles ranging from 4 (UMC1060 to 8 (UMC2002 and UMC1155 alleles per locus with a mean value of 6.50 alleles per locus. The PIC values ranged from 0.713 (UMC1060 to 0.842 (UMC2002 with an average value of 0.810 and the DI value ranged from 0.734 (UMC1060 to 0.848 (UMC2002 with an average value of 0.819. 100% of used SSR markers had PIC and DI values higher than 0.7 that means high polymorphism of chosen markers used for analysis. Probability of identity (PI was low ranged from 0.004 (UMC1072 to 0.022 (UMC1060 with an average of 0.008. A dendrogram was constructed from a genetic distance matrix based on profiles of the 10 maize SSR loci using the unweighted pair-group method with the arithmetic average (UPGMA. According to analysis, the collection of 40 diverse accessions of maize was clustered into four clusters. The first cluster contained nine genotypes of maize, while the second cluster contained the four genotypes of maize. The third cluster contained 5 maize genotypes. Cluster 4 contained five genotypes from Hungary (22.73%, two genotypes from Poland (9.10%, seven genotypes of maize from Union of Soviet Socialist Republics (31.81%, six genotypes from Czechoslovakia (27.27%, one genotype from Slovak Republic (4.55% and one genotype of maize is from Yugoslavia (4.55%. We could not distinguish 4 maize genotypes grouped in cluster 4, (Voroneskaja and Kocovska Skora and 2 Hungarian maize genotypes - Feheres Sarga Filleres and Mindszentpusztai Feher, which are genetically the closest.

Protection of macaques with diverse MHC genotypes against a heterologous SIV by vaccination with a deglycosylated live-attenuated SIV.

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Chie Sugimoto

Full Text Available HIV vaccine development has been hampered by issues such as undefined correlates of protection and extensive diversity of HIV. We addressed these issues using a previously established SIV-macaque model in which SIV mutants with deletions of multiple gp120 N-glycans function as potent live attenuated vaccines to induce near-sterile immunity against the parental pathogenic SIVmac239. In this study, we investigated the protective efficacy of these mutants against a highly pathogenic heterologous SIVsmE543-3 delivered intravenously to rhesus macaques with diverse MHC genotypes. All 11 vaccinated macaques contained the acute-phase infection with blood viral loads below the level of detection between 4 and 10 weeks postchallenge (pc, following a transient but marginal peak of viral replication at 2 weeks in only half of the challenged animals. In the chronic phase, seven vaccinees contained viral replication for over 80 weeks pc, while four did not. Neutralizing antibodies against challenge virus were not detected. Although overall levels of SIV specific T cell responses did not correlate with containment of acute and chronic viral replication, a critical role of cellular responses in the containment of viral replication was suggested. Emergence of viruses with altered fitness due to recombination between the vaccine and challenge viruses and increased gp120 glycosylation was linked to the failure to control SIV. These results demonstrate the induction of effective protective immune responses in a significant number of animals against heterologous virus by infection with deglycosylated attenuated SIV mutants in macaques with highly diverse MHC background. These findings suggest that broad HIV cross clade protection is possible, even in hosts with diverse genetic backgrounds. In summary, results of this study indicate that deglycosylated live-attenuated vaccines may provide a platform for the elucidation of correlates of protection needed for a

Genetic diversity in cultivated carioca common beans based on molecular marker analysis

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Juliana Morini Küpper Cardoso Perseguini

2011-01-01

Full Text Available A wide array of molecular markers has been used to investigate the genetic diversity among common bean species. However, the best combination of markers for studying such diversity among common bean cultivars has yet to be determined. Few reports have examined the genetic diversity of the carioca bean, commercially one of the most important common beans in Brazil. In this study, we examined the usefulness of two molecular marker systems (simple sequence repeats - SSRs and amplified fragment length polymorphisms - AFLPs for assessing the genetic diversity of carioca beans. The amount of information provided by Roger's modified genetic distance was used to analyze SSR data and Jaccards similarity coefficient was used for AFLP data. Seventy SSRs were polymorphic and 20 AFLP primer combinations produced 635 polymorphic bands. Molecular analysis showed that carioca genotypes were quite diverse. AFLPs revealed greater genetic differentiation and variation within the carioca genotypes (Gst = 98% and Fst = 0.83, respectively than SSRs and provided better resolution for clustering the carioca genotypes. SSRs and AFLPs were both suitable for assessing the genetic diversity of Brazilian carioca genotypes since the number of markers used in each system provided a low coefficient of variation. However, fingerprint profiles were generated faster with AFLPs, making them a better choice for assessing genetic diversity in the carioca germplasm.

Characterization of cowpea genotype resistance to Callosobruchus maculatus

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Maria de Jesus Passos de Castro

2013-09-01

Full Text Available The objective of this work was to characterize the resistance of 50 cowpea (Vigna unguiculata genotypes to Callosobruchus maculatus. A completely randomized design with five replicates per treatment (genotype was used. No-choice tests were performed using the 50 cowpea genotypes to evaluate the preference for oviposition and the development of the weevil. The genotypes IT85 F-2687, MN05-841 B-49, MNC99-508-1, MNC99-510-8, TVu 1593, Canapuzinho-1-2, and Sanzi Sambili show non-preference-type resistance (oviposition and feeding. IT81 D-1045 Ereto and IT81 D-1045 Enramador exhibit antibiosis against C. maculatus and descend from resistant genitors, which grants them potential to be used in future crossings to obtain cowpea varieties with higher levels of resistance.

Annual research review: Rare genotypes and childhood psychopathology--uncovering diverse developmental mechanisms of ADHD risk.

Science.gov (United States)

Scerif, Gaia; Baker, Kate

2015-03-01

Through the increased availability and sophistication of genetic testing, it is now possible to identify causal diagnoses in a growing proportion of children with neurodevelopmental disorders. In addition to developmental delay and intellectual disability, many genetic disorders are associated with high risks of psychopathology, which curtail the wellbeing of affected individuals and their families. Beyond the identification of significant clinical needs, understanding the diverse pathways from rare genetic mutations to cognitive dysfunction and emotional-behavioural disturbance has theoretical and practical utility. We overview (based on a strategic search of the literature) the state-of-the-art on causal mechanisms leading to one of the most common childhood behavioural diagnoses - attention deficit hyperactivity disorder (ADHD) - in the context of specific genetic disorders. We focus on new insights emerging from the mapping of causal pathways from identified genetic differences to neuronal biology, brain abnormalities, cognitive processing differences and ultimately behavioural symptoms of ADHD. First, ADHD research in the context of rare genotypes highlights the complexity of multilevel mechanisms contributing to psychopathology risk. Second, comparisons between genetic disorders associated with similar psychopathology risks can elucidate convergent or distinct mechanisms at each level of analysis, which may inform therapeutic interventions and prognosis. Third, genetic disorders provide an unparalleled opportunity to observe dynamic developmental interactions between neurocognitive risk and behavioural symptoms. Fourth, variation in expression of psychopathology risk within each genetic disorder points to putative moderating and protective factors within the genome and the environment. A common imperative emerging within psychopathology research is the need to investigate mechanistically how developmental trajectories converge or diverge between and within

Evaluation of nutritional quality and antioxidant potential of pigeonpea genotypes.

Science.gov (United States)

Sekhon, Japjot; Grewal, Satvir Kaur; Singh, Inderjit; Kaur, Jagmeet

2017-10-01

Three released cultivars, forty four advance breeding lines and three wild species of pigeonpea ( Cajanus cajan L. Millsp) were evaluated for nutritional, antinutritional traits and antioxidant potential so as to identify promising genotypes. The average content of total soluble sugars, starch and total soluble proteins was found to be 43.66, 360.51 and 204.54 mg/g, respectively. Antioxidant potential in terms of free radical scavenging activity (DPPH), ferric reducing antioxidant power (FRAP), reducing power, hydroxyl radical scavenging activity and superoxide anion radical scavenging activity was estimated. The diversity was observed in genotypes with all the traits. AL 1960, AL 2000, AL 2009 and AL 2046 had high total soluble proteins, medium antinutritional factors and good antioxidant potential. AL 201, AL 1931, AL 1932, AL 1960, AL 2046, AL 2049 and AL 2060 had good nutritional value as protein and starch content ranged from 20 to 23 and 42 to 52%, respectively. Wild species C. scarabaeoides 1CP15683/W15 had lower carbohydrates, proteins, and antinutritional traits while high antioxidant potential due to high total phenols, DPPH, FRAP and reducing power. The diversity observed in genotypes with all the traits could be further used to develop nutritionally important genotypes.

Genetic diversity among endangered rare Dalbergia cochinchinensis

African Journals Online (AJOL)

hocvan

Experimental Taxonomy and Genetic Diversity, Vietnam National Museum of Nature, Vietnam Academy for Science and ... Genetic diversity of the 35 genotypes of D. cochinchinensis species were evaluated by ...... Dalbergia genus at the population level of genetic .... Population genetic software for teaching and research.

Genetic diversity in radish germplasm for morphological traits and seed storage proteins

International Nuclear Information System (INIS)

Jatoi, S.A.; Siddiqui, S.U.; Masood, M.S.; Javaid, A.; Iqbal, M.; Sayal, O.U.

2011-01-01

Genetic variation of forty-nine local and exotic radish genotypes including two checks was studied for morphological traits and seed storage protein electrophoresis using sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) markers. A high variation in germplasm for root shape, root length, root colour (internal and external), flesh texture and root type was observed. Among these genotypes, the genetic variation was apparent for most of the characters like plant biomass, root weight, leaf length, root length and root diameter that indicated the potential for crop improvement in these traits through simple selection. Exotic germplasm exhibited higher variation for plant biomass, root weight and root length which could be utilized through breeding programme. Cluster analysis on the basis of genetic diversity for seven quantitative traits resulted into four clusters. No clustering was found on the basis of origin. Low level of variance was observed for SDS-PAGE electrophoresis that suggested acquisition of more germplasm. On the basis of high yield and crispy root texture some genotypes (10076, 10362, 10429, 10658, 10662 and 10667) were identified for further testing under wide range of agro-ecological conditions. (author)

Molecular and functional diversity in Capsicum landraces of ...

African Journals Online (AJOL)

The present study analyzed the diversity in 26 landraces of Capsicum from Andaman Islands using 20 morphological, 16 biochemical and 10 DNA markers. Significant differences were observed in tested landraces and 16 reference genotypes from mainland India. Biochemical markers grouped all the genotypes into eight ...

Physicochemical and sensorial quality of banana genotypes

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Ronielli Cardoso Reis

2016-03-01

Full Text Available Despite the diversity of banana varieties in Brazil, only a few cultivars have the proper agronomic traits and fruit quality for commercial exploitation. This study aimed at evaluating the physicochemical traits and sensorial acceptance of banana genotypes, in order to identify those with potential for commercial growing. Six improved banana genotypes were assessed (BRS Maravilha, PC 0101, FHIA 18, TM 2803, YB 4203 and BRS Caipira, as well as three commercial cultivars (Grand Naine, Pacovan and Prata Anã. Analyses of peel and pulp color, peel thickness, pulp yield, moisture, pH, soluble solids, titratable acidity, total carotenoids and sensorial acceptance were performed. The BRS Maravilha, FHIA 18, YB 4203 and BRS Caipira genotypes presented physicochemical traits similar to the Grand Naine, Pacovan and Prata Anã commercial cultivars. The BRS Maravilha and TM 2803 genotypes had sensorial acceptance similar to the Prata Anã and Grand Naine cultivars, and are therefore promising for commercial growing, with the advantage of being resistant to the black Sigatoka and Panama disease.

Extraordinary Genetic Diversity in a Wood Decay Mushroom.

Science.gov (United States)

Baranova, Maria A; Logacheva, Maria D; Penin, Aleksey A; Seplyarskiy, Vladimir B; Safonova, Yana Y; Naumenko, Sergey A; Klepikova, Anna V; Gerasimov, Evgeny S; Bazykin, Georgii A; James, Timothy Y; Kondrashov, Alexey S

2015-10-01

Populations of different species vary in the amounts of genetic diversity they possess. Nucleotide diversity π, the fraction of nucleotides that are different between two randomly chosen genotypes, has been known to range in eukaryotes between 0.0001 in Lynx lynx and 0.16 in Caenorhabditis brenneri. Here, we report the results of a comparative analysis of 24 haploid genotypes (12 from the United States and 12 from European Russia) of a split-gill fungus Schizophyllum commune. The diversity at synonymous sites is 0.20 in the American population of S. commune and 0.13 in the Russian population. This exceptionally high level of nucleotide diversity also leads to extreme amino acid diversity of protein-coding genes. Using whole-genome resequencing of 2 parental and 17 offspring haploid genotypes, we estimate that the mutation rate in S. commune is high, at 2.0 × 10(-8) (95% CI: 1.1 × 10(-8) to 4.1 × 10(-8)) per nucleotide per generation. Therefore, the high diversity of S. commune is primarily determined by its elevated mutation rate, although high effective population size likely also plays a role. Small genome size, ease of cultivation and completion of the life cycle in the laboratory, free-living haploid life stages and exceptionally high variability of S. commune make it a promising model organism for population, quantitative, and evolutionary genetics. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Molecular characterization of 93 genotypes of cocoa (Theobroma cacao L. with random amplified microsatellites RAMs

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Yacenia Morillo C.

2014-12-01

Full Text Available Random amplified microsatellite (RAMs markers six were used to characterize 93 genotypes of cocoa in Tumaco (Colombia. Hundred twenty seven bands were generated. The number of polymorphic loci varied between 11 and 25 for the AG and TG primers, respectively. This study differentiated the 93 genotypes into six groups with a 0.53 similarity, 0.28 mean heterozygosity (He for the population, and 0.12±0.02 genetic differentiation coefficient or Fst. A significant level of genetic diversity was evident in the T. cacao genotypes. This resource would benefit selection programs of individual trees or plant breeding programs. The genotypes clustered in a large proportion in accordance with the collection zone. This characteristic was associated with collection zones and along the rivers in the municipality of Tumaco. The RAM technique proved to be a useful tool for the determination of genetic diversity in Theobroma species.

Genotype and Phenotype Characterization of Indonesian Phytophthora infestans Isolates Collected From Java and Outside Java Island

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Dwinita Wikan Utami

2017-10-01

Full Text Available Phytophthora infestans, the cause of late blight disease, is a worldwide problem in potato and tomato production. To understand the biology and ecology of P. infestans and the mechanism of spatial and temporal factors for the variation in P. infestans, the population diversity is required to be fully characterized. The objective of this research is to characterize the diversity of P. infestans. Surveys and collection of P. infestans isolates were performed on many locations of potato's production center in Indonesia, as in Java (West Java, Central Java, and East Java and outside of Java islands (Medan, Jambi, and Makassar. The collected isolates were then analyzed for their virulence diversity via plant disease bioassays on differential varieties and genotype diversity based on fragment analysis genotypes profile using the multiplexing 20 simple sequence repeat markers. The virulence characterization showed that the isolates group from Makassar, South Sulawesi, have the broad spectrum virulence pathotype to R1, R2, R3, R4, and R5 differential plants. Simple sequence repeat genotype characterization showed that in general, the population structure of P. infestans grouping is accordance to the origin of the sampling locations. The diversity between populations is lower than diversity between isolates in one location population groups. The characters of P. infestans population showed that the population diversity of P. infestans more occurs on individual isolates in one location compared with the diversity between the population location sampling.

Brief communication genotyping of Burkholderia pseudomallei revealed high genetic variability among isolates from a single population group.

Science.gov (United States)

Zueter, Abdelrahman Mohammad; Rahman, Zaidah Abdul; Yean, Chan Yean; Harun, Azian

2015-01-01

Burkholderia pseudomallei is a soil dwelling Gram-negative bacteria predominates in Southeast Asia zone and the tropical part of Australia. Genetic diversity has been explored among various populations and environments worldwide. To date, little data is available on MLST profiling of clinical B. pseudomallei isolates in peninsular Malaysia. In this brief report, thirteen culture positive B. pseudomallei cases collected from a single population of Terengganu state in the Western Peninsular Malaysia and were confirmed by In-house TTS1-PCR. Isolates were subjected for multi-locus sequence typing (MLST) to explore their genotypic diversity and to investigate for possible clonal clustering of a certain sequence type. Patient's clinical information was examined to investigate for clinical correlation among the different genotypes. In spite of small sample set, MLST results indicated predictive results; considerable genotypic diversity, predominance and novelty among B. pseudomallei collected over a single geographically-located population in Malaysia. Massive genotypic heterogeneity was observed; 8 different sequence types with predominance of sequence type 54 and discovery of two novel sequence types. However, no clear pathogenomic or organ tropism clonal relationships were predicted.

Assessing Symbiodinium diversity in scleractinian corals via next-generation sequencing-based genotyping of the ITS2 rDNA region

KAUST Repository

Arif, Chatchanit; Daniels, Camille; Bayer, Till; Banguera Hinestroza, Eulalia; Barbrook, Adrian; Howe, Christopher J.; LaJeunesse, Todd C.; Voolstra, Christian R.

2014-01-01

The persistence of coral reef ecosystems relies on the symbiotic relationship between scleractinian corals and intracellular, photosynthetic dinoflagellates in the genus Symbiodinium. Genetic evidence indicates that these symbionts are biologically diverse and exhibit discrete patterns of environmental and host distribution. This makes the assessment of Symbiodinium diversity critical to understanding the symbiosis ecology of corals. Here, we applied pyrosequencing to the elucidation of Symbiodinium diversity via analysis of the internal transcribed spacer 2 (ITS2) region, a multicopy genetic marker commonly used to analyse Symbiodinium diversity. Replicated data generated from isoclonal Symbiodinium cultures showed that all genomes contained numerous, yet mostly rare, ITS2 sequence variants. Pyrosequencing data were consistent with more traditional denaturing gradient gel electrophoresis (DGGE) approaches to the screening of ITS2 PCR amplifications, where the most common sequences appeared as the most intense bands. Further, we developed an operational taxonomic unit (OTU)-based pipeline for Symbiodinium ITS2 diversity typing to provisionally resolve ecologically discrete entities from intragenomic variation. A genetic distance cut-off of 0.03 collapsed intragenomic ITS2 variants of isoclonal cultures into single OTUs. When applied to the analysis of field-collected coral samples, our analyses confirm that much of the commonly observed Symbiodinium ITS2 diversity can be attributed to intragenomic variation. We conclude that by analysing Symbiodinium populations in an OTU-based framework, we can improve objectivity, comparability and simplicity when assessing ITS2 diversity in field-based studies.

Assessing Symbiodinium diversity in scleractinian corals via next-generation sequencing-based genotyping of the ITS2 rDNA region

KAUST Repository

Arif, Chatchanit

2014-09-01

The persistence of coral reef ecosystems relies on the symbiotic relationship between scleractinian corals and intracellular, photosynthetic dinoflagellates in the genus Symbiodinium. Genetic evidence indicates that these symbionts are biologically diverse and exhibit discrete patterns of environmental and host distribution. This makes the assessment of Symbiodinium diversity critical to understanding the symbiosis ecology of corals. Here, we applied pyrosequencing to the elucidation of Symbiodinium diversity via analysis of the internal transcribed spacer 2 (ITS2) region, a multicopy genetic marker commonly used to analyse Symbiodinium diversity. Replicated data generated from isoclonal Symbiodinium cultures showed that all genomes contained numerous, yet mostly rare, ITS2 sequence variants. Pyrosequencing data were consistent with more traditional denaturing gradient gel electrophoresis (DGGE) approaches to the screening of ITS2 PCR amplifications, where the most common sequences appeared as the most intense bands. Further, we developed an operational taxonomic unit (OTU)-based pipeline for Symbiodinium ITS2 diversity typing to provisionally resolve ecologically discrete entities from intragenomic variation. A genetic distance cut-off of 0.03 collapsed intragenomic ITS2 variants of isoclonal cultures into single OTUs. When applied to the analysis of field-collected coral samples, our analyses confirm that much of the commonly observed Symbiodinium ITS2 diversity can be attributed to intragenomic variation. We conclude that by analysing Symbiodinium populations in an OTU-based framework, we can improve objectivity, comparability and simplicity when assessing ITS2 diversity in field-based studies.

Temporal dynamic responses of roots in contrasting tomato genotypes to cadmium tolerance.

Science.gov (United States)

Borges, Karina Lima Reis; Salvato, Fernanda; Alcântara, Berenice Kussumoto; Nalin, Rafael Storto; Piotto, Fernando Ângelo; Azevedo, Ricardo Antunes

2018-04-01

Despite numerous studies on cadmium (Cd) uptake and accumulation in crops, relatively little is available considering the temporal dynamic of Cd uptake and responses to stress focused on the root system. Here we highlighted the responses to Cd-induced stress in roots of two tomato genotypes contrasting in Cd-tolerance: the tolerant Pusa Ruby and the sensitive Calabash Rouge. Tomato genotypes growing in the presence of 35 μM CdCl 2 exhibited a similar trend of Cd accumulation in tissues, mainly in the root system and overall plants exhibited reduction in the dry matter weight. Both genotypes showed similar trends for malondialdehyde and hydrogen peroxide accumulation with increases when exposed to Cd, being this response more pronounced in the sensitive genotype. When the antioxidant machinery is concerned, in the presence of Cd the reduced glutathione content was decreased in roots while ascorbate peroxidase (APX), glutathione reductase (GR) and glutathione S-transferase (GST) activities were increased in the presence of Cd in the tolerant genotype. Altogether these results suggest APX, GR and GST as the main players of the antioxidant machinery against Cd-induced oxidative stress.

Genomic patterns in Acropora cervicornis show extensive population structure and variable genetic diversity.

Science.gov (United States)

Drury, Crawford; Schopmeyer, Stephanie; Goergen, Elizabeth; Bartels, Erich; Nedimyer, Ken; Johnson, Meaghan; Maxwell, Kerry; Galvan, Victor; Manfrino, Carrie; Lirman, Diego

2017-08-01

Threatened Caribbean coral communities can benefit from high-resolution genetic data used to inform management and conservation action. We use Genotyping by Sequencing (GBS) to investigate genetic patterns in the threatened coral, Acropora cervicornis , across the Florida Reef Tract (FRT) and the western Caribbean. Results show extensive population structure at regional scales and resolve previously unknown structure within the FRT. Different regions also exhibit up to threefold differences in genetic diversity (He), suggesting targeted management based on the goals and resources of each population is needed. Patterns of genetic diversity have a strong spatial component, and our results show Broward and the Lower Keys are among the most diverse populations in Florida. The genetic diversity of Caribbean staghorn coral is concentrated within populations and within individual reefs (AMOVA), highlighting the complex mosaic of population structure. This variance structure is similar over regional and local scales, which suggests that in situ nurseries are adequately capturing natural patterns of diversity, representing a resource that can replicate the average diversity of wild assemblages, serving to increase intraspecific diversity and potentially leading to improved biodiversity and ecosystem function. Results presented here can be translated into specific goals for the recovery of A. cervicornis , including active focus on low diversity areas, protection of high diversity and connectivity, and practical thresholds for responsible restoration.

Genotyping-by-sequencing data of 272 crested wheatgrass (Agropyron cristatum genotypes

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Pingchuan Li

2017-12-01

Full Text Available Crested wheatgrass [Agropyron cristatum L. (Gaertn.] is an important cool-season forage grass widely used for early spring grazing. However, the genomic resources for this non-model plant are still lacking. Our goal was to generate the first set of next generation sequencing data using the genotyping-by-sequencing technique. A total of 272 crested wheatgrass plants representing seven breeding lines, five cultivars and five geographically diverse accessions were sequenced with an Illumina MiSeq instrument. These sequence datasets were processed using different bioinformatics tools to generate contigs for diploid and tetraploid plants and SNPs for diploid plants. Together, these genomic resources form a fundamental basis for genomic studies of crested wheatgrass and other wheatgrass species. The raw reads were deposited into Sequence Read Archive (SRA database under NCBI accession SRP115373 (https://www.ncbi.nlm.nih.gov/sra?term=SRP115373 and the supplementary datasets are accessible in Figshare (10.6084/m9.figshare.5345092. Keywords: Crested wheatgrass, Genotyping-by-sequencing, Diploid, Tetraploid, Raw sequence data

Response of cotton genotypes to boron under-b-adequate conditions

International Nuclear Information System (INIS)

Shah, J. A.; Sial, M. A.; Hassan, Z. U.; Rajpar, I.

2015-01-01

Balanced boron (B) application is well-known to enhance the cotton production; however, the narrow range between B-deficiency and toxicity levels makes it difficult to manage. Cotton genotypes extensively differ in their response to B requirements. The adequate dose of B for one genotype may be insufficient or even toxic to other genotype. The effects of boron (B) on seed cotton yield and its various yield associated traits were studied on 10 cotton genotypes of Pakistan. The pot studies were undertaken to categorize cotton genotypes using B-deficient (control) and B-adequate (2.0 kg B ha-1) levels arranged in CRD with four repeats. The results indicated that the seed cotton yield, yield attributes and B-uptake of genotypes were comparatively decreased in B-deficient stressed treatment. Genotype NIA-Ufaq exhibited wide range of adaptation and ranked as efficient-responsive, as it produced higher seed cotton yield under both B-regimes. SAU-2 and CIM-506 were highly-efficient and remaining all genotypes were medium-efficient. Genotype Sindh-1 produced low seed cotton yield under B deficient condition and ranked as low-efficient. B-efficient cotton genotypes can be grown in B deficient soils without B application. (author)

cultivars and identification of genotype-specific fingerprints using ...

Indian Academy of Sciences (India)

Home; Journals; Journal of Genetics; Volume 89; Online resources. Diversity in Indian barley (Hordeum vulgare) cultivars and identification of genotype-specific fingerprints using microsatellite markers. S. K. Jaiswal Shree P. Pandey S. Sharma R. Prasad L. C. Prasad R. P. S. Verma Arun K. Joshi. Volume 89 Online ...

Supplementary data: Molecular assessment of genetic diversity in ...

Indian Academy of Sciences (India)

Molecular assessment of genetic diversity in cluster bean. (Cyamopsis tetragonoloba) genotypes. Rakesh Pathak, S. K. Singh, Manjit Singh and A. Henry. J. Genet. 89, 243–246. Figure 1. RAPD profile of 1–16 Cyamopsis tetragonoloba genotypes amplified with arbitrary primer OPA-16. Figure 2. RAPD profile of 17–32 ...

Clonality and Micro-Diversity of a Nationwide Spreading Genotype of Mycobacterium tuberculosis in Japan

Science.gov (United States)

Wada, Takayuki; Iwamoto, Tomotada; Tamaru, Aki; Seto, Junji; Ahiko, Tadayuki; Yamamoto, Kaori; Hase, Atushi; Maeda, Shinji; Yamamoto, Taro

2015-01-01

Mycobacterium tuberculosis transmission routes can be estimated from genotypic analysis of clinical isolates from patients. In Japan, still a middle-incidence country of TB, a unique genotype strain designated as ‘M-strain’ has been isolated nationwide recently. To ascertain the history of the wide spread of the strain, 10 clinical isolates from different areas were subjected to genome-wide analysis based on deep sequencers. Results show that all isolates possessed common mutations to those of referential strains. The greatest number of accumulated single nucleotide variants (SNVs) from the oldest coalescence was 13 nucleotides, indicating high clonality of these isolates. When an SNV common to the isolates was used as a surrogate marker of the clone, authentic clonal isolates with variation in a reliable subset of variable number of tandem repeat (VNTR) genotyping method can be selected successfully from clinical isolates populations of M. tuberculosis. When the authentic clones can also be assigned to sub-clonal groups by SNVs derived from the genomic comparison, they are classifiable into three sub-clonal groups with a bias of geographical origins. Feedback from genomic analysis of clinical isolates of M. tuberculosis to genotypic markers will be an efficient strategy for the big data in various settings for public health actions against TB. PMID:25734518

Relationship between ureB Sequence Diversity, Urease Activity and Genotypic Variations of Different Helicobacter pylori Strains in Patients with Gastric Disorders.

Science.gov (United States)

Ghalehnoei, Hossein; Ahmadzadeh, Alireza; Farzi, Nastaran; Alebouyeh, Masoud; Aghdaei, Hamid Asadzadeh; Azimzadeh, Pendram; Molaei, Mahsa; Zali, Mohammad Reza

2016-01-01

Association of the severity of Helicobacter pylori induced diseases with virulence entity of the colonized strains was proven in some studies. Urease has been demonstrated as a potent virulence factor for H. pylori. The main aim of this study was investigation of the relationships of ureB sequence diversity, urease activity and virulence genotypes of different H. pylori strains with histopathological changes of gastric tissue in infected patients suffering from different gastric disorders. Analysis of the virulence genotypes in the isolated strains indicated significant associations between the presence of severe active gastritis and cagA+ (P = 0.039) or cagA/iceA1 genotypes (P = 0.026), and intestinal metaplasia and vacA m1 (P = 0.008) or vacA s1/m2 (P = 0.001) genotypes. Our results showed a 2.4-fold increased risk of peptic ulcer (95% CI: 0.483-11.93), compared with gastritis, in the infected patients who had dupA positive strains; however this association was not statistically significant. The results of urease activity showed a significant mean difference between the isolated strains from patients with PUD and NUD (P = 0.034). This activity was relatively higher among patients with intestinal metaplasia. Also a significant association was found between the lack of cagA and increased urease activity among the isolated strains (P = 0.036). While the greatest sequence variation of ureB was detected in a strain from a patient with intestinal metaplasia, the sole determined amino acid change in UreB sequence (Ala201Thr, 30%), showed no influence on urease activity. In conclusion, the supposed role of H. pylori urease to form peptic ulcer and advancing of intestinal metaplasia was postulated in this study. Higher urease activity in the colonizing H. pylori strains that present specific virulence factors was indicated as a risk factor for promotion of histopathological changes of gastric tissue that advance gastric malignancy.

Genetic Divergence in Sugarcane Genotypes

OpenAIRE

Tahir, Mohammad; Rahman, Hidayatur; Gul, Rahmani; Ali, Amjad; Khalid, Muhammad

2012-01-01

To assess genetic divergence of sugarcane germplasm, an experiment comprising 25 sugarcane genotypes was conducted at Sugar Crops Research Institute (SCRI), Mardan, Khyber Pakhtunkhwa, Pakistan, in quadruple lattice design during 2008-09. Among the 14 parameters evaluated, majority exhibited significant differences while some showed nonsignificant mean squares. The initial correlation matrix revealed medium to high correlations. Principal Component Analysis (PCA) showed that there were two pr...

Carcass traits of four rabbit genotypes

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Ajda Kermauner

2010-01-01

Full Text Available Seventy-three rabbits of four genotypes (A - SIKA maternal line; C - SIKA sire line; AxC - hybrids between line A and C; AxCal - crossbreds between line A and the Californian breed were used to evaluate the effect of genotype on carcass traits. Rabbits were weaned at 35 days and slaughtered at 93 days of age. Rabbits were fed standard feed mixture ad libitum. The highest live weight at slaughter and dressing percentage was achieved by line C, and the lowest in line A. Hybrids between line A and C exhibited slightly worse carcass traits than rabbits in line C, but the differences were not statistically significant. The Californian breed gave worse results than crossbreeding with line C, though in most cases the differences between AxC and AxCal were not significant. The differences between genotypes in hind leg tissue composition, pH and meat colour were not statistically significant.

Genotyping of Leptospira directly in urine samples of cattle demonstrates a diversity of species and strains in Brazil.

Science.gov (United States)

Hamond, C; Pestana, C P; Medeiros, M A; Lilenbaum, W

2016-01-01

The aim of this study was to identify Leptospira in urine samples of cattle by direct sequencing of the secY gene. The validity of this approach was assessed using ten Leptospira strains obtained from cattle in Brazil and 77 DNA samples previously extracted from cattle urine, that were positive by PCR for the genus-specific lipL32 gene of Leptospira. Direct sequencing identified 24 (31·1%) interpretable secY sequences and these were identical to those obtained from direct DNA sequencing of the urine samples from which they were recovered. Phylogenetic analyses identified four species: L. interrogans, L. borgpetersenii, L. noguchii, and L. santarosai with the most prevalent genotypes being associated with L. borgpetersenii. While direct sequencing cannot, as yet, replace culturing of leptospires, it is a valid additional tool for epidemiological studies. An unexpected finding from this study was the genetic diversity of Leptospira infecting Brazilian cattle.

Genetic Diversity and Evidence for Transmission of Streptococcus mutans by DiversiLab rep-PCR.

Science.gov (United States)

Momeni, Stephanie S; Whiddon, Jennifer; Cheon, Kyounga; Ghazal, Tariq; Moser, Stephen A; Childers, Noel K

2016-09-01

This two-part study investigated the genetic diversity and transmission of Streptococcus mutans using the DiversiLab repetitive extragenic palindromic PCR (rep-PCR) approach. For children with S. mutans and participating household members, analysis for evidence of unrelated child-to-child as well as intra-familial transmission was evaluated based on commonality of genotypes. A total of 169 index children and 425 household family members from Uniontown, Alabama were evaluated for genetic diversity using rep-PCR. Thirty-four unique rep-PCR genotypes were observed for 13,906 S. mutans isolates. For transmission, 117 child and household isolates were evaluated for shared genotype (by child and by genotype cases, multiple matches possible for each child). Overall, children had 1-9 genotypes and those with multiple genotypes were 2.3 times more likely to have caries experience (decayed, missing and filled teeth/surfaces>0). Only 28% of children shared all genotypes within the household, while 72% had at least 1 genotype not shared with anyone in the household. Children had genotype(s) not shared with any household members in 157 cases. In 158 cases children and household members shared a genotype in which 55% (87/158 cases) were shared with more than one family member. Children most frequently shared genotypes with their mothers (54%; 85/158), siblings (46%; 72/158) and cousins (23%; 37/158). A reference library for S. mutans for epidemiological surveillance using the DiversiLab rep-PCR approach is detailed. The genetic diversity of S. mutans in this population demonstrated frequent commonality of genotypes. Evidence for both child-to-child and intra-familial transmission of S. mutans was observed by rep-PCR. Copyright © 2016 Elsevier B.V. All rights reserved.

Geographical Distribution of Trypanosoma cruzi Genotypes in Venezuela

Science.gov (United States)

Carrasco, Hernán J.; Segovia, Maikell; Llewellyn, Martin S.; Morocoima, Antonio; Urdaneta-Morales, Servio; Martínez, Cinda; Martínez, Clara E.; Garcia, Carlos; Rodríguez, Marlenes; Espinosa, Raul; de Noya, Belkisyolé A.; Díaz-Bello, Zoraida; Herrera, Leidi; Fitzpatrick, Sinead; Yeo, Matthew; Miles, Michael A.; Feliciangeli, M. Dora

2012-01-01

Chagas disease is an endemic zoonosis native to the Americas and is caused by the kinetoplastid protozoan parasite Trypanosoma cruzi. The parasite is also highly genetically diverse, with six discrete typing units (DTUs) reported TcI – TcVI. These DTUs broadly correlate with several epidemiogical, ecological and pathological features of Chagas disease. In this manuscript we report the most comprehensive evaluation to date of the genetic diversity of T. cruzi in Venezuela. The dataset includes 778 samples collected and genotyped over the last twelve years from multiple hosts and vectors, including nine wild and domestic mammalian host species, and seven species of triatomine bug, as well as from human sources. Most isolates (732) can be assigned to the TcI clade (94.1%); 24 to the TcIV group (3.1%) and 22 to TcIII (2.8%). Importantly, among the 95 isolates genotyped from human disease cases, 79% belonged to TcI - a DTU common in the Americas, however, 21% belonged to TcIV- a little known genotype previously thought to be rare in humans. Furthermore, were able to assign multiple oral Chagas diseases cases to TcI in the area around the capital, Caracas. We discuss our findings in the context of T. cruzi DTU distributions elsewhere in the Americas, and evaluate the impact they have on the future of Chagas disease control in Venezuela. PMID:22745843

Start codon targeted (scot polymorphism reveals genetic diversity in european old maize (zea mays l. Genotypes

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Martin Vivodík

2016-11-01

Full Text Available Maize (Zea mays L. is one of the world's most important crop plants following wheat and rice, which provides staple food to large number of human population in the world. It is cultivated in a wider range of environments than wheat and rice because of its greater adaptability. Molecular characterization is frequently used by maize breeders as an alternative method for selecting more promising genotypes and reducing the cost and time needed to develop hybrid combinations. In the present investigation 40 genotypes of maize from Czechoslovakia, Hungary, Poland, Union of Soviet Socialist Republics, Slovakia and Yugoslavia were analysed using 20 Start codon targeted (SCoT markers. These primers produced total 114 fragments across 40 maize genotypes, of which 86 (76.43% were polymorphic with an average of 4.30 polymorphic fragments per primer and number of amplified fragments ranged from 2 (SCoT 45 to 8 (SCoT 28 and SCoT 63. The polymorphic information content (PIC value ranged from 0.374 (ScoT 45 to 0.846 (SCoT 28 with an average of 0.739. The dendrogram based on hierarchical cluster analysis using UPGMA algorithm was prepared. The hierarchical cluster analysis showed that the maize genotypes were divided into two main clusters. Unique maize genotype (cluster 1, Zuta Brzica, originating from Yugoslavia separated from others. Cluster 2 was divided into two main clusters (2a and 2b. Subcluster 2a contained one Yugoslavian genotype Juhoslavanska and subcluster 2b was divided in two subclusters 2ba and 2bb. The present study shows effectiveness of employing SCoT markers in analysis of maize, and would be useful for further studies in population genetics, conservation genetics and genotypes improvement.

Assessment of genetic diversity among sugarcane cultivars using ...

African Journals Online (AJOL)

Genetic diversity based on the characterization of genetic makeup, using molecular markers is of utmost importance for breeders in crop improvement programme. A total of 26 microsatellite primers were used to determine the genetic diversity among 40 sugarcane genotypes including their parents. The polymerase chain ...

Interactive Exhibits Foster Partnership and Engage Diverse Learners at Their Local Libraries

Science.gov (United States)

LaConte, K.; Dusenbery, P.; Fitzhugh, G.; Harold, J. B.; Holland, A.

2016-12-01

Learners frequently need to access increasingly complex information to help them understand our changing world. More and more libraries are transforming themselves into places where learners not only access STEM information, but interact with professionals and undertake hands-on learning. Libraries are beginning to position themselves as part of learning ecosystems that contribute to a collective impact on the community. Traveling STEM exhibits are catalyzing these partnerships and engaging students, families, and adults in repeat visits through an accessible venue: their public library. The impact of the STAR Library Education Network's (STAR_Net) Discover Earth: A Century of Change exhibit on partnerships, the circulation of STEM resources, and the engagement of learners was studied by an external evaluation team. The STAR_Net project's summative evaluation utilized mixed methods to investigate project implementation and its outcomes. Methods included pre- and post-exhibit surveys administered to staff from each library that hosted the exhibits; interviews with staff from host libraries; patron surveys; exhibit-related circulation records; web metrics regarding the online STAR_Net community of practice; and site visits. A subset of host libraries recruited professionals, who delivered programming that connected Earth systems science, weather, climate, and conservation themes from the exhibit to local issues. Library patrons improved their knowledge about STEM topics presented in the exhibits and associated programming, and patrons viewing the exhibit reflected the demographics of their communities. In a follow-up survey, patrons reported spending an average of 60 minutes looking at the exhibit over their cumulative visits to the library. In contrast, visitors might visit a museum only once to look at a comparably-sized traveling exhibit due to barriers such as cost and distance. Exhibit host libraries reported an increase in the circulation of Earth science

Characterization of indigenous gossypium arboreum L. genotypes for various fiber quality traits

International Nuclear Information System (INIS)

Iqbal, M. A.; Abbas, A.; Zafar, Y.

2015-01-01

Diploid cotton (Gossypium arboreum L.) being an Old World cultivated cotton species, evolved in Indo-Pak subcontinent, has been known for conferring resistance to biotic and abiotic stresses. To the extent of our knowledge, there is no comprehensive report available on the characterization of G. arboreum germplasm. Hence, the present study was conducted to characterize 26 G. arboreum genotypes by deploying univariate and multivariate analysis in 2010 at NIBGE, Faisalabad. All these genotypes were characterized for boll weight, GOT percentage, micronaire value, staple length, fiber bundle strength and uniformity index. Genotypic variation was significant (p<0.01) for all the analyzed traits except boll weight. Maximum boll weight (2.47g) was observed for genotype 23718. GOT ranged from 18.75% (Haroonabad) to 36.94 percentage (DC-116).The finest fiber was obtained from synthetic (4.37 micro g/inch) and this genotype also exhibited the higher values for staple length (23.81 mm) and fiber bundle strength (27.37 g/tex). Range for uniformity index was observed from 76.19 percentage (Garohill) to 77.98 percentage (212). Principal component analysis (PCA) exhibited that first five components accounted for >63 percentage of the total variability. Cluster analysis identified four groups based on their agronomic properties. Significant relationships among different traits can be useful to select best genotypes having good fiber quality traits. These genotypes may prove a valuable resource to fuel the breeding efforts for not only broadening the genetic base of the newly developed material but can also add synergy to various cotton genomic projects. (author)

Population genetic structure of Plasmodium falciparum across a region of diverse endemicity in West Africa

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Mobegi Victor A

2012-07-01

Full Text Available Abstract Background Malaria parasite population genetic structure varies among areas of differing endemicity, but this has not been systematically studied across Plasmodium falciparum populations in Africa where most infections occur. Methods Ten polymorphic P. falciparum microsatellite loci were genotyped in 268 infections from eight locations in four West African countries (Republic of Guinea, Guinea Bissau, The Gambia and Senegal, spanning a highly endemic forested region in the south to a low endemic Sahelian region in the north. Analysis was performed on proportions of mixed genotype infections, genotypic diversity among isolates, multilocus standardized index of association, and inter-population differentiation. Results Each location had similar levels of pairwise genotypic diversity among isolates, although there were many more mixed parasite genotype infections in the south. Apart from a few isolates that were virtually identical, the multilocus index of association was not significant in any population. Genetic differentiation between populations was low (most pairwise FST values  Conclusions Although proportions of mixed genotype infections varied with endemicity as expected, population genetic structure was similar across the diverse sites. Very substantial reduction in transmission would be needed to cause fragmented or epidemic sub-structure in this region.

GENETIC DIVERGENCE AMONG Passiflora cristalina Vanderpl & Zappi. GENOTYPES BASED ON FLOWER AND FRUIT CHARACTERISTICS

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GREICIELE FARIAS DA SILVEIRA

Full Text Available ABSTRACT This study aimed to evaluate the genetic divergence among Passiflora cristalina genotypes and quantify the relative contribution of 30 flower and fruit characteristics, seeking to support the preservation and characterization of genetic resources of the species for preservation and use in future breeding programs. We evaluated 150 fruit and 150 flowers collected in 15 genotypes with naturally occurring in the municipality of Alta Floresta, MT. The characterization of genotypes was performed through 30 morphological characteristics of flowers and fruits, 21 of these for flower and 9 for fruit. Data were evaluated using the principal components and cluster methods obtained by UPGMA method from the similarity matrix (Euclidian mean distance, using the Genes software. By principal component analysis, it has been found that the first three components have absorbed 52.11% of the accumulated variation. The characteristics that most contributed to the discrimination of genotypes were fresh fruit weight, stigma length, length of corona filaments, fruit width, petal width and pulp weight, which are more responsive for the selection of P.cristalina genotypes. Smaller contributions to diversity were obtained from anther width, bract width and fruit length. The smallest contributions for diversity were obtained from the following characteristics: anther width, bract width and fruit length. Through UPGMA clustering method, it was found that there is a large genetic divergence among genotypes analyzed because all genotypes were grouped with over 50% of dissimilarity. This study identified genotypes 4, 5 and 9 as the most divergent and therefore the most suitable for breeding in future breeding programs and genetic conservation of the species.

Genotypic diversity of oscillatoriacean strains belonging to the genera Geitlerinema and Spirulina determined by 16S rDNA restriction analysis.

Science.gov (United States)

Margheri, Maria C; Piccardi, Raffaella; Ventura, Stefano; Viti, Carlo; Giovannetti, Luciana

2003-05-01

Genotypic diversity of several cyanobacterial strains mostly isolated from marine or brackish waters, belonging to the genera Geitlerinema and Spirulina, was investigated by amplified 16S ribosomal DNA restriction analysis and compared with morphological features and response to salinity. Cluster analysis was performed on amplified 16S rDNA restriction profiles of these strains along with profiles obtained from sequence data of five Spirulina-like strains, including three representatives of the new genus Halospirulina. Our strains with tightly coiled trichomes from hypersaline waters could be assigned to the Halospirulina genus. Among the uncoiled strains, the two strains of hypersaline origin clustered together and were found to be distant from their counterparts of marine and freshwater habitat. Moreover, another cluster, formed by alkali-tolerant strains with tightly coiled trichomes, was well delineated.

A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences.

Science.gov (United States)

Alcantara, Luiz Carlos Junior; Cassol, Sharon; Libin, Pieter; Deforche, Koen; Pybus, Oliver G; Van Ranst, Marc; Galvão-Castro, Bernardo; Vandamme, Anne-Mieke; de Oliveira, Tulio

2009-07-01

Human immunodeficiency virus type-1 (HIV-1), hepatitis B and C and other rapidly evolving viruses are characterized by extremely high levels of genetic diversity. To facilitate diagnosis and the development of prevention and treatment strategies that efficiently target the diversity of these viruses, and other pathogens such as human T-lymphotropic virus type-1 (HTLV-1), human herpes virus type-8 (HHV8) and human papillomavirus (HPV), we developed a rapid high-throughput-genotyping system. The method involves the alignment of a query sequence with a carefully selected set of pre-defined reference strains, followed by phylogenetic analysis of multiple overlapping segments of the alignment using a sliding window. Each segment of the query sequence is assigned the genotype and sub-genotype of the reference strain with the highest bootstrap (>70%) and bootscanning (>90%) scores. Results from all windows are combined and displayed graphically using color-coded genotypes. The new Virus-Genotyping Tools provide accurate classification of recombinant and non-recombinant viruses and are currently being assessed for their diagnostic utility. They have incorporated into several HIV drug resistance algorithms including the Stanford (http://hivdb.stanford.edu) and two European databases (http://www.umcutrecht.nl/subsite/spread-programme/ and http://www.hivrdb.org.uk/) and have been successfully used to genotype a large number of sequences in these and other databases. The tools are a PHP/JAVA web application and are freely accessible on a number of servers including: http://bioafrica.mrc.ac.za/rega-genotype/html/, http://lasp.cpqgm.fiocruz.br/virus-genotype/html/, http://jose.med.kuleuven.be/genotypetool/html/.

Diversity of Pneumocystis jirovecii Across Europe: A Multicentre Observational Study

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Alexandre Alanio

2017-08-01

Our study showed the wide population diversity across Europe, with evidence of local clusters of patients harbouring a given genotype. These data suggest a specific association between genotype and underlying disease, with evidence of a different natural history of PCP in HIV patients and renal transplant recipients.

Phylogenetic and structural diversity in the feline leukemia virus env gene.

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Shinya Watanabe

Full Text Available Feline leukemia virus (FeLV belongs to the genus Gammaretrovirus, and causes a variety of neoplastic and non-neoplastic diseases in cats. Alteration of viral env sequences is thought to be associated with disease specificity, but the way in which genetic diversity of FeLV contributes to the generation of such variants in nature is poorly understood. We isolated FeLV env genes from naturally infected cats in Japan and analyzed the evolutionary dynamics of these genes. Phylogenetic reconstructions separated our FeLV samples into three distinct genetic clusters, termed Genotypes I, II, and III. Genotype I is a major genetic cluster and can be further classified into Clades 1-7 in Japan. Genotypes were correlated with geographical distribution; Genotypes I and II were distributed within Japan, whilst FeLV samples from outside Japan belonged to Genotype III. These results may be due to geographical isolation of FeLVs in Japan. The observed structural diversity of the FeLV env gene appears to be caused primarily by mutation, deletion, insertion and recombination, and these variants may be generated de novo in individual cats. FeLV interference assay revealed that FeLV genotypes did not correlate with known FeLV receptor subgroups. We have identified the genotypes which we consider to be reliable for evaluating phylogenetic relationships of FeLV, which embrace the high structural diversity observed in our sample. Overall, these findings extend our understanding of Gammaretrovirus evolutionary patterns in the field, and may provide a useful basis for assessing the emergence of novel strains and understanding the molecular mechanisms of FeLV transmission in cats.

Revealing the Diversity of Introduced Coffea canephora Germplasm in Ecuador: Towards a National Strategy to Improve Robusta

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Rey Gastón Loor Solórzano

2017-01-01

Full Text Available Genetic resources of Coffea canephora have been introduced in several tropical countries with potential for crop development. In Ecuador, the species has been cultivated since the mid-20th century. However, little is known about the diversity and genetic structure of introduced germplasm. This paper provides an overview of the genetic and phenotypic diversity of C. canephora in Ecuador and some proposals for implementing a breeding program. Twelve SSR markers were used to analyze 1491 plants of C. canephora grown in different living collections in Ecuador, compared to 29 genotypes representing the main genetic and geographic diversity groups identified within the species. Results indicated that most of the genotypes introduced are of Congolese origin, with accessions from both main subgroups, SG1 and SG2. Some genotypes were classed as hybrids between both subgroups. Substantial phenotypic diversity was also found, and correlations were observed with genetic diversity. Ecuadorian Robusta coffee displays wide genetic diversity and we propose some ways of improving Robusta in Ecuador. A breeding program could be based on three operations: the choice of elite clones, the introduction of new material from other countries (Ivory Coast, Uganda, and the creation of new hybrid material using genotypes from the different diversity groups.

Evaluation of some Phenological and Pomological Characteristics of Selected Walnut Genotypes from Shahroud-Iran

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Sara Akhiani

2017-05-01

Full Text Available The first step in walnut breeding programs is to identify and evaluate superior genotypes of fruit trees. Hence, there are various walnut breeding programs in various areas of Iran. A study aimed to evaluate the morphological and chemical characteristics of selected superior genotypes of walnut was conducted in the Shahroud region in 2011-2012.  The following genotypes were selected in this study as the best walnut genotypes:  X-18 homogamous genotypes due to desirable late leafing;   genotype X-11 for its high percentage of kernel production, easily removal of shell, thin shell; genotype X-52 due to its kernel plumpness compared to other genotypes, thin shell and high percentage of kernel and genotype X-70 for its kernel brightness, easily kernel extracting and high percentage of kernels. The X-49 and X-5 genotypes had the highest amount of linoleic and linolenic fatty acids and higher nutritional quality compared to other genotypes. Three genotypes, X-3, X-11 and X-22, had the highest amount of oil. Genotypes X-9 and X-45 had the highest amount of protein. The difference between oil content and fatty acid compositions was presumably due to genetic diversity and ecological conditions of the studied genotypes cultivation.

Genetic diversity of Trichomonas vaginalis reinfection in HIV-positive women.

Science.gov (United States)

Conrad, Melissa D; Kissinger, Patricia; Schmidt, Norine; Martin, David H; Carlton, Jane M

2013-09-01

Recently developed genotyping tools allow better understanding of Trichomonas vaginalis population genetics and epidemiology. These tools have yet to be applied to T vaginalis collected from HIV+ populations, where understanding the interaction between the pathogens is of great importance due to the correlation between T vaginalis infection and HIV transmission. The objectives of the study were twofold: first, to compare the genetic diversity and population structure of T vaginalis collected from HIV+ women with parasites from reference populations; second, to use the genetic markers to perform a case study demonstrating the usefulness of these techniques in investigating the mechanisms of repeat infections. Repository T vaginalis samples from a previously described treatment trial were genotyped at 11 microsatellite loci. Estimates of genetic diversity and population structure were determined using standard techniques and compared with previously reported estimates of global populations. Genotyping data were used in conjunction with behavioural data to evaluate mechanisms of repeat infections. T vaginalis from HIV+ women maintain many of the population genetic characteristics of parasites from global reference populations. Although there is evidence of reduced diversity and bias towards type 1 parasites in the HIV+ population, the populations share a two-type population structure and parasite haplotypes. Genotyping/behavioural data suggest that 36% (12/33) of repeat infections in HIV+ women can be attributed to treatment failure. T vaginalis infecting HIV+ women is not genetically distinct from T vaginalis infecting reference populations. Information from genotyping can be valuable for understanding mechanisms of repeat infections.

Genotype, soil type, and locale effects on reciprocal transplant vigor, endophyte growth, and microbial functional diversity of a narrow sagebrush hybrid zone in Salt Creek Canyon, Utah

Science.gov (United States)

Miglia, K.J.; McArthur, E.D.; Redman, R.S.; Rodriguez, R.J.; Zak, J.C.; Freeman, D.C.

2007-01-01

When addressing the nature of ecological adaptation and environmental factors limiting population ranges and contributing to speciation, it is important to consider not only the plant's genotype and its response to the environment, but also any close interactions that it has with other organisms, specifically, symbiotic microorganisms. To investigate this, soils and seedlings were reciprocally transplanted into common gardens of the big sagebrush hybrid zone in Salt Creek Canyon, Utah, to determine location and edaphic effects on the fitness of parental and hybrid plants. Endophytic symbionts and functional microbial diversity of indigenous and transplanted soils and sagebrush plants were also examined. Strong selection occurred against the parental genotypes in the middle hybrid zone garden in middle hybrid zone soil; F1 hybrids had the highest fitness under these conditions. Neither of the parental genotypes had superior fitness in their indigenous soils and habitats; rather F1 hybrids with the nonindigenous maternal parent were superiorly fit. Significant garden-by-soil type interactions indicate adaptation of both plant and soil microorganisms to their indigenous soils and habitats, most notably in the middle hybrid zone garden in middle hybrid zone soil. Contrasting performances of F1 hybrids suggest asymmetrical gene flow with mountain, rather than basin, big sagebrush acting as the maternal parent. We showed that the microbial community impacted the performance of parental and hybrid plants in different soils, likely limiting the ranges of the different genotypes.

The effects of stabilizing and directional selection on phenotypic and genotypic variation in a population of RNA enzymes.

Science.gov (United States)

Hayden, Eric J; Bratulic, Sinisa; Koenig, Iwo; Ferrada, Evandro; Wagner, Andreas

2014-02-01

The distribution of variation in a quantitative trait and its underlying distribution of genotypic diversity can both be shaped by stabilizing and directional selection. Understanding either distribution is important, because it determines a population's response to natural selection. Unfortunately, existing theory makes conflicting predictions about how selection shapes these distributions, and very little pertinent experimental evidence exists. Here we study a simple genetic system, an evolving RNA enzyme (ribozyme) in which a combination of high throughput genotyping and measurement of a biochemical phenotype allow us to address this question. We show that directional selection, compared to stabilizing selection, increases the genotypic diversity of an evolving ribozyme population. In contrast, it leaves the variance in the phenotypic trait unchanged.

Frequent Spread of Plasmodium vivax Malaria Maintains High Genetic Diversity at the Myanmar-China Border, Without Distance and Landscape Barriers.

Science.gov (United States)

Lo, Eugenia; Lam, Nancy; Hemming-Schroeder, Elizabeth; Nguyen, Jennifer; Zhou, Guofa; Lee, Ming-Chieh; Yang, Zhaoqing; Cui, Liwang; Yan, Guiyun

2017-12-05

In Myanmar, civil unrest and the establishment of internally displaced person (IDP) settlements along the Myanmar-China border have impacted malaria transmission. Microsatellite markers were used to examine source-sink dynamics for Plasmodium vivax between IDP settlements and surrounding villages in the border region. Genotypic structure and diversity were compared across the 3 years following the establishment of IDP settlements, to infer demographic history. We investigated whether human migration and landscape heterogeneity contributed to P. vivax transmission. P. vivax from IDP settlements and local communities consistently exhibited high genetic diversity within populations but low polyclonality within individuals. No apparent genetic structure was observed among populations and years. P. vivax genotypes in China were similar to those in Myanmar, and parasite introduction was unidirectional. Landscape factors, including distance, elevation, and land cover, do not appear to impede parasite gene flow. The admixture of P. vivax genotypes suggested that parasite gene flow via human movement contributes to the spread of malaria both locally in Myanmar and across the international border. Our genetic findings highlight the presence of large P. vivax gene reservoirs that can sustain transmission. Thus, it is important to reinforce and improve existing control efforts along border areas. © The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.

'Ogura'-based 'CMS' lines with different nuclear backgrounds of cabbage revealed substantial diversity at morphological and molecular levels.

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Parkash, Chander; Kumar, Sandeep; Singh, Rajender; Kumar, Ajay; Kumar, Satish; Dey, Shyam Sundar; Bhatia, Reeta; Kumar, Raj

2018-01-01

A comprehensive study on characterization and genetic diversity analysis was carried out in 16 'Ogura'-based 'CMS' lines of cabbage using 14 agro-morphological traits and 29 SSR markers. Agro-morphological characterization depicted considerable variations for different horticultural traits studied. The genotype, ZHA-2, performed better for most of the economically important quantitative traits. Further, gross head weight (0.76), head length (0.60) and head width (0.83) revealed significant positive correlation with net head weight. Dendrogram based on 10 quantitative traits exhibited considerable diversity among different CMS lines and principle component analysis (PCA) indicated that net and gross head weight, and head length and width are the main components of divergence between 16 CMS lines of cabbage. In molecular study, a total of 58 alleles were amplified by 29 SSR primers, averaging to 2.0 alleles in each locus. High mean values of Shannon's Information index (0.62), expected (0.45) and observed (0.32) heterozygosity and polymorphic information content (0.35) depicted substantial polymorphism. Dendrogram based on Jaccard's similarity coefficient constructed two major groups and eight sub-groups, which revealed substantial diversity among different CMS lines. In overall, based on agro-morphological and molecular studies genotype RRMA, ZHA-2 and RCA were found most divergent. Hence, they have immense potential in future breeding programs for the high-yielding hybrid development in cabbage.

Genetic diversity analysis of mustard (Brassica spp.) germplasm ...

African Journals Online (AJOL)

sunny t

successfully cultivated between Aman and Boro rice rotation without affecting this popular cropping pattern. So, it is urgent to analyze the genetic diversity and its response for the selection of short duration mustard genotypes for increasing our cropping intensity. Diversity at marker loci is currently the most feasible strategy ...

Detection of diverse genotypes of Methicillin-resistant Staphylococcus aureus from hospital personnel and the environment in Armenia

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Hermine V. Mkrtchyan

2017-02-01

Full Text Available Abstract Background Methicillin-resistant Staphylococcus aureus (MRSA is a public health concern internationally. Studies examining a range of cohorts have been reported from various regions of the world, but little is known about the molecular epidemiology of MRSA in Armenia. Methods Between May and September 2013, twenty isolates of methicillin-resistant Staphylococcus aureus (MRSA; mecA positive were recovered from hospital personnel (n = 10; 9 females, 1 male and environmental sites (n = 10 in the maternity ward of one of the teaching hospitals in Armenia. Results Multi-locus sequence type clonal complex (MLST-CC assignments inferred from spa typing data revealed the majority belonged to 3 pandemic lineages of MRSA including: t008-CC8-SCCmecV (n = 10; 7 from personnel; t021-CC30-SCCmecIV (n = 5; all environmental; and t1523-CC45 (n = 2; 1 from personnel, one harboured SCCmecV the other was SCCmec non-typable. The remainder identified as belonging to genotype t364-CC182, both of which harboured a novel SCCmec cassette with kdp, rif5, ccrB2 and ccrC detected by PCR (both from personnel; and t325-CC88-SCCmecIV (n = 1; environmental. All MRSA were negative for the Panton-Valentine Leukocidin (PVL locus and three CC8 strains were positive for the arginine catabolic element (ACME. Conclusions In this small study, we report for the first time of the occurrence of diverse MRSA genotypes belonging to both pandemic and more sporadic international clones in Armenia harbouring the smaller SCCmec types and/or ACME, both of which have been associated with strain fitness. Further surveillance is warranted to better understand the prevalence, clinical and molecular epidemiology of MRSA throughout Armenia.

Porcine reproductive and respiratory syndrome virus: antigenic and molecular diversity of British isolates and implications for diagnosis.

Science.gov (United States)

Frossard, Jean-Pierre; Fearnley, Catherine; Naidu, Brindha; Errington, Jane; Westcott, David G; Drew, Trevor W

2012-08-17

Porcine reproductive and respiratory syndrome (PRRS) is an endemic disease of pigs, caused by PRRS virus, a member of the Arteriviridae family. First seen in Britain in 1991, the disease continues to be a significant economic and welfare problem for pig producers. To date, only PRRSV genotype 1 has been found in Britain. At the genetic level, a considerable increase has been reported in the diversity of PRRS viruses isolated in Britain between 2003 and 2007, versus the early 1990 s. In this study, the diversity has been shown to extend to the antigenic level too, with potential consequences for diagnostic methods. Antigenic diversity was assessed using a panel of twelve monoclonal antibodies, only one of which reacted with all isolates tested. Nine diverse viruses were compared as potential antigens in immunoperoxidase monolayer assays, where each one produced quite different results for a common panel of sera. As a single virus is used in each diagnostic assay, results must therefore be interpreted cautiously. For a real-time RT-PCR assay, published oligonucleotide primer and probe sequences were evaluated against available genetic sequences of British and European viruses, and were re-designed where considerable mismatches were found. The multiplex assay incorporating these modified primers to detect genotype 1 and 2 PRRS viruses was then validated for use with diagnostic sera and tissues. As the increasing degree of diversity exhibited by British strains is mirrored in other countries, PRRSV will continue to provide an ongoing challenge to diagnosis at a global, as well as national level. Crown Copyright © 2012. Published by Elsevier B.V. All rights reserved.

Evaluation of diverse wheat genotypes for potential biomass production through physiological parameters at seedling stage under controlled environment

International Nuclear Information System (INIS)

Khattak, G.S.S.

2014-01-01

Thirty wheat genotypes from UK, CIMMYT and Pakistan were evaluated under controlled environment conditions for their potential biomass production by measuring stomatal conductance (gs; porometry), leaf photosynthesis (IRGA), carbon isotope discrimination and carbon content (isotope ratio and mass analysis) at Rothamsted Research, Harpenden, UK during 2011. Amongst the dwarf genotypes, Rht2 and Rht3 showed lower stomatal conductance than Seri 32B, Seri 87B and Bathoor-07. For these 5 genotypes and another genotype Inqalab photosynthetic performance was determined by means of IRGA measurements. Of these genotypes Inqalab had the highest photosynthetic activity (A), stomatal conductance (gs), transpiration (E) and leaf intercellular CO/sub 2/ but it also had the lowest water use efficiency (A/gs) and intrinsic water use efficiency (A/E). Seri-87B had the greatest water use efficiency (A/gs) and intrinsic water use efficiency (A/E). All the Pakistani genotypes had large stomatal conductances and high 13C delta and thus may be expected to produce high biomass under irrigations and optimum inputs. (author)

Precise genotyping and recombination detection of Enterovirus

Science.gov (United States)

2015-01-01

Enteroviruses (EV) with different genotypes cause diverse infectious diseases in humans and mammals. A correct EV typing result is crucial for effective medical treatment and disease control; however, the emergence of novel viral strains has impaired the performance of available diagnostic tools. Here, we present a web-based tool, named EVIDENCE (EnteroVirus In DEep conception, http://symbiont.iis.sinica.edu.tw/evidence), for EV genotyping and recombination detection. We introduce the idea of using mixed-ranking scores to evaluate the fitness of prototypes based on relatedness and on the genome regions of interest. Using phylogenetic methods, the most possible genotype is determined based on the closest neighbor among the selected references. To detect possible recombination events, EVIDENCE calculates the sequence distance and phylogenetic relationship among sequences of all sliding windows scanning over the whole genome. Detected recombination events are plotted in an interactive figure for viewing of fine details. In addition, all EV sequences available in GenBank were collected and revised using the latest classification and nomenclature of EV in EVIDENCE. These sequences are built into the database and are retrieved in an indexed catalog, or can be searched for by keywords or by sequence similarity. EVIDENCE is the first web-based tool containing pipelines for genotyping and recombination detection, with updated, built-in, and complete reference sequences to improve sensitivity and specificity. The use of EVIDENCE can accelerate genotype identification, aiding clinical diagnosis and enhancing our understanding of EV evolution. PMID:26678286

Bacterial diversity on the surface of potato tubers in soil and the influence of the plant genotype.

Science.gov (United States)

Weinert, Nicole; Meincke, Remo; Gottwald, Christine; Heuer, Holger; Schloter, Michael; Berg, Gabriele; Smalla, Kornelia

2010-10-01

The surface of tubers might be a reservoir for bacteria that are disseminated with seed potatoes or that affect postharvest damage. The numbers of culturable bacteria and their antagonistic potential, as well as bacterial community fingerprints were analysed from tubers of seven field-grown potato genotypes, including two lines with tuber-accumulated zeaxanthin. The plant genotype significantly affected the number of culturable bacteria only at one field site. Zeaxanthin had no effect on the bacterial plate counts. In dual culture, 72 of 700 bacterial isolates inhibited at least one of the potato pathogens Rhizoctonia solani, Verticillium dahliae or Phytophthora infestans, 12 of them suppressing all three. Most of these antagonists were identified as Bacillus or Streptomyces. From tubers of two plant genotypes, including one zeaxanthin line, higher numbers of antagonists were isolated. Most antagonists showed glucanase, cellulase and protease activity, which could represent mechanisms for pathogen suppression. PCR-DGGE fingerprints of the 16S rRNA genes of bacterial communities from the tuber surfaces revealed that the potato genotype significantly affected the Pseudomonas community structure at one site. However, the genotypes showed nearly identical fingerprints for Bacteria, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, Bacillus and Streptomycetaceae. In conclusion, tuber-associated bacteria were only weakly affected by the plant genotype. © 2010 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Breeding value of primary synthetic wheat genotypes for grain yield

Science.gov (United States)

To introduce new genetic diversity into the bread wheat gene pool from its progenitor, Aegilops tauschii (Coss.) Schmalh, 33 primary synthetic hexaploid wheat genotypes (SYN) were crossed to 20 spring bread wheat (BW) cultivars at the International Wheat and Maize Improvement Center. Modified single...

Exploring origins, invasion history and genetic diversity of Imperata cylindrica (L.) P. Beauv. (Cogongrass) in the United States using genotyping by sequencing.

Science.gov (United States)

Burrell, A Millie; Pepper, Alan E; Hodnett, George; Goolsby, John A; Overholt, William A; Racelis, Alexis E; Diaz, Rodrigo; Klein, Patricia E

2015-05-01

Imperata cylindrica (Cogongrass, Speargrass) is a diploid C4 grass that is a noxious weed in 73 countries and constitutes a significant threat to global biodiversity and sustainable agriculture. We used a cost-effective genotyping-by-sequencing (GBS) approach to identify the reproductive system, genetic diversity and geographic origins of invasions in the south-eastern United States. In this work, we demonstrated the advantage of employing the closely related, fully sequenced crop species Sorghum bicolor (L.) Moench as a proxy reference genome to identify a set of 2320 informative single nucleotide and insertion-deletion polymorphisms. Genetic analyses identified four clonal lineages of cogongrass and one clonal lineage of Imperata brasiliensis Trin. in the United States. Each lineage was highly homogeneous, and we found no evidence of hybridization among the different lineages, despite geographical overlap. We found evidence that at least three of these lineages showed clonal reproduction prior to introduction to the United States. These results indicate that cogongrass has limited evolutionary potential to adapt to novel environments and further suggest that upon arrival to its invaded range, this species did not require local adaptation through hybridization/introgression or selection of favourable alleles from a broad genetic base. Thus, cogongrass presents a clear case of broad invasive success, across a diversity of environments, in a clonal organism with limited genetic diversity. © 2015 John Wiley & Sons Ltd.

Genotyping comparison of Mycobacterium leprae isolates by VNTR analysis from nasal samples in a Brazilian endemic region.

Science.gov (United States)

Lima, Luana Nepomueceno Costa; Frota, Cristiane Cunha; Suffys, Phillip Noel; Fontes, Amanda Nogueira Brum; Mota, Rosa Maria Salani; Almeida, Rosa Livia Freitas; Andrade Pontes, Maria Araci de; Gonçalves, Heitor de Sá; Kendall, Carl; Kerr, Ligia Regina Sansigolo

2018-02-06

This study analyzed the genetic diversity by MIRU-VNTR of Mycobacterium leprae isolates from nasal cavities and related to epidemiological and clinical data. The sample consisted of 48 newly diagnosed leprosy cases that tested positive for M. leprae PCR in nasal secretion (NS) attending to the National Reference Center of Dermatology Dona Libania (CDERM), Fortaleza, Brazil. Total DNA was extracted from NS of each patient and used for amplification of four M. leprae VNTR loci. Four clusters of M. leprae isolates were formed with identical genotypes. In the spatial analysis, 12 leprosy cases presented similar genotypes organized into 4 clusters. The most common genotypes in the current study was AC8b: 8, AC9: 7, AC8a: 8, GTA9: 10, which may represent a genotype of circulating strains most often in Ceará. A minimum set of four MIRU-VNTR loci was demonstrated to study the genetic diversity of M. leprae isolates from NS.

Microsatellite genotyping reveals high genetic diversity but low ...

African Journals Online (AJOL)

JMwacharos

2016-03-16

Mar 16, 2016 ... diversity and (2) Investigate population structure and extent of admixture .... to estimate and partition genetic variation within and ... K between 1 and 40 and inferred its most optimal value ... populations of 0.84 ± 0.021 with the lowest mean in ..... on population stratification and the distribution of genetic.

Genetic diversity in Trichomonas vaginalis.

Science.gov (United States)

Meade, John C; Carlton, Jane M

2013-09-01

Recent advances in genetic characterisation of Trichomonas vaginalis isolates show that the extensive clinical variability in trichomoniasis and its disease sequelae are matched by significant genetic diversity in the organism itself, suggesting a connection between the genetic identity of isolates and their clinical manifestations. Indeed, a high degree of genetic heterogeneity in T vaginalis isolates has been observed using multiple genotyping techniques. A unique two-type population structure that is both local and global in distribution has been identified, and there is evidence of recombination within each group, although sexual recombination between the groups appears to be constrained. There is conflicting evidence in these studies for correlations between T vaginalis genetic identity and clinical presentation, metronidazole susceptibility, and the presence of T vaginalis virus, underscoring the need for adoption of a common standard for genotyping the parasite. Moving forward, microsatellite genotyping and multilocus sequence typing are the most robust techniques for future investigations of T vaginalis genotype-phenotype associations.

Determination quercetin content, antioxidant and antimicrobial activity of genotype mutant Samosir shallots irradiated by gamma rays

Science.gov (United States)

Sinuraya, M.; Hanafiah, D. S.; Romulo, A.; Barus, A.

2018-02-01

The aim of the research was to study the variation in antioxidant and antimicrobial activity as well as the total quercetin content of the fifth generation genotypes mutant Samosir shallot irradiated by gamma rays. The studies conducted included the assessment of quercetin content, antioxidant and antimicrobial activity in shallot bulbs after long-term storage (6 months in the room temperature). Quercetin content of 20 selected genotype mutants of irradiated shallot bulbs along with untreated populations were calculated using quercetin (QU) as a standard. Antioxidant activities of 8 genotype mutant were determined using DPPH. Antimicrobial activity of bulb extracts were tested against six bacteria including Staphylococcus aurous, Enterococcus faecalis, Bacillus subtilis, Escherichia coli, Pseudomonas aeruginosa, and Klebsiella pneumoniae and oneyeastCandida albicans. The results showed that population of genotype mutants irradiated with dosage 2Gy, 4 Gy, 5 Gy and 6 Gy have higher quercetin content than control samples. None of the genotype mutants exhibited antibacterial inhibitory against all microorganism tested except for the sample number 2 and 6 (bulbs generated from the plants irradiated by gamma rays with dosage at 2 Gy and 6 Gy). There was also none of the genotypes observed exhibited significant antioxidant efficacy.

The role of propagule pressure, genetic diversity and microsite availability for Senecio vernalis invasion.

Directory of Open Access Journals (Sweden)

Alexandra Erfmeier

Full Text Available Genetic diversity is supposed to support the colonization success of expanding species, in particular in situations where microsite availability is constrained. Addressing the role of genetic diversity in plant invasion experimentally requires its manipulation independent of propagule pressure. To assess the relative importance of these components for the invasion of Senecio vernalis, we created propagule mixtures of four levels of genotype diversity by combining seeds across remote populations, across proximate populations, within single populations and within seed families. In a first container experiment with constant Festuca rupicola density as matrix, genotype diversity was crossed with three levels of seed density. In a second experiment, we tested for effects of establishment limitation and genotype diversity by manipulating Festuca densities. Increasing genetic diversity had no effects on abundance and biomass of S. vernalis but positively affected the proportion of large individuals to small individuals. Mixtures composed from proximate populations had a significantly higher proportion of large individuals than mixtures composed from within seed families only. High propagule pressure increased emergence and establishment of S. vernalis but had no effect on individual growth performance. Establishment was favoured in containers with Festuca, but performance of surviving seedlings was higher in open soil treatments. For S. vernalis invasion, we found a shift in driving factors from density dependence to effects of genetic diversity across life stages. While initial abundance was mostly linked to the amount of seed input, genetic diversity, in contrast, affected later stages of colonization probably via sampling effects and seemed to contribute to filtering the genotypes that finally grew up. In consequence, when disentangling the mechanistic relationships of genetic diversity, seed density and microsite limitation in colonization of

The role of propagule pressure, genetic diversity and microsite availability for Senecio vernalis invasion.

Science.gov (United States)

Erfmeier, Alexandra; Hantsch, Lydia; Bruelheide, Helge

2013-01-01

Genetic diversity is supposed to support the colonization success of expanding species, in particular in situations where microsite availability is constrained. Addressing the role of genetic diversity in plant invasion experimentally requires its manipulation independent of propagule pressure. To assess the relative importance of these components for the invasion of Senecio vernalis, we created propagule mixtures of four levels of genotype diversity by combining seeds across remote populations, across proximate populations, within single populations and within seed families. In a first container experiment with constant Festuca rupicola density as matrix, genotype diversity was crossed with three levels of seed density. In a second experiment, we tested for effects of establishment limitation and genotype diversity by manipulating Festuca densities. Increasing genetic diversity had no effects on abundance and biomass of S. vernalis but positively affected the proportion of large individuals to small individuals. Mixtures composed from proximate populations had a significantly higher proportion of large individuals than mixtures composed from within seed families only. High propagule pressure increased emergence and establishment of S. vernalis but had no effect on individual growth performance. Establishment was favoured in containers with Festuca, but performance of surviving seedlings was higher in open soil treatments. For S. vernalis invasion, we found a shift in driving factors from density dependence to effects of genetic diversity across life stages. While initial abundance was mostly linked to the amount of seed input, genetic diversity, in contrast, affected later stages of colonization probably via sampling effects and seemed to contribute to filtering the genotypes that finally grew up. In consequence, when disentangling the mechanistic relationships of genetic diversity, seed density and microsite limitation in colonization of invasive plants, a clear

Multi-Population Selective Genotyping to Identify Soybean [Glycine max (L.) Merr.] Seed Protein and Oil QTLs.

Science.gov (United States)

Phansak, Piyaporn; Soonsuwon, Watcharin; Hyten, David L; Song, Qijian; Cregan, Perry B; Graef, George L; Specht, James E

2016-06-01

Plant breeders continually generate ever-higher yielding cultivars, but also want to improve seed constituent value, which is mainly protein and oil, in soybean [Glycine max (L.) Merr.]. Identification of genetic loci governing those two traits would facilitate that effort. Though genome-wide association offers one such approach, selective genotyping of multiple biparental populations offers a complementary alternative, and was evaluated here, using 48 F2:3 populations (n = ∼224 plants) created by mating 48 high protein germplasm accessions to cultivars of similar maturity, but with normal seed protein content. All F2:3 progeny were phenotyped for seed protein and oil, but only 22 high and 22 low extreme progeny in each F2:3 phenotypic distribution were genotyped with a 1536-SNP chip (ca 450 bimorphic SNPs detected per mating). A significant quantitative trait locus (QTL) on one or more chromosomes was detected for protein in 35 (73%), and for oil in 25 (52%), of the 48 matings, and these QTL exhibited additive effects of ≥ 4 g kg(-1) and R(2) values of 0.07 or more. These results demonstrated that a multiple-population selective genotyping strategy, when focused on matings between parental phenotype extremes, can be used successfully to identify germplasm accessions possessing large-effect QTL alleles. Such accessions would be of interest to breeders to serve as parental donors of those alleles in cultivar development programs, though 17 of the 48 accessions were not unique in terms of SNP genotype, indicating that diversity among high protein accessions in the germplasm collection is less than what might ordinarily be assumed. Copyright © 2016 Phansak et al.

Naturally occurring resistance mutations within the core and NS5B regions in hepatitis C genotypes, particularly genotype 5a, in South Africa.

Science.gov (United States)

Prabdial-Sing, N; Blackard, J T; Puren, A J; Mahomed, A; Abuelhassan, W; Mahlangu, J; Vermeulen, M; Bowyer, S M

2016-03-01

Approximately 1 million South Africans are infected with Hepatitis C virus (HCV). The standard of care (SOC) in South Africa is combination therapy (pegylated interferon and ribavirin). HCV genotypes and/or mutations in the core/non-structural regions have been associated with response to therapy and/or disease progression. This study examines mutations in the core (29-280 amino acids, including ∼ 90 E1 amino acids) and NS5B (241-306 amino acids) regions on pre-treatment isolates from patients attending Johannesburg hospitals or asymptomatic South African blood donors. Diversity within known CD4+ and CD8+ T-cell epitopes was also explored. Samples grouped into subtypes 1a(N = 10) 1b(N = 12), 3a(N = 5), 4a(N = 3) and 5a(N = 61). Two mutations, associated with interferon resistance-R70Q and T110N-were present in 29 genotype 5a core sequences. No resistance mutation to NS5B nucleotide inhibitors, sofosbuvir was found. Six putative CD8+ and one CD4+ T-cell epitope sequence in the core region showed binding scores of <300 IC50nM to HLA alleles frequently observed in the South African population. No known CD8+ and CD4+ T-cell epitopes were mapped in the NS5B region. The analysis begs the question whether those infected with genotype 5a will benefit better on interferon-free combination therapies. This study provides new insight into one of the lesser studied HCV genotypes and compares the diversity seen in a large pre-treatment cohort with other subtypes. Copyright © 2015 Elsevier B.V. All rights reserved.

Analysis of genetic diversity in female, male and half sibs willow ...

African Journals Online (AJOL)

The genetic diversity among genotypes of Salix sp. was found to be high, suggesting the importance and feasibility of introducing elite genotypes from different origins for Salix germplasm conservation and breeding programs. Keywords: Salix sp., half sibs, molecular markers, genomic DNA fingerprinting. African Journal of ...

Genetic Diversity and Population Structure of Cowpea (Vigna unguiculata L. Walp).

Science.gov (United States)

Xiong, Haizheng; Shi, Ainong; Mou, Beiquan; Qin, Jun; Motes, Dennis; Lu, Weiguo; Ma, Jianbing; Weng, Yuejin; Yang, Wei; Wu, Dianxing

2016-01-01

The genetic diversity of cowpea was analyzed, and the population structure was estimated in a diverse set of 768 cultivated cowpea genotypes from the USDA GRIN cowpea collection, originally collected from 56 countries. Genotyping by sequencing was used to discover single nucleotide polymorphism (SNP) in cowpea and the identified SNP alleles were used to estimate the level of genetic diversity, population structure, and phylogenetic relationships. The aim of this study was to detect the gene pool structure of cowpea and to determine its relationship between different regions and countries. Based on the model-based ancestry analysis, the phylogenetic tree, and the principal component analysis, three well-differentiated genetic populations were postulated from 768 worldwide cowpea genotypes. According to the phylogenetic analyses between each individual, region, and country, we may trace the accession from off-original, back to the two candidate original areas (West and East of Africa) to predict the migration and domestication history during the cowpea dispersal and development. To our knowledge, this is the first report of the analysis of the genetic variation and relationship between globally cultivated cowpea genotypes. The results will help curators, researchers, and breeders to understand, utilize, conserve, and manage the collection for more efficient contribution to international cowpea research.

Habitat predictors of genetic diversity for two sympatric wetland-breeding amphibian species.

Science.gov (United States)

McKee, Anna M; Maerz, John C; Smith, Lora L; Glenn, Travis C

2017-08-01

Population genetic diversity is widely accepted as important to the conservation and management of wildlife. However, habitat features may differentially affect evolutionary processes that facilitate population genetic diversity among sympatric species. We measured genetic diversity for two pond-breeding amphibian species (Dwarf salamanders, Eurycea quadridigitata ; and Southern Leopard frogs, Lithobates sphenocephalus ) to understand how habitat characteristics and spatial scale affect genetic diversity across a landscape. Samples were collected from wetlands on a longleaf pine reserve in Georgia. We genotyped microsatellite loci for both species to assess population structures and determine which habitat features were most closely associated with observed heterozygosity and rarefied allelic richness. Both species exhibited significant population genetic structure; however, structure in Southern Leopard frogs was driven primarily by one outlier site. Dwarf salamander allelic richness was greater at sites with less surrounding road area within 0.5 km and more wetland area within 1.0 and 2.5 km, and heterozygosity was greater at sites with more wetland area within 0.5 km. In contrast, neither measure of Southern Leopard frog genetic diversity was associated with any habitat features at any scale we evaluated. Genetic diversity in the Dwarf salamander was strongly associated with land cover variables up to 2.5 km away from breeding wetlands, and/or results suggest that minimizing roads in wetland buffers may be beneficial to the maintenance of population genetic diversity. This study suggests that patterns of genetic differentiation and genetic diversity have associations with different habitat features across different spatial scales for two syntopic pond-breeding amphibian species.

Evaluation of Populus and Salix continuously irrigated with landfill leachate I. Genotype-specific elemental phytoremediation.

Science.gov (United States)

Zalesny, Ronald S; Bauer, Edmund O

2007-01-01

There is a need for the identification and selection of specific tree genotypes that can sequester elements from contaminated soils, with elevated rates of uptake. We irrigated Populus (DN17, DN182, DN34, NM2, NM6) and Salix (94003, 94012, S287, S566, SX61) genotypes planted in large soil-filled containers with landfill leachate or municipal water and tested for differences in inorganic element concentrations (P, K, Ca, Mg, S, Zn, B, Mn, Fe, Cu, Al, Na, and Cl) in the leaves, stems, and roots. Trees were irrigated with leachate or water during the final 12 wk of the 18-wk study. Genotype-specific uptake existed. For genera, tissue concentrations exhibited four responses. First, Populus had the greatest uptake of P, K, S, Cu, and Cl. Second, Salix exhibited the greatest uptake of Zn, B, Fe, and Al. Third, Salix had greater concentrations of Ca and Mg in leaves, while Populus had greater concentrations in stems and roots. Fourth, Populus had greater concentrations of Mn and Na in leaves and stems, while Salix had greater concentrations in roots. Populus deltoides x P. nigra clones exhibited better overall phytoremediation than the P. nigra x P. maximowiczii genotypes tested. Phytoremediation for S. purpurea clones 94003 and 94012 was generally less than for other Salix genotypes. Overall, concentrations of elements in the leaves, stems, and roots corroborated those in the plant-sciences literature. Uptake was dependent upon the specific genotype for most elements. Our results corroborated the need for further testing and selecting of specific clones for various phytoremediation needs, while providing a baseline for future researchers developing additional studies and resource managers conducting on-site remediation.

Genotypic analysis of Mucor from the platypus in Australia.

Science.gov (United States)

Connolly, J H; Stodart, B J; Ash, G J

2010-01-01

Mucor amphibiorum is the only pathogen known to cause significant morbidity and mortality in the free-living platypus (Ornithorhynchus anatinus) in Tasmania. Infection has also been reported in free-ranging cane toads (Bufo marinus) and green tree frogs (Litoria caerulea) from mainland Australia but has not been confirmed in platypuses from the mainland. To date, there has been little genotyping specifically conducted on M. amphibiorum. A collection of 21 Mucor isolates representing isolates from the platypus, frogs and toads, and environmental samples were obtained for genotypic analysis. Internal transcribed spacer (ITS) region sequencing and GenBank comparison confirmed the identity of most of the isolates. Representative isolates from infected platypuses formed a clade containing the reference isolates of M. amphibiorum from the Centraal Bureau voor Schimmelcultures repository. The M. amphibiorum isolates showed a close sequence identity with Mucor indicus and consisted of two haplotypes, differentiated by single nucleotide polymorphisms within the ITS1 and ITS2 regions. With the exception of isolate 96-4049, all isolates from platypuses were in one haplotype. Multilocus fingerprinting via the use of intersimple sequence repeats polymerase chain reaction identified 19 genotypes. Two major clusters were evident: 1) M. amphibiorum and Mucor racemosus; and 2) Mucor circinelloides, Mucor ramosissimus, and Mucor fragilis. Seven M. amphibiorum isolates from platypuses were present in two subclusters, with isolate 96-4053 appearing genetically distinct from all other isolates. Isolates classified as M. circinelloides by sequence analysis formed a separate subcluster, distinct from other Mucor spp. The combination of sequencing and multilocus fingerprinting has the potential to provide the tools for rapid identification of M. amphibiorum. Data presented on the diversity of the pathogen and further work in linking genetic diversity to functional diversity will provide

Genotypic Diversity within a Single Pseudomonas aeruginosa Strain Commonly Shared by Australian Patients with Cystic Fibrosis.

Directory of Open Access Journals (Sweden)

Anna Sze Tai

Full Text Available In cystic fibrosis (CF, Pseudomonas aeruginosa undergoes intra-strain genotypic and phenotypic diversification while establishing and maintaining chronic lung infections. As the clinical significance of these changes is uncertain, we investigated intra-strain diversity in commonly shared strains from CF patients to determine if specific gene mutations were associated with increased antibiotic resistance and worse clinical outcomes. Two-hundred-and-one P. aeruginosa isolates (163 represented a dominant Australian shared strain, AUST-02 from two Queensland CF centres over two distinct time-periods (2001-2002 and 2007-2009 underwent mexZ and lasR sequencing. Broth microdilution antibiotic susceptibility testing in a subset of isolates was also performed. We identified a novel AUST-02 subtype (M3L7 in adults attending a single Queensland CF centre. This M3L7 subtype was multi-drug resistant and had significantly higher antibiotic minimum inhibitory concentrations than other AUST-02 subtypes. Prospective molecular surveillance using polymerase chain reaction assays determined the prevalence of the 'M3L7' subtype at this centre during 2007-2009 (170 patients and 2011 (173 patients. Three-year clinical outcomes of patients harbouring different strains and subtypes were compared. MexZ and LasR sequences from AUST-02 isolates were more likely in 2007-2009 than 2001-2002 to exhibit mutations (mexZ: odds ratio (OR = 3.8; 95% confidence interval (CI: 1.1-13.5 and LasR: OR = 2.5; 95%CI: 1.3-5.0. Surveillance at the adult centre in 2007-2009 identified M3L7 in 28/509 (5.5% P. aeruginosa isolates from 13/170 (7.6% patients. A repeat survey in 2011 identified M3L7 in 21/519 (4.0% P. aeruginosa isolates from 11/173 (6.4% patients. The M3L7 subtype was associated with greater intravenous antibiotic and hospitalisation requirements, and a higher 3-year risk of death/lung transplantation, than other AUST-02 subtypes (adjusted hazard ratio [HR] = 9.4; 95%CI: 2

Genotypic and Phenotypic Analysis of Dairy Lactococcus lactis Biodiversity in Milk: Volatile Organic Compounds as Discriminating Markers

Science.gov (United States)

Dhaisne, Amandine; Guellerin, Maeva; Laroute, Valérie; Laguerre, Sandrine; Le Bourgeois, Pascal; Loubiere, Pascal

2013-01-01

The diversity of nine dairy strains of Lactococcus lactis subsp. lactis in fermented milk was investigated by both genotypic and phenotypic analyses. Pulsed-field gel electrophoresis and multilocus sequence typing were used to establish an integrated genotypic classification. This classification was coherent with discrimination of the L. lactis subsp. lactis bv. diacetylactis lineage and reflected clonal complex phylogeny and the uniqueness of the genomes of these strains. To assess phenotypic diversity, 82 variables were selected as important dairy features; they included physiological descriptors and the production of metabolites and volatile organic compounds (VOCs). Principal-component analysis (PCA) demonstrated the phenotypic uniqueness of each of these genetically closely related strains, allowing strain discrimination. A method of variable selection was developed to reduce the time-consuming experimentation. We therefore identified 20 variables, all associated with VOCs, as phenotypic markers allowing discrimination between strain groups. These markers are representative of the three metabolic pathways involved in flavor: lipolysis, proteolysis, and glycolysis. Despite great phenotypic diversity, the strains could be divided into four robust phenotypic clusters based on their metabolic orientations. Inclusion of genotypic diversity in addition to phenotypic characters in the classification led to five clusters rather than four being defined. However, genotypic characters make a smaller contribution than phenotypic variables (no genetic distances selected among the most contributory variables). This work proposes an original method for the phenotypic differentiation of closely related strains in milk and may be the first step toward a predictive classification for the manufacture of starters. PMID:23709512

Biotyping and genotyping (MLVA16 of Brucella abortus isolated from cattle in Brazil, 1977 to 2008.

Directory of Open Access Journals (Sweden)

Sílvia Minharro

Full Text Available Brucellosis is a worldwide distributed zoonosis that causes important economic losses to animal production. In Brazil, information on the distribution of biovars and genotypes of Brucella spp. is scarce or unavailable. This study aimed (i to biotype and genotype 137 Brazilian cattle isolates (from 1977 to 2008 of B. abortus and (ii to analyze their distribution. B. abortus biovars 1, 2 and 3 (subgroup 3b were confirmed and biovars 4 and 6 were first described in Brazil. Genotyping by the panel 1 revealed two groups, one clustering around genotype 40 and another around genotype 28. Panels 2A and 2B disclosed a high diversity among Brazilian B. abortus strains. Eighty-nine genotypes were found by MLVA16. MLVA16 panel 1 and 2 showed geographic clustering of some genotypes. Biotyping and MLVA16 genotyping of Brazilian B. abortus isolates were useful to better understand the epidemiology of bovine brucellosis in the region.

Genetic diversity of bread wheat genotypes in Iran for some nutritional value and baking quality traits.

Science.gov (United States)

Amiri, Reza; Sasani, Shahryar; Jalali-Honarmand, Saeid; Rasaei, Ali; Seifolahpour, Behnaz; Bahraminejad, Sohbat

2018-02-01

Genetic variation among 78 irrigated bread wheat genotypes was studied for their nutritional value and baking quality traits as well as some agronomic traits. The experiment was conducted in a randomized complete block design with three replicates under normal and terminal drought stress conditions in Kermanshah, Iran during 2012-2013 cropping season. The results of combined ANOVA indicated highly significant genotypic differences for all traits. All studied traits except grain yield, hectoliter weight and grain fiber content were significantly affected by genotype × environment interaction. Drought stress reduced grain yield, thousand kernel weight, gluten index, grain starch content and hectoliter weight and slightly promoted grain protein and fiber contents, falling number, total gluten and ratio of wet gluten to grain protein content. Grain yield by 31.66% and falling number by 9.20% attained the highest decrease and increase due to drought stress. There were negative and significant correlations among grain yield with grain protein and fiber contents under both conditions. Results of cluster analysis showed that newer genotypes had more grain yield and gluten index than older ones, but instead, they had the lower grain protein and fiber contents. It is thought that wheat breeders have bred cultivars with high grain yield, low protein content, and improved bread-making attributes during last seven decades. While older genotypes indicated significantly higher protein contents, and some of them had higher gluten index. We concluded from this study that it is imperative for breeders to pay more attention to improve qualitative traits coordinated to grain yield.

stability analysis of food barley genotypes in northern ethiopia

African Journals Online (AJOL)

ACSS

interaction and stability for barley grain yield and yield related traits in the growing ... that the environments were diverse; causing most of the variation in grain yield. ... component axes IPCA1, IPCA2 and IPCA3, which explained 58.06, 27.11 and ..... AMMI analysis of variance for grain yield (t ha-1) of food barley genotypes ...

Visualization of Genome Diversity in German Shepherd Dogs

OpenAIRE

Sally-Anne Mortlock; Rachel Booth; Hamutal Mazrier; Mehar S. Khatkar; Peter Williamson

2016-01-01

A loss of genetic diversity may lead to increased disease risks in subpopulations of dogs. The canine breed structure has contributed to relatively small effective population size in many breeds and can limit the options for selective breeding strategies to maintain diversity. With the completion of the canine genome sequencing project, and the subsequent reduction in the cost of genotyping on a genomic scale, evaluating diversity in dogs has become much more accurate and accessible. This pro...

Whole genome analysis of porcine astroviruses detected in Japanese pigs reveals genetic diversity and possible intra-genotypic recombination.

Science.gov (United States)

Ito, Mika; Kuroda, Moegi; Masuda, Tsuneyuki; Akagami, Masataka; Haga, Kei; Tsuchiaka, Shinobu; Kishimoto, Mai; Naoi, Yuki; Sano, Kaori; Omatsu, Tsutomu; Katayama, Yukie; Oba, Mami; Aoki, Hiroshi; Ichimaru, Toru; Mukono, Itsuro; Ouchi, Yoshinao; Yamasato, Hiroshi; Shirai, Junsuke; Katayama, Kazuhiko; Mizutani, Tetsuya; Nagai, Makoto

2017-06-01

Porcine astroviruses (PoAstVs) are ubiquitous enteric virus of pigs that are distributed in several countries throughout the world. Since PoAstVs are detected in apparent healthy pigs, the clinical significance of infection is unknown. However, AstVs have recently been associated with a severe neurological disorder in animals, including humans, and zoonotic potential has been suggested. To date, little is known about the epidemiology of PoAstVs among the pig population in Japan. In this report, we present an analysis of nearly complete genomes of 36 PoAstVs detected by a metagenomics approach in the feces of Japanese pigs. Based on a phylogenetic analysis and pairwise sequence comparison, 10, 5, 15, and 6 sequences were classified as PoAstV2, PoAstV3, PoAstV4, and PoAstV5, respectively. Co-infection with two or three strains was found in individual fecal samples from eight pigs. The phylogenetic trees of ORF1a, ORF1b, and ORF2 of PoAstV2 and PoAstV4 showed differences in their topologies. The PoAstV3 and PoAstV5 strains shared high sequence identities within each genotype in all ORFs; however, one PoAstV3 strain and one PoAstV5 strain showed considerable sequence divergence from the other PoAstV3 and PoAstV5 strains, respectively, in ORF2. Recombination analysis using whole genomes revealed evidence of multiple possible intra-genotype recombination events in PoAstV2 and PoAstV4, suggesting that recombination might have contributed to the genetic diversity and played an important role in the evolution of Japanese PoAstVs. Copyright © 2017 Elsevier B.V. All rights reserved.

Genotype modulates testosterone-dependent activity and reactivity in male mice.

Science.gov (United States)

Broida, J; Svare, B

1983-03-01

Adult castration significantly reduced the homecage locomotor activity of both inbred C57BL/6J and DBA/2J and outbred Rockland-Swiss (R-S) male mice. Castrated C57BL animals exhibited greater reductions in this behavior than did the other genotypes. Locomotor activity in a novel environment (reactivity) was also reduced by castration but only for inbred males. In both test situations, postcastration reductions in ambulation were prevented by implants of testosterone (T)-containing Silastic capsules. Thus, testicular hormones promote activity and reactivity in the male mouse in a genotype-dependent fashion.

Genotype X Environment Interaction for Yield of Pickling Cucumber in 24 U.S. Environments

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Dia Mahendra

2018-02-01

Full Text Available Reliable yield performance is important in cucumber because seed companies prefer to market cultivars adapted to multiple rather than single regions of the U.S. Also, growers benefit by using a cultivar that performs well in many environments. Future performance of cultivars is also important. The objectives of the study were to (i evaluate the yield of cucumber genotypes over successive years and in different locations, and (ii identify cucumber genotypes with high stability for yield. A diverse set of 22 pickling genotypes was evaluated over 3 years (1986, 1987 and 1988 and in 7 locations across the United States. Yield traits were evaluated using once-over harvest and counting the number of fruit that were marketable, culled or oversize. Total yield, marketable yield (total minus culled fruit, early yield (number of oversize fruit, percent culls and fruit per plant were calculated. Data were analyzed with SASGxE and RGxE programs using SAS and R programming languages, respectively. There were strong effects of environment(E as well as genotype(G xE interaction for all traits. Genotypes ‘Regal F1’, ‘Calypso F1’, ‘Carolina F1’, ‘Gy 3’, ‘Gy 14’ and ‘Fremont F1’ had high marketable yield and medium to high stability for all traits. There was an advantage of hybrids over inbreds for trait performance. Hybrids fell into a single cluster with large prediction intervals. Based on the stability statistics and divisive clusters, it appears possible to breed stable cucumber genotypes with high yield. The genotype with highest performance for marketable yield, greatest stability for yield, lowest 1-R2 ratio value (diverse and representative were ‘Marbel F1’ and Gy 14.

Correlation of Lactobacillus rhamnosus Genotypes and Carbohydrate Utilization Signatures Determined by Phenotype Profiling.

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Ceapa, Corina; Lambert, Jolanda; van Limpt, Kees; Wels, Michiel; Smokvina, Tamara; Knol, Jan; Kleerebezem, Michiel

2015-08-15

Lactobacillus rhamnosus is a bacterial species commonly colonizing the gastrointestinal (GI) tract of humans and also frequently used in food products. While some strains have been studied extensively, physiological variability among isolates of the species found in healthy humans or their diet is largely unexplored. The aim of this study was to characterize the diversity of carbohydrate utilization capabilities of human isolates and food-derived strains of L. rhamnosus in relation to their niche of isolation and genotype. We investigated the genotypic and phenotypic diversity of 25 out of 65 L. rhamnosus strains from various niches, mainly human feces and fermented dairy products. Genetic fingerprinting of the strains by amplified fragment length polymorphism (AFLP) identified 11 distinct subgroups at 70% similarity and suggested niche enrichment within particular genetic clades. High-resolution carbohydrate utilization profiling (OmniLog) identified 14 carbon sources that could be used by all of the strains tested for growth, while the utilization of 58 carbon sources differed significantly between strains, enabling the stratification of L. rhamnosus strains into three metabolic clusters that partially correlate with the genotypic clades but appear uncorrelated with the strain's origin of isolation. Draft genome sequences of 8 strains were generated and employed in a gene-trait matching (GTM) analysis together with the publicly available genomes of L. rhamnosus GG (ATCC 53103) and HN001 for several carbohydrates that were distinct for the different metabolic clusters: l-rhamnose, cellobiose, l-sorbose, and α-methyl-d-glucoside. From the analysis, candidate genes were identified that correlate with l-sorbose and α-methyl-d-glucoside utilization, and the proposed function of these genes could be confirmed by heterologous expression in a strain lacking the genes. This study expands our insight into the phenotypic and genotypic diversity of the species L. rhamnosus

Diversity arrays technology (DArT) markers in apple for genetic linkage maps

NARCIS (Netherlands)

Schouten, H.J.; Weg, van de W.E.; Carling, J.; Khan, S.A.; McKay, S.J.; Kaauwen, van M.P.W.

2012-01-01

Diversity Arrays Technology (DArT) provides a high-throughput whole-genome genotyping platform for the detection and scoring of hundreds of polymorphic loci without any need for prior sequence information. The work presented here details the development and performance of a DArT genotyping array for

The Genetic Diversity and Phylogenetic Characteritics of Rotavirus VP4(P Genotypes in Children With Acute Diarrhea

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Haghshenas Z

2011-11-01

Full Text Available Background: Acute gastroenteritis is a major cause of morbidity and mortality among children in developing countries. Rotaviruses are recognized as the most common etiologic factors of gastroenteritis. In this study, we determined the epidemiologic features, clinical symptoms and molecular structure of rotavirus VP4(P genotypes in children with acute diarrhea in Bahrami Hospital in Tehran Iran, during 2009 for justifying the routine use of rotavirus vaccines in children. Methods: One hundred fifty fecal samples from 150 children with acute diarrhea in Bahrami Pediatric Hospital in Tehran, Iran were collected from January to December 2009. The patients’ mean age was 20.90+18.19 years (ranging from 1 month to 14 years. Fecal samples were transported on ice to the laboratory of virology department of Pasture Institute of Iran. The demographic and clinical data for each case were entered in an author-devised questionnaire. Group A rotavirus was detected by dsRNA-PAGE. Subsequently, rotavirus genotyping (VP4 was performed by semi-nested multiple RT-PCR and the phylogenetic tree of the Rotavirus nucleotides was constructed. The data were analyzed by statistical tests including Wilcoxon signed and Mann-Whitney U. Results: Rotavirus was isolated in 19.3% of the samples, more than 90% of which had long RNA patterns. The predominant genotype (VP4 was P[8] (86% and other genotypes respectively were P[6] (6.9% and P[4] (6.9%. Conclusion: A high prevalence of the P[8] genotype was found to be the cause of acute diarrhea. The analysis of P[8] genotype sequence showed a high level of similarity of the virus in this study with those of other Asian countries.

Effect of participatory selection of varieties on the identification of outstanding common bean genotypes (Phaseolus vulgaris L.

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Alexis Lamz Piedra

2017-10-01

Full Text Available Among the main factors affecting bean production is poor distribution of varieties for different environmental conditions in which its are grown. The aim of this work was to evaluate the impact of participatory selection of foreign genetic materials and national commercial and pre-commercial common bean in identifying genotypes for their outstanding performance and resistance to common bacteriosis (Xanthomonas campestris pv. phaseoli (Smith Dye (Xcp. In the "El Mulato" farm belonging to the Empowered Cooperative of Credit and Services (CCSF "Orlando Cuellar" in the municipality San José de las Lajas, Mayabeque, two experiments were conducted. In the first one, 15 genotypes were planted in 13 September 2014 (early season in experimental plots to develop a diversity Fair and evaluate the natural incidence of common bean bacteriosis. In the second experiment, they were sown on 25 December (late season the materials selected by farmers with superior agronomic performance (7 genotypes to validate the stability of its performance. Among the results, an effective range of 93,33 % between the selected materials and selective criteria that this diversity was identified were high performance, resistance to common bacteriosis and color of beans. It was found that the selection of the diversity of beans by farmers is not influenced by the origin of materials and participatory selection identified common bean genotypes with high yield potential and stability between planting seasons.

Quantification and diversity in the black seeds (nigella sativa L.) gene stock of pakistan for their composition of mineral nutrients

International Nuclear Information System (INIS)

Iqbal, M.S.; Qureshi, A.S.; Ghafoor, A.

2009-01-01

Nigella saliva (L.) a member of family Ranunculaceae is an annual herbaceous plant indigenous to the Mediterranean region that contains more than 100 nutrients and had been used for edible and medicinal purposes in major parts of the world since long. Present study is on the analysis of thirty four accessions with two check genotypes for genetic diversity based on thirteen mineral nutrients. High variation for Fe, Ca, Cu, Mg, Pb, Zn, Co, Mn, Na, P, B, K and N indicated the scope of sample selection for these characters. Coefficient of correlation studies revealed that Cu had significantly positive correlation with Ca, whereas Mg was significantly correlated with Ca and Cu. Linkages of desirable traits are suggested to be broken through novel techniques for maximum exploitation of genomic diversity for valuable phyto-chemicals. Based on principal component analysis, first four factors contributed 62 percent of the variability amongst genotypes for mineral nutrients. Eigen value> I exhibited 23.57 % of variation for component I, 17.28 % for component 2 and 12.43 % of variation for component 3, respectively. Moreover, it also reflects the potential of improvement, through building broad based gene pool by acquiring more samples from diverse geographical areas. These principal components could be selected individually for the improvement of specific mineral nutrients for multipurpose use and applications. Six clusters were observed for 36 genotypes based on mineral nutrients. The genotypes Pk-020877, Pk-020749, Pk-020876, Pk-020545, Pk-020561, Pk-020781 and Pk-020729, Pk-020620, Pk-020561, Pk-020631, Pk-020879, Pk-020868 produced the highest N (5.56), Fe (0.74), Ca (10.83), Mg (11.56), Pb (0.09), Zn (0.09), Na (0.68), P (0.66), B (39.58), and K (0.99), whereas Pk-020873 produced lowest N (1.67), Pk-020766 Fe (0.10), Pk-020576 Ca (7.38), Pk-020585 Mg (9.40), check-2 Pb (0.02), Pk-020872 Zn (0.01), Pk-020781 and Pk-020877 Na (0.17), check-2 P (0.50), Pk-020585 B (13

Cercospora zeina from Maize in South Africa Exhibits High Genetic Diversity and Lack of Regional Population Differentiation.

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Muller, Mischa F; Barnes, Irene; Kunene, Ncobile T; Crampton, Bridget G; Bluhm, Burton H; Phillips, Sonia M; Olivier, Nicholas A; Berger, Dave K

2016-10-01

South Africa is one of the leading maize-producing countries in sub-Saharan Africa. Since the 1980s, Cercospora zeina, a causal agent of gray leaf spot of maize, has become endemic in South Africa, and is responsible for substantial yield reductions. To assess genetic diversity and population structure of C. zeina in South Africa, 369 isolates were collected from commercial maize farms in three provinces (KwaZulu-Natal, Mpumalanga, and North West). These isolates were evaluated with 14 microsatellite markers and species-specific mating type markers that were designed from draft genome sequences of C. zeina isolates from Africa (CMW 25467) and the United States (USPA-4). Sixty alleles were identified across 14 loci, and gene diversity values within each province ranged from 0.18 to 0.35. High levels of gene flow were observed (Nm = 5.51), and in a few cases, identical multilocus haplotypes were found in different provinces. Overall, 242 unique multilocus haplotypes were identified with a low clonal fraction of 34%. No distinct population clusters were identified using STRUCTURE, principal coordinate analysis, or Weir's theta θ statistic. The lack of population differentiation was supported by analysis of molecular variance tests, which indicated that only 2% of the variation was attributed to variability between populations from each province. Mating type ratios of MAT1-1 and MAT1-2 idiomorphs from 335 isolates were not significantly different from a 1:1 ratio in all provinces, which provided evidence for sexual reproduction. The draft genome of C. zeina CMW 25467 exhibited a complete genomic copy of the MAT1-1 idiomorph as well as exonic fragments of MAT genes from both idiomorphs. The high level of gene diversity, shared haplotypes at different geographical locations within South Africa, and presence of both MAT idiomorphs at all sites indicates widespread dispersal of C. zeina between maize fields in the country as well as evidence for sexual recombination. The

An Interactive Exhibition about Animal Skeletons: Did the Visitors Learn Any Zoology?

Science.gov (United States)

Tunnicliffe, Sue Dale; Laterveer-de Beer, Manon

2002-01-01

Explores museum visitors' understanding of skeleton exhibits and whether such exhibits increase their understanding of the zoology displayed. The exhibition under study focused on the diversity of vertebrae skeletons which were arranged according to the mode of locomotion. (DDR)

Digital phenotyping for quantification of genetic diversity in inbred guava (Psidium guajava) families.

Science.gov (United States)

Krause, W; Viana, A P; Cavalcante, N R; Ambrósio, M; Santos, E A; Vieira, H D

2017-03-22

Digital image analysis of seeds has been used for the identification of cultivars, determination of seed color and mechanical damage, and classification of different seed sizes. The aim of the present study was to evaluate the efficiency of digital image analysis of seeds for the quantification of genetic diversity among genotypes of inbred guava (Psidium guajava L.) families. The SAS Mini equipment, which consists of a capture module and a software program for analysis, was employed for the capture and analysis of the seed images. Different genetic diversity quantification strategies were tested using the Ward-Modified Location Model method. The set of variables related to geometry of the seeds was the largest contributor to divergence among the guava genotypes. The use of seed descriptors obtained by digital image analysis via the SAS system was efficient at quantifying the genetic diversity among genotypes of inbred guava families associated with the use of the Ward-Modified Location Model method.

CRISPR associated diversity within a population of Sulfolobus islandicus.

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Nicole L Held

2010-09-01

Full Text Available Predator-prey models for virus-host interactions predict that viruses will cause oscillations of microbial host densities due to an arms race between resistance and virulence. A new form of microbial resistance, CRISPRs (clustered regularly interspaced short palindromic repeats are a rapidly evolving, sequence-specific immunity mechanism in which a short piece of invading viral DNA is inserted into the host's chromosome, thereby rendering the host resistant to further infection. Few studies have linked this form of resistance to population dynamics in natural microbial populations.We examined sequence diversity in 39 strains of the archeaon Sulfolobus islandicus from a single, isolated hot spring from Kamchatka, Russia to determine the effects of CRISPR immunity on microbial population dynamics. First, multiple housekeeping genetic markers identify a large clonal group of identical genotypes coexisting with a diverse set of rare genotypes. Second, the sequence-specific CRISPR spacer arrays split the large group of isolates into two very different groups and reveal extensive diversity and no evidence for dominance of a single clone within the population.The evenness of resistance genotypes found within this population of S. islandicus is indicative of a lack of strain dominance, in contrast to the prediction for a resistant strain in a simple predator-prey interaction. Based on evidence for the independent acquisition of resistant sequences, we hypothesize that CRISPR mediated clonal interference between resistant strains promotes and maintains diversity in this natural population.

Geographic distribution of hepatitis C virus genotype 6 subtypes in Thailand.

Science.gov (United States)

Akkarathamrongsin, Srunthron; Praianantathavorn, Kesmanee; Hacharoen, Nisachol; Theamboonlers, Apiradee; Tangkijvanich, Pisit; Tanaka, Yasuhito; Mizokami, Masashi; Poovorawan, Yong

2010-02-01

The nucleotide sequence of hepatitis C virus (HCV) genotype 6 found mostly in south China and south-east Asia, displays profound genetic diversity. The aim of this study to determine the genetic variability of HCV genotype 6 (HCV-6) in Thailand and locate the subtype distribution of genotype 6 in various geographic areas. Four hundred nineteen anti-HCV positive serum samples were collected from patients residing in - the central part of the country. HCV RNA positive samples based on reverse transcriptase- polymerase chain reaction (RT-PCR) of the 5'UTR were amplified with primers specific for the core and NS5B regions. Nucleotide sequences of both regions were analyzed for the genotype by phylogenetic analysis. To determine geographic distribution of HCV-6 subtypes, a search of the international database on subtype distribution in the respective countries was conducted. Among 375 HCV RNA positive samples, 71 had HCV-6 based on phylogenetic analysis of partial core and NS5B regions. The subtype distribution in order of predominance was 6f (56%), 6n (22%), 6i (11%), 6j (10%), and 6e (1%). Among the 13 countries with different subtypes of HCV-6, most sequences have been reported from Vietnam. Subtype 6f was found exclusively in Thailand where five distinct HCV-6 subtypes are circulating. HCV-6, which is endemic in south China and south-east Asia, displays profound genetic diversity and may have evolved over a considerable period of time. (c) 2009 Wiley-Liss, Inc.

A quantitative and qualitative comparison of illumina MiSeq and 454 amplicon sequencing for genotyping the highly polymorphic major histocompatibility complex (MHC) in a non-model species.

Science.gov (United States)

Razali, Haslina; O'Connor, Emily; Drews, Anna; Burke, Terry; Westerdahl, Helena

2017-07-28

High-throughput sequencing enables high-resolution genotyping of extremely duplicated genes. 454 amplicon sequencing (454) has become the standard technique for genotyping the major histocompatibility complex (MHC) genes in non-model organisms. However, illumina MiSeq amplicon sequencing (MiSeq), which offers a much higher read depth, is now superseding 454. The aim of this study was to quantitatively and qualitatively evaluate the performance of MiSeq in relation to 454 for genotyping MHC class I alleles using a house sparrow (Passer domesticus) dataset with pedigree information. House sparrows provide a good study system for this comparison as their MHC class I genes have been studied previously and, consequently, we had prior expectations concerning the number of alleles per individual. We found that 454 and MiSeq performed equally well in genotyping amplicons with low diversity, i.e. amplicons from individuals that had fewer than 6 alleles. Although there was a higher rate of failure in the 454 dataset in resolving amplicons with higher diversity (6-9 alleles), the same genotypes were identified by both 454 and MiSeq in 98% of cases. We conclude that low diversity amplicons are equally well genotyped using either 454 or MiSeq, but the higher coverage afforded by MiSeq can lead to this approach outperforming 454 in amplicons with higher diversity.

Impact of marker ascertainment bias on genomic selection accuracy and estimates of genetic diversity.

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Nicolas Heslot

Full Text Available Genome-wide molecular markers are often being used to evaluate genetic diversity in germplasm collections and for making genomic selections in breeding programs. To accurately predict phenotypes and assay genetic diversity, molecular markers should assay a representative sample of the polymorphisms in the population under study. Ascertainment bias arises when marker data is not obtained from a random sample of the polymorphisms in the population of interest. Genotyping-by-sequencing (GBS is rapidly emerging as a low-cost genotyping platform, even for the large, complex, and polyploid wheat (Triticum aestivum L. genome. With GBS, marker discovery and genotyping occur simultaneously, resulting in minimal ascertainment bias. The previous platform of choice for whole-genome genotyping in many species such as wheat was DArT (Diversity Array Technology and has formed the basis of most of our knowledge about cereals genetic diversity. This study compared GBS and DArT marker platforms for measuring genetic diversity and genomic selection (GS accuracy in elite U.S. soft winter wheat. From a set of 365 breeding lines, 38,412 single nucleotide polymorphism GBS markers were discovered and genotyped. The GBS SNPs gave a higher GS accuracy than 1,544 DArT markers on the same lines, despite 43.9% missing data. Using a bootstrap approach, we observed significantly more clustering of markers and ascertainment bias with DArT relative to GBS. The minor allele frequency distribution of GBS markers had a deficit of rare variants compared to DArT markers. Despite the ascertainment bias of the DArT markers, GS accuracy for three traits out of four was not significantly different when an equal number of markers were used for each platform. This suggests that the gain in accuracy observed using GBS compared to DArT markers was mainly due to a large increase in the number of markers available for the analysis.

Impact of Marker Ascertainment Bias on Genomic Selection Accuracy and Estimates of Genetic Diversity

Science.gov (United States)

Heslot, Nicolas; Rutkoski, Jessica; Poland, Jesse; Jannink, Jean-Luc; Sorrells, Mark E.

2013-01-01

Genome-wide molecular markers are often being used to evaluate genetic diversity in germplasm collections and for making genomic selections in breeding programs. To accurately predict phenotypes and assay genetic diversity, molecular markers should assay a representative sample of the polymorphisms in the population under study. Ascertainment bias arises when marker data is not obtained from a random sample of the polymorphisms in the population of interest. Genotyping-by-sequencing (GBS) is rapidly emerging as a low-cost genotyping platform, even for the large, complex, and polyploid wheat (Triticum aestivum L.) genome. With GBS, marker discovery and genotyping occur simultaneously, resulting in minimal ascertainment bias. The previous platform of choice for whole-genome genotyping in many species such as wheat was DArT (Diversity Array Technology) and has formed the basis of most of our knowledge about cereals genetic diversity. This study compared GBS and DArT marker platforms for measuring genetic diversity and genomic selection (GS) accuracy in elite U.S. soft winter wheat. From a set of 365 breeding lines, 38,412 single nucleotide polymorphism GBS markers were discovered and genotyped. The GBS SNPs gave a higher GS accuracy than 1,544 DArT markers on the same lines, despite 43.9% missing data. Using a bootstrap approach, we observed significantly more clustering of markers and ascertainment bias with DArT relative to GBS. The minor allele frequency distribution of GBS markers had a deficit of rare variants compared to DArT markers. Despite the ascertainment bias of the DArT markers, GS accuracy for three traits out of four was not significantly different when an equal number of markers were used for each platform. This suggests that the gain in accuracy observed using GBS compared to DArT markers was mainly due to a large increase in the number of markers available for the analysis. PMID:24040295

Genotyping of polymorphic effectors of Toxoplasma gondii isolates from China

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Weisheng Cheng

2017-11-01

Full Text Available Abstract Background Toxoplasma gondii is an opportunistic protozoan apicomplexan and obligate intracellular parasite that infects a wide range of animals and humans. Rhoptry proteins 5 (ROP5, ROP16, ROP18 and dense granules 15 (GRA15 are the important effectors secreted by T. gondii which link to the strain virulence for mice and modulate the host’s response to the parasite. Little has been known about these molecules as well as GRA3 in type Chinese 1 strains that show polymorphism among strains of archetypical genotypes. This study examined the genetic diversity of these effectors and its correlated virulence in mice among T. gondii isolates from China. Results Twenty-one isolates from stray cats were detected, of which 15 belong to Chinese 1, and 6 to ToxoDB #205. Wh6 isolate, a Chinese 1 strain, has an avirulent phenotype. PCR-RFLP results of ROP5 and ROP18 presented few variations among the strains. Genotyping of GRA15 and ROP16 revealed that all the strains belong to type II allele except Xz7 which carries type I allele. ROP16 amino acid alignment at 503 locus demonstrated that 17 isolates are featured as type I or type III (ROP16I/III, and the other 4 as type II (ROP16II. The strains investigated may be divided into four groups based on GRA3 amino acid alignment, and all isolates of type Chinese 1 belong to the μ-1 allele except Wh6 which is identical to type II strain. Conclusions PCR-RFLP and sequence alignment analyses of ROP5, ROP16, ROP18, GRA3, and GRA15 in T. gondii revealed that strains with the same genotype may have variations in some of their key genes. GRA3 variation exhibited by Wh6 strain may be associated with the difference in phenotype and pathogenesis.

Characterization of genetic diversity in chickpea using SSR markers, Start Codon Targeted Polymorphism (SCoT) and Conserved DNA-Derived Polymorphism (CDDP).

Science.gov (United States)

Hajibarat, Zahra; Saidi, Abbas; Hajibarat, Zohreh; Talebi, Reza

2015-07-01

To evaluate the genetic diversity among 48 genotypes of chickpea comprising cultivars, landraces and internationally developed improved lines genetic distances were evaluated using three different molecular marker techniques: Simple Sequence Repeat (SSR); Start Codon Targeted (SCoT) and Conserved DNA-derived Polymorphism (CDDP). Average polymorphism information content (PIC) for SSR, SCoT and CDDP markers was 0.47, 0.45 and 0.45, respectively, and this revealed that three different marker types were equal for the assessment of diversity amongst genotypes. Cluster analysis for SSR and SCoT divided the genotypes in to three distinct clusters and using CDDP markers data, genotypes grouped in to five clusters. There were positive significant correlation (r = 0.43, P SSR markers. These results suggest that efficiency of SSR, SCOT and CDDP markers was relatively the same in fingerprinting of chickpea genotypes. To our knowledge, this is the first detailed report of using targeted DNA region molecular marker (CDDP) for genetic diversity analysis in chickpea in comparison with SCoT and SSR markers. Overall, our results are able to prove the suitability of SCoT and CDDP markers for genetic diversity analysis in chickpea for their high rates of polymorphism and their potential for genome diversity and germplasm conservation.

Tenofovir alafenamide demonstrates broad cross-genotype activity against wild-type HBV clinical isolates and maintains susceptibility to drug-resistant HBV isolates in vitro.

Science.gov (United States)

Liu, Yang; Miller, Michael D; Kitrinos, Kathryn M

2017-03-01

Tenofovir alafenamide (TAF) is a novel prodrug of tenofovir (TFV). This study evaluated the antiviral activity of TAF against wild-type genotype A-H HBV clinical isolates as well as adefovir-resistant, lamivudine-resistant, and entecavir-resistant HBV isolates. Full length HBV genomes or the polymerase/reverse transcriptase (pol/RT) region from treatment-naïve patients infected with HBV genotypes A-H were amplified and cloned into an expression vector under the control of a CMV promoter. In addition, 11 drug resistant HBV constructs were created by site-directed mutagenesis of a full length genotype D construct. Activity of TAF was measured by transfection of each construct into HepG2 cells and assessment of HBV DNA levels following treatment across a range of TAF concentrations. TAF activity in vitro was similar against wild-type genotype A-H HBV clinical isolates. All lamivudine- and entecavir-resistant isolates and 4/5 adefovir-resistant isolates were found to be sensitive to inhibition by TAF in vitro as compared to the wild-type isolate. The adefovir-resistant isolate rtA181V + rtN236T exhibited low-level reduced susceptibility to TAF. TAF is similarly active in vitro against wild-type genotype A-H HBV clinical isolates. The TAF sensitivity results for all drug-resistant isolates are consistent with what has been observed with the parent drug TFV. The in vitro cell-based HBV phenotyping assay results support the use of TAF in treatment of HBV infected subjects with diverse HBV genotypes, in both treatment-naive and treatment-experienced HBV infected patients. Copyright © 2016 Elsevier B.V. All rights reserved.

Cerebral and non-cerebral coenurosis: on the genotypic and phenotypic diversity of Taenia multiceps.

Science.gov (United States)

Christodoulopoulos, Georgios; Dinkel, Anke; Romig, Thomas; Ebi, Dennis; Mackenstedt, Ute; Loos-Frank, Brigitte

2016-12-01

We characterised the causative agents of cerebral and non-cerebral coenurosis in livestock by determining the mitochondrial genotypes and morphological phenotypes of 52 Taenia multiceps isolates from a wide geographical range in Europe, Africa, and western Asia. Three studies were conducted: (1) a morphological comparison of the rostellar hooks of cerebral and non-cerebral cysts of sheep and goats, (2) a morphological comparison of adult worms experimentally produced in dogs, and (3) a molecular analysis of three partial mitochondrial genes (nad1, cox1, and 12S rRNA) of the same isolates. No significant morphological or genetic differences were associated with the species of the intermediate host. Adult parasites originating from cerebral and non-cerebral cysts differed morphologically, e.g. the shape of the small hooks and the distribution of the testes in the mature proglottids. The phylogenetic analysis of the mitochondrial haplotypes produced three distinct clusters: one cluster including both cerebral isolates from Greece and non-cerebral isolates from tropical and subtropical countries, and two clusters including cerebral isolates from Greece. The majority of the non-cerebral specimens clustered together but did not form a monophyletic group. No monophyletic groups were observed based on geography, although specimens from the same region tended to cluster. The clustering indicates high intraspecific diversity. The phylogenetic analysis suggests that all variants of T. multiceps can cause cerebral coenurosis in sheep (which may be the ancestral phenotype), and some variants, predominantly from one genetic cluster, acquired the additional capacity to produce non-cerebral forms in goats and more rarely in sheep.

Characterization of casein gene complex and genetic diversity analysis in Indian goats.

Science.gov (United States)

Rout, P K; Kumar, A; Mandal, A; Laloe, D; Singh, S K; Roy, R

2010-04-01

Milk protein polymorphism plays an important role in genetic diversity analysis, phylogenetic studies, establishing geographical diversity, conservation decision, and improving breeding goals. Milk protein polymorphism in Indian goat breeds has not been well studied; therefore, an investigation was carried out to analyze the genetic structure of the casein gene and milk protein diversity at six milk protein loci in nine Indian goat breeds/genetic groups from varied agro-climatic zones. Milk protein genotyping was carried out in 1098 individual milk samples by SDS-PAGE at alphaS1-CN (CSN1S1), beta-CN (CSN2), alphaS2-CN (CSN1S2), kappa-CN (CSN3), beta-LG, and alpha-LA loci. Indian goats exhibited alphaS1-casein A allele in higher frequency in the majority of breeds except Ganjam and local goats. The alphaS1-casein A allele frequencies varied from 0.45 to 0.77. A total of 16 casein haplotypes were observed in seven breeds and breed specific haplotypes were observed with respect to geographic region. The average number of alleles was lowest in Ganjam (1.66 +/- 0.81) and highest in Sirohi goats (2.50 +/- 1.05). Expected heterozygosity at six different loci demonstrated genetic diversity and breed fragmentation. Neighbor-Joining tree was built basing on Nei's distance. There was about 16.95% variability due to differences between breeds, indicating a strong subdivision. Principal component analysis was carried out to highlight the relationship among breeds. The variability among goat breeds was contributed by alphaS2-CN, beta-LG and alphaS1-CN. The Indian goats exhibited alphaS1-CN (CSN1S1) A allele in higher frequency in all the breeds indicating the higher casein yield in their milk.

Historical distribution and molecular diversity of Bacillus anthracis, Kazakhstan.

Science.gov (United States)

Aikembayev, Alim M; Lukhnova, Larissa; Temiraliyeva, Gulnara; Meka-Mechenko, Tatyana; Pazylov, Yerlan; Zakaryan, Sarkis; Denissov, Georgiy; Easterday, W Ryan; Van Ert, Matthew N; Keim, Paul; Francesconi, Stephen C; Blackburn, Jason K; Hugh-Jones, Martin; Hadfield, Ted

2010-05-01

To map the distribution of anthrax outbreaks and strain subtypes in Kazakhstan during 1937-2005, we combined geographic information system technology and genetic analysis by using archived cultures and data. Biochemical and genetic tests confirmed the identity of 93 archived cultures in the Kazakhstan National Culture Collection as Bacillus anthracis. Multilocus variable number tandem repeat analysis genotyping identified 12 genotypes. Cluster analysis comparing these genotypes with previously published genotypes indicated that most (n = 78) isolates belonged to the previously described A1.a genetic cluster, 6 isolates belonged to the A3.b cluster, and 2 belonged to the A4 cluster. Two genotypes in the collection appeared to represent novel genetic sublineages; 1 of these isolates was from Krygystan. Our data provide a description of the historical, geographic, and genetic diversity of B. anthracis in this Central Asian region.

Genetic diversity as assessed by morphological and microsatellite ...

African Journals Online (AJOL)

lap

2012-10-18

Oct 18, 2012 ... Genetic diversity in 20 elite greengram [Vigna radiata (L.) R. Wilczek] ... bean and cowpea were successfully amplified across 20 greengram genotypes of .... PCR amplified products were subjected to electrophoresis in a.

Genetic diversity of Echinococcus spp. in Russia.

Science.gov (United States)

Konyaev, Sergey V; Yanagida, Tetsuya; Nakao, Minoru; Ingovatova, Galina M; Shoykhet, Yakov N; Bondarev, Alexandr Y; Odnokurtsev, Valeriy A; Loskutova, Kyunnyay S; Lukmanova, Gulnur I; Dokuchaev, Nikolai E; Spiridonov, Sergey; Alshinecky, Mikhail V; Sivkova, Tatyana N; Andreyanov, Oleg N; Abramov, Sergey A; Krivopalov, Anton V; Karpenko, Sergey V; Lopatina, Natalia V; Dupal, Tamara A; Sako, Yasuhito; Ito, Akira

2013-11-01

In Russia, both alveolar and cystic echinococcoses are endemic. This study aimed to identify the aetiological agents of the diseases and to investigate the distribution of each Echinococcus species in Russia. A total of 75 Echinococcus specimens were collected from 14 host species from 2010 to 2012. Based on the mitochondrial DNA sequences, they were identified as Echinococcus granulosus sensu stricto (s.s.), E. canadensis and E. multilocularis. E. granulosus s.s. was confirmed in the European Russia and the Altai region. Three genotypes, G6, G8 and G10 of E. canadensis were detected in Yakutia. G6 was also found in the Altai region. Four genotypes of E. multilocularis were confirmed; the Asian genotype in the western Siberia and the European Russia, the Mongolian genotype in an island of Baikal Lake and the Altai Republic, the European genotype from a captive monkey in Moscow Zoo and the North American genotype in Yakutia. The present distributional record will become a basis of public health to control echinococcoses in Russia. The rich genetic diversity demonstrates the importance of Russia in investigating the evolutionary history of the genus Echinococcus.

Performance of Different Tomato Genotypes in the Arid Tropics of Sudan during the Summer Season. II. Generative Development

Directory of Open Access Journals (Sweden)

Adil H.A. Abdelmageed

2009-10-01

Full Text Available Eleven tomato genotypes of diverse origin were grown in Shambat, University of Khartoum, Sudan, in a randomized block design with three replications for two successive seasons (2002/2003, 2003/2004. The same genotypes were firstly evaluated under glasshouse conditions at the Humboldt University of Berlin, Germany during 2002. Highly significant differences were encountered among the different genotypes for most of the generative characters, such as number of days to flowering, number of flowers per plant, number of fruits per plant, fruit fresh weight per plant and fruit set percentage. Based on results obtained from this study, the genotype ‘Summerset’ proved to be high yielding under high temperature conditions in comparison to other genotypes.

[Study on VNTR diversity of clinical Mycobacterium tuberculosis isolates from Qinghai].

Science.gov (United States)

Li, Bin; Liu, Haican; Wang, Zhaofen; Ma, Yongcheng; Su, Xiaodong; Jiang, Mingxia; Wan, Kanglin; Liu, Shou; Zhao, Xiuqin; Qu, Shugen

2015-10-01

To investigate the variable number tandem repeats (VNTR) genetic polymorphisms, genotyping and distribution pattern of clinical Mycobacterium (M.) tuberculosis isolates from Qinghai province. The clinical M. tuberculosis strains isolated from the patients with tuberculosis and related background data were collected from Qinghai Provincial Center for Disease Control and Prevention from 2009 to 2012. Genotyping was conducted by using multiple locus VNTR analysis (MLVA). Genomic DNA was extracted and 15 VNTR loci were amplified with PCR and the PCR products were detected with gel electrophoresis. The VNTR diversity and clusters of genotyping were analyzed with BioNumerics (Version 5.0). A total of 251 clinical M. tuberculosis isolates were analyzed with 15 VNTR loci showing that there were great genetic diversity in these isolates. Six of the 15 VNTR loci, showed that the Hunter-Gaston index (HGI) were higher than 0.6, in which the highest resolution was MIRU26. The clusters of genotyping showed that these isolates could be categorized into four gene clusters and 238 genotypes. The four gene clusters accounted for 4.9%, 91.9%, 1.6% and 1.6% of the clinical isolates, respectively. The results showed that there is great variety of VNTR genetic polymorphisms in clinical M. tuberculosis isolates in Qinghai province.

Effects of MAOA-genotype, alcohol consumption, and aging on violent behavior.

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Tikkanen, Roope; Sjöberg, Rickard L; Ducci, Francesca; Goldman, David; Holi, Matti; Tiihonen, Jari; Virkkunen, Matti

2009-03-01

Environmental factors appear to interact with a functional polymorphism (MAOA-LPR) in the promoter region of the monoamine oxidase A gene (MAOA) in determining some forms of antisocial behavior. However, how MAOA-LPR modulates the effects of other factors such as alcohol consumption related to antisocial behavior is not completely understood. This study examines the conjunct effect of MAOA-LPR, alcohol consumption, and aging on the risk for violent behavior. Recidivism in severe impulsive violent behavior was assessed after 7 to 15 years in a sample of 174 Finnish alcoholic offenders, the majority of whom exhibited antisocial or borderline personality disorder or both, and featured impulsive temperament traits. The risk for committing new acts of violence increased by 2.3% for each kilogram of increase in yearly mean alcohol consumption (p = 0.004) and decreased by 7.3% for every year among offenders carrying the high activity MAOA genotype. In contrast, alcohol consumption and aging failed to affect violent behavior in the low activity MAOA genotyped offenders. MAOA-LPR showed no main effect on the risk for recidivistic violence. Violent offenders carrying the high activity MAOA genotype differ in several ways from carriers with the low activity MAOA risk allele previously associated with antisocial behavior. Finnish high activity MAOA genotyped risk alcoholics exhibiting antisocial behavior, high alcohol consumption, and abnormal alcohol-related impulsive and uncontrolled violence might represent an etiologically distinct alcohol dependence subtype.

Short communication. Genotyping and phylogenetic analysis of bovine viral diarrhea virus (BVDV) isolates in Kosovo

OpenAIRE

Izedin Goga; Kristaq Berxholi; Beqe Hulaj; Driton Sylejmani; Boris Yakobson; Yehuda Stram

2014-01-01

Three serum samples positive in Antigen ELISA BVDV have been tested to characterise genetic diversity of bovine viral diarrhea virus (BVDV) in Kosovo. Samples were obtained in 2011 from heifers and were amplified by reverse transcription-polymerase chain reaction, sequenced and analysed by computer-assisted phylogenetic analysis. Amplified products and nucleotide sequence showed that all 3 isolates belonged to BVDV 1 genotype and 1b sub genotype. These results enrich the extant knowledge of B...

Insights into the genetic structure and diversity of 38 South Asian Indians from deep whole-genome sequencing.

Science.gov (United States)

Wong, Lai-Ping; Lai, Jason Kuan-Han; Saw, Woei-Yuh; Ong, Rick Twee-Hee; Cheng, Anthony Youzhi; Pillai, Nisha Esakimuthu; Liu, Xuanyao; Xu, Wenting; Chen, Peng; Foo, Jia-Nee; Tan, Linda Wei-Lin; Koo, Seok-Hwee; Soong, Richie; Wenk, Markus Rene; Lim, Wei-Yen; Khor, Chiea-Chuen; Little, Peter; Chia, Kee-Seng; Teo, Yik-Ying

2014-05-01

South Asia possesses a significant amount of genetic diversity due to considerable intergroup differences in culture and language. There have been numerous reports on the genetic structure of Asian Indians, although these have mostly relied on genotyping microarrays or targeted sequencing of the mitochondria and Y chromosomes. Asian Indians in Singapore are primarily descendants of immigrants from Dravidian-language-speaking states in south India, and 38 individuals from the general population underwent deep whole-genome sequencing with a target coverage of 30X as part of the Singapore Sequencing Indian Project (SSIP). The genetic structure and diversity of these samples were compared against samples from the Singapore Sequencing Malay Project and populations in Phase 1 of the 1,000 Genomes Project (1 KGP). SSIP samples exhibited greater intra-population genetic diversity and possessed higher heterozygous-to-homozygous genotype ratio than other Asian populations. When compared against a panel of well-defined Asian Indians, the genetic makeup of the SSIP samples was closely related to South Indians. However, even though the SSIP samples clustered distinctly from the Europeans in the global population structure analysis with autosomal SNPs, eight samples were assigned to mitochondrial haplogroups that were predominantly present in Europeans and possessed higher European admixture than the remaining samples. An analysis of the relative relatedness between SSIP with two archaic hominins (Denisovan, Neanderthal) identified higher ancient admixture in East Asian populations than in SSIP. The data resource for these samples is publicly available and is expected to serve as a valuable complement to the South Asian samples in Phase 3 of 1 KGP.

Measles virus genotypes circulating in India, 2011-2015.

Science.gov (United States)

Vaidya, Sunil R; Chowdhury, Deepika T

2017-05-01

The Government of India is accepted to participate in the measles elimination and rubella control goal 2020, hence genetic characterization of measles viruses (MeV) becomes essential. At National Reference Laboratory (National Institute of Virology, Pune), the throat swabs/urine specimens (n = 380) or PCR products (n = 219) obtained from the suspected measles cases were referred for the molecular testing and subsequently, MeV nucleoprotein (N) gene sequencing/genotyping. In addition, 2,449 suspected measles cases, mainly from the Maharashtra state were referred for the laboratory diagnosis. A detailed study was performed on N gene sequences obtained during last two decades. Indian MeV sequences obtained during 2011-2015 were compared with 1996-2010 sequences and genetic divergence was studied. Circulation of measles genotypes B3 (n = 3), D4 (n = 49), and D8 (n = 351) strains were observed in 19 States and three Union Territories of India. In addition, 64 measles viruses were isolated from 253 throat swab or urine specimens obtained from the suspected measles cases. During 2011-2015, 67.9% (1,663/2,449) suspected measles cases were laboratory confirmed. Molecular studies showed circulation of measles genotype B3 in India along with prominently circulating genotypes D4 and D8 except D7 strains. The genetic diversion within Indian B3, D4, and D8 genotypes was 0.3%, 1.1%, and 2.1%, respectively. The genetic divergence of Indian B3, D4, and D8 measles strains with the WHO reference sequences was 2.5%, 2.6%, and 1.8%, respectively. It is crucial data for national immunization program. More measles/rubella genotyping studies are necessary to track transmission and to support measles elimination and rubella control. J. Med. Virol. 89:753-758, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Genotyping and Molecular Identification of Date Palm Cultivars Using Inter-Simple Sequence Repeat (ISSR) Markers.

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Ayesh, Basim M

2017-01-01

Molecular markers are credible for the discrimination of genotypes and estimation of the extent of genetic diversity and relatedness in a set of genotypes. Inter-simple sequence repeat (ISSR) markers rapidly reveal high polymorphic fingerprints and have been used frequently to determine the genetic diversity among date palm cultivars. This chapter describes the application of ISSR markers for genotyping of date palm cultivars. The application involves extraction of genomic DNA from the target cultivars with reliable quality and quantity. Subsequently the extracted DNA serves as a template for amplification of genomic regions flanked by inverted simple sequence repeats using a single primer. The similarity of each pair of samples is measured by calculating the number of mono- and polymorphic bands revealed by gel electrophoresis. Matrices constructed for similarity and genetic distance are used to build a phylogenetic tree and cluster analysis, to determine the molecular relatedness of cultivars. The protocol describes 3 out of 9 tested primers consistently amplified 31 loci in 6 date palm cultivars, with 28 polymorphic loci.

Interaction in Short rotation coppice willow, Salix viminalis genotype mixtures

Energy Technology Data Exchange (ETDEWEB)

Begley, D. [Department of Biological Sciences, Queen' s University Belfast, Newforge Lane, Belfast BT9 5PX, Northern Ireland (United Kingdom); McCracken, A.R. [Applied Plant Science and Biometrics Division, Agri-Food and Biosciences Institute, 18A Newforge Lane, Belfast BT9 5PX, Northern Ireland (United Kingdom)]|[Northern Ireland Horticulture and Plant Breeding Station, Applied Plant Science and Biometrics Division, Agri-Food and Biosciences Institute, Loughgall, Co., Armagh BT61 8JB, Northern Ireland (United Kingdom); Dawson, W.M. [Northern Ireland Horticulture and Plant Breeding Station, Applied Plant Science and Biometrics Division, Agri-Food and Biosciences Institute, Loughgall, Co., Armagh BT61 8JB, Northern Ireland (United Kingdom); Watson, S. [Applied Plant Science and Biometrics Division, Agri-Food and Biosciences Institute, 18A Newforge Lane, Belfast BT9 5PX, Northern Ireland (United Kingdom)

2009-02-15

Seven straight Salix viminalis genotypes with different levels of rust (Melampsora epitea) susceptibility were grown as mono-plots as well as being incorporated into a range of mixtures. Two 3-year harvests (2003 and 2006) were taken. Disease progress was followed on each of the individual genotypes throughout each growing season 2001-2006. In 2003 there were small but significant yield increases from the mixtures compared to the yield of individual components grown as mono-plots. These differences were not evident at the second harvest in 2006. No consistent effect of mixtures on reducing rust on the most susceptible genotype, Salix viminalis '77082' were observed. In some years, e.g. 2003, at certain times during the growing season, significant reductions were observed on Salix viminalis '77082' in certain 3-way mixtures compared to mono-plots. These, however, were not repeated consistently in subsequent years. It was concluded that the current commercial practice in many parts of Europe of planting mixtures as a disease control strategy will only be effective if there is sufficient genetic diversity between the Salix genotypes incorporated into the mixture. (author)

Allelopathic activity of pakistan wheat genotypes against wild oat (Avena fatua L.)

International Nuclear Information System (INIS)

Mahmood, K.; Khaliq, A.; Cheema, Z.A.; Arshad, M.

2013-01-01

Wheat allelopathy can be manipulated for sustainable weed management in wheat based cropping systems. Bioassays were conducted to quantify the allelopathic potential of 35 indigenous wheat genotypes against germination and seedling growth of wild oat (Avena fatua L.). Foliar application of aqueous extracts of wheat straw, surface mulching and incorporation of wheat straw of different genotypes were employed for bioassays study. Results revealed the suppressive allelopathic activity of different wheat genotypes manifested in the form of impaired germination and retarded seedling growth of wild oat. A highly significant genotypic variation in allelopathic potential was observed for different traits. Germination of wild oat was decreased by 10-84% over control by different wheat genotypes. Likewise, over 70% reductions in seedling root and shoot dry weight of wild oat was also observed in V6007. Wheat genotypes viz. V6007, AS 2000, V6111, V6034, V4611, V7189, Uqa b 2000, Chanab 2000, Bhakkar 2002, Pak 81 and Rohtas 90 showed strongly inhibitory allelopathic activity against seedling growth of wild oat. V6007 exhibited highest suppression of wild oat. These studies confirm the suppressive allelopathic potential of indigenous wheat genotypes against wild oat that needs further to be explored under natural conditions. (author)

Genetic Diversity and Structure of the Apiosporina morbosa Populations on Prunus spp.

Science.gov (United States)

Zhang, Jinxiu; Fernando, W G Dilantha; Remphrey, William R

2005-08-01

ABSTRACT Populations of Apiosporina morbosa collected from 15 geographic locations in Canada and the United States and three host species, Prunus virginiana, P. pensylvanica, and P. padus, were evaluated using the sequence-related amplified polymorphism (SRAP) technique to determine their genetic diversity and population differentiation. Extensive diversity was detected in the A. morbosa populations, including 134 isolates from Canada and the United States, regardless of the origin of the population. The number of polymorphic loci varied from 6.9 to 82.8% in the geographic populations, and from 41.4 to 79.3% in the populations from four host genotypes based on 58 polymorphic fragments. In all, 44 to 100% of isolates in the geographic populations and 43.6 to 76.2% in populations from four host genotypes represented unique genotypes. Values of heterozygosity (H) varied from 2.8 to 28.3% in the geographic populations and 10.2 to 26.1% in the populations from four host genotypes. In general, the A. morbosa populations sampled from wild chokecherry showed a higher genetic diversity than those populations collected from other host species, whereas the populations isolated from cultivated chokecherry, P. virginiana 'Shubert Select', showed a reduction of genetic diversity compared with populations from wild P. virginiana. Significant population differentiation was found among both the geographic populations (P virginiana were closely clustered, and no population differentiation was detected except for the populations from Morris, Morden, and Winnipeg, Manitoba, Canada. Furthermore, the populations from P. virginiana in the same geographic locations had higher genetic identity and closer genetic distance to each other compared with those from different locations. Four populations from P. virginiana, P. pensylvanica, and P. padus, were significantly differentiated from each other (P P> = 0.334). Indirect estimation of gene flow showed that significant restricted gene flow

Genetic diversity of Aspergillus fumigatus in indoor hospital environments.

Science.gov (United States)

Araujo, Ricardo; Amorim, António; Gusmão, Leonor

2010-09-01

Environmental isolates of Aspergillus fumigatus are less studied than those recovered from clinical sources. In the present study, the genetic diversity among such environmental isolates was assessed, as well as their dispersion ability and the acquisition of new strains in 19 medical units of the same hospital. A. fumigatus isolates were genotyped using a single multiplex PCR-based reaction with eight microsatellite markers and an insertion/deletion polymorphism. A total of 130 unique genotypes were found among a total of 250 A. fumigatus isolates. Genotypic diversity ranged from 0.86 to 1 in samples from hospital rooms, and there was no correlation between these samples and the presence of high-efficiency particulate air filters or any other air filtration system. Four of the six most prevalent A. fumigatus strains were recovered from water samples. The occurrence of microvariation was common among environmental isolates, which affected each of the microsatellite markers. The assessment of the genetic diversity of A. fumigatus is a useful tool for illustrating the presence or absence of specific clonal populations in a clinical setting. A. fumigatus populations were highly dynamic indoors, and new populations were found in just a few months. Due to the high indoor dispersion capability of A. fumigatus, more attention should be given to strains with increased pathogenic potential or reduced susceptibility to anti-fungal drugs.

True-slime-mould-inspired hydrostatically coupled oscillator system exhibiting versatile behaviours

International Nuclear Information System (INIS)

Umedachi, Takuya; Ito, Kentaro; Idei, Ryo; Ishiguro, Akio

2013-01-01

Behavioural diversity is an indispensable attribute of living systems, which makes them intrinsically adaptive and responsive to the demands of a dynamically changing environment. In contrast, conventional engineering approaches struggle to suppress behavioural diversity in artificial systems to reach optimal performance in given environments for desired tasks. The goals of this research include understanding the essential mechanism that endows living systems with behavioural diversity and implementing the mechanism in robots to exhibit adaptive behaviours. For this purpose, we have focused on an amoeba-like unicellular organism: the plasmodium of true slime mould. Despite the absence of a central nervous system, the plasmodium exhibits versatile spatiotemporal oscillatory patterns and switches spontaneously among these patterns. By exploiting this behavioural diversity, it is able to exhibit adaptive behaviour according to the situation encountered. Inspired by this organism, we built a real physical robot using hydrostatically coupled oscillators that produce versatile oscillatory patterns and spontaneous transitions among the patterns. The experimental results show that exploiting physical hydrostatic interplay—the physical dynamics of the robot—allows simple phase oscillators to promote versatile behaviours. The results can contribute to an understanding of how a living system generates versatile and adaptive behaviours with physical interplays among body parts. (paper)

Genotype-Phenotype Correlation of Maternally Inherited Disorders due to Mutations in Mitochondrial DNA

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Peterus Thajeb

2006-09-01

Full Text Available Mitochondrial disorders are heterogeneous systemic ailments that are most often caused by maternal inheritance of a variety of mutations of the mitochondrial (mt DNA. Paternal inheritance and somatic mutation are rare. The disorders are well recognized not only for the genotypic heterogeneity, but also the phenotypic variation among the affected members of a single family. The genotype-phenotype correlation of the diversity of the syndromic and non-syndromic features of mitochondrial disorders are discussed. Some aspects of the molecular mechanisms of this heterogeneity, and the histopathologic findings are highlighted.

Mycobacterial Interspersed Repetitive-Unit–Variable-Number Tandem-Repeat (MIRU-VNTR) Genotyping of Mycobacterium intracellulare for Strain Comparison with Establishment of a PCR-Based Database

Science.gov (United States)

Iakhiaeva, Elena; McNulty, Steven; Brown Elliott, Barbara A.; Falkinham, Joseph O.; Williams, Myra D.; Vasireddy, Ravikiran; Wilson, Rebecca W.; Turenne, Christine

2013-01-01

Strain comparison is important to population genetics and to evaluate relapses in patients with Mycobacterium avium complex (MAC) lung disease, but the “gold standard” of pulsed-field gel electrophoresis (PFGE) is time-consuming and complex. We used variable-number tandem repeats (VNTR) for fingerprinting of respiratory isolates of M. intracellulare from patients with underlying bronchiectasis, to establish a nonsequence-based database for population analysis. Different genotypes identified by PFGE underwent species identification using a 16S rRNA gene multiplex PCR. Genotypes of M. intracellulare were confirmed by internal transcribed spacer 1 (ITS1) sequencing and characterized using seven VNTR primers. The pattern of VNTR amplicon sizes and repeat number defined each specific VNTR type. Forty-two VNTR types were identified among 84 genotypes. PFGE revealed most isolates with the same VNTR type to be clonal or exhibit similar grouping of bands. Repetitive sequence-based PCR (rep-PCR) showed minimal pattern diversity between VNTR types compared to PFGE. Fingerprinting of relapse isolates from 31 treated patients using VNTR combined with 16S multiplex PCR unambiguously and reliably distinguished different genotypes from the same patient, with results comparable to those of PFGE. VNTR for strain comparison is easier and faster than PFGE, is as accurate as PFGE, and does not require sequencing. Starting with a collection of 167 M. intracellulare isolates, VNTR distinguished M. intracellulare into 42 clonal groups. Comparison of isolates from different geographic areas, habitats, and clinical settings is now possible. PMID:23175249

Mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) genotyping of mycobacterium intracellulare for strain comparison with establishment of a PCR-based database.

Science.gov (United States)

Iakhiaeva, Elena; McNulty, Steven; Brown Elliott, Barbara A; Falkinham, Joseph O; Williams, Myra D; Vasireddy, Ravikiran; Wilson, Rebecca W; Turenne, Christine; Wallace, Richard J

2013-02-01

Strain comparison is important to population genetics and to evaluate relapses in patients with Mycobacterium avium complex (MAC) lung disease, but the "gold standard" of pulsed-field gel electrophoresis (PFGE) is time-consuming and complex. We used variable-number tandem repeats (VNTR) for fingerprinting of respiratory isolates of M. intracellulare from patients with underlying bronchiectasis, to establish a nonsequence-based database for population analysis. Different genotypes identified by PFGE underwent species identification using a 16S rRNA gene multiplex PCR. Genotypes of M. intracellulare were confirmed by internal transcribed spacer 1 (ITS1) sequencing and characterized using seven VNTR primers. The pattern of VNTR amplicon sizes and repeat number defined each specific VNTR type. Forty-two VNTR types were identified among 84 genotypes. PFGE revealed most isolates with the same VNTR type to be clonal or exhibit similar grouping of bands. Repetitive sequence-based PCR (rep-PCR) showed minimal pattern diversity between VNTR types compared to PFGE. Fingerprinting of relapse isolates from 31 treated patients using VNTR combined with 16S multiplex PCR unambiguously and reliably distinguished different genotypes from the same patient, with results comparable to those of PFGE. VNTR for strain comparison is easier and faster than PFGE, is as accurate as PFGE, and does not require sequencing. Starting with a collection of 167 M. intracellulare isolates, VNTR distinguished M. intracellulare into 42 clonal groups. Comparison of isolates from different geographic areas, habitats, and clinical settings is now possible.

Role of abscisic acid and proline in salinity tolerance of wheat genotypes

International Nuclear Information System (INIS)

Shafi, M.; Bakht, J.; Khan, M.J.; Raziuddin; Khan, M.A.

2011-01-01

Wheat genotypes were evaluated for salinity tolerance under 3 diverse environments of Yar Hussain, Baboo Dehari (District Swabi KPK Pakistan) and Khitab Koroona (District Charsadda KPK Pakistan). Eleven genotypes (Local, SR-24, SR-25, SR-7, SR-22, SR-4, SR-20, SR-19, SR-2, SR-23 and SR-40) were tested for their salinity tolerance. These locations had different salinity profile (i.e. Yar Hussain, EC. 3-3.5 dS m/sup -1/; Baboo Dehari, EC. 4-4.5 dS m/sup -1/ and Khitab Koroona, EC. 5-5.30 dSm/sup -1/). Different locations and wheat genotypes had a significant (p < 0.05) effect on endogenous shoot proline, shoot ABA (3, 6 and 9 weeks after emergence) and straw yield. Maximum endogenous shoot proline and ABA levels (3, 6 and 9 weeks after emergence) were recorded in genotype SR-40 followed by genotype SR-23. The results further indicated that minimum endogenous shoot proline and ABA concentrations (3, 6 and 9 weeks after emergence) were recorded at Yar Hussain. Maximum endogenous shoot proline and ABA concentration (3, 6 and 9 weeks after emergence) were observed at Khitab Koroona. (author)

Genome-wide Differences in DNA Methylation Changes in Two Contrasting Rice Genotypes in Response to Drought Conditions

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Wensheng Wang

2016-11-01

Full Text Available Differences in drought stress tolerance within diverse rice genotypes have been attributed to genetic diversity and epigenetic alterations. DNA methylation is an important epigenetic modification that influences diverse biological processes, but its effects on rice drought stress tolerance are poorly understood. In this study, methylated DNA immunoprecipitation sequencing and an Affymetrix GeneChip rice genome array were used to profile the DNA methylation patterns and transcriptomes of the drought-tolerant introgression line DK151 and its drought-sensitive recurrent parent IR64 under drought and control conditions. The introgression of donor genomic DNA induced genome-wide DNA methylation changes in DK151 plants. A total of 1190 differentially methylated regions (DMRs were detected between the two genotypes under normal growth conditions, and the DMR-associated genes in DK151 plants were mainly related to stress response, programmed cell death, and nutrient reservoir activity, which are implicated to constitutive drought stress tolerance. A comparison of the DNA methylation changes in the two genotypes under drought conditions indicated that DK151 plants have a more stable methylome, with only 92 drought-induced DMRs, than IR64 plants with 506 DMRs. Gene ontology analyses of the DMR-associated genes in drought-stressed plants revealed that changes to the DNA methylation status of genotype-specific genes are associated with the epigenetic regulation of drought stress responses. Transcriptome analysis further helped to identify a set of 12 and 23 DMR-associated genes that were differentially expressed in DK151 and IR64, respectively, under drought stress compared with respective controls. Correlation analysis indicated that DNA methylation has various effects on gene expression, implying that it affects gene expression directly or indirectly through diverse regulatory pathways. Our results indicate that drought-induced alterations to DNA

Genotypic variation influences reproductive success and thermal stress tolerance in the reef building coral, Acropora palmata

Science.gov (United States)

Baums, I. B.; Devlin-Durante, M. K.; Polato, N. R.; Xu, D.; Giri, S.; Altman, N. S.; Ruiz, D.; Parkinson, J. E.; Boulay, J. N.

2013-09-01

The branching coral Acropora palmata is a foundation species of Caribbean reefs that has been decimated in recent decades by anthropogenic and natural stressors. Declines in population density and genotypic diversity likely reduce successful sexual reproduction in this self-incompatible hermaphrodite and might impede recovery. We investigated variation among genotypes in larval development under thermally stressful conditions. Six two-parent crosses and three four-parent batches were reared under three temperatures and sampled over time. Fertilization rates differed widely with two-parent crosses having lower fertilization rates (5-56 %, mean 22 % ± 22 SD) than batches (from 31 to 87 %, mean 59 % ± 28 SD). Parentage analysis of larvae in batch cultures showed differences in gamete compatibility among parents, coinciding with significant variation in both sperm morphology and egg size. While all larval batches developed more rapidly at increased water temperatures, rate of progression through developmental stages varied among batches, as did swimming speed. Together, these results indicate that loss of genotypic diversity exacerbates already severe limitations in sexual reproductive success of A. palmata. Nevertheless, surviving parental genotypes produce larvae that do vary in their phenotypic response to thermal stress, with implications for adaptation, larval dispersal and population connectivity in the face of warming sea surface temperatures.

Genetic diversity among endangered rare Dalbergia ...

African Journals Online (AJOL)

Genetic diversity among endangered rare Dalbergia cochinchinensis (Fabaceae) genotypes in Vietnam revealed by random amplified polymorphic DNA (RAPD) ... The number of amplified fragments varied from 1 (OPR15, OPB05, RA142, OPR08, UBC348, OPE14 and OPO04) to 8 (OPP19) and their sizes ranged from 250 ...

Single Nucleotide Polymorphisms in Common Bean: Their Discovery and Genotyping Using a Multiplex Detection System

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E. Gaitán-Solís

2008-11-01

Full Text Available Single nucleotide polymorphism (SNP markers are by far the most common form of DNA polymorphism in a genome. The objectives of this study were to discover SNPs in common bean ( L. by comparing sequences from coding and noncoding regions obtained from the GenBank and genomic DNA and to compare sequencing results with those obtained using single base extension (SBE assays on the Luminex-100 system for use in high-throughput germplasm evaluation. We assessed the frequency of SNPs in 47 fragments of common bean DNA, using SBE as the evaluation methodology. We conducted a sequence analysis of 10 genotypes of cultivated and wild beans belonging to the Mesoamerican and Andean genetic pools of . For the 10 genotypes evaluated, a total of 20,964 bp of sequence were analyzed in each genotype and compared, resulting in the discovery of 239 SNPs and 133 InDels, giving an average SNP frequency of one per 88 bp and an InDel frequency of one per 157 bp. This is the equivalent of a nucleotide diversity (θ of 6.27 × 10. Comparisons with the SNP genotypes previously obtained by direct sequencing showed that the SBE assays on the Luminex-100 were accurate, with 2.5% being miscalled and 1% showing no signal. These results indicate that the Luminex-100 provides a high-throughput system that can be used to analyze SNPs in large samples of genotypes both for purposes of assessing diversity and also for mapping studies.

Elevated temperature is more effective than elevated [CO2 ] in exposing genotypic variation in Telopea speciosissima growth plasticity: implications for woody plant populations under climate change.

Science.gov (United States)

Huang, Guomin; Rymer, Paul D; Duan, Honglang; Smith, Renee A; Tissue, David T

2015-10-01

Intraspecific variation in phenotypic plasticity is a critical determinant of plant species capacity to cope with climate change. A long-standing hypothesis states that greater levels of environmental variability will select for genotypes with greater phenotypic plasticity. However, few studies have examined how genotypes of woody species originating from contrasting environments respond to multiple climate change factors. Here, we investigated the main and interactive effects of elevated [CO2 ] (CE ) and elevated temperature (TE ) on growth and physiology of Coastal (warmer, less variable temperature environment) and Upland (cooler, more variable temperature environment) genotypes of an Australian woody species Telopea speciosissima. Both genotypes were positively responsive to CE (35% and 29% increase in whole-plant dry mass and leaf area, respectively), but only the Coastal genotype exhibited positive growth responses to TE . We found that the Coastal genotype exhibited greater growth response to TE (47% and 85% increase in whole-plant dry mass and leaf area, respectively) when compared with the Upland genotype (no change in dry mass or leaf area). No intraspecific variation in physiological plasticity was detected under CE or TE , and the interactive effects of CE and TE on intraspecific variation in phenotypic plasticity were also largely absent. Overall, TE was a more effective climate factor than CE in exposing genotypic variation in our woody species. Our results contradict the paradigm that genotypes from more variable climates will exhibit greater phenotypic plasticity in future climate regimes. © 2015 John Wiley & Sons Ltd.

Selection and Evaluation of Maize Genotypes Tolerance to Low Phosphorus Soils

Energy Technology Data Exchange (ETDEWEB)

Yang, J. C.; Jiang, H. M.; Zhang, J. F.; Li, L. L.; Li, G. H. [Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing (China)

2013-11-15

Maize species differ in their ability to take up phosphorus (P) from the soil, and these differences are attributed to the morphology and physiology of plants relative to their germplasm base. An effective method of increasing P efficiency in maize is to select and evaluate genotypes that can produce a high yield under P deficient conditions. In this study, 116 maize inbred lines with various genetic backgrounds collected from several Agricultural Universities and Institutes in China were evaluated in a field experiment to identify genotypic differences in P efficiency in 2007. Overall, 15 maize inbred lines were selected from the 116 inbred lines during the 5-year field experimental period based on their 100-grain weight in P-deficient soil at maturity, when compared to the characteristics exhibited in P-sufficient soil. All of the selected lines were evaluated in field experiments from 2008 to 2010 for their tolerance to low-P at the seedling and maturity stages. Inhibition (%) was used and defined as the parameter measured under P limitation compared to the parameters measured under P sufficiency to evaluate the genotypic variation in tolerance. Inhibition of root length, root surface area, volume, root: shoot ratio and P uptake efficiency could be used as indices to assess the genotypic tolerance to P limitation. Low-P tolerant genotypes could uptake more P and accumulate more dry matter at the seedling stage. A strong relationship between the total biomass and root length was exhibited. In order to understand the mechanisms of the genotypic tolerance to low-P soil to utilize P from the sparing soluble P forms, 5 maize genotypes selected out of the 15 maize inbred lines, according to the four quadrant distribution, was used as the criteria in a {sup 32}P isotope tracer experiment to follow the recovery of {sup 32}P in soil P fractions. The {sup 32}P tracer results showed a higher rate for water- soluble P transformation to slowly available P in P deficient soil

Comparative analysis of full genomic sequences among different genotypes of dengue virus type 3

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Lin Ting-Hsiang

2008-05-01

Full Text Available Abstract Background Although the previous study demonstrated the envelope protein of dengue viruses is under purifying selection pressure, little is known about the genetic differences of full-length viral genomes of DENV-3. In our study, complete genomic sequencing of DENV-3 strains collected from different geographical locations and isolation years were determined and the sequence diversity as well as selection pressure sites in the DENV genome other than within the E gene were also analyzed. Results Using maximum likelihood and Bayesian approaches, our phylogenetic analysis revealed that the Taiwan's indigenous DENV-3 isolated from 1994 and 1998 dengue/DHF epidemics and one 1999 sporadic case were of the three different genotypes – I, II, and III, each associated with DENV-3 circulating in Indonesia, Thailand and Sri Lanka, respectively. Sequence diversity and selection pressure of different genomic regions among DENV-3 different genotypes was further examined to understand the global DENV-3 evolution. The highest nucleotide sequence diversity among the fully sequenced DENV-3 strains was found in the nonstructural protein 2A (mean ± SD: 5.84 ± 0.54 and envelope protein gene regions (mean ± SD: 5.04 ± 0.32. Further analysis found that positive selection pressure of DENV-3 may occur in the non-structural protein 1 gene region and the positive selection site was detected at position 178 of the NS1 gene. Conclusion Our study confirmed that the envelope protein is under purifying selection pressure although it presented higher sequence diversity. The detection of positive selection pressure in the non-structural protein along genotype II indicated that DENV-3 originated from Southeast Asia needs to monitor the emergence of DENV strains with epidemic potential for better epidemic prevention and vaccine development.

Genetic diversity of high performance cultivars of upland and irrigated Brazilian rice.

Science.gov (United States)

Coelho, G R C; Brondani, C; Hoffmann, L V; Valdisser, P A M R; Borba, T C O; Mendonça, J A; Rodrigues, L A; de Menezes, I P P

2017-09-21

The objective of this study was to analyze the diversity and discrimination of high-performance Brazilian rice cultivars using microsatellite markers. Twenty-nine rice cultivars belonging to EMBRAPA Arroz e Feijão germplasm bank in Brazil were genotyped by 24 SSR markers to establish their structure and genetic discrimination. It was demonstrated that the analyzed germplasm of rice presents an expressive and significant genetic diversity with low heterogeneity among the cultivars. All 29 cultivars were differentiated genetically, and were organized into two groups related to their upland and irrigated cultivation systems. These groups showed a high genetic differentiation, with greater diversity within the group that includes the cultivars for irrigated system. The genotyping data of these cultivars, with the morphological e phenotypical data, are valuable information to be used by rice breeding programs to develop new improved cultivars.

Characterisation and determination of virus resistance among cowpea [Vigna unguiculata (L.) Walp.] Genotypes

International Nuclear Information System (INIS)

Tettey, Carlos Kweku

2017-07-01

Several households in Ghana feed on cowpea [Vigna unguiculata (L.) Walp.] which serves as good source of protein. However, cowpea viral diseases and the lack of adaptable cultivars have become a limiting factor in cowpea production. This work therefore sought to explore morphogenetic diversity and viral resistance traits in cowpea germplasm to improve productivity. Thirty-eight exotic and local cowpea genotypes were cultivated at the Teaching and Research Field of the School of Agriculture, the University of Cape Coast. Two plants were maintained per stand at planting distance of 50 cm x 30 cm with three replications in a randomized complete block layout during the major (June – September) and minor seasons (November – February). The cowpea genotypes were characterised using both morphological and molecular methods to assess diversity in the coastal savanna agro-ecological zone of Ghana. They were also screened for resistance to cowpea viruses using visual scale on-field and DAS-ELISA protocol. The cowpeas showed significant (P < 0.05) variations in plant height, canopy diameter, number of branches, area of leaf, days to 50% flowering, days to pod maturity, pod length, number of seeds per pod and hundred seed weight. There were significant and positive correlations between pod weight and seed yield (r = 0.985, P < 0.05), plant height and canopy diameter (r = 0.576, P < 0.05), canopy diameter and number of branches (r = 0.576) as well as pod length and the number of seeds per pod (r = 0.530, P < 0.05). Hundred seed weight ranged from 10.03 g to 22.7 g. On the whole, 23 quantitative and qualitative parameters differentiated the cowpea genotypes into two main clusters with sub-clusters. Genomic analysis involving nine polymorphic SSR primers showed a mean genetic diversity of 0.7, polymorphic information content of 0.67 and allele frequency of 0.4 among the cowpea genotypes, which were differentiated into two main clusters with sub-clusters. Incidence and severity

Genetic diversity of Brucella abortus and Brucella melitensis in Kazakhstan using MLVA-16.

Science.gov (United States)

Shevtsov, Alexandr; Ramanculov, Erlan; Shevtsova, Elena; Kairzhanova, Alma; Tarlykov, Pavel; Filipenko, Maxim; Dymova, Maya; Abisheva, Gulzada; Jailbekova, Aygul; Kamalova, Dinara; Chsherbakov, Andrei; Tulegenov, Samat; Akhmetova, Assel; Sytnik, Igor; Karibaev, Talgat; Mukanov, Kasim

2015-08-01

Brucellosis is an endemic disease in Central Asia characterized by high infection rates in humans and animals. Currently, little is known about the genetic diversity of Brucella spp. circulating in the region, despite the high prevalence of brucellosis. This study aimed to analyze the genetic diversity of Brucella melitensis and Brucella abortus strains circulating in the Republic of Kazakhstan. We genotyped 128 B. melitensis and 124 B. abortus strains collected in regions with the highest prevalence of brucellosis. Genotyping was performed using multi-locus variable-number tandem-repeat analysis (MLVA). Analysis of a subset of 8 loci (MLVA-8) of 128 B. melitensis strains identified genotypes 42 (n=108), 43 (n=2), and 63 (n=19) related to the 'East Mediterranean' group. An MLVA-16 assay sorted 128 B. melitensis strains into 25 different genotypes. Excluding one variable locus, MLVA-15 of B. melitensis was distinct from strains originating in the Mediterranean region; however, 77% of them were identical to strains isolated in China. A minimum spanning tree for B. melitensis using MLVA-15 analysis clustered the local strains together with strains previously collected in China. MLVA-8 analysis of 124 B. abortus strains identified them as genotype 36, suggesting Eurasian distribution of this lineage. Complete MLVA-16 assay analysis clustered the strains into five genotypes, revealing little diversity of B. abortus when compared on the global scale. A minimum spanning tree for B. abortus obtained using MLVA-15 analysis clustered the 2 most prevalent genotypes (n=117) together with strains previously collected in China. Thus, MLVA analysis was used to characterize 252 strains of Brucella collected in Kazakhstan. The analysis revealed genetic homogeneity among the strains. Interestingly, identical MLVA-15 profiles were found in seemingly unrelated outbreaks in China, Turkey, and Kazakhstan. Further analysis is needed for better understanding of the epidemiology of

[Observation of genetic diversity in dental plaque of elder people with root caries].

Science.gov (United States)

Ma, Shan-fen; Liang, Jing-ping; Jiang, Yun-tao; Zhu, Cai-lian

2011-08-01

Bacterial community in dental plaque of elder people was analyzed to learn about the microhabitat composition and diversity. Dental plaque samples were collected from 25 elders. PCR-based denaturing gradient gel electrophoresis (PCR-DGGE) was used to evaluate the microbial diversity by displaying PCR-generated 16SrDNA fragments that migrate at different distances, reflecting the different sequence of fragment. SPSS12.0 software was used to analyze the variance of genotypes between different groups of bacteria. Genotypes of bacteria in dental plaques in the root caries group was significantly more than the other two groups. Crown caries group and caries-free group had no significant difference. The genetic diversity of the dental plaque microflora in the root caries group is significantly higher than coronal caries group and caries-free group.

Genetic dissimilarity among sweet potato genotypes using morphological and molecular descriptors

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Elisângela Knoblauch Viega de Andrade

2017-08-01

Full Text Available This study aimed to evaluate the genetic dissimilarity among sweet potato genotypes using morphological and molecular descriptors. The experiment was conducted in the Olericulture Sector at Federal University of Jequitinhonha and Mucuri Valleys (UFVJM and evaluated 60 sweet potato genotypes. For morphological characterization, 24 descriptors were used. For molecular characterization, 11 microsatellite primers specific for sweet potatoes were used, obtaining 210 polymorphic bands. Morphological and molecular diversity was obtained by dissimilarity matrices based on the coefficient of simple matching and the Jaccard index for morphological and molecular data, respectively. From these matrices, dendrograms were built. There is a large amount of genetic variability among sweet potato genotypes of the germplasm bank at UFVJM based on morphological and molecular characterizations. There was no duplicate suspicion or strong association between morphological and molecular analyses. Divergent accessions have been identified by molecular and morphological analyses, which can be used as parents in breeding programmes to produce progenies with high genetic variability.

Assessment of adaptability and stability of grain yield in bread wheat genotypes under different sowing times in Punjab

International Nuclear Information System (INIS)

Anwar, J.; Hussain, M.; Ali, M.A.; Subhani, G.M.; Munir, M.

2011-01-01

Twenty advanced lines/genotypes of wheat including two check varieties were sown under two different sowing times through out the Punjab province at 18 different locations with diverse environments to study their stability and adaptability. Normal sowing was done in second week of November 2007 while the delayed sowing was completed during second week of December 2007 during crop season 2007-08. The pooled analysis of variance showed significant differences among environments and genotypes for grain yield demonstrating the presence of considerable variations (p<0.01) among genotypes as well as diversity of growing environments at various locations for both normal and late sown wheat crops. The highest average grain yield was obtained at Jalandar Seed Farm, Arifwala and Pak. German Farm, Multan for normal and delayed sown crops, respectively. Most of the locations emerged as high yielding in normal sowing compared to late sown crop. Dendrograms of 18 locations based on the average yield of 20 wheat genotypes grown under normal and late sown crop revealed two main clusters. Under both normal and late sowing, none of the varieties exceeded the check Seher-2006, however, the check was followed by the advanced lines V-04022 and V-05066 for normal sown crop and Shafaq-2006, V-05066 and V-04022 under delayed sowing. All the genotypes revealed decline in grain yield for late sown wheat crop. The analysis of stability based on mean grain yield, regression coefficient and deviation from regression advocated that the cultivars V-05066 and V-03BT007 were most stable and adapted to diverse environmental conditions of Punjab. These cultivars revealed unit regression and non-significant deviations from regression. The check variety Seher-2006 produced maximum yield for both sowing times that suggested its consistent and stable performance across the environments. (author)

Emergence of hepatitis C virus genotype 4: phylogenetic analysis reveals three distinct epidemiological profiles

NARCIS (Netherlands)

de Bruijne, Joep; Schinkel, Janke; Prins, Maria; Koekkoek, Sylvie M.; Aronson, Sem J.; van Ballegooijen, Marijn W.; Reesink, Hendrik W.; Molenkamp, Richard; van de Laar, Thijs J. W.

2009-01-01

Hepatitis C virus (HCV) genotype 4 (HCV-4) infection is considered to be difficult to treat and has become increasingly prevalent in European countries, including The Netherlands. Using a molecular epidemiological approach, the present study investigates the genetic diversity and evolutionary origin

Assessment of sorghum genetic resources for genetic diversity and drought tolerance using molecular markers and agro-morphological traits

Energy Technology Data Exchange (ETDEWEB)

Abu Assar, A H; Salih, M; Ali, A M [Agricultural Research Corporation (ARC), P.O. Box 126 Wad Medani (Sudan); Uptmoor, R [Institute of Vegetable and Fruit Science, University of Hannover, Herrengauser Strabe 2.30419 Hanover (Greece); Abdelmula, A A [Department of Agronomy, Faculty of Agriculture, University of Khartoum, postal code: 13314 Shambat (Sudan); Ordon, F [Institute of Eqidemiology and Resistance, Federal Centre for Breeding Research on Cultivated Plants, Theodor-Roemer-Weg 4, D-06449 Aschersleben (Greece); Wagner, C; Friedt, W [Institute of Crop Science and Plant Breedin 1, Heinrich-Buff-Ring 26-32, D-35392 Giessen (Greece)

2009-07-01

Forty sorghum genotype were investigated for genetic diversity and drought tolerance. Diversity parameters were estimated using 16 simple sequence repeats markers. For assessment of drought tolerance, the genotype were field evaluated under normal and drought stress condition for two seasons in three environments, in Sudan. In total, 98 SSRs alleles were detected with an average of 6.1 alleles per locus. The estimated polymorphic information contents ranged from 0.33 to 0.86. The genetic similarity ranged from 0.00 to 0.88 with a low mean of 0.32. The dendrogram, generated from the UPGMA cluster analysis, showed two main clusters differentiated into nine sub-clusters with close relationship to morphological characters and pedigree information. Mantel statistics revealed a good fit of the cophenetic values to the original data set (r= 0.88). The overall mean genetic diversity was 0.67. Significant differences were detected among genotypes under both normal and drought stressed conditions for all measured traits. Based on the relative yield, the most drought-tolerant genotypes were Arfa Gadamak, Wad Ahmed, El-Najada, Korcola, ICSR 92003 And Sham Sham. Drought five days delay in flowering, and the earliest genotypes were PI 569695, PI 570446, PI 569953, Dwarf White Milo and PI 56995. (Author)

Assessment of sorghum genetic resources for genetic diversity and drought tolerance using molecular markers and agro-morphological traits

International Nuclear Information System (INIS)

Abu Assar, A. H.; Salih, M.; Ali, A. M.; Uptmoor, R.; Abdelmula, A. A.; Ordon, F.; Wagner, C.; Friedt, W.

2009-01-01

Forty sorghum genotype were investigated for genetic diversity and drought tolerance. Diversity parameters were estimated using 16 simple sequence repeats markers. For assessment of drought tolerance, the genotype were field evaluated under normal and drought stress condition for two seasons in three environments, in Sudan. In total, 98 SSRs alleles were detected with an average of 6.1 alleles per locus. The estimated polymorphic information contents ranged from 0.33 to 0.86. The genetic similarity ranged from 0.00 to 0.88 with a low mean of 0.32. The dendrogram, generated from the UPGMA cluster analysis, showed two main clusters differentiated into nine sub-clusters with close relationship to morphological characters and pedigree information. Mantel statistics revealed a good fit of the cophenetic values to the original data set (r= 0.88). The overall mean genetic diversity was 0.67. Significant differences were detected among genotypes under both normal and drought stressed conditions for all measured traits. Based on the relative yield, the most drought-tolerant genotypes were Arfa Gadamak, Wad Ahmed, El-Najada, Korcola, ICSR 92003 And Sham Sham. Drought five days delay in flowering, and the earliest genotypes were PI 569695, PI 570446, PI 569953, Dwarf White Milo and PI 56995. (Author)

Molecular epidemiology of American/Asian genotype DENV-2 in Peru.

Science.gov (United States)

Cruz, Cristhopher D; Forshey, Brett M; Juarez, Diana S; Guevara, Carolina; Leguia, Mariana; Kochel, Tadeusz J; Halsey, Eric S

2013-08-01

During the past decade, countries in South America have reported dengue hemorrhagic fever (DHF) associated with American/Asian genotype of dengue virus serotype 2 (DENV-2). DENV-2 strains have been associated with large outbreaks of dengue fever and DHF in numerous regions of Peru since the mid-1990s, but studies to address the origins, distribution, and genetic diversity of DENV-2 strains have been limited. To address this knowledge gap, we sequenced the envelope gene region of DENV-2 isolates from Peru, Ecuador, Paraguay, and Bolivia. Sequences were aligned and compared to a global sample of DENV-2 viruses. Phylogenetic analysis confirmed the circulation of two DENV-2 genotypes in Peru: American (prior to 2001) and American/Asian (2000 to present). American/Asian genotype variants can be classified into two lineages, and these were introduced into Peru from the north (Ecuador, Colombia, and/or Venezuela) and the east (Brazil and Bolivia). American/Asian lineage II replaced lineage I after 2009. We estimate the time to the most recent common ancestor for American/Asian DENV-2 genotype in the Americas was in 1980, and 1984 and 1989 for lineages I and II, respectively. In light of evidence for increased virulence of lineage II of American/Asian DENV-2, our results support the need for continuous monitoring for the emergence of new DENV genotypes that may be associated with severe disease. Copyright © 2013. Published by Elsevier B.V.

Does Sex Trade with Violence among Genotypes in Drosophila melanogaster?

Science.gov (United States)

Cabral, Larry G.; Foley, Brad R.; Nuzhdin, Sergey V.

2008-01-01

The evolutionary forces shaping the ability to win competitive interactions, such as aggressive encounters, are still poorly understood. Given a fitness advantage for competitive success, variance in aggressive and sexual display traits should be depleted, but a great deal of variation in these traits is consistently found. While life history tradeoffs have been commonly cited as a mechanism for the maintenance of variation, the variability of competing strategies of conspecifics may mean there is no single optimum strategy. We measured the genetically determined outcomes of aggressive interactions, and the resulting effects on mating success, in a panel of diverse inbred lines representing both natural variation and artificially selected genotypes. Males of one genotype which consistently lost territorial encounters with other genotypes were nonetheless successful against males that were artificially selected for supernormal aggression and dominated all other lines. Intransitive patterns of territorial success could maintain variation in aggressive strategies if there is a preference for territorial males. Territorial success was not always associated with male mating success however and females preferred ‘winners’ among some male genotypes, and ‘losers’ among other male genotypes. This suggests that studying behaviour from the perspective of population means may provide limited evolutionary and genetic insight. Overall patterns of competitive success among males and mating transactions between the sexes are consistent with mechanisms proposed for the maintenance of genetic variation due to nonlinear outcomes of competitive interactions. PMID:18414669

Linking Diversity and Differentiation

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Hans-Rolf Gregorius

2010-03-01

Full Text Available Generally speaking, the term differentiation refers to differences between collections for the distribution of specified traits of their members, while diversity deals with (effective numbers of trait states (types. Counting numbers of types implies discrete traits such as alleles and genotypes in population genetics or species and taxa in ecology. Comparisons between the concepts of differentiation and diversity therefore primarily refer to discrete traits. Diversity is related to differentiation through the idea that the total diversity of a subdivided collection should be composed of the diversity within the subcollections and a complement called “diversity between subcollections”. The idea goes back to the perception that the mixing of differentiated collections increases diversity. Several existing concepts of “diversity between subcollections” are based on this idea. Among them, β-diversity and fixation (inadvertently called differentiation are the most prominent in ecology and in population genetics, respectively. The pertaining measures are shown to quantify the effect of differentiation in terms of diversity components, though from a dual perspective: the classical perspective of differentiation between collections for their type compositions, and the reverse perspective of differentiation between types for their collection affiliations. A series of measures of diversity-oriented differentiation is presented that consider this dual perspective at two levels of diversity partitioning: the overall type or subcollection diversity and the joint type-subcollection diversity. It turns out that, in contrast with common notions, the measures of fixation (such as FST or GST refer to the perspective of type rather than subcollection differentiation. This unexpected observation strongly suggests that the popular interpretations of fixation measures must be reconsidered.

Impact of irrigation intervals, nitrogen fertilizer levels and heritability on spineless performance in safflower genotypes

International Nuclear Information System (INIS)

Ragab, A.I.; Kassem, M.

2003-01-01

The present study was conducted to study the impact of irrigation intervals, nitrogen fertilizer levels on spineless percentages, meanwhile, heritability and genetic gain were determind for further selection for eight safflower genotype, during 1998/1999-1999/2000 seasons, at nuclear research center-inshas. Concerning irrigation intervals, results showed that spineless percentages of safflower genotypes were markedly increased with the increasing of irrigation intervals, this eans that increase of drought conditions leds to increase the spineless percentages in all the genotypes. Regarding nitrogen fertilizer levels, results exhibited that spineless percentages were increased with the increasing of nitrogen fertilizer levels for all the studied genotypes. Combined analysis of variance chowed highly significant effect for irrigation intervals, fertilizer levels, years and genotypes for spineles trait. The first order interaction, second order interaction and third order interaction were highly significant suggesting that spineless trait was affected the environmental factors

Insights into the genetic structure and diversity of 38 South Asian Indians from deep whole-genome sequencing.

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Lai-Ping Wong

2014-05-01

Full Text Available South Asia possesses a significant amount of genetic diversity due to considerable intergroup differences in culture and language. There have been numerous reports on the genetic structure of Asian Indians, although these have mostly relied on genotyping microarrays or targeted sequencing of the mitochondria and Y chromosomes. Asian Indians in Singapore are primarily descendants of immigrants from Dravidian-language-speaking states in south India, and 38 individuals from the general population underwent deep whole-genome sequencing with a target coverage of 30X as part of the Singapore Sequencing Indian Project (SSIP. The genetic structure and diversity of these samples were compared against samples from the Singapore Sequencing Malay Project and populations in Phase 1 of the 1,000 Genomes Project (1 KGP. SSIP samples exhibited greater intra-population genetic diversity and possessed higher heterozygous-to-homozygous genotype ratio than other Asian populations. When compared against a panel of well-defined Asian Indians, the genetic makeup of the SSIP samples was closely related to South Indians. However, even though the SSIP samples clustered distinctly from the Europeans in the global population structure analysis with autosomal SNPs, eight samples were assigned to mitochondrial haplogroups that were predominantly present in Europeans and possessed higher European admixture than the remaining samples. An analysis of the relative relatedness between SSIP with two archaic hominins (Denisovan, Neanderthal identified higher ancient admixture in East Asian populations than in SSIP. The data resource for these samples is publicly available and is expected to serve as a valuable complement to the South Asian samples in Phase 3 of 1 KGP.

Application of high-resolution DNA melting for genotyping in lepidopteran non-model species: Ostrinia furnacalis (Crambidae.

Directory of Open Access Journals (Sweden)

FengBo Li

Full Text Available Development of an ideal marker system facilitates a better understanding of the genetic diversity in lepidopteran non-model organisms, which have abundant species, but relatively limited genomic resources. Single nucleotide polymorphisms (SNPs discovered within single-copy genes have proved to be desired markers, but SNP genotyping by current techniques remain laborious and expensive. High resolution melting (HRM curve analysis represents a simple, rapid and inexpensive genotyping method that is primarily confined to clinical and diagnostic studies. In this study, we evaluated the potential of HRM analysis for SNP genotyping in the lepidopteran non-model species Ostrinia furnacalis (Crambidae. Small amplicon and unlabeled probe assays were developed for the SNPs, which were identified in 30 females of O. furnacalis from 3 different populations by our direct sequencing. Both assays were then applied to genotype 90 unknown female DNA by prior mixing with known wild-type DNA. The genotyping results were compared with those that were obtained using bi-directional sequencing analysis. Our results demonstrated the efficiency and reliability of the HRM assays. HRM has the potential to provide simple, cost-effective genotyping assays and facilitates genotyping studies in any non-model lepidopteran species of interest.

Determination of processing and nutritional quality attributes of potato genotypes in Pakistan

International Nuclear Information System (INIS)

Abbas, G.; Hafiz, I.A.; Hussain, A.

2011-01-01

The acceptability of potatoes for processing as french fries is largely dependent on the quality of the end products. Processing industry is totally dependent on the quality parameters of tuber to satisfy the increasing demand of customers. Thirty two potato genotypes for processing and yield quality traits were assessed for screening. Significant differences in all the quality parameters and various characteristics were found, while the genotypes; 394021-120, 9625, Kiran, NARC 2002-1, NARC 1-2006/1 and VR 90-217 gave the highest results regarding yield and quality of potato tubers except kiran, which has a high yield but low quality characters. The tuber sizes an d weight was also significantly different among genotypes except weight of big size tubers. Variations existed among genotypes in tuber characteristics (skin color, tuber shape, eye depth, flesh color and general appearance). The results regarding correlation studies indicated that french fry color exhibited negative correlation with reducing sugar (r = -0.7046), total sugars (r = -0.6659) and positive correlation with dry matter (r = 0.5013).This screening is helpful to the ongoing efforts to select the best genotype for the emerging processing industry of Pakistan. (author)

An XML-based interchange format for genotype-phenotype data.

Science.gov (United States)

Whirl-Carrillo, M; Woon, M; Thorn, C F; Klein, T E; Altman, R B

2008-02-01

Recent advances in high-throughput genotyping and phenotyping have accelerated the creation of pharmacogenomic data. Consequently, the community requires standard formats to exchange large amounts of diverse information. To facilitate the transfer of pharmacogenomics data between databases and analysis packages, we have created a standard XML (eXtensible Markup Language) schema that describes both genotype and phenotype data as well as associated metadata. The schema accommodates information regarding genes, drugs, diseases, experimental methods, genomic/RNA/protein sequences, subjects, subject groups, and literature. The Pharmacogenetics and Pharmacogenomics Knowledge Base (PharmGKB; www.pharmgkb.org) has used this XML schema for more than 5 years to accept and process submissions containing more than 1,814,139 SNPs on 20,797 subjects using 8,975 assays. Although developed in the context of pharmacogenomics, the schema is of general utility for exchange of genotype and phenotype data. We have written syntactic and semantic validators to check documents using this format. The schema and code for validation is available to the community at http://www.pharmgkb.org/schema/index.html (last accessed: 8 October 2007). (c) 2007 Wiley-Liss, Inc.

Empirical evaluation of DArT, SNP, and SSR marker-systems for genotyping, clustering, and assigning sugar beet hybrid varieties into populations

Science.gov (United States)

Dominant and co-dominant molecular markers are routinely used in plant genetic diversity research. In the present study we assessed the success-rate of three marker-systems for estimating genotypic diversity, clustering varieties into populations, and assigning a single variety into the expected pop...

The geographical patterns of symbiont diversity in the invasive legume Mimosa pudica can be explained by the competitiveness of its symbionts and by the host genotype.

Science.gov (United States)

Melkonian, Rémy; Moulin, Lionel; Béna, Gilles; Tisseyre, Pierre; Chaintreuil, Clémence; Heulin, Karine; Rezkallah, Naïma; Klonowska, Agnieszka; Gonzalez, Sophie; Simon, Marcelo; Chen, Wen-Ming; James, Euan K; Laguerre, Gisèle

2014-07-01

Variations in the patterns of diversity of symbionts have been described worldwide on Mimosa pudica, a pan-tropical invasive species that interacts with both α and β-rhizobia. In this study, we investigated if symbiont competitiveness can explain these variations and the apparent prevalence of β- over α-rhizobia. We developed an indirect method to measure the proportion of nodulation against a GFP reference strain and tested its reproducibility and efficiency. We estimated the competitiveness of 54 strains belonging to four species of β-rhizobia and four of α-rhizobia, and the influence of the host genotype on their competitiveness. Our results were compared with biogeographical patterns of symbionts and host varieties. We found: (i) a strong strain effect on competitiveness largely explained by the rhizobial species, with Burkholderia phymatum being the most competitive species, followed by B. tuberum, whereas all other species shared similar and reduced levels of competitiveness; (ii) plant genotype can increase the competitiveness of Cupriavidus taiwanensis. The latter data support the likelihood of the strong adaptation of C. taiwanensis with the M. pudica var. unijuga and help explain its prevalence as a symbiont of this variety over Burkholderia species in some environments, most notably in Taiwan. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

Genetic diversity of Echinococcus granulosus in center of Iran.

Science.gov (United States)

Pestechian, Nader; Hosseini Safa, Ahmad; Tajedini, Mohammadhasan; Rostami-Nejad, Mohammad; Mousavi, Mohammad; Yousofi, Hosseinali; Haghjooy Javanmard, Shaghayegh

2014-08-01

Hydatid cyst caused by Echinococcus granulosus is one of the most important parasitic diseases around the world and many countries in Asia, including Iran, are involved with this infection. This disease can cause high mortality in humans as well as economic losses in livestock. To date, several molecular methods have been used to determine the genetic diversity of E. granulosus. So far, identification of E. granulosus using real-time PCR fluorescence-based quantitative assays has not been studied worldwide, also in Iran. Therefore, the aim of this study was to investigate the genetic diversity of E. granulosus from center of Iran using real-time PCR method. A total of 71 hydatid cysts were collected from infected sheep, goat, and cattle slaughtered in Isfahan, Iran during 2013. DNA was extracted from protoscolices and/or germinal layers from each individual cyst and used as template to amplify the mitochondrial cytochrome c oxidase subunit 1 gene (cox1) (420 bp). Five cattle isolates out of 71 isolates were sterile and excluded from further investigation. Overall, of 66 isolates, partial sequences of the cox1 gene of E. granulosus indicated the presence of genotypes G1 in 49 isolates (74.2%), G3 in 15 isolates (22.7%), and G6 in 2 isolates (3.0%) in infected intermediate hosts. Sixteen sequences of G1 genotype had microgenetic variants, and they were compared to the original sequence of cox1. However, isolates identified as G3 and G6 genotypes were completely consistent with original sequences. G1 genotype in livestock was the dominant genotype in Isfahan region, Iran.

Effects of ghrelin gene genotypes on the growth traits in Chinese cattle.

Science.gov (United States)

Zhang, Ai-ling; Zhang, Li; Zhang, Liang-zhi; Zhang, Cun-fang; Lan, Xian-yong; Zhang, Chun-lei; Chen, Hong

2012-06-01

Ghrelin is an important peptide that stimulates food intake and regulates energy balance of animals. Single nucleotide polymorphisms of ghrelin gene in three Chinese cattle populations were investigated through PCR-SSCP and DNA sequencing. Five over-lapped DNA fragments were analyzed and a total of three ones exhibited different genotypes. Three genotypes and four SNPs (-415 A > G, -414 T > C, -321 C > A, and -172 A > G) were found on the -544 to +35 bp region (G-1) of ghrelin gene. On the locus of -1037 to -509 bp (G-2), two genotypes and one SNP (-726 A > T) were discovered. And in the exon1, exon2, and intron1 (G-4 locus, (+4 to +427)), two genotypes and one SNP were detected (+205 C > T, located in intron1). Positions of the five SNPs in the 5′ regulatory region might be the transcription factor binding sites. The SNPs at -415 and -414 in the core binding sequence were found to cause the change of the site. Though the SNP at -172 did not change the binding site, it generated one new site at the same time. The frequencies of the genotypes varied differently in the three breeds. Results of ANOVA showed that G-1 was correlative to the ischium width (IW) of Nanyang cattle aged 18 months (p = 0.043). The least square analysis between genotypes at G-1 locus and growth traits in Nanyang cattle showed that the individuals (aged 18 months) with C genotype had greater IW than that of the other two genotypes. The C genotype might serve as one potential candidate genetic marker for cattle growth and development.

Characterization of a Wheat Breeders' Array suitable for high-throughput SNP genotyping of global accessions of hexaploid bread wheat (Triticum aestivum).

Science.gov (United States)

Allen, Alexandra M; Winfield, Mark O; Burridge, Amanda J; Downie, Rowena C; Benbow, Harriet R; Barker, Gary L A; Wilkinson, Paul A; Coghill, Jane; Waterfall, Christy; Davassi, Alessandro; Scopes, Geoff; Pirani, Ali; Webster, Teresa; Brew, Fiona; Bloor, Claire; Griffiths, Simon; Bentley, Alison R; Alda, Mark; Jack, Peter; Phillips, Andrew L; Edwards, Keith J

2017-03-01

Targeted selection and inbreeding have resulted in a lack of genetic diversity in elite hexaploid bread wheat accessions. Reduced diversity can be a limiting factor in the breeding of high yielding varieties and crucially can mean reduced resilience in the face of changing climate and resource pressures. Recent technological advances have enabled the development of molecular markers for use in the assessment and utilization of genetic diversity in hexaploid wheat. Starting with a large collection of 819 571 previously characterized wheat markers, here we describe the identification of 35 143 single nucleotide polymorphism-based markers, which are highly suited to the genotyping of elite hexaploid wheat accessions. To assess their suitability, the markers have been validated using a commercial high-density Affymetrix Axiom ® genotyping array (the Wheat Breeders' Array), in a high-throughput 384 microplate configuration, to characterize a diverse global collection of wheat accessions including landraces and elite lines derived from commercial breeding communities. We demonstrate that the Wheat Breeders' Array is also suitable for generating high-density genetic maps of previously uncharacterized populations and for characterizing novel genetic diversity produced by mutagenesis. To facilitate the use of the array by the wheat community, the markers, the associated sequence and the genotype information have been made available through the interactive web site 'CerealsDB'. © 2016 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Does genetic diversity hinder parasite evolution in social insect colonies?

DEFF Research Database (Denmark)

Hughes, William Owen Hamar; Boomsma, Jacobus Jan

2006-01-01

of host genetic diversity on parasite evolution by carrying out serial passages of a virulent fungal pathogen through leaf-cutting ant workers of known genotypes. Parasite virulence increased over the nine-generation span of the experiment while spore production decreased. The effect of host relatedness...... upon virulence appeared limited. However, parasites cycled through more genetically diverse hosts were more likely to go extinct during the experiment and parasites cycled through more genetically similar hosts had greater spore production. These results indicate that host genetic diversity may indeed...

Variability in amino acid digestibility of triticale grain from diverse genotypes as studied in cecectomized laying hens.

Science.gov (United States)

Zuber, T; Maurer, H P; Möhring, J; Nautscher, N; Siegert, W; Rosenfelder, P; Rodehutscord, M

2016-12-01

Triticale, an anthropogenic hybrid grain, is increasing in importance as a feed grain for laying hens. However, our limited knowledge of its nutritional qualities and their impact on hen performance prevents optimization of its use. The present study investigated the digestibility of amino acids ( AA: ) in triticale grain in laying hens, and additionally examined relationships between AA digestibility and chemical and physical characteristics of the grain. Twenty genotypes of triticale were grown under standardized agronomic and environmental conditions and were characterized according to their physical properties (thousand-seed weight, test weight, falling number, extract viscoelasticity), chemical composition (proximate nutrients, non-starch polysaccharides, AA, minerals, inositol phosphates) and gross energy concentration. Additionally, the in vitro solubility of nitrogen was determined. The animal trial comprised 4 Latin Squares (6 × 6) distributed among 2 subsequent runs. Twelve cecectomized LSL-Classic hens were individually housed in metabolism cages and either fed a basal diet containing 500 g/kg cornstarch or one of 20 triticale diets, each replacing the cornstarch with one triticale genotype, for 8 d. During the last 4 d, feed intake was recorded and excreta were collected quantitatively. Amino acid digestibility of the triticale genotypes was calculated by linear regression. The digestibility of all AA differed significantly between the 20 genotypes, including Lys (digestibility range 68 to 80%), Met (77 to 86%), Thr (68 to 78%) and Trp (74 to 83%). However, AA digestibility only correlated with characteristics of the grain in few cases, without a consistent pattern among AA. Equations to predict AA digestibility based on the grain's physical and chemical characteristics were calculated by multiple linear regression. The explanatory power (adjusted R 2 ;) of these prediction equations was below 0.7 for most AA and thus not sufficiently precise to be

Environmental Influences on Pigeonpea-Fusarium udum Interactions and Stability of Genotypes to Fusarium Wilt

Science.gov (United States)

Sharma, Mamta; Ghosh, Raju; Telangre, Rameshwar; Rathore, Abhishek; Saifulla, Muhammad; Mahalinga, Dayananda M.; Saxena, Deep R.; Jain, Yogendra K.

2016-01-01

Fusarium wilt (Fusarium udum Butler) is an important biotic constraint to pigeonpea (Cajanus cajan L.) production worldwide. Breeding for fusarium wilt resistance continues to be an integral part of genetic improvement of pigeonpea. Therefore, the study was aimed at identifying and validating resistant genotypes to fusarium wilt and determining the magnitude of genotype × environment (G × E) interactions through multi-environment and multi-year screening. A total of 976 genotypes including germplasm and breeding lines were screened against wilt using wilt sick plot at Patancheru, India. Ninety two genotypes resistant to wilt were tested for a further two years using wilt sick plot at Patancheru. A Pigeonpea Wilt Nursery (PWN) comprising of 29 genotypes was then established. PWN was evaluated at nine locations representing different agro-climatic zones of India for wilt resistance during two crop seasons 2007/08 and 2008/09. Genotypes (G), environment (E), and G × E interactions were examined by biplot which partitioned the main effect into G, E, and G × E interactions with significant levels (p ≤ 0.001) being obtained for wilt incidence. The genotype contributed 36.51% of resistance variation followed by the environment (29.32%). A GGE biplot integrated with a boxplot and multiple comparison tests enabled us to identify seven stable genotypes (ICPL 20109, ICPL 20096, ICPL 20115, ICPL 20116, ICPL 20102, ICPL 20106, and ICPL 20094) based on their performance across diverse environments. These genotypes have broad based resistance and can be exploited in pigeonpea breeding programs. PMID:27014287

Diversidade bacteriana da rizosfera de genótipos de milho contrastantes na eficiência de uso de fósforo Bacterial diversity in the rhizosphere of maize genotypes contrasting for phosphorus use efficiency

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Christiane Abreu de Oliveira

2009-11-01

Full Text Available O objetivo deste trabalho foi avaliar a diversidade funcional e genética de bactérias associadas à rizosfera de genótipos de milho contrastantes quanto à eficiência de uso de fósforo, por meio do teste de fontes de carbono no sistema EcoPlate e da eletroforese em gel de gradiente desnaturante (DGGE dos fragmentos amplificados dos genes 16S ribossomais (rDNA das bactérias. Foram coletadas amostras de solo da rizosfera de linhagens e híbridos contrastantes quanto à eficiência de uso de fósforo, cultivados em Latossolo Vermelho-Escuro fase cerrado, com baixo e alto teor de P. Bactérias da rizosfera de híbridos e linhagens eficientes, sob estresse de P, analisadas pelo sistema EcoPlate, tenderam a se agrupar conforme a análise de componentes principais, o que indica que utilizaram fontes de carbono semelhantes. Não houve diferença na diversidade bacteriana, analisada pela DGGE, entre bactérias associadas a genótipos eficientes e ineficientes no uso de P. Com base no sequenciamento do 16S rDNA, foi verificado que a rizosfera de genótipos de milho sob estresse de P parece selecionar grupos específicos de bactérias. A estrutura populacional genética e metabólica de bactérias da rizosfera foi mais influenciada pelo teor de fósforo no solo do que pela eficiência das plantas em usar o fósforo.The objective of this work was to evaluate the functional and genetic diversity of bacteria associated to the rhizosphere of maize genotypes contrasting for phosphorus use efficiency by means of the EcoPlate carbon source test and denaturing gradient gel electrophoresis (DGGE of amplified 16S ribosomal DNA (rDNA fragments of bacteria. Rhizosphere soil samples of maize genotypes (hybrids and lineages contrasting for phosphorus use efficiency cultivated in an Oxisol with high and low P content were collected. Bacteria from the rhizosphere of P-efficient maize genotypes under P stress conditions analyzed by the EcoPlate system tended to group

Genetic diversity assessment in brassica germplasm based on morphological attributes

International Nuclear Information System (INIS)

Ali, I.; Ali, N.; Ali, S.; Hussain, I.; Khan, S. A.; Tahira, R.

2015-01-01

Genetic diversity of 28 Brassica genotypes was studied using different morphological attributes. Data were recorded on days to maturity (DM), plant height (PH), primary branches plant (PBPP), pod length (PL), seed pod (SP), 1000 - seed weight (1000 - SW), yield plant (YPP) and oil (percentage). Three checks (Pakola, CM and TA), were used to check the performance of collected materials with already available brassica varieties. significant statistical differences were observed among the tested genotypes based on the studied morphological traits. Among the tested genotypes, genotype keelboat proved to be superior as compared to other studied genotypes due to maximum level of studied traits like pod length (7.03 cm), seed pod (32.33), 1000 - seed weight (5.38 g), seed yield plant (110.8 g) and oil content (52.9 percentage. The highest level of performance recorded by kalabat in terms of branches plant, pod length (cm), number of seed pod, seed yield plant (g), 1000 - seed weight (g) and oil content (percentage), indicates that this genotype is genetically different and superior than the other studied genotype. Therefore, genotype kalabat can be either used as variety after adaptability trials over a larger area or included in Brassica breeding programmes as a good source of genetic variation. (author)

Effect of Genotypic and Environmental Differences on Flax (Linum usitatissimum L.)

International Nuclear Information System (INIS)

Amer, I.M; Moustafa, H.A.M.

2006-01-01

Genotype X environment (GE) interactions for some flax characters nd their effects on yield of three divergent mutant lines two local cultivars were studied over five environmental conditions (three years and different soils) at Inshas, Egypt. the obtained results reveled that the variance due to environmental conditions were greater than the variance due to genotypes, or GE interaction for all studied traits. the variances due to GE interactions were greater than the variances for genotypes in seed yield and its related traits and vice versa in straw yield and its related traits. the environmental conditions exhibited greater effect on the local cultivars than on mutant lines. the mutant line 25 gave the highest seeds and straw yield / plant over all environments. adaptability and performance stability of a line over years and sites are interested for flax producer for growing a cultivar with high yield and performance stability at his location

Analysis of the genetic diversity of four rabbit genotypes using ...

African Journals Online (AJOL)

Dr.Ola

2013-05-15

May 15, 2013 ... diseases or market conditions. A considerable number of genetic diversity studies for several livestock species have been carried out during recent years by research. *Corresponding author. E-mail: ola.galal@agr.kfs.edu.eg or olagalal2002@yahoo.com , Tel/Fax: +2-0479102930. Abbreviations: APRI ...

In vitro application of integrated selection index for screening drought tolerant genotypes in common wheat

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Ezatollah FARSHADFAR

2016-10-01

Full Text Available This experiment was conducted on 20 wheat genotypes during 2010-2011 growing season at the Razi University, Kermanshah, Iran. A completely randomized design with six replications was used for callus induction and a 20 × 2 factorial experiment with three replications was used for response of genotypes to in vitro drought stress. ANOVA exhibited highly significant differences among the genotypes for callus growth rate, relative fresh mass growth, relative growth rate, callus water content, percent of callus chlorosis and proline content under stress condition (15 % PEG. PCA showed that the integrated selection index was correlated with callus growth index, relative fresh mass growth, relative growth rate and proline content indicating that these screening techniques can be useful for selecting drought tolerant genotypes. Screening drought tolerant genotypes and in vitro indicators of drought tolerance using mean rank, standard deviation of ranks and biplot analysis, discriminated genotypes 2, 18 and 10 as the most drought tolerant. Therefore they are recommended to be used as parents for genetic analysis, gene mapping and improvement of drought tolerance.

Cowpea Nodules Harbor Non-rhizobial Bacterial Communities that Are Shaped by Soil Type Rather than Plant Genotype.

Science.gov (United States)

Leite, Jakson; Fischer, Doreen; Rouws, Luc F M; Fernandes-Júnior, Paulo I; Hofmann, Andreas; Kublik, Susanne; Schloter, Michael; Xavier, Gustavo R; Radl, Viviane

2016-01-01

Many studies have been pointing to a high diversity of bacteria associated to legume root nodules. Even though most of these bacteria do not form nodules with legumes themselves, it was shown that they might enter infection threads when co-inoculated with rhizobial strains. The aim of this work was to describe the diversity of bacterial communities associated with cowpea ( Vigna unguiculata L. Walp) root nodules using 16S rRNA gene amplicon sequencing, regarding the factors plant genotype and soil type. As expected, Bradyrhizobium was the most abundant genus of the detected genera. Furthermore, we found a high bacterial diversity associated to cowpea nodules; OTUs related to the genera Enterobacter, Chryseobacterium, Sphingobacterium , and unclassified Enterobacteriacea were the most abundant. The presence of these groups was significantly influenced by the soil type and, to a lesser extent, plant genotype. Interestingly, OTUs assigned to Chryseobacterium were highly abundant, particularly in samples obtained from an Ultisol soil. We confirmed their presence in root nodules and assessed their diversity using a target isolation approach. Though their functional role still needs to be addressed, we postulate that Chryseobacterium strains might help cowpea plant to cope with salt stress in semi-arid regions.

Genotype X/C recombinant (putative genotype I) of hepatitis B virus is rare in Hanoi, Vietnam--genotypes B4 and C1 predominate.

Science.gov (United States)

Phung, Thi Bich Thuy; Alestig, Erik; Nguyen, Thanh Liem; Hannoun, Charles; Lindh, Magnus

2010-08-01

There are eight known genotypes of hepatitis B virus, A-H, and several subgenotypes, with rather well-defined geographic distributions. HBV genotypes were evaluated in 153 serum samples from Hanoi, Vietnam. Of the 87 samples that could be genotyped, genotype B was found in 67 (77%) and genotype C in 19 (22%). All genotype C strains were of subgenotype C1, and the majority of genotype B strains were B4, while a few were B2. The genotype X/C recombinant strain, identified previously in Swedish patients of indigenous Vietnamese origin, was found in one sample. This variant, proposed to be classified as genotype I, has been found recently also by others in Vietnam and Laos. The current study indicates that the genotype X/C recombinant may represent approximately 1% of the HBV strains circulating in Vietnam. (c) 2010 Wiley-Liss, Inc.

Effect of halopriming on the induction of nacl salt tolerance in different wheat genotypes

International Nuclear Information System (INIS)

Muhammad, Z.; Hussain, F.; Rehmanullah, M.; Majeed, A.

2015-01-01

Salinity is a major environmental stress limiting plant growth and productivity of wide range of crops with impairing effects on germination and yield. The present study was conducted to assess the induction of salt tolerance in seven wheat genotypes (Bakhtawar-92, Bhakar-2002, Fakhar-e-Sarhad, Khyber-87, Nasir-2000, Pirsabak-2005, and Uqab-2000) at germination and seedling stage through halo-priming with NaCl. Seeds of each wheat genotype were halo-primed separately. Halo-primed seeds of each wheat genotype were subjected to 0.02 (control), 2, 4, 6 and 8 dS/m NaCl salinity under laboratory conditions. Germination percentage age varied significantly among various wheat genotypes; however, differences between different salt concentrations were non-significant. All the seedling growth characters (germination, plumule growth, fresh and dry weight of seedling and moisture contents) exhibited significant differences among wheat genotypes as well as under the applied salt concentration except for radicle growth which varied non-significantly under salt stress. Interaction between various wheat genotypes and salt concentration was also significant for all the seedling growth characters, while it was non-significant for germination percentage age. It is concluded that NaCl proved to be effective priming agents in inducing salt tolerance in the tested wheat genotypes. (author)

Genetic diversity of Escherichia coli isolates from surface water and groundwater in a rural environment.

Science.gov (United States)

Gambero, Maria Laura; Blarasin, Monica; Bettera, Susana; Giuliano Albo, Jesica

2017-10-01

The genetic characteristics among Escherichia coli strains can be grouped by origin of isolation. Then, it is possible to use the genotypes as a tool to determine the source of water contamination. The aim of this study was to define water aptitude for human consumption in a rural basin and to assess the diversity of E. coli water populations. Thus, it was possible to identify the main sources of fecal contamination and to explore linkages with the hydrogeological environment and land uses. The bacteriological analysis showed that more than 50% of samples were unfit for human consumption. DNA fingerprinting analysis by BOX-PCR indicated low genotypic diversity of E. coli isolates taken from surface water and groundwater. The results suggested the presence of a dominant source of fecal contamination. The relationship between low genotypic diversity and land use would prove that water contamination comes from livestock. The genetic diversity of E. coli isolated from surface water was less than that identified in groundwater because of the different hydraulic features of both environments. Furthermore, each one of the two big strain groups identified in this basin is located in different sub-basins, showing that hydrological dynamics exerts selective pressure on bacteria DNA.

Caenorhabditis briggsae recombinant inbred line genotypes reveal inter-strain incompatibility and the evolution of recombination.

Directory of Open Access Journals (Sweden)

Joseph A Ross

2011-07-01

Full Text Available The nematode Caenorhabditis briggsae is an emerging model organism that allows evolutionary comparisons with C. elegans and exploration of its own unique biological attributes. To produce a high-resolution C. briggsae recombination map, recombinant inbred lines were generated from reciprocal crosses between two strains and genotyped at over 1,000 loci. A second set of recombinant inbred lines involving a third strain was also genotyped at lower resolution. The resulting recombination maps exhibit discrete domains of high and low recombination, as in C. elegans, indicating these are a general feature of Caenorhabditis species. The proportion of a chromosome's physical size occupied by the central, low-recombination domain is highly correlated between species. However, the C. briggsae intra-species comparison reveals striking variation in the distribution of recombination between domains. Hybrid lines made with the more divergent pair of strains also exhibit pervasive marker transmission ratio distortion, evidence of selection acting on hybrid genotypes. The strongest effect, on chromosome III, is explained by a developmental delay phenotype exhibited by some hybrid F2 animals. In addition, on chromosomes IV and V, cross direction-specific biases towards one parental genotype suggest the existence of cytonuclear epistatic interactions. These interactions are discussed in relation to surprising mitochondrial genome polymorphism in C. briggsae, evidence that the two strains diverged in allopatry, the potential for local adaptation, and the evolution of Dobzhansky-Muller incompatibilities. The genetic and genomic resources resulting from this work will support future efforts to understand inter-strain divergence as well as facilitate studies of gene function, natural variation, and the evolution of recombination in Caenorhabditis nematodes.

Short communication. Genotyping and phylogenetic analysis of bovine viral diarrhea virus (BVDV isolates in Kosovo

Directory of Open Access Journals (Sweden)

Izedin Goga

2014-03-01

Full Text Available Three serum samples positive in Antigen ELISA BVDV have been tested to characterise genetic diversity of bovine viral diarrhea virus (BVDV in Kosovo. Samples were obtained in 2011 from heifers and were amplified by reverse transcription-polymerase chain reaction, sequenced and analysed by computer-assisted phylogenetic analysis. Amplified products and nucleotide sequence showed that all 3 isolates belonged to BVDV 1 genotype and 1b sub genotype. These results enrich the extant knowledge of BVDV and represent the first documented data about Kosovo BVDV isolates.

Development of a single nucleotide polymorphism barcode to genotype Plasmodium vivax infections.

Directory of Open Access Journals (Sweden)

Mary Lynn Baniecki

2015-03-01

Full Text Available Plasmodium vivax, one of the five species of Plasmodium parasites that cause human malaria, is responsible for 25-40% of malaria cases worldwide. Malaria global elimination efforts will benefit from accurate and effective genotyping tools that will provide insight into the population genetics and diversity of this parasite. The recent sequencing of P. vivax isolates from South America, Africa, and Asia presents a new opportunity by uncovering thousands of novel single nucleotide polymorphisms (SNPs. Genotyping a selection of these SNPs provides a robust, low-cost method of identifying parasite infections through their unique genetic signature or barcode. Based on our experience in generating a SNP barcode for P. falciparum using High Resolution Melting (HRM, we have developed a similar tool for P. vivax. We selected globally polymorphic SNPs from available P. vivax genome sequence data that were located in putatively selectively neutral sites (i.e., intergenic, intronic, or 4-fold degenerate coding. From these candidate SNPs we defined a barcode consisting of 42 SNPs. We analyzed the performance of the 42-SNP barcode on 87 P. vivax clinical samples from parasite populations in South America (Brazil, French Guiana, Africa (Ethiopia and Asia (Sri Lanka. We found that the P. vivax barcode is robust, as it requires only a small quantity of DNA (limit of detection 0.3 ng/μl to yield reproducible genotype calls, and detects polymorphic genotypes with high sensitivity. The markers are informative across all clinical samples evaluated (average minor allele frequency > 0.1. Population genetic and statistical analyses show the barcode captures high degrees of population diversity and differentiates geographically distinct populations. Our 42-SNP barcode provides a robust, informative, and standardized genetic marker set that accurately identifies a genomic signature for P. vivax infections.

Development of a Single Nucleotide Polymorphism Barcode to Genotype Plasmodium vivax Infections

Science.gov (United States)

Baniecki, Mary Lynn; Faust, Aubrey L.; Schaffner, Stephen F.; Park, Daniel J.; Galinsky, Kevin; Daniels, Rachel F.; Hamilton, Elizabeth; Ferreira, Marcelo U.; Karunaweera, Nadira D.; Serre, David; Zimmerman, Peter A.; Sá, Juliana M.; Wellems, Thomas E.; Musset, Lise; Legrand, Eric; Melnikov, Alexandre; Neafsey, Daniel E.; Volkman, Sarah K.; Wirth, Dyann F.; Sabeti, Pardis C.

2015-01-01

Plasmodium vivax, one of the five species of Plasmodium parasites that cause human malaria, is responsible for 25–40% of malaria cases worldwide. Malaria global elimination efforts will benefit from accurate and effective genotyping tools that will provide insight into the population genetics and diversity of this parasite. The recent sequencing of P. vivax isolates from South America, Africa, and Asia presents a new opportunity by uncovering thousands of novel single nucleotide polymorphisms (SNPs). Genotyping a selection of these SNPs provides a robust, low-cost method of identifying parasite infections through their unique genetic signature or barcode. Based on our experience in generating a SNP barcode for P. falciparum using High Resolution Melting (HRM), we have developed a similar tool for P. vivax. We selected globally polymorphic SNPs from available P. vivax genome sequence data that were located in putatively selectively neutral sites (i.e., intergenic, intronic, or 4-fold degenerate coding). From these candidate SNPs we defined a barcode consisting of 42 SNPs. We analyzed the performance of the 42-SNP barcode on 87 P. vivax clinical samples from parasite populations in South America (Brazil, French Guiana), Africa (Ethiopia) and Asia (Sri Lanka). We found that the P. vivax barcode is robust, as it requires only a small quantity of DNA (limit of detection 0.3 ng/μl) to yield reproducible genotype calls, and detects polymorphic genotypes with high sensitivity. The markers are informative across all clinical samples evaluated (average minor allele frequency > 0.1). Population genetic and statistical analyses show the barcode captures high degrees of population diversity and differentiates geographically distinct populations. Our 42-SNP barcode provides a robust, informative, and standardized genetic marker set that accurately identifies a genomic signature for P. vivax infections. PMID:25781890

Deciphering the Diversities of Astroviruses and Noroviruses in Wastewater Treatment Plant Effluents by a High-Throughput Sequencing Method.

Science.gov (United States)

Prevost, B; Lucas, F S; Ambert-Balay, K; Pothier, P; Moulin, L; Wurtzer, S

2015-10-01

Although clinical epidemiology lists human enteric viruses to be among the primary causes of acute gastroenteritis in the human population, their circulation in the environment remains poorly investigated. These viruses are excreted by the human population into sewers and may be released into rivers through the effluents of wastewater treatment plants (WWTPs). In order to evaluate the viral diversity and loads in WWTP effluents of the Paris, France, urban area, which includes about 9 million inhabitants (approximately 15% of the French population), the seasonal occurrence of astroviruses and noroviruses in 100 WWTP effluent samples was investigated over 1 year. The coupling of these measurements with a high-throughput sequencing approach allowed the specific estimation of the diversity of human astroviruses (human astrovirus genotype 1 [HAstV-1], HAstV-2, HAstV-5, and HAstV-6), 7 genotypes of noroviruses (NoVs) of genogroup I (NoV GI.1 to NoV GI.6 and NoV GI.8), and 16 genotypes of NoVs of genogroup II (NoV GII.1 to NoV GII.7, NoV GII.9, NoV GII.12 to NoV GII.17, NoV GII.20, and NoV GII.21) in effluent samples. Comparison of the viral diversity in WWTP effluents to the viral diversity found by analysis of clinical data obtained throughout France underlined the consistency between the identified genotypes. However, some genotypes were locally present in effluents and were not found in the analysis of the clinical data. These findings could highlight an underestimation of the diversity of enteric viruses circulating in the human population. Consequently, analysis of WWTP effluents could allow the exploration of viral diversity not only in environmental waters but also in a human population linked to a sewerage network in order to better comprehend viral epidemiology and to forecast seasonal outbreaks. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Molecular epidemiology and genetic diversity of hepatitis B virus genotype E in an isolated Afro-Colombian community.

Science.gov (United States)

Alvarado Mora, Mónica Viviana; Romano, Camila Malta; Gomes-Gouvêa, Michele Soares; Gutierrez, Maria Fernanda; Carrilho, Flair José; Pinho, João Renato Rebello

2010-02-01

Hepatitis B virus (HBV) infection is a significant public health concern with 350 million chronic carriers worldwide. Eight HBV genotypes (A-H) have been described so far. Genotype E (HBV/E) is widely distributed in West Africa and has rarely been found in other continents, except for a few cases in individuals with an African background. In this study, we characterized HBV genotypes in Quibdó, Colombia, by partial S/P gene sequencing, and found, for the first time, HBV/E circulating in nine Afro-Colombian patients who had no recent contact with Africa. The presence of HBV/E in this community as a monophyletic group suggests that it was a result of a recent introduction by some Afro-descendent contact or, alternatively, that the virus came with slaves brought to Colombia. By using sequences with sampling dates, we estimated the substitution rate to be about 3.2 x 10(-4) substitutions per site per year, which resulted in a time to the most recent common ancestor (TMRCA) of 29 years. In parallel, we also estimated the TMRCA for HBV/E by using two previously estimated substitution rates (7.7 x 10(-4) and 1.5 x 10(-5) substitutions per site per year). The TMRCA was around 35 years under the higher rate and 1500 years under the slower rate. In sum, this work reports for the first time the presence of an exclusively African HBV genotype circulating in South America. We also discuss the time of the entry of this virus into America based on different substitution rates estimated for HBV.

Raps markers for genetic diversity analysis in rice (Oryza sativa L)

Energy Technology Data Exchange (ETDEWEB)

Alvarez, A; Fuentes, Jorge L [Centro de Estudios Aplicados al Desarrollo Nuclear, La Habana (Cuba); Deus, Juan E [Instituto de Investigaciones del Arroz, Habana (Cuba); Duque, Maria C [Centro Internacional de la Agricultura Tropical. Proyecto de Arroz , Cali (Colombia)

1999-07-01

The establishment of relationships between genotypes existing in gene banks that may be used in new crosses, and about genetic diversity in available germplasm, is very useful for plant breeders. In this work, a genetic diversity analysis among 20 varieties of the Cuban rice germplasm bank was performed by using RAPD markers. Twenty four decamer primers were screened which produced 61 polymorphic bands out of 105 consistent and reproducible amplified fragments (58.1 %). The proportion of polymorphic bands varied for each primer, with an average of 3 polymorphic bands per primer, these results agreed with previous reports on RAPD polymorphism in rice germplasm. Depending on the primer, 1 to 7 distinct patterns were obtained among the screened genotypes. Pair-wise genetic distances between genotypes were computed based on Dice's coefficient. Three major, statistically robust groups were obtained in the UPGMA dendrogram (A, B and C) which clearly corresponded to different genetic pools. Additionally, more insight could be gained according to the sub-grouping pattern within group A, which included the principal semi-dwarf commercial varieties. The present study allowed to prove the efficiency of RAPD markers for genetic diversity analysis in closely related germplasm, particularly for the semi-dwarf Cuban commercial rice cultivars. Also, the existence of a narrow genetic base among these varieties has been confirmed, pointing at the urgent necessity of widen it.

Raps markers for genetic diversity analysis in rice (Oryza sativa L)

International Nuclear Information System (INIS)

Alvarez, A.; Fuentes, Jorge L.; Deus, Juan E.; Duque, Maria C.

1999-01-01

The establishment of relationships between genotypes existing in gene banks that may be used in new crosses, and about genetic diversity in available germplasm, is very useful for plant breeders. In this work, a genetic diversity analysis among 20 varieties of the Cuban rice germplasm bank was performed by using RAPD markers. Twenty four decamer primers were screened which produced 61 polymorphic bands out of 105 consistent and reproducible amplified fragments (58.1 %). The proportion of polymorphic bands varied for each primer, with an average of 3 polymorphic bands per primer, these results agreed with previous reports on RAPD polymorphism in rice germplasm. Depending on the primer, 1 to 7 distinct patterns were obtained among the screened genotypes. Pair-wise genetic distances between genotypes were computed based on Dice's coefficient. Three major, statistically robust groups were obtained in the UPGMA dendrogram (A, B and C) which clearly corresponded to different genetic pools. Additionally, more insight could be gained according to the sub-grouping pattern within group A, which included the principal semi-dwarf commercial varieties. The present study allowed to prove the efficiency of RAPD markers for genetic diversity analysis in closely related germplasm, particularly for the semi-dwarf Cuban commercial rice cultivars. Also, the existence of a narrow genetic base among these varieties has been confirmed, pointing at the urgent necessity of widen it

Comparison of Three Different Commercial Kits for the Human Papilloma Virus Genotyping.

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Lim, Yong Kwan; Choi, Jee-Hye; Park, Serah; Kweon, Oh Joo; Park, Ae Ja

2016-11-01

High-risk type human papilloma virus (HPV) is the most important cause of cervical cancer. Recently, real-time polymerase chain reaction and reverse blot hybridization assay-based HPV DNA genotyping kits are developed. So, we compared the performances of different three HPV genotyping kits using different analytical principles and methods. Two hundred positive and 100 negative cervical swab specimens were used. DNA was extracted and all samples were tested by the MolecuTech REBA HPV-ID, Anyplex II HPV28 Detection, and HPVDNAChip. Direct sequencing was performed as a reference method for confirming high-risk HPV genotypes 16, 18, 45, 52, and 58. Although high-level agreement results were observed in negative samples, three kits showed decreased interassay agreement as screening setting in positive samples. Comparing the genotyping results, three assays showed acceptable sensitivity and specificity for the detection of HPV 16 and 18. Otherwise, various sensitivities showed in the detection of HPV 45, 52, and 58. The three assays had dissimilar performance of HPV screening capacity and exhibited moderate level of concordance in HPV genotyping. These discrepant results were unavoidable due to difference in type-specific analytical sensitivity and lack of standardization; therefore, we suggested that the efforts to standardization of HPV genotyping kits and adjusting analytical sensitivity would be important for the best clinical performance. © 2016 Wiley Periodicals, Inc.

Morphological and molecular genetic diversity of Syrian indigenous ...

African Journals Online (AJOL)

Domestic goats in Syria may provide an interesting source of genetic variability due to its proximity to the centers of domestication. This study aimed to assess the morphological variation, genetic diversity and population substructure of the Syrian goat populations. Commonly, three goat genotypes are distinguished in Syria, ...

Preliminary Studies of the Performance of Quinoa (Chenopodium quinoa Willd.) Genotypes under Irrigated and Rainfed Conditions of Central Malawi.

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Maliro, Moses F A; Guwela, Veronica F; Nyaika, Jacinta; Murphy, Kevin M

2017-01-01

The goal of sustainable intensification of agriculture in Malawi has led to the evaluation of innovative, regionally novel or under-utilized crop species. Quinoa ( Chenopodium quinoa Willd.) has the potential to provide a drought tolerant, nutritious alternative to maize. We evaluated 11 diverse varieties of quinoa for their yield and agronomic performance at two locations, Bunda and Bembeke, in Malawi. The varieties originated from Ecuador, Chile and Bolivia in South America; the United States and Canada in North America; and, Denmark in Europe, and were chosen based on their variation in morphological and agronomic traits, and their potential for adaptation to the climate of Malawi. Plant height, panicle length, days to maturity, harvest index, and seed yield were recorded for each variety under irrigation at Bunda and Bembeke, and under rainfed conditions at Bunda. Plant height was significantly influenced by both genotype and environment. There were also significant differences between the two locations for panicle length whereas genotype and genotype × environment (G × E) interaction were not significantly different. Differences were found for genotype and G × E interaction for harvest index. Notably, differences for genotype, environment and G × E were found for grain yield. Seed yield was higher at Bunda (237-3019 kg/ha) than Bembeke (62-692 kg/ha) under irrigated conditions. The highest yielding genotype at Bunda was Titicaca (3019 kg/ha) whereas Multi-Hued was the highest (692 kg/ha) at Bembeke. Strong positive correlations between seed yield and (1) plant height ( r = 0.74), (2) days to maturity ( r = 0.76), and (3) biomass ( r = 0.87) were found under irrigated conditions. The rainfed evaluations at Bunda revealed significant differences in seed yield, plant biomass, and seed size among the genotypes. The highest yielding genotype was Black Seeded (2050 kg/ha) followed by Multi-Hued (1603 kg/ha) and Bio-Bio (1446 kg/ha). Ecuadorian (257 kg/ha) was

Genetic diversity studies in pea (Pisum sativum L.) using simple sequence repeat markers.

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Kumari, P; Basal, N; Singh, A K; Rai, V P; Srivastava, C P; Singh, P K

2013-03-13

The genetic diversity among 28 pea (Pisum sativum L.) genotypes was analyzed using 32 simple sequence repeat markers. A total of 44 polymorphic bands, with an average of 2.1 bands per primer, were obtained. The polymorphism information content ranged from 0.657 to 0.309 with an average of 0.493. The variation in genetic diversity among these cultivars ranged from 0.11 to 0.73. Cluster analysis based on Jaccard's similarity coefficient using the unweighted pair-group method with arithmetic mean (UPGMA) revealed 2 distinct clusters, I and II, comprising 6 and 22 genotypes, respectively. Cluster II was further differentiated into 2 subclusters, IIA and IIB, with 12 and 10 genotypes, respectively. Principal component (PC) analysis revealed results similar to those of UPGMA. The first, second, and third PCs contributed 21.6, 16.1, and 14.0% of the variation, respectively; cumulative variation of the first 3 PCs was 51.7%.

Forecasting Brassica rapa: Merging climate models with genotype specific process models for evaluation whole species response to climate change.

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Pleban, J. R.; Mackay, D. S.; Ewers, B. E.; Weinig, C.; Guadagno, C. L.

2016-12-01

Human society has modified agriculture management practices and utilized a variety of breeding approaches to adapt to changing environments. Presently a dual pronged challenge has emerged as environmental change is occurring more rapidly while the demand of population growth on food supply is rising. Knowledge of how current agricultural practices will respond to these challenges can be informed through crafted prognostic modeling approaches. Amongst the uncertainties associated with forecasting agricultural production in a changing environment is evaluation of the responses across the existing genotypic diversity of crop species. Mechanistic models of plant productivity provide a means of genotype level parameterization allowing for a prognostic evaluation of varietal performance under changing climate. Brassica rapa represents an excellent species for this type of investigation because of its wide cultivation as well as large morphological and physiological diversity. We incorporated genotypic parameterization of B. rapa genotypes based on unique CO2 assimilation strategies, vulnerabilities to cavitation, and root to leaf area relationships into the TREES model. Three climate drivers, following the "business-as-usual" greenhouse gas emissions scenario (RCP 8.5) from Coupled Model Intercomparison Project, Phase 5 (CMIP5) were considered: temperature (T) along with associated changes in vapor pressure deficit (VPD), increasing CO2, as well as alternatives in irrigation regime across a temporal scale of present day to 2100. Genotypic responses to these drivers were evaluated using net primary productivity (NPP) and percent loss hydraulic conductance (PLC) as a measure of tolerance for a particular watering regime. Genotypic responses to T were witnessed as water demand driven by increases in VPD at 2050 and 2100 drove some genotypes to greater PLC and in a subset of these saw periodic decreases in NPP during a growing season. Genotypes able to withstand the greater

Displaying lives: the narrative of objects in biographical exhibitions

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Caterina Albano

2007-03-01

Full Text Available Biographical exhibitions are a museum practice that asks for critical consideration. Grounding the argument in critical theory, social studies and museum theory, the article explores the narrative function of objects in biographical exhibitions by addressing the social significance of objects in relation to biography and their relevance when presented into an exhibition display. Central is the concept of objects as ‘biographical relics’ that are culturally fetishized in biographical narratives. This raises questions about biographical reliability and the cultural role that such objects plays in exhibition narratives as bearers of reality and as metonymical icons of the biographical subject. The article considers examples of biographical exhibitions of diverse figures such as Gregor Mendel, Madame de Pompadour and Roland Barthes, and the role that personal items, but also portraits and photographs, play in them.

Diversity and activity of biosurfactant-producing Pseudomonas in the rhizosphere of black pepper in Vietnam.

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Tran, H; Kruijt, M; Raaijmakers, J M

2008-03-01

Phytophthora capsici is a major pathogen of black pepper and zoospores play an important role in the infection process. Fluorescent pseudomonads that produce biosurfactants with zoosporicidal activities were isolated from the black pepper rhizosphere in Vietnam, and their genotypic diversity and potential to control Phy. capsici root rot was determined. Biosurfactant-producing pseudomonads were genotypically and biochemically characterized by BOX-polymerase chain reaction (PCR), 16S-rDNA sequencing, reverse-phase-high-performance liquid chromatography and liquid chromatography-mass spectrometry analyses. Biosurfactant-producing fluorescent pseudomonads make up c. 1.3% of the culturable Pseudomonas population in the rhizosphere of black pepper. Although BOX-PCR revealed substantial genotypic diversity, the isolates were shown to produce the same biosurfactants and were all identified as Pseudomonas putida. When applied to black pepper stem cuttings, several of the biosurfactant-producing strains provided significant disease control. In absence of the disease, several of the bacterial strains promoted shoot and root growth of black pepper stem cuttings. Biosurfactant-producing pseudomonads indigenous to the rhizosphere of black pepper plants are genotypically diverse and provide a novel resource for the control of Phy. capsici root rot and growth promotion of black pepper stem cuttings. The results of this study provide a strong basis for further development of supplementary strategies with antagonistic bacteria to control foot and root rot of black pepper and to promote plant growth.

Genetic diversity and phylogeography of highly zoonotic Echinococcus granulosus genotype G1 in the Americas (Argentina, Brazil, Chile and Mexico) based on 8279bp of mtDNA.

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Laurimäe, Teivi; Kinkar, Liina; Andresiuk, Vanessa; Haag, Karen Luisa; Ponce-Gordo, Francisco; Acosta-Jamett, Gerardo; Garate, Teresa; Gonzàlez, Luis Miguel; Saarma, Urmas

2016-11-01

Echinococcus granulosus is a taeniid cestode and the etiological agent of an infectious zoonotic disease known as cystic echinococcosis (CE) or hydatid disease. CE is a serious public health concern in many parts of the world, including the Americas, where it is highly endemic in many regions. Echinococcus granulosus displays high intraspecific genetic variability and is divided into multiple genotypes (G1-G8, G10) with differences in their biology and etiology. Of these, genotype G1 is responsible for the majority of human and livestock infections and has the broadest host spectrum. However, despite the high significance to the public and livestock health, the data on genetic variability and regional genetic differences of genotype G1 in America are scarce. The aim of this study was to evaluate the genetic variability and phylogeography of G1 in several countries in America by sequencing a large portion of the mitochondrial genome. We analysed 8279bp of mtDNA for 52 E. granulosus G1 samples from sheep, cattle and pigs collected in Argentina, Brazil, Chile and Mexico, covering majority of countries in the Americas where G1 has been reported. The phylogenetic network revealed 29 haplotypes and a high haplotype diversity (Hd=0.903). The absence of phylogeographic segregation between different regions in America suggests the importance of animal transportation in shaping the genetic structure of E. granulosus G1. In addition, our study revealed many highly divergent haplotypes, indicating a long and complex evolutionary history of E. granulosus G1 in the Americas. Copyright © 2016 Elsevier B.V. All rights reserved.

Estimation of genetic variability among elite wheat genotypes using random amplified polymorphic DNA (RAPD) analysis

International Nuclear Information System (INIS)

BIBI, S.; Khan, I.A.; Naqvi, M.H.; Siddiqui, M.A.; Yasmeen, S.; Seema, M.

2012-01-01

Twenty four wheat varieties/lines were assessed through RAPD for genetic diversity. Of forty primers, thirteen were able to amplify the genomic DNA and yielded 269 polymorphic bands. The percentage of the polymorphic loci was 86.22%. Nei's genetic diversity (h) ranged from 0.248 to 0.393, with an average of 0.330. Shanon's index ranged from 0.382 to 0.567, with an average of 0.487. The proportion of genetic variation among the populations ( Ds) accounted for 28.58 % of the whole genetic diversity. The level of gene flow (Nm) was 1.25. Some specific RAPD bands were also identified, variety C-591, and QM-4531 contain a specific segment of 4.9 kbp. Whereas SARC-1 and PKV-1600 amplified a specific DNA segment with primer A-09. Marvi-2000 contains two specific segments of 3.2 kb and 200 bp amplified with primer B-07. Genetically most similar genotypes were C-591 and Pasban-90 (76%) and most dissimilar genotypes were Rawal-87 and Khirman (36.1%). On the basis of results, 24 wheat varieties under study could be divided into 'two' groups and five clusters 'A' to 'E. (author)

Distribution of Porphyromonas gingivalis fimA genotypes in primary endodontic infections.

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Rôças, Isabela N; Siqueira, José F

2010-03-01

Long fimbriae (FimA) are important virulence factors of Porphyromonas gingivalis. Based on the diversity of the fimA gene, this species is classified into 6 genotypes. This study surveyed samples from primary endodontic infections for the presence of these P. gingivalis fimA variants. Genomic DNA isolated from samples taken from 25 root canals of teeth with chronic apical periodontitis and 25 aspirates from acute apical abscess was used as template in polymerase chain reaction (PCR) assays directed toward the detection of the different P. gingivalis fimA genotypes. Porphyromonas gingivalis was detected by a 16S rRNA gene-based PCR in 36% of the total number of cases sampled (44% of chronic apical periodontitis and 28% of abscess aspirates). In cases of chronic apical periodontitis, P. gingivalis variant type IV was the most prevalent (24%), followed by types I (20%), II (16%), and III (8%). In acute abscess samples, variant type II was the most prevalent (12%), followed by types III and IV (8% of each) and type I (4%). Combinations of up to 3 different genotypes were detected in a few cases. No single fimA genotype variant or combination thereof was significantly associated with symptoms. Overall, fimA types IV (16%), II (14%), and I (12%) were the most prevalent. Findings demonstrated that different P. gingivalis fimA genotypes can be present in primary endodontic infections. Copyright 2010 Mosby, Inc. All rights reserved.

Genetic characterization of Toxoplasma gondii from Brazilian wildlife revealed abundant new genotypes.

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Vitaliano, S N; Soares, H S; Minervino, A H H; Santos, A L Q; Werther, K; Marvulo, M F V; Siqueira, D B; Pena, H F J; Soares, R M; Su, C; Gennari, S M

2014-12-01

This study aimed to isolate and genotype T. gondii from Brazilian wildlife. For this purpose, 226 samples were submitted to mice bioassay and screened by PCR based on 18S rRNA sequences. A total of 15 T. gondii isolates were obtained, including samples from four armadillos (three Dasypus novemcinctus, one Euphractus sexcinctus), three collared anteaters (Tamandua tetradactyla), three whited-lipped peccaries (Tayassu pecari), one spotted paca (Cuniculus paca), one oncilla (Leopardus tigrinus), one hoary fox (Pseudalopex vetulus), one lineated woodpecker (Dryocopus lineatus) and one maned wolf (Chrysocyon brachyurus). DNA from the isolates, originated from mice bioassay, and from the tissues of the wild animal, designated as "primary samples", were genotyped by PCR-restriction fragment length polymorphism (PCR/RFLP), using 12 genetic markers (SAG1, SAG2, alt.SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L258, PK1, CS3 and Apico). A total of 17 genotypes were identified, with 13 identified for the first time and four already reported in published literature. Results herein obtained corroborate previous studies in Brazil, confirming high diversity and revealing unique genotypes in this region. Given most of genotypes here identified are different from previous studies in domestic animals, future studies on T. gondii from wildlife is of interest to understand population genetics and structure of this parasite.

Genetic characterization of Toxoplasma gondii from Brazilian wildlife revealed abundant new genotypes

Directory of Open Access Journals (Sweden)

S.N. Vitaliano

2014-12-01

Full Text Available This study aimed to isolate and genotype T. gondii from Brazilian wildlife. For this purpose, 226 samples were submitted to mice bioassay and screened by PCR based on 18S rRNA sequences. A total of 15 T. gondii isolates were obtained, including samples from four armadillos (three Dasypus novemcinctus, one Euphractus sexcinctus, three collared anteaters (Tamandua tetradactyla, three whited-lipped peccaries (Tayassu pecari, one spotted paca (Cuniculus paca, one oncilla (Leopardus tigrinus, one hoary fox (Pseudalopex vetulus, one lineated woodpecker (Dryocopus lineatus and one maned wolf (Chrysocyon brachyurus. DNA from the isolates, originated from mice bioassay, and from the tissues of the wild animal, designated as “primary samples”, were genotyped by PCR–restriction fragment length polymorphism (PCR/RFLP, using 12 genetic markers (SAG1, SAG2, alt.SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L258, PK1, CS3 and Apico. A total of 17 genotypes were identified, with 13 identified for the first time and four already reported in published literature. Results herein obtained corroborate previous studies in Brazil, confirming high diversity and revealing unique genotypes in this region. Given most of genotypes here identified are different from previous studies in domestic animals, future studies on T. gondii from wildlife is of interest to understand population genetics and structure of this parasite.

Concordance between botanical groups and genetic diversity in peanut

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Ingrid Pinheiro Machado

Full Text Available ABSTRACT The aims of this study were to characterize peanut accessions of germplasm collection of the CCA/UFC and check consistency between the pre-existing botanical groups to estimates of genetic diversity. For this were conducted a trial with 43 accessions of peanut in a randomized block design with three replications. To characterization were used 21 morphological descriptors, where revealed large genetic variation. The mass hundred grains trait showed the main discriminating factors, with relative percentage of 22.1%. The cluster obtained with the linkage complete method, it was possible to view the dendrogram the formation of seven groups based on the Mahalanobis distance. By principal components analysis was identified phenotypic diversity among genotypes. The first three components explained 81% of the total variation. Subsequently, built a three-dimensional scatter chart for access of visualization, eight groups being formed. There was medium magnitude of agreement between the botanical groups and genetic diversity, both by the dendrogram and graphic dispersion proving the dissimilarity between genotypes of different botanic groups. Therefore, crossings between group access botanical Spanish or Valencia with those belonging to the Virginia group should generate segregating populations with high genetic potential.

Relatedness of Indian flax genotypes (Linum usitatissimum L.): an inter-simple sequence repeat (ISSR) primer assay.

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Rajwade, Ashwini V; Arora, Ritu S; Kadoo, Narendra Y; Harsulkar, Abhay M; Ghorpade, Prakash B; Gupta, Vidya S

2010-06-01

The objective of this study was to analyze the genetic relationships, using PCR-based ISSR markers, among 70 Indian flax (Linum usitatissimum L.) genotypes actively utilized in flax breeding programs. Twelve ISSR primers were used for the analysis yielding 136 loci, of which 87 were polymorphic. The average number of amplified loci and the average number of polymorphic loci per primer were 11.3 and 7.25, respectively, while the percent loci polymorphism ranged from 11.1 to 81.8 with an average of 63.9 across all the genotypes. The range of polymorphism information content scores was 0.03-0.49, with an average of 0.18. A dendrogram was generated based on the similarity matrix by the Unweighted Pair Group Method with Arithmetic Mean (UPGMA), wherein the flax genotypes were grouped in five clusters. The Jaccard's similarity coefficient among the genotypes ranged from 0.60 to 0.97. When the omega-3 alpha linolenic acid (ALA) contents of the individual genotypes were correlated with the clusters in the dendrogram, the high ALA containing genotypes were grouped in two clusters. This study identified SLS 50, Ayogi, and Sheetal to be the most diverse genotypes and suggested their use in breeding programs and for developing mapping populations.

High genetic diversity and fine-scale spatial structure in the marine flagellate Oxyrrhis marina (Dinophyceae uncovered by microsatellite loci.

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Chris D Lowe

2010-12-01

Full Text Available Free-living marine protists are often assumed to be broadly distributed and genetically homogeneous on large spatial scales. However, an increasing application of highly polymorphic genetic markers (e.g., microsatellites has provided evidence for high genetic diversity and population structuring on small spatial scales in many free-living protists. Here we characterise a panel of new microsatellite markers for the common marine flagellate Oxyrrhis marina. Nine microsatellite loci were used to assess genotypic diversity at two spatial scales by genotyping 200 isolates of O. marina from 6 broad geographic regions around Great Britain and Ireland; in one region, a single 2 km shore line was sampled intensively to assess fine-scale genetic diversity. Microsatellite loci resolved between 1-6 and 7-23 distinct alleles per region in the least and most variable loci respectively, with corresponding variation in expected heterozygosities (H(e of 0.00-0.30 and 0.81-0.93. Across the dataset, genotypic diversity was high with 183 genotypes detected from 200 isolates. Bayesian analysis of population structure supported two model populations. One population was distributed across all sampled regions; the other was confined to the intensively sampled shore, and thus two distinct populations co-occurred at this site. Whilst model-based analysis inferred a single UK-wide population, pairwise regional F(ST values indicated weak to moderate population sub-division (0.01-0.12, but no clear correlation between spatial and genetic distance was evident. Data presented in this study highlight extensive genetic diversity for O. marina; however, it remains a substantial challenge to uncover the mechanisms that drive genetic diversity in free-living microorganisms.

Genetic diversity of wild and cultivated genotypes of pigeonpea through RAPD and SSR markers.

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Walunjkar, Babasaheb C; Parihar, Akarsh; Singh, Nirbhay Kumar; Parmar, L D

2015-03-01

Eight wild and four cultivated pigeonpea genotypes were subjected to RAPD and microsatellite analysis, with 40 primers each. Out of these, eight RAPD and five SSR primers were found polymorphic. RAPD primers showed 100% polymorphism and produced a total of 517 DNA fragments, whereas SSR primers produced 67 fragments and they too showed 100% polymorphism. The RAPD markers revealed highest similarity co-efficient of 0.93 (GT-100 and ICPL-87), whereas the highest similarity co-efficient obtained with SSR markers was 1.00 (GTH-1 and GT-100). Average PIC value obtained with RAPD and SSR were 0.90 and 0.18, respectively. The arithmetic mean heterozygosity and marker index were 0.90 and 22.47 respectively with RAPD marker, whereas the corresponding values for SSR markers were 0.18 and 33.66. Moreover; the four wild genotypes (Cajanus scarabaeoides, Rhyncosia rufescence, Cajanus cajanifolius and Rhyncosia canna) and the four cultivars (GTH-1, GT-100, ICPL-87 and GT-1) grouped distinctly in the same subgroups of the dendrograms obtained with both RAPD and SSR analysis. Therefore, the findings of SSR supplement and validate the results obtained with RAPD analysis.

Diversity of cacao trees in Waslala, Nicaragua: associations between genotype spectra, product quality and yield potential.

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Trognitz, Bodo; Cros, Emile; Assemat, Sophie; Davrieux, Fabrice; Forestier-Chiron, Nelly; Ayestas, Eusebio; Kuant, Aldo; Scheldeman, Xavier; Hermann, Michael

2013-01-01

The sensory quality and the contents of quality-determining chemical compounds in unfermented and fermented cocoa from 100 cacao trees (individual genotypes) representing groups of nine genotype spectra (GG), grown at smallholder plantings in the municipality of Waslala, Nicaragua, were evaluated for two successive harvest periods. Cocoa samples were fermented using a technique mimicking recommended on-farm practices. The sensory cocoa quality was assessed by experienced tasters, and seven major chemical taste compounds were quantified by near infrared spectrometry (NIRS). The association of the nine, partially admixed, genotype spectra with the analytical and sensory quality parameters was tested. The individual parameters were analyzed as a function of the factors GG and harvest (including the date of fermentation), individual trees within a single GG were used as replications. In fermented cocoa, significant GG-specific differences were observed for methylxanthines, theobromine-to-caffeine (T/C) ratio, total fat, procyanidin B5 and epicatechin, as well as the sensory attributes global score, astringency, and dry fruit aroma, but differences related to harvest were also apparent. The potential cocoa yield was also highly determined by the individual GG, although there was significant tree-to-tree variation within every single GG. Non-fermented samples showed large harvest-to-harvest variation of their chemical composition, while differences between GG were insignificant. These results suggest that selection by the genetic background, represented here by groups of partially admixed genotype spectra, would be a useful strategy toward enhancing quality and yield of cocoa in Nicaragua. Selection by the GG within the local, genetically segregating populations of seed-propagated cacao, followed by clonal propagation of best-performing individuals of the selected GG could be a viable alternative to traditional propagation of cacao by seed from open pollination. Fast and

Diversity of cacao trees in Waslala, Nicaragua: associations between genotype spectra, product quality and yield potential.

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Bodo Trognitz

Full Text Available The sensory quality and the contents of quality-determining chemical compounds in unfermented and fermented cocoa from 100 cacao trees (individual genotypes representing groups of nine genotype spectra (GG, grown at smallholder plantings in the municipality of Waslala, Nicaragua, were evaluated for two successive harvest periods. Cocoa samples were fermented using a technique mimicking recommended on-farm practices. The sensory cocoa quality was assessed by experienced tasters, and seven major chemical taste compounds were quantified by near infrared spectrometry (NIRS. The association of the nine, partially admixed, genotype spectra with the analytical and sensory quality parameters was tested. The individual parameters were analyzed as a function of the factors GG and harvest (including the date of fermentation, individual trees within a single GG were used as replications. In fermented cocoa, significant GG-specific differences were observed for methylxanthines, theobromine-to-caffeine (T/C ratio, total fat, procyanidin B5 and epicatechin, as well as the sensory attributes global score, astringency, and dry fruit aroma, but differences related to harvest were also apparent. The potential cocoa yield was also highly determined by the individual GG, although there was significant tree-to-tree variation within every single GG. Non-fermented samples showed large harvest-to-harvest variation of their chemical composition, while differences between GG were insignificant. These results suggest that selection by the genetic background, represented here by groups of partially admixed genotype spectra, would be a useful strategy toward enhancing quality and yield of cocoa in Nicaragua. Selection by the GG within the local, genetically segregating populations of seed-propagated cacao, followed by clonal propagation of best-performing individuals of the selected GG could be a viable alternative to traditional propagation of cacao by seed from open

Diversity of Cacao Trees in Waslala, Nicaragua: Associations between Genotype Spectra, Product Quality and Yield Potential

Science.gov (United States)

Trognitz, Bodo; Cros, Emile; Assemat, Sophie; Davrieux, Fabrice; Forestier-Chiron, Nelly; Ayestas, Eusebio; Kuant, Aldo; Scheldeman, Xavier; Hermann, Michael

2013-01-01

The sensory quality and the contents of quality-determining chemical compounds in unfermented and fermented cocoa from 100 cacao trees (individual genotypes) representing groups of nine genotype spectra (GG), grown at smallholder plantings in the municipality of Waslala, Nicaragua, were evaluated for two successive harvest periods. Cocoa samples were fermented using a technique mimicking recommended on-farm practices. The sensory cocoa quality was assessed by experienced tasters, and seven major chemical taste compounds were quantified by near infrared spectrometry (NIRS). The association of the nine, partially admixed, genotype spectra with the analytical and sensory quality parameters was tested. The individual parameters were analyzed as a function of the factors GG and harvest (including the date of fermentation), individual trees within a single GG were used as replications. In fermented cocoa, significant GG-specific differences were observed for methylxanthines, theobromine-to-caffeine (T/C) ratio, total fat, procyanidin B5 and epicatechin, as well as the sensory attributes global score, astringency, and dry fruit aroma, but differences related to harvest were also apparent. The potential cocoa yield was also highly determined by the individual GG, although there was significant tree-to-tree variation within every single GG. Non-fermented samples showed large harvest-to-harvest variation of their chemical composition, while differences between GG were insignificant. These results suggest that selection by the genetic background, represented here by groups of partially admixed genotype spectra, would be a useful strategy toward enhancing quality and yield of cocoa in Nicaragua. Selection by the GG within the local, genetically segregating populations of seed-propagated cacao, followed by clonal propagation of best-performing individuals of the selected GG could be a viable alternative to traditional propagation of cacao by seed from open pollination. Fast and

Clonal genotype of Geomyces destructans among bats with White Nose Syndrome, New York, USA.

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Rajkumar, Sunanda S; Li, Xiaojiang; Rudd, Robert J; Okoniewski, Joseph C; Xu, Jianping; Chaturvedi, Sudha; Chaturvedi, Vishnu

2011-07-01

The dispersal mechanism of Geomyces destructans, which causes geomycosis (white nose syndrome) in hibernating bats, remains unknown. Multiple gene genealogic analyses were conducted on 16 fungal isolates from diverse sites in New York State during 2008-2010. The results are consistent with the clonal dispersal of a single G. destructans genotype.

Assessing genetic diversity among six populations of Gossypium arboreum L. using microsatellites markers.

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Sethi, Khushboo; Siwach, Priyanka; Verma, Surender Kumar

2015-10-01

Among the four cultivated cotton species, G. hirsutum (allotetraploid) presently holds a primary place in cultivation. Efforts to further improve this primary cotton face the constraints of its narrow genetic base due to repeated selective breeding and hence demands enrichment of diversity in the gene pool. G. arboreum (diploid species) is an invaluable genetic resource with great potential in this direction. Based on the dispersal and domestication in different directions from Indus valley, different races of G. arboreum have evolved, each having certain traits like drought and disease resistance, which the tetraploid cotton lack. Due to lack of systematic, race wise characterization of G. arboreum germplasm, it  has not been explored fully. During the present study, 100 polymorphic SSR loci were  used to genotype 95 accessions belonging to 6 races of G. arboreum producing 246 polymorphic alleles; mean number of effective alleles was 1.505. AMOVA showed 14 % of molecular variance among population groups, 34 % among individuals and remaining 52 % within individuals. UPGMA dendrogram, based on Nei's genetic distance, distributed the six populations in two major clusters of 3 populations each; race 'bengalense' was found more close to 'cernuum' than the others. The clustering of 95 genotypes by UPGMA tree generation as well as PCoA analysis clustered 'bengalense' genotypes into one group along with some genotypes of 'cernuum', while rest of the genotypes made separate clusters. Outcomes of this research should be helpful in identifying the genotypes for their further utilization in hybridization program to obtain high level of germplasm diversity.

Genotypes and subgenotypes of hepatitis B virus circulating in an endemic area in Peru.

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Ramírez-Soto, Max Carlos; Bracho, Maria Alma; González-Candelas, Fernando; Huichi-Atamari, Milagros

2018-01-01

Although hepatitis B virus (HBV) infection is still endemic in Abancay, Peru, two decades after vaccination against hepatitis B started in the area, little is known about the diversity and circulation of genotypes and subgenotypes of the virus. To identify the genotypes and subtypes of HBV circulating in Abancay, complete genome sequences of 11 treatment-naive HBV-infected patients were obtained, and phylogenetic analysis was conducted with these and additional sequences from GenBank. Genotyping revealed the presence of genotype F in all the samples from Abancay. Subgenotype F1b was dominant and only one isolate belonged to subgenotype F4, which represents the first description of this subgenotype in Peru. Phylogenetic analysis revealed that most subgenotype F1b isolates from Peru clustered in a subgroup along with two sequences from Argentina, whereas two clusters with two HBV/F1b sequences each were indicative of recent epidemiological linkage, but only one could be verified by independent data. These results suggest that the HBV subgenotype F1b seems to be the predominant subgenotype in Abancay, Peru.

Variation for N Uptake System in Maize: Genotypic Response to N Supply

KAUST Repository

Garnett, Trevor

2015-11-09

An understanding of the adaptations made by plants in their nitrogen (N) uptake systems in response to reduced N supply is important to the development of cereals with enhanced N uptake efficiency (NUpE). Twenty seven diverse genotypes of maize (Zea mays, L.) were grown in hydroponics for 3 weeks with limiting or adequate N supply. Genotypic response to N was assessed on the basis of biomass characteristics and the activities of the nitrate (NO−3) and ammonium (NH+4) high-affinity transport systems. Genotypes differed greatly for the ability to maintain biomass with reduced N. Although, the N response in underlying biomass and N transport related characteristics was less than that for biomass, there were clear relationships, most importantly, lines that maintained biomass at reduced N maintained net N uptake with no change in size of the root relative to the shoot. The root uptake capacity for both NO−3 and NH+4 increased with reduced N. Transcript levels of putative NO−3 and NH+4 transporter genes in the root tissue of a subset of the genotypes revealed that predominately ZmNRT2 transcript levels responded to N treatments. The correlation between the ratio of transcripts of ZmNRT2.2 between the two N levels and a genotype\\'s ability to maintain biomass with reduced N suggests a role for these transporters in enhancing NUpE. The observed variation in the ability to capture N at low N provides scope for both improving NUpE in maize and also to better understand the N uptake system in cereals.

Epidemiology of Brucellosis and Genetic Diversity of Brucella abortus in Kazakhstan.

Science.gov (United States)

Shevtsova, Elena; Shevtsov, Alexandr; Mukanov, Kasim; Filipenko, Maxim; Kamalova, Dinara; Sytnik, Igor; Syzdykov, Marat; Kuznetsov, Andrey; Akhmetova, Assel; Zharova, Mira; Karibaev, Talgat; Tarlykov, Pavel; Ramanculov, Erlan

2016-01-01

Brucellosis is a major zoonotic infection in Kazakhstan. However, there is limited data on its incidence in humans and animals, and the genetic diversity of prevalent strains is virtually unstudied. Additionally, there is no detailed overview of Kazakhstan brucellosis control and eradication programs. Here, we analyzed brucellosis epidemiological data, and assessed the effectiveness of eradication strategies employed over the past 70 years to counteract this infection. We also conducted multiple loci variable-number tandem repeat analysis (MLVA) of Brucella abortus strains found in Kazakhstan. We analyzed official data on the incidence of animal brucellosis in Kazakhstan. The records span more than 70 years of anti-brucellosis campaigns, and contain a brief description of the applied control strategies, their effectiveness, and their impact on the incidence in humans. The MLVA-16 method was used to type 94 strains of B. abortus and serial passages of B. abortus 82, a strain used in vaccines. MLVA-8 and MLVA-11 analyses clustered strains into a total of four and seven genotypes, respectively; it is the first time that four of these genotypes have been described. MLVA-16 analysis divided strains into 28 distinct genotypes having genetic similarity coefficient that varies from 60 to100% and a Hunter & Gaston diversity index of 0.871. MST analysis reconstruction revealed clustering into "Kazakhstani-Chinese (Central Asian)", "European" and "American" lines. Detection of multiple genotypes in a single outbreak confirms that poorly controlled trade of livestock plays a crucial role in the spread of infection. Notably, the MLVA-16 profile of the B. abortus 82 strain was unique and did not change during 33 serial passages. MLVA genotyping may thus be useful for epidemiological monitoring of brucellosis, and for tracking the source(s) of infection. We suggest that countrywide application of MLVA genotyping would improve the control of brucellosis in Kazakhstan.

High Levels of Genetic Diversity of Plasmodium falciparum Populations in Papua New Guinea despite Variable Infection Prevalence

Science.gov (United States)

Barry, Alyssa E.; Schultz, Lee; Senn, Nicholas; Nale, Joe; Kiniboro, Benson; Siba, Peter M.; Mueller, Ivo; Reeder, John C.

2013-01-01

High levels of genetic diversity in Plasmodium falciparum populations are an obstacle to malaria control. Here, we investigate the relationship between local variation in malaria epidemiology and parasite genetic diversity in Papua New Guinea (PNG). Cross-sectional malaria surveys were performed in 14 villages spanning four distinct malaria-endemic areas on the north coast, including one area that was sampled during the dry season. High-resolution msp2 genotyping of 2,147 blood samples identified 761 P. falciparum infections containing a total of 1,392 clones whose genotypes were used to measure genetic diversity. Considerable variability in infection prevalence and mean multiplicity of infection was observed at all of the study sites, with the area sampled during the dry season showing particularly striking local variability. Genetic diversity was strongly associated with multiplicity of infection but not with infection prevalence. In highly endemic areas, differences in infection prevalence may not translate into a decrease in parasite population diversity. PMID:23400571

Determination of the resistance types to Spodoptera cosmioides (Walker (Lepidoptera: Noctuidae in soybean genotypes

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Arlindo Leal Boiça Júnior

2015-04-01

Full Text Available The aim of this work was to evaluate the resistance types in soybean genotypes to Spodoptera cosmioides (Walker in laboratory. Soybean genotypes assessed were as follows: ‘IAC 100’ (resistance standard, ‘BR16’ (susceptible standard, ‘Dowling’, PI 227687, PI 274454, ‘IGRA RA 626 RR’, PI 227682, ‘BRSGO 8360’, ‘IGRA RA 516 RR’ and ‘P 98Y11 RR’. Free-choice and no-choice feeding non-preference tests were done using two newly-hatched larvae per genotype or one third-instar larva per genotype in both tests. Larvae attractiveness was evaluated in different times, and at the end of the experiments the leaf area consumed was quantified. In the antibiosis test, newly-hatched larvae were individualized into Petri dishes, where leaflets of the genotypes were offered over the larval stage, and the following biological parameters were assessed: period and viability of larvae, pupae and overall (larvae + pupae, weight of larvae and pupae, sex ratio and adults longevity. Overall, in the feeding preference tests, significant differences were not found in leaf consumption among the genotypes. In the antibiosis assay, genotypes PI 227687, PI 227682 and ‘IAC 100’ caused 100% larval mortality and the lowest weight of larvae, ranging between 37.65 and 85.56 mg. All soybean genotypes evaluated do not exhibit feeding non-preference type resistance to S. cosmioides, and PI 227687, PI 227682 and ‘IAC 100’ highlighted for possessing antibiosis.

Assessment of genetic diversity among moderately drought tolerant landraces of rice using RAPD markers

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Md. Shariful Islam

2013-01-01

Full Text Available Genetic diversity and relationships among six rice genotypes were investigated using five random amplified polymorphic DNA (RAPD markers. A total of 69 alleles were amplified, of which 66 were polymorphic. The size of the amplified alleles was between 0.25 and 2.35 kbp. The number of polymorphic alleles detected with each primer ranged from 7 to 24 with an average of 13.2 per primer and the polymorphism information content (PIC values varied from 0.8672 to 0.9471. Pair-wise similarity estimated the range of 0.308 to 0.718 among all the genotypes and the highest genetic similarity was found between Maloti and BRRI dhan53. Cluster analysis using UPGMA (unweighted pair group method with arithmetic averages revealed three clusters at genetic similarity of 46%. A moderately drought tolerant landrace, Boalia, formed a single cluster and the remaining genotypes grouped into distinct clusters based on their relatedness. The results showed a high level of genetic diversity among studied genotypes and this information will assist in conservation as well as selection of parents during breeding programs for the development of drought tolerant rice varieties in near future.

H. pylori clinical isolates have diverse babAB genotype distributions over different topographic sites of stomach with correlation to clinical disease outcomes

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Sheu Shew-Meei

2012-05-01

Full Text Available Abstract Background Intragenomic recombination between babA and babB mediates antigenic variations and may help H. pylori colonization. This study determined whether variable genotypes of babA and babB correlate to different clinical disease outcomes, and can distribute over the different gastric niches. Results This study enrolled 92 clinical strains (45 from peptic ulcer, 27 from gastritis, and 20 from gastric cancer to detect whether the babA and babB are at locus A or B by PCR reactions using the primers designed from the upstream and variable region of the babA and babB genes. Four genotypes of babA and babB (A B, AB B, A AB, AB AB were found. The distribution of the 4 genotypes in 92 clinical strains was significantly different among patients with different gastric diseases (p vs. 9.7%, p p p > 0.05. Besides, the study enrolled 19 patients to verify whether variable genotypes of babAB existed in the different gastric niches. Among the patients infected with more than one babAB genotypes over antrum and corpus, there were higher rate of genotypes as A B or AB AB in isolates from antrum than in those from corpus (75.0 % vs. 16.7%, p  Conclusions The H. pylori isolate with the AB AB genotype correlates with an increased gastric cancer risk, and colonize in an antrum predominant manner.

In vitro regeneration of some Iranian alfalfa (Medicago sativa L. genotypes via somatic embryogenesis

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Majid Shokrpour

2014-12-01

Full Text Available An effective in vitro regeneration system is one of the prerequisites for genetic manipulation of alfalfa (Medicago sativa L. varieties and genotypes. In this research, somatic embryogenesis of four alfalfa genotypes, 6-18 (synthetic, 4-14 (Kara Yonje- Karakozlu, 3-27 (Kara Yonje Maraghe and y-6 (Regen-SY, were investigated using leaf and petiole explants. Formation of callus and somatic embryogenesis was significantly influenced by the explant type and interaction of genotype and culture medium. Petiole explants of genotype 4-14 produced the highest yield of callus (0.406 gr fresh weight of callus. Percentage of somatic embryogenesis and the number of embryos per callus in petiole explants of genotype 4-14 was higher than those of other genotypes and explants. In genotype 6-18, the highest percentage of somatic embryogenesis was achieved on MS medium containing 5 mg/L 2,4-D and 2 mg/L kinetin. There was no significant differences between genotypes and explants in terms of embryo conversion to plantlet, and on average, 58% of somatic embryos converted to plantlet on MS medium. The petiole explants of genotype 6-18 did not exhibit somatic embryogenesis response in medium containing low ratio of 2,4-D:Kinetin (5 mg/L 2,4-D and 2 mg/L kinetin. While, these explants showed somatic embryogenesis in higher ratio of 2,4-D:Kinetin (5:1. The plantlet conversion efficiency of somatic embryos produced through this study was relatively higher and therefore, the method presented in this study could be used in alfalfa genetic manipulation and molecular studies.

A century of potato breeding: improvement, diversification, and diversity

Science.gov (United States)

Breeding within potato has relied almost entirely on phenotypic selection and little is known of the underlying genetic elements being acted upon. To characterize the effects of this selection on phenotypic and genotypic diversity within cultivated potato, the SolCAP 8300 Infinium SNP chip was utili...

Molecular evaluation of genetic diversity and association studies in ...

Indian Academy of Sciences (India)

In the present study, we tested rice genotypes that included un(der)exploited landraces of Tamil Nadu along with indica and japonica test cultivars to ascertain their genetic diversity structure. Highly polymorphic microsatellite markers were used for generating marker segregation data. A novel measure, allele discrimination ...

Common genotypes of hepatitis B virus

International Nuclear Information System (INIS)

Idrees, M.; Khan, S.; Riazuddin, S.

2004-01-01

Objective: To find out the frequency of common genotypes of hepatitis-B virus (HBV). Subjects and Methods: HBV genotypes were determined in 112 HBV DNA positive sera by a simple and precise molecular genotyping system base on PCR using type-specific primers for the determination of genotypes of HBV A through H. Results: Four genotypes (A,B,C and D) out of total eight reported genotypes so far were identified. Genotypes A, B and C were predominant. HBV genotype C was the most predominant in this collection, appearing in 46 samples (41.7%). However, the genotypes of a total of 5 (4.46%) samples could not be determined with the present genotyping system. Mixed genotypes were seen in 8(7.14% HBV) isolates. Five of these were infected with genotypes A/D whereas two were with genotypes C/D. One patient was infected with 4 genotypes (A/B/C/D). Genotype A (68%) was predominant in Sindh genotype C was most predominant in North West Frontier Province (NWFP) (68.96) whereas genotype C and B were dominant in Punjab (39.65% and 25.86% respectively). Conclusion: All the four common genotypes of HBV found worldwide (A,B,C and D) were isolated. Genotype C is the predominant Genotypes B and C are predominant in Punjab and N.W.F.P. whereas genotype A is predominant in Sindh. (author)

Genotype I of Japanese Encephalitis Virus Virus-like Particles Elicit Sterilizing Immunity against Genotype I and III Viral Challenge in Swine.

Science.gov (United States)

Fan, Yi-Chin; Chen, Jo-Mei; Lin, Jen-Wei; Chen, Yi-Ying; Wu, Guan-Hong; Su, Kuan-Hsuan; Chiou, Ming-Tang; Wu, Shang-Rung; Yin, Ji-Hang; Liao, Jiunn-Wang; Chang, Gwong-Jen J; Chiou, Shyan-Song

2018-05-10

Swine are a critical amplifying host involved in human Japanese encephalitis (JE) outbreaks. Cross-genotypic immunogenicity and sterile protection are important for the current genotype III (GIII) virus-derived vaccines in swine, especially now that emerging genotype I (GI) JE virus (JEV) has replaced GIII virus as the dominant strain. Herein, we aimed to develop a system to generate GI JEV virus-like particles (VLPs) and evaluate the immunogenicity and protection of the GI vaccine candidate in mice and specific pathogen-free swine. A CHO-heparan sulfate-deficient (CHO-HS(-)) cell clone, named 51-10 clone, stably expressing GI-JEV VLP was selected and continually secreted GI VLPs without signs of cell fusion. 51-10 VLPs formed a homogeneously empty-particle morphology and exhibited similar antigenic activity as GI virus. GI VLP-immunized mice showed balanced cross-neutralizing antibody titers against GI to GIV viruses (50% focus-reduction micro-neutralization assay titers 71 to 240) as well as potent protection against GI or GIII virus infection. GI VLP-immunized swine challenged with GI or GIII viruses showed no fever, viremia, or viral RNA in tonsils, lymph nodes, and brains as compared with phosphate buffered saline-immunized swine. We thus conclude GI VLPs can provide sterile protection against GI and GIII viruses in swine.

Molecular characterization and multi-locus genotypes of Enterocytozoon bieneusi from captive red kangaroos (Macropus Rufus in Jiangsu province, China.

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Zhijun Zhong

Full Text Available Enterocytozoon bieneusi is the most common pathogen of microsporidian species infecting humans worldwide. Although E. bieneusi has been found in a variety of animal hosts, information on the presence of E. bieneusi in captive kangaroos in China is limited. The present study was aimed at determining the occurrence and genetic diversity of E. bieneusi in captive kangaroos. A total of 61 fecal specimens (38 from red kangaroos and 23 from grey kangaroos were collected from Nanjing Hongshan Forest Zoo and Hongshan Kangaroo Breeding Research Base, Jiangsu province, China. Using the nested PCR amplification ITS gene of rRNA of E. bieneusi, totally 23.0% (14/61 of tested samples were PCR-positive with three genotypes (i.e. one known genotype, CHK1, and two novel genotypes, CSK1 and CSK2. Multi-locus sequence typing using three microsatellites (MS1, MS3, and MS7 and one minisatellite (MS4 revealed one, five, two, and one types at these four loci, respectively. In phylogenetic analysis, the two genotypes, CHK1 and CSK1, were clustered into a new group of unknown zoonotic potential, and the novel genotype CSK2 was clustered into a separate clade with PtEb and PtEbIX. To date, this is the first report on the presence of E. bieneusi in captive red kangaroos in Jiangsu province, China. Furthermore, a high degree of genetic diversity was observed in the E. bieneusi genotype and seven MLGs (MLG1-7 were found in red kangaroos. Our findings suggest that infected kangaroo may act as potential reservoirs of E. bieneusi and be source to transmit infections to other animal.

Molecular epidemiology and genetic diversity of Orientia tsutsugamushi from patients with scrub typhus in 3 regions of India.

Science.gov (United States)

Varghese, George M; Janardhanan, Jeshina; Mahajan, Sanjay K; Tariang, David; Trowbridge, Paul; Prakash, John A J; David, Thambu; Sathendra, Sowmya; Abraham, O C

2015-01-01

Scrub typhus, an acute febrile illness that is widespread in the Asia-Pacific region, is caused by the bacterium Orientia tsutsugamushi, which displays high levels of antigenic variation. We conducted an investigation to identify the circulating genotypes of O. tsutsugamushi in 3 scrub typhus-endemic geographic regions of India: South India, Northern India, and Northeast India. Eschar samples collected during September 2010-August 2012 from patients with scrub typhus were subjected to 56-kDa type-specific PCR and sequencing to identify their genotypes. Kato-like strains predominated (61.5%), especially in the South and Northeast, followed by Karp-like strains (27.7%) and Gilliam and Ikeda strains (2.3% each). Neimeng-65 genotype strains were also observed in the Northeast. Clarifying the genotypic diversity of O. tsutsugamushi in India enhances knowledge of the regional diversity among circulating strains and provides potential resources for future region-specific diagnostic studies and vaccine development.

Genotyping of Brucella melitensis and Brucella abortus strains currently circulating in Xinjiang, China.

Science.gov (United States)

Sun, Ming-Jun; Di, Dong-Dong; Li, Yan; Zhang, Zhi-Cheng; Yan, Hao; Tian, Li-Li; Jing, Zhi-Gang; Li, Jin-Ping; Jiang, Hai; Fan, Wei-Xing

2016-10-01

Brucellosis is a well-known zoonotic disease that can cause severe economic and healthcare losses. Xinjiang, one of the biggest livestock husbandry sectors in China, has gone through increasing incidence of brucellosis in cattle and small ruminants recently. In this paper, 50 B. melitensis strains and 9 B. abortus strains collected from across Xinjiang area (from 2010 to 2015) were genotyped using multiple locus variable-number tandem-repeat (VNTR) analysis (MLVA) and multi-locus sequence typing (MLST). Based on 8 loci (MLVA-8), 50 B. melitensis strains were classified into three genotypes. Genotypes 42 (n=38, 76%) and 63 (n=11, 22%) were part of the East Mediterranean group, and one genotype with pattern of 1-5-3-13-2-4-3-2 represents a single-locus variant from genotype 63. MLVA-16 resolved 50 B. melitensis strains into 28 genotypes, of which 15 are unique to Xinjiang and 10 are in common with those in adjacent country Kazakhstan and neighboring provinces of China. Minimum Spanning Tree (MST) analysis implies that B. melitensis strains collected from across Kazakhstan, Xinjiang and China areas may share a common origin. Nine B. abortus strains were sorted into three genotypes by MLVA-8, genotypes 36 (n=7, 77.8%), 86 (n=1, 11.1%) and a new genotype with pattern of 4-5-3-13-2-2-3-1. Each B. abortus strain showed distinct MLVA-16 genotypes, suggesting that B. abortus species may possess more genetic diversity than B. melitensis. Using MLST, most B. melitensis strains (n=49) were identified as sequence type ST8, and most B. abortus strains (n=8) were recognized as ST2. Two new sequence types, ST37 and ST38, represented by single strain from B. melitensis and B. abortus species respectively, were also detected in this study. These results could facilitate the pathogen surveillance in the forthcoming eradication programs and serve as a guide in source tracking in case of new outbreaks occur. Copyright © 2016 Elsevier B.V. All rights reserved.

Clonal Genotype of Geomyces destructans among Bats with White Nose Syndrome, New York, USA

OpenAIRE

Rajkumar, Sunanda S.; Li, Xiaojiang; Rudd, Robert J.; Okoniewski, Joseph C.; Xu, Jianping; Chaturvedi, Sudha; Chaturvedi, Vishnu

2011-01-01

The dispersal mechanism of Geomyces destructans, which causes geomycosis (white nose syndrome) in hibernating bats, remains unknown. Multiple gene genealogic analyses were conducted on 16 fungal isolates from diverse sites in New York State during 2008–2010. The results are consistent with the clonal dispersal of a single G. destructans genotype.

Cowpea Nodules Harbor Non-rhizobial Bacterial Communities that Are Shaped by Soil Type Rather than Plant Genotype

Science.gov (United States)

Leite, Jakson; Fischer, Doreen; Rouws, Luc F. M.; Fernandes-Júnior, Paulo I.; Hofmann, Andreas; Kublik, Susanne; Schloter, Michael; Xavier, Gustavo R.; Radl, Viviane

2017-01-01

Many studies have been pointing to a high diversity of bacteria associated to legume root nodules. Even though most of these bacteria do not form nodules with legumes themselves, it was shown that they might enter infection threads when co-inoculated with rhizobial strains. The aim of this work was to describe the diversity of bacterial communities associated with cowpea (Vigna unguiculata L. Walp) root nodules using 16S rRNA gene amplicon sequencing, regarding the factors plant genotype and soil type. As expected, Bradyrhizobium was the most abundant genus of the detected genera. Furthermore, we found a high bacterial diversity associated to cowpea nodules; OTUs related to the genera Enterobacter, Chryseobacterium, Sphingobacterium, and unclassified Enterobacteriacea were the most abundant. The presence of these groups was significantly influenced by the soil type and, to a lesser extent, plant genotype. Interestingly, OTUs assigned to Chryseobacterium were highly abundant, particularly in samples obtained from an Ultisol soil. We confirmed their presence in root nodules and assessed their diversity using a target isolation approach. Though their functional role still needs to be addressed, we postulate that Chryseobacterium strains might help cowpea plant to cope with salt stress in semi-arid regions. PMID:28163711

High quality copy number and genotype data from FFPE samples using Molecular Inversion Probe (MIP) microarrays

Energy Technology Data Exchange (ETDEWEB)

Wang, Yuker; Carlton, Victoria E.H.; Karlin-Neumann, George; Sapolsky, Ronald; Zhang, Li; Moorhead, Martin; Wang, Zhigang C.; Richardson, Andrea L.; Warren, Robert; Walther, Axel; Bondy, Melissa; Sahin, Aysegul; Krahe, Ralf; Tuna, Musaffe; Thompson, Patricia A.; Spellman, Paul T.; Gray, Joe W.; Mills, Gordon B.; Faham, Malek

2009-02-24

A major challenge facing DNA copy number (CN) studies of tumors is that most banked samples with extensive clinical follow-up information are Formalin-Fixed Paraffin Embedded (FFPE). DNA from FFPE samples generally underperforms or suffers high failure rates compared to fresh frozen samples because of DNA degradation and cross-linking during FFPE fixation and processing. As FFPE protocols may vary widely between labs and samples may be stored for decades at room temperature, an ideal FFPE CN technology should work on diverse sample sets. Molecular Inversion Probe (MIP) technology has been applied successfully to obtain high quality CN and genotype data from cell line and frozen tumor DNA. Since the MIP probes require only a small ({approx}40 bp) target binding site, we reasoned they may be well suited to assess degraded FFPE DNA. We assessed CN with a MIP panel of 50,000 markers in 93 FFPE tumor samples from 7 diverse collections. For 38 FFPE samples from three collections we were also able to asses CN in matched fresh frozen tumor tissue. Using an input of 37 ng genomic DNA, we generated high quality CN data with MIP technology in 88% of FFPE samples from seven diverse collections. When matched fresh frozen tissue was available, the performance of FFPE DNA was comparable to that of DNA obtained from matched frozen tumor (genotype concordance averaged 99.9%), with only a modest loss in performance in FFPE. MIP technology can be used to generate high quality CN and genotype data in FFPE as well as fresh frozen samples.

Sequence and phylogenetic analysis of virulent Newcastle disease virus isolates from Pakistan during 2009–2013 reveals circulation of new sub genotype

International Nuclear Information System (INIS)

Siddique, Naila; Naeem, Khalid; Abbas, Muhammad Athar; Ali Malik, Akbar; Rashid, Farooq; Rafique, Saba; Ghafar, Abdul; Rehman, Abdul

2013-01-01

Despite observing the standard bio-security measures at commercial poultry farms and extensive use of Newcastle disease vaccines, a new genotype VII-f of Newcastle disease virus (NDV) got introduced in Pakistan during 2011. In this regard 300 ND outbreaks recorded so far have resulted into huge losses of approximately USD 200 million during 2011–2013. A total of 33 NDV isolates recovered during 2009–2013 throughout Pakistan were characterized biologically and phylogenetically. The phylogenetic analysis revealed a new velogenic sub genotype VII-f circulating in commercial and domestic poultry along with the earlier reported sub genotype VII-b. Partial sequencing of Fusion gene revealed two types of cleavage site motifs; lentogenic 112 GRQGRL 117 and velogenic 112 RRQKRF 117 along with some point mutations indicative of genetic diversity. We report here a new sub genotype of virulent NDV circulating in commercial and backyard poultry in Pakistan and provide evidence for the possible genetic diversity which may be causing new NDV out breaks. - Highlights: • The first report of isolation of new genotype VII-f of virulent Newcastle disease virus (NDV) in Pakistan. • We report the partial Fusion gene sequences of new genotype VII-f of virulent NDV from Pakistan. • We report the phylogenetic relationship of new NDV strains with reported NDV strains. • Provide outbreak history of new virulent NDV strain in commercial and backyard poultry in Pakistan. • We provide possible evidence for the role of backyard poultry in NDV outbreaks

Genotypic and epitope characteristics of group A porcine rotavirus strains circulating in Canada.

Science.gov (United States)

Naseer, Omer; Jarvis, Matthew C; Ciarlet, Max; Marthaler, Douglas G

2017-07-01

Surveillance of Rotavirus A (RVA) infections in North America swine populations are limited and not performed over a significant time period to properly assess the diversity of RVA strains in swine. The VP7 (G) and VP4 (P) genes of 32 Canadian RVA strains, circulating between 2009 and 2015 were sequenced, identifying the G3P[13], G5P[7], G9P[7], G9[13], and G9[19] genotype combinations. The Canadian RVA strains were compared to the RVA strains present in the swine ProSystems RCE rotavirus vaccine. The comparison revealed multiple amino acid differences in the G and P antigenic epitopes, regardless of the G and P genotypes but specifically in the Canadian G3, P[13] and P[19] genotypes. Our study further contributes to the characterization of RVA's evolution and disease mitigation among swine, which may optimize target vaccine design, thereby minimizing RVA disease in this economically important animal population. Copyright © 2017 Elsevier Inc. All rights reserved.

Longitudinal genotyping of Candida dubliniensis isolates reveals strain maintenance, microevolution, and the emergence of itraconazole resistance.

LENUS (Irish Health Repository)

Fleischhacker, M

2010-05-01

We investigated the population structure of 208 Candida dubliniensis isolates obtained from 29 patients (25 human immunodeficiency virus [HIV] positive and 4 HIV negative) as part of a longitudinal study. The isolates were identified as C. dubliniensis by arbitrarily primed PCR (AP-PCR) and then genotyped using the Cd25 probe specific for C. dubliniensis. The majority of the isolates (55 of 58) were unique to individual patients, and more than one genotype was recovered from 15 of 29 patients. A total of 21 HIV-positive patients were sampled on more than one occasion (2 to 36 times). Sequential isolates recovered from these patients were all closely related, as demonstrated by hybridization with Cd25 and genotyping by PCR. Six patients were colonized by the same genotype of C. dubliniensis on repeated sampling, while strains exhibiting altered genotypes were recovered from 15 of 21 patients. The majority of these isolates demonstrated minor genetic alterations, i.e., microevolution, while one patient acquired an unrelated strain. The C. dubliniensis strains could not be separated into genetically distinct groups based on patient viral load, CD4 cell count, or oropharyngeal candidosis. However, C. dubliniensis isolates obtained from HIV-positive patients were more closely related than those recovered from HIV-negative patients. Approximately 8% (16 of 194) of isolates exhibited itraconazole resistance. Cross-resistance to fluconazole was only observed in one of these patients. Two patients harboring itraconazole-resistant isolates had not received any previous azole therapy. In conclusion, longitudinal genotyping of C. dubliniensis isolates from HIV-infected patients reveals that isolates from the same patient are generally closely related and may undergo microevolution. In addition, isolates may acquire itraconazole resistance, even in the absence of prior azole therapy.

Eco-epidemiology of Novel Bartonella Genotypes from Parasitic Flies of Insectivorous Bats.

Science.gov (United States)

Sándor, Attila D; Földvári, Mihály; Krawczyk, Aleksandra I; Sprong, Hein; Corduneanu, Alexandra; Barti, Levente; Görföl, Tamás; Estók, Péter; Kováts, Dávid; Szekeres, Sándor; László, Zoltán; Hornok, Sándor; Földvári, Gábor

2018-04-29

Bats are important zoonotic reservoirs for many pathogens worldwide. Although their highly specialized ectoparasites, bat flies (Diptera: Hippoboscoidea), can transmit Bartonella bacteria including human pathogens, their eco-epidemiology is unexplored. Here, we analyzed the prevalence and diversity of Bartonella strains sampled from 10 bat fly species from 14 European bat species. We found high prevalence of Bartonella spp. in most bat fly species with wide geographical distribution. Bat species explained most of the variance in Bartonella distribution with the highest prevalence of infected flies recorded in species living in dense groups exclusively in caves. Bat gender but not bat fly gender was also an important factor with the more mobile male bats giving more opportunity for the ectoparasites to access several host individuals. We detected high diversity of Bartonella strains (18 sequences, 7 genotypes, in 9 bat fly species) comparable with tropical assemblages of bat-bat fly association. Most genotypes are novel (15 out of 18 recorded strains have a similarity of 92-99%, with three sequences having 100% similarity to Bartonella spp. sequences deposited in GenBank) with currently unknown pathogenicity; however, 4 of these sequences are similar (up to 92% sequence similarity) to Bartonella spp. with known zoonotic potential. The high prevalence and diversity of Bartonella spp. suggests a long shared evolution of these bacteria with bat flies and bats providing excellent study targets for the eco-epidemiology of host-vector-pathogen cycles.

[A study on genotype of 271 mycobacterium tuberculosis isolates in 6 prefectures in Yunnan Province].

Science.gov (United States)

Chen, L Y; Yang, X; Ru, H H; Yang, H J; Yan, S Q; Ma, L; Chen, J O; Yang, R; Xu, L

2018-01-06

Objective: To understand the characteristics of genotypes of Mycobacterium tuberculosis isolates in Yunnan province, and provide the molecular epidemiological evidence for prevention and control of tuberculosis in Yunnan Province. Methods: Mycobacterium Tuberculosis isolates were collected from 6 prefectures of Yunnan province in 2014 and their Genetypes of Mycobacterium tuberculosis isolates were obtained using spoligotyping and multiple locus variable numbers of tandem repeats analysis (MLVA). The results of spoligotyping were entered into the SITVITWEB database to obtain the Spoligotyping International Type (SIT) patterns and the sublineages of MTB isolates. The genoyping patterns were clustered with BioNumerics (version 5.0). Results: A total of 271 MTB isolates represented patients were collected from six prefectures in Yunnan province. Out of these patients, 196 (72.3%) were male. The mean age of the patients was (41.9±15.1) years. The most MTB isolates were from Puer, totally 94 iusolates(34.69%). Spoligotyping analysis revealed that 151 (55.72%) MTB isolates belonged to the Beijing genotype, while the other 120 (44.28%) were from non-Beijing genotype; 40 genotypes were consisted of 24 unique genotypes and 16 clusters. The 271 isolates were differentiated into 30 clusters (2 to 17 isolates per cluster) and 177 unique genotypes, showing a clustering rate of 23.62%. Beijing genotype strains showed higher clustering rate than non-Beijing genotype strains (29.14% vs 16.67%). The HGI of 12-locus VNTR in total MTB strains, Beijing genotype strains and non-Beijing genotype was 0.993, 0.982 and 0.995 respectively. Conclusion: The Beijing genotype was the predominant genotype in Yunnan Province, the characteristics of Mycobacterium tuberculosis showed high genetic diversity. The genotyping data reflect the potential recent ongoing transmission in some area, which highlights the urgent need for early diagnosis and treatment of the infectious TB cases, to cut off the

Impact of inter-genotypic recombination and probe cross-reactivity on the performance of the Abbott RealTime HCV Genotype II assay for hepatitis C genotyping.

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Sridhar, Siddharth; Yip, Cyril C Y; Chan, Jasper F W; To, Kelvin K W; Cheng, Vincent C C; Yuen, Kwok-Yung

2018-05-01

The Abbott RealTime HCV Genotype II assay (Abbott-RT-HCV assay) is a real-time PCR based genotyping method for hepatitis C virus (HCV). This study measured the impact of inter-genotypic recombination and probe cross-reactivity on the performance of the Abbott-RT-HCV assay. 517 samples were genotyped using the Abbott-RT-HCV assay over a one-year period, 34 (6.6%) were identified as HCV genotype 1 without further subtype designation raising the possibility of inaccurate genotyping. These samples were subjected to confirmatory sequencing. 27 of these 34 (79%) samples were genotype 1b while five (15%) were genotype 6. One HCV isolate was an inter-genotypic 1a/4o recombinant. This is a novel natural HCV recombinant that has never been reported. Inter-genotypic recombination and probe cross-reactivity can affect the accuracy of the Abbott-RT-HCV assay, both of which have significant implications on antiviral regimen choice. Confirmatory sequencing of ambiguous results is crucial for accurate genotyping. Copyright © 2018 Elsevier Inc. All rights reserved.

Multiple genotypes within aecial clusters in Puccinia graminis and Puccinia coronata: improved understanding of the biology of cereal rust fungi.

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Berlin, Anna; Samils, Berit; Andersson, Björn

2017-01-01

Cereal rust fungi ( Puccinia spp.) are among the most economically important plant pathogens. These fungi have a complex life cycle, including five spore stages and two hosts. They infect one grass host on which they reproduce clonally and cause the cereal rust diseases, while the alternate host is required for sexual reproduction. Although previous studies clearly demonstrate the importance of the alternate host in creating genetic diversity in cereal rust fungi, little is known about the amount of novel genotypes created in each successful completion of a sexual reproduction event. In this study, single sequence repeat markers were used to study the genotypic diversity within aecial clusters by genotyping individual aecial cups. Two common cereal rusts, Puccinia graminis causing stem rust and Puccinia coronata the causal agent of crown rust were investigated. We showed that under natural conditions, a single aecial cluster usually include several genotypes, either because a single pycnial cluster is fertilized by several different pycniospores, or because aecia within the cluster are derived from more than one fertilized adjoining pycnial cluster, or a combination of both. Our results imply that although sexual events in cereal rust fungi in most regions of the world are relatively rare, the events that occur may still significantly contribute to the genetic variation within the pathogen populations.

Evaluation of the Abbott Real Time HCV genotype II assay for Hepatitis C virus genotyping.

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Sariguzel, Fatma Mutlu; Berk, Elife; Gokahmetoglu, Selma; Ercal, Baris Derya; Celik, Ilhami

2015-01-01

The determination of HCV genotypes and subtypes is very important for the selection of antiviral therapy and epidemiological studies. The aim of this study was to evaluate the performance of Abbott Real Time HCV Genotype II assay in HCV genotyping of HCV infected patients in Kayseri, Turkey. One hundred patients with chronic hepatitis C admitted to our hospital were evaluated between June 2012 and December 2012, HCV RNA levels were determined by the COBAS® AmpliPrep/COBAS® TaqMan® 48 HCV test. HCV genotyping was investigated by the Abbott Real Time HCV Genotype II assay. With the exception of genotype 1, subtypes of HCV genotypes could not be determined by Abbott assay. Sequencing analysis was used as the reference method. Genotypes 1, 2, 3 and 4 were observed in 70, 4, 2 and 24 of the 100 patients, respectively, by two methods. The concordance between the two systems to determine HCV major genotypes was 100%. Of 70 patients with genotype 1, 66 showed infection with subtype 1b and 4 with subtype 1a by Abbott Real Time HCV Genotype II assay. Using sequence analysis, 61 showed infection with subtype 1b and 9 with subtype 1a. In determining of HCV genotype 1 subtypes, the difference between the two methods was not statistically significant (P>0.05). HCV genotype 4 and 3 samples were found to be subtype 4d and 3a, respectively, by sequence analysis. There were four patients with genotype 2. Sequence analysis revealed that two of these patients had type 2a and the other two had type 2b. The Abbott Real Time HCV Genotype II assay yielded results consistent with sequence analysis. However, further optimization of the Abbott Real Time HCV Genotype II assay for subtype identification of HCV is required.

Diversity of the subspecies Bifidobacterium animalis subsp. lactis.

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Bunesova, Vera; Killer, Jiri; Javurkova, Barbora; Vlkova, Eva; Tejnecky, Vaclav; Musilova, Sarka; Rada, Vojtech

2017-04-01

Strains of Bifidobacterium animalis subsp. lactis are well-known health-promoting probiotics used commercially. B. animalis subsp. lactis has been isolated from different sources, and little is known about animal isolates of this taxon. The aim of this study was to examine the genotypic and phenotypic diversity between B. animalis subsp. lactis strains different animal hosts including Cameroon sheep, Barbary sheep, okapi, mouflon, German shepard and to compare to BB12, food isolates and the collection strain DSM 10140. Ten strains of B. animalis subsp. lactis from different sources were characterised by phenotyping, fingerprinting, and multilocus sequence typing (MLST). Regardless of origin, MLST and phylogenetic analyses revealed a close relationship between strains of B. animalis subsp. lactis with commercial and animal origin with the exception of isolates from ovine cheese, mouflon and German Shepard dog. Moreover, isolates from dog and mouflon showed significant differences in fermentation profiles and peptide mass fingerprints (MALDI-TOF). Results indicated phenotypic and genotypic diversity among strains of B. animalis subsp. lactis. Copyright © 2017 Elsevier Ltd. All rights reserved.

The genotypic structure of a multi-host bumblebee parasite suggests a role for ecological niche overlap.

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Rahel M Salathé

Full Text Available The genotypic structure of parasite populations is an important determinant of ecological and evolutionary dynamics of host-parasite interactions with consequences for pest management and disease control. Genotypic structure is especially interesting where multiple hosts co-exist and share parasites. We here analyze the natural genotypic distribution of Crithidia bombi, a trypanosomatid parasite of bumblebees (Bombus spp., in two ecologically different habitats over a time period of three years. Using an algorithm to reconstruct genotypes in cases of multiple infections, and combining these with directly identified genotypes from single infections, we find a striking diversity of infection for both data sets, with almost all multi-locus genotypes being unique, and are inferring that around half of the total infections are resulting from multiple strains. Our analyses further suggest a mixture of clonality and sexuality in natural populations of this parasite species. Finally, we ask whether parasite genotypes are associated with host species (the phylogenetic hypothesis or whether ecological factors (niche overlap in flower choice shape the distribution of parasite genotypes (the ecological hypothesis. Redundancy analysis demonstrates that in the region with relatively high parasite prevalence, both host species identity and niche overlap are equally important factors shaping the distribution of parasite strains, whereas in the region with lower parasite prevalence, niche overlap more strongly contributes to the distribution observed. Overall, our study underlines the importance of ecological factors in shaping the natural dynamics of host-parasite systems.

Coronavirus Infection and Diversity in Bats in the Australasian Region.

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Smith, C S; de Jong, C E; Meers, J; Henning, J; Wang, L- F; Field, H E

2016-03-01

Following the SARS outbreak, extensive surveillance was undertaken globally to detect and identify coronavirus diversity in bats. This study sought to identify the diversity and prevalence of coronaviruses in bats in the Australasian region. We identified four different genotypes of coronavirus, three of which (an alphacoronavirus and two betacoronaviruses) are potentially new species, having less than 90% nucleotide sequence identity with the most closely related described viruses. We did not detect any SARS-like betacoronaviruses, despite targeting rhinolophid bats, the putative natural host taxa. Our findings support the virus-host co-evolution hypothesis, with the detection of Miniopterus bat coronavirus HKU8 (previously reported in Miniopterus species in China, Hong Kong and Bulgaria) in Australian Miniopterus species. Similarly, we detected a novel betacoronavirus genotype from Pteropus alecto which is most closely related to Bat coronavirus HKU9 identified in other pteropodid bats in China, Kenya and the Philippines. We also detected possible cross-species transmission of bat coronaviruses, and the apparent enteric tropism of these viruses. Thus, our findings are consistent with a scenario wherein the current diversity and host specificity of coronaviruses reflects co-evolution with the occasional host shift.

Genetic and Biochemical Diversity of Paenibacillus larvae Isolated from Tunisian Infected Honey Bee Broods

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Chadlia Hamdi

2013-01-01

Full Text Available Paenibacillus larvae is the causative agent of American foulbrood (AFB, a virulent disease of honeybee (Apis mellifera larvae. In Tunisia, AFB has been detected in many beekeeping areas, where it causes important economic losses, but nothing is known about the diversity of the causing agent. Seventy-five isolates of P. larvae, identified by biochemical tests and 16S rRNA gene sequencing, were obtained from fifteen contaminated broods showing typical AFB symptoms, collected in different locations in the northern part of the country. Using BOX-PCR, a distinct profile of P. larvae with respect to related Paenibacillus species was detected which may be useful for its identification. Some P. larvae-specific bands represented novel potential molecular markers for the species. BOX-PCR fingerprints indicated a relatively high intraspecific diversity among the isolates not described previously with several molecular polymorphisms identifying six genotypes on polyacrylamide gel. Polymorphisms were also detected in several biochemical characters (indol production, nitrate reduction, and methyl red and oxidase tests. Contrary to the relatively high intraspecies molecular and phenotypic diversity, the in vivo virulence of three selected P. larvae genotypes did not differ significantly, suggesting that the genotypic/phenotypic differences are neutral or related to ecological aspects other than virulence.

Dry matter content and fruit size affect flavour and texture of novel Actinidia deliciosa genotypes.

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Nardozza, Simona; Gamble, Joanna; Axten, Lauren G; Wohlers, Mark W; Clearwater, Michael J; Feng, Jinquan; Harker, F Roger

2011-03-15

Previous studies with commercial kiwifruit cultivars have demonstrated that the taste of fruit with higher dry matter content (DM) is more liked by consumers. A unique replicated trial of kiwifruit genotypes (10 high/low DM × small/large-fruited genotypes) has provided an opportunity to consider how the genetic propensity for a kiwifruit to accumulate DM affects fruit flavour and texture. In the present study, eating-ripe fruit from each of the genotypes were assessed using a trained sensory panel and the relationships between these sensory attributes and fresh weight, DM, flesh firmness and soluble solids content (SSC) were explored. The genotypes provided a diversity of flavour and texture attributes, each of which varied in perceived intensity of the sensory experience. High-DM genotypes had higher SSC and were perceived as sweeter than low-DM genotypes. Sweet taste was closely associated with the perception of the tropical flavour and high-DM genotypes were found to have more tropical notes. Fruit size was associated with fruit texture, and small fruit were characterised by a firmer and more fibrous core. Large high-DM fruit were perceived as juicier than those of all other genotypes. Genotypes were perceived differently from one another, and differences in fruit size and DM content were reflected in fruit sensorial properties. This study is unique in demonstrating interactions between fruit size, DM and sensory properties. These findings could be relevant not only to kiwifruit but to fruiting crop breeders in general, because of the demonstrated potential for effects of fruit size and DM content on sweetness, flavour and fruit texture. Copyright © 2010 Society of Chemical Industry.

Contrasting microsatellite diversity in the evolutionary lineages of Phytophthora lateralis.

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Vettraino, AnnaMaria; Brasier, Clive M; Webber, Joan F; Hansen, Everett M; Green, Sarah; Robin, Cecile; Tomassini, Alessia; Bruni, Natalia; Vannini, Andrea

2017-02-01

Following recent discovery of Phytophthora lateralis on native Chamaecyparis obtusa in Taiwan, four phenotypically distinct lineages were discriminated: the Taiwan J (TWJ) and Taiwan K (TWK) in Taiwan, the Pacific Northwest (PNW) in North America and Europe and the UK in west Scotland. Across the four lineages, we analysed 88 isolates from multiple sites for microsatellite diversity. Twenty-one multilocus genotypes (MLGs) were resolved with high levels of diversity of the TWK and PNW lineages. No alleles were shared between the PNW and the Taiwanese lineages. TWK was heterozygous at three loci, whereas TWJ isolates were homozygous apart from one isolate, which exhibited a unique allele also present in the TWK lineage. PNW lineage was heterozygous at three loci. The evidence suggests its origin may be a yet unknown Asian source. North American and European PNW isolates shared all their alleles and also a dominant MLG, consistent with a previous proposal that this lineage is a recent introduction into Europe from North America. The UK lineage was monomorphic and homozygous at all loci. It shared its alleles with the PNW and the TWJ and TWK lineages, hence a possible origin in a recent hybridisation event between a Taiwan lineage and PNW cannot be ruled out. Copyright © 2016 British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Diversity rankings among bacterial lineages in soil.

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Youssef, Noha H; Elshahed, Mostafa S

2009-03-01

We used rarefaction curve analysis and diversity ordering-based approaches to rank the 11 most frequently encountered bacterial lineages in soil according to diversity in 5 previously reported 16S rRNA gene clone libraries derived from agricultural, undisturbed tall grass prairie and forest soils (n=26,140, 28 328, 31 818, 13 001 and 53 533). The Planctomycetes, Firmicutes and the delta-Proteobacteria were consistently ranked among the most diverse lineages in all data sets, whereas the Verrucomicrobia, Gemmatimonadetes and beta-Proteobacteria were consistently ranked among the least diverse. On the other hand, the rankings of alpha-Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes and Chloroflexi varied widely in different soil clone libraries. In general, lineages exhibiting largest differences in diversity rankings also exhibited the largest difference in relative abundance in the data sets examined. Within these lineages, a positive correlation between relative abundance and diversity was observed within the Acidobacteria, Actinobacteria and Chloroflexi, and a negative diversity-abundance correlation was observed within the Bacteroidetes. The ecological and evolutionary implications of these results are discussed.

Genetic diversity of Toxoplama gondii isolates from Ethiopian feral cats

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Recent studies indicate greater genetic variability among isolates of Toxoplasma gondii worldwide than previously thought. However, there is no information on genetic diversity of T. gondii from any host in Ethiopia. In the present study, genotyping was performed on viable T. gondii isolates by bioa...

Specific gene expression responses to parasite genotypes reveal redundancy of innate immunity in vertebrates.

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David Haase

Full Text Available Vertebrate innate immunity is the first line of defense against an invading pathogen and has long been assumed to be largely unspecific with respect to parasite/pathogen species. However, recent phenotypic evidence suggests that immunogenetic variation, i.e. allelic variability in genes associated with the immune system, results in host-parasite genotype-by-genotype interactions and thus specific innate immune responses. Immunogenetic variation is common in all vertebrate taxa and this reflects an effective immunological function in complex environments. However, the underlying variability in host gene expression patterns as response of innate immunity to within-species genetic diversity of macroparasites in vertebrates is unknown. We hypothesized that intra-specific variation among parasite genotypes must be reflected in host gene expression patterns. Here we used high-throughput RNA-sequencing to examine the effect of parasite genotypes on gene expression patterns of a vertebrate host, the three-spined stickleback (Gasterosteus aculeatus. By infecting naïve fish with distinct trematode genotypes of the species Diplostomum pseudospathaceum we show that gene activity of innate immunity in three-spined sticklebacks depended on the identity of an infecting macroparasite genotype. In addition to a suite of genes indicative for a general response against the trematode we also find parasite-strain specific gene expression, in particular in the complement system genes, despite similar infection rates of single clone treatments. The observed discrepancy between infection rates and gene expression indicates the presence of alternative pathways which execute similar functions. This suggests that the innate immune system can induce redundant responses specific to parasite genotypes.

Cytogenetics of Physalis peruviana L. and Physalis floridana Rydb. genotypes with differential response to Fusarium oxysporum

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Sara A. Liberato G.

2014-01-01

Full Text Available Vascular wilt caused by the fungus Fusarium oxysporumis considered the main constraint of cape gooseberry, Physalis peruviana, production in Colombia. P. peruvianaand P. floridana genotypes with differential resistance responses against F. oxysporum have been identified previously. In the present study, the genotypes were evaluated in order to complement the knowledge of cytogenetics diversity in Physalisand to design hybridization strategies to support breeding of cape gooseberry crop. The chromosome number in mitotic dividing cells from root-tips of tissue culture plantlets was determined, from which the average mitotic hour was estimated at 12:00 hours for P. peruviana and 10:00 for P. floridana. Chromosomic complements of 2n = 4x = 48 and 2n = 2x = 24 were found for each one of the two species. Additionally, flow cytometry analyses detected variation within P. peruviana with a nuclear DNA content of 2.33 pg for the 2n = 24 genotype and variations ranged from 5.77 to 8.12 pg for 2n = 48 genotypes. In P. floridanaDNA content was 2.29 pg in the 2n = 24 genotype and 4.03 pg in the 2n = 48 genotype. There was a significant effect (α = 0.01 of the number of chromosomes on nuclear DNA content for the two species.

Assesment of corn (zea mays l.) genotypes in relation to nitrogen fertilization under irrigated cropping conditions in Turkey