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Sample records for genetic variability outcrossing

  1. Local-scale patterns of genetic variability, outcrossing, and spatial structure in natural stands of Arabidopsis thaliana.

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    Kirsten Bomblies

    2010-03-01

    Full Text Available As Arabidopsis thaliana is increasingly employed in evolutionary and ecological studies, it is essential to understand patterns of natural genetic variation and the forces that shape them. Previous work focusing mostly on global and regional scales has demonstrated the importance of historical events such as long-distance migration and colonization. Far less is known about the role of contemporary factors or environmental heterogeneity in generating diversity patterns at local scales. We sampled 1,005 individuals from 77 closely spaced stands in diverse settings around Tübingen, Germany. A set of 436 SNP markers was used to characterize genome-wide patterns of relatedness and recombination. Neighboring genotypes often shared mosaic blocks of alternating marker identity and divergence. We detected recent outcrossing as well as stretches of residual heterozygosity in largely homozygous recombinants. As has been observed for several other selfing species, there was considerable heterogeneity among sites in diversity and outcrossing, with rural stands exhibiting greater diversity and heterozygosity than urban stands. Fine-scale spatial structure was evident as well. Within stands, spatial structure correlated negatively with observed heterozygosity, suggesting that the high homozygosity of natural A. thaliana may be partially attributable to nearest-neighbor mating of related individuals. The large number of markers and extensive local sampling employed here afforded unusual power to characterize local genetic patterns. Contemporary processes such as ongoing outcrossing play an important role in determining distribution of genetic diversity at this scale. Local "outcrossing hotspots" appear to reshuffle genetic information at surprising rates, while other stands contribute comparatively little. Our findings have important implications for sampling and interpreting diversity among A. thaliana accessions.

  2. Plant genetics: increased outcrossing in hothead mutants.

    Science.gov (United States)

    Peng, Peng; Chan, Simon W-L; Shah, Govind A; Jacobsen, Steve E

    2006-09-28

    Arising from: S. J. Lolle, J. L. Victor, J. M. Young & R. E. Pruitt 434, 505-509 (2005); Lolle et al. reply. Lolle et al. report that loss-of-function alleles of the HOTHEAD (HTH) gene in Arabidopsis thaliana are genetically unstable, giving rise to wild-type revertants. On the basis of the reversion of many other genetic markers in hth plants, they suggested a model in which a cache of extragenomic information could cause genes to revert to the genotype of previous generations. In our attempts to reproduce this phenomenon, we discovered that hth mutants show a marked tendency to outcross (unlike wild-type A. thaliana, which is almost exclusively self-fertilizing). Moreover, when hth plants are grown in isolation, their genetic inheritance is completely stable. These results may provide an alternative explanation for the genome wide non-mendelian inheritance reported by Lolle et al.

  3. Intrapopulation fixation index dynamics in finite populations with variable outcrossing rates

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    Coelho Alexandre Siqueira Guedes

    2003-01-01

    Full Text Available The intrapopulation fixation index ( f is inversely related to the outcrossing rate (t. Results obtained from data on molecular markers of natural populations have shown that these values are highly variable, even when measured in the same group of individuals. It is thus suggested that factors besides those described in Wright's genetic equilibrium must be operating. Using simulated data sets this study shows that the finite size condition of a population is sufficient to spread the estimated f values along a range at equilibrium, as opposed to keeping them at the theoretical equilibrium point. The variation in outcrossing rates can amplify this range considerably. Correlation between estimated f values obtained from different loci in this condition showed to be negatively related to the outcrossing rates, and positively related to the variance of these rates along generations. The finite size of populations associated to small fluctuations in t mean values over time may explain the usually reported high variation among estimated f values of different loci.

  4. Outcrossing and coexistence of genetically modified with (genetically) unmodified crops: a case study of the situation in the Netherlands.

    NARCIS (Netherlands)

    Wiel, van de C.C.M.; Lotz, L.A.P.

    2006-01-01

    With the introduction of genetically modified (GM) crops the EU has demanded that individual member states enact measures to prevent inadvertent admixture ¿ through outcrossing ¿ of genetically modified organisms (GMOs) with products from conventional and organic farming. A literature review on outc

  5. Genetic rescue of an endangered domestic animal through outcrossing with closely related breeds

    DEFF Research Database (Denmark)

    Strønen, Astrid Vik; Salmela, Elina; Baldursdottir, Birna K.

    2017-01-01

    Genetic rescue, outcrossing with individuals from a related population, is used to augment genetic diversity in populations threatened by severe inbreeding and extinction. The endangered Norwegian Lundehund dog underwent at least two severe bottlenecks in the 1940s and 1960s that each left only......: Norwegian Buhund, Icelandic Sheepdog, and Norrbottenspets. Examination of single nucleotide polymorphism (SNP) genotypes based on 165K loci in 48 dogs from the four breeds revealed substantially lower genetic diversity for the Lundehund (HE 0.035) than for other breeds (HE 0.209-0.284). Analyses of genetic...... structure with > 15K linkage disequilibrium-pruned SNPs showed four distinct genetic clusters. Pairwise FST values between Lundehund and the candidate breeds were highest for Icelandic Sheepdog, followed by Buhund and Norrbottenspets. We assessed the presence of outlier loci among candidate breeds...

  6. Outcrossing potential between 11 important genetically modified crops and the Chilean vascular flora.

    Science.gov (United States)

    Sánchez, Miguel A; Cid, Pablo; Navarrete, Humberto; Aguirre, Carlos; Chacón, Gustavo; Salazar, Erika; Prieto, Humberto

    2016-02-01

    The potential impact of genetically modified (GM) crops on biodiversity is one of the main concerns in an environmental risk assessment (ERA). The likelihood of outcrossing and pollen-mediated gene flow from GM crops and non-GM crops are explained by the same principles and depend primarily on the biology of the species. We conducted a national-scale study of the likelihood of outcrossing between 11 GM crops and vascular plants in Chile by use of a systematized database that included cultivated, introduced and native plant species in Chile. The database included geographical distributions and key biological and agronomical characteristics for 3505 introduced, 4993 native and 257 cultivated (of which 11 were native and 246 were introduced) plant species. Out of the considered GM crops (cotton, soya bean, maize, grape, wheat, rice, sugar beet, alfalfa, canola, tomato and potato), only potato and tomato presented native relatives (66 species total). Introduced relative species showed that three GM groups were formed having: a) up to one introduced relative (cotton and soya bean), b) up to two (rice, grape, maize and wheat) and c) from two to seven (sugar beet, alfalfa, canola, tomato and potato). In particular, GM crops presenting introduced noncultivated relative species were canola (1 relative species), alfalfa (up to 4), rice (1), tomato (up to 2) and potato (up to 2). The outcrossing potential between species [OP; scaled from 'very low' (1) to 'very high' (5)] was developed, showing medium OPs (3) for GM-native relative interactions when they occurred, low (2) for GMs and introduced noncultivated and high (4) for the grape-Vitis vinifera GM-introduced cultivated interaction. This analytical tool might be useful for future ERA for unconfined GM crop release in Chile.

  7. Diversity, genetic structure and evidence of outcrossing in British populations of the rock fern Adiantum capillus-veneris using microsatellites.

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    Pryor, K V; Young, J E; Rumsey, F J; Edwards, K J; Bruford, M W; Rogers, H J

    2001-08-01

    Microsatellites were isolated and a marker system was developed in the fern Adiantum capillus-veneris. Polymorphic markers were then used to study the genetic diversity and structure of populations within the UK and Ireland where this species grows at the northern edge of its range, requiring a specific rock habitat and limited to a few scattered populations. Three dinucleotide loci detected a high level of diversity (23 alleles and 28 multilocus genotypes) across the UK and Ireland, with nearly all variation partitioned among rather than within populations. Of 17 populations represented by multiple samples, all except four were monomorphic. Heterozygosity was detected in three populations, all within Glamorgan, Wales (UK), showing evidence of outcrossing. We make inferences on the factors determining the observed levels and patterns of genetic variation and the possible evolutionary history of the populations.

  8. Life history and past demography maintain genetic structure, outcrossing rate, contemporary pollen gene flow of an understory herb in a highly fragmented rainforest

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    Pilar Suárez-Montes

    2016-12-01

    Full Text Available Introduction Theory predicts that habitat fragmentation, by reducing population size and increasing isolation among remnant populations, can alter their genetic diversity and structure. A cascade of effects is expected: genetic drift and inbreeding after a population bottleneck, changes in biotic interactions that may affect, as in the case of plants, pollen dynamics, mating system, reproductive success. The detection of the effects of contemporary habitat fragmentation on the genetic structure of populations are conditioned by the magnitude of change, given the few number of generations since the onset of fragmentation, especially for long-lived organisms. However, the present-day genetic structure of populations may bear the signature of past demography events. Here, we examine the effects of rainforest fragmentation on the genetic diversity, population structure, mating system (outcrossing rate, indirect gene flow and contemporary pollen dynamics in the understory herb Aphelandra aurantiaca. Also, we assessed its present-day genetic structure under different past demographic scenarios. Methods Twelve populations of A. aurantiaca were sampled in large (4, medium (3, and small (5 forest fragments in the lowland tropical rainforest at Los Tuxtlas region. Variation at 11 microsatellite loci was assessed in 28–30 reproductive plants per population. In two medium- and two large-size fragments we estimated the density of reproductive plants, and the mating system by analyzing the progeny of different mother plants per population. Results Despite prevailing habitat fragmentation, populations of A. aurantiaca possess high genetic variation (He = 0.61, weak genetic structure (Rst = 0.037, and slight inbreeding in small fragments. Effective population sizes (Ne were large, but slightly lower in small fragments. Migrants derive mostly from large and medium size fragments. Gene dispersal is highly restricted but long distance gene dispersal events

  9. Outcrossing in Florida and California commercial avocado (Persea americana Mill) orchards estimated using microsatellite markers and the development of a genetic linkage map

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    Avocado has an unusual flowering mechanism, diurnally synchronous protogynous dichogamy, which promotes cross pollination. Comemrcial groves usually contain pollinizer rows adjacent to the more desirable commercial cultivars. Conflicting results on the effect of pollinizer rows on out-crossing rates...

  10. High outcrossing rates in fields with mixed sorghum landraces: how are landraces maintained?

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    Barnaud, A; Trigueros, G; McKey, D; Joly, H I

    2008-11-01

    The effect of mating system on genetic diversity is a major theme in plant evolutionary genetics, because gene flow plays a large role in structuring the genetic variability within and among populations. Understanding crop mating systems and their consequences for gene flow can aid in managing agricultural systems and conserving genetic resources. We evaluated the extent of pollen flow, its links with farming practices and its impact on the dynamics of diversity of sorghum in fields of Duupa farmers in Cameroon. Duupa farmers grow numerous landraces mixed in a field, a practice that favours extensive pollen flow. We estimated parameters of the mating system of five landraces representative of the genetic diversity cultivated in the study site, using a direct method based on progeny array. The multilocus outcrossing rate calculated from all progenies was 18% and ranged from 0 to 73% among progenies. Outcrossing rates varied greatly among landraces, from 5 to 40%. Our results also showed that individual maternal plants were usually pollinated by more than eight pollen donors, except for one landrace (three pollen donors). Although the biological traits of sorghum (inflorescence morphology, floral traits, phenology) and the spatial planting practices of Duupa farmers led to extensive pollen flow among landraces, selection exerted by farmers appears to be a key parameter affecting the fate of new genetic combinations from outcrossing events. Because both natural and human-mediated factors shape evolution in crop populations, understanding evolutionary processes and designing in situ conservation measures requires that biologists and anthropologists work together.

  11. Ambiguous genetic relationships among coconut (Cocos nucifera L.) cultivars: the effects of outcrossing, sample source and size, and method of analysis.

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    A prior analysis of eight coconut cultivars with 15 microsatellite (SSR) markers drew unexpected relationships between two of the out-crossing tall cultivars evaluated: ‘Atlantic Tall’ and ‘Panama Tall’. We further investigated the relationships between these eight cultivars by increasing the number...

  12. An AFLP estimation of the outcrossing rate of Spondias tuberosa (Anacardiaceae), an endemic species to the Brazilian semiarid region.

    Science.gov (United States)

    Fernandes Santos, Carlos Antonio; de Souza Gama, Renata Natália Cândido

    2013-06-01

    The umbu tree (Spondias tuberosa) is one of the most important endemic species to the Brazilian tropical semiarid region. The umbu tree has edible fruits with a peculiar flavor that are consumed in natura or in a semi-industrialized form, such as jams, candies and juices. The majority of endemic species to Brazilian semiarid region have not been studied or sampled to form germ-plasm collections, which increases the risk of losing genetic variability of the adapted species to xerophytic conditions. The aim of this study was to estimate outcrossing rates in S. tuberosa using a multilocus mixed model in order to guide genetic resources and breeding programs of this species. DNA samples were extracted from 92 progenies of umbu trees, which were distributed among 12 families. These trees were planted by seed in 1991 in Petrolina, PE, Brazil. The experimental design was a randomized block, with a total of 42 progenies sampled in three regions. The experimental units were composed by five plants and five replications. The outcrossing rate was estimated by the multilocus model, which is available in the MLTR software, and was based on 17 polymorphic AFLP bands obtained from AAA_CTG and AAA_CTC primer combinations. The observed heterozygotes ranged from 0.147 to 0.499, with a maximum frequency estimated for the AAA_CTC 10 amplicon. The multilocus outcrossing estimation (t(m)) was 0.804 +/- 0.072, while the single-locus (t(s)) was 0.841 +/- 0.079, which suggests that S. tuberosa is predominantly an outcrossing species. The difference between t(m) and t(s) was -0.037 +/- 0.029, which indicates that biparental inbreeding was nearly absent. The mean inbreeding coefficient or fixation index (F) among maternal plants was--0.103 +/- 0.045, and the expected F was 0.108, which indicates that there was no excess of heterozygotes in the maternal population. The outcrossing estimates obtained in the present study indicate that S. tuberosa is an open-pollinated species. Biometrical

  13. Genetic variability of grey snow mould (Typhula incarnata).

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    Vergara, Georgina V; Bughrara, Suleiman S; Jung, Geunhwa

    2004-11-01

    Randomly amplified polymorphic DNA (RAPD) markers were used to assess the genetic diversity of isolates of grey snow mould ('gray snow mold'), Typhula incarnata, taken from infected turfgrasses from 40 different locations in the northern USA. Data from 115 markers using 37 RAPD primers showed 48 % polymorphism. The distance coefficients between isolates indicate the wide genetic diversity of T. incarnata across the sample area. Dendrograms generated using neighbour-joining (NJ) bootstrap analyses showed three clades and suggest possible recent colonization from common founder groups. Partitioning of the genetic variance using analysis of molecular variance (AMOVA) of four groups based on geographic locations (Michigan, lower and upper peninsula; Minnesota; Wisconsin) showed that genetic variation attributable among groups and within groups was 12.67 and 87.33 %, respectively. No correlation was found between geographic distance and pairwise genetic distance of the groups. High outcrossing and sexual recombination of T. incarnata may well be key factors explaining the genetic variability as shown with the low Fixation index (FST) and high average of genetic diversity per locus within groups.

  14. Genetic variation in variability

    NARCIS (Netherlands)

    Mulder, Herman; Gienapp, Phillip; Visser, Marcel E.

    2016-01-01

    Variation in traits is essential for natural selection to operate and genetic and environmental effects can contribute to this phenotypic variation. From domesticated populations, we know that families can differ in their level of within-family variance, which leads to the intriguing situation th

  15. Molecular genetic variability, population structure and mating system in tropical forages

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    Melissa Garcia

    2013-09-01

    Full Text Available Microsatellite (SSR markers were developed for the following tropical forage species, using accessions available from the plant genetic resources (PGR collections held by EMBRAPA (Brazilian Agricultural Research Corporation: Brachiaria brizantha, B. humidicola, Panicum maximum, Paspalum spp., Stylosanthes capitata, S. guianensis, S. macrocephala, Calopogonium mucunoides and Centrosema spp. The markers were used to analyze population structure and genetic diversity, evolution and origin of the genetic variability in the center of origin, mating systems and genetic resources in EMBRAPA’s germplasm bank. The results shed light on the amount of genetic variation within and between populations, revealed the need in some cases for further plant collection to adequately represent the species in PGR collections, allowed us to assemble core collections (subsets of the total collections that should contain most of the available diversity and (in the case of the legumes showed the need to avoid unwanted outcrossing when regenerating conserved material. The data will allow plant breeders to better select accessions for hybrid production, discriminate between genotypes and use marker-assisted selection in breeding programs. Our results will also underpin the construction of genetic maps, mapping of genes of agronomic interest and numerous other studies on genetic variability, population structure, gene flow and reproductive systems for the tropical forage species studied in this work.

  16. Estimating Out-Crossing Rate of Bg 379-2 Using Morphological Markers and Confirmation by Molecular Markers

    Institute of Scientific and Technical Information of China (English)

    L. H. M. Y. K. SOMARATNE; A.S.M.T.ABAYAWICKRAMA; I. P. WICKRAMASINGHE; W. L. G. SAMARASINGHE

    2012-01-01

    Rice is largely self-fertilized and accordingly a field population of rice is completely composed of near homozygotes.Due to the emergence of off-types,homozygosity will be affected.With the time,this will cause the reduction of genetic purity in some rice varieties.One of the reasons has been suspected to be the high out-crossing frequencies of such varieties.Studies were conducted at the Rice Research and Development Institute,Batalagoda,Sri Lanka to estimate the out-crossing rote of Bg 379-2,a variety having the problem of maintaining genetic purity.Bg 379-2 was allowed to out-cross with Bg 450 and the number of outcrossed plants were counted using dominant morphological markers such as short-round grain and purple culm of pollen donor.A molecular confirmation of out-crossing was also performed using sequence tagged site (STS) molecular marker pTA248.The variety Bg 379-2 showed a potential out-crossing rate of 3.41% and an average out-crossing rate of 1.29% using dominant morphological markers.Polymorphism was clearly detected between parents and out-crossed plants as well as selfed plants of Bg 379-2 using their banding patterns.A similar study can be performed to determine the out-crossing rates of other varieties which show high percentage of off-types in the population for the better understanding of the breeding behavior of the varieties.

  17. Natural variation of outcrossing in the hermaphroditic nematode Pristionchus pacificus

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    Click Arielle

    2009-04-01

    Full Text Available Abstract Background Evolution of selfing can be associated with an increase in fixation of deleterious mutations, which in certain conditions can lead to species extinction. In nematodes, a few species evolved self-fertilization independently, making them excellent model systems to study the evolutionary consequences of this type of mating system. Results Here we determine various parameters that influence outcrossing in the hermaphroditic nematode Pristionchus pacificus and compare them to the better known Caenorhabditis elegans. These nematode species are distinct in terms of genetic diversity, which could be explained by differences in outcrossing rates. We find that, similarly to C. elegans, P. pacificus males are generated at low frequencies from self-fertilizing hermaphrodites and are relatively poor mating partners. Furthermore, crosses between different isolates reveal that hybrids have lower brood sizes than the pure strains, which is a sign of outbreeding depression. In contrast to C. elegans, P. pacificus has lower brood sizes and the male X-bearing sperm is able to outcompete the X-nullo sperm. Conclusion The results indicate that there is no evidence of any selection acting very strongly on P. pacificus males.

  18. Calculating Outcrossing Rates used in Decision Support Systems for Ships

    DEFF Research Database (Denmark)

    Nielsen, Ulrik Dam

    2008-01-01

    Onboard decision support systems (DSS) are used to increase the operational safety of ships. Ideally, DSS can estimate - in the statistical sense - future ship responses on a time scale of the order of 1-3 hours taking into account speed and course changes. The calculations depend on both...... operational and environmental parameters that are known only in the statistical sense. The present paper suggests a procedure to incorporate random variables and associated uncertainties in calculations of outcrossing rates, which are the basis for risk-based DSS. The procedure is based on parallel system...... analysis, and the paper derives and describes the main ideas. The concept is illustrated by an example, where the limit state of a non-linear ship response is considered. The results from the parallel system analysis are in agreement with corresponding Monte Carlo simulations. However, the computational...

  19. Genetic variability, heritability and genetic advance of quantitative ...

    African Journals Online (AJOL)

    ONOS

    2010-05-10

    May 10, 2010 ... clusters/plant, number of pods/plant, number of seeds/pod, yield/plant and 100 seed weight of black gram in M2 ... Key words: Genetic variability, gamma rays, quantitative traits, black gram. ... MATERIALS AND METHODS.

  20. Induction of genetic variability in oat

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    Jefferson Luis Meirelles Coimbra

    2007-01-01

    Full Text Available Genetic variability in plants can be maximized through techniques of induction to make selection of genotypeswith improved adaptation to cultivation conditions possible. For oat, these techniques are important for a sustainabledevelopment through plant breeding programs in southern Brazil. The effects of mutagens (one physical: 60Co gamma raysand two chemical agents: ethyl - methanesulfonate and methyl-methanesulfonate were compared in the segregating M2 andM3 generations derived from artificial hybridization and induced mutation to compare mechanisms of widening the geneticvariability of oat. The methodologies increased the genetic variability in the trait vegetative cycle effectively, by either increasingor reducing the number of days from emergence to full heading; both can be applied in oat breeding programs.

  1. Genetic variability of Italian Heavy Draught Horse

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    Fabio Maretto

    2010-01-01

    Full Text Available This study aimed to analyze the genetic variability of the Italian Heavy Draught Horse (IHDH breed using a panel of 23 microsatellite markers. We also compared the population structure of the IHDH to other two unrelated breeds (Italian Haflinger, IH and Quarter Horse, QH. The IHDH showed a genetic variability comparable with other European heavy draught horse breeds and with the IH and QH breeds analyzed. Clustering analyses using a posterior Bayesian approach clearly differentiated the three breeds; it also showed a fragmentation of the IHDH in three subpopulations that need to be further investigated. These findings are an indicator of the present situation of the IHDH and will contribute to the conservation and implementation of the selection programme for this breed.

  2. Genetic basis of pain variability: recent advances.

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    Young, Erin E; Lariviere, William R; Belfer, Inna

    2012-01-01

    An estimated 15-50% of the population experiences pain at any given time, at great personal and societal cost. Pain is the most common reason patients seek medical attention, and there is a high degree of individual variability in reporting the incidence and severity of symptoms. Research suggests that pain sensitivity and risk for chronic pain are complex heritable traits of polygenic origin. Animal studies and candidate gene testing in humans have provided some progress in understanding the heritability of pain, but the application of the genome-wide association methodology offers a new tool for further elucidating the genetic contributions to normal pain responding and pain in clinical populations. Although the determination of the genetics of pain is still in its infancy, it is clear that a number of genes play a critical role in determining pain sensitivity or susceptibility to chronic pain. This review presents an update of the most recent findings that associate genetic variation with variability in pain and an overview of the candidate genes with the highest translational potential.

  3. Genetic variability in three Amazon parrot species

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    IF. Lopes

    Full Text Available Parrots of the genus Amazona are among the most threatened species of the Order Pscittaciformes. This work describes allozyme polymorphisms in three Amazon parrot species - the Blue-fronted Amazon (Amazona aestiva, the Orange-winged Amazon (Amazona amazonica, and the Festive Amazon (Amazona festiva -, and provides useful data for the evaluation of their genetic variability. We electrophoretically analyzed blood samples from 68 wild-caught individuals, maintained in captivity in three Brazilian zoos. Eight of the ten studied enzyme loci exhibited polymorphism. Glucosephosphate isomerase (Gpi proved to be a diagnostic locus for the identification of these Amazon species. The expected average heterozygosity of the Blue-fronted Amazon (0.060 differed significantly from the expected heterozygosities of the Orange-winged Amazon and the Festive Amazon (0.040 and 0.039, respectively. This result was discussed as a consequence of hybridization between two geographic A. aestiva subspecies, and alternatively as a particular trait of this species. Genetic variability of the Blue-fronted Amazon compared to birds in general is not low on a species-wide level, despite the fact that this parrot is one of the most illegally traded species. Allozyme analysis proved to be an useful tool in monitoring the genetic variation within the genus Amazona and can be applied in the management program of other threatened species of this genus.

  4. Milk metabolites and their genetic variability.

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    Wittenburg, D; Melzer, N; Willmitzer, L; Lisec, J; Kesting, U; Reinsch, N; Repsilber, D

    2013-04-01

    The composition of milk is crucial to evaluate milk performance and quality measures. Milk components partly contribute to breeding scores, and they can be assessed to judge metabolic and energy status of the cow as well as to serve as predictive markers for diseases. In addition to the milk composition measures (e.g., fat, protein, lactose) traditionally recorded during milk performance test via infrared spectroscopy, novel techniques, such as gas chromatography-mass spectrometry, allow for a further analysis of milk into its metabolic components. Gas chromatography-mass spectrometry is suitable for measuring several hundred metabolites with high throughput, and thus it is applicable to study sources of genetic and nongenetic variation of milk metabolites in dairy cows. Heritability and mode of inheritance of metabolite measurements were studied in a linear mixed model approach including expected (pedigree) and realized (genomic) relationship between animals. The genetic variability of 190 milk metabolite intensities was analyzed from 1,295 cows held on 18 farms in Mecklenburg-Western Pomerania, Germany. Besides extensive pedigree information, genotypic data comprising 37,180 single nucleotide polymorphism markers were available. Goodness of fit and significance of genetic variance components based on likelihood ratio tests were investigated with a full model, including marker- and pedigree-based genetic effects. Broad-sense heritability varied from zero to 0.699, with a median of 0.125. Significant additive genetic variance was observed for highly heritable metabolites, but dominance variance was not significantly present. As some metabolites are particularly favorable for human nutrition, for instance, future research should address the identification of locus-specific genetic effects and investigate metabolites as the molecular basis of traditional milk performance test traits.

  5. Genetic variability of sorghum landraces from lower Eastern Kenya ...

    African Journals Online (AJOL)

    Reuben M. Muasya

    2016-02-24

    Feb 24, 2016 ... Key words: Genetic variability, landraces, simple sequence repeats, sorghum. ... determining the fate of new genetic combinations from ..... Systematics and evolution of Sorghum Sect. ... Farm Management Handbook of Kenya, ... environment for genetic marker analysis. ... Introduction to population biology.

  6. Outcrossing rates and relatedness estimates in pecan (Carya illinoinensis) populations.

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    Rüter, B; Hamrick, J L; Wood, B W

    2000-01-01

    Estimates of single and multilocus outcrossing rates as well as relatedness among progeny of individual seed trees were obtained for 14 populations of pecan [Carya illinoinensis (Wangenh.) K. Koch]. Mean outcrossing estimates were not significantly different from 1.0 and relatedness values indicate that most progeny within families are half sibs. Biparental inbreeding was insignificant in all study sites, and inbreeding coefficients indicated that populations were close to inbreeding equilibrium.

  7. Genetic Variability Under the Seedbank Coalescent.

    Science.gov (United States)

    Blath, Jochen; González Casanova, Adrián; Eldon, Bjarki; Kurt, Noemi; Wilke-Berenguer, Maite

    2015-07-01

    We analyze patterns of genetic variability of populations in the presence of a large seedbank with the help of a new coalescent structure called the seedbank coalescent. This ancestral process appears naturally as a scaling limit of the genealogy of large populations that sustain seedbanks, if the seedbank size and individual dormancy times are of the same order as those of the active population. Mutations appear as Poisson processes on the active lineages and potentially at reduced rate also on the dormant lineages. The presence of "dormant" lineages leads to qualitatively altered times to the most recent common ancestor and nonclassical patterns of genetic diversity. To illustrate this we provide a Wright-Fisher model with a seedbank component and mutation, motivated from recent models of microbial dormancy, whose genealogy can be described by the seedbank coalescent. Based on our coalescent model, we derive recursions for the expectation and variance of the time to most recent common ancestor, number of segregating sites, pairwise differences, and singletons. Estimates (obtained by simulations) of the distributions of commonly employed distance statistics, in the presence and absence of a seedbank, are compared. The effect of a seedbank on the expected site-frequency spectrum is also investigated using simulations. Our results indicate that the presence of a large seedbank considerably alters the distribution of some distance statistics, as well as the site-frequency spectrum. Thus, one should be able to detect from genetic data the presence of a large seedbank in natural populations.

  8. Pollination by sexual deception promotes outcrossing and mate diversity in self-compatible clonal orchids.

    Science.gov (United States)

    Whitehead, M R; Linde, C C; Peakall, R

    2015-08-01

    The majority of flowering plants rely on animals as pollen vectors. Thus, plant mating systems and pollen dispersal are strongly influenced by pollinator behaviour. In Australian sexually deceptive orchids pollinated by male thynnine wasps, outcrossing and extensive pollen flow is predicted due to floral deception, which minimizes multiple flower visitations within patches, and the movement of pollinators under mate-search rather than foraging behaviours. This hypothesis was tested using microsatellite markers to reconstruct and infer paternity in two clonal, self-compatible orchids. Offspring from naturally pollinated Chiloglottis valida and C. aff. jeanesii were acquired through symbiotic culture of seeds collected over three seasons. In both species, outcrossing was extensive (tm  = 0.924-1.00) despite clone sizes up to 11 m wide. The median pollen flow distance based on paternity for both taxa combined was 14.5 m (n = 18, range 0-69 m), being larger than typically found by paternity analyses in other herbaceous plants. Unexpectedly for orchids, some capsules were sired by more than one father, with an average of 1.35 pollen donors per fruit. This is the first genetic confirmation of polyandry in orchid capsules. Further, we report a possible link between multiple paternity and increased seed fitness. Together, these results demonstrate that deceptive pollination by mate-searching wasps enhances offspring fitness by promoting both outcrossing and within-fruit paternal diversity.

  9. Genetic variability of Euglena agilis (Euglenophyceae

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    Bożena Zakryś

    2011-01-01

    Full Text Available The results of the internal transcribed spacer (ITS2 of extrachromosomal rDNA and the chloroplast SSU rDNA sequence analysis presented here confirmed elevated genetic polymorphism revealed earlier by RFLP and RAPD for seven clones of the cosmopolitan species - Euglena agilis Carter. High diversity among these clonal strains was not reflected by morphological criteria, with the exception of the only one character - the ability of the cell in its non-motile dividing states (palmella to produce mucus and form a slimy envelope. Evolutionary adaptation as formation of slimy envelope may be attributed to different survival strategy of the species by which it adapts to life in a highly variable environment.

  10. THE EFFECTS OF POPULATION-SIZE AND PLANT-DENSITY ON OUTCROSSING RATES IN LOCALLY ENDANGERED SALVIA-PRATENSIS

    NARCIS (Netherlands)

    VANTREUREN, R; BIJLSMA, R; OUBORG, NJ; VANDELDEN, W

    Multilocus outcrossing rates were estimated in natural and experimental populations of Salvia pratensis, an entomophilous, gynodioecious, protandrous perennial. Male steriles were used to check the estimation procedure of outcrossing rates in hermaphrodites. Estimates of outcrossing rates in

  11. Family Outcrossing Rates of Pinus caribaea Morelet var. caribaea in Seed Orchard and Natural Populations

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Family outcrossing rates of Pinus caribaea var. caribaea populations that differed in origin and management were estimated by using isozyme markers. The family outcrossing rates were estimated by (1)fixing the probability of pollen gene frequency (p); (2) allowing pollen gene frequency to vary among families. The estimates of family outcrossing rates for all the populations varied widely among families (clones of the seed orchard), ranging from 0.39 to 2.0. The average family outcrossing rates of both m...

  12. Genetic variability among Andrographis paniculata in Chhattisgarh ...

    African Journals Online (AJOL)

    Preeti minz

    2013-09-25

    Sep 25, 2013 ... 2 Department of Bio and Nano Technology, Guru Jambheshwar University of Science &Technology, Hisar ... Genetic tools that use hybridization, polymerase chain ... based molecular markers have been found to be useful in.

  13. Improving linkage analysis in outcrossed forest trees - an example from Acacia mangium.

    Science.gov (United States)

    Butcher, A.; Williams, R.; Whitaker, D.; Ling, S.; Speed, P.; Moran, F.

    2002-05-01

    Mapping in forest trees generally relies on outbred pedigrees in which genetic segregation is the result of meiotic recombination from both parents. The currently available mapping packages are not optimal for outcrossed pedigrees as they either cannot order phase-ambiguous data or only use pairwise information when ordering loci within linkage groups. A new package, OUTMAP, has been developed for mapping codominant loci in outcrossed trees. A comparison of maps produced using linkage data from two pedigrees of Acacia mangium Willd demonstrated that the marker orders produced using OUTMAP were consistently of higher likelihood than those produced by JOINMAP. In addition, the maps were produced more efficiently, without the need for recoding data or the detailed investigation of pairwise recombination fractions which was necessary to select the optimal marker order using JOINMAP. Distances between markers often varied from those calculated by JOINMAP, resulting in an increase in the estimated genome length. OUTMAP can be used with all segregation types to determine phase and to calculate the likelihood of alternative marker orders, with a choice of three optimisation methods.

  14. Genetics Home Reference: common variable immune deficiency

    Science.gov (United States)

    ... or Free article on PubMed Central Park JH, Resnick ES, Cunningham-Rundles C. Perspectives on common variable ... on PubMed or Free article on PubMed Central Resnick ES, Cunningham-Rundles C. The many faces of ...

  15. Using genetic programming to discover nonlinear variable interactions.

    Science.gov (United States)

    Westbury, Chris; Buchanan, Lori; Sanderson, Michael; Rhemtulla, Mijke; Phillips, Leah

    2003-05-01

    Psychology has to deal with many interacting variables. The analyses usually used to uncover such relationships have many constraints that limit their utility. We briefly discuss these and describe recent work that uses genetic programming to evolve equations to combine variables in nonlinear ways in a number of different domains. We focus on four studies of interactions from lexical access experiments and psychometric problems. In all cases, genetic programming described nonlinear combinations of items in a manner that was subsequently independently verified. We discuss the general implications of genetic programming and related computational methods for multivariate problems in psychology.

  16. Genetic variability of marine shrimp in the Brazilian industry

    Directory of Open Access Journals (Sweden)

    Rodrigo Maggioni

    2013-08-01

    Full Text Available The objective of this work was to estimate the genetic variability level and distribution in Brazilian broodstocks of marine shrimp (Litopenaeus vannamei. Nine of the country's largest hatcheries were evaluated using codominant and highly polymorphic microsatellite markers. The results obtained from genotyping of ten microsatellite loci are indicative of genetic variability that is compatible with that found in wild populations of L. vannamei in Mexico and Central America. A possible explanation is the highly diversified and relatively recent origin of the available broodstocks. Bayesian analysis detected a signal for five founding populations. The distribution of genetic distances partially reflects geographical location, and this information will be useful for the creation of new broodstocks. Therefore, L. vannamei genetic variability among nine of the largest national hatcheries can be considered high.

  17. Red mangrove life history variables along latitudinal and anthropogenic stress gradients.

    Science.gov (United States)

    Proffitt, C Edward; Travis, Steven

    2014-06-01

    Mangroves migrate northward in Florida and colonize marshes historically dominated by salt marsh species. In theory, this migration should be facilitated by greater numbers of propagules stemming from increased reproductive activity and greater genetic variability caused by outcrossing. We aimed to determine if stand reproduction and % outcrossing were affected by cold stress (stress increases with latitude), anthropogenic stress (human population density as a proxy), and years since a major hurricane. Further, we wished to determine if mutation rate varied with the stressors and if that affected stand reproduction. Both coasts of Florida from the southern Florida Keys to Tampa Bay on the Gulf of Mexico coast, and Merritt Island on the Atlantic coast. We conducted field surveys of frequency of reproducing trees (104,211 trees surveyed in 102 forested stands), incidence of trees showing albinism in propagules, and% outcrossing estimated from the ratio of albino:normal propagules. Structural equation modeling (SEM) was used to test a conceptual model that served as a multivariate hypothesis. Reproductive frequencies varied by site and increased with latitude although more strongly on the Gulf coast. Our SEM results indicate that outcrossing increases in this predominately selfing species under conditions of cold and anthropogenic stress, and that this increases reproductive output in the population. Further, we find that increased mutation rates suppress stand reproductive output but there is no significant relationship between outcrossing and mutation rate. Tree size responded to stressors but did not affect stand reproduction. Reproduction increased with years since major hurricane. Potential for colonization of northern Florida salt marshes by mangroves is enhanced by increased reproductive rates that provides more propagules and outcrossing that should enhance genetic variation thereby promoting adaptation to novel environmental conditions. Natural (cold) stress

  18. Genetic variability for tuber yield, quality, and virus disease complex ...

    African Journals Online (AJOL)

    Genetic variability for tuber yield, quality, and virus disease complex traits in Uganda ... Silk and Sowola which showed high flowering ability failed to fertilise and set ... Up to five genes may be involved in â-carotene synthesis and probably in ...

  19. Parental influences on pathogen resistance in brown trout embryos and effects of outcrossing within a river network.

    Science.gov (United States)

    Clark, Emily S; Stelkens, Rike B; Wedekind, Claus

    2013-01-01

    Phenotypic plasticity can increase tolerance to heterogeneous environments but the elevations and slopes of reaction norms are often population specific. Disruption of locally adapted reaction norms through outcrossing can lower individual viability. Here, we sampled five genetically distinct populations of brown trout (Salmo trutta) from within a river network, crossed them in a full-factorial design, and challenged the embryos with the opportunistic pathogen Pseudomonas fluorescens. By virtue of our design, we were able to disentangle effects of genetic crossing distance from sire and dam effects on early life-history traits. While pathogen infection did not increase mortality, it was associated with delayed hatching of smaller larvae with reduced yolk sac reserves. We found no evidence of a relationship between genetic distance (W, FST) and the expression of early-life history traits. Moreover, hybrids did not differ in phenotypic means or reaction norms in comparison to offspring from within-population crosses. Heritable variation in early life-history traits was found to remain stable across the control and pathogen environments. Our findings show that outcrossing within a rather narrow geographical scale can have neutral effects on F1 hybrid viability at the embryonic stage, i.e. at a stage when environmental and genetic effects on phenotypes are usually large.

  20. Parental influences on pathogen resistance in brown trout embryos and effects of outcrossing within a river network.

    Directory of Open Access Journals (Sweden)

    Emily S Clark

    Full Text Available Phenotypic plasticity can increase tolerance to heterogeneous environments but the elevations and slopes of reaction norms are often population specific. Disruption of locally adapted reaction norms through outcrossing can lower individual viability. Here, we sampled five genetically distinct populations of brown trout (Salmo trutta from within a river network, crossed them in a full-factorial design, and challenged the embryos with the opportunistic pathogen Pseudomonas fluorescens. By virtue of our design, we were able to disentangle effects of genetic crossing distance from sire and dam effects on early life-history traits. While pathogen infection did not increase mortality, it was associated with delayed hatching of smaller larvae with reduced yolk sac reserves. We found no evidence of a relationship between genetic distance (W, FST and the expression of early-life history traits. Moreover, hybrids did not differ in phenotypic means or reaction norms in comparison to offspring from within-population crosses. Heritable variation in early life-history traits was found to remain stable across the control and pathogen environments. Our findings show that outcrossing within a rather narrow geographical scale can have neutral effects on F1 hybrid viability at the embryonic stage, i.e. at a stage when environmental and genetic effects on phenotypes are usually large.

  1. Genetic variability assessment in the genus Passiflora by SSR markers

    Directory of Open Access Journals (Sweden)

    Claudia Lougon Paiva

    2014-09-01

    Full Text Available The genus Passiflora encompasses many species that are endemic to the Brazilian territory, including some with economic value. Studies on genetic diversity in this genus are fundamental because they allow understanding genetic variability and distance. The present study aimed to determine the genetic variability and distances among 10 species of the genus Passiflora by using microsatellite markers (Simple Sequence Repeat, SSR. Twenty-eight heterologous microsatellite markers were tested, but only 12 were used in the diversity analysis because they amplified in at least 80% of the species. A clear separation was observed among the subgenuses studied, as well as wide variation among the accessions of Passiflora. This knowledge enables breeders to explore diversity and transfer favorable alleles found in wild species.

  2. Constraints on the Genetic and Antigenic Variability of Measles Virus.

    Science.gov (United States)

    Beaty, Shannon M; Lee, Benhur

    2016-04-21

    Antigenic drift and genetic variation are significantly constrained in measles virus (MeV). Genetic stability of MeV is exceptionally high, both in the lab and in the field, and few regions of the genome allow for rapid genetic change. The regions of the genome that are more tolerant of mutations (i.e., the untranslated regions and certain domains within the N, C, V, P, and M proteins) indicate genetic plasticity or structural flexibility in the encoded proteins. Our analysis reveals that strong constraints in the envelope proteins (F and H) allow for a single serotype despite known antigenic differences among its 24 genotypes. This review describes some of the many variables that limit the evolutionary rate of MeV. The high genomic stability of MeV appears to be a shared property of the Paramyxovirinae, suggesting a common mechanism that biologically restricts the rate of mutation.

  3. Genetic influence on inflammation variables in the elderly

    DEFF Research Database (Denmark)

    de Maat, Moniek P M; Bladbjerg, Else Marie; Hjelmborg, Jacob v. B.

    2004-01-01

    BACKGROUND: Inflammation variables (C-reactive protein [CRP], fibrinogen, and soluble intercellular adhesion molecule-1 [sICAM-1]) have been identified as risk factors for cardiovascular disease. It is still not known how much the regulation of inflammatory risk factors is determined by genetic...... factors, and the aim of this study was to determine the heritability of these inflammation variables and of the acute phase regulating cytokines interleukin-6 (IL-6) and tumor necrosis factor-alpha (TNF-alpha) at older ages. METHODS AND RESULTS: The heritability of CRP, fibrinogen, sICAM-1, IL-6, and TNF...... factors accounted for 20% to 55% of the variation in plasma levels of the inflammation variables. The highest heritability was found for sICAM-1. The genetic polymorphisms we studied explained only a small, insignificant part of the heritability. CONCLUSIONS: This study in elderly twins provides evidence...

  4. Genetic variability and population structure of Salvia lachnostachys: implications for breeding and conservation programs.

    Science.gov (United States)

    Erbano, Marianna; Schühli, Guilherme Schnell E; Santos, Élide Pereira Dos

    2015-04-08

    The genetic diversity and population structure of Salvia lachnostachys Benth were assessed. Inter Simple Sequence Repeat (ISSR) molecular markers were used to investigate the restricted distribution of S. lachnostachys in Parana State, Brazil. Leaves of 73 individuals representing three populations were collected. DNA was extracted and submitted to PCR-ISSR amplification with nine tested primers. Genetic diversity parameters were evaluated. Our analysis indicated 95.6% polymorphic loci (stress value 0.02) with a 0.79 average Simpson's index. The Nei-Li distance dendrogram and principal component analysis largely recovered the geographical origin of each sample. Four major clusters were recognized representing each collected population. Nei's gene diversity and Shannon's information index were 0.25 and 0.40 respectively. As is typical for outcrossing herbs, the majority of genetic variation occurred at the population level (81.76%). A high gene flow (Nm = 2.48) was observed with a correspondingly low fixation index. These values were generally similar to previous studies on congeneric species. The results of principal coordinate analysis (PCA) and of arithmetic average (UPGMA) were consistent and all three populations appear distinct as in STRUCTURE analysis. In addition, this analysis indicated a majority intrapopulation genetic variation. Despite the human pressure on natural populations our study found high levels of genetic diversity for S. lachnostachys. This was the first molecular assessment for this endemic species with medicinal proprieties and the results can guide for subsequent bioprospection, breeding programs or conservation actions.

  5. Molecular variability and genetic relationship among Brazilian strains of the sugarcane smut fungus.

    Science.gov (United States)

    Benevenuto, Juliana; Longatto, Daniel P; Reis, Gislaine V; Mielnichuk, Natalia; Palhares, Alessandra C; Carvalho, Giselle; Saito, Suzane; Quecine, Maria C; Sanguino, Alvaro; Vieira, Maria Lucia C; Camargo, Luis Eduardo A; Creste, Silvana; Monteiro-Vitorello, Claudia B

    2016-12-01

    Sporisorium scitamineum is the fungus that causes sugarcane smut disease. Despite of the importance of sugarcane for Brazilian agribusiness and the persistence of the pathogen in most cropping areas, genetic variation studies are still missing for Brazilian isolates. In this study, sets of isolates were analyzed using two molecular markers (AFLP and telRFLP) and ITS sequencing. Twenty-two whips were collected from symptomatic plants in cultivated sugarcane fields of Brazil. A total of 41 haploid strains of compatible mating types were selected from individual teliospores and used for molecular genetic analyses. telRFLP and ITS analyses were expanded to six Argentine isolates, where the sugarcane smut was first recorded in America. Genetic relationship among strains suggests the human-mediated dispersal of S. scitamineum within the Brazilian territory and between the two neighboring countries. Two genetically distinct groups were defined by the combined analysis of AFLP and telRFLP. The opposite mating-type strains derived from single teliospores were clustered together into these main groups, but had not always identical haplotypes. telRFLP markers analyzed over two generations of selfing and controlled outcrossing confirmed the potential for emergence of new variants and occurrence of recombination, which are relevant events for evolution of virulence and environmental adaptation.

  6. Genetic variability in five species of Anostomidae (Ostariophysi - Characiformes

    Directory of Open Access Journals (Sweden)

    Chiari Lucimara

    1999-01-01

    Full Text Available Genetic variability was studied in five fish species (Anostomidae: Schizodon intermedius and S. nasutus and Leporinus friderici, L. elongatus and L. obtusidens, collected at one location on the Tibagi River (Paraná, Brazil. The protein data from seven systems coded collectively for 19 loci in the liver, muscle and heart. Nine of these loci were polymorphic. The estimated proportion of polymorphism loci ( varied from 16.7% in S. intermedius to 36.9% in L. friderici; the mean heterozygosity observed (o was 0.027 ± 0.015 and 0.109 ± 0.042, respectively. The estimated value of the genetic identity among L. friderici and S. intermedius (0.749 and S. nasutus (0.787 suggested that these are "congeneric" species. Morphological characteristics indicate that these species belong to distinct genera, while isoenzymatic data show that they are very similar at the genetic/biochemical level.

  7. Genetic variations involved in interindividual variability in carotenoid status.

    OpenAIRE

    Borel, Patrick

    2012-01-01

    International audience; As shown in most clinical studies dedicated to carotenoids, there is a huge interindividual variability in absorption, and blood and tissue responses, of dietary carotenoids. The recent discovery that several proteins are involved in carotenoid metabolism in humans has prompted a possible explanation for this phenomenon: genetic variants in genes encoding for these proteins may affect their expression or activity, and in turn carotenoid metabolism and carotenoid status...

  8. Genetic variability of broodstocks of restocking programs in Brazil

    Directory of Open Access Journals (Sweden)

    Nelson Lopera-Barrero

    2015-09-01

    Full Text Available Objective. The aim of this study was evaluate the genetic diversity of the following broodstocks: piapara (Leporinus elongatus, dourado (Salminus brasiliensis, jundiá (Rhamdia quelen and cachara (Pseudoplatystoma fasciatum already useful for restocking programs in the Paranapanema, Iguaçu and Paraná Brazilian Rivers. Materials and methods. Samples from the caudal fin of 122 fish were analyzed. DNA was extracted by NaCl protocol. PCR products were separated by a horizontal agarose gel electrophoresis. The fragments were visualized by staining with ethidium bromide. Results. The amplification of 25 primers generated different fragments in studied species that allowed characterizing 440 fragments of 100-2900 bp. High percentage of polymorphic fragments (66.67 to 86.29, Shannon index (0.365 to 0.486 and genetic diversity of Nei (0.248 to 0.331 were detected. Conclusions. The level of genetic variability in the broodstocks was adequate for allowing their use in restocking programs in the studied Rivers. However, periodical monitoring studies of genetic variability in these stocks, the mating system, reproductive system and general management must be made to guarantee the preservation of wild populations.

  9. Assessment of genetic and chemical variability in Thymus caramanicus.

    Science.gov (United States)

    Hadian, Javad; Bigdeloo, Mahdi; Nazeri, Vahideh; Khadivi-Khub, Abdollah

    2014-05-01

    Thymus caramanicus is an endemic species grown in Iran with interesting pharmacological and biological properties. In the present work, essential oil compositions and inter-simple sequences repeat (ISSR) markers were used to estimate the relationships among and within seven populations of T. caramanicus, belonging to three provinces in Iran. The studied individuals were distinguished on the basis of ISSR markers and constituents of essential oil. A total of 127 band positions were produced by 12 ISSR primers, of which 105 were found polymorphic with 82.68% polymorphism. Genetic similarity values among individuals ranged between 0.15 and 0.82 which was indicative of a high level of genetic variation. On the basis of their genetic similarities, ISSR analysis allowed to group the samples into two main clusters. One of these included populations originated from Kerman and Isfahan provinces, and the other cluster consists of populations from Semnan province. Chemical compounds of essential oils were found variable in the various individuals and all samples were principally composed of phenolic constituents (carvacrol and/or thymol). As a consequence, the plants were classified into two major chemotypes including carvacrol and thymol/carvacrol. A relationship between genetic and chemical variability and geographic distribution has been observed in studied populations of T. caramanicus.

  10. FUS and TDP43 genetic variability in FTD and CBS.

    Science.gov (United States)

    Huey, Edward D; Ferrari, Raffaele; Moreno, Jorge H; Jensen, Christopher; Morris, Christopher M; Potocnik, Felix; Kalaria, Rajesh N; Tierney, Michael; Wassermann, Eric M; Hardy, John; Grafman, Jordan; Momeni, Parastoo

    2012-05-01

    This study aimed to evaluate genetic variability in the FUS and TDP-43 genes, known to be mainly associated with amyotrophic lateral sclerosis (ALS), in patients with the diagnoses of frontotemporal lobar degeneration (FTLD) and corticobasal syndrome (CBS). We screened the DNA of 228 patients for all the exons and flanking introns of FUS and TDP-43 genes. We identified 2 novel heterozygous missense mutations in FUS: P106L (g.22508384C>T) in a patient with behavioral variant frontotemporal dementia (bvFTD) and Q179H in several members of a family with behavioral variant FTD. We also identified the N267S mutation in TDP-43 in a CBS patient, previously only reported in 1 ALS family and 1 FTD patient. Additionally, we identified 2 previously reported heterozygous insertion and deletion mutations in Exon 5 of FUS; Gly174-Gly175 del GG (g. 4180-4185 delGAGGTG) in an FTD patient and Gly175-Gly176 ins GG (g. 4185-4186 insGAGGTG) in a patient with diagnosis of CBS. Not least, we have found a series of variants in FUS also in neurologically normal controls. In summary, we report that genetic variability in FUS and TDP-43 encompasses a wide range of phenotypes (including ALS, FTD, and CBS) and that there is substantial genetic variability in FUS gene in neurologically normal controls. Copyright © 2012 Elsevier Inc. All rights reserved.

  11. Cryptosporidium,Giardia, Cryptococcus, Pneumocystis genetic variability: cryptic biological species or clonal near-clades?

    Directory of Open Access Journals (Sweden)

    Michel Tibayrenc

    2014-04-01

    Full Text Available An abundant literature dealing with the population genetics and taxonomy of Giardia duodenalis, Cryptosporidium spp., Pneumocystis spp., and Cryptococcus spp., pathogens of high medical and veterinary relevance, has been produced in recent years. We have analyzed these data in the light of new population genetic concepts dealing with predominant clonal evolution (PCE recently proposed by us. In spite of the considerable phylogenetic diversity that exists among these pathogens, we have found striking similarities among them. The two main PCE features described by us, namely highly significant linkage disequilibrium and near-clading (stable phylogenetic clustering clouded by occasional recombination, are clearly observed in Cryptococcus and Giardia, and more limited indication of them is also present in Cryptosporidium and Pneumocystis. Moreover, in several cases, these features still obtain when the near-clades that subdivide the species are analyzed separately ("Russian doll pattern". Lastly, several sets of data undermine the notion that certain microbes form clonal lineages simply owing to a lack of opportunity to outcross due to low transmission rates leading to lack of multiclonal infections ("starving sex hypothesis". We propose that the divergent taxonomic and population genetic inferences advanced by various authors about these pathogens may not correspond to true evolutionary differences and could be, rather, the reflection of idiosyncratic practices among compartmentalized scientific communities. The PCE model provides an opportunity to revise the taxonomy and applied research dealing with these pathogens and others, such as viruses, bacteria, parasitic protozoa, and fungi.

  12. Cryptosporidium,Giardia, Cryptococcus, Pneumocystis genetic variability: cryptic biological species or clonal near-clades?

    Science.gov (United States)

    Tibayrenc, Michel; Ayala, Francisco J

    2014-04-01

    An abundant literature dealing with the population genetics and taxonomy of Giardia duodenalis, Cryptosporidium spp., Pneumocystis spp., and Cryptococcus spp., pathogens of high medical and veterinary relevance, has been produced in recent years. We have analyzed these data in the light of new population genetic concepts dealing with predominant clonal evolution (PCE) recently proposed by us. In spite of the considerable phylogenetic diversity that exists among these pathogens, we have found striking similarities among them. The two main PCE features described by us, namely highly significant linkage disequilibrium and near-clading (stable phylogenetic clustering clouded by occasional recombination), are clearly observed in Cryptococcus and Giardia, and more limited indication of them is also present in Cryptosporidium and Pneumocystis. Moreover, in several cases, these features still obtain when the near-clades that subdivide the species are analyzed separately ("Russian doll pattern"). Lastly, several sets of data undermine the notion that certain microbes form clonal lineages simply owing to a lack of opportunity to outcross due to low transmission rates leading to lack of multiclonal infections ("starving sex hypothesis"). We propose that the divergent taxonomic and population genetic inferences advanced by various authors about these pathogens may not correspond to true evolutionary differences and could be, rather, the reflection of idiosyncratic practices among compartmentalized scientific communities. The PCE model provides an opportunity to revise the taxonomy and applied research dealing with these pathogens and others, such as viruses, bacteria, parasitic protozoa, and fungi.

  13. Does beekeeping reduce genetic variability in Melipona scutellaris (Apidae, Meliponini)?

    Science.gov (United States)

    Carvalho-Zilse, G A; Costa-Pinto, M F F; Nunes-Silva, C G; Kerr, W E

    2009-06-30

    Many factors have contributed to reductions in wild populations of stingless bees, such as: deforestation, displacement and destruction of nests by honey gatherers, as well as use of insecticides and other agrochemicals. All of these can potentially affect the populational structure of native species. We analyzed genetic variability and populational structure of Melipona scutellaris, based on five microsatellite loci, using heterologous primers of M. bicolor. Samples were taken from 43 meliponaries distributed among 30 sites of four northeastern states of Brazil (Pernambuco, Alagoas, Sergipe, and Bahia). Thirty-one alleles were found to be well distributed among the populations, with sizes ranging from 85 to 146 bp. In general, there was a variable distribution and frequency of alleles among populations, with either exclusive and/or fixed alleles at some sites. The population of Pernambuco was the most polymorphic, followed by Bahia, Alagoas and Sergipe. The heterozygosity was Ho = 0.36 on average, much lower than what has been reported for M. bicolor (Ho = 0.65). Most populations were not under Hardy-Weinberg equilibrium. We found a higher variation within rather than among populations, indicating no genetic structuring in those bees maintained in meliponaries. This apparent homogenization may be due to intense beekeeping activity, including exchange of genetic material among beekeepers. Based on our findings, we recommend more studies of meliponaries and of wild populations in order to help orient management and conservation of these native pollinators.

  14. Outcrossing between an agroforestry plantation and remnant native populations of Eucalyptus loxophleba.

    Science.gov (United States)

    Sampson, Jane F; Byrne, Margaret

    2008-06-01

    Gene dispersal among populations of a species is an important force influencing their genetic structure. Dispersal may also occur between taxa that would normally be isolated when nonendemic, domesticated or transgenic species are planted within the natural range of interfertile taxa. Such a mosaic of populations is typical of many agricultural landscapes, and investigations are needed to assess the risks of genetic contamination of the endemic populations but a combination of approaches may be necessary because of the limitations of research in this landscape. This study used microsatellite markers and a range of analyses (mating system, paternity exclusion, Bayesian assignment) to examine gene dispersal between remnants of the endemic Eucalyptus loxophleba ssp. supralaevis and a plantation of a nonendemic subspecies. Our results indicate that remnant populations are connected by significant dispersal to pollen sources up to 1.94 km away including the plantation. The combined analyses showed that the pollen pool and outcrossing rates of individuals within remnants varied significantly probably because of asynchronous flowering and that the likelihood of paternity was not correlated with spatial proximity. More than half of all progeny had male parents from outside their stand with the largest proportions estimated to come from the plantation by exclusion (42.4%) or Bayesian analyses (18.8-76%). Fragmentation may not be associated with decreased gene dispersal between populations of tree species, natural or planted, so that the distances required to buffer endemic trees in fragmented rural landscapes are likely to be large.

  15. Genetic variability of six French meat sheep breeds in relation to their genetic management

    Directory of Open Access Journals (Sweden)

    Coralie Danchin-Burge

    2003-11-01

    Full Text Available Abstract Some demographic parameters, the genetic structure and the evolution of the genetic variability of six French meat sheep breeds were analysed in relation with their management. Four of these breeds are submitted to more or less intense selection: the Berrichon du Cher (BCH, Blanc du Massif Central (BMC, Charollais (CHA and Limousin (LIM; the other two breeds are under conservation: the Roussin de La Hague (RLH and Solognot (SOL. Genealogical data of the recorded animals born from 1970 to 2000 and of their known ancestors were used. The most balanced contributions of the different flocks to the sire-daughter path was found in the SOL. In the BCH, a single flock provided 43% of the sire-AI sire path, whereas the contributions of the flocks were more balanced in the BMC and LIM (the only other breeds where AI is used to a substantial amount. The distribution of the expected genetic contribution of the founder animals was found to be unbalanced, especially in the BCH and LIM. The effective numbers of ancestors (founders or not for the ewes born from 1996 to 2000 were equal to 35 (BCH, 144 (BMC, 112 (CHA, 69 (LIM, 40 (RLH and 49 (SOL. Inbreeding was not analysed in the BMC, due to incomplete pedigree information. From 1980 on, the rates of inbreeding, in percentage points per year, were +0.112 (BCH, +0.045 (CHA, +0.036 (LIM, +0.098 (RLH and +0.062 (SOL. The implications of the observed trends on genetic variability are discussed in relation to the genetic management of each breed. The need for a larger selection basis in the BCH, the efficiency of the rules applied in the SOL to preserve the genetic variability and the need for a more collective organisation in the CHA and RLH are outlined.

  16. Genetic Variability and Population Structure of Salvia lachnostachys: Implications for Breeding and Conservation Programs

    Directory of Open Access Journals (Sweden)

    Marianna Erbano

    2015-04-01

    Full Text Available The genetic diversity and population structure of Salvia lachnostachys Benth were assessed. Inter Simple Sequence Repeat (ISSR molecular markers were used to investigate the restricted distribution of S. lachnostachys in Parana State, Brazil. Leaves of 73 individuals representing three populations were collected. DNA was extracted and submitted to PCR-ISSR amplification with nine tested primers. Genetic diversity parameters were evaluated. Our analysis indicated 95.6% polymorphic loci (stress value 0.02 with a 0.79 average Simpson’s index. The Nei-Li distance dendrogram and principal component analysis largely recovered the geographical origin of each sample. Four major clusters were recognized representing each collected population. Nei’s gene diversity and Shannon’s information index were 0.25 and 0.40 respectively. As is typical for outcrossing herbs, the majority of genetic variation occurred at the population level (81.76%. A high gene flow (Nm = 2.48 was observed with a correspondingly low fixation index. These values were generally similar to previous studies on congeneric species. The results of principal coordinate analysis (PCA and of arithmetic average (UPGMA were consistent and all three populations appear distinct as in STRUCTURE analysis. In addition, this analysis indicated a majority intrapopulation genetic variation. Despite the human pressure on natural populations our study found high levels of genetic diversity for S. lachnostachys. This was the first molecular assessment for this endemic species with medicinal proprieties and the results can guide for subsequent bioprospection, breeding programs or conservation actions.

  17. Genetic Variability in Susceptibility to Occupational Respiratory Sensitization

    Directory of Open Access Journals (Sweden)

    Berran Yucesoy

    2011-01-01

    Full Text Available Respiratory sensitization can be caused by a variety of substances at workplaces, and the health and economic burden linked to allergic respiratory diseases continues to increase. Although the main factors that affect the onset of the symptoms are the types and intensity of allergen exposure, there is a wide range of interindividual variation in susceptibility to occupational/environmental sensitizers. A number of gene variants have been reported to be associated with various occupational allergic respiratory diseases. Examples of genes include, but are not limited to, genes involved in immune/inflammatory regulation, antioxidant defenses, and fibrotic processes. Most of these variants act in combination with other genes and environmental factors to modify disease progression, severity, or resolution after exposure to allergens. Therefore, understanding the role of genetic variability and the interaction between genetic and environmental/occupational factors provides new insights into disease etiology and may lead to the development of novel preventive and therapeutic strategies. This paper will focus on the current state of knowledge regarding genetic influences on allergic respiratory diseases, with specific emphasis on diisocyanate-induced asthma and chronic beryllium disease.

  18. Comparison of external genetic of Wareng and Kampung Chicken, observed from introgression rate and genetic variability

    Directory of Open Access Journals (Sweden)

    T Sartika

    2008-12-01

    Full Text Available Wareng and Kampung chicken are Indonesian native chicken that have good potential to be dual purpose chicken. Information on these chickens has not hast’n widely published so that their genetic potential is unknown. The purpose of this research is to collect basic data of the external genetic characteristic from Wareng and Kampung chickens consisting feather color, feather pattern, feather feature, feather shine, shank color and comb shape; to identify rate of introgression imported breed (Rhode Island Red, White Leghorn and Barred Plymouth Rock, the purity and genetic variability of Wareng and Kampung chickens. This study was carried out at the Research Institute for Animal Production, Ciawi, Bogor. Materials used were 361 of Wareng chickens (313 females, 48 males and 439 of Kampung chickens (352 females, 87 males. Data were analyzed using formulas to identify gene frequency, rate of introgression of purity native gene frequency and the genetic variability. The result showed that the control of gene constitution on external characteristic of Wareng chicken was I_ E_ bb S_ Id_ pp and ii e+ _bb ss idid pp on Kampung chicken. Wareng chicken own constitution of gene the same as with White Leghorn (II EE SS BB IdId pp. Wareng Chicken is not containing frequency of original gene of Indonesian local chicken (Kampung. The level of influence value (rate of introgression from Europe and American chicken for Wareng chicken was of equal to 84% and 25% to Kampung chicken. So that the purity for Wareng chicken was 16% and 75% was for Kampung chicken. The variability genetic of Kampung chickens (39% higher than Wareng chicken (16%.

  19. Microsatellite variability reveals high genetic diversity and low genetic differentiation in a critical giant panda population

    Institute of Scientific and Technical Information of China (English)

    Jiandong YANG; Zhihe ZHANG; Fujun SHEN; Xuyu YANG; Liang ZHANG; Limin CHEN; Wenping ZHANG; Qing ZHU; Rong HOU

    2011-01-01

    Understanding present patterns of genetic diversity is critical in order to design effective conservation and management strategies for endangered species.Tangjiahe Nature Reserve (NR) is one of the most important national reserves for giant pandas Ailuropoda melanoleuca in China.Previous studies have shown that giant pandas in Tangjiahe NR may be threatened by population decline and fragmentation.Here we used 10 microsatellite DNA markers to assess the genetic variability in the Tangjiahe population.The results indicate a low level of genetic differentiation between the Hongshihe and Motianling subpopulations in the reserve.Assignment tests using the Bayesian clustering method in STRUCTURE identified one genetic cluster from 42 individuals of the two subpopulations.All individuals from the same subpopulation were assigned to one cluster.This indicates high gene flow between subpopulations.F statistic analyses revealed a low Fls-value of 0.024 in the total population and implies a randomly mating population in Tangjiahe NR.Additionally,our data show a high level of genetic diversity for the Tangjiahe population.Mean allele number (A),Allelic richness (AR) and mean expected heterozygosity (HE) for the Tangiiahe population was 5.9,5.173 and 0.703,respectively.This wild giant panda population can be restored through concerted effort [Current Zoology 57 (6):717-724,2011].

  20. Microsatellite variability reveals high genetic diversity and low genetic differentiation in a critical giant panda population

    Directory of Open Access Journals (Sweden)

    Jiandong YANG, Zhihe ZHANG, Fujun SHEN, Xuyu YANG, Liang ZHANG, Limin CHEN, Wenping ZHANG, Qing ZHU, Rong HOU

    2011-12-01

    Full Text Available Understanding present patterns of genetic diversity is critical in order to design effective conservation and management strategies for endangered species. Tangjiahe Nature Reserve (NR is one of the most important national reserves for giant pandas Ailuropoda melanoleuca in China. Previous studies have shown that giant pandas in Tangjiahe NR may be threatened by population decline and fragmentation. Here we used 10 microsatellite DNA markers to assess the genetic variability in the Tangjiahe population. The results indicate a low level of genetic differentiation between the Hongshihe and Motianling subpopulations in the reserve. Assignment tests using the Bayesian clustering method in STRUCTURE identified one genetic cluster from 42 individuals of the two subpopulations. All individuals from the same subpopulation were assigned to one cluster. This indicates high gene flow between subpopulations. F statistic analyses revealed a low FIS-value of 0.024 in the total population and implies a randomly mating population in Tangjiahe NR. Additionally, our data show a high level of genetic diversity for the Tangjiahe population. Mean allele number (A, Allelic richness (AR and mean expected heterozygosity (HE for the Tangjiahe population was 5.9, 5.173 and 0.703, respectively. This wild giant panda population can be restored through concerted effort [Current Zoology 57 (6: 717–724, 2011].

  1. Adenoviral targeting using genetically incorporated camelid single variable domains.

    Science.gov (United States)

    Kaliberov, Sergey A; Kaliberova, Lyudmila N; Buggio, Maurizio; Tremblay, Jacqueline M; Shoemaker, Charles B; Curiel, David T

    2014-08-01

    The unique ability of human adenovirus serotype 5 (Ad5) to accomplish efficient transduction has allowed the use of Ad5-based vectors for a range of gene therapy applications. Several strategies have been developed to alter tropism of Ad vectors to achieve a cell-specific gene delivery by using fiber modifications via genetic incorporation of targeting motifs. In this study, we have explored the utility of novel anti-human carcinoembryonic antigen (hCEA) single variable domains derived from heavy chain (VHH) camelid family of antibodies to achieve targeted gene transfer. To obtain anti-CEA VHHs, we produced a VHH-display library from peripheral blood lymphocytes RNA of alpacas at the peak of immune response to the hCEA antigen (Ag). We genetically incorporated an anti-hCEA VHH into a de-knobbed Ad5 fiber-fibritin chimera and demonstrated selective targeting to the cognate epitope expressed on the membrane surface of target cells. We report that the anti-hCEA VHH used in this study retains Ag recognition functionality and provides specificity for gene transfer of capsid-modified Ad5 vectors. These studies clearly demonstrated the feasibility of retargeting of Ad5-based gene transfer using VHHs.

  2. Clinical Characteristics and Genetic Variability of Human Rhinovirus in Mexico

    Directory of Open Access Journals (Sweden)

    Hilda Montero

    2012-01-01

    Full Text Available Human rhinovirus (HRV is a leading cause of acute respiratory infection (ARI in young children and infants worldwide and has a high impact on morbidity and mortality in this population. Initially, HRV was classified into two species: HRV-A and HRV-B. Recently, a species called HRV-C and possibly another species, HRV-D, were identified. In Mexico, there is little information about the role of HRV as a cause of ARI, and the presence and importance of species such as HRV-C are not known. The aim of this study was to determine the clinical characteristics and genetic variability of HRV in Mexican children. Genetic characterization was carried out by phylogenetic analysis of the 5′-nontranslated region (5′-NTR of the HRV genome. The results show that the newly identified HRV-C is circulating in Mexican children more frequently than HRV-B but not as frequently as HRV-A, which was the most frequent species. Most of the cases of the three species of HRV were in children under 2 years of age, and all species were associated with very mild and moderate ARI.

  3. Increasing genetic variability in black oats using gamma irradiation.

    Science.gov (United States)

    Silveira, G; Moliterno, E; Ribeiro, G; Costa, P M A; Woyann, L G; Tessmann, E W; Oliveira, A C; Cruz, C D

    2014-12-04

    The black oat (Avena strigosa Schreb) is commonly used for forage, soil cover, and green manure. Despite its importance, little improvement has been made to this species, leading to high levels of genotypic disuniformity within commercial cultivars. The objective of this study was to evaluate the efficiency of different doses of gamma rays [(60)Co] applied to black oat seeds on the increase of genetic variability of agronomic traits. We applied doses of 0, 10, 50, 100, and 200 Gy to the genotype ALPHA 94087 through exposure to [(60)Co]. Two experiments were conducted in the winter of 2008. The first aimed to test forage trait measurements such as plant height, dry matter yield, number of surviving tillers, and seedling stand. The second test assessed seed traits, such as yield and dormancy levels. Gamma irradiation seems not to increase seed yield in black oats, but it was effective in generating variability for the other traits. Tiller number and plant height are important selection traits to increase dry matter yield. Selection in advanced generations of mutant populations can increase the probability of identifying superior genotypes.

  4. Genetic variability and correlation studies in sunflower (Helianthus annuus L.

    Directory of Open Access Journals (Sweden)

    Sheshaiah and Shankergoud I.

    2015-06-01

    Full Text Available The present study was conducted in order to investigate genetic variability and to understand the relationship and contribution of characters towards total dry matter and root length. The investigation was carried out at Main Agricultural Research Station, UAS, Raichur during Rabi 2012-13, 32 genotypes were evaluated in RBD fashion under root structures. At flowering stage all morphological and root characters were scored. The total dry matter content was assessed after drying the root, stem, leaf, petiole and flower of the plant at 70 0C in an oven.. High GCV coupled with high PCV recorded for most of the characters except stem girth, SPAD reading and number of leaves, indicating more variability for these traits and are less influenced by the environment. High heritability coupled with high GAM reported for all the traits under study suggested for the greater effectiveness for selection and improvement expected for these traits in future generations. The total dry matter and root length had very highly significant positive association with plant height, root volume, fresh root weight, dry root weight, fresh stem weight, dry stem weight, fresh leaf weight and dry leaf weight indicating the importance of root characters in determining the moisture stress tolerance and putforthing the total dry matter content of the plant.

  5. Genetic Variability of Apolipoprotein E in Different Populations from Venezuela

    Directory of Open Access Journals (Sweden)

    M. T. Fernández-Mestre

    2005-01-01

    Full Text Available The genetic variation at the Apolipoprotein E locus (APOE is an important determinant of plasma lipids and has been implicated in various human pathological conditions. The objective of the present study was to estimate the distribution of APOE alleles in five Venezuelan communities: two Amerindian tribes (Bari and Yucpa, one Negroid population from Curiepe, one Caucasoid population from Colonia Tovar and the mestizo urban population living in Caracas. The APOE*3 allele was the most common allele in all populations studied. However, a significant increase in the APOE*2 allele frequency in the Mestizo (18.96% and Negroid (16.25% populations was found. Similar to results reported in other Native American populations we have found that the APOE*2 allele is completely absent in the Bari and Yucpa Amerindians. Frequencies found in the Colonia Tovar population are in agreement with those reported in the population of Germany, indicating a high degree of relatedness. The results support the notion that the distribution of the APOE alleles shows ethnic variability.

  6. Reproductive strategies and genetic variability in tropical freshwater fish

    Directory of Open Access Journals (Sweden)

    Maria Dolores Peres Lassala

    2007-01-01

    Full Text Available We estimated the genetic variability of nine fish species from the Brazilian upper Paraná River floodplain (Astyanax altiparanae, Hoplias malabaricus, Leporinus lacustris, Loricariichthys platymetopon, Parauchenipterus galeatus, Pimelodus maculatus, Rhaphiodon vulpinus, Roeboides paranensis and Serrasalmus marginatus based on data for 36 putative allozyme loci obtained using corn starch gel electrophoresis of 13 enzymatic systems: aspartate aminotransferase (EC 2.6.1.1, acid phosphatase (EC 3.1.3.2, esterase (EC 3.1.1.1, glycerol-3-phosphate dehydrogenase (EC 1.1.1.8, glucose-6-phosphate dehydrogenase (EC 1.1.1.49, glucose-6-phosphate isomerase (EC 5.3.1.9, Iditol dehydrogenase (EC 1.1.1.14, isocitrate dehydrogenase - NADP+ (EC 1.1.1.42, L-lactate dehydrogenase (EC 1.1.1.27, malate dehydrogenase (EC 1.1.1.37, malate dehydrogenase-NADP+ (EC 1.1.1.40, phosphoglucomutase (EC 5.4.2.2 and superoxide dismutase, (EC 1.15.1.1. The mean expected heterozygosity varied from zero to 0.147. When data from the literature for 75 species of tropical fish were added to the nine species of this study, the heterozygosity values differed significantly among the groups of different reproductive strategies. The highest mean heterozygosity was for the non-migratory without parental care, followed by the long-distance migratory, and the lowest mean was for the non-migratory with parental care or internal fecundation.

  7. STUDY OF GENETIC VARIABILITY OF TRITICALE VARIETIES BY SSR MARKERS

    Directory of Open Access Journals (Sweden)

    Jana Ondroušková

    2013-04-01

    Full Text Available For the detection of genetic variability ten genotypes of winter triticale (×Triticosecale Wittmack, 2n = 6x = 42; BBAARR were selected: nine varieties and one breeding line with good bread-making quality KM 4-09 with the chromosome translocation 1R.1D 5+10-2. 25 microsatellites markers located in the genome A, B, D and R were chosen for analysis. Eighty-four alleles were detected with an average of 3.36 alleles per locus were detected. For each microsatellite statistical values were calculated diversity index (DI, probabilities of identity (PI and polymorphic information content (PIC were calculated and averages statistical values are: DI 0.55, PI 0.27 and 0.5 PIC. Overall dendrogram based on the UPGMA method (Jaccards similarity coefficient significantly distinguished two groups of genotypes and these groups were divided into sub-clusters. A set of 5 SSR markers (Xwms0752, Xbarc128, Xrems1237, Xwms0861 and Xbrac170 which have the calculated PIC value higher than 0.68 that are sufficient for the identification of the analyzed genotypes was described.

  8. Rapid evolution of reproductive isolation between incipient outcrossing and selfing Clarkia species.

    Science.gov (United States)

    Briscoe Runquist, Ryan D; Chu, Eric; Iverson, Justin L; Kopp, Jason C; Moeller, David A

    2014-10-01

    A major goal of speciation research is to understand the processes involved in the earliest stages of the evolution of reproductive isolation (RI). One important challenge has been to identify systems where lineages have very recently diverged and opportunities for hybridization are present. We conducted a comprehensive examination of the components of RI across the life cycle of two subspecies of Clarkia xantiana, which diverged recently (ca. 65,000 bp). One subspecies is primarily outcrossing, but self-compatible, whereas the other is primarily selfing. The subspecies co-occur in a zone of sympatry but hybrids are rarely observed. Premating barriers resulted in nearly complete isolation in both subspecies with flowering time and pollinator preference (for the outcrosser over the selfer) as the strongest barriers. We found that the outcrosser had consistently more competitive pollen, facilitating hybridization in one direction, but no evidence for pollen-pistil interactions as an isolating barrier. Surprisingly, postzygotic isolation was detected at the stage of hybrid seed development, but in no subsequent life stages. This crossing barrier was asymmetric with crosses from the selfer to outcrosser most frequently failing. Collectively, the results provide evidence for rapid evolution of multiple premating and postzygotic barriers despite a very recent divergence time.

  9. Making genetic biodiversity measurable : a review of statistical multivariate methods to study variability at gene level

    OpenAIRE

    2011-01-01

    Measures of agro-ecosystems genetic variability are essential to sustain scientific-based actions and policies tending to protect the ecosystem services they provide. To build the genetic variability datum it is necessary to deal with a large number and different types of variables. Molecular marker data is highly dimensional by nature, and frequently additional types of information are obtained, as morphological and physiological traits. This way, gene...

  10. NOTE - Genetic variability among cassava accessions based on SSR markers

    Directory of Open Access Journals (Sweden)

    Márcia de Nazaré Oliveira Ribeiro

    2011-01-01

    Full Text Available The aim of this study was to characterize and estimate the genetic similarity among 93 cassava accessions. The DNAamplification was performed with 14 microsatellite primers. The amplification products were separated by a polyacrylamide gelelectrophoresis, showing a polymorphism formation, through which the accessions were discriminated against. The genetic similarityamong accessions of cassava was estimated by the Dice coefficient. Cluster analysis was carried out using the UPGMA method. Thepolymorphic primers amplified a total of 26 alleles with 2-4 alleles per loci. The genetic similarity ranged from 0.16 to 0.96. Theaverage values for observed and expected heterozygosity were 0.18 and 0.46, respectively. Twenty genetic similarity clusters weredetermined, demonstrating diversity among accessions, suggesting the possibility of heterotic hybrid generation.

  11. Considerations for Managing Agricultural Co-Existence between Transgenic and Non-Transgenic Cultivars of Outcrossing Perennial Forage Plants in Dairy Pastures

    Directory of Open Access Journals (Sweden)

    Kevin F. Smith

    2016-11-01

    Full Text Available Many of the major forage species used in agriculture are outcrossing and rely on the exchange of pollen between individuals for reproduction; this includes the major species used for dairy production in grazing systems: perennial ryegrass (Lolium perenne L. and white clover (Trifolium repens L.. Cultivars of these species have been co-existing since contrasting cultivars were developed using plant breeding, but the consequences and need for strategies to manage co-existence have been made more prominent with the advent of genetic modification. Recent technological developments have seen the experimental evaluation of genetically modified (GM white clover and perennial ryegrass, although there is no current commercial growing of GM cultivars of these species. Co-existence frameworks already exist for two major cross-pollinated grain crops (canola and maize in Europe, and for alfalfa (Medicago sativa L. in the US, so many of the principles that the industry has developed for co-existence in these crops such as detection techniques, segregation, and agronomic management provide lessons and guidelines for outcrossing forage species, that are discussed in this paper.

  12. Pollen Performance in Clarkia Taxa with Contrasting Mating Systems: Implications for Male Gametophytic Evolution in Selfers and Outcrossers

    Directory of Open Access Journals (Sweden)

    Alisa A. Hove

    2013-04-01

    Full Text Available We tested three predictions regarding the joint evolution of pollen performance and mating system. First, due to the potential for intense intrasexual competition in outcrossing populations, we predicted that outcrossers would produce faster-growing pollen than their selfing relatives. Second, if elevated competition promotes stronger selection on traits that improve pollen performance, then, among-plant variation in pollen performance would be lower in outcrossers than in selfers. Third, given successive generations of adaptation to the same maternal genotype in selfers, we predicted that, in selfing populations (but not in outcrossing ones, pollen would perform better following self- than cross-pollinations. We tested these predictions in field populations of two pairs of Clarkia (Onagraceae sister taxa. Consistent with our predictions, one outcrosser (C. unguiculata exhibited faster pollen germination and less variation in pollen tube growth rate (PTGR among pollen donors than its selfing sister species, C. exilis. Contrary to our predictions, the selfing C. xantiana ssp. parviflora exhibited faster PTGR than the outcrossing ssp. xantiana, and these taxa showed similar levels of variation in this trait. Pollen performance following self- vs. cross-pollinations did not differ within either selfing or outcrossing taxa. While these findings suggest that mating system and pollen performance may jointly evolve in Clarkia, other factors clearly contribute to pollen performance in natural populations.

  13. Economic Statistical Design of Variable Sampling Interval X¯$\\overline X $ Control Chart Based on Surrogate Variable Using Genetic Algorithms

    Directory of Open Access Journals (Sweden)

    Lee Tae-Hoon

    2016-12-01

    Full Text Available In many cases, a X¯$\\overline X $ control chart based on a performance variable is used in industrial fields. Typically, the control chart monitors the measurements of a performance variable itself. However, if the performance variable is too costly or impossible to measure, and a less expensive surrogate variable is available, the process may be more efficiently controlled using surrogate variables. In this paper, we present a model for the economic statistical design of a VSI (Variable Sampling Interval X¯$\\overline X $ control chart using a surrogate variable that is linearly correlated with the performance variable. We derive the total average profit model from an economic viewpoint and apply the model to a Very High Temperature Reactor (VHTR nuclear fuel measurement system and derive the optimal result using genetic algorithms. Compared with the control chart based on a performance variable, the proposed model gives a larger expected net income per unit of time in the long-run if the correlation between the performance variable and the surrogate variable is relatively high. The proposed model was confined to the sample mean control chart under the assumption that a single assignable cause occurs according to the Poisson process. However, the model may also be extended to other types of control charts using a single or multiple assignable cause assumptions such as VSS (Variable Sample Size X¯$\\overline X $ control chart, EWMA, CUSUM charts and so on.

  14. Genetic variability and relationships for populations of Cerastoderma edule and of the C. Glaucum complex

    Science.gov (United States)

    Hummel, H.; Wolowicz, M.; Bogaards, R. H.

    Genetic variability and relationships of populations of the cockles Cerastoderma edule and of the C. glaucum complex in Europe were determined by means of isoenzyme electrophoresis. Distinct isoenzyme markers allowed a clear distinction between these two taxa. C edule showed a higher genetic intra-population variability than the other cockle species. The imbalance of the genotypes within popuulation and the inter-population differentiation of the C. glaucum complex are stronger than in C. edule. The genetic variability is related to the different habitats of the species, the members of the C. glaucum complex living in more isolated areas and having more limited gene flow.

  15. Genetic variability of fatty acids in bovine milk

    Directory of Open Access Journals (Sweden)

    Soyeurt H.

    2008-01-01

    Full Text Available Fatty acids composition of bovine milk influences the technological properties of butterfat and also presents some potential benefits for human health. Impact of feeding on fat composition is well described in the literature; less information is available about the impact of genetics. Based on few studies, essentially conducted to isolate some feeding effect, the breed seemed to influence the fatty acids composition. The variation in the activity of δ-9 desaturase, key enzyme in the production of monounsaturated fatty acids and conjugated linoleic acids in milk, could explain these differences. Very few studies have been focussing on the estimation of genetic parameters of fatty acids composition. However, the moderate heritability estimates observed by these studies for the major fatty acids could suggest a potential genetic effect.

  16. Sylvatic plague reduces genetic variability in black-tailed prairie dogs.

    Science.gov (United States)

    Trudeau, Kristie M; Britten, Hugh B; Restani, Marco

    2004-04-01

    Small, isolated populations are vulnerable to loss of genetic diversity through in-breeding and genetic drift. Sylvatic plague due to infection by the bacterium Yersinia pestis caused an epizootic in the early 1990s resullting in declines and extirpations of many black-tailed prairie dog (Cynomys ludovicianus) colonies in north-central Montana, USA. Plague-induced population bottlenecks may contribute to significant reductions in genetic variability. In contrast, gene flow maintains genetic variability within colonies. We investigated the impacts of the plague epizootic and distance to nearest colony on levels of genetic variability in six prairie dog colonies sampled between June 1999 and July 2001 using 24 variable randomly amplified polymorphic DNA (RAPD) markers. Number of effective alleles per locus (n(e)) and gene diversity (h) were significantly decreased in the three colonies affected by plague that were recovering from the resulting bottlenecks compared with the three colonies that did not experience plague. Genetic variability was not significantly affected by geographic distance between colonies. The majority of variance in gene fieqnencies was found within prairie clog colonies. Conservation of genetic variability in black-tailed prairie dogs will require the preservation of both large and small colony complexes and the gene flow amonog them.

  17. Genetic variables of various manifestations of osteochondrosis and their correlations between and within joints in Dutch warmblood horses

    NARCIS (Netherlands)

    Grevenhof, van E.M.; Schurink, A.; Ducro, B.J.; Weeren, van P.R.; Tartwijk, van J.M.F.M.

    2009-01-01

    Osteochondrosis (OC) is an important orthopedic developmental disorder in many horse populations. A review of the literature revealed widely variable heritability estimates for the disorder. We estimated the genetic variables (heritabilities and genetic correlations) of various manifestations of OC.

  18. Genetic variability in Sudanese Acacia senegal (L.) assessed by ...

    African Journals Online (AJOL)

    TUOYO

    2010-07-26

    Jul 26, 2010 ... Gum Arabic producing agroforestry tree species in. Sudan. A. senegal .... Algadamblia 4, simmer 2, Simmer 1 and Nabg as sisters,. (Alphil 1, alphil 2 as .... RAPD markers could be used for differentiating Acacia senegal genotypes ... the result of genetic stability due to long overlapping generations, and a ...

  19. Genetics Home Reference: familial focal epilepsy with variable foci

    Science.gov (United States)

    ... Med Genet. 2016 Aug;53(8):503-10. doi: 10.1136/jmedgenet-2016-103883. Review. Citation on PubMed Baulac S, Ishida S, Marsan E, Miquel C, Biraben A, Nguyen DK, Nordli D, Cossette P, ... 2015 Apr;77(4):675-83. doi: 10.1002/ana.24368. Epub 2015 Mar 13. ...

  20. Genetic Variability in Barley (Hordeum vulgare l.) Landraces from ...

    African Journals Online (AJOL)

    The phenotypic frequencies of morphological characters (qualitative ... of genetic variation among segregating progeny for pure line cultivar development ...... provided discrimination between landraces according to their origin because the .... categories of descriptors evolving along different evolutionary lines (Asfaw, 1989b ...

  1. Genetic Variability in Soybean (Glycine max L.) for Low Soil ...

    African Journals Online (AJOL)

    Abush Tesfaye

    The application of inorganic P fertilizers is one of the possibilities for addressing the problem of low P ..... (2011), traits combining such high H2 and genetic advance are predominantly controlled ..... Genstat Release 11.1 (PC/Windows). Wang ...

  2. Bayesian methods for meta-analysis of causal relationships estimated using genetic instrumental variables

    DEFF Research Database (Denmark)

    2010-01-01

    Genetic markers can be used as instrumental variables, in an analogous way to randomization in a clinical trial, to estimate the causal relationship between a phenotype and an outcome variable. Our purpose is to extend the existing methods for such Mendelian randomization studies to the context...... of multiple genetic markers measured in multiple studies, based on the analysis of individual participant data. First, for a single genetic marker in one study, we show that the usual ratio of coefficients approach can be reformulated as a regression with heterogeneous error in the explanatory variable....... This can be implemented using a Bayesian approach, which is next extended to include multiple genetic markers. We then propose a hierarchical model for undertaking a meta-analysis of multiple studies, in which it is not necessary that the same genetic markers are measured in each study. This provides...

  3. Genetic variability of Dactylopius opuntiae (Hemiptera, Dactylopiidae) on forage cactus in northeast Brazil.

    Science.gov (United States)

    Silva, D M P; do E S Mergulhão, A C; de Medeiros, L V; Figueiredo, M V B; Burity, H A

    2013-10-30

    The carmine cochineal Dactylopius opuntiae is a key pest in productive fields of forage cactus in Pernambuco, Brazil. Species identification by means of molecular markers assists in understanding the genetic profile, underpins morphological characterization, and supports the monitoring of populations in integrated management programs designed to control this pest. We evaluated the genetic variability of natural populations of D. opuntiae. Genetic variability was analyzed with ISSR and RAPD primers in 24 populations from 12 municipalities of Pernambuco State in Brazil. Morphological characterization confirmed that D. opuntiae was the only cochineal species present in all samples. Nine ISSR primers and six RAPD produced a total of 62 and 58 polymorphic fragments, respectively. Both types of markers showed an average genetic similarity of 80% regardless of the geographic origin of samples. The low genetic variability demonstrates a high degree of relatedness among these D. opuntiae populations.

  4. Genetic variability in the mitochondrial DNA of the Danish Pine marten

    DEFF Research Database (Denmark)

    Pertoldi, Cino; Muñoz, Joaquin; Madsen, Aksel Bo;

    2008-01-01

    Here we study genetic differentiation and changes over time in genetic variability in the rare pine marten Martes martes. Samples from three isolated geographic regions: Jutland and Sealand (Denmark) and southern Scania (southernmost Sweden), were genotyped by sequencing the hypervariable domain ...

  5. Genetic Instrumental Variable (GIV) Regression: Explaining Socioeconomic and Health Outcomes in Non-Experimental Data

    NARCIS (Netherlands)

    T.A. DiPrete (Thomas); C. Burik (Casper); Ph.D. Koellinger (Philipp)

    2017-01-01

    textabstractWe introduce Genetic Instrumental Variables (GIV) regression – a method to estimate causal effects in non-experimental data with many possible applications in the social sciences and epidemiology. In non-experimental data, genetic correlation between the outcome and the exposure of

  6. Outcrossing rates in a natural stand and in a seed orchard of Pinus peuce

    Directory of Open Access Journals (Sweden)

    P. Zhelev

    2013-12-01

    Full Text Available The mating system parameters were studied in a natural stand and in a seed orchard of the Balkan endemic, Pinus peuce Griseb. bymeans of isozyme gene markers. The results indicate that the multilocus estimates of the outcrossing rates are low relative to otherwidespread conifers but concord to these reported for other pine species with limited area of distribution. No significant differenceswere detected between the natural stand and the seed orchard estimates. Multilocus estimates of outcrossing rate were within the range0.77-0.79, while mean single-locus estimates were lower (0.69-0.73. The results indicate that at least 20% of the progeny of Pinus peuceis due to self-fertilization. Possible reasons for the results observed and the implications for tree breeding and gene conservation are discussed.

  7. Outcrossing rates in a natural stand and in a seed orchard of Pinus peuce

    Directory of Open Access Journals (Sweden)

    P. Zhelev

    2013-12-01

    Full Text Available The mating system parameters were studied in a natural stand and in a seed orchard of the Balkan endemic, Pinus peuce Griseb. bymeans of isozyme gene markers. The results indicate that the multilocus estimates of the outcrossing rates are low relative to otherwidespread conifers but concord to these reported for other pine species with limited area of distribution. No significant differenceswere detected between the natural stand and the seed orchard estimates. Multilocus estimates of outcrossing rate were within the range0.77-0.79, while mean single-locus estimates were lower (0.69-0.73. The results indicate that at least 20% of the progeny of Pinus peuceis due to self-fertilization. Possible reasons for the results observed and the implications for tree breeding and gene conservation are discussed.

  8. Microbialite genetic diversity and composition relate to environmental variables.

    Science.gov (United States)

    Centeno, Carla M; Legendre, Pierre; Beltrán, Yislem; Alcántara-Hernández, Rocío J; Lidström, Ulrika E; Ashby, Matthew N; Falcón, Luisa I

    2012-12-01

    Microbialites have played an important role in the early history of life on Earth. Their fossilized forms represent the oldest evidence of life on our planet dating back to 3500 Ma. Extant microbialites have been suggested to be highly productive and diverse communities with an evident role in the cycling of major elements, and in contributing to carbonate precipitation. Although their ecological and evolutionary importance has been recognized, the study of their genetic diversity is yet scanty. The main goal of this study was to analyse microbial genetic diversity of microbialites living in different types of environments throughout Mexico, including desert ponds, coastal lagoons and a crater-lake. We followed a pyrosequencing approach of hypervariable regions of the 16S rRNA gene. Results showed that microbialite communities were very diverse (H' = 6-7) and showed geographic variation in composition, as well as an environmental effect related to pH and conductivity, which together explained 33% of the genetic variation. All microbialites had similar proportions of major bacterial and archaeal phyla. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  9. Genetic components of litter size variability in sheep

    Directory of Open Access Journals (Sweden)

    Chevalet Claude

    2001-05-01

    Full Text Available Abstract Classical selection for increasing prolificacy in sheep leads to a concomitant increase in its variability, even though the objective of the breeder is to maximise the frequency of an intermediate litter size rather than the frequency of high litter sizes. For instance, in the Lacaune sheep breed raised in semi-intensive conditions, ewes lambing twins represent the economic optimum. Data for this breed, obtained from the national recording scheme, were analysed. Variance components were estimated in an infinitesimal model involving genes controlling the mean level as well as its environmental variability. Large heritability was found for the mean prolificacy, but a high potential for increasing the percentage of twins at lambing while reducing the environmental variability of prolificacy is also suspected. Quantification of the response to such a canalising selection was achieved.

  10. Genetic components of litter size variability in sheep

    Science.gov (United States)

    SanCristobal-Gaudy, Magali; Bodin, Loys; Elsen, Jean-Michel; Chevalet, Claude

    2001-01-01

    Classical selection for increasing prolificacy in sheep leads to a concomitant increase in its variability, even though the objective of the breeder is to maximise the frequency of an intermediate litter size rather than the frequency of high litter sizes. For instance, in the Lacaune sheep breed raised in semi-intensive conditions, ewes lambing twins represent the economic optimum. Data for this breed, obtained from the national recording scheme, were analysed. Variance components were estimated in an infinitesimal model involving genes controlling the mean level as well as its environmental variability. Large heritability was found for the mean prolificacy, but a high potential for increasing the percentage of twins at lambing while reducing the environmental variability of prolificacy is also suspected. Quantification of the response to such a canalising selection was achieved. PMID:11403747

  11. A comparison of floral integration between selfing and outcrossing species: a meta-analysis.

    Science.gov (United States)

    Fornoni, Juan; Ordano, Mariano; Pérez-Ishiwara, Rubén; Boege, Karina; Domínguez, César A

    2016-02-01

    Floral integration is thought to be an adaptation to promote cross-fertilization, and it is often assumed that it increases morphological matching between flowers and pollinators, increasing the efficiency of pollen transfer. However, the evidence for this role of floral integration is limited, and recent studies have suggested a possible positive association between floral integration and selfing. Although a number of explanations exist to account for this inconsistency, to date there has been no attempt to examine the existence of an association between floral integration and mating system. This study hypothesized that if pollinator-mediated pollen movement among plants (outcrossing) is the main factor promoting floral integration, species with a predominantly outcrossing mating system should present higher levels of floral integration than those with a predominantly selfing mating system. A phylogenetically informed meta-analysis of published data was performed in order to evaluate whether mating system (outcrossing vs. selfing) accounts for the variation in floral integration among 64 species of flowering plants. Morphometric floral information was used to compare intra-floral integration among traits describing sexual organs (androecium and gynoecium) and those corresponding to the perianth (calix and corolla). The analysis showed that outcrossing species have lower floral integration than selfing species. This pattern was caused by significantly higher integration of sexual traits than perianth traits, as integration of the latter group remained unchanged across mating categories. The results suggest that the evolution of selfing is associated with concomitant changes in intra-floral integration. Thus, floral integration of sexual traits should be considered as a critical component of the selfing syndrome. © The Author 2015. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email

  12. Outcrossing and paternity analysis of Pinus densiflora (Japanese red pine) by microsatellite polymorphism.

    Science.gov (United States)

    Lian, C; Miwa, M; Hogetsu, T

    2001-07-01

    This study employed microsatellite loci to analyse outcrossing rate and pollen dispersal in Japanese red pine (Pinus densiflora) in an isolated stand. The average offspring outcrossing rate for 29 cones was 0.955. Significant differences in outcrossing rates between offspring groups on individual branches that extended in different directions at different heights were not detected. Male parents of 874 offspring collected from the maternal tree were assessed by exclusion using polymorphisms at three microsatellite loci. Paternity analysis indicated that at least 31% of the offspring were fertilized by pollen from trees outside the stand. The average distance of pollen migration within the study stand was 68 m, with a maximum value of 325 m. There was excess mating with nearby P. densiflora trees, of which only a few were predominant pollen donors. In addition, a weakly directional bias in P. densiflora pollination was also detected in the study stand, suggesting that female strobili on a branch of the maternal tree were more easily fertilized by pollen from trees in that direction.

  13. Genetic variability of Verbascum populations from metal polluted and unpolluted sites

    Directory of Open Access Journals (Sweden)

    Danilović Gordana

    2015-01-01

    Full Text Available Mullein (Verbascum plants have extensive distribution and can grow in variable environmental conditions. Seed was collected from mullein plants grown at 4 locations, two metals contaminated and two metal uncontaminated areas. Genetic variability of progeny was examined. Populations collected from unpolluted areas were genetically more similar than those collected from polluted areas as revealed by RAPD and SSR markers and UPGMA analysis. The results indicate that there is genetic differentiation between examined populations and therefore they represent suitable material for further investigation of plant adaptation mechanisms to increased metal content. [Projekat Ministarstva nauke Republike Srbije, br. III43010

  14. Bayesian methods for meta-analysis of causal relationships estimated using genetic instrumental variables

    DEFF Research Database (Denmark)

    Burgess, Stephen; Thompson, Simon G; Andrews, G

    2010-01-01

    Genetic markers can be used as instrumental variables, in an analogous way to randomization in a clinical trial, to estimate the causal relationship between a phenotype and an outcome variable. Our purpose is to extend the existing methods for such Mendelian randomization studies to the context o...

  15. Identifying genetic variants for heart rate variability in the acetylcholine pathway

    NARCIS (Netherlands)

    Riese, Harriëtte; Muñoz Venegas, Loretto; Hartman, Catharina A; Ding, Xiuhua; Su, Shaoyong; Oldehinkel, Albertine J; van Roon, Arie M; van der Most, Peter J; Lefrandt, Joop; Gansevoort, Ronald; van der Harst, Pim; Verweij, Niek; Licht, Carmilla M M; Boomsma, Dorret I; Hottenga, Jouke-Jan; Willemsen, Gonneke; Penninx, Brenda W J H; Nolte, Ilja M; de Geus, Eco J C; Wang, Xiaoling; Snieder, Harold

    2014-01-01

    Heart rate variability is an important risk factor for cardiovascular disease and all-causemortality. The acetylcholine pathway plays a key role in explaining heart rate variability in humans. We assessed whether 443 genotyped and imputed common genetic variants in eight key genes (CHAT, SLC18A3,

  16. Genetic variability in captive populations of the stingless bee Tetragonisca angustula.

    Science.gov (United States)

    Santiago, Leandro R; Francisco, Flávio O; Jaffé, Rodolfo; Arias, Maria C

    2016-08-01

    Low genetic variability has normally been considered a consequence of animal husbandry and a major contributing factor to declining bee populations. Here, we performed a molecular analysis of captive and wild populations of the stingless bee Tetragonisca angustula, one of the most commonly kept species across South America. Microsatellite analyses showed similar genetic variability between wild and captive populations However, captive populations showed lower mitochondrial genetic variability. Male-mediated gene flow, transport and division of nests are suggested as the most probable explanations for the observed patterns of genetic structure. We conclude that increasing the number of colonies kept through nest divisions does not negatively affect nuclear genetic variability, which seems to be maintained by small-scale male dispersal and human-mediated nest transport. However, the transport of nests from distant localities should be practiced with caution given the high genetic differentiation observed between samples from western and eastern areas. The high genetic structure verified is the result of a long-term evolutionary process, and bees from distant localities may represent unique evolutionary lineages.

  17. GENETIC VARIABILITY AND CORRELATION STUDIES IN BRINJAL (SOLANUM MELONGENA L.)

    OpenAIRE

    Bhukya Ravi Nayak; P. K. Nagre

    2013-01-01

    The present investigation was conducted at Department of Horticulture, Horticulture Garden, Dr. PDKV, Akola (M.S.), during kharif 2012-13. The experimental material comprised of 20 genotypes along with one check of brinjal and the experimental was laid out in randomized block design with three replications. Variability studies revealed that highly significant differences were recorded among the varieties for all characters. Correlation and path analysis revealed that fruit length, diameter, w...

  18. Variables Affecting Secondary School Students' Willingness to Eat Genetically Modified Food Crops

    Science.gov (United States)

    Maes, Jasmien; Bourgonjon, Jeroen; Gheysen, Godelieve; Valcke, Martin

    2017-04-01

    A large-scale cross-sectional study (N = 4002) was set up to determine Flemish secondary school students' willingness to eat genetically modified food (WTE) and to link students' WTE to previously identified key variables from research on the acceptance of genetic modification (GM). These variables include subjective and objective knowledge about genetics and biotechnology, perceived risks and benefits of GM food crops, trust in information from different sources about GM, and food neophobia. Differences between WTE-related variables based on students' grade level, educational track, and gender were analyzed. The students displayed a rather indecisive position toward GM food and scored weakly on a genetics and biotechnology knowledge test. WTE correlated most strongly with perceived benefits and subjective and objective knowledge. The results have clear implications for education, as they reiterate the need to strengthen students' scientific knowledge base and to introduce a GM-related debate at a much earlier stage in their school career.

  19. Genetic fidelity and variability of micropropagated cassava plants (Manihot esculenta Crantz) evaluated using ISSR markers.

    Science.gov (United States)

    Vidal, Á M; Vieira, L J; Ferreira, C F; Souza, F V D; Souza, A S; Ledo, C A S

    2015-07-14

    Molecular markers are efficient for assessing the genetic fidelity of various species of plants after in vitro culture. In this study, we evaluated the genetic fidelity and variability of micropropagated cassava plants (Manihot esculenta Crantz) using inter-simple sequence repeat markers. Twenty-two cassava accessions from the Embrapa Cassava & Fruits Germplasm Bank were used. For each accession, DNA was extracted from a plant maintained in the field and from 3 plants grown in vitro. For DNA amplification, 27 inter-simple sequence repeat primers were used, of which 24 generated 175 bands; 100 of those bands were polymorphic and were used to study genetic variability among accessions of cassava plants maintained in the field. Based on the genetic distance matrix calculated using the arithmetic complement of the Jaccard's index, genotypes were clustered using the unweighted pair group method using arithmetic averages. The number of bands per primer was 2-13, with an average of 7.3. For most micropropagated accessions, the fidelity study showed no genetic variation between plants of the same accessions maintained in the field and those maintained in vitro, confirming the high genetic fidelity of the micropropagated plants. However, genetic variability was observed among different accessions grown in the field, and clustering based on the dissimilarity matrix revealed 7 groups. Inter-simple sequence repeat markers were efficient for detecting the genetic homogeneity of cassava plants derived from meristem culture, demonstrating the reliability of this propagation system.

  20. Assessing genetic variability in two ancient chicken breeds of Padova area

    Directory of Open Access Journals (Sweden)

    Martino Cassandro

    2010-01-01

    Full Text Available Genetic diversity in two ancient indigenous chicken breeds of the Veneto region was assessed using Amplified Fragment Length Polymorphism (AFLP markers. A total of 63 individuals were analysed using three selected AFLP primer combinations that produced 66 clear polymorphisms. The breeds analyzed were the Padovana and the Polverara (two ancient breeds and a reference broiler line. The expected heterozygosity (Het did not differ significantly among breeds. The variability at AFLP loci was largely maintained across breeds, as indicated by the coefficient of genetic differentiation (Gst value. The lowest genetic distance is found between the Padovana and Polverara breeds suggesting that they could be genetically close.

  1. Genetic variability in the Florida manatee (Trichechus manatus)

    Science.gov (United States)

    McClenaghan, Leroy R.; O'Shea, Thomas J.

    1988-01-01

    Tissue was obtained from 59 manatee (Trichechus manatus) carcasses salvaged from 20 counties in Florida. Allozyme phenotypes at 24 structural loci were determined by gel electrophoresis. Averages for the proportion of polymorphic loci and mean heterozygosity were 0.300 (range, 0.167-0.417) and 0.050 (range, 0.028-0.063), respectively. These estimates are equivalent to or higher than those generally reported for other species of marine mammals and do not support the hypothesis that body size and heterozygosity in mammals are related inversely. Among-region gene diversity accounted for only 4% of the total diversity. High rates of gene flow probably account for genetic homogeneity across regions. An F-statistic analysis revealed a general tendency toward excess homozygosity within regions. Management efforts to prevent future reductions in population size that would erode existing genic diversity should continue.

  2. Influence from genetic variability on opioid use for cancer pain: a European genetic association study of 2294 cancer pain patients

    DEFF Research Database (Denmark)

    Klepstad, P; Fladvad, T; Skorpen, F;

    2011-01-01

    Cancer pain patients need variable opioid doses. Preclinical and clinical studies suggest that opioid efficacy is related to genetic variability. However, the studies have small samples, findings are not replicated, and several candidate genes have not been studied. Therefore, a study of genetic...... variability with opioid doses in a large population using a confirmatory validation population was warranted. We recruited 2294 adult European patients using a World Health Organization (WHO) step III opioid and analyzed single nucleotide polymorphisms (SNPs) in genes with a putative influence on opioid...... mechanisms. The patients' mean age was 62.5 years, and the average pain intensity was 3.5. The patients' primary opioids were morphine (n=830), oxycodone (n=446), fentanyl (n=699), or other opioids (n=234). Pain intensity, time on opioids, age, gender, performance status, and bone or CNS metastases predicted...

  3. Genetic variability of Triatoma flavida and Triatoma bruneri (Hemiptera: Reduviidae by RAPD-PCR technique

    Directory of Open Access Journals (Sweden)

    Jorge Fraga

    2011-02-01

    Full Text Available The Triatominae (Hemiptera:Reduviidae contains the principal and potential Chagas disease vectors present in Mexico, Central America and South America. Triatoma flavida and T. bruneri are Cuban species. These species are closely related according to morphology and were considered synonyms until 1981, when they were separated on the grounds of external characters of the body and the morphology of male genitalia. The present study seeks to analyze genetic polymorphism of T. flavida and T. bruneri populations using RAPD techniques, and to assess the genetic relationship between these species. Ten random primers were used to evaluate the genetic variability among species using RAPD-PCR. The genetic flow among them was calculated. The dendrogram based on calculated Jaccard distances showed two clearly distinguishable clusters which coincided with the studied species. Within each species, moderate genetic differentiation (Fst 0.05-0.15 and migration rates (N > 1 were found among populations, that reveal gene flow and genetic homogeneity. Between species, the Fst value showed a high genetic differentiation and the migration rate was insufficient to maintain genetic homogeneity, and confirmed the absence of gene flow between them. Our results confirm the genetic variability among T. flavida and T. bruneri species.

  4. Genetic variability of Triatoma flavida and Triatoma bruneri (Hemiptera: Reduviidae) by RAPD-PCR technique.

    Science.gov (United States)

    Fraga, Jorge; Rodriguez, Jinnay; Fuentes, Omar; Hernández, Yenin; Castex, Mayda; Gonzalez, Raul; Fernández-Calienes, Aymé

    2011-01-01

    The Triatominae (Hemiptera:Reduviidae) contains the principal and potential Chagas disease vectors present in Mexico, Central America and South America. Triatoma flavida and T. bruneri are Cuban species. These species are closely related according to morphology and were considered synonyms until 1981, when they were separated on the grounds of external characters of the body and the morphology of male genitalia. The present study seeks to analyze genetic polymorphism of T. flavida and T. bruneri populations using RAPD techniques, and to assess the genetic relationship between these species. Ten random primers were used to evaluate the genetic variability among species using RAPD-PCR. The genetic flow among them was calculated. The dendrogram based on calculated Jaccard distances showed two clearly distinguishable clusters which coincided with the studied species. Within each species, moderate genetic differentiation (Fst 0.05-0.15) and migration rates (N > 1) were found among populations, that reveal gene flow and genetic homogeneity. Between species, the Fst value showed a high genetic differentiation and the migration rate was insufficient to maintain genetic homogeneity, and confirmed the absence of gene flow between them. Our results confirm the genetic variability among T. flavida and T. bruneri species.

  5. Effects of HBV Genetic Variability on RNAi Strategies

    Directory of Open Access Journals (Sweden)

    Nattanan Panjaworayan

    2011-01-01

    Full Text Available RNAi strategies present promising antiviral strategies against HBV. RNAi strategies require base pairing between short RNAi effectors and targets in the HBV pregenome or other RNAs. Natural variation in HBV genotypes, quasispecies variation, or mutations selected by the RNAi strategy could potentially make these strategies less effective. However, current and proposed antiviral strategies against HBV are being, or could be, designed to avoid this. This would involve simultaneous targeting of multiple regions of the genome, or regions in which variation or mutation is not tolerated. RNAi strategies against single genotypes or against variable regions of the genome would need to have significant other advantages to be part of robust therapies.

  6. Genetic diversity and variability in two Italian autochthonous donkey genetic types assessed by microsatellite markers

    Directory of Open Access Journals (Sweden)

    Donato Matassino

    2014-01-01

    Full Text Available Since 13rd century, Italian domestic autochthonous donkey population has been characterised by Mediterranean grey mousy cruciate ancestral phenotype, currently typical of Amiata donkey (AD genetic type. This phenotype persisted up to the 16th century when a marked introduction of Hispanic and French big sized and dark bay or darkish coloured sires occurred. In the context of a safeguard programme of Latial Equide resources, the aim of this research was to evaluate the genetic diversity and similarity between the AD breed and an autochthonous donkey population native from Lazio, the Viterbese donkey (VD, using molecular markers. A total of 135 animals (50 AD and 85 VD were genetically characterised by using 16 short tandem repeat markers. A high genetic differentiation between populations (FST=0.158; P<0.01 and a low betweenbreeds genetic similarity (0.233±0.085 were observed. Correspondence analysis, the result of STRUCTURE software analysis and analysis of molecular variance would seem to indicate genetically different entities as well. It would be desirable to increase the number of comparison with other breeds to better understand the origin of VD. Moreover, results obtained in this study suggest that the loss of genetic variation observed in VD could mainly derive from unnoticed sub-population structuring (Wahlund effect, rather than to other factors such as inbreeding, null alleles or selection influence.

  7. Genetic variation in variability: phenotypic variability of fledging weight and its evolution in a songbird population

    NARCIS (Netherlands)

    Mulder, H.A.; Gienapp, P; Visser, ME

    2016-01-01

    Variation in traits is essential for natural selection to operate and genetic and environmental effects can contribute to this phenotypic variation. From domesticated populations, we know that families can differ in their level of within-family variance, which leads to the intriguing situation that

  8. Genetic variation in variability : phenotypic variability of fledging weight and its evolution in a songbird population

    NARCIS (Netherlands)

    Mulder, Han A.; Gienapp, P; Visser, Marcel

    2016-01-01

    Variation in traits is essential for natural selection to operate and genetic and environmental effects can contribute to this phenotypic variation. From domesticated populations we know that families can differ in their level of within-family variance, which leads to the intriguing situation that w

  9. AFLP estimation of the outcrossing rate of Spondias tuberosa (Anacardiaceae, an endemic species to the Brazilian semiarid region Una estimación AFLP de la tasa de fecundación cruzada de Spondias tuberosa (Anacardiaceae, una especie endémica de la región semiárida de Brasil

    Directory of Open Access Journals (Sweden)

    Carlos Antonio Fernandes Santos

    2013-06-01

    Full Text Available The umbu tree (Spondias tuberosa is one of the most important endemic species to the Brazilian tropical semiarid region. The umbu tree has edible fruits with a peculiar flavor that are consumed in natura or in a semi-industrialized form, such as jams, candies and juices. The majority of endemic species to Brazilian semiarid region have not been studied or sampled to form germ- plasm collections, which increases the risk of losing genetic variability of the adapted species to xerophytic conditions. The aim of this study was to estimate outcrossing rates in S. tuberosa using a multilocus mixed model in order to guide genetic resources and breeding programs of this species. DNA samples were extracted from 92 progenies of umbu trees, which were distributed among 12 families. These trees were planted by seed in 1991 in Petrolina, PE, Brazil. The experimental design was a randomized block, with a total of 42 progenies sampled in three regions. The experimental units were composed by five plants and five replications. The out- crossing rate was estimated by the multilocus model, which is available in the MLTR software, and was based on 17 polymorphic AFLP bands obtained from AAA_CTG and AAA_CTC primer combinations. The observed heterozygotes ranged from 0.147 to 0.499, with a maximum frequency estimated for the AAA_CTC_10 ampli- con. The multilocus outcrossing estimation ( was 0.804±0.072, while the single-locus ( was 0.841±0.079, which suggests that S. tuberosa is predominantly an outcrossing species. The difference between and was -0.037±0.029, which indicates that biparental inbreeding was nearly absent. The mean inbreeding coefficient or fixation index ( among maternal plants was - 0.103±0.045, and the expected was 0.108, which indicates that there was no excess of heterozygotes in the maternal population. The outcrossing estimates obtained in the present study indicate that S. tuberosa is an open-pollinated species. Biometrical models applied

  10. Genetic variability and population structure of endangered Panax ginseng in the Russian Primorye

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    Muzarok Tamara I

    2010-06-01

    Full Text Available Abstract Background The natural habitat of wild P. ginseng is currently found only in the Russian Primorye and the populations are extremely exhausted and require restoration. Analysis of the genetic diversity and population structure of an endangered species is a prerequisite for conservation. The present study aims to investigate the patterns and levels of genetic polymorphism and population structures of wild P. ginseng with the AFLP method to (1 estimate the level of genetic diversity in the P. ginseng populations in the Russian Primorsky Krai, (2 calculate the distribution of variability within a population and among populations and (3 examine the genetic relationship between the populations. Methods Genetic variability and population structure of ten P. ginseng populations were investigated with Amplified Fragment Length Polymorphism (AFLP markers. The genetic relationships among P. ginseng plants and populations were delineated. Results The mean genetic variability within populations was high. The mean level of polymorphisms was 55.68% at the population level and 99.65% at the species level. The Shannon's index ranged between 0.1602 and 0.3222 with an average of 0.2626 at the population level and 0.3967 at the species level. The analysis of molecular variances (AMOVA showed a significant population structure in P. ginseng. The partition of genetic diversity with AMOVA suggested that the majority of the genetic variation (64.5% was within populations of P. ginseng. The inter-population variability was approximately 36% of the total variability. The genetic relationships among P. ginseng plants and populations were reconstructed by Minimum Spanning tree (MS-tree on the basis of Euclidean distances with ARLEQUIN and NTSYS, respectively. The MS-trees suggest that the southern Uss, Part and Nad populations may have promoted P. ginseng distribution throughout the Russian Primorye. Conclusion The P. ginseng populations in the Russian Primorye

  11. Genetic variability of Taenia saginata inferred from mitochondrial DNA sequences.

    Science.gov (United States)

    Rostami, Sima; Salavati, Reza; Beech, Robin N; Babaei, Zahra; Sharbatkhori, Mitra; Harandi, Majid Fasihi

    2015-04-01

    Taenia saginata is an important tapeworm, infecting humans in many parts of the world. The present study was undertaken to identify inter- and intraspecific variation of T. saginata isolated from cattle in different parts of Iran using two mitochondrial CO1 and 12S rRNA genes. Up to 105 bovine specimens of T. saginata were collected from 20 slaughterhouses in three provinces of Iran. DNA were extracted from the metacestode Cysticercus bovis. After PCR amplification, sequencing of CO1 and 12S rRNA genes were carried out and two phylogenetic analyses of the sequence data were generated by Bayesian inference on CO1 and 12S rRNA sequences. Sequence analyses of CO1 and 12S rRNA genes showed 11 and 29 representative profiles respectively. The level of pairwise nucleotide variation between individual haplotypes of CO1 gene was 0.3-2.4% while the overall nucleotide variation among all 11 haplotypes was 4.6%. For 12S rRNA sequence data, level of pairwise nucleotide variation was 0.2-2.5% and the overall nucleotide variation was determined as 5.8% among 29 haplotypes of 12S rRNA gene. Considerable genetic diversity was found in both mitochondrial genes particularly in 12S rRNA gene.

  12. Genetic variation in variability: Phenotypic variability of fledging weight and its evolution in a songbird population.

    Science.gov (United States)

    Mulder, Han A; Gienapp, Philip; Visser, Marcel E

    2016-09-01

    Variation in traits is essential for natural selection to operate and genetic and environmental effects can contribute to this phenotypic variation. From domesticated populations, we know that families can differ in their level of within-family variance, which leads to the intriguing situation that within-family variance can be heritable. For offspring traits, such as birth weight, this implies that within-family variance in traits can vary among families and can thus be shaped by natural selection. Empirical evidence for this in wild populations is however lacking. We investigated whether within-family variance in fledging weight is heritable in a wild great tit (Parus major) population and whether these differences are associated with fitness. We found significant evidence for genetic variance in within-family variance. The genetic coefficient of variation (GCV) was 0.18 and 0.25, when considering fledging weight a parental or offspring trait, respectively. We found a significant quadratic relationship between within-family variance and fitness: families with low or high within-family variance had lower fitness than families with intermediate within-family variance. Our results show that within-family variance can respond to selection and provides evidence for stabilizing selection on within-family variance. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

  13. Genetic variability testing of neurodevelopmental genes in schizophrenic patients.

    Science.gov (United States)

    Terzić, Tea; Kastelic, Matej; Dolžan, Vita; Plesničar, Blanka Kores

    2015-05-01

    This study investigated the associations between single nucleotide polymorphisms in the neurodevelopmental Disrupted In Schizophrenia 1 (DISC1 ), neuregulin 1 (NRG1), brain-derived neurotrophic factor (BDNF) and NOTCH4 genes and the clinical symptoms and the occurrence of treatment-resistant schizophrenia in the Slovenian population. We included 138 schizophrenia patients, divided into treatment-responsive and treatment-resistant group and 94 healthy blood donors. All subjects were genotyped for eight polymorphisms (DISC1 rs6675281, DISC1 rs821616, NRG1 rs3735781, NRG1 rs3735782, NRG1 rs10503929, NRG1 rs3924999, BDNF rs6265, NOTCH rs367398) and investigated for associations with clinical variables. NOTCH4 rs367398 AA/AG was significantly associated with worse Positive and Negative Syndrome Scale (PANSS) and Clinical Global Impression (CGI) score. NOTCH4 rs367398 was not statistically significantly associated with the occurrence of treatment-resistant schizophrenia after the correction for multiple testing. Our data indicate that NOTCH4 polymorphism can influence clinical symptoms in Slovenian patients with schizophrenia.

  14. Loss of genetic variability at the transferrin locus in five hatchery stocks of tambaqui (Colossoma macropomum

    Directory of Open Access Journals (Sweden)

    Calcagnotto Daniela

    2000-01-01

    Full Text Available Knowledge and conservation of the genetic variability in stocks maintained as live gene banks have become a high priority task for Brazilian fish culture. The aim of the present survey was to assess the transferrin allelic diversity of five hatchery stocks of tambaqui (Colossoma macropomum. The tambaqui stock from Pentecoste, the oldest maintained in Brazilian hatchery stations, retained three of the six alleles detected in wild populations of tambaqui from the Amazon River. Other hatchery stocks, directly or indirectly derived from the Pentecoste stock, did not show transferrin allelic variability. Insufficient number of founders and genetic drift due to sampling errors seem to be the main causes leading to loss of genetic diversity in tambaqui hatchery stocks. Appropriate management strategies are required in order to improve the genetic potential of tambaqui stocks in Brazil.

  15. Disentangling the effects of genetic, prenatal and parenting influences on children’s cortisol variability

    OpenAIRE

    MARCEAU, KRISTINE; Ram, Nilam; Neiderhiser, Jenae M.; Laurent, Heidemarie K.; Daniel S Shaw; Fisher, Phil; Natsuaki, Misaki N.; Leve, Leslie D.

    2013-01-01

    Developmental plasticity models hypothesize the role of genetic and prenatal environmental influences on the development of the hypothalamic–pituitary–adrenal (HPA) axis and highlight that genes and the prenatal environment may moderate early postnatal environmental influences on HPA functioning. This article examines the interplay of genetic, prenatal and parenting influences across the first 4.5 years of life on a novel index of children’s cortisol variability. Repeated measures data were o...

  16. Genetic variability of lactoferrin content estimated by mid-infrared spectrometry in bovine milk

    OpenAIRE

    Soyeurt, Hélène; Colinet, Frédéric; Arnould, Valérie; Dardenne, Pierre; Bertozzi, Carlo; Renaville, Robert; Portetelle, Daniel; Gengler, Nicolas

    2007-01-01

    The effects of lactoferrin (LF) on the immune system have already been shown by many studies. Unfortunately, the current methods used to measure LF levels in milk do not permit the study of the genetic variability of lactoferrin or the performance of routine genetic evaluations. The first aim of this research was to derive a calibration equation permitting the prediction of LF in milk by mid-infrared spectrometry (MIR). The calibration with partial least squares on 69 ...

  17. Hybrid model based on Genetic Algorithms and SVM applied to variable selection within fruit juice classification.

    Science.gov (United States)

    Fernandez-Lozano, C; Canto, C; Gestal, M; Andrade-Garda, J M; Rabuñal, J R; Dorado, J; Pazos, A

    2013-01-01

    Given the background of the use of Neural Networks in problems of apple juice classification, this paper aim at implementing a newly developed method in the field of machine learning: the Support Vector Machines (SVM). Therefore, a hybrid model that combines genetic algorithms and support vector machines is suggested in such a way that, when using SVM as a fitness function of the Genetic Algorithm (GA), the most representative variables for a specific classification problem can be selected.

  18. Influence from genetic variability on opioid use for cancer pain: a European genetic association study of 2294 cancer pain patients

    DEFF Research Database (Denmark)

    Klepstad, P; Fladvad, T; Skorpen, F;

    2011-01-01

    Cancer pain patients need variable opioid doses. Preclinical and clinical studies suggest that opioid efficacy is related to genetic variability. However, the studies have small samples, findings are not replicated, and several candidate genes have not been studied. Therefore, a study of genetic...... mechanisms. The patients' mean age was 62.5 years, and the average pain intensity was 3.5. The patients' primary opioids were morphine (n=830), oxycodone (n=446), fentanyl (n=699), or other opioids (n=234). Pain intensity, time on opioids, age, gender, performance status, and bone or CNS metastases predicted......C, HTR3D, HTR3E, HTR1, or CNR1 showed significant associations with opioid dose in both the development and the validation analyzes. These findings do not support the use of pharmacogenetic analyses for the assessed SNPs to guide opioid treatment. The study also demonstrates the importance...

  19. Disentangling the effects of genetic, prenatal and parenting influences on children's cortisol variability.

    Science.gov (United States)

    Marceau, Kristine; Ram, Nilam; Neiderhiser, Jenae M; Laurent, Heidemarie K; Shaw, Daniel S; Fisher, Phil; Natsuaki, Misaki N; Leve, Leslie D

    2013-11-01

    Developmental plasticity models hypothesize the role of genetic and prenatal environmental influences on the development of the hypothalamic-pituitary-adrenal (HPA) axis and highlight that genes and the prenatal environment may moderate early postnatal environmental influences on HPA functioning. This article examines the interplay of genetic, prenatal and parenting influences across the first 4.5 years of life on a novel index of children's cortisol variability. Repeated measures data were obtained from 134 adoption-linked families, adopted children and both their adoptive parents and birth mothers, who participated in a longitudinal, prospective US domestic adoption study. Genetic and prenatal influences moderated associations between inconsistency in overreactive parenting from child age 9 months to 4.5 years and children's cortisol variability at 4.5 years differently for mothers and fathers. Among children whose birth mothers had high morning cortisol, adoptive fathers' inconsistent overreactive parenting predicted higher cortisol variability, whereas among children with low birth mother morning cortisol adoptive fathers' inconsistent overreactive parenting predicted lower cortisol variability. Among children who experienced high levels of prenatal risk, adoptive mothers' inconsistent overreactive parenting predicted lower cortisol variability and adoptive fathers' inconsistent overreactive parenting predicted higher cortisol variability, whereas among children who experienced low levels of prenatal risk there were no associations between inconsistent overreactive parenting and children's cortisol variability. Findings supported developmental plasticity models and uncovered novel developmental, gene × environment and prenatal × environment influences on children's cortisol functioning.

  20. Genetic variability of an endangered Bromeliaceae species (Pitcairnia albiflos) from the Brazilian Atlantic rainforest.

    Science.gov (United States)

    Domingues, R; Machado, M A; Forzza, R C; Melo, T D; Wohlres-Viana, S; Viccini, L F

    2011-10-13

    Pitcairnia albiflos is a Bromeliaceae species endemic to Brazil that has been included as data-deficient in the extinction risk list of Brazilian flora. We analyzed genetic variability in P. albiflos populations using RAPD markers to investigate population structure and reproductive mechanisms and also to evaluate the actual extinction risk level of this species. Leaves of 56 individuals of P. albiflos from three populations were collected: Urca Hill (UH, 20 individuals), Chacrinha State Park (CSP, 24 individuals) and Tijuca National Park (TNP, 12 individuals). The RAPD technique was effective in characterizing the genetic diversity in the P. albiflos populations since it was possible to differentiate the populations and to identify exclusive bands for at least two of them. Even if there is low genetic diversity among them (CSP-UH = 0.463; CSP-TNP = 0.440; UH-TNP = 0.524), the populations seem to be isolated according to the low genetic diversity observed within them (H(pop) CSP = 0.060; H(pop) UH = 0.042; H(pop) TNP = 0.130). This fact might be the result of clonal and self-reproduction predominance and also from environmental degradation around the collection areas. Consequently, it would be important to protect all populations both in situ and ex situ to prevent the decrease of genetic variability. The low genetic variability among individuals of the same population confirms the inclusion of this species as critically endangered in the risk list for Brazilian flora.

  1. Dynamics of genetic variability in Anastrepha fraterculus (Diptera: Tephritidae) during adaptation to laboratory rearing conditions.

    Science.gov (United States)

    Parreño, María A; Scannapieco, Alejandra C; Remis, María I; Juri, Marianela; Vera, María T; Segura, Diego F; Cladera, Jorge L; Lanzavecchia, Silvia B

    2014-01-01

    Anastrepha fraterculus is one of the most important fruit fly plagues in the American continent and only chemical control is applied in the field to diminish its population densities. A better understanding of the genetic variability during the introduction and adaptation of wild A. fraterculus populations to laboratory conditions is required for the development of stable and vigorous experimental colonies and mass-reared strains in support of successful Sterile Insect Technique (SIT) efforts. The present study aims to analyze the dynamics of changes in genetic variability during the first six generations under artificial rearing conditions in two populations: a) a wild population recently introduced to laboratory culture, named TW and, b) a long-established control line, named CL. Results showed a declining tendency of genetic variability in TW. In CL, the relatively high values of genetic variability appear to be maintained across generations and could denote an intrinsic capacity to avoid the loss of genetic diversity in time. The impact of evolutionary forces on this species during the adaptation process as well as the best approach to choose strategies to introduce experimental and mass-reared A. fraterculus strains for SIT programs are discussed.

  2. Transfer of intracolonial genetic variability through gametes in Acropora hyacinthus corals

    Science.gov (United States)

    Schweinsberg, M.; González Pech, R. A.; Tollrian, R.; Lampert, K. P.

    2014-03-01

    In recent years, the new phenomenon of intracolonial genetic variability within a single coral colony has been described. This connotes that coral colonies do not necessarily consist of only a single genotype, but may contain several distinct genotypes. Harboring more than one genotype could improve survival under stressful environmental conditions, e.g., climate change. However, so far it remained unclear whether the intracolonial genetic variability of the adult coral is also present in the gametes. We investigated the occurrence of intracolonial genetic variability in 14 mature colonies of the coral Acropora hyacinthus using eight microsatellite loci. A grid was placed over each colony before spawning, and the emerging egg/sperm bundles were collected separately in each grid. The underlying tissues as well as the egg/sperm bundles were genotyped to determine whether different genotypes were present. Within the 14 mature colonies, we detected 10 colonies with more than one genotype (intracolonial genetic variability). Four out of these 10 mature colonies showed a transfer of different genotypes via the eggs to the next generation. In two out of these four cases, we found additional alleles, and in the two other cases, we found only a subset of alleles in the unfertilized eggs. Our results suggest that during reproduction of A. hyacinthus, more than one genotype per colony is able to reproduce. We discuss the occurrence of different genotypes within a single coral colony and the ability for those to release eggs which are genetically distinct.

  3. Use of the IRAP marker to study genetic variability in Pseudocercospora fijiensis populations.

    Science.gov (United States)

    de Queiroz, Casley Borges; Santana, Mateus Ferreira; da Silva, Gilvan Ferreira; Mizubuti, Eduardo Seiti Gomide; de Araújo, Elza Fernandes; de Queiroz, Marisa Vieira

    2014-03-01

    Pseudocercospora fijiensis is the etiological agent of black Sigatoka, which is currently considered as one of the most destructive banana diseases in all locations where it occurs. It is estimated that a large portion of the P. fijiensis genome consists of transposable elements, which allows researchers to use transposon-based molecular markers in the analysis of genetic variability in populations of this pathogen. In this context, the inter-retrotransposon-amplified polymorphism (IRAP) was used to study the genetic variability in P. fijiensis populations from different hosts and different geographical origins in Brazil. A total of 22 loci were amplified and 77.3 % showed a polymorphism. Cluster analysis revealed two major groups in Brazil. The observed genetic diversity (H E) was 0.22, and through molecular analysis of variance, it was determined that the greatest genetic variability occurs within populations. The discriminant analysis of principal components revealed no structuring related to the geographical origin of culture of the host. The IRAP-based marker system is a suitable tool for the study of genetic variability in P. fijiensis.

  4. [Detection of genetic variability in Cercospora kikuchii isolates from a single soybean field].

    Science.gov (United States)

    Lurá, M C; Di Conza, J A; González, A M; Latorre Rapela, M G; Turino, L; Ibáñez, M M; Iacona, V

    2007-01-01

    Detection of genetic variability in Cercospora kikuchii isolates from a single soybean field. Current knowledge about epidemiology and population structure of Cercospora kikuchii is little developed and no studies regarding this subject have been reported in Argentina. The aim of this work was to select primers to study genetic variability in C. kikuchii isolated from the same soybean field using RAPD (Random Amplified Polymorphism DNA). RAPD was applied to the DNA of 5 C. kikuchii, isolated from diseased tissue of the soybean in the same field, another isolate, from a strain collection. Out of seven primers, five of them proved to be useful to study the population of C. kikuchii isolates.

  5. Improved Genetic Algorithm with Two-Level Approximation for Truss Optimization by Using Discrete Shape Variables

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    Shen-yan Chen

    2015-01-01

    Full Text Available This paper presents an Improved Genetic Algorithm with Two-Level Approximation (IGATA to minimize truss weight by simultaneously optimizing size, shape, and topology variables. On the basis of a previously presented truss sizing/topology optimization method based on two-level approximation and genetic algorithm (GA, a new method for adding shape variables is presented, in which the nodal positions are corresponding to a set of coordinate lists. A uniform optimization model including size/shape/topology variables is established. First, a first-level approximate problem is constructed to transform the original implicit problem to an explicit problem. To solve this explicit problem which involves size/shape/topology variables, GA is used to optimize individuals which include discrete topology variables and shape variables. When calculating the fitness value of each member in the current generation, a second-level approximation method is used to optimize the continuous size variables. With the introduction of shape variables, the original optimization algorithm was improved in individual coding strategy as well as GA execution techniques. Meanwhile, the update strategy of the first-level approximation problem was also improved. The results of numerical examples show that the proposed method is effective in dealing with the three kinds of design variables simultaneously, and the required computational cost for structural analysis is quite small.

  6. The accumulation of genetic diversity within a canopy-stored seed bank.

    Science.gov (United States)

    Ayre, David; O'Brien, Eleanor; Ottewell, Kym; Whelan, Rob

    2010-07-01

    Many plants regenerate after fire from a canopy-stored seed bank, in which seed are housed in fire resistant confructescences (cones) that remain on maternal plants. This strategy would be favoured if plants accumulate a sufficiently large and genetically diverse seed bank during interfire intervals. We use a 16-year demographic study and surveys of microsatellite variation to quantify and explain the rate of accumulation of genetic diversity within the canopy seed bank of the shrub Banksia spinulosa. Flowering and fruit set were highly variable. An initial sample in 1991 of 354 reproductively mature plants generated 426 cones over 16 years, of which only 55 cones from 40 maternal plants persisted until 2005. By genotyping seed from these 55 cones we demonstrated that genetic diversity accumulated rapidly within the seed bank. Resampling revealed that diversity was determined by the number, not the age, of cones. Cones were widely distributed among plants, outcrossing rates were high (mean t(m) = 1.00 +/- 0.04) and biparental inbreeding low. Adults displayed little evidence of isolation by distance and the genotypic diversity of seed cohorts was independent of the density of neighbouring potential sires. We therefore estimate that within at least 13 individual years the number of cones produced per year (14-63) would have contained 100% of the adult genetic diversity. We conclude that a highly outcrossed mating system and relatively widespread pollen dispersal ensure the rapid development of a genetically diverse and spatially and temporally homogeneous seed bank.

  7. Genetic variability in mitochondrial and nuclear genes of Larus dominicanus (Charadriiformes, Laridae from the Brazilian coast

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    Gisele Pires de Mendonça Dantas

    2012-01-01

    Full Text Available Several phylogeographic studies of seabirds have documented low genetic diversity that has been attributed to bottleneck events or individual capacity for dispersal. Few studies have been done in seabirds on the Brazilian coast and all have shown low genetic differentiation on a wide geographic scale. The Kelp Gull is a common species with a wide distribution in the Southern Hemisphere. In this study, we used mitochondrial and nuclear markers to examine the genetic variability of Kelp Gull populations on the Brazilian coast and compared this variability with that of sub-Antarctic island populations of this species. Kelp Gulls showed extremely low genetic variability for mitochondrial markers (cytb and ATPase and high diversity for a nuclear locus (intron 7 of the β-fibrinogen. The intraspecific evolutionary history of Kelp Gulls showed that the variability found in intron 7 of the β-fibrinogen gene was compatible with the variability expected under neutral evolution but suggested an increase in population size during the last 10,000 years. However, none of the markers revealed evidence of a bottleneck population. These findings indicate that the recent origin of Kelp Gulls is the main explanation for their nuclear diversity, although selective pressure on the mtDNA of this species cannot be discarded.

  8. Genetic variability in mitochondrial and nuclear genes of Larus dominicanus (Charadriiformes, Laridae) from the Brazilian coast

    Science.gov (United States)

    de Mendonça Dantas, Gisele Pires; Meyer, Diogo; Godinho, Raquel; Ferrand, Nuno; Morgante, João Stenghel

    2012-01-01

    Several phylogeographic studies of seabirds have documented low genetic diversity that has been attributed to bottleneck events or individual capacity for dispersal. Few studies have been done in seabirds on the Brazilian coast and all have shown low genetic differentiation on a wide geographic scale. The Kelp Gull is a common species with a wide distribution in the Southern Hemisphere. In this study, we used mitochondrial and nuclear markers to examine the genetic variability of Kelp Gull populations on the Brazilian coast and compared this variability with that of sub-Antarctic island populations of this species. Kelp Gulls showed extremely low genetic variability for mitochondrial markers (cytb and ATPase) and high diversity for a nuclear locus (intron 7 of the β-fibrinogen). The intraspecific evolutionary history of Kelp Gulls showed that the variability found in intron 7 of the β-fibrinogen gene was compatible with the variability expected under neutral evolution but suggested an increase in population size during the last 10,000 years. However, none of the markers revealed evidence of a bottleneck population. These findings indicate that the recent origin of Kelp Gulls is the main explanation for their nuclear diversity, although selective pressure on the mtDNA of this species cannot be discarded. PMID:23271950

  9. Exploring the genetic variability in water use efficiency: Evaluation of inter and intra cultivar genetic diversity in grapevines.

    Science.gov (United States)

    Tortosa, Ignacio; Escalona, José Mariano; Bota, Josefina; Tomás, Magdalena; Hernández, Esther; Escudero, Enrique García; Medrano, Hipólito

    2016-10-01

    Genetic improvement of crop Water Use Efficiency (WUE) is a general goal because the increasing water scarcity and the trend to a more sustainable agriculture. For grapevines, this subject is relevant and need an urgent response because their wide distribution in semi-arid areas. New cultivars are difficult to introduce in viticulture due to the narrow dependency of consumer appreciation often linked to a certain particular wine taste. Clones of reputed cultivars would presumably be more accepted but little is known on the intra-cultivar genetic variability of the WUE. The present work compares, on the basis of two field assays, the variability of intrinsic water use efficiency (WUEi) in a large collection of cultivars in contrast with a collection of clones of Tempranillo cultivar. The results show that clonal variability of WUEi was around 80% of the inter-cultivar, thus providing a first assessment on the opportunity for clonal selection by WUE. Plotting the WUEi data against stem water potential or stomatal conductance it was possible to identify cultivars and clones out of the confidence intervals of this linear regression thus with significantly higher and lower WUEi values. The present results contribute to open the expectative for a genetic improvement of grapevine WUE. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  10. Estimates of genetic variability and association studies in quantitative plant traits of Eruca spp. landraces

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    Bozokalfa Kadri Mehmet

    2010-01-01

    Full Text Available Despite the increasing of economical importance of rocket plant limited information is available on genetic variability for the agronomic traits among Eruca spp. Hence, heritability and association studies of plant properties are necessities for a successful further rocket breeding programme. The objective of this study was to examine phenotypic and genotypic variability, broad sense heritability, genetic advance, genotypic and phenotypic correlation and mean for agronomic traits of rocket plant. The magnitude of phenotypic coefficient of variation values for all the traits were higher than the corresponding values and broad sense heritability estimates exceeded 65% for all traits. Phenotypic coefficients of variability (PCV ranged from 7.60 to 34.34% and genotypic coefficients of variability (GCV ranged between 5.58% for petiole thickness and 34.30% for plant weight. The results stated that plant weight, siliqua width, seed per siliqua and seed weight could be useful character for improved Eruca spp. breeding programme.

  11. Evidence for Outcrossing via the Buller Phenomenon in a Substrate Simultaneously Inoculated with Spores and Mycelium of Agaricus bisporus

    Science.gov (United States)

    Callac, Philippe; Spataro, Cathy; Caille, Aurélie; Imbernon, Micheline

    2006-01-01

    In Agaricus bisporus, traditional cultivars and most of the wild populations belong to A. bisporus var. bisporus, which has a predominantly pseudohomothallic life cycle in which most meiospores are heterokaryons (n + n). A lower proportion of homokaryotic (n) meiospores, which typify the heterothallic life cycle, also are produced. In wild populations, pseudohomothallism was thought previously to play a major role, but recent analyses have found that significant outcrossing also may occur. We inoculated a standard substrate for A. bisporus cultivation simultaneously with homokaryotic mycelium from one parent and spores from a second parent. Culture trays produced numerous sporocarps that could theoretically have resulted from five different reproductive modes (pseudohomothallism, selfing or outcrossing via heterothallism, and selfing or outcrossing via the Buller phenomenon [i.e., between a homokaryon and a heterokaryon]). Most or all of the sporocarps resulted from outcrossing between the inoculated homokaryon and the inoculated heterokaryotic spores (or mycelia that grew from them). These data broaden our understanding of population dynamics under field conditions and provide an outcrossing method that could be used in commercial breeding programs. PMID:16597931

  12. VARIABILITY AND GENETIC STRUCTURE IN A COMMERCIAL FIELD OF TEQUILA PLANTS, Agave tequilana WEBER (AGAVACEAE

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    Martha Isabel Torres-Moran

    2013-01-01

    Full Text Available Crops of the tequila plant (Agave tequilana are produced mainly from offshoots of mother plants in established commercial fields. This propagation method is significant, as it is believed that it facilitates the spread of disease because of the crop’s low genetic variability and is also necessary because it is regulate the use of just that variety in tequila industry. Different levels of genetic variability have been reported for A. tequilana and so we tested individuals from representative cultivation zones to determine the actual variability in fields and to assess the genetic structure of populations in commercial plantations. Four additional Agave spp. were used as a control group while Fourcrea spp. individuals were used as an external group. Morphological traits and molecular markers were analyzed. The differences between A. tequilana individuals collected from southern Jalisco state and those collected in the principal Denomination of Origin zone confirmed the existence of different genotypes, which were conserved in different regions by asexual propagation. Leaf length, plant height and number of leaves were the most significant variables that explained the variability within the A. tequilana group. At the molecular level, we found genetic differentiation with a minimum similarity of 0.253 (Jaccard’s coefficient and genetic structure analysis indicated five groups with significant genotypic differences. Genetic structure analysis, grouped accessions according to the dispersion of plant material from the initial sites of cultivation. These results might facilitate the correlation of different groups with crop yield or tequila quality and the establishment of elite lines for breeding programs. It is recommendable in a future, to determinate the different levels of inulines produced by each detected group.

  13. High levels of genetic differentiation and selfing in the Brazilian cerrado fruit tree Dipteryx alata Vog. (Fabaceae)

    Science.gov (United States)

    2010-01-01

    Dipteryx alata is a native fruit tree species of the cerrado (Brazilian savanna) that has great economic potential because of its multiple uses. Knowledge of how the genetic variability of this species is organized within and among populations would be useful for genetic conservation and breeding programs. We used nine simple sequence repeat (SSR) primers developed for Dipteryx odorata to evaluate the genetic structure of three populations of D. alata located in central Brazil based on a leaf sample analysis from 101 adults. The outcrossing rate was evaluated using 300 open-pollinated offspring from 25 seed-trees. Pollen dispersal was measured by parentage analysis. We used spatial genetic structure (SGS) to test the minimal distance for harvesting seeds in conservation and breeding programs. Our data indicate that the populations studied had a high degree of genetic diversity and population structure, as suggested by the high level of divergence among populations . The estimated outcrossing rate suggested a mixed mating system, and the intrapopulation fixation index was influenced by SGS. We conclude that seed harvesting for genetic conservation and breeding programs requires a minimum distance between trees of 196 m to avoid collecting seeds from related seed-trees. PMID:21637609

  14. High levels of genetic differentiation and selfing in the Brazilian cerrado fruit tree Dipteryx alata Vog. (Fabaceae

    Directory of Open Access Journals (Sweden)

    Roberto Tarazi

    2010-01-01

    Full Text Available Dipteryx alata is a native fruit tree species of the cerrado (Brazilian savanna that has great economic potential because of its multiple uses. Knowledge of how the genetic variability of this species is organized within and among populations would be useful for genetic conservation and breeding programs. We used nine simple sequence repeat (SSR primers developed for Dipteryx odorata to evaluate the genetic structure of three populations of D. alata located in central Brazil based on a leaf sample analysis from 101 adults. The outcrossing rate was evaluated using 300 open-pollinated offspring from 25 seed-trees. Pollen dispersal was measured by parentage analysis. We used spatial genetic structure (SGS to test the minimal distance for harvesting seeds in conservation and breeding programs. Our data indicate that the populations studied had a high degree of genetic diversity and population structure, as suggested by the high level of divergence among populations . The estimated outcrossing rate suggested a mixed mating system, and the intrapopulation fixation index was influenced by SGS. We conclude that seed harvesting for genetic conservation and breeding programs requires a minimum distance between trees of 196 m to avoid collecting seeds from related seed-trees.

  15. Molecular variability and genetic structure of Chrysodeixis includens (Lepidoptera: Noctuidae), an important soybean defoliator in Brazil.

    Science.gov (United States)

    Palma, Janine; Maebe, Kevin; Guedes, Jerson Vanderlei Carús; Smagghe, Guy

    2015-01-01

    This study provides the first genetic characterization of the soybean looper, Chrysodeixis includens (Walker, 1857), an important defoliating pest species of soybean crops in Brazil. Population genetic variability and the genetic structure of C. includens populations were evaluated by using ISSR markers with samples from the major soybean producing regions in Brazil in the growing seasons 2011/2012. Seven different primers were applied for population characterization of the molecular variability and genetic structure of 8 soybean looper populations from 8 states of Brazil. The seven ISSR loci generated 247 bands in 246 individuals of C. includens sampled. The expected heterozygosity (HE) in the populations varied between 0.093 and 0.106, while the overall HE was 0.099, indicating low genetic diversity. The analysis of molecular variance indicated that 98% of the variability was expressed among individuals within populations (FST = 0.021, p = 0.001). The low level of polymorphism over all populations, the high levels of gene flow, and the low genetic structure are indicatives of the exchange of genetic information between the different sampled regions. Population structuring suggests the presence of two major groups which do not correlate with their geographic sampling location in Brazil. These results may indicate recent recolonization of C. includens in Brazil or migration patterns following source-sink dynamics. Furthermore, the presence of two groups within C. includens suggests that a study on development of resistance or any other genetic-based trait needs to be evaluated on both groups, and pest management in soybean fields should be aware that differences may come to the control strategies they use.

  16. Molecular variability and genetic structure of Chrysodeixis includens (Lepidoptera: Noctuidae, an important soybean defoliator in Brazil.

    Directory of Open Access Journals (Sweden)

    Janine Palma

    Full Text Available This study provides the first genetic characterization of the soybean looper, Chrysodeixis includens (Walker, 1857, an important defoliating pest species of soybean crops in Brazil. Population genetic variability and the genetic structure of C. includens populations were evaluated by using ISSR markers with samples from the major soybean producing regions in Brazil in the growing seasons 2011/2012. Seven different primers were applied for population characterization of the molecular variability and genetic structure of 8 soybean looper populations from 8 states of Brazil. The seven ISSR loci generated 247 bands in 246 individuals of C. includens sampled. The expected heterozygosity (HE in the populations varied between 0.093 and 0.106, while the overall HE was 0.099, indicating low genetic diversity. The analysis of molecular variance indicated that 98% of the variability was expressed among individuals within populations (FST = 0.021, p = 0.001. The low level of polymorphism over all populations, the high levels of gene flow, and the low genetic structure are indicatives of the exchange of genetic information between the different sampled regions. Population structuring suggests the presence of two major groups which do not correlate with their geographic sampling location in Brazil. These results may indicate recent recolonization of C. includens in Brazil or migration patterns following source-sink dynamics. Furthermore, the presence of two groups within C. includens suggests that a study on development of resistance or any other genetic-based trait needs to be evaluated on both groups, and pest management in soybean fields should be aware that differences may come to the control strategies they use.

  17. Genetic diversity and the mating system in a fragmented population of Tsoongiodendron odorum

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    Xia Wang

    2012-11-01

    Full Text Available Habitat fragmentation is one of the most serious threats to plant diversity. In general, fragmentation negatively impacts the genetic variability of plant populations due to increased random geneticdrift, inbreeding, and reductions in gene flow. To investigate the effect of habitat fragmentation on genetic diversity and the mating system of Tsoongiodendron odorum, in this study, we analyzed genetic diversity and the mating system in hierarchical levels at the population, stands, and the individual scales in a fragmented T.odorum population. We sampled and mapped 61 adult individuals from the population. Using eight microsatellite loci, we genotyped a total of 780 seeds from 15 maternal trees for the mating system analysis. The results revealed moderate levels of genetic diversity in both adults (HE = 0.522 and seeds (HE = 0.499 with no significant differences between the two ontogenic stages. In addition, we did not observe asignificant increase in the seeds inbreeding coefficient. Results from the multilocus mating system analysis indicated that T. odorum was an outbreeding species with a multilocus outcrossing rate (tm of 1.000. A small number of biparental inbreeding and correlated mating events were detected in this fragmented population. We found a small number of effective pollen donors (Nep is between 3.7 and 5.4, which seems to be a common character of insect-pollinated canopy trees. Minor differences in outcrossing rates were detected among stands, and more pollen donors were found in smaller stands. However, outcrossing rate was significantly different among individuals, and a few selfing events were detected in some seed trees. These results may provide fundamental information required to establish long term conservation strategies for this endangered tree which is endemic to China.

  18. Genetic variability in common wheat germplasm based on coefficients of parentage

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    Fernanda Bered

    2002-01-01

    Full Text Available The characterization of genetic variability and an estimate of the genetic relationship among varieties are essential to any breeding program, because artificial crosses among less similar parents allow a larger segregation and the combination of different favorable alleles. Genetic variability can be evaluated in different ways, including the Coefficient of Parentage (COP, which estimates the probability of two alleles in two different individuals being identical by descent. In this study, we evaluated the degree of genetic relationship among 53 wheat genotypes, and identified the ancestor genotypes which contributed the most to the current wheat germplasm, as a prediction of the width of the genetic base of this cereal. The results revealed a mean COP of 0.07 and the formation of 22 similarity groups. The ancestor genotypes Ciano 67 and Mentana were those which contributed the most to the current wheat germplasm. According to the COP analyses, the genetic base of wheat rests on a small number of ancestral genotypes.

  19. Exome Sequence Analysis Suggests that Genetic Burden Contributes to Phenotypic Variability and Complex Neuropathy

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    Claudia Gonzaga-Jauregui

    2015-08-01

    Full Text Available Charcot-Marie-Tooth (CMT disease is a clinically and genetically heterogeneous distal symmetric polyneuropathy. Whole-exome sequencing (WES of 40 individuals from 37 unrelated families with CMT-like peripheral neuropathy refractory to molecular diagnosis identified apparent causal mutations in ∼45% (17/37 of families. Three candidate disease genes are proposed, supported by a combination of genetic and in vivo studies. Aggregate analysis of mutation data revealed a significantly increased number of rare variants across 58 neuropathy-associated genes in subjects versus controls, confirmed in a second ethnically discrete neuropathy cohort, suggesting that mutation burden potentially contributes to phenotypic variability. Neuropathy genes shown to have highly penetrant Mendelizing variants (HPMVs and implicated by burden in families were shown to interact genetically in a zebrafish assay exacerbating the phenotype established by the suppression of single genes. Our findings suggest that the combinatorial effect of rare variants contributes to disease burden and variable expressivity.

  20. Genetic variability in wild genotypes of Passiflora cincinnata based on RAPD markers.

    Science.gov (United States)

    Cerqueira-Silva, C B M; Conceição, L D H C S; Santos, E S L; Cardoso-Silva, C B; Pereira, A S; Oliveira, A C; Corrêa, R X

    2010-12-21

    The genetic diversity and characteristics of commercial interest of Passiflora species make it useful to characterize wild germplasm, because of their potential use for fruit, ornamental and medicinal purposes. We evaluated genetic diversity, using RAPD markers, of 32 genotypes of Passiflora cincinnata collected from the wild in the region of Vitória da Conquista, Bahia, Brazil. Thirteen primers generated 95 polymorphic markers and only one monomorphic marker. The mean genetic distance between the genotypes estimated by the complement of the Dice index was 0.51 (ranging from 0.20-0.85), and genotype grouping based on the UPGMA algorithm showed wide variability among the genotypes. This type of information contributes to identification and conservation of the biodiversity of this species and for the identification of pairs of divergent individuals for maximum exploitation of existing variability.

  1. Genetic variability in progenies of Eucalyptus dunnii Maiden for resistance to Puccinia psidii

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    Cleber da Silva Pinto

    2014-10-01

    Full Text Available This study investigated the genetic variability in progenies of Eucalyptus dunnii Maiden for resistance against rust (Puccinia psidii. Field experiments were installed in two regions with different soil-climatic conditions. Open-pollinated progenies were established in a randomized complete block design. Sixty and 48 progenies were evaluated under field conditions at two sites, respectively, with six replications and eight trees per plot. In another experiment in a controlled environment, 53 progenies were evaluated in randomized blocks with six replications and nine plants per plot. The following traits were evaluated: plant height, severity of pest attack and the most susceptible stage to the leaf disease. The genetic variability for rust resistance in the E. dunnii population under study was high, with a genetic coefficient of variation of 36.07%; 7% of the evaluated progenies were rust-resistant. It indicates a high potential for selection and breeding of the species.

  2. Exome sequence analysis suggests genetic burden contributes to phenotypic variability and complex neuropathy

    Science.gov (United States)

    Gonzaga-Jauregui, Claudia; Harel, Tamar; Gambin, Tomasz; Kousi, Maria; Griffin, Laurie B.; Francescatto, Ludmila; Ozes, Burcak; Karaca, Ender; Jhangiani, Shalini; Bainbridge, Matthew N.; Lawson, Kim S.; Pehlivan, Davut; Okamoto, Yuji; Withers, Marjorie; Mancias, Pedro; Slavotinek, Anne; Reitnauer, Pamela J; Goksungur, Meryem T.; Shy, Michael; Crawford, Thomas O.; Koenig, Michel; Willer, Jason; Flores, Brittany N.; Pediaditrakis, Igor; Us, Onder; Wiszniewski, Wojciech; Parman, Yesim; Antonellis, Anthony; Muzny, Donna M.; Katsanis, Nicholas; Battaloglu, Esra; Boerwinkle, Eric; Gibbs, Richard A.; Lupski, James R.

    2015-01-01

    Charcot-Marie-Tooth (CMT) disease is a clinically and genetically heterogeneous distal symmetric polyneuropathy. Whole-exome sequencing (WES) of 40 individuals from 37 unrelated families with CMT-like peripheral neuropathy refractory to molecular diagnosis identified apparent causal mutations in ~45% (17/37) of families. Three candidate disease genes are proposed, supported by a combination of genetic and in vivo studies. Aggregate analysis of mutation data revealed a significantly increased number of rare variants across 58 neuropathy associated genes in subjects versus controls; confirmed in a second ethnically discrete neuropathy cohort, suggesting mutation burden potentially contributes to phenotypic variability. Neuropathy genes shown to have highly penetrant Mendelizing variants (HMPVs) and implicated by burden in families were shown to interact genetically in a zebrafish assay exacerbating the phenotype established by the suppression of single genes. Our findings suggest that the combinatorial effect of rare variants contributes to disease burden and variable expressivity. PMID:26257172

  3. Gene flow in genetically engineered perennial grasses: Lessons for modification of dedicated bioenergy crops

    Science.gov (United States)

    The potential ecological consequences of the commercialization of genetically engineered (GD) crops have been the subject of intense debate, particularly when the GE crops are perennial and capable of outcrossing to wild relatives. The essential ecological impact issues for engi...

  4. Genetic variability and evolutionary dynamics of viruses of the family Closteroviridae

    Directory of Open Access Journals (Sweden)

    Luis eRubio

    2013-06-01

    Full Text Available RNA viruses have a great potential for genetic variation, rapid evolution and adaptation. Characterization of the genetic variation of viral populations provides relevant information on the processes involved in virus evolution and epidemiology and it is crucial for designing reliable diagnostic tools and developing efficient and durable disease control strategies. Here we performed an updated analysis of sequences available in Genbank and reviewed present knowledge on the genetic variability and evolutionary processes of viruses of the family Closteroviridae. Several factors have shaped the genetic structure and diversity of closteroviruses. I A strong negative selection seems to be responsible for the high genetic stability in space and time for some viruses. II Long distance migration, probably by human transport of infected propagative plant material, have caused that genetically similar virus isolates are found in distant geographical regions. III Recombination between divergent sequence variants have generated new genotypes and plays an important role for the evolution of some viruses of the family Closteroviridae. IV Interaction between virus strains or between different viruses in mixed infections may alter accumulation of certain strains. V Host change or virus transmission by insect vectors induced changes in the viral population structure due to positive selection of sequence variants with higher fitness for host-virus or vector-virus interaction (adaptation or by genetic drift due to random selection of sequence variants during the population bottleneck associated to the transmission process.

  5. Genetic analysis of Phytophthora infestans populations in the Nordic European countries reveals high genetic variability

    DEFF Research Database (Denmark)

    Brurberg, May Bente; Elameen, Abdelhameed; Le, Ving Hong

    2011-01-01

    Late blight, caused by the oomycete Phytophthora infestans, is the most important disease of potato (Solanum tuberosum). The pathogen is highly adaptable and to get an overview of the genetic variation in the Nordic countries, Denmark, Finland, Norway and Sweden we have analyzed 200 isolates from...... different fields using nine simple-sequence repeat (SSR) markers. Forty-nine alleles were detected among the nine SSR loci and isolates from all four Nordic countries shared the most common alleles across the loci. In total 169 multilocus genotypes (based on seven loci) were identified among 191 isolates....... The genotypic diversities, quantified by a normalized Shannon’s diversity index (Hs), were 0.95 for the four Nordic countries. The low FST value of 0.04 indicates that the majority of variation is found within the four Nordic countries. The large number of genotypes and the frequency distribution of mating...

  6. Multi-taxa integrated landscape genetics for zoonotic infectious diseases: deciphering variables influencing disease emergence.

    Science.gov (United States)

    Leo, Sarah S T; Gonzalez, Andrew; Millien, Virginie

    2016-05-01

    Zoonotic disease transmission systems involve sets of species interacting with each other and their environment. This complexity impedes development of disease monitoring and control programs that require reliable identification of spatial and biotic variables and mechanisms facilitating disease emergence. To overcome this difficulty, we propose a framework that simultaneously examines all species involved in disease emergence by integrating concepts and methods from population genetics, landscape ecology, and spatial statistics. Multi-taxa integrated landscape genetics (MTILG) can reveal how interspecific interactions and landscape variables influence disease emergence patterns. We test the potential of our MTILG-based framework by modelling the emergence of a disease system across multiple species dispersal, interspecific interaction, and landscape scenarios. Our simulations showed that both interspecific-dependent dispersal patterns and landscape characteristics significantly influenced disease spread. Using our framework, we were able to detect statistically similar inter-population genetic differences and highly correlated spatial genetic patterns that imply species-dependent dispersal. Additionally, species that were assigned coupled-dispersal patterns were affected to the same degree by similar landscape variables. This study underlines the importance of an integrated approach to investigating emergence of disease systems. MTILG is a robust approach for such studies and can identify potential avenues for targeted disease management strategies.

  7. Intra and inter populational genetic variability in Maytenus ilicifolia Mart. ex Reiss. 1861, through RAPD markers

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    AJ. Mossi

    Full Text Available Maytenus ilicifolia is a medicinal plant largely used in the South Brazilian folk medicine. The aim of this study was to quantify the intra and inter populational genetic variability in three populations of M. ilicifolia, focusing on the genetic conservation of this species, which has been threatened by anthropic action. RAPD (Random Amplified Polymorphic DNA markers were used to analyze 30 plants of each of the three populations collected in the Alto Uruguai Gaúcho region. Fourteen selected primers generated a total of 158 bands, 71.5% of which were polymorphic. The comparison of Jaccard’s distances showed that the intra populational variation was higher than the inter populational variability, and cluster analysis allowed the separation of the three populations. Just 7.6% of the bands were specific of at least two populations. Data indicate that the analyzed M. ilicifolia populations represent a single genetic pool, and therefore any of the population thoroughly can represent the overall genetic variability of the species in the sampled region.

  8. Genetic variability in Bracco Italiano dog breed assessed by pedigree data

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    Francesca Cecchi

    2013-07-01

    Full Text Available The Bracco Italiano is one of the oldest pointing dog breed, used for hunting ever since the Renaissance time. The complete electronic record of the breed was downloaded from the ENCI database [whole population (WP = 24,613 animals registered since 1970 to 2011] with the aim to estimate genetic variability in Bracco Italiano dog breed using pedigree records. Up to 97% of the individuals had registered parents and 86% registered grand-fathers. Average generation interval was 4.68±0.545 for stallions and 4.08±0.321 year for dams. Reference population (RP was defined as the population of interest that include living reproductive animals approaching the last three generations and include 9006 dogs of which 34% were inbreds. The number of ancestors was 564 in WP and 188 in RP, while the effective number of ancestors was 46 and 34 respectively. To explain 50% of the genetic variability, a total of 18 and 9 ancestors enough, respectively in the WP and RP. The average inbreeding coefficient in the RP resulted 6.7% while the average increase in inbreeding was estimated to be 1.29% (Ne=38.86. Nevertheless a regular monitoring of genetic variability of the population is important and must be adopted, in order to avoid the danger of an excessive increase of inbreeding in the future, which would result in significant inbreeding depression and in significant loss of genetic variation.

  9. Genetic Variability and Microdistribution of Triatoma infestans Genotypes and Trypanosoma cruzi Clones in Arequipa Region (Peru

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    Brenière Simone F

    1997-01-01

    Full Text Available The genetic variability of Triatoma infestans and Trypanosoma cruzi populations was studied by isoenzyme analysis in two distinct areas of Arequipa province (Peru; one, Santa Rita de Siguas, being an endemic area for Chagas' disease, the second, Arequipa, recently infected. Analysis of T. infestans genetic variability indicates, (i temporal stability of genotypes found in Santa Rita de Siguas, (ii high genetic differences between Arequipa and Santa Rita de Siguas populations suggesting minor contact between them, (iii multiple origin of the T. infestans population in Arequipa, and (iv poor dispersal capacity of T. infestans: the panmictic unit could be reduce to a house. Parasite isoenzyme analysis was performed in 29 Peruvian stocks of T. cruzi, mainly isolated from bugs taken in a single locality, Santa Rita de Siguas. The results show, (i a high genetic polymorphism, (ii nine different multilocus genotypes were detected and clustered in two different clades, (iii most of the parasite isolates pertained to one of the clade and were genetically similar to those analyzed 12 years before. This sample allowed the study of the mating system of T. cruzi in strict sympatic conditions and gave more strength to the hypothesis of the clonal structure of T. cruzi populations

  10. Genetic variability and microdistribution of Triatoma infestans genotypes and Trypanosoma cruzi clones in Arequipa region (Peru).

    Science.gov (United States)

    Brenière, S F; Lopez, J; Vargas, F; Barnabé, C

    1997-01-01

    The genetic variability of Triatoma infestans and Trypanosoma cruzi populations was studied by isoenzyme analysis in two distinct areas of Arequipa province (Peru); one, Santa Rita de Siguas, being an endemic area for Chagas' disease, the second, Arequipa, recently infected. Analysis of T. infestans genetic variability indicates, (i) temporal stability of genotypes found in Santa Rita de Siguas, (ii) high genetic differences between Arequipa and Santa Rita de Siguas populations suggesting minor contact between them, (iii) multiple origin of the T. infestans population in Arequipa, and (iv) poor dispersal capacity of T. infestans: the panmictic unit could be reduce to a house. Parasite isoenzyme analysis was performed in 29 Peruvian stocks of T. cruzi, mainly isolated from bugs taken in a single locality, Santa Rita de Siguas. The results show, (i) a high genetic polymorphism, (ii) nine different multilocus genotypes were detected and clustered in two different clades, (iii) most of the parasite isolates pertained to one of the clade and were genetically similar to those analyzed 12 years before. This sample allowed the study of the mating system of T. cruzi in strict sympathic conditions and gave more strength to the hypothesis of the clonal structure of T. cruzi populations.

  11. Loss of genetic variability induced by Agroecosystems: Chrysoperla externa (Hagen) (Neuroptera: Chrysopidae) as a case study.

    Science.gov (United States)

    Morales, A C; Lavagnini, T C; Freitas, S

    2013-02-01

    Four species of green lacewings occur in Brazil, of which Chrysoperla externa (Hagen) (Neuroptera: Chrysopidae) exhibits the widest geographical distribution. Chrysoperla externa is a predatory insect that is potentially useful as a biological control agent of agricultural pests. Studies on the genetic diversity of lacewing populations are essential to reduce the environmental and economic harm that may be caused by organisms with a low ability to adapt to the adverse and/or different environmental conditions to which they are exposed. We used the cytochrome oxidase I mitochondrial gene as a molecular marker to investigate the genetic diversity of green lacewing species collected from native and agroecosystem environments. Populations derived from native areas showed higher rates of genetic variability compared to populations from agroecosystems. Demographic changes in the form of population expansion were observed in agroecosystems, whereas populations in the native environment appeared stable over time. A statistical analysis showed significant genetic structure between each of the sampled groups, combined with its complete absence within each group, corroborating each group's identity. We infer that the loss of variability exhibited by populations from the agroecosystems is the result of genetic drift by means of the founder effect, a similar effect that has been observed in other introduced populations. Agroecosystems might therefore function as exotic areas for green lacewings, even when these areas are within the normal range of the species.

  12. Degree of intraspecific genetic divergence and variability in three Sciaenid species

    Digital Repository Service at National Institute of Oceanography (India)

    Menezes, M.R.; Taniguchi, N.; Seki, S.

    stream_size 31514 stream_content_type text/plain stream_name Jap_J_Ichthyol_37_39.pdf.txt stream_source_info Jap_J_Ichthyol_37_39.pdf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 Japan.,." Journal...(Cultural Fisheries, Faculty of Agriculture, Kocbi University, Nankoku 7&3, Japan Abstrllct Genetic variations in Nibea mitsukurii, N. albijfora and Pennahia argentara from different localities were assayed electrophoretically. The genetic variability in N. mirsukurii...

  13. Genetics and Forest Seed Handling

    DEFF Research Database (Denmark)

    Schmidt, Lars Holger

    2016-01-01

    High genetic quality seed is obtained from seed sources that match the planting site, have a good outcrossing rate, and are superior in some desirable characters. Non-degraded natural forests and plantations may be used as untested seed sources, which can sometimes be managed to promote outbreedi...

  14. Genetics of Forest Seed Handling

    DEFF Research Database (Denmark)

    Schmidt, Lars Holger

    2016-01-01

    High genetic quality seed is obtained from seed sources that match the planting site, have a good outcrossing rate, and are superior in some desirable characters. Non-degraded natural forests and plantations may be used as untested seed sources, which can sometimes be managed to promote outbreeding...

  15. Genetic variability and population structure of the mushroom Pleurotus eryngii var. tuoliensis.

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    Mengran Zhao

    Full Text Available The genetic diversity of 123 wild strains of Pleurotus eryngii var. tuoliensis, which were collected from nine geographical locations in Yumin, Tuoli, and Qinghe counties in the Xinjiang Autonomous Region of China, was analysed using two molecular marker systems (inter-simple sequence repeat and start codon targeted. At the variety level, the percentage of polymorphic loci and Nei's gene diversity index for P. eryngii var. tuoliensis was 96.32% and 0.238, respectively. At the population level, Nei's gene diversity index ranged from 0.149 to 0.218 with an average of 0.186, and Shannon's information index ranged from 0.213 to 0.339 with an average of 0.284. These results revealed the abundant genetic variability in the wild resources of P. eryngii var. tuoliensis. Nei's gene diversity analysis indicated that the genetic variance was mainly found within individual geographical populations, and the analysis of molecular variance revealed low but significant genetic differentiation among local and regional populations. The limited gene flow (Nm = 1.794 was inferred as a major reason for the extent of genetic differentiation of P. eryngii var. tuoliensis. The results of Mantel tests showed that the genetic distance among geographical populations of P. eryngii var. tuoliensis was positively correlated with the geographical distance and the longitudinal distances (rGo = 0.789 and rLn = 0.873, respectively, which indicates that geographical isolation is an important factor for the observed genetic differentiation. Nine geographical populations of P. eryngii var. tuoliensis were divided into three groups according to their geographical origins, which revealed that the genetic diversity was closely related to the geographical distribution of this wild fungus.

  16. Genetic Variability Overrides the Impact of Parental Cell Type and Determines iPSC Differentiation Potential

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    Aija Kyttälä

    2016-02-01

    Full Text Available Reports on the retention of somatic cell memory in induced pluripotent stem cells (iPSCs have complicated the selection of the optimal cell type for the generation of iPSC biobanks. To address this issue we compared transcriptomic, epigenetic, and differentiation propensities of genetically matched human iPSCs derived from fibroblasts and blood, two tissues of the most practical relevance for biobanking. Our results show that iPSC lines derived from the same donor are highly similar to each other. However, genetic variation imparts a donor-specific expression and methylation profile in reprogrammed cells that leads to variable functional capacities of iPSC lines. Our results suggest that integration-free, bona fide iPSC lines from fibroblasts and blood can be combined in repositories to form biobanks. Due to the impact of genetic variation on iPSC differentiation, biobanks should contain cells from large numbers of donors.

  17. Genetic variability of two populations of Pseudoplatystoma reticulatum from the Upper Paraguay River Basin

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    Marcia Matos de Abreu

    2009-01-01

    Full Text Available Catfishes of the genus Pseudoplatystoma are very important species due to both their high commercial value and their ecological role as voracious predators. They undertake lengthy migratory movements during their life-cycle, this including reproductive migration which occurs from October to December in the rainy season. In the present study, seven microsatellite loci were analyzed to access genetic variability in two samples of P. reticulatum from the Upper Paraguay Basin. The loci were highly polymorphic (mean = 7.28. According to all analysis, the two samples of P. reticulatum revealed pronounced genetic differentiation. Fst value was 0.2290, Rst value 0.1067 and AMOVA 22.90% (Fst and 10.67% (Rst, all being highly significant (p < 0.001. The division of the fishes into two groups was confirmed by microsatellite multi-locus Bayesian assignment testing. The results obtained present evidence of genetic structuring in a P. reticulatum population.

  18. Genetic Polymorphism of Aedes albopictus Population Inferred From ND5 Gene Variabilities In Subang Jaya, Malaysia.

    Science.gov (United States)

    Adilah-Amrannudin, Nurul; Hamsidi, Mayamin; Ismail, Nurul-Ain; Ismail, Rodziah; Dom, Nazri Che; Ahmad, Abu Hassan; Mastuki, Mohd Fahmi; Basri, Tengku Shahrul Anuar Tengku Ahmad; Khalid, Adira; Muslim, Mohammad; Daud, Nurul Amalina Ahmad; Camalxaman, Siti Nazrina

    2016-12-01

    This study was performed to establish the genetic variability of Aedes albopictus within Subang Jaya, Selangor, Malaysia, by using the nicotinamide adenine dinucleotide dehydrogenase 5 subunit (ND5) mitochondrial DNA (mtDNA) marker. A total of 90 samples were collected from 9 localities within an area of the Subang Jaya Municipality. Genetic variability was determined through the amplification and sequencing of a fragment of the ND5 gene. Eight distinct mtDNA haplotypes were identified. The evolutionary relationship of the local haplotypes alongside 28 reference strains was used to construct a phylogram, the analysis of which revealed low genetic differentiation in terms of both nucleotide and haplotype diversity. Bayesian method was used to infer the phylogenetic tree, revealing a unique relationship between local isolates. The study corroborates the reliability of ND5 to identify distinct lineages for polymorphism-based studies and supplements the existing body of knowledge regarding its genetic diversity. This in turn could potentially aid existing vector control strategies to help mitigate the risk and spread of the dengue virus.

  19. Genetic variability of Echinococcus granulosus based on the mitochondrial 16S ribosomal RNA gene.

    Science.gov (United States)

    Wang, Ning; Wang, Jiahai; Hu, Dandan; Zhong, Xiuqin; Jiang, Zhongrong; Yang, Aiguo; Deng, Shijin; Guo, Li; Tsering, Dawa; Wang, Shuxian; Gu, Xiaobin; Peng, Xuerong; Yang, Guangyou

    2015-06-01

    Echinococcus granulosus is the etiological agent of cystic echinococcosis, a major zoonotic disease of both humans and animals. In this study, we assessed genetic variability and genetic structure of E. granulosus in the Tibet plateau, using the complete mitochondrial 16 S ribosomal RNA gene for the first time. We collected and sequenced 62 isolates of E. granulosus from 3 populations in the Tibet plateau. A BLAST analysis indicated that 61 isolates belonged to E. granulosus sensu stricto (genotypes G1-G3), while one isolate belonged to E. canadensis (genotype G6). We detected 16 haplotypes with a haplotype network revealing a star-like expansion, with the most common haplotype occupying the center of the network. Haplotype diversity and nucleotide diversity were low, while negative values were observed for Tajima's D and Fu's Fs. AMOVA results and Fst values revealed that the three geographic populations were not genetically differentiated. Our results suggest that a population bottleneck or population expansion has occurred in the past, and that this explains the low genetic variability of E. granulosus in the Tibet Plateau.

  20. Genetic variability and homozygosity in a F4 castor bean population by microsatellite markers

    Directory of Open Access Journals (Sweden)

    Edna Lobo Machado

    2016-01-01

    Full Text Available ABSTRACT The objectives of this study were to identify the genetic variability and estimate the level of homozygosity in a castor bean F4 population using microsatellite markers (SSR. To this end, it was performed the genotyping of the population through 53 pairs of SSR primers. Allele frequencies were estimated by number of alleles per locus, expected heterozygosity (He, observed heterozygosity (Ho and polymorphic information content (PIC. An array of genetic dissimilarity was generated by Nei and Li index, and hierarchical cluster analysis was performed using the Unweighted Pair-Group Method Averages (UPGMA method. Polymorphism was detected in a total of eight loci (15.09% of the 53 evaluated, with the presence of two alleles per locus. Allele frequencies varied between 0.71 and 0.53, and the PIC, between 0.32 and 0.37. The average observed heterozygosity Ho (0.30 was lower than the expected heterozygosity He (0.47. Five dissimilar groups were formed, showing that there is genetic variability among the evaluated genotypes. The highest genetic dissimilarity was 0.708 and the lowest, 0.00. The percentages of homozygous genotypes varied from 25 to 75%. These results show that controlled selfing in castor bean raises the level of homozygosity, important for the breeding program.

  1. Genetic and environmental influences on blood pressure variability: a study in twins.

    Science.gov (United States)

    Xu, Xiaojing; Ding, Xiuhua; Zhang, Xinyan; Su, Shaoyong; Treiber, Frank A; Vlietinck, Robert; Fagard, Robert; Derom, Catherine; Gielen, Marij; Loos, Ruth J F; Snieder, Harold; Wang, Xiaoling

    2013-04-01

    Blood pressure variability (BPV) and its reduction in response to antihypertensive treatment are predictors of clinical outcomes; however, little is known about its heritability. In this study, we examined the relative influence of genetic and environmental sources of variance of BPV and the extent to which it may depend on race or sex in young twins. Twins were enrolled from two studies. One study included 703 white twins (308 pairs and 87 singletons) aged 18-34 years, whereas another study included 242 white twins (108 pairs and 26 singletons) and 188 black twins (79 pairs and 30 singletons) aged 12-30 years. BPV was calculated from 24-h ambulatory blood pressure recording. Twin modeling showed similar results in the separate analysis in both twin studies and in the meta-analysis. Familial aggregation was identified for SBP variability (SBPV) and DBP variability (DBPV) with genetic factors and common environmental factors together accounting for 18-40% and 23-31% of the total variance of SBPV and DBPV, respectively. Unique environmental factors were the largest contributor explaining up to 82-77% of the total variance of SBPV and DBPV. No sex or race difference in BPV variance components was observed. The results remained the same after adjustment for 24-h blood pressure levels. The variance in BPV is predominantly determined by unique environment in youth and young adults, although familial aggregation due to additive genetic and/or common environment influences was also identified explaining about 25% of the variance in BPV.

  2. Genetic variability of rice recurrent selection populations as affected by male sterility or manual recombination

    Directory of Open Access Journals (Sweden)

    Letícia da Silveira Pinheiro

    2012-06-01

    Full Text Available The objective of this work was to determine the effect of male sterility or manual recombination on genetic variability of rice recurrent selection populations. The populations CNA-IRAT 4, with a gene for male sterility, and CNA 12, which was manually recombined, were evaluated. Genetic variability among selection cycles was estimated using14 simple sequence repeat (SSR markers. A total of 926 plants were analyzed, including ten genitors and 180 individuals from each of the evaluated cycles (1, 2 and 5 of the population CNA-IRAT 4, and 16 genitors and 180 individuals from each of the cycles (1 and 2 of CNA 12. The analysis allowed the identification of alleles not present among the genitors for both populations, in all cycles, especially for the CNA-IRAT 4 population. These alleles resulted from unwanted fertilization with genotypes that were not originally part of the populations. The parameters of Wright's F-statistic (F IS and F IT indicated that the manual recombination expands the genetic variability of the CNA 12 population, whereas male sterility reduces the one of CNA-IRAT 4.

  3. [Environmental and genetic variables related with alterations in language acquisition in early childhood].

    Science.gov (United States)

    Moriano-Gutierrez, A; Colomer-Revuelta, J; Sanjuan, J; Carot-Sierra, J M

    2017-01-01

    A great deal of research has addressed problems in the correct acquisition of language, but with few overall conclusions. The reasons for this lie in the individual variability, the existence of different measures for assessing language and the fact that a complex network of genetic and environmental factors are involved in its development. To review the environmental and genetic variables that have been studied to date, in order to gain a better under-standing of the causes of specific language impairment and create new evidence that can help in the development of screening systems for the early detection of these disorders. The environmental variables related with poorer early child language development include male gender, low level of education of the mother, familial history of problems with language or psychiatric problems, perinatal problems and health problems in early childhood. Bilingualism seems to be a protective factor. Temperament and language are related. Within the genetic factors there are several specific genes associated with language, two of which have a greater influence on its physiological acquisition: FOXP2 and CNTNAP2. The other genes that are most related with specific language disorders are ATP2C2, CMIP, ROBO2, ZNF277 and NOP9. The key to comprehending the development of specific language disorders lies in reaching an understanding of the true role played by genes in the ontogenesis, in the regulation of the different developmental processes, and how this role is modulated by the environment.

  4. Do clones degenerate over time? Explaining the genetic variability of asexuals through population genetic models

    Directory of Open Access Journals (Sweden)

    Drozd Pavel

    2011-03-01

    Full Text Available Abstract Background Quest for understanding the nature of mechanisms governing the life span of clonal organisms lasts for several decades. Phylogenetic evidence for recent origins of most clones is usually interpreted as proof that clones suffer from gradual age-dependent fitness decay (e.g. Muller's ratchet. However, we have shown that a neutral drift can also qualitatively explain the observed distribution of clonal ages. This finding was followed by several attempts to distinguish the effects of neutral and non-neutral processes. Most recently, Neiman et al. 2009 (Ann N Y Acad Sci.:1168:185-200. reviewed the distribution of asexual lineage ages estimated from a diverse array of taxa and concluded that neutral processes alone may not explain the observed data. Moreover, the authors inferred that similar types of mechanisms determine maximum asexual lineage ages in all asexual taxa. In this paper we review recent methods for distinguishing the effects of neutral and non-neutral processes and point at methodological problems related with them. Results and Discussion We found that contemporary analyses based on phylogenetic data are inadequate to provide any clear-cut answer about the nature and generality of processes affecting evolution of clones. As an alternative approach, we demonstrate that sequence variability in asexual populations is suitable to detect age-dependent selection against clonal lineages. We found that asexual taxa with relatively old clonal lineages are characterised by progressively stronger deviations from neutrality. Conclusions Our results demonstrate that some type of age-dependent selection against clones is generally operational in asexual animals, which cover a wide taxonomic range spanning from flatworms to vertebrates. However, we also found a notable difference between the data distribution predicted by available models of sequence evolution and those observed in empirical data. These findings point at the

  5. Genetic variability of Amorphophallus muelleri Blume in Java based on Random Amplified Polymorphic DNA

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    DIYAH MARTANTI

    2008-10-01

    Full Text Available Amorphophallus muelleri Blume (Araceae is valued for its glucomanan content for use in food industry (healthy diet food, paper industry, pharmacy and cosmetics. The species is triploid (2n=3x=39 and the seed is developed apomictically. The present research is aimed to identify genetic variability of six population of A. muelleri from Java (consisted of 50 accessions using random amplified polymorphic DNA (RAPD. The six populations of the species are: East Java: (1 Silo-Jember, (2 Saradan-Madiun, (3 IPB (cultivated, from Saradan-Madiun, (4 Panti-Jember, (5 Probolinggo; and Central Java: (6 Cilacap. The results showed that five RAPD primers generated 42 scorable bands of which 29 (69.05% were polymorphic. Size of the bands varied from 300bp to 1.5kbp. The 50 accessions of A. muelleri were divided into two main clusters, some of them were grouped based on their populations, and some others were not. The range of individual genetic dissimilarity was from 0.02 to 0.36. The results showed that among six populations investigated, Saradan population showed the highest levels of genetic variation with mean values of na = 1.500+ 0.5061, ne = 1.3174 + 0.3841, PLP = 50% and He = 0, 0.1832+0.2054, whereas Silo-Jember population showed the lowest levels of genetic variation with mean values na = 1.2619+ 0.4450, ne = 1.1890 + 0.3507, PLP = 26.19% and He = 0.1048+0.1887. Efforts to conserve, domesticate, cultivate and improve genetically should be based on the genetic properties of each population and individual within population, especially Saradan population which has the highest levels of genetic variation, need more attention for its conservation.

  6. Identifying genetic variants for heart rate variability in the acetylcholine pathway.

    Directory of Open Access Journals (Sweden)

    Harriëtte Riese

    Full Text Available Heart rate variability is an important risk factor for cardiovascular disease and all-cause mortality. The acetylcholine pathway plays a key role in explaining heart rate variability in humans. We assessed whether 443 genotyped and imputed common genetic variants in eight key genes (CHAT, SLC18A3, SLC5A7, CHRNB4, CHRNA3, CHRNA, CHRM2 and ACHE of the acetylcholine pathway were associated with variation in an established measure of heart rate variability reflecting parasympathetic control of the heart rhythm, the root mean square of successive differences (RMSSD of normal RR intervals. The association was studied in a two stage design in individuals of European descent. First, analyses were performed in a discovery sample of four cohorts (n = 3429, discovery stage. Second, findings were replicated in three independent cohorts (n = 3311, replication stage, and finally the two stages were combined in a meta-analysis (n = 6740. RMSSD data were obtained under resting conditions. After correction for multiple testing, none of the SNPs showed an association with RMSSD. In conclusion, no common genetic variants for heart rate variability were identified in the largest and most comprehensive candidate gene study on the acetylcholine pathway to date. Future gene finding efforts for RMSSD may want to focus on hypothesis free approaches such as the genome-wide association study.

  7. Identifying Genetic Variants for Heart Rate Variability in the Acetylcholine Pathway

    Science.gov (United States)

    Riese, Harriëtte; Muñoz, Loretto M.; Hartman, Catharina A.; Ding, Xiuhua; Su, Shaoyong; Oldehinkel, Albertine J.; van Roon, Arie M.; van der Most, Peter J.; Lefrandt, Joop; Gansevoort, Ron T.; van der Harst, Pim; Verweij, Niek; Licht, Carmilla M. M.; Boomsma, Dorret I.; Hottenga, Jouke-Jan; Willemsen, Gonneke; Penninx, Brenda W. J. H.; Nolte, Ilja M.; de Geus, Eco J. C.; Wang, Xiaoling; Snieder, Harold

    2014-01-01

    Heart rate variability is an important risk factor for cardiovascular disease and all-cause mortality. The acetylcholine pathway plays a key role in explaining heart rate variability in humans. We assessed whether 443 genotyped and imputed common genetic variants in eight key genes (CHAT, SLC18A3, SLC5A7, CHRNB4, CHRNA3, CHRNA, CHRM2 and ACHE) of the acetylcholine pathway were associated with variation in an established measure of heart rate variability reflecting parasympathetic control of the heart rhythm, the root mean square of successive differences (RMSSD) of normal RR intervals. The association was studied in a two stage design in individuals of European descent. First, analyses were performed in a discovery sample of four cohorts (n = 3429, discovery stage). Second, findings were replicated in three independent cohorts (n = 3311, replication stage), and finally the two stages were combined in a meta-analysis (n = 6740). RMSSD data were obtained under resting conditions. After correction for multiple testing, none of the SNPs showed an association with RMSSD. In conclusion, no common genetic variants for heart rate variability were identified in the largest and most comprehensive candidate gene study on the acetylcholine pathway to date. Future gene finding efforts for RMSSD may want to focus on hypothesis free approaches such as the genome-wide association study. PMID:25384021

  8. Genetic variability of Echinococcus granulosus from the Tibetan plateau inferred by mitochondrial DNA sequences.

    Science.gov (United States)

    Yan, Ning; Nie, Hua-Ming; Jiang, Zhong-Rong; Yang, Ai-Guo; Deng, Shi-Jin; Guo, Li; Yu, Hua; Yan, Yu-Bao; Tsering, Dawa; Kong, Wei-Shu; Wang, Ning; Wang, Jia-Hai; Xie, Yue; Fu, Yan; Yang, De-Ying; Wang, Shu-Xian; Gu, Xiao-Bin; Peng, Xue-Rong; Yang, Guang-You

    2013-09-01

    To analyse genetic variability and population structure, 84 isolates of Echinococcus granulosus (Cestoda: Taeniidae) collected from various host species at different sites of the Tibetan plateau in China were sequenced for the whole mitochondrial nad1 (894 bp) and atp6 (513 bp) genes. The vast majority were classified as G1 genotype (n=82), and two samples from human patients in Sichuan province were identified as G3 genotype. Based on the concatenated sequences of nad1+atp6, 28 different haplotypes (NA1-NA28) were identified. A parsimonious network of the concatenated sequence haplotypes showed star-like features in the overall population, with NA1 as the major haplotype in the population networks. By AMOVA it was shown that variation of E. granulosus within the overall population was the main pattern of the total genetic variability. Neutrality indexes of the concatenated sequence (nad1+atp6) were computed by Tajima's D and Fu's Fs tests and showed high negative values for E. granulosus, indicating significant deviations from neutrality. FST and Nm values suggested that the populations were not genetically differentiated.

  9. Epigenetic variability in the genetically uniform forest tree species Pinus pinea L.

    Science.gov (United States)

    Sáez-Laguna, Enrique; Guevara, María-Ángeles; Díaz, Luis-Manuel; Sánchez-Gómez, David; Collada, Carmen; Aranda, Ismael; Cervera, María-Teresa

    2014-01-01

    There is an increasing interest in understanding the role of epigenetic variability in forest species and how it may contribute to their rapid adaptation to changing environments. In this study we have conducted a genome-wide analysis of cytosine methylation pattern in Pinus pinea, a species characterized by very low levels of genetic variation and a remarkable degree of phenotypic plasticity. DNA methylation profiles of different vegetatively propagated trees from representative natural Spanish populations of P. pinea were analyzed with the Methylation Sensitive Amplified Polymorphism (MSAP) technique. A high degree of cytosine methylation was detected (64.36% of all scored DNA fragments). Furthermore, high levels of epigenetic variation were observed among the studied individuals. This high epigenetic variation found in P. pinea contrasted with the lack of genetic variation based on Amplified Fragment Length Polymorphism (AFLP) data. In this manner, variable epigenetic markers clearly discriminate individuals and differentiates two well represented populations while the lack of genetic variation revealed with the AFLP markers fail to differentiate at both, individual or population levels. In addition, the use of different replicated trees allowed identifying common polymorphic methylation sensitive MSAP markers among replicates of a given propagated tree. This set of MSAPs allowed discrimination of the 70% of the analyzed trees.

  10. Genetic variability and heritability in cultivated okra [Abel moschus esculentus (L.) Moench

    Energy Technology Data Exchange (ETDEWEB)

    Nwangburuka, C. C.; Denton, O. A.; Khinde, O. B.; Ojo, D. K.; Popoola, A. R.

    2012-11-01

    Twenty-nine okra accessions from different agro-ecological regions in Nigeria were grown during the rainy and dry seasons, between 2006 and 2007 at Abeokuta (derived savanah) and Ilishan (rainforest) and assessed to determine their genetic variability, heritability and genetic advance from eight yield related characters. The experiment was laid out in a Randomized Complete Block Design with five replications. There was high genotypic coefficient of variability, % broad-sense heritability and genetic advance in traits such as plant height (26.2, 90.7, 51.5), fresh pod length (23.9, 98.5, 48.8), fresh pod width (23.9, 98.5, 48.8), mature pod length (28.6, 98.5, 52.3), branching per plant (29.3, 82.3, 54.8) and pod weight per plant (33.9, 90.0, 63.3), suggesting the effect of additive genes and reliability of selection based on phenotype of these traits for crop improvement. The positive and significant phenotypic and genotypic correlation between plant height at maturity, fresh pod width, seeds per pod and pods per plant, branches per plant with seed weight per plant and pod weight per plant, suggests that selection on the basis of the phenotype of these characters will lead to high seed and pod yield in okra. (Author) 26 refs.

  11. Optimization of cocoa butter analog synthesis variables using neural networks and genetic algorithm.

    Science.gov (United States)

    Shekarchizadeh, Hajar; Tikani, Reza; Kadivar, Mahdi

    2014-09-01

    Cocoa butter analog was prepared from camel hump fat and tristearin by enzymatic interesterification in supercritical carbon dioxide (SC-CO2) using immobilized Thermomyces lanuginosus lipase (Lipozyme TL IM) as a biocatalyst. Optimal process conditions were determined using neural networks and genetic algorithm optimization. Response surfaces methodology was used to design the experiments to collect data for the neural network modelling. A general regression neural network model was developed to predict the response of triacylglycerol (TAG) distribution of cocoa butter analog from the process pressure, temperature, tristearin/camel hump fat ratio, water content, and incubation time. A genetic algorithm was used to search for a combination of the process variables for production of most similar cocoa butter analog to the corresponding cocoa butter. The combinations of the process variables during genetic algorithm optimization were evaluated using the neural network model. The pressure of 10 MPa; temperature of 40 °C; SSS/CHF ratio of 0.6:1; water content of 13 % (w/w); and incubation time of 4.5 h were found to be the optimum conditions to achieve the most similar cocoa butter analog to the corresponding cocoa butter.

  12. Genetic variability in maned wolf based on heterologous short-tandem repeat markers from domestic dog.

    Science.gov (United States)

    Salim, D C; Akimoto, A A; Carvalho, C B; Oliveira, S F; Grisolia, C K; Moreira, J R; Klautau-Guimarães, M N

    2007-06-20

    The maned wolf (Chrysocyon brachyurus) is the largest South American canid. Habitat loss and fragmentation, due to agricultural expansion and predatory hunting, are the main threats to this species. It is included in the official list of threatened wildlife species in Brazil, and is also protected by IUCN and CITES. Highly variable genetic markers such as microsatellites have the potential to resolve genetic relationships at all levels of the population structure (among individuals, demes or metapopulations) and also to identify the evolutionary unit for strategies for the conservation of the species. Tests were carried out to verify whether a class of highly polymorphic tetranucleotide repeats described for the domestic dog effectively amplifies DNA in the maned wolf. All five loci studied were amplified; however, one of these, was shown to be monomorphic in 69 maned wolf samples. The average allele number and estimated heterozygosity per polymorphic locus were 4.3 and 67%, respectively. The genetic variability found for this species, which is considered threatened with extinction, showed similar results when compared to studies of other canids.

  13. Genetic variability of garlic accessions as revealed by agro-morphological traits evaluated under different environments.

    Science.gov (United States)

    Hoogerheide, E S S; Azevedo Filho, J A; Vencovsky, R; Zucchi, M I; Zago, B W; Pinheiro, J B

    2017-05-31

    The cultivated garlic (Allium sativum L.) displays a wide phenotypic diversity, which is derived from natural mutations and phenotypic plasticity, due to dependence on soil type, moisture, latitude, altitude and cultural practices, leading to a large number of cultivars. This study aimed to evaluate the genetic variability shown by 63 garlic accessions belonging to Instituto Agronômico de Campinas and the Escola Superior de Agricultura "Luiz de Queiroz" germplasm collections. We evaluated ten quantitative characters in experimental trials conducted under two localities of the State of São Paulo: Monte Alegre do Sul and Piracicaba, during the agricultural year of 2007, in a randomized blocks design with five replications. The Mahalanobis distance was used to measure genetic dissimilarities. The UPGMA method and Tocher's method were used as clustering procedures. Results indicated significant variation among accessions (P < 0.01) for all evaluated characters, except for the percentage of secondary bulb growth in MAS, indicating the existence of genetic variation for bulb production, and germplasm evaluation considering different environments is more reliable for the characterization of the genotypic variability among garlic accessions, since it diminishes the environmental effects in the clustering of genotypes.

  14. Genetic variability of the neogregarine Apicystis bombi, an etiological agent of an emergent bumblebee disease.

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    Jafar Maharramov

    Full Text Available The worldwide spread of diseases is considered a major threat to biodiversity and a possible driver of the decline of pollinator populations, particularly when novel species or strains of parasites emerge. Previous studies have suggested that populations of introduced European honeybee (Apis mellifera and bumblebee species (Bombus terrestris and Bombus ruderatus in Argentina share the neogregarine parasite Apicystis bombi with the native bumblebee (Bombus dahlbomii. In this study we investigated whether A. bombi is acting as an emergent parasite in the non-native populations. Specifically, we asked whether A. bombi, recently identified in Argentina, was introduced by European, non-native bees. Using ITS1 and ITS2 to assess the parasite's intraspecific genetic variation in bees from Argentina and Europe, we found a largely unstructured parasite population, with only 15% of the genetic variation being explained by geographic location. The most abundant haplotype in Argentina (found in all 9 specimens of non-native species was identical to the most abundant haplotype in Europe (found in 6 out of 8 specimens. Similarly, there was no evidence of structuring by host species, with this factor explaining only 17% of the genetic variation. Interestingly, parasites in native Bombus ephippiatus from Mexico were genetically distant from the Argentine and European samples, suggesting that sufficient variability does exist in the ITS region to identify continent-level genetic structure in the parasite. Thus, the data suggest that A. bombi from Argentina and Europe share a common, relatively recent origin. Although our data did not provide information on the direction of transfer, the absence of genetic structure across space and host species suggests that A. bombi may be acting as an emergent infectious disease across bee taxa and continents.

  15. Structure and Genetic Variability of the Oceanic Whitetip Shark, Carcharhinus longimanus, Determined Using Mitochondrial DNA

    Science.gov (United States)

    Camargo, Sâmia M.; Coelho, Rui; Chapman, Demian; Howey-Jordan, Lucy; Brooks, Edward J.; Fernando, Daniel; Mendes, Natalia J.; Hazin, Fabio H. V.; Oliveira, Claudio; Santos, Miguel N.; Foresti, Fausto; Mendonça, Fernando F.

    2016-01-01

    Information regarding population structure and genetic connectivity is an important contribution when establishing conservation strategies to manage threatened species. The oceanic whitetip shark, Carcharhinus longimanus, is a highly migratory, large-bodied, pelagic shark listed by the IUCN (International Union for Conservation of Nature) Red List as "vulnerable" throughout its range and “critically endangered” in the western north Atlantic. In 2014, the species was protected globally under Appendix II of CITES (Convention on International Trade in Endangered Species), limiting and regulating trade. This study used partial sequences of mitochondrial DNA (mtDNA) control region to determine the population genetic structure of oceanic whitetip sharks across the Atlantic and Indian Oceans. 724 base pairs were obtained from 215 individuals that identifed nine polymorphic sites and defined 12 distinct haplotypes. Total nucleotide diversity (π) was 0.0013 and haplotype diversity (h) was 0.5953. The Analysis of Molecular Variance (AMOVA) evidenced moderate levels of population structure (ɸST = 0.1039) with restricted gene flow between the western and eastern Atlantic Ocean, and a strong relationship between the latter region and the Indian Ocean. Even though the oceanic whitetip is a highly migratory animal the results presented here show that their genetic variability is slightly below average of other pelagic sharks. Additionally, this study recommends that at least two populations in the Atlantic Ocean should be considered distinct (eastern and western Atlantic) and conservation efforts should be focused in areas with the greatest genetic diversity by environmental managers. PMID:27187497

  16. Structure and Genetic Variability of the Oceanic Whitetip Shark, Carcharhinus longimanus, Determined Using Mitochondrial DNA.

    Science.gov (United States)

    Camargo, Sâmia M; Coelho, Rui; Chapman, Demian; Howey-Jordan, Lucy; Brooks, Edward J; Fernando, Daniel; Mendes, Natalia J; Hazin, Fabio H V; Oliveira, Claudio; Santos, Miguel N; Foresti, Fausto; Mendonça, Fernando F

    2016-01-01

    Information regarding population structure and genetic connectivity is an important contribution when establishing conservation strategies to manage threatened species. The oceanic whitetip shark, Carcharhinus longimanus, is a highly migratory, large-bodied, pelagic shark listed by the IUCN (International Union for Conservation of Nature) Red List as "vulnerable" throughout its range and "critically endangered" in the western north Atlantic. In 2014, the species was protected globally under Appendix II of CITES (Convention on International Trade in Endangered Species), limiting and regulating trade. This study used partial sequences of mitochondrial DNA (mtDNA) control region to determine the population genetic structure of oceanic whitetip sharks across the Atlantic and Indian Oceans. 724 base pairs were obtained from 215 individuals that identifed nine polymorphic sites and defined 12 distinct haplotypes. Total nucleotide diversity (π) was 0.0013 and haplotype diversity (h) was 0.5953. The Analysis of Molecular Variance (AMOVA) evidenced moderate levels of population structure (ɸST = 0.1039) with restricted gene flow between the western and eastern Atlantic Ocean, and a strong relationship between the latter region and the Indian Ocean. Even though the oceanic whitetip is a highly migratory animal the results presented here show that their genetic variability is slightly below average of other pelagic sharks. Additionally, this study recommends that at least two populations in the Atlantic Ocean should be considered distinct (eastern and western Atlantic) and conservation efforts should be focused in areas with the greatest genetic diversity by environmental managers.

  17. Genetic variability analysis of Byrsonima crassifolia germplasm collected in Pará State using ISSR markers.

    Science.gov (United States)

    Rodrigues, S M; Moura, E F; Ramos, G K S; Oliveira, M S P

    2016-10-17

    Native of the Amazon, the nanche (Byrsonima crassifolia) is a fruit cultivated by family farmers and used in cooking; as such, it represents an opportunity for regional agribusiness. The Embrapa Eastern Amazon set up an active germplasm bank (BAG) consisting of 22 accessions sampled in 11 municipalities of Pará State. Due to its economic potential, there is an interest to advance the genetic breeding program of this species. The aim of this study was to characterize the BAG nanche collection using inter-simple sequence repeat (ISSR) markers. Accessions were genotyped using 23 pre-selected ISSR primers resulting in 109 amplified polymorphic and 51 monomorphic bands. With eight polymorphic bands each, the most polymorphic primers were UBC 809 and UBC 848. An unweighted pair-group method with arithmetic average cluster analysis based on Jaccard's coefficient indicated that the individuals clustered into two distinct groups. Accessions Igarapé Açu-2 and Augusto Corrêa-Pl 1 were most similar. The genetic dissimilarity values ranged from 0.10 to 0.59. We conclude that the ISSR markers were efficient in detecting polymorphisms in the nanche accessions, and that it is possible to infer the genetic variability among accessions of the collection. This demonstrate the importance of using molecular markers in poorly studied species and the advantages that this information can bring to the genetic improvement of such species.

  18. Assessment of genetic variability of fish personality traits using rainbow trout isogenic lines.

    Science.gov (United States)

    Millot, Sandie; Péan, Samuel; Labbé, Laurent; Kerneis, Thierry; Quillet, Edwige; Dupont-Nivet, Mathilde; Bégout, Marie-Laure

    2014-07-01

    The study of inter-individual variability of personality in fish is a growing field of interest but the genetic basis of this complex trait is still poorly investigated due to the difficulty in controlling fish genetic origin and life history. When available, isogenic lines that allow performing independent tests on different individuals having identical genotype constitute a very relevant experimental material to disentangle the genetic and environmental components of behavioural individuality. We took advantage of heterozygous isogenic lines to investigate the personality in rainbow trout through the analysis of their reactions to different experimental situations. To this end, seven to ten rainbow trout isogenic lines were screened for their spatial exploratory behaviour, their flight response toward a stressor and their risk taking behaviour. Results showed that some lines seemed less sensitive to new events or environmental changes and could be defined as low responsive, while others were very sensitive and defined as high responsive. The use of isogenic lines highlighted the importance of genetic factors, in combination with life history, in the expression of personality in domesticated fish.

  19. Genetic variability and identification of the intermediate snail hosts of Schistosoma mansoni

    Directory of Open Access Journals (Sweden)

    Teofânia HDA Vidigal

    1998-01-01

    Full Text Available Studies based on shell or reproductive organ morphology and genetic considerations suggest extensive intraspecific variation in Biomphalaria snails. The high variability at the morphological and genetic levels, as well as the small size of some specimens and similarities between species complicate the correct identification of these snails. Here we review our work using methods based on polymerase chain reaction (PCR amplification for analysis of genetic variation and identification of Biomphalaria snails from Brazil, Argentina, Uruguay and Paraguay. Arbitrarily primed-PCR revealed that the genome of B. glabrata exihibits a remarkable degree of intraespecific polymorphism. Low stringency-PCR using primers for 18S rRNA permited the identification of B. glabrata, B. tenagophila and B. occidentalis. The study of individuals obtained from geographically distinct populations exhibits significant intraspecific DNA polymorphism, however specimens from the same species, exhibit some species specific LSPs. We also showed that PCR-restriction fragment of length polymorphism of the internal transcribed spacer region of Biomphalaria rDNA, using DdeI permits the differentiation of the three intermediate hosts of Schistosoma mansoni. The molecular biological techniques used in our studies are very useful for the generation of new knowledge concerning the systematics and population genetics of Biomphalaria snails.

  20. Structure and Genetic Variability of the Oceanic Whitetip Shark, Carcharhinus longimanus, Determined Using Mitochondrial DNA.

    Directory of Open Access Journals (Sweden)

    Sâmia M Camargo

    Full Text Available Information regarding population structure and genetic connectivity is an important contribution when establishing conservation strategies to manage threatened species. The oceanic whitetip shark, Carcharhinus longimanus, is a highly migratory, large-bodied, pelagic shark listed by the IUCN (International Union for Conservation of Nature Red List as "vulnerable" throughout its range and "critically endangered" in the western north Atlantic. In 2014, the species was protected globally under Appendix II of CITES (Convention on International Trade in Endangered Species, limiting and regulating trade. This study used partial sequences of mitochondrial DNA (mtDNA control region to determine the population genetic structure of oceanic whitetip sharks across the Atlantic and Indian Oceans. 724 base pairs were obtained from 215 individuals that identifed nine polymorphic sites and defined 12 distinct haplotypes. Total nucleotide diversity (π was 0.0013 and haplotype diversity (h was 0.5953. The Analysis of Molecular Variance (AMOVA evidenced moderate levels of population structure (ɸST = 0.1039 with restricted gene flow between the western and eastern Atlantic Ocean, and a strong relationship between the latter region and the Indian Ocean. Even though the oceanic whitetip is a highly migratory animal the results presented here show that their genetic variability is slightly below average of other pelagic sharks. Additionally, this study recommends that at least two populations in the Atlantic Ocean should be considered distinct (eastern and western Atlantic and conservation efforts should be focused in areas with the greatest genetic diversity by environmental managers.

  1. A genetic algorithm for variable selection in logistic regression analysis of radiotherapy treatment outcomes.

    Science.gov (United States)

    Gayou, Olivier; Das, Shiva K; Zhou, Su-Min; Marks, Lawrence B; Parda, David S; Miften, Moyed

    2008-12-01

    A given outcome of radiotherapy treatment can be modeled by analyzing its correlation with a combination of dosimetric, physiological, biological, and clinical factors, through a logistic regression fit of a large patient population. The quality of the fit is measured by the combination of the predictive power of this particular set of factors and the statistical significance of the individual factors in the model. We developed a genetic algorithm (GA), in which a small sample of all the possible combinations of variables are fitted to the patient data. New models are derived from the best models, through crossover and mutation operations, and are in turn fitted. The process is repeated until the sample converges to the combination of factors that best predicts the outcome. The GA was tested on a data set that investigated the incidence of lung injury in NSCLC patients treated with 3DCRT. The GA identified a model with two variables as the best predictor of radiation pneumonitis: the V30 (p=0.048) and the ongoing use of tobacco at the time of referral (p=0.074). This two-variable model was confirmed as the best model by analyzing all possible combinations of factors. In conclusion, genetic algorithms provide a reliable and fast way to select significant factors in logistic regression analysis of large clinical studies.

  2. Genetic variability of bottle gourd Lagenaria siceraria (Mol. Standley and its morphological characterization by multivariate analysis

    Directory of Open Access Journals (Sweden)

    Mladenović Emina

    2012-01-01

    Full Text Available A wide range of bottle gourd Lagenaria siceraria (Mol. Standley germplasm was collected from different parts of the world. Genetic resource preservation and determination of genetic variability was carried out as a foundation for future breeding work. The germplasm diversity collected in Serbia is a result of its adaptation to diverse ecological conditions and farmers’ selection in accordance with their preference and ethnobotanical utilization. The broad intraspecific variation of the plant, fruit and seed morphology is a direct result of the research carried out. Principal component analysis (PCA of L. siceraria with 13 quantitative traits showed continuous variation among accessions, primarily due to fruit and seed size and shape. The evident reduction in trait variation is a direct result of the preference for ornamental use that favored certain shapes and sizes of the fruit, which has not significantly changed over the centuries.

  3. Genetic variability of lactoferrin content estimated by mid-infrared spectrometry in bovine milk.

    Science.gov (United States)

    Soyeurt, H; Colinet, F G; Arnould, V M-R; Dardenne, P; Bertozzi, C; Renaville, R; Portetelle, D; Gengler, N

    2007-09-01

    The effects of lactoferrin (LF) on the immune system have already been shown by many studies. Unfortunately, the current methods used to measure LF levels in milk do not permit the study of the genetic variability of lactoferrin or the performance of routine genetic evaluations. The first aim of this research was to derive a calibration equation permitting the prediction of LF in milk by mid-infrared spectrometry (MIR). The calibration with partial least squares on 69 samples showed a ratio of standard error of cross-validation to standard deviation equal to 1.98. Based on this value, the calibration equation was used to establish an LF indicator trait (predicted LF; pLF) on a large number of milk samples (n = 7,690). A subsequent study of its variability was conducted, which confirmed that stage of lactation and lactation number influence the overall pLF level. Small differences in mean pLF among 7 dairy breeds were also observed. The pLF content of Jersey milk was significantly higher than that in Holstein milk. Therefore, the choice of breed could change the expected LF level. Heritability estimated for pLF was 19.7%. The genetic and phenotypic correlations between somatic cell score and pLF were 0.04 and 0.26, respectively. As somatic cell score increases in presence of mastitis, this observation seems to indicate that pLF, or a function of observed pLF, compared with expected LF might have potential as an indicator of mastitis. The negative genetic correlation (-0.36) between milk yield and pLF could indicate an undesirable effect of selection for high milk production on the overall LF level.

  4. Influence of immunoprotection on genetic variability of cysteine proteinases from Haemonchus contortus adult worms.

    Science.gov (United States)

    Martín, S; Molina, J M; Hernández, Y I; Ferrer, O; Muñoz, Ma C; López, A; Ortega, L; Ruiz, A

    2015-11-01

    The limitations associated with the use of anthelmintic drugs in the control of gastrotintestinal nematodosis, such as the emergence of anthelmintic resistance, have stimulated the study of the immunological control of many parasites. In the case of Haemonchus contortus, several vaccination trials using native and recombinant antigens have been conducted. A group of antigens with demonstrated immunoprotective value are cathepsin B - like proteolytic enzymes of the cysteine proteinase type. These enzymes, which have been observed in both excretory-secretory products and somatic extracts of H. contortus, may vary among different geographic isolates and on strains isolated from different hosts, or even from the same host, as has been demonstrated in some comparative studies of genetic variability. In the present study, we evaluated the genetic variability of the worms that fully developed their endogenous cycle in immunised sheep and goat in order to identify the alleles of most immunoprotective value. To address these objectives, groups of sheep and goats were immunised with PBS soluble fractions enriched for cysteine proteinases from adult worms of H. contortus from either a strain of H. contortus isolated from goats of Gran Canaria Island (SP) or a strain isolated from sheep of North America (NA). The results confirmed the immunoprophylactic value of this type of enzyme against haemonchosis in both sheep and goats in association with increased levels of specific IgG. The genetic analysis demonstrated that the immunisation had a genetic selection on proteinase-encoding genes. In all the immunised animals, allelic frequencies were statistically different from those observed in non-immunised control animals in the four analysed genes. The reduction in the allelic frequencies suggests that parasites expressing these proteases are selectively targeted by the vaccine, and hence they should be considered in any subunit vaccine approach to control haemonchosis in small

  5. Insecticide resistance and genetic variability in natural populations of Aedes (Stegomyia aegypti (Diptera: Culicidae from Colombia

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    Oscar A. Aguirre-Obando

    2015-02-01

    Full Text Available Mosquito control prevails as the most efficient method to protect humans from the dengue virus, despite recent efforts to find a vaccine for this disease. We evaluated insecticide resistance and genetic variability in natural populations of Aedes aegypti (Linnaeus, 1762 from Colombia. This is the first Colombian study examining kdr mutations and population structure. Bioassays with larvae of three mosquito populations (Armenia, Calarcá and Montenegro were performed according to the World Health Organization (WHO guidelines, using Temephos. For the analysis of the Val1016Ile mutation and genetic diversity, we sampled recently-emerged adults from four mosquito populations (Armenia, Calarcá, Montenegro and Barcelona. Following the WHO protocol, bioassays implemented with larvae showed resistance to Temephos in mosquito populations from Armenia (77% ± 2 and Calarcá (62% ± 14, and an incipient altered susceptibility at Montenegro (88% ± 8. The RR95 of mosquito populations ranged from 3.7 (Montenegro to 6.0 (Calarca. The Val1016Ile mutation analysis of 107 genotyped samples indicates that 94% of the specimens were homozygous for the wild allele (1016Val and 6% were heterozygous (Val1016Ile. The 1016Ile allele was not found in Barcelona. Genetic variability analysis found three mitochondrial lineages with low genetic diversity and gene flow. In comparison with haplotypes from the American continent, those from this study suggest connections with Mexican and North American populations. These results confirm that a continuous monitoring and managing program of A. aegypti resistance in the state of Quindío is required.

  6. Evaluating Genetic Variability of Sorghum Mutant Lines Tolerant to Acid Soil

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    W. Puspitasari

    2012-12-01

    Full Text Available High rainfall in some parts in Indonesia causes soil become acidic. The main constraint of acid soil is phosphor (P deficiency and aluminum (Al toxicity which decrease plant productivity. To overcome this problem, it is important to develop a crop variety tolerant to such conditions. Sorghum is probably one of the potential crops to meet that objective. Sorghum has been reported to have wide adaptability to various agro-ecology and can be used as food and animal feed. Unfortunately, sorghum is not Indonesian origin so its genetic variability is still low. From previous breeding works with induced mutation, some promising mutant lines have been developed. These mutant lines were included in the experiment carried out in Tenjo with soil condition was classified as acid soil with pH 4.8 and exchangeable-Al content 2.43 me/100 g. The objectives of this experiment were to study the magnitude of genetic variability of agronomy and grain quality characters in sorghum in order to facilitate the breeding improvement of the species. Plant materials used in this study were ten genotypes, including 6 mutant lines and 4 control varieties. The randomized block design with three replications was used in the experiment. The genetic variabilities of agronomic and grain quality characters existed among genotypes, such as plant height, number of leaves, stalk diameter, biomass weight, panicle length, grain yield per plant, 100 seed weight and tannin content in the grain. The broad sense heritabilities of agronomic characters were estimated ranging from medium to high. Grain yield showed significantly positive correlation with agronomic characters observed, but it was negatively correlated with protein content

  7. Evaluating Genetic Variability of Sorghum Mutant Lines Tolerant to Acid Soil

    Directory of Open Access Journals (Sweden)

    W. Puspitasari

    2012-08-01

    Full Text Available High rainfall in some parts in Indonesia causes soil become acidic. The main constraint of acid soil is phosphor (P deficiency and aluminum (Al toxicity which decrease plant productivity. To overcome this problem, it is important to develop a crop variety tolerant to such conditions. Sorghum is probably one of the potential crops to meet that objective. Sorghum has been reported to have wide adaptability to various agro-ecology and can be used as food and animal feed. Unfortunately, sorghum is not Indonesian origin so its genetic variability is still low. From previous breeding works with induced mutation, some promising mutant lines have been developed. These mutant lines were included in the experiment carried out in Tenjo with soil condition was classified as acid soil with pH 4.8 and exchangeable-Al content 2.43 me/100 g. The objectives of this experiment were to study the magnitude of genetic variability of agronomy and grain quality characters in sorghum in order to facilitate the breeding improvement of the species. Plant materials used in this study were ten genotypes, including 6 mutant lines and 4 control varieties. The randomized block design with three replications was used in the experiment. The genetic variabilities of agronomic and grain quality characters existed among genotypes, such as plant height, number of leaves, stalk diameter, biomass weight, panicle length, grain yield per plant, 100 seed weight and tannin content in the grain. The broad sense heritabilities of agronomic characters were estimated ranging from medium to high. Grain yield showed significantly positive correlation with agronomic characters observed, but it was negatively correlated with protein content

  8. Heirloom tomato cultivars and local populations as sources of genetic variability for breeding

    Directory of Open Access Journals (Sweden)

    Glogovac Svetlana

    2010-01-01

    Full Text Available Five local tomato populations and fourteen heirloom cultivars were analyzed in this study. The analyzed genotypes represent a part of tomato collection of Institute of Field and Vegetable Crops in Novi Sad. The following fruit and plant traits were analyzed: growth type, fruit color, fruit shape index, fruit weight, number of locules and dry matter content. Cluster analysis was performed so as to group the analyzed genotypes by homology and divergence. The aim of this article was to determine the importance of heirloom cultivars and local populations as sources of genetic variability in tomato breeding process.

  9. [Phenotypic variability in a family with genetically verified familial hemiplegic migraine type 2].

    Science.gov (United States)

    Hogaard, Nina; Klit, Henriette; Vogel, Ida; Thelle, Thomas

    2015-01-26

    After playing handball, a 13-year-old girl developed a comatose condition during 7-10 days with hemiparesis and aphasia. From age three to nine she was treated for partial epilepsy. She never had symptoms of migraine. Her father had childhood epilepsy and at the age of 40 and 44 he experienced two attacks with prolonged coma, fever, seizures, hemiparesis and aphasia. His mother had symptoms of severe hemiplegic migraine. Father and daughter were genetically tested and an earlier described mutation in ATP1A2 gene was found. These cases illustrate the phenotypic variability in familial hemiplegic migraine type 2.

  10. A Novel Sliding Mode Variable Structure Controller Based on a Genetic Algorithm

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    A novel control method has been proposed by using the genetic algorithm ( GA ) for nonlinear and complex plants. The proposed control strategy is based on a variable structure control, it overcomes the defects of other adaptive methods such as strong dependence to the system. A GA is used to learn to optimally select integral coefficient C. Simulation results verified the effectiveness of the controller. For position control of Direct Current (DC) motor in practice, this method has good performance and strong robustness, and both dynamic and steady performances were improved.

  11. Microsatellite DNA typing for assessment of genetic variability in Marwari breed of Indian goat

    Directory of Open Access Journals (Sweden)

    Anoop Singh Yadav

    2015-07-01

    Full Text Available Aim: To estimate existing within-breed genetic variability in Marwari goats under field conditions and the generated data that can be used to determine genetic relationships with other breed of goats. Materials and Methods: A total of 146 blood samples of goats of Marwari breed were randomly collected from genetically unrelated animals from different villages of Bikaner Districts of Rajasthan, India. Genomic DNA was extracted from whole blood using proteinase K-digestion followed by standard phenol–chloroform extraction procedure at room temperature and confirmed through horizontal electrophoresis on 0.8% agarose gel containing ethidium bromide. Fifteen caprine microsatellite markers were used to estimate genetic variability among the goats of Marwari breed in terms of allelic and genotype frequencies, heterozygosities and polymorphism information content (PIC value. Results: A total of 74 alleles were contributed by Marwari goat across all 15 microsatellite loci. The number of alleles per locus varied from two (ILSTS-087 to 9 (ILSTS-058 alleles, with a mean of 4.93 whereas the effective number of allele varied from 1.35 (ILSTS-005 to 3.129 (ILSTS011 with a mean of 2.36. The effective number of allele is lesser than observed number at all the loci. Allelic sizes ranged from 125 bp (ILSTS-028 and ILSTS-033 to 650 bp (ILSTS-011 and ILSTS-019. The expected heterozygosity ranged from 0.240 (locus ILSTS-005 to 0.681 (locus ILSTS-011, with an average value of 0.544. The observed heterozygosity (Ho ranged from 0.1428 (locus ILSTS-087 to 0.9285 (locus ILSTS-034, with an average value of 0.5485 indicates substantial and very good number of heterozygotes, in the population. The highest PIC value (1.1886 was observed at ILSTS-044 locus and least (0.0768 at ILSTS-065 locus for Marwari goat. Conclusion: Microsatellite analysis revealed a high level of polymorphism across studied microsatellite markers and informativeness of the markers for genetic

  12. [Cercospora kikuchii isolated from Province of Santa Fe (Argentina): genetic variability and cercosporin production].

    Science.gov (United States)

    González, Ana María; Turino, Ludmila; Latorre Rapela, María Gabriela; Lurá, María Cristina

    2008-12-31

    The aims of the present study were to analyze the genetic variability of Cercospora kikuchii isolates and the in vitro cercosporin production, of these isolates obtained from soybean at the central-northern region of Santa Fe province (Argentina). Also the relationship between RAPD profiles and toxin production was also assessed. The strain C. kikuchii NBRC 6711 and 13 soybean isolates with symptoms of leaf blight were tested. Cercosporin production was analyzed by growing the fungus on Potato Dextrose Agar, extracting the toxin in alkaline medium and determining its concentration by spectrophotometry. The population of C. kikuchii studied showed variability, both genotypically, nine different groups were encountered, and have the ability to produce cercosporin. No relationship was found between toxin production and the RAPD profiles.

  13. Taxa de polinização cruzada em cubiu Natural outcrossing in cocona

    Directory of Open Access Journals (Sweden)

    Waldelice Oliveira de Paiva

    1999-01-01

    Full Text Available Com o objetivo de avaliar a frequência de hibridação natural em Cubiu (Solanum sessiliflorum Dunal foram avaliadas em Manaus, AM, duas cultivares que se diferenciavam pela presença ou ausência de pigmentação de antocianina nos ramos, pecíolos e nervuras das folha. A taxa de polinização cruzada foi avaliada em três épocas do florescimento das plantas e foi estimada em 31%. Durante o desenvolvimento da cultura, observou-se grande presença de abelhas dos gêneros (Apidae Paratrigona, Trigona e Melipona e coleópteros Crysomelidae.In order to evaluate the natural rates of outcrossing in cocona (Solanum sessiliflorum Dunal, two cultivars, one with antocyanin presence and other without antocyanin, were planted in Manaus, AM, Brazil. The percentage of cross-polination was evaluated in three plant flowering periods and was estimated in 31%. During the period of cultivation, high presence of beas of Apidae genus Paratrigona, Trigona and Melipona and beetle Crysomelidae were observed.

  14. Evidence for Outcrossing via the Buller Phenomenon in a Substrate Simultaneously Inoculated with Spores and Mycelium of Agaricus bisporus

    OpenAIRE

    Callac, Philippe; Spataro, Cathy; Caille, Aurélie; Imbernon, Micheline

    2006-01-01

    In Agaricus bisporus, traditional cultivars and most of the wild populations belong to A. bisporus var. bisporus, which has a predominantly pseudohomothallic life cycle in which most meiospores are heterokaryons (n + n). A lower proportion of homokaryotic (n) meiospores, which typify the heterothallic life cycle, also are produced. In wild populations, pseudohomothallism was thought previously to play a major role, but recent analyses have found that significant outcrossing also may occur. We...

  15. SSR-based detection of genetic variability in the charcoal root rot pathogen Macrophomina phaseolina.

    Science.gov (United States)

    Jana, Tarakanta; Sharma, Tilak R; Singh, Nagendra K

    2005-01-01

    Macrophomina phaseolina, the causal agent of charcoal root or collar rot, is an important plant pathogen especially in soybean and cotton. Single primers of simple sequence repeats (SSR) or microsatellite markers have been used for the characterization of genetic variability of different populations of M. phaseolina obtained from soybean and cotton grown in India and the USA. Genetic similarity between isolates was calculated, and cluster analysis was used to generate a dendrogram showing relationships between isolates collected from the two hosts. Forty isolates could be clustered into three major groups corresponding to their hosts and geographical region. The wide distribution of microsatellites in M. phaseolina genome was assessed by agarose gel electrophoresis of the PCR products generated by direct amplification of inter SSR regions DNA. This is the first report of the use of microsatellite markers to characterize the charcoal root rot pathogen. The SSR fingerprints (0.25-3.5 kb) generated using DNA from different populations of M. phaseolina of two hosts indicated that these repeats are interspersed within the genome of this pathogen. The variability found within closely related isolates of M. phaseolina indicated that such microsatellites are useful in population studies and represents a step towards identification of potential isolate diagnostic markers specific to soybean and cotton.

  16. Phenotypic effects of genetic variability in human clock genes on circadian and sleep parameters

    Indian Academy of Sciences (India)

    Malcolm Von Schantz

    2008-12-01

    Circadian rhythms and sleep are two separate but intimately related processes. Circadian rhythms are generated through the precisely controlled, cyclic expression of a number of genes designated clock genes. Genetic variability in these genes has been associated with a number of phenotypic differences in circadian as well as sleep parameters, both in mouse models and in humans. Diurnal preferences as determined by the selfreported Horne–Östberg (HÖ) questionnaire, has been associated with polymorphisms in the human genes CLOCK, PER1, PER2 and PER3. Circadian rhythm-related sleep disorders have also been associated with mutations and polymorphisms in clock genes, with the advanced type cosegrating in an autosomal dominant inheritance pattern with mutations in the genes PER2 and CSNK1D, and the delayed type associating without discernible Mendelian inheritance with polymorphisms in CLOCK and PER3. Several mouse models of clock gene null alleles have been demonstrated to have affected sleep homeostasis. Recent findings have shown that the variable number tandem polymorphism in PER3, previously linked to diurnal preference, has profound effects on sleep homeostasis and cognitive performance following sleep loss, confirming the close association between the processes of circadian rhythms and sleep at the genetic level.

  17. Genetic variability in the endophytic fungus Guignardia citricarpa isolated from citrus plants

    Directory of Open Access Journals (Sweden)

    Chirlei Glienke-Blanco

    2002-01-01

    Full Text Available During some phases of of their life-cycle endophytic fungi colonize plants asymptomatically being found most frequently inside the aerial part of plant tissues. After surface disinfection of apparently healthy leaves from three varieties of mandarin orange and one tangor, and after incubation on appropriate culture medium, 407 fungal isolates were obtained, giving a total infection frequency of 81%. No fungal growth was observed from disinfected seeds, indicating that fungi are probably not transmitted via seeds. Of the fungal isolates, 27% belonged to the genus Guignardia, with 12 isolates being identified as Guignardia citricarpa Kiely, which is described as a citrus pathogen. The isolates were variable in respect to the presence of sexual structures and growth rates. Most of the isolates produces mature asci, supporting the hypothesis that they are nonpathogenic endophytes, which recently were identified as G. mangiferae. High intraspecific genetic variability (an average similarity coefficient of 0.6 was detected using random amplified polymorphic DNA (RAPD markers generated by seven different primers. The highest similarity coefficient (0.9 was between isolates P15 and M86 and the smallest (0.22 between isolates P15 and C145. These results did not allow us to establish an association between genetic similarity of the fungal isolates and the citrus varieties from which they were obtained.

  18. Characterization of Fusarium verticillioides strains isolated from maize in Italy: fumonisin production, pathogenicity and genetic variability.

    Science.gov (United States)

    Covarelli, Lorenzo; Stifano, Simonetta; Beccari, Giovanni; Raggi, Lorenzo; Lattanzio, Veronica Maria Teresa; Albertini, Emidio

    2012-08-01

    Fusarium verticillioides (teleomorph Gibberella moniliformis) is the main fungal agent of ear and kernel rot of maize (Zea mays L.) worldwide, including Italy. F.verticillioides is a highly toxigenic species since it is able to produce the carcinogenic mycotoxins fumonisins. In this study, 25 F. verticillioides strains, isolated from maize in different regions of Italy were analyzed for their ability to produce fumonisins, their pathogenicity and their genetic variability. A further referenced strain of G. moniliformis isolated from maize in USA was also used as outgroup. The fumonisins B₁, B₂, and B₃ were analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Pathogenicity tests were carried out by symptom observation and determination of growth parameters after inoculation of maize seeds, seedlings and wounded detached leaves. Total genomic DNA was used for Amplified Fragment Length Polymorphism (AFLP) analysis. About 20% of the analyzed strains were unable to produce fumonisins in in vitro experiments on inoculated maize flour, while, among fumonisin producers, a great variability was observed, with values ranging from 1 to 115 mg kg⁻¹. The different analyzed strains showed a wide range of pathogenicity in terms of effect on seed germination, seedling development and of symptoms produced on detached leaves, which were not correlated with the different in vitro fumonisin production. AFLP analysis indicated the presence of genetic diversity not only between the Italian strains and the American reference but also among the Italian isolates. Copyright © 2012 Elsevier Ltd. All rights reserved.

  19. The link between genetic variation and variability in vaccine responses: systematic review and meta-analyses.

    Science.gov (United States)

    Posteraro, Brunella; Pastorino, Roberta; Di Giannantonio, Paolo; Ianuale, Carolina; Amore, Rosarita; Ricciardi, Walter; Boccia, Stefania

    2014-03-26

    Although immune response to vaccines can be influenced by several parameters, human genetic variations are thought to strongly influence the variability in vaccine responsiveness. Systematic reviews and meta-analyses are needed to clarify the genetic contribution to this variability, which may affect the efficacy of existing vaccines. We performed a systematic literature search to identify all studies describing the associations of allelic variants or single nucleotide polymorphisms in immune response genes with vaccine responses until July 2013. The studies fulfilling inclusion criteria were meta-analyzed. Thirteen studies (11,686 subjects) evaluated the associations of human leukocyte antigen (HLA) and other immunity gene variations with the responses to single vaccines, including MMR-II (measles and rubella virus), HepB (hepatitis virus), influenza virus, and MenC (serogroup C meningococcus) vaccines. Seven HLA genetic variants were included in the meta-analyses. The pooled ORs showed that DRB1*07 (2.46 [95% CI=1.60-3.77]; P for heterogeneity=0.117; I(2)=49.1%), DQA1*02:01 (2.21 [95% CI=1.22-4.00]; P for heterogeneity=0.995; I(2)=0.0%), DQB1*02:01 (2.03 [95% CI=1.35-3.07]; P for heterogeneity=0.449; I(2)=0.0%), and DQB1*03:03 (3.31 [95% CI=1.12-9.78]; P for heterogeneity=0.188; I(2)=42.4%) were associated with a significant decrease of antibody responses to MMR-II, HepB, and influenza vaccines. The pooled ORs showed that DRB1*13 (0.52 [95% CI=0.32-0.84]; P for heterogeneity=0.001; I(2)=85.1%) and DRB1*13:01 (0.19 [95% CI=0.06-0.58]; P for heterogeneity=0.367; I(2)=0.0%) were associated with a significant increase of antibody responses to the above vaccines. While our findings reinforce the concept that individuals with a particular HLA allelic composition are more likely to respond efficiently to vaccines, future studies should be encouraged to further elucidate the link between genetic variation and variability of the human immune response to vaccines

  20. Genetic Variability of Macrophomina phaseolina Isolates from Dry Beans in Turkey

    Directory of Open Access Journals (Sweden)

    Serkan Yeşil

    2016-04-01

    Full Text Available Charcoal rot is a soil and seed borne, economically important fungal disease on dry bean in Turkey. Twenty bean isolates of M. phaseolina collected from different locations in Turkey during 2008 and 2012 years were studied for genetic variability using random amplified polymorphic DNA (RAPD assay, chlorate sensitivity on medium supplemented with 120mM of potassium, phenotype of colony, and pathogenicity. Isolates were identified as M. phaseolina based on morhological features and PCR assays using species-specific primers (MPKF1and MPKR1. Isolates of M. phaseolina were analysed for their aggressiveness on the susceptible bean cv. Akman 98, by soil inoculation method. Isolates exhibiting a dense chlorate phenotype were chlorate-resistant, while those possessing feathery and restricted chlorate phenotypes were chlorate-sensitive. More than half of the isolates (55% were resistant to chlorate and produced dense phenotype, while 35% isolates showed feathery and two isolates (10% showed restricted growth. DNA from 20 isolates was subjected to genetic diversity analysis by the RAPD method using 14 randomly chosen 10-base random primers, and low genetic diversity (33.3% was observed among the tested isolates.

  1. Genetic loci associated with heart rate variability and their effects on cardiac disease risk

    Science.gov (United States)

    Nolte, Ilja M.; Munoz, M. Loretto; Tragante, Vinicius; Amare, Azmeraw T.; Jansen, Rick; Vaez, Ahmad; von der Heyde, Benedikt; Avery, Christy L.; Bis, Joshua C.; Dierckx, Bram; van Dongen, Jenny; Gogarten, Stephanie M.; Goyette, Philippe; Hernesniemi, Jussi; Huikari, Ville; Hwang, Shih-Jen; Jaju, Deepali; Kerr, Kathleen F.; Kluttig, Alexander; Krijthe, Bouwe P.; Kumar, Jitender; van der Laan, Sander W.; Lyytikäinen, Leo-Pekka; Maihofer, Adam X.; Minassian, Arpi; van der Most, Peter J.; Müller-Nurasyid, Martina; Nivard, Michel; Salvi, Erika; Stewart, James D.; Thayer, Julian F.; Verweij, Niek; Wong, Andrew; Zabaneh, Delilah; Zafarmand, Mohammad H.; Abdellaoui, Abdel; Albarwani, Sulayma; Albert, Christine; Alonso, Alvaro; Ashar, Foram; Auvinen, Juha; Axelsson, Tomas; Baker, Dewleen G.; de Bakker, Paul I. W.; Barcella, Matteo; Bayoumi, Riad; Bieringa, Rob J.; Boomsma, Dorret; Boucher, Gabrielle; Britton, Annie R.; Christophersen, Ingrid; Dietrich, Andrea; Ehret, George B.; Ellinor, Patrick T.; Eskola, Markku; Felix, Janine F.; Floras, John S.; Franco, Oscar H.; Friberg, Peter; Gademan, Maaike G. J.; Geyer, Mark A.; Giedraitis, Vilmantas; Hartman, Catharina A.; Hemerich, Daiane; Hofman, Albert; Hottenga, Jouke-Jan; Huikuri, Heikki; Hutri-Kähönen, Nina; Jouven, Xavier; Junttila, Juhani; Juonala, Markus; Kiviniemi, Antti M.; Kors, Jan A.; Kumari, Meena; Kuznetsova, Tatiana; Laurie, Cathy C.; Lefrandt, Joop D.; Li, Yong; Li, Yun; Liao, Duanping; Limacher, Marian C.; Lin, Henry J.; Lindgren, Cecilia M.; Lubitz, Steven A.; Mahajan, Anubha; McKnight, Barbara; zu Schwabedissen, Henriette Meyer; Milaneschi, Yuri; Mononen, Nina; Morris, Andrew P.; Nalls, Mike A.; Navis, Gerjan; Neijts, Melanie; Nikus, Kjell; North, Kari E.; O'Connor, Daniel T.; Ormel, Johan; Perz, Siegfried; Peters, Annette; Psaty, Bruce M.; Raitakari, Olli T.; Risbrough, Victoria B.; Sinner, Moritz F.; Siscovick, David; Smit, Johannes H.; Smith, Nicholas L.; Soliman, Elsayed Z.; Sotoodehnia, Nona; Staessen, Jan A.; Stein, Phyllis K.; Stilp, Adrienne M.; Stolarz-Skrzypek, Katarzyna; Strauch, Konstantin; Sundström, Johan; Swenne, Cees A.; Syvänen, Ann-Christine; Tardif, Jean-Claude; Taylor, Kent D.; Teumer, Alexander; Thornton, Timothy A.; Tinker, Lesley E.; Uitterlinden, André G.; van Setten, Jessica; Voss, Andreas; Waldenberger, Melanie; Wilhelmsen, Kirk C.; Willemsen, Gonneke; Wong, Quenna; Zhang, Zhu-Ming; Zonderman, Alan B.; Cusi, Daniele; Evans, Michele K.; Greiser, Halina K.; van der Harst, Pim; Hassan, Mohammad; Ingelsson, Erik; Järvelin, Marjo-Riitta; Kääb, Stefan; Kähönen, Mika; Kivimaki, Mika; Kooperberg, Charles; Kuh, Diana; Lehtimäki, Terho; Lind, Lars; Nievergelt, Caroline M.; O'Donnell, Chris J.; Oldehinkel, Albertine J.; Penninx, Brenda; Reiner, Alexander P.; Riese, Harriëtte; van Roon, Arie M.; Rioux, John D.; Rotter, Jerome I.; Sofer, Tamar; Stricker, Bruno H.; Tiemeier, Henning; Vrijkotte, Tanja G. M.; Asselbergs, Folkert W.; Brundel, Bianca J. J. M.; Heckbert, Susan R.; Whitsel, Eric A.; den Hoed, Marcel; Snieder, Harold; de Geus, Eco J. C.

    2017-01-01

    Reduced cardiac vagal control reflected in low heart rate variability (HRV) is associated with greater risks for cardiac morbidity and mortality. In two-stage meta-analyses of genome-wide association studies for three HRV traits in up to 53,174 individuals of European ancestry, we detect 17 genome-wide significant SNPs in eight loci. HRV SNPs tag non-synonymous SNPs (in NDUFA11 and KIAA1755), expression quantitative trait loci (eQTLs) (influencing GNG11, RGS6 and NEO1), or are located in genes preferentially expressed in the sinoatrial node (GNG11, RGS6 and HCN4). Genetic risk scores account for 0.9 to 2.6% of the HRV variance. Significant genetic correlation is found for HRV with heart rate (−0.74heart rhythm regulation, with a key role for genetic variants (GNG11, RGS6) that influence G-protein heterotrimer action in GIRK-channel induced pacemaker membrane hyperpolarization. PMID:28613276

  2. Genetic variability among 18 cultivars of cooking bananas and plantains by RAPD and ISSR markers

    Directory of Open Access Journals (Sweden)

    YUYU SURYASARI POERBA

    2010-07-01

    Full Text Available Poerba YS, Ahmad F (2010 Genetic variability among 18 cultivars of cooking bananas and plantains by RAPD and ISSR markers. Biodiversitas 11: 118-123. This study was done to assess the molecular diversity of 36 accessions (18 cultivars of the plantain and cooking bananas (Musa acuminata x M. balbisiana, AAB, ABB subgroups based on Random amplified polymorphic DNA (RAPD and and Inter Simple Sequence Repeats (ISSR markers and to determine genetic relationships in the bananas. RAPD and ISSR fingerprinting of these banana varieties was carried out by five primers of RAPDs and two primers of ISSRs. RAPD primers produced 63 amplified fragments varying from 250 to 2500 bp in size. 96.82% of the amplification bands were polymorphic. ISSR primers produced 26 amplified fragments varying from 350 bp to 2000 bp in size. The results showed that 92.86% of the amplification bands were polymorphic. The range of genetic distance of 18 cultivars was from 0.06-0.67.

  3. Genetic variability in Colombian Creole cattle populations estimated by pedigree information.

    Science.gov (United States)

    Martínez, R A; García, D; Gallego, J L; Onofre, G; Pérez, J; Cañón, J

    2008-03-01

    The genetic structure of 4 Colombian Creole cattle breeds, namely, Costeño con Cuernos, Blanco Orejinegro (BON), Romosinuano (ROMO), and Sanmartinero (SM), was studied with an analysis of the available pedigree data. The comparison between the effective number of founders (f(e)) and the effective number of ancestors (f(a)) revealed a decrease in the genetic variation that was rather important for the ROMO and San Martinero breeds, which had the lowest f(a)/f(e) ratios (0.34 and 0.53, respectively). All breeds showed similar values for the number of equivalent generations traced, ranging from 3.1 in BON to 4.8 in ROMO. These 2 populations also had the lowest and the highest population sizes, respectively. The lowest average inbreeding coefficient considering the whole pedigree was obtained by BON (0.18%), whereas the highest was attained by ROMO (1.22%). Finally, the percentage of individuals with an inbreeding level greater than 6.25% in the reference population was high, indicating that the existing conservation management strategies could be improved to successfully maintain the genetic variability of these populations.

  4. Determination of genetic variability of traditional varieties of Brazilian rice using microsatellite markers

    Directory of Open Access Journals (Sweden)

    Claudio Brondani

    2006-01-01

    Full Text Available The rice (Oryza sativa breeding program of the Rice and Bean research center of the Brazilian agricultural company Empresa Brasileira de Pesquisa Agropecuária (Embrapa is well established and provides new cultivars every year to attend the demand for improved high yielding varieties with tolerance to biotic and abiotic stresses. However, the elite genitors used to compose new populations for selection are closely related, contributing to the yield plateau reached in the last 20 years. To overcome this limit, it is necessary to broaden the genetic basis of the cultivars using diverse germplasm such as wild relatives or traditional varieties, with the latter being more practical because they are more easily crossed with elite germplasm to accelerate the recovery of modern plant types in the breeding lines. The objective of our study was to characterize the allelic diversity of 192 traditional varieties of Brazilian rice using 12 simple sequence repeat (SSR or microsatellite markers. The germplasm was divided into 39 groups by common name similarity. A total of 176 alleles were detected, 30 of which (from 23 accessions were exclusive. The number of alleles per marker ranged from 6 to 22, with an average of 14.6 alleles per locus. We identified 16 accessions as a mixture of pure lines or heterozygous plants. Dendrogram analysis identified six clusters of identical accessions with different common names and just one cluster with identical accessions with the same common name, indicating that SSR markers are fundamental to determining the genetic relationship between landraces. A subset of 24 landraces, representatives of the 13 similarity groups plus the 11 accessions not grouped, was the most variable set of genotypes analyzed. These accessions can be used as genitors to increase the genetic variability available to rice breeding programs.

  5. Genetic and virulence variability among Erwinia tracheiphila strains recovered from different cucurbit hosts.

    Science.gov (United States)

    Rojas, E Saalau; Dixon, P M; Batzer, J C; Gleason, M L

    2013-09-01

    The causal agent of cucurbit bacterial wilt, Erwinia tracheiphila, has a wide host range in the family Cucurbitaceae, including economically important crops such as muskmelon (Cucumis melo), cucumber (C. sativus), and squash (Cucurbita spp.). Genetic variability of 69 E. tracheiphila strains was investigated by repetitive-element polymerase chain reaction (rep-PCR) using BOXA1R and ERIC1-2 primers. Fingerprint profiles revealed significant variability associated with crop host; strains isolated from Cucumis spp. were clearly distinguishable from Cucurbita spp.-isolated strains regardless of geographic origin. Twelve E. tracheiphila strains isolated from muskmelon, cucumber, or summer squash were inoculated onto muskmelon and summer squash seedlings, followed by incubation in a growth chamber. Wilt symptoms were assessed over 3 weeks, strains were reisolated, and rep-PCR profiles were compared with the inoculated strains. Wilting occurred significantly faster when seedlings were inoculated with strains that originated from the same crop host genus (P<0.001). In the first run of the experiment, cucumber and muskmelon strains caused wilting on muskmelon seedlings at a median of 7.8 and 5.6 days after inoculation (dai), respectively. Summer squash seedlings wilted 18.0, 15.7, and 5.7 dai when inoculated with muskmelon-, cucumber-, and squash-origin strains, respectively. In a second run of the experiment, cucumber and muskmelon strains caused wilting on muskmelon at 7.0 and 6.9 dai, respectively, whereas summer squash seedlings wilted at 23.6, 29.0 and 9.0 dai when inoculated with muskmelon-, cucumber-, and squash-origin strains, respectively. Our results provide the first evidence of genetic diversity within E. tracheiphila and suggest that strain specificity is associated with plant host. This advance is a first step toward understanding the genetic and population structure of E. tracheiphila.

  6. Foot-and-Mouth Disease Virus Serotype O Phylodynamics: Genetic Variability Associated with Epidemiological Factors in Pakistan

    DEFF Research Database (Denmark)

    Brito, B. P.; Perez, A. M.; Jamal, S. M.;

    2013-01-01

    One of the most challenging aspects of foot-and-mouth disease (FMD) control is the high genetic variability of the FMD virus (FMDV). In endemic settings such as the Indian subcontinent, this variability has resulted in the emergence of pandemic strains that have spread widely and caused devastati...... into Europe (Bulgaria) and Africa (Libya)....

  7. Climate variables explain neutral and adaptive variation within salmonid metapopulations: the importance of replication in landscape genetics.

    Science.gov (United States)

    Hand, Brian K; Muhlfeld, Clint C; Wade, Alisa A; Kovach, Ryan P; Whited, Diane C; Narum, Shawn R; Matala, Andrew P; Ackerman, Michael W; Garner, Brittany A; Kimball, John S; Stanford, Jack A; Luikart, Gordon

    2016-02-01

    Understanding how environmental variation influences population genetic structure is important for conservation management because it can reveal how human stressors influence population connectivity, genetic diversity and persistence. We used riverscape genetics modelling to assess whether climatic and habitat variables were related to neutral and adaptive patterns of genetic differentiation (population-specific and pairwise FST ) within five metapopulations (79 populations, 4583 individuals) of steelhead trout (Oncorhynchus mykiss) in the Columbia River Basin, USA. Using 151 putatively neutral and 29 candidate adaptive SNP loci, we found that climate-related variables (winter precipitation, summer maximum temperature, winter highest 5% flow events and summer mean flow) best explained neutral and adaptive patterns of genetic differentiation within metapopulations, suggesting that climatic variation likely influences both demography (neutral variation) and local adaptation (adaptive variation). However, we did not observe consistent relationships between climate variables and FST across all metapopulations, underscoring the need for replication when extrapolating results from one scale to another (e.g. basin-wide to the metapopulation scale). Sensitivity analysis (leave-one-population-out) revealed consistent relationships between climate variables and FST within three metapopulations; however, these patterns were not consistent in two metapopulations likely due to small sample sizes (N = 10). These results provide correlative evidence that climatic variation has shaped the genetic structure of steelhead populations and highlight the need for replication and sensitivity analyses in land and riverscape genetics.

  8. Climate variables explain neutral and adaptive variation within salmonid metapopulations: The importance of replication in landscape genetics

    Science.gov (United States)

    Hand, Brian K; Muhlfeld, Clint C.; Wade, Alisa A.; Kovach, Ryan; Whited, Diane C.; Narum, Shawn R.; Matala, Andrew P; Ackerman, Michael W.; Garner, B. A.; Kimball, John S; Stanford, Jack A.; Luikart, Gordon

    2016-01-01

    Understanding how environmental variation influences population genetic structure is important for conservation management because it can reveal how human stressors influence population connectivity, genetic diversity and persistence. We used riverscape genetics modelling to assess whether climatic and habitat variables were related to neutral and adaptive patterns of genetic differentiation (population-specific and pairwise FST) within five metapopulations (79 populations, 4583 individuals) of steelhead trout (Oncorhynchus mykiss) in the Columbia River Basin, USA. Using 151 putatively neutral and 29 candidate adaptive SNP loci, we found that climate-related variables (winter precipitation, summer maximum temperature, winter highest 5% flow events and summer mean flow) best explained neutral and adaptive patterns of genetic differentiation within metapopulations, suggesting that climatic variation likely influences both demography (neutral variation) and local adaptation (adaptive variation). However, we did not observe consistent relationships between climate variables and FST across all metapopulations, underscoring the need for replication when extrapolating results from one scale to another (e.g. basin-wide to the metapopulation scale). Sensitivity analysis (leave-one-population-out) revealed consistent relationships between climate variables and FST within three metapopulations; however, these patterns were not consistent in two metapopulations likely due to small sample sizes (N = 10). These results provide correlative evidence that climatic variation has shaped the genetic structure of steelhead populations and highlight the need for replication and sensitivity analyses in land and riverscape genetics.

  9. Genetic variability among the wild boars (Sus scrofa scrofa, crossbred animals and pigs using microsatellite markers (STRs

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    Paula Viana Correa da Silva

    2011-04-01

    Full Text Available The aim of this work was to study the genetic variability among the wild boars, crossbred animals and pigs using microsatellite markers. Five genetic groups were studied. The fragments of three microsatellites developed for Sus scrofa domestica - IGF1, ACTG2 and TNFB - were amplified through PCR technique to evaluate the expected intra populacion variability (He and observed (Ho heterozygosity, and endogamy coefficient (F IS within each population and inter population variability F IS , testing relationship among five genetic groups to establish the genetic distance among them. The high level of observed heterozygosity values varied between 0.537 and 0.7871. Generally, F IS was low, suggesting that the endogamy did not exist between the tested animals.

  10. Variability in seed traits and genetic divergence in a clonal seed orchard of Dalbergia sissoo Roxb.

    Institute of Scientific and Technical Information of China (English)

    Ombir singh; Altaf Hussain Soft

    2012-01-01

    The variations in seed and pod traits,genetic superiority and genetic divergence were evaluated for a Clonal Seed Orchard (CSO) of Dalbergia sissoo Roxb.at Bithmera,India consisting of 20 clones from different agro-climatic conditions of four northern states (Uttar Pradesh,Uttarakhand,Haryana and Rajasthan).The seeds and pods of various clones in the orchard exhibited significant variability in size,weight and other characters.Significant positive correlations were observed between seed length and seed width (p<0.05),seed length and seed thickness (p<0.01),seed length and seed weight (p<0.0l),seed thickness and seed weight (p<0.01),seed length and germination value (p<0.05).The genetic parameters for seed and pod traits also showed a wide range of variations in the orchard.Heritability values were found to be over 50 vpereent for most of the seed and pod traits.Seed weight,seed length and seed thickness showed high heritability values coupled with maximum genetic gain for these characters.Ward's minimum variance dendrogram of clones of D.sissoo showed three distinct clusters; cluster 1 was the largest with 12 better clones whereas cluster 2 and 3 consisting of seven moderate clones and one poor clone,respectively.Mean cluster values showed sufficient variation among the clusters for seed weight,germination value and seed length.The possible hybridization between best clones of cluster 1 to the disease resistant clone of cluster 2 (resistant against deadly Gandoderma lucidum root rot disease of D.sissoo) is also suggested for further breeding programmes of the species.The deployment of clone 194 (better performed and disease resistant) is also recommended in future plantation programmes of D.sissoo in northern India.

  11. [Genetic variability of juniper tall (Juniperus excelsa Bieb.) in the northern and southern limits of the natural distribution].

    Science.gov (United States)

    Korshikov, I I; Nikolaeva, A V

    2013-01-01

    Genetic structure, subdivision and differentiation of six populations of juniper tall (Juniperus excelsa Bieb.) of the Crimean Mountains and of one population in Lebanon were investigated using 18 polymorphic allozyme loci as genetic markers. The high level of genetic variability of J. excelsa was established in the northern and the southern limits of its natural habitat. The mean values of the main indicators of genetic polymorphism were: P99 = 1,000, A = 3,167, H(E) = 0,370, H(o) = 0,405. Subdivision and differentiation of populations were low (F(ST) = 0,032, D(N) = 0,026) indicating similarity of their gene pools.

  12. Components of genetic variability and heritability of grain yield of silage maize

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    Sečanski Mile D.

    2004-01-01

    Full Text Available The aim of the present study was to evaluate the following parameters for the grain yield of silage maize: variability of inbred lines and their diallel hybrids, superior-parent heterosis and components of genetic variability and heritability on the basis of the diallel set. The two-year four-replicate trial was set up according to the randomized complete-block design at Zemun Polje. It was determined that a genotype, year and their interaction significantly affected variability of this trait. The highest. i.e. the lowest grain yield, on the average for both investigation years. was recorded in the silage maize inbred lines ZPLB402 and ZPLB405. respectively. The analysis of components of genetic variance for grain yield shows that the additive component (D was lower than the dominant (H1 and H2 genetic variance, while a positive component F and the frequency of dominant (u and recessive (v genes for this observed trait point to prevalence of dominant genes over recessive ones. Furthermore. this is confirmed by the ratio of dominant to recessive genes in parental genotypes for grain yield (Kd/Kr> 1 that is greater than unity in both years of investigation. The estimated value of the average degree of dominance (H1/D1/2 exceeds unity, pointing out to superdominance in inheritance of this trait in both years of investigation. Results of Vr/Vr regression analysis indicate superdominance in inheritance of grain yield. Moreover. a registered presence of non-allelic interaction points out to the need to study effects of epistasis, as it can have a greater significance in certain hybrids. A greater value of dominant than additive variance resulted in high values of broad-sense heritability for grain yield in both investigation years (98.71%, i.e. 97.19% in 1997, i.e. 1998, respectively. and low values of narrow-sense heritability (11.9% in 1997 and 12.2% in 1998.

  13. SOUR CHERRY (Prunus cerasus L. GENETIC VARIABILITY AND PHOTOSYNTHETIC EFFICIENCY DURING DROUGHT

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    Marija Viljevac

    2012-12-01

    Full Text Available Sour cherry is an important fruit in Croatian orchards. Cultivar Oblačinska is predominant in existing orchards with noted intracultivar phenotypic heterogeneity. In this study, the genetic variability of 22 genotypes of cvs. Oblačinska, Maraska and Cigančica, as well as standard cvs. Kelleris 14, Kelleris 16, Kereška, Rexelle and Heimann conserved were investigated. Two types of molecular markers were used: microsatellite markers (SSR in order to identify intercultivar, and AFLP in order to identify intracultivar variabilities. A set of 12 SSR markers revealed small genetic distance between cvs. Maraska and Oblačinska while cv. Cigančica is affined to cv. Oblačinska. Furthermore, cvs. Oblačinska, Cigančica and Maraska were characterized compared to standard ones. AFLP markers didn`t confirm significant intracultivar variability of cv. Oblačinska although the variability has been approved at the morphological, chemical and pomological level. Significant corelation between SSR and AFLP markers was found. Identification of sour cherry cultivars tolerant to drought will enable the sustainability of fruit production with respect to the climate change in the future. For this purpose, the tolerance of seven sour cherry genotypes (cvs. Kelleris 16, Maraska, Cigančica and Oblačinska represented by 4 genotypes: OS, 18, D6 and BOR to drought conditions was tested in order to isolate genotypes with the desired properties. In the greenhouse experiment, cherry plants were exposed to drought stress. The leaf relative water content, OJIP test parameters which specify efficiency of the photosynthetic system based on measurements of chlorophyll a fluorescence, and concentrations of photo-synthetic pigments during the experiment were measured as markers of drought tolerance. Photosynthetic performance index (PIABS comprises three key events in the reaction centre of photosystem II affecting the photosynthetic activity: the absorption of energy

  14. Genetic variability in environmental isolates of Legionella pneumophila from Comunidad Valenciana (Spain).

    Science.gov (United States)

    Coscollá, Mireia; Gosalbes, María José; Catalán, Vicente; González-Candelas, Fernando

    2006-06-01

    Legionella pneumophila is associated to recurrent outbreaks in several Comunidad Valenciana (Spain) localities, especially in Alcoi, where social and climatic conditions seem to provide an excellent environment for bacterial growth. We have analysed the nucleotide sequences of three loci from 25 environmental isolates from Alcoi and nearby locations sampled over 3 years. The analysis of these isolates has revealed a substantial level of genetic variation, with consistent patterns of variability across loci, and comparable to that found in a large, European-wide sampling of clinical isolates. Among the tree loci studied, fliC showed the highest level of nucleotide diversity. The analysis of isolates sampled in different years revealed a clear differentiation, with samples from 2001 being significantly distinct from those obtained in 2002 and 2003. Furthermore, although linkage disequilibrium measures indicate a clonal nature for population structure in this sample, the presence of some recombination events cannot be ruled out.

  15. MORPHOLOGICAL TRAITS AS TOOL TO VERIFY GENETIC VARIABILITY OF INTERSPECIFIC DRAGON FRUIT HYBRIDS

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    ADRIANA DE CASTRO CORREIA DA SILVA

    Full Text Available ABSTRACT With recent cultivation in Brazil, the dragon fruit still have lacks related to the selection of promising materials and there are not yet commercial varieties in the country. Therefore, manual pollination cross were held in 2010, between plants of H. undatus x H. polyrhizus and H. undatus x H. setaceus. Aiming evaluate the genetic diversity of the progenies for future use in breeding program, based on cladodes characteristics, six characters were assessed: length and diameter of stem, distance between areoles, arch height, number and size of spines/areole. From the Euclidean distance matrix analysis was constructed a dendrogram by the UPGMA method. There was great variability among hybrids, and eight of them have shown promise for use in breeding program.

  16. Copy number variants and genetic traits: closer to the resolution of phenotypic to genotypic variability.

    Science.gov (United States)

    Beckmann, Jacques S; Estivill, Xavier; Antonarakis, Stylianos E

    2007-08-01

    A considerable and unanticipated plasticity of the human genome, manifested as inter-individual copy number variation, has been discovered. These structural changes constitute a major source of inter-individual genetic variation that could explain variable penetrance of inherited (Mendelian and polygenic) diseases and variation in the phenotypic expression of aneuploidies and sporadic traits, and might represent a major factor in the aetiology of complex, multifactorial traits. For these reasons, an effort should be made to discover all common and rare copy number variants (CNVs) in the human population. This will also enable systematic exploration of both SNPs and CNVs in association studies to identify the genomic contributors to the common disorders and complex traits.

  17. α-synuclein genetic variability: A biomarker for dementia in Parkinson disease.

    Science.gov (United States)

    Guella, Ilaria; Evans, Daniel M; Szu-Tu, Chelsea; Nosova, Ekaterina; Bortnick, Stephanie F; Goldman, Jennifer G; Dalrymple-Alford, John C; Geurtsen, Gert J; Litvan, Irene; Ross, Owen A; Middleton, Lefkos T; Parkkinen, Laura; Farrer, Matthew J

    2016-06-01

    The relationship between Parkinson disease (PD), PD with dementia (PDD), and dementia with Lewy bodies (DLB) has long been debated. Although PD is primarily considered a motor disorder, cognitive impairment is often present at diagnosis, and only ∼20% of patients remain cognitively intact in the long term. Alpha-synuclein (SNCA) was first implicated in the pathogenesis of the disease when point mutations and locus multiplications were identified in familial parkinsonism with dementia. In worldwide populations, SNCA genetic variability remains the most reproducible risk factor for idiopathic PD. However, few investigators have looked at SNCA variability in terms of cognitive outcomes. We have used targeted high-throughput sequencing to characterize the 135kb SNCA locus in a large multinational cohort of patients with PD, PDD, and DLB and healthy controls. An analysis of 43 tagging single nucleotide polymorphisms across the SNCA locus shows 2 distinct association profiles for symptoms of parkinsonism and/or dementia, respectively, toward the 3' or the 5' of the SNCA gene. In addition, we define a specific haplotype in intron 4 that is directly associated with PDD. The PDD risk haplotype has been interrogated at single nucleotide resolution and is uniquely tagged by an expanded TTTCn repeat. Our data show that PD, PDD, and DLB, rather than a disease continuum, have distinct genetic etiologies albeit within one genomic locus. Such results may serve as prognostic biomarkers to these disorders, to inform physicians and patients, and to assist in the design and stratification of clinical trials aimed at disease modification. Ann Neurol 2016;79:991-999. © 2016 American Neurological Association.

  18. Epidemiology and genetic variability of HHV-8/KSHV in Pygmy and Bantu populations in Cameroon.

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    Edouard Betsem

    2014-05-01

    Full Text Available BACKGROUND: Kaposi's sarcoma associated herpesvirus (KSHV/HHV-8 is the causal agent of all forms of Kaposi sarcoma. Molecular epidemiology of the variable K1 region identified five major subtypes exhibiting a clear geographical clustering. The present study is designed to gain new insights into the KSHV epidemiology and genetic diversity in Cameroon. METHODOLOGY/PRINCIPAL FINDINGS: Bantu and Pygmy populations from remote rural villages were studied. Antibodies directed against latent nuclear antigens (LANA were detected by indirect immunofluorescence using BC3 cells. Peripheral blood cell DNAs were subjected to a nested PCR amplifying a 737 bp K1 gene fragment. Consensus sequences were phylogenetically analyzed. We studied 2,063 persons (967 females, 1,096 males, mean age 39 years, either Bantus (1,276 or Pygmies (787. The Bantu group was older (42 versus 35 years: P<10(-4. KSHV anti-LANA seroprevalence was of 37.2% (768/2063, with a significant increase with age (P<10(-4 but no difference according to sex. Seroprevalence, as well as the anti-LANA antibodies titres, were higher in Bantus (43.2% than in Pygmies (27.6% (P<10(-4, independently of age. We generated 29 K1 sequences, comprising 24 Bantus and five Pygmies. These sequences belonged to A5 (24 cases or B (five cases subtypes. They exhibited neither geographical nor ethnic aggregation. A5 strains showed a wide genetic diversity while the B strains were more homogenous and belonged to the B1 subgroup. CONCLUSION: These data demonstrate high KSHV seroprevalence in the two major populations living in Southern and Eastern Cameroon with presence of mostly genetically diverse A5 but also B K1 subtypes.

  19. Variability, heritability and genetic association in vegetable amaranth (Amaranthus tricolor L.)

    Energy Technology Data Exchange (ETDEWEB)

    Sarker, U.; Islam, Md T.; Rabbani, Md G.; Oba, S.

    2015-07-01

    Forty three vegetable amaranth (Amaranthus tricolor L.) genotypes selected from different eco-geographic regions of Bangladesh were evaluated during 3 years (2012-2014) for genetic variability, heritability and genetic association among mineral elements and quality and agronomic traits in randomized complete block design (RCBD) with five replications. The analysis showed that vegetable amaranth is a rich source of K, Ca, Mg, proteins and dietary fibre with average values among the 43 genotypes (1.014%, 2.476%, 2.984, 1.258% and 7.81%, respectively). Six genotypes (VA13, VA14, VA16, VA18, VA26, VA27) showed a biological yield >2000 g/m2 and high mineral, protein and dietary fibre contents; eleven genotypes had high amount of minerals, protein and dietary fibre with above average biological yield; nine genotypes had below average biological yield but were rich in minerals, protein and dietary fibre. Biological yield exhibited a strong positive correlation with leaf area, shoot weight, shoot/root weight and stem base diameter. Insignificant genotypic correlation was observed among mineral, quality and agronomic traits, except K vs. Mg, protein vs. dietary fibre and stem base diameter vs. Ca. Some of these genotypes can be used for improvement of vegetable amaranth regarding mineral, protein and dietary fibre content without compromising yield loss. (Author)

  20. Prioritizing individual genetic variants after kernel machine testing using variable selection.

    Science.gov (United States)

    He, Qianchuan; Cai, Tianxi; Liu, Yang; Zhao, Ni; Harmon, Quaker E; Almli, Lynn M; Binder, Elisabeth B; Engel, Stephanie M; Ressler, Kerry J; Conneely, Karen N; Lin, Xihong; Wu, Michael C

    2016-12-01

    Kernel machine learning methods, such as the SNP-set kernel association test (SKAT), have been widely used to test associations between traits and genetic polymorphisms. In contrast to traditional single-SNP analysis methods, these methods are designed to examine the joint effect of a set of related SNPs (such as a group of SNPs within a gene or a pathway) and are able to identify sets of SNPs that are associated with the trait of interest. However, as with many multi-SNP testing approaches, kernel machine testing can draw conclusion only at the SNP-set level, and does not directly inform on which one(s) of the identified SNP set is actually driving the associations. A recently proposed procedure, KerNel Iterative Feature Extraction (KNIFE), provides a general framework for incorporating variable selection into kernel machine methods. In this article, we focus on quantitative traits and relatively common SNPs, and adapt the KNIFE procedure to genetic association studies and propose an approach to identify driver SNPs after the application of SKAT to gene set analysis. Our approach accommodates several kernels that are widely used in SNP analysis, such as the linear kernel and the Identity by State (IBS) kernel. The proposed approach provides practically useful utilities to prioritize SNPs, and fills the gap between SNP set analysis and biological functional studies. Both simulation studies and real data application are used to demonstrate the proposed approach.

  1. Basil (Ocimum basilicum Genetic Variability and Viral Disease Assessment in Nigeria

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    O.D. Ojo

    2012-01-01

    Full Text Available The study aims at assessing Basil’s genetic phenotypic variability and viral disease incidence in Nigeria for sustainable pathological interventions. Basil (Ocimum basilicum is important for it’s medicinal and nutritive value. It is highly adaptable as a potential crop in the tropics and could therefore enhance the food security of sub Saharan Africa nations. Germplasm seed evaluation and characterization was therefore carried out from the nationwide National Horticultural Research Institute (NIHORT seed collection survey to expand NIHORT basil genetic base. The field layout was completely randomized design with five replications. The treatments were: O. basilicum, O. gratissimum and the local basil. Treatments were randomly allocated per replication. There were significant phenotypic differences in the O. basilicum variety. These differences were observed in the plant coloration ranging from deep to light purple coloration of stem, leaf, leaf vein and petiole. Our observations also revealed for the first time significant tolerance to Venial Mottle Mosaic Virus (VMMV in the purple colored compared to the green O. basilicum in the early stages of growth till 50% anthesis. This is the first report of this observation in the African continent. Tolerance to VMMV symptoms increased significantly (LSD 5% with purplish coloration. We concluded that inducement of purplish coloration in Basil through breeding might improve tolerance to VMMV and thereby increase market value of Basil with sustainable pathological interventions.

  2. Variability, heritability and genetic association in vegetable amaranth (Amaranthus tricolorL.

    Directory of Open Access Journals (Sweden)

    Umakanta Sarker

    2015-06-01

    Full Text Available Forty three vegetable amaranth (Amaranthus tricolor L. genotypes selected from different eco-geographic regions of Bangladesh were evaluated during 3 years (2012-2014 for genetic variability, heritability and genetic association among mineral elements and quality and agronomic traits in randomized complete block design (RCBD with five replications. The analysis showed that vegetable amaranth is a rich source of K, Ca, Mg, proteins and dietary fibre with average values among the 43 genotypes (1.014%, 2.476%, 2.984, 1.258% and 7.81%, respectively. Six genotypes (VA13, VA14, VA16, VA18, VA26, VA27 showed a biological yield >2000 g/m2 and high mineral, protein and dietary fibre contents; eleven genotypes had high amount of minerals, protein and dietary fibre with above average biological yield; nine genotypes had below average biological yield but were rich in minerals, protein and dietary fibre. Biological yield exhibited a strong positive correlation with leaf area, shoot weight, shoot/root weight and stem base diameter. Insignificant genotypic correlation was observed among mineral, quality and agronomic traits, except K vs. Mg, protein vs. dietary fibre and stem base diameter vs. Ca. Some of these genotypes can be used for improvement of vegetable amaranth regarding mineral, protein and dietary fibre content without compromising yield loss.

  3. A colony of dog guides: analysis of the genetic variability assessed by pedigree data

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    Roberta Ciampolini

    2010-01-01

    Full Text Available The study presents the analysis of the genetic variability in a colony of dog guides. Three breeds, Labrador (L, Golden Retriever (GR, and German Shepherd (GS, were evaluated. Pedigrees data on 370 L, 260 GR, and 85 GS dogs bred for guide by the National Guide Dog School (SNCG of Scandicci (Florence, Italy were used. Data were available beginning from 1994. The average coefficient of coancestry and the mean F were 0.8% and 0.45% in GR, 0.7% and 0.38% in L, 1.0% and 0.49% in GS, respectively. The rate of increase in inbreeding was lower in L population (0.17 than in GR population (0.54, while in GS only the dogs with 5 e 7 traced generations resulted inbred. The results of this research point out that the genetic management of the dogs seems to be carefully and rationally monitored. Nevertheless, the population that may require a greater attention seems to be the GR, where a higher increase of the coefficient of inbreeding per generation is observed; therefore, the importation of germplasm from other working dogs is desirable in order to avoid in future an excessive increase of the inbreeding that could lead to adverse consequences for dogs health and fertility.

  4. Variability of yield traits and disease resistance in winter triticale genetic resources accessions

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    Wanda Kociuba

    2014-07-01

    Full Text Available A systematic gathering of winter triticale accessions was started in Poland in 1982 by the Institute of Genetics, Breeding and Seed Science at the Agricultural University in Lublin (at present its name is: Institute of Genetics, Breeding and Plant Biotechnology at the University of Life Sciences in Lublin. First, breeding lines obtained in local breeding stations were gathered. Next, accessions were imported from the following world gene banks: Beltsville, Gatersleben, and VIR. Interesting hybrid materials obtained in research centers were also included in the collection. Now, the collection includes 2349 accessions (1329 of winter triticale and 1020 of spring triticale. The evaluation is conducted in a 4-year cycle of field experiments using the same methods. The gathered accessions represent a large range of variability of both morphological and commercial traits. The large differentiation of accessions especially concerns traits such as: plant height, number and weight of grains per spi- ke, protein content in grain, field resistance to powdery mildew, brown rust and leaf and spike diseases.

  5. GENETIC VARIABILITY OF CULTURED PLANT TISSUES UNDER NORMAL CONDITIONS AND UNDER STRESS

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    Dolgikh Yu.I.

    2012-08-01

    Full Text Available The genetic variability induced by in vitro conditions known as somaclonal variation is of practical interest due to its potential uses in plant breeding but, on the other hand, if clonal propagation or transformation is main goal, it becomes an unwelcome phenomenon. Thus, it is important to know frequency, the genomic distribution, the mechanisms and factors influencing somaclonal variation. We studied variability of PCR-based DNA markers of cultured tissues and regenerated plants of maize and bread wheat. The original A188 line of maize and the somaclones obtained were tested using 38 RAPD and 10 ISSR primers. None of the A188 plants showed variation in the RAPD and ISSR spectra for any of the primers used. However, the PCR spectra obtained from the somaclones demonstrated some variations, i.e., 22 RAPD primers and 6 ISSR primers differentiated at least one somaclonal variant from the progenitor line. Six SCAR markers were developed based on several RAPD and ISSR fragments. The inheritance of these SCAR markers was verified in the selfing progeny of each somaclone in the R1–R4 generations and in the hybrids, with A188 as the parental line in the F1 and F2 generations. These markers were sequenced and bioinformatic searches were performed to understand the molecular events that may underlie the variability observed in the somaclones. All changes were found in noncoding sequences and were induced by different molecular events, such as the insertion of long terminal repeat transposon, precise miniature inverted repeat transposable element (MITE excision, microdeletion, recombination, and a change in the pool of mitochondrial DNA. In two groups of independently produced somaclones, the same features (morphological, molecular were variable, which confirms the theory of ‘hot spots’ occurring in the genome. The presence of the same molecular markers in the somaclones and in different non-somaclonal maize variants suggests that in some cases

  6. Pedigree analysis of the Turkish Arab horse population: structure, inbreeding and genetic variability.

    Science.gov (United States)

    Duru, S

    2017-09-01

    The aim of this study was to evaluate genetic variability in the Turkish Arab horse population using pedigree information. This study is the first detailed pedigree analysis of the breed in Turkey. Pedigree data were collected from the National Studbook. The pedigree data for 23 668 horses, born between 1904 and 2014, were used in the analysis. From this data set, a reference population (RP) of 14 838 animals symbolising the last generation was defined. Demographic parameters, the inbreeding level (F), the average relatedness (AR), the effective population size (N e), the effective number of founders (f e), the effective number of ancestors (f a) and the number of founder genome equivalents (f g) were calculated for the population. The average generation interval for the RP was 12.2±4.6 years, whereas the calculated pedigree completeness levels were 98.2%, 96.6% and 95.0% for the first, second and third known generations. The mean equivalent generations (t), the average complete generations and the mean maximum generations for the RP were 7.8, 5.4 and 12.2, respectively, whereas the mean F and AR were 4.6% and 9.5% for the RP. The rate of inbred animals was 94.2% for the RP, whereas the number of founders, the number of ancestors and the f e, f a and f g were 342, 223, 40, 22 and 9.6 for the RP. The large differences observed between f e, and the number of founders demonstrates that genetic diversity decreased between the founder and the RP. Contribution of the 14 most influential founder to the RP was 50.0%, whereas just eight ancestral horses can account for 50% of the genetic variability. N e estimated via an individual increase in inbreeding per generation ( $$ \\hskip3pt{\\bar{\\hskip-2ptN}_{{\\rm e}} } $$ ), and paired increase in coancestry $$\\left(\\! \\hskip3pt{\\bar{\\hskip-2ptN}_{{ eC}} } \\right)$$ , were 74.4±3.9 and 73.5±0.58, respectively. The inbreeding increases with the pedigree knowledge. In addition, the decrease in inbreeding in last years

  7. First evidence of genetic intraspecific variability and occurrence of Entamoeba gingivalis in HIV(+)/AIDS.

    Science.gov (United States)

    Cembranelli, Sibeli B S; Souto, Fernanda O; Ferreira-Paim, Kennio; Richinho, Túlio T; Nunes, Poliana L; Nascentes, Gabriel A N; Ferreira, Thatiana B; Correia, Dalmo; Lages-Silva, Eliane

    2013-01-01

    Entamoeba gingivalis is considered an oral commensal but demonstrates a pathogenic potential associated with periodontal disease in immunocompromised individuals. Therefore, this study evaluated the occurrence, opportunistic conditions, and intraspecific genetic variability of E. gingivalis in HIV(+)/AIDS patients. Entamoeba gingivalis was studied using fresh examination (FE), culture, and PCR from bacterial plaque samples collected from 82 HIV(+)/AIDS patients. Genetic characterization of the lower ribosomal subunit of region 18S (18S-SSU rRNA) was conducted in 9 positive samples using low-stringency single specific primer PCR (LSSP-PCR) and sequencing analysis. Entamoeba gingivalis was detected in 63.4% (52/82) of the samples. No association was detected between the presence of E. gingivalis and the CD4(+) lymphocyte count (≤200 cells/mm(3) (p = 0.912) or viral load (p = 0.429). The LSSP-PCR results helped group E. gingivalis populations into 2 polymorphic groups (68.3% similarity): group I, associated with 63.6% (7/11) of the samples, and group II, associated with 36.4% (4/11) of the samples, which shared 74% and 83.7% similarity and association with C and E isolates from HIV(-) individuals, respectively. Sequencing of 4 samples demonstrated 99% identity with the reference strain ATCC 30927 and also showed 2 divergent clusters, similar to those detected by LSSP-PCR. Opportunistic behavior of E. gingivalis was not detected, which may be related to the use of highly active antiretroviral therapy by all HIV(+)/AIDS patients. The high occurrence of E. gingivalis in these patients can be influenced by multifactorial components not directly related to the CD4(+) lymphocyte counts, such as cholesterol and the oral microbiota host, which could mask the potential opportunistic ability of E. gingivalis. The identification of the 18S SSU-rRNA polymorphism by LSSP-PCR and sequencing analysis provides the first evidence of genetic variability in E. gingivalis

  8. Tomato second cycle hybrids as a source of genetic variability for fruit quality traits

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    Pereira da Costa JH

    2016-11-01

    Full Text Available The objective of this study was to investigate the phenotypic and molecular variability in a F2 generation derived from a SCH (Second Cycle Hybrid in order to detect QTLs for some fruit traits of tomato. Genome coverage at different levels was achieved by three types of molecular markers (polypeptides, sequence-related amplified polymorphism-SRAP and amplified restriction fragment polymorphism - AFLP. Different degrees of polymorphism were detected by SRAP and AFLP at the DNA structure level and also by polypeptides at the DNA expression level. The first two markers, associated with phenotypic variation, detected QTLs involved in important agronomic traits such as fruit shelf life, soluble solids content, pH, and titratable acidity. New gene blocks originated by recombination during the first cycle of crossing were detected. This study confirmed that the observed phenotypic differences represent a new gene rearrangement and that these new gene blocks are responsible for the presence of the genetic variability detected for these traits.

  9. Genetic variability in three Italian beef cattle breeds derived from pedigree information

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    Francesco Filippini

    2010-01-01

    Full Text Available The aim of the present work was to estimate genetic variability in Chianina (CH, Marchigiana (MC and Romagnola (RO breeds using pedigree information. Different approaches based on probability of identity-by-descent (effective population size through an increase in inbreeding Ne or probability of gene origin (total number of founders f, effective number of founders fe, ancestors fa and founder genomes fg were used. Reference populations were defined using female animals born between 1996 and 2000 where both parents are known. Generation intervals were 5.35, 4.93 and 5.15 years for CH, MC and RO, respectively. The total number of founders were 7092, 11947, 3928, for CH, MC and RO, respectively. Complete generation equivalent showed the relative high quality of pedigree information: 5.66 for CH, 4.54 for MC and 4.95 for RO. For CH, MC and RO, respectively, a fe value of 152.1, 70.9 and 89.8, a fa value of 73.6, 48.0 and 59.5 and a fg value of 39.5, 25.0 and 38.5, were calculated. When inbreeding was used effective population sizes were 138, 122 and 124 for CH, MC and RO, respectively. Parameters derived from the probabilities of gene origin were variable among the investigated breeds and the results for MC demonstrate the need to pay specific attention to breeding strategies.

  10. Genetic variability of Brazilian populations of Lymnaea columella (Gastropoda: Lymnaeidae), an intermediate host of Fasciola hepatica (Trematoda: Digenea).

    Science.gov (United States)

    Cardoso, Paula Cristina Marques; Caldeira, Roberta Lima; Lovato, Maria Bernadete; Coelho, Paulo Marcos Zech; Berne, Maria Elisabeth Aires; Müller, Gertrud; Carvalho, Omar dos Santos

    2006-03-01

    In Brazil, Lymnaea columella is the most important intermediate host of Fasciola hepatica, the etiological agent of fasciolosis, which is a parasitic disease of veterinarian and human importance. Random amplified polymorphic DNA (RAPD) was used to investigate the genetic variability within and among nine Brazilian populations of L. columella comprising 205 individuals. A number of four primers were used for analysis of molecular variance (AMOVA). Out of 83 RAPD markers, 63 (76%) were polymorphic and revealed 119 unique RAPD profiles. The levels of genetic variability found in the populations were low and most of the genetic variation was interpopulational (81.6%) when compared to intrapopulational variability (18.4%). These results are in accordance with the dynamics and distribution of the populations analyzed.

  11. Genetic characterization of Toxoplasma gondii isolates from Portugal, Austria, and Israel reveals higher genetic variability within the type II lineage

    Science.gov (United States)

    This study compared genetic diversity of Toxoplasma gondii isolates from Portugal, Austria and Israel. For this, we genotyped 90 T. gondii isolates (16 from Portugal, 67 from Austria and 7 from Israel) using 10 nested PCR-restriction length polymorphism (RFLP) genetic markers and 15 microsatellite (...

  12. Induced genetic variability and correlation studies for yield and its component traits in Groundnut (Arachis hypogaea L.

    Directory of Open Access Journals (Sweden)

    Channayya P. Hiremath , H. L. Nadaf and Keerthi,C.M

    2011-03-01

    Full Text Available Groundnut is one of the principal economic oilseed crops of the world, which has been exposed extensively to mutagenictreatments for induction of genetic variability. In the present experiment, estimates of genetic variability, heritability and geneticadvance were assessed for 12 different quantitative traits in the mutants derived from two Spanish Bunch groundnut cultivars, viz.TPG-41 and GPBD-4 with chemical and physical mutagenic agents. Wide genetic variations were observed for most of thequantitative traits studied as evidenced by higher mean, range, PCV and GCV values. Further genetic improvement throughselection for yield improvement should rely on number of primary branches per plant, 100-kernel weight, SMK% and shellingper cent as these mutants recorded higher genetic variability, heritability and genetic advance for these quantitative traits. Podyield was positively and significantly associated with number of primary branches, pod weight per plant, 100-kernel weight,sound matured per cent kernel and oil yield. These results clearly indicate that idirect selection for yield in groundnut is possiblethrough simultaneous improvement of these yield components

  13. The assessment of genetic variability and taxonomic affi nity of local pummelo accessions from Yogyakarta, Indonesia based on RAPD

    Directory of Open Access Journals (Sweden)

    Ratna Susandarini

    2016-02-01

    Full Text Available Pummelo (Citrus maxima is one of three biotypes considered as true species within the genus Citrus.A major issue of pummelo taxonomy in Indonesia is the high number of cultivars showing variability inphenotypic characters but of unknown genetic diversity. In this study, the assessment of genetic variabilityand taxonomic affi nity of local accessions of C. maxima from Yogyakarta was examined based on RAPDfi ngerprinting. The availability of universal primers and technical simplicity makes RAPD as a molecular toolof choice for the assessment of genetic variability at various taxonomic levels. In this study, 13 accessions of C.maxima collected from Yogyakarta were observed for their genetic variability. An additional three registeredcultivars were included for comparative purpose. Two decamer primers used for the amplifi cation of DNAproduced 222 bands with 174 of them were polymorphic. The data was subjected to cluster analysis to observethe grouping of accessions and taxonomic affi nity. Results indicated high genetic variability among accessions.The dendrogram constructed using UPGMA method based on simple matching coeffi cient showed twomain clusters were which was in line to morphological characters. The grouping of accessions showed cleardifferentiation between accessions bearing white and those with reddish fruit fl esh, and thus demonstratestaxonomic value of this study in recognizing important agronomic character for this tropical fruit crop.

  14. Behavior Genetics and the Within-Person Variability of Daily Interpersonal Styles: The Heritability of Flux, Spin and Pulse

    OpenAIRE

    Markey, Patrick M.; Racine, Sarah E.; Markey, Charlotte N; Hopwood, Christopher J.; Keel, Pamela K.; Burt, S. Alexandra; Neale, Michael C.; Sisk, Cheryl L.; Boker, Steven M.; Kelly L. Klump

    2014-01-01

    A classical twin study was used to estimate the magnitude of genetic and environmental influences on four measurements of within-person variability: dominance flux, warmth flux, spin and pulse. Flux refers to the variability of an individual’s interpersonal dominance and warmth. Spin measures changes in the tone of interpersonal styles and pulse measures changes in the intensity of interpersonal styles. Daily reports of interpersonal styles were collected from 494 same-sex female twins (142 m...

  15. Data from: Genetic variation in variability: phenotypic variability of fledging weight and its evolution in a songbird population

    NARCIS (Netherlands)

    Mulder, H.A.; Gienapp, P.; Visser, M.E.

    2016-01-01

    Variation in traits is essential for natural selection to operate and genetic and environmental effects can contribute to this phenotypic variation. From domesticated populations, we know that families can differ in their level of within-family variance, which leads to the intriguing situation that

  16. Occurrence and genetic variability of Phlebotomus papatasi in an urban area of southern Italy

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    Dantas-Torres Filipe

    2010-08-01

    Full Text Available Abstract Background A phlebotomine sand fly was noticed in the second floor of an old building in a highly urbanized area of southern Italy. A short-term entomological survey was carried out in the subsequent weeks to this event, allowing the collection of additional phlebotomine sand flies that were later identified as Phlebotomus papatasi. We assessed the genetic variability among P. papatasi sequences obtained in this study and those available from Italy using a mitochondrial DNA (mtDNA fragment (from cytochrome b gene to NADH1 and the internal transcribed spacer 2 (ITS2 as genetic markers. Results From 9 June to 19 July, eight males and seven females (two blood-fed of P. papatasi were collected in the old town of Bari (southern Italy. The insects were found near the bed and in the bathroom and potential blood sources (e.g., pigeons and dogs for them were common in the neighbourhood. Again, five females of P. papatasi collected in Valenzano, another urban area in the province of Bari, were also identified and included in the genetic study. The mtDNA sequences (945 bp obtained from Bari and Valenzano were identical except for a single transition (T ↔ C at the 793 nucleotide residue. Pairwise comparison of the last 440 bp of the mtDNA fragment analyzed herein with other sequences of P. papatasi from Italy revealed a nucleotide variation ranging from 0.2 to 1.3%. Three ITS2 sequence types were detected within specimens collected in Valenzano, one of them identical to that from Bari. Pairwise comparison of ITS2 sequences of P. papatasi from Italy revealed a nucleotide variation up to 1.8%. Conclusions This study reports the occurrence of P. papatasi in an urban area of southern Italy and shows a low nucleotide difference among ITS2 and mtDNA sequences of this species available from Italy. The presence of P. papatasi in urban areas might represent a risk for human health, particularly for the potential transmission of sandfly fever viruses.

  17. Genetic variability of the whitefly Bemisia tabaci and its secondary endosymbionts in the Arabian Peninsula

    KAUST Repository

    Ragab, Alaa I.

    2013-05-01

    the Q biotype. All endosymbionts were detected, with Hamiltonella as the most predominant. Several instances of co-infection by two or more endosymbionts were observed. Samples from the geographically isolated and mountainous region of Fayfa demonstrated higher genetic variability compared to the other locations, leading to the possible identification of a new haplotype, as well as the first time identification of the A biotype in the region.

  18. Worldwide genetic variability of the Duffy binding protein: insights into Plasmodium vivax vaccine development.

    Directory of Open Access Journals (Sweden)

    Taís Nóbrega de Sousa

    Full Text Available The dependence of Plasmodium vivax on invasion mediated by Duffy binding protein (DBP makes this protein a prime candidate for development of a vaccine. However, the development of a DBP-based vaccine might be hampered by the high variability of the protein ligand (DBP(II, known to bias the immune response toward a specific DBP variant. Here, the hypothesis being investigated is that the analysis of the worldwide DBP(II sequences will allow us to determine the minimum number of haplotypes (MNH to be included in a DBP-based vaccine of broad coverage. For that, all DBP(II sequences available were compiled and MNH was based on the most frequent nonsynonymous single nucleotide polymorphisms, the majority mapped on B and T cell epitopes. A preliminary analysis of DBP(II genetic diversity from eight malaria-endemic countries estimated that a number between two to six DBP haplotypes (17 in total would target at least 50% of parasite population circulating in each endemic region. Aiming to avoid region-specific haplotypes, we next analyzed the MNH that broadly cover worldwide parasite population. The results demonstrated that seven haplotypes would be required to cover around 60% of DBP(II sequences available. Trying to validate these selected haplotypes per country, we found that five out of the eight countries will be covered by the MNH (67% of parasite populations, range 48-84%. In addition, to identify related subgroups of DBP(II sequences we used a Bayesian clustering algorithm. The algorithm grouped all DBP(II sequences in six populations that were independent of geographic origin, with ancestral populations present in different proportions in each country. In conclusion, in this first attempt to undertake a global analysis about DBP(II variability, the results suggest that the development of DBP-based vaccine should consider multi-haplotype strategies; otherwise a putative P. vivax vaccine may not target some parasite populations.

  19. Genetic variability in the natural populations of Lasioderma serricorne (F.) (Coleoptera: Anobiidae), detected by RAPD markers and by esterase isozymes.

    Science.gov (United States)

    Coelho-Bortolo, T; Mangolin, C A; Lapenta, A S

    2016-02-01

    Lasioderma serricorne (F.) is a small cosmopolitan beetle regarded as a destructive pest of several stored products such as grains, flour, spices, dried fruit and tobacco. Chemical insecticides are one of the measures used against the pest. However, intensive insecticide use has resulted in the appearance of resistant insect populations. Therefore, for the elaboration of more effective control programs, it is necessary to know the biological aspects of L. serricorne. Among these aspects, the genetic variability knowledge is very important and may help in the development of new control methods. The objective of this study was to evaluate the genetic variability of 11 natural populations of L. serricorne collected respectively in three and four towns in the states of Paraná and São Paulo, Brazil, using 20 primers random amplified polymorphic DNA (RAPD) and polymorphisms of esterases. These primers produced 352 polymorphic bands. Electrophoretic analysis of esterases allowed the identification of four polymorphic loci (Est-2, Est-4, Est-5 and Est-6) and 18 alleles. Results show that populations are genetically differentiated and there is a high level of genetic variability within populations. The high degree of genetic differentiation is not directly correlated to geographical distance. Thus, our data indicate that movement of infested commodities may contribute to the dissemination of L. serricorne, facilitating gene flow.

  20. The effects of selective breeding against scrapie susceptibility on the genetic variability of the Latxa Black-Faced sheep breed

    Directory of Open Access Journals (Sweden)

    Legarra Andrés

    2006-09-01

    Full Text Available Abstract Breeding sheep populations for scrapie resistance could result in a loss of genetic variability. In this study, the effect on genetic variability of selection for increasing the ARR allele frequency was estimated in the Latxa breed. Two sources of information were used, pedigree and genetic polymorphisms (fifteen microsatellites. The results based on the genealogical information were conditioned by a low pedigree completeness level that revealed the interest of also using the information provided by the molecular markers. The overall results suggest that no great negative effect on genetic variability can be expected in the short time in the population analysed by selection of only ARR/ARR males. The estimated average relationship of ARR/ARR males with reproductive females was similar to that of all available males whatever its genotype: 0.010 vs. 0.012 for a genealogical relationship and 0.257 vs. 0.296 for molecular coancestry, respectively. However, selection of only ARR/ARR males implied important losses in founder animals (87 percent and low frequency alleles (30 percent in the ram population. The evaluation of mild selection strategies against scrapie susceptibility based on the use of some ARR heterozygous males was difficult because the genetic relationships estimated among animals differed when pedigree or molecular information was used, and the use of more molecular markers should be evaluated.

  1. A genetic algorithm-based approach to flexible flow-line scheduling with variable lot sizes.

    Science.gov (United States)

    Lee, I; Sikora, R; Shaw, M J

    1997-01-01

    Genetic algorithms (GAs) have been used widely for such combinatorial optimization problems as the traveling salesman problem (TSP), the quadratic assignment problem (QAP), and job shop scheduling. In all of these problems there is usually a well defined representation which GA's use to solve the problem. We present a novel approach for solving two related problems-lot sizing and sequencing-concurrently using GAs. The essence of our approach lies in the concept of using a unified representation for the information about both the lot sizes and the sequence and enabling GAs to evolve the chromosome by replacing primitive genes with good building blocks. In addition, a simulated annealing procedure is incorporated to further improve the performance. We evaluate the performance of applying the above approach to flexible flow line scheduling with variable lot sizes for an actual manufacturing facility, comparing it to such alternative approaches as pair wise exchange improvement, tabu search, and simulated annealing procedures. The results show the efficacy of this approach for flexible flow line scheduling.

  2. Emergence and genetic variability of Anaplasma species in small ruminants and ticks from Central Europe.

    Science.gov (United States)

    Derdáková, Markéta; Stefančíková, Astéria; Spitalská, Eva; Tarageľová, Veronika; Košťálová, Tatiana; Hrkľová, Gabriela; Kybicová, Kateřina; Schánilec, Pavel; Majláthová, Viktória; Várady, Marián; Peťko, Branislav

    2011-12-15

    Anaplasmoses are common tick-borne zoonotic bacterial diseases of livestock and free-living ungulates from the genus Anaplasma that are recently emerging in Central Europe. The main aim of this study was to analyze the prevalence and genetic variability of Anaplasma phagocytophilum and Anaplasma ovis in small ruminants and questing ticks from six different sites in Slovakia and the Czech Republic using the PCR of the msp4 gene followed by the sequence analysis. At two farms from southeastern Slovakia, 66.1% small ruminants were infected with A. ovis in contrast to one positive animal from both sites in northern Slovakia. It was represented by two different genotypes. A. phagocytophilum was present in all tested flocks with the infection prevalence ranging from 0.9% to 5.7%. None of the tested questing ticks carried A. ovis. A. phagocytophilum was detected in 1.1% and 7.8% of questing Ixodes ricinus ticks collected around the farms located in southeastern and northern Slovakia, respectively. A. phagocytophilum revealed higher intraspecific diversity than A. ovis. Copyright © 2011 Elsevier B.V. All rights reserved.

  3. Evolving Neural Network Using Variable String Genetic Algorithm for Color Infrared Aerial Image Classification

    Institute of Scientific and Technical Information of China (English)

    FU Xiaoyang; P E R Dale; ZHANG Shuqing

    2008-01-01

    Coastal wetlands are characterized by complex patterns both in their geomorphic and ecological features.Besides field observations,it is necessary to analyze the land cover of wetlands through the color infrared (CIR) aerial photography or remote sensing image.In this paper,we designed an evolving neural network classifier using variable string genetic algorithm (VGA) for the land cover classification of CIR aerial image.With the VGA,the classifier that we designed is able to evolve automatically the appropriate number of hidden nodes for modeling the neural network topology optimally and to find a near-optimal set of connection weights globally.Then,with backpropagation algorithm (BP),it can find the best connection weights.The VGA-BP classifier,which is derived from hybrid algorithms mentioned above,is demonstrated on CIR images classification effectively.Compared with standard classifiers,such as Bayes maximum-likelihood classifier,VGA classifier and BP-MLP (multi-layer perception) classifier,it has shown that the VGA-BP classifier can have better performance on highly resolution land cover classification.

  4. Genetic variability and limited clonality of Mycoplasma hyorhinis in pig herds.

    Science.gov (United States)

    Trüeb, Bettina; Catelli, Elena; Luehrs, Adrian; Nathues, Heiko; Kuhnert, Peter

    2016-08-15

    Mycoplasma hyorhinis is a common inhabitant of the upper respiratory tract and tonsils of pigs. Its role as a possible pathogen remains controversial. In order to gain more insight into the epidemiology and population structure of M. hyorhinis we genetically characterized 60 isolates by multi locus sequence typing (MLST). The M. hyorhinis strains originated from Swiss and German pig herds with knowledge on the clinical background. The MLST scheme of Tocqueville et al. (J. Clin. Microbiol. 2014) was optimized, primers for the six MLST gene fragments were newly designed to allow amplification and sequencing with a single protocol. A total of 27 ST were observed with the 60 strains, 26 of those were previously unknown types. Generally identical genotypes were observed within a farm but they differed between farms. The identical genotype was also observed in three different Swiss farms. On the other hand different genotypes within a farm were found with three German farms. The Swiss isolates formed a distinct cluster but otherwise there was no geographical nor a clinical association with specific clusters observed. Data shows a high variability of M. hyorhinis comparable to what is observed for Mycoplasma hyopneumoniae. Similar to this pathogen the population structure of M. hyorhinis also shows some limited clonality with predominant genotypes within an animal and a single farm but different ones between farms. The comparable population structure of M. hyopneumoniae and M. hyorhinis could indicate a similar evolution of the two species in the common pig host.

  5. Genetic variability and social structure of colonies in Acromyrmex heyeri and A. striatus (Hymenoptera: Formicidae

    Directory of Open Access Journals (Sweden)

    E. DIEHI

    Full Text Available The breeding structure of both colony and population of social insects can be examined by genetic analysis. Colonies of the leaf-cutting ants Acromyrmex heyeri and A. striatus (Myrmicinae, Attini were thus analyzed for isoenzyme systems MDH, a-GPDH, and AMY to describe genotype variability and social structure. A total of five loci were investigated (three for amylase and one for each other system. Ninety-seven colonies of A. heyeri and 103 of A. striatus were sampled in different localities in Southern Brazil (State of Rio Grande do Sul. The genotypes found show the occurrence of monogyny and polygyny associated or not with polyandry, which indicates that the social organization is colony-specific. The polygyny and polyandry observed are likely to be responsible for the great genotypic diversity of the colonies. The average inbreeding coefficient per colony was higher in A. striatus than in A. heyeri, which may reflect the different patterns of production of sexual individuals and nuptial flight of those two species.

  6. A Variable Interval Rescheduling Strategy for Dynamic Flexible Job Shop Scheduling Problem by Improved Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    Lei Wang

    2017-01-01

    Full Text Available In real-world manufacturing systems, production scheduling systems are often implemented under random or dynamic events like machine failure, unexpected processing times, stochastic arrival of the urgent orders, cancellation of the orders, and so on. These dynamic events will lead the initial scheduling scheme to be nonoptimal and/or infeasible. Hence, appropriate dynamic rescheduling approaches are needed to overcome the dynamic events. In this paper, we propose a dynamic rescheduling method based on variable interval rescheduling strategy (VIRS to deal with the dynamic flexible job shop scheduling problem considering machine failure, urgent job arrival, and job damage as disruptions. On the other hand, an improved genetic algorithm (GA is proposed for minimizing makespan. In our improved GA, a mix of random initialization population by combining initialization machine and initialization operation with random initialization is designed for generating high-quality initial population. In addition, the elitist strategy (ES and improved population diversity strategy (IPDS are used to avoid falling into the local optimal solution. Experimental results for static and several dynamic events in the FJSP show that our method is feasible and effective.

  7. Influence of sex and genetic variability on expression of X-linked genes in human monocytes.

    Science.gov (United States)

    Castagné, Raphaële; Zeller, Tanja; Rotival, Maxime; Szymczak, Silke; Truong, Vinh; Schillert, Arne; Trégouët, David-Alexandre; Münzel, Thomas; Ziegler, Andreas; Cambien, François; Blankenberg, Stefan; Tiret, Laurence

    2011-11-01

    In humans, the fraction of X-linked genes with higher expression in females has been estimated to be 5% from microarray studies, a proportion lower than the 25% of genes thought to escape X inactivation. We analyzed 715 X-linked transcripts in circulating monocytes from 1,467 subjects and found an excess of female-biased transcripts on the X compared to autosomes (9.4% vs 5.5%, pgenes not previously known to escape inactivation, the most significant one was EFHC2 whose 20% of variability was explained by sex. We also investigated cis expression quantitative trait loci (eQTLs) by analyzing 15,703 X-linked SNPs. The frequency and magnitude of X-linked cis eQTLs were quite similar in males and females. Few genes exhibited a stronger genetic effect in females than in males (ARSD, DCX, POLA1 and ITM2A). These genes would deserve further investigation since they may contribute to sex pathophysiological differences.

  8. The influence of herbivory on pre- and postzygotic stages of reproduction following open, self, and outcross pollination.

    Science.gov (United States)

    Ghyselen, Céline; Bonte, Dries; Brys, Rein

    2015-12-01

    Herbivory affects pollination success and reproductive output in plants. However, the different stages in the process from pollination to seed maturation have hardly been investigated within the context of herbivory. Herbivory might affect these stages via its effect on geitonogamous pollination and thereby the proportion of self pollen delivered to the stigma and/or via its effect on the nutritional capacity of the maternal plant. Plants of monocarpic Cynoglossum officinale were experimentally subjected to root herbivory and exposed to natural open pollination in combination with self and outcross hand pollination. We quantified pollen germination, pollen tube competition intensity, pollen tube attrition, fruit set, and seed initiation, abortion, and maturation. Although root herbivory did not affect pollen germination or pollen tube attrition, fruit set and seed initiation and maturation were negatively affected by herbivory, but for seed initiation only in the case of outcross- and open-pollinated flowers. The intensity of pollen tube competition positively affected seed initiation, but only in plants infested with the herbivore. Our study demonstrates that herbivory did not affect the early stages following pollination, but significantly impacted later postpollination stages such as fruit set and seed maturation and selection based on pollen tube competition intensity on zygote development. Our findings suggest that decreased nutritional capacity of the mother plant in response to root herbivory rather than herbivory effects on pollen quality was responsible for the lower fruit and seed production in infested plants. © 2015 Botanical Society of America.

  9. The evolution of transposable elements in natural populations of self-fertilizing Arabidopsis thaliana and its outcrossing relative Arabidopsis lyrata

    Directory of Open Access Journals (Sweden)

    Gaut Brandon S

    2010-01-01

    Full Text Available Abstract Background Transposable Elements (TEs make up the majority of plant genomes, and thus understanding TE evolutionary dynamics is key to understanding plant genome evolution. Plant reproductive systems are diverse and mating type variation is one factor among many hypothesized to influence TE evolutionary dynamics. Here, we collected a large TE-display data set in self-fertilizing Arabidopsis thaliana, and compared it to data gathered in outcrossing Arabidopsis lyrata. We analyzed seven TE families in four natural populations of each species to tease apart the effects of mating system, demography, transposition, and selection in determining patterns of TE diversity. Results Measures of TE band differentiation were largely consistent across TE families. However, patterns of diversity in A. thaliana Ac elements differed significantly from that other TEs, perhaps signaling a lack of recent transposition. Across TE families, we estimated higher allele frequencies and lower selection coefficients on A. thaliana TE insertions relative to A. lyrata TE insertions. Conclusions The differences in TE distributions between the two Arabidopsis species represents a synthesis of evolutionary forces that include the transposition dynamics of individual TE families and the demographic histories of populations. There are also species-specific differences that could be attributed to the effects of mating system, including higher overall allele frequencies in the selfing lineage and a greater proportion of among population TE diversity in the outcrossing lineage.

  10. Calculation of mean outcrossing rates of non-Gaussian processes with stochastic input parameters - Reliability of containers stowed on ships in severe sea

    DEFF Research Database (Denmark)

    Nielsen, Ulrik Dam

    2010-01-01

    Mean outcrossing rates can be used as a basis for decision support for ships in severe sea. The article describes a procedure for calculating the mean outcrossing rate of non-Gaussian processes with stochastic input parameters. The procedure is based on the first-order reliability method (FORM......) and stochastic parameters are incorporated by carrying out a number of FORM calculations corresponding to combinations of specific values of the stochastic parameters. Subsequently, the individual FORM calculation is weighted according to the joint probability with which the specific combination of parameter....... The results of the procedure are compared with brute force simulations obtained by Monte Carlo simulation (MCS) and good agreement is observed. Importantly, the procedure requires significantly less CPU time compared to MCS to produce mean outcrossing rates....

  11. Comparison of gSSR and EST-SSR markers for analyzing genetic variability among tomato cultivars (Solanum lycopersicum L.).

    Science.gov (United States)

    Zhou, R; Wu, Z; Jiang, F L; Liang, M

    2015-10-27

    In order to study genetic variability and develop better strategies for the utilization of 48 tomato cultivars from America, China, the Netherlands, and Portugal, genomic simple sequence repeat (gSSR) and EST-derived SSR (EST-SSR) markers were applied. In all, 15 of 82 gSSR and 18 of 115 EST-SSR markers showed polymorphic loci. There were 995 and 2072 clear fragments amplified by polymorphic gSSR and EST-SSR markers, respectively. The total and average number of alleles detected by EST-SSRs (75, 4.2) was more than gSSRs (54, 3.6) as a result of some multi-locus EST-SSRs. A lower polymorphism information content value was found in gSSRs (0.529) compared to EST-SSRs (0.620). Similarity coefficient matrixes of the 48 tomato cultivars were established based on the gSSRs and EST-SSRs, and UPGMA dendrograms were constructed from the gSSRs and EST-SSRs similarity coefficient matrixes. A high similarity was observed between the gSSRs and EST-SSRs dendrograms. Genetic variability of four tomato populations from different countries showed that the observed number of alleles and Nei's genetic diversity were highest in the American population, and the effective number of alleles was highest in the Dutch population. The estimated genetic structure showed some tomato cultivars from different countries shared a common genetic background, which might be related to gene flow. It was inferred that both gSSR and EST-SSR markers were effective to assess genetic variability of tomato cultivars, and the combination of both markers could be more effective for genetic diversity analysis in tomato.

  12. Effect of genetic homogeneity on behavioural variability in an object recognition test in cloned Göttingen minipigs

    DEFF Research Database (Denmark)

    Søndergaard, Lene Vammen; Herskin, Mette S.; Ladewig, Jan;

    2012-01-01

    The number of animals used in research should be limited as much as possible. Among cloned animals, genetic variation is minimal and to the extent that behaviour is genetically determined inter-individual variability is expected to be higher among naturally bred animals. However, the cloning...... in these behavioural variables in cloned minipigs is less than in naturally bred control subjects and therefore does not directly support the hypothesis that cloning may be used to replicate animals in order to reduce group size in experimentation animals....... were subjected to a behavioural test of memory, the spontaneous object recognition test, from an early age. At ages 1 and 2 years no evidence of memory decline was found, yet the data showed striking behavioural variability among the cloned groups. The aim of the present study was to investigate...

  13. Genetic Control of the Variable Innate Immune Response to Asymptomatic Bacteriuria

    Science.gov (United States)

    Hernández, Jenny Grönberg; Sundén, Fredrik; Connolly, John; Svanborg, Catharina; Wullt, Björn

    2011-01-01

    The severity of urinary tract infection (UTI) reflects the quality and magnitude of the host response. While strong local and systemic innate immune activation occurs in patients with acute pyelonephritis, the response to asymptomatic bacteriuria (ABU) is low. The immune response repertoire in ABU has not been characterized, due to the inherent problem to distinguish bacterial differences from host-determined variation. In this study, we investigated the host response to ABU and genetic variants affecting innate immune signaling and UTI susceptibility. Patients were subjected to therapeutic urinary tract inoculation with E. coli 83972 to ensure that they were exposed to the same E. coli strain. The innate immune response repertoire was characterized in urine samples, collected from each patient before and after inoculation with bacteria or PBS, if during the placebo arm of the study. Long-term E. coli 83972 ABU was established in 23 participants, who were followed for up to twelve months and the innate immune response was quantified in 233 urine samples. Neutrophil numbers increased in all but two patients and in an extended urine cytokine/chemokine analysis (31 proteins), the chemoattractants IL-8 and GRO-α, RANTES, Eotaxin-1 and MCP-1, the T cell chemoattractant and antibacterial peptide IP-10, inflammatory regulators IL-1-α and sIL-1RA and the T lymphocyte/dendritic cell product sIL-2Rα were detected and variably increased, compared to sterile samples. IL-6, which is associated with symptomatic UTI, remained low and numerous specific immune mediators were not detected. The patients were also genotyped for UTI-associated IRF3 and TLR4 promoter polymorphisms. Patients with ABU associated TLR4 polymorphisms had low neutrophil numbers, IL-6, IP-10, MCP-1 and sIL-2Rα concentrations. Patients with the ABU-associated IRF3 genotype had lower neutrophils, IL-6 and MCP-1 responses than the remaining group. The results suggest that the host-specific, low immune

  14. Genetic control of the variable innate immune response to asymptomatic bacteriuria.

    Directory of Open Access Journals (Sweden)

    Jenny Grönberg-Hernández

    Full Text Available The severity of urinary tract infection (UTI reflects the quality and magnitude of the host response. While strong local and systemic innate immune activation occurs in patients with acute pyelonephritis, the response to asymptomatic bacteriuria (ABU is low. The immune response repertoire in ABU has not been characterized, due to the inherent problem to distinguish bacterial differences from host-determined variation. In this study, we investigated the host response to ABU and genetic variants affecting innate immune signaling and UTI susceptibility. Patients were subjected to therapeutic urinary tract inoculation with E. coli 83972 to ensure that they were exposed to the same E. coli strain. The innate immune response repertoire was characterized in urine samples, collected from each patient before and after inoculation with bacteria or PBS, if during the placebo arm of the study. Long-term E. coli 83972 ABU was established in 23 participants, who were followed for up to twelve months and the innate immune response was quantified in 233 urine samples. Neutrophil numbers increased in all but two patients and in an extended urine cytokine/chemokine analysis (31 proteins, the chemoattractants IL-8 and GRO-α, RANTES, Eotaxin-1 and MCP-1, the T cell chemoattractant and antibacterial peptide IP-10, inflammatory regulators IL-1-α and sIL-1RA and the T lymphocyte/dendritic cell product sIL-2Rα were detected and variably increased, compared to sterile samples. IL-6, which is associated with symptomatic UTI, remained low and numerous specific immune mediators were not detected. The patients were also genotyped for UTI-associated IRF3 and TLR4 promoter polymorphisms. Patients with ABU associated TLR4 polymorphisms had low neutrophil numbers, IL-6, IP-10, MCP-1 and sIL-2Rα concentrations. Patients with the ABU-associated IRF3 genotype had lower neutrophils, IL-6 and MCP-1 responses than the remaining group. The results suggest that the host

  15. Analysis of genetic variability in three species of Pimelodidae (Ostariophysi - Siluriformes

    Directory of Open Access Journals (Sweden)

    Fernanda S. de Almeida

    1998-12-01

    Full Text Available Genetic variability of three Pimelodidae species, Pimelodus maculatus, Iheringichthys labrosus, and Pinirampus pirinampu, collected at one site in the Tibagi River, was comparatively analyzed using protein data for six systems which code 15 loci in liver, muscle, and heart. The proportion of polymorphic loci ( for P. maculatus, I. labrosus, and P. pirinampu was 13.33, 20, and 6.67%, respectively, and mean heterozigosity was 6, 8.3, and 4.3%. The genetic identity value (I was 0.32 between P. maculatus and I. labrosus, 0.37 between P. maculatus and P. pirinampu, and 0.58 between I. labrosus and P. pirinampu. This value suggests that these two latter species are congeneric. However, morphological characteristics place these species in distinct genera.A variabilidade genética de 3 espécies da família Pimelodidae, Pimelodus maculatus, Iheringichthys labrosus e Pinirampus pirinampu, coletadas em um ponto do rio Tibagi, foi analisada comparativamente utilizando dados protéicos de 6 sistemas que codificam 15 locos em fígado, músculo e coração. A proporção de locos polimórficos ( para P. maculatus, I. labrosus e P. pirinampu foi de 13,33, 20 e 6,67%, respectivamente, e a heterozigosidade média foi de 6, 8,3 e 4,3%. A identidade genética (I foi de 0,32 entre P. maculatus e I. labrosus, 0,37 entre P. maculatus e P. pirinampu e 0,58 entre I. labrosus e P. pirinampu. O valor de I (0,58 encontrado entre I. labrosus e P. pirinampu sugere que estas são espécies congenéricas. No entanto, as características morfológicas colocam estas espécies em gêneros distintos. Os resultados obtidos nesse estudo podem ser úteis para um melhor conhecimento de espécies de Pimelodidae. Elas também reforçam a necessidade da preservação do rio Tibagi (Paraná - Brasil através de uma análise cuidadosa no caso de construção de hidroelétricas.

  16. Deltamethrin flea-control preserves genetic variability of black-tailed prairie dogs during a plague outbreak

    Science.gov (United States)

    Jones, P.H.; Biggins, D.E.; Eads, D.A.; Eads, S.L.; Britten, H.B.

    2012-01-01

    Genetic variability and structure of nine black-tailed prairie dog (BTPD, Cynomys ludovicianus) colonies were estimated with 15 unlinked microsatellite markers. A plague epizootic occurred between the first and second years of sampling and our study colonies were nearly extirpated with the exception of three colonies in which prairie dog burrows were previously dusted with an insecticide, deltamethrin, used to control fleas (vectors of the causative agent of plague, Yersinia pestis). This situation provided context to compare genetic variability and structure among dusted and non-dusted colonies pre-epizootic, and among the three dusted colonies pre- and post-epizootic. We found no statistical difference in population genetic structures between dusted and non-dusted colonies pre-epizootic. On dusted colonies, gene flow and recent migration rates increased from the first (pre-epizootic) year to the second (post-epizootic) year which suggested dusted colonies were acting as refugia for prairie dogs from surrounding colonies impacted by plague. Indeed, in the dusted colonies, estimated densities of adult prairie dogs (including dispersers), but not juveniles (non-dispersers), increased from the first year to the second year. In addition to preserving BTPDs and many species that depend on them, protecting colonies with deltamethrin or a plague vaccine could be an effective method to preserve genetic variability of prairie dogs. ?? 2011 Springer Science+Business Media B.V.

  17. Genetic variability of a population of Aedes aegypti from Paraná, Brazil, using the mitochondrial ND4 gene

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    Adriana L. Twerdochlib

    2012-06-01

    Full Text Available Genetic variability of a population of Aedes aegypti from Paraná, Brazil, using the mitochondrial ND4 gene. To analyze the genetic variability of populations of Aedes aegypti, 156 samples were collected from 10 municipalities in the state of Paraná, Brazil. A 311 base pairs (bp region of the NADH dehydrogenase subunit 4 (ND4 mitochondrial gene was examined. An analysis of this fragment identified eight distinct haplotypes. The mean genetic diversity was high (h = 0.702; p = 0.01556. AMOVA analysis indicated that most of the variation (67% occurred within populations and the F ST value (0.32996 was highly significant. F ST values were significant in most comparisons among cities. The isolation by distance was not significant (r = -0.1216 and p = 0, 7550, indicating that genetic distance is not related to geographic distance. Neighbor-joining analysis showed two genetically distinct groups within Paraná. The DNA polymorphism and AMOVA data indicate a decreased gene flow in populations from Paraná, which can result in increased vectorial competence.

  18. Genetic variability of wild cherry (Prunus avium L.) seed stands in Slovenia as revealed by nuclear microsatellite loci.

    Science.gov (United States)

    Jarni, Kristjan; De Cuyper, Bart; Brus, Robert

    2012-01-01

    Microsatellite markers were used to describe the genetic variability of four seed stands of wild cherry (Prunus avium L.). One hundred and thirty one individuals were genotyped at ten nuclear microsatellite loci. Total genetic diversity was high (H(E) = 0.704), while differences between stands were small but significant (F(ST) = 0.053, G'(ST) = 0.234). There was a significant amount of clonal reproduction in one stand, with only 11 genotypes identified among 36 trees. One stand showed a significant excess (F(IS) = -0.044) of heterozygosity, and one showed a deficit (F(IS) = 0.044). Our results demonstrate the importance of taking into account the biological and genetic characteristics of species in forest management, especially when determining a new seed stand. The small genetic differences found between seed stands indicate that a large number of stands are not required. However, they should be carefully selected and should possess adequate genetic variability to ensure low relatedness between seed trees.

  19. Genetic variability of wild cherry (Prunus avium L. seed stands in Slovenia as revealed by nuclear microsatellite loci.

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    Kristjan Jarni

    Full Text Available Microsatellite markers were used to describe the genetic variability of four seed stands of wild cherry (Prunus avium L.. One hundred and thirty one individuals were genotyped at ten nuclear microsatellite loci. Total genetic diversity was high (H(E = 0.704, while differences between stands were small but significant (F(ST = 0.053, G'(ST = 0.234. There was a significant amount of clonal reproduction in one stand, with only 11 genotypes identified among 36 trees. One stand showed a significant excess (F(IS = -0.044 of heterozygosity, and one showed a deficit (F(IS = 0.044. Our results demonstrate the importance of taking into account the biological and genetic characteristics of species in forest management, especially when determining a new seed stand. The small genetic differences found between seed stands indicate that a large number of stands are not required. However, they should be carefully selected and should possess adequate genetic variability to ensure low relatedness between seed trees.

  20. GENETIC VARIABILITY OF POLYMESODA EROSA POPULATION IN THE SEGARA ANAKAN CILACAP

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    AGUS NURYANTO

    2010-01-01

    Full Text Available Mud clams, Polymesoda erosa, in the Segara Anakan Cilacap are highly exploited by the local communities for daily consumption. This is presumed causing population decline and potentially causing loss of genetic diversity. Genetic diversity level within population can be obtained by population genetic study using molecular marker such as randomly amplified polymorphic DNA (RAPD. Here we amplified RAPD marker using ten arbitrary primers to assess genetic diversity of P. erosa population in the Segara Anakan Cilacap to provide genetic data for its sustainable use. The results proved that the use of RAPD marker has high polymorphisms. The mud clam population also showed a high level of heterozygosity and genetic diversity. This has important implication for the management plan towards sustainable use of P. erosa in the Segara Anakan Cilacap.

  1. Chinese Xibe population genetic composition according to linkage groups of X-chromosomal STRs: population genetic variability and interpopulation comparisons.

    Science.gov (United States)

    Meng, Hao-Tian; Shen, Chun-Mei; Zhang, Yu-Dang; Dong, Qian; Guo, Yu-Xin; Yang, Guang; Yan, Jiang-Wei; Liu, Yao-Shun; Mei, Ting; Shi, Jian-Feng; Zhu, Bo-Feng

    2017-09-01

    The Xibe population is one of China's officially recognised populations and is now distributed separately from west to east in the northern part of China. X-chromosomal short tandem repeats have a special inheritance pattern, and could be used as complements in forensic application, especially for complex or deficiency cases. This study obtained the allelic and haplotypic frequencies of 19 X-STR loci in the Xibe population from Xinjiang Uygur Autonomous Region, China, and studied the genetic differentiations between the Xibe and other populations. The combined power of discrimination in females and males and mean exclusion chances in deficiency cases, normal trios and duo cases was at least 0.999 999 994. In the haplotypic study, the Xibe population showed a more similar pattern of haplotype distribution with Asian populations than populations from other continents, while allelic study also indicated a closer relationship between the Xibe and Asian populations. The 19 X-STR loci would be useful in forensic application in the studied population. The Xibe population showed a closer genetic relationship with Asian populations in the study, and more population data would be necessary for more detailed genetic relationship studies.

  2. Adaptive genetic variability and differentiation of Croatian and Austrian Quercus robur L. populations at a drought prone field trial

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    Saša Bogdan

    2017-07-01

    Full Text Available Provenance trials, where populations of different geographical origin are tested in a common environment (common garden test, are a tool suited to allow the study of intraspecific adaptive genetic variation. Research of pedunculate oak (Quercus robur L. adaptive genetic variability through analyses of populations in common garden tests has a long tradition. However, pedunculated oak populations originating south-eastern from the Alps have been scarcely studied in this way. This study addresses the adaptive genetic variability and differentiation of pedunculate oak populations originating from Austria and Croatia in a provenance/progeny field trial. Studied plants were six years old and were growing at the trial for three years. After two years of unusually low precipitations height and survival were analysed. The total mean height of all plants in the trial was 137.8 cm and ranged from 123.0 cm to 151.8 cm. The overall mean survival rate was rather high (0.85. Mean population survival ranged from 0.64 to 0.94. Individual narrow-sense heritabilities (hi2, family mean heritabilities (hf2, the coefficients of additive genetic variation (CVA and quantitative genetic differentiation coefficients (QST were calculated. A multivariate regression tree (MRT analysis was used to determine the pattern of genetic differentiation of the populations. Individual heritabilities for height ranged between 0.00 and 0.39. Family mean heritabilities for height were rather low in most populations as well (<0.5. Family mean heritabilities for survival were higher than for height (ranging between 0.00 and 0.77. Calculated QST coefficients (0.25 for height and 0.14 for survival indicated between-population genetic differentiation. The populations were separated into two clusters by MRT analysis regarding a climatic variable, namely Hargreaves’ reference evapotranspiration. Populations originating from comparatively more humid habitats were grouped in the first

  3. Nonequilibrium Conditions Explain Spatial Variability in Genetic Structuring of Little Penguin (Eudyptula minor).

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    Burridge, Christopher P; Peucker, Amanda J; Valautham, Sureen K; Styan, Craig A; Dann, Peter

    2015-01-01

    Factors responsible for spatial structuring of population genetic variation are varied, and in many instances there may be no obvious explanations for genetic structuring observed, or those invoked may reflect spurious correlations. A study of little penguins (Eudyptula minor) in southeast Australia documented low spatial structuring of genetic variation with the exception of colonies at the western limit of sampling, and this distinction was attributed to an intervening oceanographic feature (Bonney Upwelling), differences in breeding phenology, or sea level change. Here, we conducted sampling across the entire Australian range, employing additional markers (12 microsatellites and mitochondrial DNA, 697 individuals, 17 colonies). The zone of elevated genetic structuring previously observed actually represents the eastern half of a genetic cline, within which structuring exists over much shorter spatial scales than elsewhere. Colonies separated by as little as 27 km in the zone are genetically distinguishable, while outside the zone, homogeneity cannot be rejected at scales of up to 1400 km. Given a lack of additional physical or environmental barriers to gene flow, the zone of elevated genetic structuring may reflect secondary contact of lineages (with or without selection against interbreeding), or recent colonization and expansion from this region. This study highlights the importance of sampling scale to reveal the cause of genetic structuring. © The American Genetic Association 2015.

  4. Genetic variability among populations of the sand fly Lutzomyia (Lutzomyia) longipalpis (Diptera: Psychodidae) from Central America.

    Science.gov (United States)

    Mutebi, J P; Rowton, E; Herrero, M V; Ponce, C; Belli, A; Valle, S; Lanzaro, G C

    1998-03-01

    Eleven Central American populations of Lutzomyia longipalpis (Lutz & Neiva) were analyzed for genetic variation at 16 enzyme loci. The aim was to study the genetic structure among populations within this region and to identify demes that may represent different sibling species. Genotypic frequencies within populations agreed with Hardy-Weinberg expectations, indicating that there were no sympatric sibling species among these 11 populations. Levels of genetic distance between pairs of populations were very low (migration rates among populations (Nm) were low (3.7), indicating that gene flow was restricted. These data explained observed genetic substructuring when all genotypes were pooled.

  5. Analysis of Genetic Variability among thirty accessions of Andean Lupin (Lupinus mutabilis Sweet using ISSR molecular markers

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    Michelle C. Chirinos-Arias

    2015-03-01

    Full Text Available In order to make the genetic variability analysis among thirty accessions of andean lupine (L. mutabilis Sweet belonging to Agrarian Innovation National Institute (INIA Seed Bank. DNA was extracted from 300 plants and we made bulks. We standardized amplification protocol of Inter Simple Sequence Repeat (ISSR primers, we chose the most polymorphic primers to run in acrylamide gel. We found 255 ISSR loci with 8 primers. It was found high genetic variability of the samples under study by ISSR markers. Also observed relatively high polymorphism for autogamous species such as andean lupine. Finally phenograms showed a relationship with the geographical location, possibly due to in situ gene flow due to the exchange or sale of seeds in markets near the collection area.

  6. Behavior Genetics and the Within-Person Variability of Daily Interpersonal Styles: The Heritability of Flux, Spin and Pulse.

    Science.gov (United States)

    Markey, Patrick M; Racine, Sarah E; Markey, Charlotte N; Hopwood, Christopher J; Keel, Pamela K; Burt, S Alexandra; Neale, Michael C; Sisk, Cheryl L; Boker, Steven M; Klump, Kelly L

    2014-04-01

    A classical twin study was used to estimate the magnitude of genetic and environmental influences on four measurements of within-person variability: dominance flux, warmth flux, spin and pulse. Flux refers to the variability of an individual's interpersonal dominance and warmth. Spin measures changes in the tone of interpersonal styles and pulse measures changes in the intensity of interpersonal styles. Daily reports of interpersonal styles were collected from 494 same-sex female twins (142 monozygotic pairs and 105 dizygotic pairs) over 45 days. For dominance flux, warmth flux, and spin, genetic effects accounted for a larger proportion of variance (37%, 24%, and 30%, respectively) than shared environmental effects (14%, 13%, 0%, respectively), with the remaining variance due to the non-shared environment (62%, 50%, 70% respectively). Pulse appeared to be primarily influenced by the non-shared environment, although conclusions about the contribution of familial influences were difficult to draw from this study.

  7. Genetic variability of an unusual apomictic triploid cactus--Haageocereus tenuis Ritter--from the Coast of Central Peru.

    Science.gov (United States)

    Arakaki, Mónica; Speranza, Pablo; Soltis, Pamela S; Soltis, Douglas E

    2013-01-01

    Haageocereus tenuis is a prostrate cactus restricted to a small area of 2 km(2) near the city of Lima, Peru. The species is triploid and propagates mainly through stem fragmentation. In addition, propagation via agamospermy is documented and adventitious embryony is also inferred as a mechanism. Although seedling recruitment has not been observed in nature, we have shown that asexually produced seeds are viable. About 45 adult individuals, plus 9 individuals obtained from seeds, were sampled and 5 microsatellite markers were used to assess genetic variability. Microsatellite analysis confirms that individuals from the only existing population are genetically identical and that the population likely represents a single clone. The absence of mutations in any individual, even in highly variable microsatellite loci, may indicate that the species is also of recent origin. Other prostrate species of Haageocereus are suspected to be occasional apomicts. This phenomenon has significant implications for the evolutionary biology and ecology of Haageocereus and other clonal Cactaceae.

  8. Genetics

    Science.gov (United States)

    ... Inheritance; Heterozygous; Inheritance patterns; Heredity and disease; Heritable; Genetic markers ... The chromosomes are made up of strands of genetic information called DNA. Each chromosome contains sections of ...

  9. [Macrogeographic genetic variability in the gastropod mollusk Littorina sitkana from the northwest Pacific].

    Science.gov (United States)

    Zaslavskaya, N I; Pudovkin, A I

    2005-03-01

    Variation at four highly polymorphic allozyme loci (inorganic pyrophosphatase, peptidase, and two esterase loci) was examined in 25 settlements of the marine snail Littorina sitkana (Mollusca, Gastropoda). The sampling localities covered a wide part of the species range: from the Peter the Great Bay (the Sea of Japan) at the southwest to the Mednyi Island (Commander Islands) at the northeast. Like other littorines lacking the pelagic stage, L. sitkana was characterized by significant genetic differentiation (G(ST) for the pooled sample was 0.310). Cluster analysis and nonmetric multidimensional scaling conducted on a matrix of pairwise genetic distances between all of the settlements studied revealed four genetically different groups: southern Primorye, northern Prymorye, Sakhalin, and Kuril-Commanders. The population-genetic structure of the L. sitkana settlements is close to that described by the isolation-by-distance and stepping-stone models: the geographic and the genetic distances between the most settlements examined are distinctly correlated.

  10. GENOTYPIC VARIABILITY, HERITABILITY AND GENETIC ADVANCE IN ETHIOPIAN MUSTARD (BRASSICA CARINATA A.BRAUN. GENOTYPES AT NORTHWESTERN ETHIOPIA

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    Tesfaye W. Mekonnen

    2015-07-01

    Full Text Available The assessment of genetic variability is fundamental for the purpose of to identify the most important traits in Ethiopian mustard breeding program. The objective of the study was to estimate variability, heritability and genetic advance on thirty six morphological characters of Ethiopian mustard (Brassica carinata genotypes were evaluated Adet Agricultural Research Center, Ethiopia. The experiment was laid out in simple lattice design. ANOVA of the experiment showed highly significant (p<0.01 for Day of maturity, grain filling period, number of pod per plot, secondary branches  per plant, harvest index, seed yield per plot, seed yield per hectare and oil content. Significant differences (p<0.01 were noted for day of flowering, plant height, primary branch per plant, biomass per plot, oil yield per plot. High phenotypic coefficient of variation (PCV was recorded for days to flowering, grain filling period, plant height, secondary branches per plant, harvest index, oil yield per plot, seed yield per plot and hectare. The magnitudes of PCV and genotypic coefficient of variation (GCV were high for grain filling period, plant height and secondary branches per plant. Heritability estimates were high for days to maturity, grain-filling period, days to flowering, plant height, biomass per plot, secondary branches per plant, primary branches per plant, oil content and oil yield per plot. High heritability was coupled with high genetic advance as percent of mean for plant height, grain filling period, secondary branches per plant were recorded. The study showed that there are variation in the extent of genetic variability, heritability and genetic advance in traits under study which can facilitate selection for further improvement of important traits of Ethiopian mustard.

  11. Patterns of Genetic Variability in Island Populations of the Cane Toad (Rhinella marina) from the Mouth of the Amazon

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    Bessa-Silva, Adam Rick; Vallinoto, Marcelo; Sodré, Davidson; da Cunha, Divino Bruno; Hadad, Dante; Asp, Nils Edvin; Sampaio, Iracilda; Schneider, Horacio; Sequeira, Fernando

    2016-01-01

    The Amazonian coast has several unique geological characteristics resulting from the interaction between drainage pattern of the Amazon River and the Atlantic Ocean. It is one of the most extensive and sedimentologically dynamic regions of the world, with a large number of continental islands mostly formed less than 10,000 years ago. The natural distribution of the cane toad (Rhinella marina), one of the world’s most successful invasive species, in this complex Amazonian system provides an intriguing model for the investigation of the effects of isolation or the combined effects of isolation and habitat dynamic changes on patterns of genetic variability and population differentiation. We used nine fast-evolving microsatellite loci to contrast patterns of genetic variability in six coastal (three mainlands and three islands) populations of the cane toad near the mouth of the Amazon River. Results from Bayesian multilocus clustering approach and Discriminant Analyses of Principal Component were congruent in showing that each island population was genetically differentiated from the mainland populations. All FST values obtained from all pairwise comparisons were significant, ranging from 0.048 to 0.186. Estimates of both recent and historical gene flow were not significantly different from zero across all population pairs, except the two mainland populations inhabiting continuous habitats. Patterns of population differentiation, with a high level of population substructure and absence/restricted gene flow, suggested that island populations of R. marina are likely isolated since the Holocene sea-level rise. However, considering the similar levels of genetic variability found in both island and mainland populations, it is reliable to assume that they were also isolated for longer periods. Given the genetic uniqueness of each cane toad population, together with the high natural vulnerability of the coastal regions and intense human pressures, we suggest that these

  12. Population structure and genetic variability in the Murrah dairy breed of water buffalo in Brazil accessed via pedigree analysis.

    Science.gov (United States)

    Malhado, Carlos Henrique Mendes; Malhado, Ana Claudia Mendes; Carneiro, Paulo Luiz Souza; Ramos, Alcides Amorim; Ambrosini, Diego Pagung; Pala, Akin

    2012-12-01

    The objective of this study was to use pedigree analysis to evaluate the population structure and genetic variability in the Murrah dairy breed of water buffalo (Bubalus bubalis) in Brazil. Pedigree analysis was performed on 5,061 animals born between 1972 and 2002. The effective number of founders (fe) was 60, representing 6.32 % of the potential number of founders. The effective number of ancestors (fa) was 36 and the genetic contribution of the 17 most influent ancestors explained 50 % of the genetic variability in the population. The ratio fe/fa (effective number of founders/effective number of ancestors), which expresses the effect of population bottlenecks, was 1.66. Completeness level for the whole pedigree was 76.8, 49.2, 27.7, and 12.8 % for, respectively, the first, second, third, and fourth known parental generations. The average inbreeding values for the whole analyzed pedigree and for inbreed animals were, respectively, 1.28 and 7.64 %. The average relatedness coefficient between individuals of the population was estimated to be 2.05 %-the highest individual coefficient was 10.31 %. The actual inbreeding and average relatedness coefficient are probably higher than estimated due to low levels of pedigree completeness. Moreover, the inbreeding coefficient increased with the addition of each generation to the pedigree, indicating that incomplete pedigrees tend to underestimate the level of inbreeding. Introduction of new sires with the lowest possible average relatedness coefficient and the use of appropriate mating strategies are recommended to keep inbreeding at acceptable levels and increase the genetic variability in this economically important species, which has relatively low numbers compared to other commercial cattle breeds. The inclusion of additional parameters, such as effective number of founders, effective number of ancestors, and fe/fa ratio, provides better resolution as compared to the inclusion of inbreeding coefficient and may help

  13. Genetic variability studies for yield and its component traits in RIL population of blackgram (Vigna mungo (L. Hepper

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    Sowmini.K and Jayamani. P

    2013-03-01

    Full Text Available Blackgram or Urdbean, being a fourth important pulse crop in India has low genetic variability, low harvest index and nosignificant improvement in its productivity till date. An inter sub specific mapping population was developed by crossingVBN(Bg 5 x Vigna mungo var. silvestris 22/10 by single seed decent method. The genetic variability parameters werestudied in a RIL (Recombinant Inbred Line population consisting of 193 lines and their parents. The higher estimates ofPCV were observed for all the traits when compared with GCV. However, GCV was found to be high for the traits singleplant yield, number of clusters per plant and number of pods per plant. High heritability per cent was observed for days tomaturity, number of seeds per pod and hundred seed weight. High genetic advance as per cent of mean was observed forplant height, number of clusters per plant, number of pods per plant, single plant yield and hundred seed weight. Highheritability coupled with high genetic advance as per cent of mean was observed for hundred seed weight. Transgressivesegregants were observed for all the traits. These could be used further for yield testing apart from utilizing it as prebreeding material. The mapping population could be used for mapping of genes for important traits.

  14. Genetic variability of the pattern of night melatonin blood levels in relation to coat changes development in rabbits.

    Science.gov (United States)

    Allain, Daniel; Malpaux, Benoit; Puechal, François; Thébault, René Gérard; De Rochambeau, Hubert; Chemineau, Philippe

    2004-01-01

    To assess the genetic variability in both the nocturnal increase pattern of melatonin concentration and photoresponsiveness in coat changes, an experiment on 422 Rex rabbits (from 23 males) raised under a constant light programme from birth was performed. The animals were sampled at 12 weeks of age, according to 4 periods over a year. Blood samples were taken 7 times during the dark phase and up to 1 h after the lighting began. Maturity of the fur was assessed at pelting. Heritability estimates of blood melatonin concentration (0.42, 0.17 and 0.11 at mid-night, 13 and 15 h after lights-out respectively) and strong genetic correlations between fur maturity and melatonin levels at the end of the dark phase (-0.64) indicates that (i) the variability of the nocturnal pattern of melatonin levels is under genetic control and (ii) the duration of the nocturnal melatonin increase is a genetic component of photoresponsiveness in coat changes.

  15. Genetic variability of the pattern of night melatonin blood levels in relation to coat changes development in rabbits

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    Chemineau Philippe

    2004-03-01

    Full Text Available Abstract To assess the genetic variability in both the nocturnal increase pattern of melatonin concentration and photoresponsiveness in coat changes, an experiment on 422 Rex rabbits (from 23 males raised under a constant light programme from birth was performed. The animals were sampled at 12 weeks of age, according to 4 periods over a year. Blood samples were taken 7 times during the dark phase and up to 1 h after the lighting began. Maturity of the fur was assessed at pelting. Heritability estimates of blood melatonin concentration (0.42, 0.17 and 0.11 at mid-night, 13 and 15 h after lights-out respectively and strong genetic correlations between fur maturity and melatonin levels at the end of the dark phase (-0.64 indicates that (i the variability of the nocturnal pattern of melatonin levels is under genetic control and (ii the duration of the nocturnal melatonin increase is a genetic component of photoresponsiveness in coat changes.

  16. From homothally to heterothally: Mating preferences and genetic variation within clones of the dinoflagellate Gymnodinium catenatum

    Science.gov (United States)

    Figueroa, Rosa Isabel; Rengefors, Karin; Bravo, Isabel; Bensch, Staffan

    2010-02-01

    The chain-forming dinoflagellate Gymnodinium catenatum Graham is responsible for outbreaks of paralytic shellfish poisoning (PSP), a human health threat in coastal waters. Sexuality in this species is of great importance in its bloom dynamics, and has been shown to be very complex but lacks an explanation. For this reason, we tested if unreported homothallic behavior and rapid genetic changes may clarify the sexual system of this alga. To achieve this objective, 12 clonal strains collected from the Spanish coast were analyzed for the presence of sexual reproduction. Mating affinity results, self-compatibility studies, and genetic fingerprinting (amplified fragment length polymorphism, AFLP) analysis on clonal strains, showed three facts not previously described for this species: (i) That there is a continuous mating system within G. catenatum, with either self-compatible strains (homothallic), or strains that needed to be outcrossed (heterothallic), and with a range of differences in cyst production among the crosses. (ii) There was intraclonal genetic variation, i.e. genetic variation within an asexual lineage. Moreover, the variability among homothallic clones was smaller than among the heterothallic ones. (iii) Sibling strains (the two strains established by the germination of one cyst) increased their intra- and inter-sexual compatibility with time. To summarize, we have found that G. catenatum's sexual system is much more complex than previously described, including complex homothallic/heterothallic behaviors. Additionally, high rates of genetic variability may arise in clonal strains, although explanations for the mechanisms responsible are still lacking.

  17. High genetic variability in endophytic fungi from the genus Diaporthe isolated from common bean (Phaseolus vulgaris L.) in Brazil.

    Science.gov (United States)

    Dos Santos, T T; de Souza Leite, T; de Queiroz, C B; de Araújo, E F; Pereira, O L; de Queiroz, M V

    2016-02-01

    The goals of the present study were to identify, to analyse the phylogenetic relations and to evaluate the genetic variability in Diaporthe endophytic isolates from common bean. Diaporthe sp., D. infecunda and D. phaseolorum strains were identified using multilocus phylogeny (rDNA ITS region; EF1-α, β-tubulin, and calmodulin genes). IRAP (Inter-Retrotransposon Amplified Polymorphism) and REMAP (Retrotransposon-Microsatellite Amplified Polymorphism) molecular markers reveal the existence of high genetic variability, especially among D. infecunda isolates. It was concluded that the multilocus phylogenetic approach was more effective than individual analysis of ITS sequences, in identifying the isolates to species level, and that IRAP and REMAP markers can be used for studying the genetic variability in the genus Diaporthe particularly at the intraspecific level. The combined use of molecular tools such as multilocus phylogenetic approach and molecular markers, as performed in this study, is the best way to distinguish endophytic strains of Diaporthe isolated from common bean (Phaseolus vulgaris L.). © 2015 The Society for Applied Microbiology.

  18. Genetic variability and structure of jaguar (Panthera onca) in Mexican zoos.

    Science.gov (United States)

    Rueda-Zozaya, Pilar; Mendoza-Martínez, Germán D; Martínez-Gómez, Daniel; Monroy-Vilchis, Octavio; Godoy, José Antonio; Sunny, Armando; Palomares, Francisco; Chávez, Cuauhtémoc; Herrera-Haro, José

    2016-02-01

    Genealogical records of animals (studbook) are created to avoid reproduction between closely related individuals, which could cause inbreeding, particularly for such endangered species as the Panthera onca (Linnaeus, 1758). Jaguar is the largest felid in the Americas and is considered an important ecological key species. In Mexico, wild jaguar populations have been significantly reduced in recent decades, and population decline typically accompany decreases in genetic variation. There is no current census of captive jaguars in Mexico, and zoos do not follow a standardized protocol in breeding programs based on genetic studies. Here, we emphasise the importance of maintaining an adequate level of genetic variation and propose the implementation of standardised studbooks for jaguars in Mexico, mainly to avoid inbreeding. In addition, achieving the aims of studbook registration would provide a population genetic characterisation that could serve as a basis for ex situ conservation programmes.

  19. Characterization of Genetic Variability and Population Structure of the Tick Amblyomma aureolatum (Acari: Ixodidae).

    Science.gov (United States)

    Ogrzewalska, Maria; Schwarcz, Kaiser; Bajay, Miklos M; Bajay, Stephanie K; Pinheiro, José B; Zucchi, Maria I; Pinter, Adriano; Labruna, Marcelo B

    2016-07-01

    The hard tick Amblyomma aureolatum (Pallas) is a vector of the bacterium Rickettsia rickettsii, the etiologic agent of Brazilian spotted fever (BSF) in parts of Brazil. Despite its wide distribution in southeastern South America and its public health importance, there is no information about genetic variation of this species that might help to understand the epidemiology of BSF. Using data from eight microsatellite markers and ticks from six localities, we used a population genetics approach to test the hypothesis that tick populations from areas with the presence of R. rickettsii are genetically different from ticks from areas without R. rickettsii Contrary to expectations, we found low genetic structure between studied regions. Thus, the presence of R. rickettsii in the specific area is more likely correlated with ecological and the environmental conditions or due to unknown gene coding regions of A. aureolatum genome that would be related to R. rickettsii infection resistance.

  20. Genetic variability and population structure of Plasmodium falciparum parasite populations from different malaria ecological regions of Kenya.

    Science.gov (United States)

    Ingasia, Luicer A; Cheruiyot, Jelagat; Okoth, Sheila Akinyi; Andagalu, Ben; Kamau, Edwin

    2016-04-01

    Transmission intensity, movement of human and vector hosts, biogeographical features, and malaria control measures are some of the important factors that determine Plasmodium falciparum parasite genetic variability and population structure. Kenya has different malaria ecologies which might require different disease intervention methods. Refined parasite population genetic studies are critical for informing malaria control and elimination strategies. This study describes the genetic diversity and population structure of P. falciparum parasites from the different malaria ecological zones in Kenya. Twelve multi-locus microsatellite (MS) loci previously described were genotyped in 225 P. falciparum isolates collected between 2012 and 2013 from five sites; three in lowland endemic regions (Kisumu, Kombewa, and Malindi) and two in highland, epidemic regions (Kisii and Kericho). Parasites from the lowland endemic and highland epidemic regions of western Kenya had high genetic diversity compared to coastal lowland endemic region of Kenya [Malindi]. The Kenyan parasites had a mean genetic differentiation index (FST) of 0.072 (p=0.011). The multi-locus genetic analysis of the 12 MS revealed all the parasites had unique haplotypes. Significant linkage disequilibrium (LD) was observed in all the five parasite populations. Kisumu had the most significant index of association values (0.16; pmalaria has been on the decline. The presence of significant LD suggests that there is occurrence of inbreeding in the parasite population. Parasite populations from Kisii showed the strongest evidence for epidemic population structure whereas the rest of the regions showed panmixia. Defining the genetic diversity of the parasites in different ecological regions of Kenya after introduction of the artemether-lumefantrine is important in refining the spread of drug resistant strains and malaria transmission for more effective control and eventual elimination of malaria in Kenya. Copyright

  1. Cryptosporidium,Giardia, Cryptococcus, Pneumocystis genetic variability: cryptic biological species or clonal near-clades?

    OpenAIRE

    2014-01-01

    An abundant literature dealing with the population genetics and taxonomy of Giardia duodenalis, Cryptosporidium spp., Pneumocystis spp., and Cryptococcus spp., pathogens of high medical and veterinary relevance, has been produced in recent years. We have analyzed these data in the light of new population genetic concepts dealing with predominant clonal evolution (PCE) recently proposed by us. In spite of the considerable phylogenetic diversity that exists among these pathogens, we have found ...

  2. The genetic variability of the Podolica cattle breed from the Gargano area. Preliminary results

    Directory of Open Access Journals (Sweden)

    Dario Cianci

    2010-01-01

    Full Text Available The Podolica cattle breed is autochthonous of Southern Italy and denoted by its particular rusticity. This study presents the preliminary results of the genetic characterization of the Podolica breed using DNA STR markers. A total of 20 microsatellite loci were analysed in 79 individuals reared in the Gargano area. Number of polymorphisms, allele fre- quencies, deviations from Hardy-Weinberg proportions, linkage disequilibrium between loci and genetic similarities between animals were calculated. The results showed a high deficiency of heterozygotes, the observed mean of het- erozygosis being 0.449, whereas the expected mean was 0.766. Many markers showed also deviations from the Hardy- Weinberg proportions and significant linkage disequilibrium between loci. However the genetic similarity within the pop- ulation was low (0.281 and the average number of alleles per locus was high (10, representing a high genetic vari- ability. In order to explain these results, a stratification of the breed in sub-populations with a high interior genetic homo- geneity but markedly differentiated one from each other could be hypothesized; this situation probably derived from non- random mating within each herd (consanguinity and from the lack of exchange of genetic material between the herds. A further study is needed on a wider sample and extending the analysis to FAO-ISAG microsatellite panel in order to con- firm this hypothesis. This could eventually provide the information necessary for the correct management of the repro- ductive schemes and for genomic traceability of meat production.

  3. Genetic variability of Appaloosa horses: a study of a closed breeding population from Argentina

    Directory of Open Access Journals (Sweden)

    Claudia Malena CORBI-BOTTO,Sebastian Andres SADABA,Elina Ines FRANCISCO,Paula Belen KALEMKERIAN,Juan Pedro LIRON,Egle Etel VILLEGAS-CASTAGNASSO,Guillermo GIOVAMBATTISTA,Pilar PERAL-GARCIA,Silvina DIAZ

    2014-09-01

    Full Text Available The genetic diversity and structure of 72 Appaloosa horses belonging to a closed breeding population from an ecological reserve in Buenos Aires, Argentina, was investigated using eight microsatellite markers from the International Society for Animal Genetics panel. Our data showed that this Appaloosa horse population had an elevated degree of genetic diversity (He= 0.746 and did not present a significant increase of homozygous individuals (FIS~0. However, the short tandem repeats, AHT5, ASB2, HTG10 and VHL20, were not in Hardy–Weinberg equilibrium (P-value<0.05. Genetic relationships between this population and other well known horse breeds showed that Appaloosa horses from Argentina could have had their origin in the horses of the Nez Perce's people in Idaho while other Appaloosa horses may have had influences from Andalusian and Lusitano breeds. This closed breeding population conserves an important degree of Appaloosa genetic diversity and notwithstanding its particular breeding characteristics, represents a valuable genetic resource for conservation.

  4. The value of small habitat islands for the conservation of genetic variability in a steppe grass species

    Science.gov (United States)

    Wódkiewicz, Maciej; Dembicz, Iwona; Moysiyenko, Ivan I.

    2016-10-01

    The habitat loss and fragmentation due to agricultural land-conversion affected the steppe throughout its range. In Ukraine, 95% of steppe was destroyed in the last two centuries. Remaining populations are confined to few refuges, like nature reserves, loess ravines, and kurgans (small burial mounds), the latter being often subject to destruction by archeological excavations. Stipa capillata L. is a typical grass species of Eurasian steppes and extrazonal dry grasslands, that was previously used as a model species in studies on steppe ecology. The aim of our research was to assess genetic diversity of S. capillata populations within different types of steppe refuges (loess ravines, biosphere reserve, kurgan) and to evaluate the value of the latter group for the preservation of genetic diversity in the study species. We assessed genetic diversity of 266 individuals from 15 populations (nine from kurgans, three from loess ravines and three from Askania-Nova Biosphere Reserve) with eight Universal Rice Primers (URPs). Studied populations showed high intra-population variability (I: 0.262-0.419, PPB: 52.08-82.64%). Populations from kurgans showed higher genetic differentiation (ΦST = 0.247) than those from loess ravines (ΦST = 0.120) and the biosphere reserve (ΦST = 0.142). Although the diversity metrics were to a small extent lower for populations from kurgans than from larger refugia we conclude that all studied populations of the species still preserve high genetic variability and are valuable for protection. To what extent this pattern holds true under continuous fragmentation in the future must be carefully monitored.

  5. Deriving estimates of individual variability in genetic potentials of performance traits for 3 dairy breeds, using a model of lifetime nutrient partitioning

    DEFF Research Database (Denmark)

    Phuong, H N; Martin, O; de Boer, I J M;

    2015-01-01

    , body reserve usage, and growth for different genotypes of cow. Moreover, it can be used to separate genetic variability in performance between individual cows from environmental noise. The model enables simulation of the effects of a genetic selection strategy on lifetime efficiency of individual cows......, which has a main advantage of including the rearing costs, and thus, can be used to explore the impact of future selection on animal performance and efficiency.......This study explored the ability of an existing lifetime nutrient partitioning model for simulating individual variability in genetic potentials of dairy cows. Generally, the model assumes a universal trajectory of dynamic partitioning of priority between life functions and genetic scaling...

  6. Genetic variability of the common Snook Centropomus undecimalis (Perciformes: Centropomidae) in connected marine and riverine environments.

    Science.gov (United States)

    Hernández-Vidal, Ulises; Lesher-Gordillo, Julia; Contreras-Sánchez, Wilfrido M; Chiappa-Carrara, Xavier

    2014-06-01

    The Common Snook, Centropomus undecimalis, inhabits riverine and marine areas of Southern Gulf of Mexico, where it is subject to intense use and exploitation. It has been reported that the genetic identification of fish stocks constitutes a valuable tool for wild population management; nevertheless, there is no available information on the genetic identification on fish stocks of this species in the region. The aim of this study was to determine the genetic relationship between C. undecimalis captured in marine and freshwater environments of the Gulf of Mexico and the San Pedro River. For this, muscle tissue samples of 79 specimens were obtained from areas located more than 300km apart. The genotype of each individual was determined using seven microsatellite primer pairs. Five primers amplified efficiently presenting between six and 28 alleles per locus. High levels of heterozygosis were observed in samples from both environments. Deviation from HWE due to an excess of heterozygotes was observed. The values of genetic difference indicate an absence of population structure (F(ST) = 0.0075 and R(ST) = (0.016, p = 0.051) and similarity in the allele frequencies, defined by Nei's index (0.805). Data showed the existence of a high gene flow due to the number of migrants (Nm = 18.7). Our results suggest that individuals living in these environments belong to the same genetic population. We suggest the development of management and protection plans for this fish species population in the wild.

  7. Genetic variability of the Bracco Italiano dog breed based on microsatellite polimorphysm

    Directory of Open Access Journals (Sweden)

    Silvano Presciuttini

    2011-10-01

    Full Text Available The Bracco Italiano is one of the oldest breeds of Italian pointing dogs, used for hunting ever since Renaissance times. After the Second World War it was included among the breeds officially recorded by the ENCI (the Italian Cynological Club, and since 1970 more than 23,000 animals have been registered; there are currently approximately 750 births per year. In this paper, we present the breed characterization of the population at the molecular level using 21 STR markers from the panels recommended for the 2006, 2008 and 2010 ISAG canine comparison test. Number of alleles, allele frequencies, deviations from Hardy-Weinberg proportions, linkage disequilibrium among loci, genetic similarity, genetic distances and molecular co-ancestry-based parameters were calculated. The number of alleles ranged from 3 to 9 (mean 6.43 whereas the expected heterozygosity ranged from 0.44 to 0.81 (mean 0.64. There was a high genetic similarity within the whole population (0.455 showing the great homogeneity of the sampled animals, as confirmed also by the small kinship distance (0.336, by the high values of the self molecular coancestry (0.703 and of the inbreeding coefficient (0.406. These results suggest the need for a careful genetic management of the population in order to avoid the risk of an excessive increase in the inbreeding level which would result in significant inbreeding depression and in significant loss of genetic variation.

  8. Genetic variability and resistance of cultivars of cowpea [Vigna unguiculata (L.) Walp] to cowpea weevil (Callosobruchus maculatus Fabr.).

    Science.gov (United States)

    Vila Nova, M X; Leite, N G A; Houllou, L M; Medeiros, L V; Lira Neto, A C; Hsie, B S; Borges-Paluch, L R; Santos, B S; Araujo, C S F; Rocha, A A; Costa, A F

    2014-03-31

    The cowpea weevil (Callosobruchus maculatus Fabr.) is the most destructive pest of the cowpea bean; it reduces seed quality. To control this pest, resistance testing combined with genetic analysis using molecular markers has been widely applied in research. Among the markers that show reliable results, the inter-simple sequence repeats (ISSRs) (microsatellites) are noteworthy. This study was performed to evaluate the resistance of 27 cultivars of cowpea bean to cowpea weevil. We tested the resistance related to the genetic variability of these cultivars using ISSR markers. To analyze the resistance of cultivars to weevil, a completely randomized test design with 4 replicates and 27 treatments was adopted. Five pairs of the insect were placed in 30 grains per replicate. Analysis of variance showed that the number of eggs and emerged insects were significantly different in the treatments, and the means were compared by statistical tests. The analysis of the large genetic variability in all cultivars resulted in the formation of different groups. The test of resistance showed that the cultivar Inhuma was the most sensitive to both number of eggs and number of emerged adults, while the TE96-290-12-G and MNC99-537-F4 (BRS Tumucumaque) cultivars were the least sensitive to the number of eggs and the number of emerged insects, respectively.

  9. Genetic variability of woolly aphid (Adelges laricis Vall.) resistance in European larch (Larix decidua Mill.)

    Energy Technology Data Exchange (ETDEWEB)

    Blada, I. [Forest Research Inst., Bucharest (Romania)

    1995-12-31

    One hundred and eleven clones of European larch were exposed to the woolly aphid and then outplanted in three locations using a randomized complete block design. At ages 11 and 19 years resistance was measured on 102 clones at 2 locations. Highly significant genetic differences were observed among the clones at both locations and at both ages. Highly significant clone x location, clone x location x age interactions were also observed. Differences between the most resistant and most susceptible clones was 483%. Sufficient genetic variation for a breeding program was present. Broad-sense heritability estimates for Adelges resistance varied by location. Significant age to age, location to location and age to location phenotypic correlation for resistance were found. Larch resistance seems to be under polygenic control. A substantial genetic gain could be achieved by selecting the best clones and using vegetative propagation, including somaclonal embryogenesis, for multiplication. 23 refs, 2 figs, 8 tabs

  10. Study of genetic variability in Vitis vinifera L. germplasm by high-throughput Vitis18kSNP array: the case of Georgian genetic resources.

    Science.gov (United States)

    De Lorenzis, Gabriella; Chipashvili, Ramaz; Failla, Osvaldo; Maghradze, David

    2015-06-23

    Georgia, in the Caucasian region, is considered the first domestication centre of grapevine. This country is characterized by high morphological variability of cultivated (Vitis vinifera L. subsp. sativa (DC.) Hegi) and wild (Vitis vinifera L. subsp. sylvestris (Gmel.) Hegi) compartments. The main objective of this study was to investigate the level of genetic diversity obtained by the novel custom Vitis18kSNP array, in order to analyse 71 grapevine accessions representative of wild and cultivated Georgian germplasms. The number of loci successfully amplified was 15,317 out of 18,775 SNP and 79 % of loci resulted polymorphic. Sixty-eight unique profiles were identified, 42 for the sativa and 26 for the sylvestris compartment. Cluster analysis highlighted two main groups, one for cultivars and another for wild individuals, while a genetic structure according to accession taxonomic status and cultivar geographical origin was revealed by multivariate analysis, differentiating clearly the genotypes into 3 main groups, two groups including cultivars and one for wild individuals, even though a considerable overlapping area was observed. Pattern of genetic diversity structure presented an additional proof that grapevine domestication events took place in the Caucasian region contributing to the crop evolution. Our results demonstrated a moderate differentiation between sativa and sylvestris compartments, even though a connection between several samples of both subspecies may be assumed for the occurrence of cross hybridization events among native wild populations and the cultivated accessions. Nevertheless, first degree relationships have not been discovered between wild and cultivated individuals.

  11. Genetic variability of pain perception and treatment--clinical pharmacological implications.

    Science.gov (United States)

    Lötsch, Jörn

    2011-06-01

    Evidence of a genetic control of pain has led to efforts to exploit genotyping information from pain patients for the development of analgesics and for the selection of pharmacological approaches to pain. Research on translating the genetic bases of familial insensitivity to pain has contributed to the discovery of crucial molecular pathways of pain and to the identification of new analgesic targets (e.g., the Na(v)1.7 sodium channel, neurotrophic tyrosine kinase receptors, nerve growth factor). Moreover, human genetic variants leading to enhanced or reduced function of specific molecular pathways are employed as substitutes for the lack of modulator molecules usable in humans, enabling nociceptive or anti-nociceptive pathways in humans to be studied before drug development. Translational approaches have also been used to verify the importance of experimentally discovered pain pathways in humans, such as GTP cyclohydrolase 1 and the potassium channel K(v)9.1. In addition to these uses of genetics as a research tool, an individualized pharmacological therapy based on the patient's genotype has been attempted. In terms of analgesics in clinical use, such an approach is at the present time only marginally available. For future analgesic targeting, for example, Na(v)1.7 or TRPA1, the genotype may be the target of a selective cure for syndromes caused by increased-function mutations in the coding genes. The consideration of human genetics in drug studies may accelerate analgesic drug development while reducing cost because the clinical success may be partly anticipated by including information of functional genetic variants that mimic the action of future analgesics. These developments show that genotyping information obtained from studies on pain patients plays a role in the clinical pharmacology of pain.

  12. Exploring the role of genetic variability and lifestyle in oxidative stress response for healthy aging and longevity.

    Science.gov (United States)

    Dato, Serena; Crocco, Paolina; D'Aquila, Patrizia; de Rango, Francesco; Bellizzi, Dina; Rose, Giuseppina; Passarino, Giuseppe

    2013-08-08

    Oxidative stress is both the cause and consequence of impaired functional homeostasis characterizing human aging. The worsening efficiency of stress response with age represents a health risk and leads to the onset and accrual of major age-related diseases. In contrast, centenarians seem to have evolved conservative stress response mechanisms, probably derived from a combination of a diet rich in natural antioxidants, an active lifestyle and a favorable genetic background, particularly rich in genetic variants able to counteract the stress overload at the level of both nuclear and mitochondrial DNA. The integration of these factors could allow centenarians to maintain moderate levels of free radicals that exert beneficial signaling and modulator effects on cellular metabolism. Considering the hot debate on the efficacy of antioxidant supplementation in promoting healthy aging, in this review we gathered the existing information regarding genetic variability and lifestyle factors which potentially modulate the stress response at old age. Evidence reported here suggests that the integration of lifestyle factors (moderate physical activity and healthy nutrition) and genetic background could shift the balance in favor of the antioxidant cellular machinery by activating appropriate defense mechanisms in response to exceeding external and internal stress levels, and thus possibly achieving the prospect of living a longer life.

  13. Relative contributions of neutral and non-neutral genetic differentiation to inform conservation of steelhead trout across highly variable landscapes

    Science.gov (United States)

    Matala, Andrew P; Ackerman, Michael W; Campbell, Matthew R; Narum, Shawn R

    2014-01-01

    Mounting evidence of climatic effects on riverine environments and adaptive responses of fishes have elicited growing conservation concerns. Measures to rectify population declines include assessment of local extinction risk, population ecology, viability, and genetic differentiation. While conservation planning has been largely informed by neutral genetic structure, there has been a dearth of critical information regarding the role of non-neutral or functional genetic variation. We evaluated genetic variation among steelhead trout of the Columbia River Basin, which supports diverse populations distributed among dynamic landscapes. We categorized 188 SNP loci as either putatively neutral or candidates for divergent selection (non-neutral) using a multitest association approach. Neutral variation distinguished lineages and defined broad-scale population structure consistent with previous studies, but fine-scale resolution was also detected at levels not previously observed. Within distinct coastal and inland lineages, we identified nine and 22 candidate loci commonly associated with precipitation or temperature variables and putatively under divergent selection. Observed patterns of non-neutral variation suggest overall climate is likely to shape local adaptation (e.g., potential rapid evolution) of steelhead trout in the Columbia River region. Broad geographic patterns of neutral and non-neutral variation demonstrated here can be used to accommodate priorities for regional management and inform long-term conservation of this species. PMID:25067950

  14. Contribution of VPS35 genetic variability to LBD in the Flanders-Belgian population

    NARCIS (Netherlands)

    Verstraeten, Aline; Wauters, Eline; Crosiers, David; Meeus, Bram; Corsmit, Ellen; Elinck, Ellen; Mattheijssens, Maria; Peeters, Karin; Cras, Patrick; Pickut, Barbara; Vandenberghe, Rik; Engelborghs, Sebastiaan; De Deyn, Peter Paul; Van Broeckhoven, Christine; Theuns, Jessie

    2012-01-01

    VPS35 was recently identified as a novel autosomal dominant gene for Parkinson disease. In this study, we aimed to determine the contribution of simple and complex VPS35 variations to the genetic etiology of the spectrum of Lewy body disorders (LBD) in a Flanders-Belgian patient cohort (n = 677). We

  15. Correlations among Jamaican 12th-Graders' Five Variables and Performance in Genetics

    Science.gov (United States)

    Bloomfield, Deen-Paul; Soyibo, Kola

    2008-01-01

    This study was aimed at finding out if the level of performance of selected Jamaican Grade 12 students on an achievement test on the concept of genetics was satisfactory; if there were statistically significant differences in their performance on the concept linked to their gender, self-esteem, cognitive abilities in biology, school-type and…

  16. Proteomic studies related to genetic determinants of variability in protein concentrations

    NARCIS (Netherlands)

    Horvatovich, Peter; Franke, Lude; Bischoff, Rainer

    2014-01-01

    Genetic variation has multiple effects on the proteome. It may influence the expression level of proteins, modify their sequences through single nucleotide polymorphisms, the occurrence of allelic variants, or alternative splicing (ASP) events. This perspective paper summarizes the major effects of

  17. Mean Platelet Volume and Arterial Stiffness – Clinical Relationship and Common Genetic Variability

    Science.gov (United States)

    Panova-Noeva, Marina; Arnold, Natalie; Hermanns, M. Iris; Prochaska, Jürgen H.; Schulz, Andreas; Spronk, Henri M.; Binder, Harald; Pfeiffer, Norbert; Beutel, Manfred; Blankenberg, Stefan; Zeller, Tanja; Lotz, Johannes; Münzel, Thomas; Lackner, Karl J.; ten Cate, Hugo; Wild, Philipp S.

    2017-01-01

    Vessel wall stiffening is an important clinical parameter, but it is unknown whether platelets, key elements in the pathogenesis of arterial thrombosis, are associated with arterial stiffness. The present studies sought to determine whether mean platelet volume (MPV), a potential marker of platelet activation, is linked to vascular elasticity as assessed by the augmentation index (AIx), in 15,010 individuals from the population-based Gutenberg Health Study. Multivariable analysis showed that MPV in both males (β 0.776; 95thCI [0.250;1.16]; p = 0.0024) and females (β 0.881[0.328;1.43]; p = 0.0018) is strongly associated with AIx. Individuals with MPV and AIx above the sex-specific medians had worse survival. Association analysis between MPV-related genetic variants and arterial stiffness identified four genetic variants in males and one in females related with AIx. Cox regression analysis for mortality identified one of these joint genetic variants close to ring finger protein 145 gene (RNF145, rs10076782) linked with increased mortality (hazard ratio 2.02; 95thCI [1.35;3.02]; p = 0.00061). Thus, these population-based data demonstrate a close relation between platelet volume as a potential marker of platelet activation and arterial stiffness in both sexes. Further research is warranted to further elucidate the mechanisms underlying larger platelets‘ role in arterial stiffening including the role of shared common genetics. PMID:28059166

  18. [Genetic variability and phylogenetic analysis of 39 short tandem repeat loci in Beijing Han population].

    Science.gov (United States)

    Xiuyan, Ruan; Weini, Wang; Yaran, Yang; Bingbing, Xie; Jing, Chen; Yacheng, Liu; Jiangwei, Yan

    2015-07-01

    In this study, we studied the genetic polymorphisms of short tandem repeat (STR) loci from 13 CODIS and 26 non-CODIS system in Beijing Han population for the first time, and established a database of 39 STR loci whose forensic parameters were further evaluated. Our results demonstrated no significant deviation from the Hardy-Weinberg equilibrium of 39 STR loci and no pairwise linkage disequilibrium between them. The power of discriminations, expected heterozygosity, polymorphic information content, and power of exclusion of 39 STR loci ranged from 0.7740-0.9818, 0.6000-0.9350, 0.5317-0.9047 and 0.2909-0.8673. The cumulated discrimination power and cumulative probability of exclusion were 0.999999999999999999999999999999999999999964971 and 0.999999999973878, respectively. Moreover, the genetic distance was calculated based on allele frequency and phylogenetic tree was built using STR loci data from Beijing Han and other 11 Chinese ethnic groups.This study provides important basic data for Chinese forensic DNA database and population genetics database, and has important significance in carrying out forensic individual identification, paternity testing, and population genetic study.

  19. Genetic variability in spotted seatrout (Cynoscion nebulosus), determined with microsatellite DNA markers

    Science.gov (United States)

    Ward, R.; Bowers, K.; Hensley, R.; Mobley, B.; Belouski, E.

    2007-01-01

    Variation in the allele frequencies of five microsatellite loci was surveyed in 1256 individual spotted seatrout (Cynoscion nebulosus) obtained from 12 bays and estuaries from Laguna Madre, Texas, to Charlotte Harbor, Florida, to St. John's River on the Florida Atlantic Coast. Texas and Louisiana collection sites were resampled each year for two to four years (1998-2001). Genetic differentiation was observed. Spotted seatrout from Florida waters were strongly differentiated from spotted seatrout collected in Louisiana and Texas. The greatest genetic discontinuity was observed between Tampa Bay and Charlotte Harbor, and Charlotte Harbor seatrout were most similar to Atlantic Coast spotted seatrout. Texas and Louisiana samples were not strongly structured within the northwestern Gulf of Mexico and there was little evidence of temporal differentiation within bays. These findings are contrary to those of earlier analyses with allozymes and mitochondrial DNA (mtDNA) where evidence of spatial differentiation was found for spotted seatrout resident on the Texas coast. The differences in genetic structure observed among these markers may reflect differences in response to selective pressure, or may be due to differences in underlying genetic processes.

  20. Variability in anthocyanin content among Abutilon theophrasti, and Urena lobata genetic resources .

    Science.gov (United States)

    Plants contain bioactive phytochemicals and nutraceuticals to be utilized in the pharmaceutical and nutraceutical markets. Sixty-two accessions of Abutilon theophrasti, Basella alba, and Urena lobata are conserved at the USDA, ARS, Plant Genetic Resources Conservation Unit, Griffin, GA. Anthocyanins...

  1. Genetic variability in apomictic mangosteen (Garcinia mangostana and its close relatives (Garcinia spp. based on ISSR markers

    Directory of Open Access Journals (Sweden)

    SOBIR

    2011-04-01

    Full Text Available Sobir, Poerwanto R, Santosa E, Sinaga S, Mansyah E (2011 Genetic variability in apomictic mangosteen (Garcinia mangostana and its close relatives (Garcinia spp. based on ISSR markers. Biodiversitas 12: 59-63. In order to reveal phylogenetic relationship of mangosteen and several close relatives (Garcinia spp., we employed seven ISSR dinucleotide primer systems on eleven close relatives of mangosteen and 28 mangosteen accessions from four islands in Indonesia (Sumatra, Java, Kalimantan and Lombok. ISSR analysis successfully amplified 43 bands on average 6.1 fragments for each primer system, and these all fragments were polymorphic. Seven close relatives of mangosteen were separated with mangosteen accessions at 0.22 level of dissimilarity, while other four including G. malaccensis, were clustered with mangosteen accessions, this results supported proposal that G. malaccensis was allopolyploid derivative of mangosteen. Clustering pattern among mangosteen accessions, however, not represented their origin, indicated that distribution of the accessions was not linked to their genetic properties.

  2. Genetic variability of Herpailurus yagouaroundi, Puma concolor and Panthera onca (Mammalia, Felidae studied using Felis catus microsatellites

    Directory of Open Access Journals (Sweden)

    Vanessa Roma Moreno

    2006-01-01

    Full Text Available We used four microsatellite loci (Fca08, Fca45, Fca77 and Fca96 from the domestic cat, Felis catus, to investigate genetic variability in specimens of Herpailurus yagouaroundi (jaguarundi, otter cat, eyra, Puma concolor (cougar, mountain lion, puma and Panthera onca (jaguar held in various Brazilian zoos. Samples of DNA from the cats were PCR amplified and then sequenced before being analyzed using the CERVUS program. Our results show a mean polymorphic information content (PIC of 0.83 for H. yagouaroundi, 0.66 for P. concolor and 0.69 for P. onca and a mean of 10.3 alleles for the Fca08 locus, 5.3 for Fca 45, 9 for Fca 77 and 14 for Fca 96. These results indicate a relatively high level of genetic diversity for the specimens studied.

  3. Chicken meat quality: genetic variability and relationship with growth and muscle characteristics

    Directory of Open Access Journals (Sweden)

    Santé-Lhoutellier Véronique

    2008-08-01

    Full Text Available Abstract Background The qualitative properties of the meat are of major importance for poultry breeding, since meat is now widely consumed as cuts or as processed products. The aim of this study was to evaluate the genetic parameters of several breast meat quality traits and their genetic relationships with muscle characteristics in a heavy commercial line of broilers. Results Significant levels of heritability (averaging 0.3 were obtained for breast meat quality traits such as pH at 15 min post-slaughter, ultimate pH (pHu, color assessed by lightness L*, redness a* and yellowness b*, drip loss, thawing-cooking loss and shear-force. The rate of decrease in pH early post-mortem and the final pH of the meat were shown to be key factors of chicken meat quality. In particular, a decrease in the final pH led to paler, more exudative and tougher breast meat. The level of glycogen stored in breast muscle estimated by the Glycolytic Potential (GP at slaughter time was shown to be highly heritable (h2 0.43. There was a very strong negative genetic correlation (rg with ultimate meat pH (rg -0.97, suggesting a common genetic control for GP and pHu. While breast muscle weight was genetically positively correlated with fiber size (rg 0.76, it was negatively correlated with the level of glycogen stored in the muscle (rg -0.58, and as a consequence it was positively correlated with the final pH of the meat (rg 0.84. Conclusion This genetic study confirmed that selection should be useful to improve meat characteristics of meat-type chickens without impairing profitability because no genetic conflict was detected between meat quality and meat quantity. Moreover, the results suggested relevant selection criteria such as ultimate pH, which is strongly related to color, water-holding capacity and texture of the meat in this heavy chicken line.

  4. Life history traits in selfing versus outcrossing annuals: exploring the 'time-limitation' hypothesis for the fitness benefit of self-pollination

    Directory of Open Access Journals (Sweden)

    Aarssen Lonnie W

    2005-02-01

    Full Text Available Abstract Background Most self-pollinating plants are annuals. According to the 'time-limitation' hypothesis, this association between selfing and the annual life cycle has evolved as a consequence of strong r-selection, involving severe time-limitation for completing the life cycle. Under this model, selection from frequent density-independent mortality in ephemeral habitats minimizes time to flower maturation, with selfing as a trade-off, and / or selection minimizes the time between flower maturation and ovule fertilization, in which case selfing has a direct fitness benefit. Predictions arising from this hypothesis were evaluated using phylogenetically-independent contrasts of several life history traits in predominantly selfing versus outcrossing annuals from a data base of 118 species distributed across 14 families. Data for life history traits specifically related to maturation and pollination times were obtained by monitoring the start and completion of different stages of reproductive development in a greenhouse study of selfing and outcrossing annuals from an unbiased sample of 25 species involving five pair-wise family comparisons and four pair-wise genus comparisons. Results Selfing annuals in general had significantly shorter plant heights, smaller flowers, shorter bud development times, shorter flower longevity and smaller seed sizes compared with their outcrossing annual relatives. Age at first flower did not differ significantly between selfing and outcrossing annuals. Conclusions This is the first multi-species study to report these general life-history differences between selfers and outcrossers among annuals exclusively. The results are all explained more parsimoniously by selection associated with time-limitation than by selection associated with pollinator/mate limitation. The shorter bud development time reported here for selfing annuals is predicted explicitly by the time-limitation hypothesis for the fitness benefit of

  5. Intra-individual Variability in Prodromal Huntington Disease and Its Relationship to Genetic Burden.

    Science.gov (United States)

    Musso, Mandi; Westervelt, Holly James; Long, Jeffrey D; Morgan, Erin; Woods, Steven Paul; Smith, Megan M; Lu, Wenjing; Paulsen, Jane S

    2015-01-01

    The current study sought to examine the utility of intra-individual variability (IIV) in distinguishing participants with prodromal Huntington disease (HD) from nongene-expanded controls. IIV across 15 neuropsychological tasks and within-task IIV using a self-paced timing task were compared as a single measure of processing speed (Symbol Digit Modalities Test [SDMT]) in 693 gene-expanded and 191 nongene-expanded participants from the PREDICT-HD study. After adjusting for depressive symptoms and motor functioning, individuals estimated to be closest to HD diagnosis displayed higher levels of across- and within-task variability when compared to controls and those prodromal HD participants far from disease onset (F ICV(3,877)=11.25; p<.0001; F PacedTiming(3,877)=22.89; p<.0001). When prodromal HD participants closest to HD diagnosis were compared to controls, Cohen's d effect sizes were larger in magnitude for the within-task variability measure, paced timing (-1.01), and the SDMT (-0.79) and paced tapping coefficient of variation (CV) (-0.79) compared to the measures of across-task variability [CV (0.55); intra-individual standard deviation (0.26)]. Across-task variability may be a sensitive marker of cognitive decline in individuals with prodromal HD approaching disease onset. However, individual neuropsychological tasks, including a measure of within-task variability, produced larger effect sizes than an index of across-task IIV in this sample.

  6. Variability, heritability and genetic advance in some agronomic and forage quality characters of spring triticale in western Canada.

    Science.gov (United States)

    Aljarrah, Mazen; Oatway, Lori; Albers, Susan; Bergen, Colin

    2014-01-01

    The aim of this study was to estimate variability, broad sense heritability, and genetic advance for dry matter yield (DMY), days to anthesis (ANTH), plant height (HT), in-vitro fiber digestibility-30h (IVFD), lignin (LIGN), starch (STAR %), crude protein content (CP %), acid detergent fiber (ADF) and neutral detergent fiber (NDF) in spring triticale genotypes. Eighteen genotypes were tested at the Field Crop Development Centre (FCDC) in Lacombe, Alberta in 2010-2011 and 2011-2012 growing season. The experimental design was randomized complete block design with 3 replicates. Combined analysis of variance was carried out using SAS Enterprise 4.2 statistical package. Heritability was estimated following the variance component method. Simple correlation coefficients were determined among all traits using two years average data. The genotype mean squares were significant (P ≤ 0.05) for DMY, ANTH, HT, IFVD, ADF, NDF, STAR %, LIGN, and CP %. The effect of year was also highly significant on all studied traits. The phenotypic coefficient of variation was higher than the genetic coefficient of variation for all traits, indicating high influence of the environment on these traits. The significant genetic variability and the high heritability combined with high genetic advance of HT, STAR% and ADF in triticale genotypes suggested that selection could be successfully practiced for those traits. Correlation analysis showed significant and positive correlation of DMY with ANTH and HT, indicating that late and tall genotypes are more suitable as a forage type and they tend to produce more biomass yield. However, DMY did not show any significant correlation with the digestibility. IVFD and STAR % were negatively correlated with LIGN. In general, these results indicated that breeding for low lignin and high starch content will improve the digestibility in triticale genotypes. The preliminary results of this study were promising. Further research must include more diverse

  7. Genetic variables of various manifestations of osteochondrosis and their correlations between and within joints in Dutch warmblood horses.

    Science.gov (United States)

    van Grevenhof, E M; Schurink, A; Ducro, B J; van Weeren, P R; van Tartwijk, J M F M; Bijma, P; van Arendonk, J A M

    2009-06-01

    Osteochondrosis (OC) is an important orthopedic developmental disorder in many horse populations. A review of the literature revealed widely variable heritability estimates for the disorder. We estimated the genetic variables (heritabilities and genetic correlations) of various manifestations of OC. Femoropatellar, tarsocrural, and metacarpophalangeal and metatarsophalangeal joints of 811 randomly selected yearlings from the Royal Warmblood Studbook of The Netherlands, descending from 32 representative stallions, were scored for OC at 28 predilection sites. At each site, OC was scored in 5 categories, distinguishing between flattened bone contours and fragments. At the animal level, the overall heritability of OC was 0.23, the heritability of flattened bone contours was 0.08, and the heritability of fragments was 0.22. At the joint level, heritability was greatest in the tarsocrural joints, intermediate in the metacarpophalangeal and metatarsophalangeal joints, and least in the femoropatellar joints. The heritability estimates for the contralateral joint homologs were very similar. The genetic correlation between the tarsocrural and femoropatellar joint was strong, whereas correlations between the metacarpophalangeal and metatarsophalangeal and other joints were moderate. The genetic correlation between flattened bone contours and fragments at the animal level was 0.80. Scoring OC on a 5-point categorical scale resulted in greater heritability on the observed scale than when analyzing OC as a binary trait. Our results suggest that selection against OC could best be performed by taking into account the OC status of all 4 joints, the femoropatellar, the tarsocrural, and the metacarpophalangeal and metatarsophalangeal joints, and discerning between flattened bone contours and fragments.

  8. Genetic variability of sexual size dimorphism in a natural population of Drosophila melanogaster: an isofemale-line approach

    Indian Academy of Sciences (India)

    Jean R. David; Patricia Gibert; Sandrine Mignon-Grasteau; Hélène Legout; Georges Pétavy; Catherine Beaumont; Brigitte Moreteau

    2003-12-01

    Most animal species exhibit sexual size dimorphism (SSD). SSD is a trait difficult to quantify for genetical purposes since it must be simultaneously measured on two kinds of individuals, and it is generally expressed either as a difference or as a ratio between sexes. Here we ask two related questions: What is the best way to describe SSD, and is it possible to conveniently demonstrate its genetic variability in a natural population? We show that a simple experimental design, the isofemale-line technique (full-sib families), may provide an estimate of genetic variability, using the coefficient of intraclass correlation. We consider two SSD indices, the female–male difference and the female/male ratio. For two size-related traits, wing and thorax length, we found that both SSD indices were normally distributed. Within each family, the variability of SSD was estimated by considering individual values in one sex (the female) with respect to the mean value in the other sex (the male). In a homogeneous sample of 30 lines of Drosophila melanogaster, both indices provided similar intraclass correlations, on average 0.21, significantly greater than zero but lower than those for the traits themselves: 0.50 and 0.36 for wing and thorax length respectively. Wing and thorax length were strongly positively correlated within each sex. SSD indices of wing and thorax length were also positively correlated, but to a lesser degree than for the traits themselves. For comparative evolutionary studies, the ratio between sexes seems a better index of SSD since it avoids scaling effects among populations or species, permits comparisons between different traits, and has an unambiguous biological significance. In the case of D. melanogaster grown at 25°C, the average female/male ratios are very similar for the wing (1.16) and the thorax (1.15), and indicate that, on average, these size traits are 15–16% longer in females.

  9. Assessing the intra-species genetic variability in the clonal pathogen Campylobacter fetus: CRISPRs are highly polymorphic DNA markers.

    Science.gov (United States)

    Calleros, Lucía; Betancor, Laura; Iraola, Gregorio; Méndez, Alejandra; Morsella, Claudia; Paolicchi, Fernando; Silveyra, Silvia; Velilla, Alejandra; Pérez, Ruben

    2017-01-01

    Campylobacter fetus is a Gram-negative, microaerophilic bacterium that infects animals and humans. The subspecies Campylobacter fetus subsp. fetus (Cff) affects a broad range of vertebrate hosts and induces abortion in cows and sheep. Campylobacter fetus subsp. venerealis (Cfv) is restricted to cattle and causes the endemic disease bovine genital campylobacteriosis, which triggers reproductive problems and is responsible for major economic losses. Campylobacter fetus subsp. testudinum (Cft) has been isolated mostly from apparently healthy reptiles belonging to different species but also from ill snakes and humans. Genotypic differentiation of Cff and Cfv is difficult, and epidemiological information is scarce because there are few methods to study the genetic diversity of the strains. We analyze the efficacy of MLST, ribosomal sequences (23S gene and internal spacer region), and CRISPRs to assess the genetic variability of C. fetus in bovine and human isolates. Sequences retrieved from complete genomes were included in the analysis for comparative purposes. MLST and ribosomal sequences had scarce or null variability, while the CRISPR-cas system structure and the sequence of CRISPR1 locus showed remarkable diversity. None of the sequences here analyzed provided evidence of a genetic differentiation of Cff and Cfv in bovine isolates. Comparison of bovine and human isolates with Cft strains showed a striking divergence. Inter-host differences raise the possibility of determining the original host of human infections using CRISPR sequences. CRISPRs are the most variable sequences analyzed in C. fetus so far, and constitute excellent representatives of a dynamic fraction of the genome. CRISPR typing is a promising tool to characterize isolates and to track the source and transmission route of C. fetus infections.

  10. Variabilidad gen��tica de los caballos criollos del Uruguay Genetic variability of uruguayan creole horse

    Directory of Open Access Journals (Sweden)

    L. KELLY

    2002-01-01

    Full Text Available El caballo Criollo del Uruguay (CCU corresponde al biotipo de caballo de trabajo americano, adaptado y criado en vastas zonas ganaderas. El objetivo de este trabajo es estudiar su variabilidad genética y establecer la diferenciación entre las subpoblaciones que componen la muestra con el fin de analizar la variabilidad entre las mismas. El estudio se realiza mediante 16 marcadores genéticos (7 grupos sanguíneos y 9 polimorfismos bioquímicos, analizándose 145 CCU pertenecientes a 4 Departamentos del país. Los sistemas electroforéticos analizados dentro de las 4 subpoblaciones (A, B, C, D se encontraron en equilibrio génico. La variabilidad genética racial se estimó mediante el Índice de Heterocigosidad media esperada (IH para los 16 marcadores genéticos (MG, el número total de variantes y el índice de consanguinidad (f. Los resultados fueron: 0.424, 62 y 0,049 respectivamente. La variabilidad de cada una de las subpoblaciones se evaluó mediante el índice F de fijación de Wright (F y el IH. Todas las subpoblaciones presentaron F negativo, siendo la de menor variabilidad la B (IH= 0.265. Se calculó la distancia genética de Nei entre las 4 subpoblaciones. Esta fue en orden creciente con respecto a la A: C (0.007, D (0.014 y B (0.058. Se realizó un análisis de "cluster" mediante el método de UPGMA, obteniéndose un dendograma en el que se agrupan las subpoblaciones A, C y D. Se puede concluir que el CCU tiene una variabilidad genética de intermedia a alta, conservando el polimorfismos de las razas ancestrales. En cuanto a la variabilidad intrapoblacional se comprueba la presencia de una línea (B dentro de la razaThe Uruguayan Creole Horse corresponds to the biotype of American horse for work, adapted and bred in vast cattle areas. The objective of this work is to study its genetic variability and to establish the differentiation among farms included in the sample with the purpose of analyzing the variability among them. The

  11. Mid-infrared prediction of milk titratable acidity and its genetic variability in first-parity cows

    OpenAIRE

    Colinet, Frédéric; Vanlierde, Amélie; Vanden Bossche, sandrine; Sindic, Marianne; Dehareng, Frédéric; Sinnaeve, Georges; Vandenplas, Jérémie; Soyeurt, Hélène; Bastin, Catherine; Gengler, Nicolas

    2012-01-01

    Coagulation of milkhas a direct effect on cheese yield. Among several parameters, titratable acidity of milk (TA) influences all the phases of milk coagulation. In order to study the genetic variability of this trait on a large scale, mid-infrared (MIR) chemometric methods were used to predict TA. A total of 507 milk samples collected in the Walloon Region of Belgium from individual cows were analyzed using a MIR spectrometer. TA was recorded as Dornic degree. An equation to predict TA from m...

  12. Genetic variability of glutathione S-transferase enzymes in human populations: functional inter-ethnic differences in detoxification systems.

    Science.gov (United States)

    Polimanti, Renato; Carboni, Cinzia; Baesso, Ilenia; Piacentini, Sara; Iorio, Andrea; De Stefano, Gian Franco; Fuciarelli, Maria

    2013-01-01

    Glutathione S-Transferase enzymes (GSTs) constitute the principal Phase II superfamily which plays a key role in cellular detoxification and in other biological processes. Studies of GSTs have revealed that genetic polymorphisms are present in these enzymes and that some of these are Loss-of-Function (LoF) variants, which affect enzymatic functions and are related to different aspects of human health. The aim of this study was to analyze functional genetic differences in GST enzymes among human populations. Attention was focused on LoF polymorphisms of GSTA1, GSTM1, GSTO1, GSTO2, GSTP1 and GSTT1 genes. These LoF variants were analyzed in 668 individuals belonging to six human groups with different ethnic backgrounds: Amhara and Oromo from Ethiopia; Colorado and Cayapa Amerindians and African Ecuadorians from Ecuador; and one sample from central Italy. The HapMap database was used to compare our data with reference populations and to analyze the haplotype and Linkage Disequilibrium diversity in different ethnic groups. Our results highlighted that ethnicity strongly affects the genetic variability of GST enzymes. In particular, GST haplotypes/variants with functional impact showed significant differences in human populations, according to their ethnic background. These data underline that human populations have different structures in detoxification genes, suggesting that these ethnic differences influence disease risk or response to drugs and therefore have implications for genetic association studies involving GST enzymes. In conclusion, our investigation provides data about the distribution of important LoF variants in GST genes in human populations. This information may be useful for designing and interpreting genetic association studies.

  13. Shared language, diverging genetic histories: high-resolution analysis of Y-chromosome variability in Calabrian and Sicilian Arbereshe.

    Science.gov (United States)

    Sarno, Stefania; Tofanelli, Sergio; De Fanti, Sara; Quagliariello, Andrea; Bortolini, Eugenio; Ferri, Gianmarco; Anagnostou, Paolo; Brisighelli, Francesca; Capelli, Cristian; Tagarelli, Giuseppe; Sineo, Luca; Luiselli, Donata; Boattini, Alessio; Pettener, Davide

    2016-04-01

    The relationship between genetic and linguistic diversification in human populations has been often explored to interpret some specific issues in human history. The Albanian-speaking minorities of Sicily and Southern Italy (Arbereshe) constitute an important portion of the ethnolinguistic variability of Italy. Their linguistic isolation from neighboring Italian populations and their documented migration history, make such minorities particularly effective for investigating the interplay between cultural, geographic and historical factors. Nevertheless, the extent of Arbereshe genetic relationships with the Balkan homeland and the Italian recipient populations has been only partially investigated. In the present study we address the genetic history of Arbereshe people by combining highly resolved analyses of Y-chromosome lineages and extensive computer simulations. A large set of slow- and fast-evolving molecular markers was typed in different Arbereshe communities from Sicily and Southern Italy (Calabria), as well as in both the putative Balkan source and Italian sink populations. Our results revealed that the considered Arbereshe groups, despite speaking closely related languages and sharing common cultural features, actually experienced diverging genetic histories. The estimated proportions of genetic admixture confirm the tight relationship of Calabrian Arbereshe with modern Albanian populations, in accordance with linguistic hypotheses. On the other hand, population stratification and/or an increased permeability of linguistic and geographic barriers may be hypothesized for Sicilian groups, to account for their partial similarity with Greek populations and their higher levels of local admixture. These processes ultimately resulted in the differential acquisition or preservation of specific paternal lineages by the present-day Arbereshe communities.

  14. Genetic Variability of the Essential Oil Content of Melissa officinalis1.

    Science.gov (United States)

    Adzet, T; Ponz, R; Wolf, E; Schulte, E

    1992-12-01

    The essential oil content of various populations of MELISSA OFFICINALIS L. (Lamiaceae), cultivated under Mediterranean climatic conditions (Ebro-Delta, Spain) has been investigated during five years of selection and improvement of the genetic plant material. Starting with an essential oil content of 0.2-0.3%, a content of more than 0.5% was obtained as a result of genetic improvement. A weak negative correlation between the content of essential oil and phenotypical growth parameters such as the number of branches per plant and height was observed. No correlation between biomass production per plant and essential oil content could be found. By the method of hybridization, M. OFFICINALIS synthetics with a high yield of biomass and essential oil content were selected.

  15. Genetics of glioblastoma: a window into its imaging and histopathologic variability.

    Science.gov (United States)

    Belden, Clifford J; Valdes, Pablo A; Ran, Cong; Pastel, David A; Harris, Brent T; Fadul, Camilo E; Israel, Mark A; Paulsen, Keith; Roberts, David W

    2011-10-01

    Glioblastoma is a highly malignant brain tumor that relentlessly defies therapy. Efforts over the past decade have begun to tease out the biochemical details that lead to its aggressive behavior and poor prognosis. There is hope that this new understanding will lead to improved treatment strategies for patients with glioblastoma, in the form of targeted, molecularly based therapies that are individualized to specific changes in individual tumors. However, these new therapies have the potential to fundamentally alter the biologic behavior of glioblastoma and, as a result, its imaging appearance. Knowledge about common genetic alterations and the resultant cellular and tissue changes (ie, induced angiogenesis and abnormal cell survival, proliferation, and invasion) in glioblastomas is important as a basis for understanding imaging findings before treatment. It is equally critical that radiologists understand which genetic pathway is targeted by each specific therapeutic agent or class of agents in order to accurately interpret changes in the imaging appearances of treated tumors.

  16. Hierarchical spatial structure of genetically variable nucleopolyhedroviruses infecting cyclic populations of western tent caterpillars.

    Science.gov (United States)

    Cooper, Dawn; Cory, Jenny S; Myers, Judith H

    2003-04-01

    The cyclic population dynamics of western tent caterpillars, Malacosoma californicum pluviale, are associated with epizootics of a nucleopolyhedrovirus, McplNPV. Given the dynamic fluctuations in host abundance and levels of viral infection, host resistance and virus virulence might be expected to change during different phases of the cycle. As a first step in determining if McplNPV virulence and population structure change with host density, we used restriction fragment length polymorphism (RFLP) analysis to examine the genetic diversity of McplNPV infecting western tent caterpillar populations at different spatial scales. Thirteen dominant genetic variants were identified in 39 virus isolates (individual larvae) collected from field populations during one year of low host density, and another distinct variant was discovered among nine additional isolates in two subsequent years of declining host density. The distribution of these genetic variants was not random and indicated that the McplNPV population was structured at several spatial levels. A high proportion of the variation could be explained by family grouping, which suggested that isolates collected within a family were more likely to be the same than isolates compared among populations. Additionally, virus variants from within populations (sites) were more likely to be the same than isolates collected from tent caterpillar populations on different islands. This may indicate that there is limited mixing of virus among tent caterpillar families and populations when host population density is low. Thus there is potential for the virus to become locally adapted to western tent caterpillar populations in different sites. However, no dominant genotype was observed at any site. Whether and how selection acts on the genetically diverse nucleopolyhedrovirus populations as host density changes will be investigated over the next cycle of tent caterpillar populations.

  17. Common genetic variability in ESR1 and EGF in relation to endometrial cancer risk and survival

    OpenAIRE

    Einarsdóttir, K; Darabi, H; Czene, K.; Li, Y; Low, Y.L.; Y. Q. Li; Bonnard, C.; Wedrén, S.; Liu, E. T.; Hall, P; Liu, J; Humphreys, K.

    2009-01-01

    We investigated common genetic variation in the entire ESR1 and EGF genes in relation to endometrial cancer risk, myometrial invasion and endometrial cancer survival. We genotyped a dense set of single-nucleotide polymorphisms (SNPs) in both genes and selected haplotype tagging SNPs (tagSNPs). The tagSNPs were genotyped in 713 Swedish endometrial cancer cases and 1567 population controls and the results incorporated into logistic regression and Cox proportional hazards models. We found five a...

  18. Optimization of cocoa butter analog synthesis variables using neural networks and genetic algorithm

    OpenAIRE

    Shekarchizadeh, Hajar; Tikani, Reza; Kadivar, Mahdi

    2012-01-01

    Cocoa butter analog was prepared from camel hump fat and tristearin by enzymatic interesterification in supercritical carbon dioxide (SC-CO2) using immobilized Thermomyces lanuginosus lipase (Lipozyme TL IM) as a biocatalyst. Optimal process conditions were determined using neural networks and genetic algorithm optimization. Response surfaces methodology was used to design the experiments to collect data for the neural network modelling. A general regression neural network model was developed...

  19. Genetic variability and nitrogenase activity of cyanobacterial communities associated with tropical seagrass meadows (western Indian Ocean)

    OpenAIRE

    Hamisi, Mariam

    2010-01-01

    Tropical seagrass ecosystems are highly productive and important for sustaining marine life and associated coastal societies. In this study, the diversity and role of nitrogen-fixing cyanobacteria associated with five common seagrass genera in coastal regions of the western Indian Ocean (WIO; Tanzania) were examined, as well as the impact of anthropogenic activities. Cyanobacteria were characterized morphologically and genetically (16S rRNA and nifH gene phylogeny), as were diel variations in...

  20. High genetic variability of HIV-1 in female sex workers from Argentina

    Directory of Open Access Journals (Sweden)

    Carr Jean K

    2007-08-01

    Full Text Available Abstract Background A cross-sectional study on 625 Female Sex Workers (FSWs was conducted between 2000 and 2002 in 6 cities in Argentina. This study describes the genetic diversity and the resistance profile of the HIV-infected subjects. Results Seventeen samples from HIV positive FSWs were genotyped by env HMA, showing the presence of 9 subtype F, 6 subtype B and 2 subtype C. Sequence analysis of the protease/RT region on 16 of these showed that 10 were BF recombinants, three were subtype B, two were subtype C, and one sample presented a dual infection with subtype B and a BF recombinant. Full-length genomes of five of the protease/RT BF recombinants were also sequenced, showing that three of them were CRF12_BF. One FSW had a dual HIV-1 infection with subtype B and a BF recombinant. The B sections of the BF recombinant clustered closely with the pure B sequence isolated from the same patient. Major resistance mutations to antiretroviral drugs were found in 3 of 16 (18.8% strains. Conclusion The genetic diversity of HIV strains among FSWs in Argentina was extensive; about three-quarters of the samples were infected with diverse BF recombinants, near twenty percent had primary ART resistance and one sample presented a dual infection. Heterosexual transmission of genetically diverse, drug resistant strains among FSWs and their clients represents an important and underestimated threat, in Argentina.

  1. Genetic variability and individual assignment of Chinese indigenous sheep populations (Ovis aries) using microsatellites.

    Science.gov (United States)

    Niu, L L; Li, H B; Ma, Y H; Du, L X

    2012-02-01

    The purpose of this study was to assess the genetic characteristics of six breeds of Chinese local sheep using 19 microsatellite loci and to effectively validate statistical methods for individual assignment based on informative microsatellites. All the six breeds deviated from Hardy-Weinberg equilibrium expectations, while the majority of markers complied. The polymorphism information content (PIC) of overall loci for the six populations ranged from 0.283 (SRCRSP5) to 0.852 (OarVH72). Tibetan sheep were the most diverse population with the highest mean allelic richness (6.895), while Ujmuqin (UQ) harboured the lowest allelic richness (6.000). The F-statistics for the six populations were F(IS)  = -0.172, F(IT)  = -0.082 and F(ST)  = 0.077, respectively. Furthermore, the pair-wise F(IS) revealed a moderate genetic differentiation among populations (P individual assignment will ensure a powerful detection of individual origin, with accuracy up to 91.87%, when the likelihood-based method is used. Overall, these findings shed light onto the genetic characteristics of Chinese indigenous sheep and offer a set of microsatellite loci that is simple, economic and highly informative for individual assignment of Chinese sheep.

  2. Genetic variability and selection for laticiferous system characters in Hevea brasiliensis

    Directory of Open Access Journals (Sweden)

    Paulo de Souza Gonçalves

    2005-09-01

    Full Text Available Six laticiferous system characters were investigated in 22 three-year-old, half-sib rubber tree [Hevea brasiliensis (Willd. ex Adr. de Juss. Muell.-Arg.] progenies, evaluated at three sites (Votuporanga, Pindorama and Jaú, all in the São Paulo State, Brazil. The traits examined were: average rubber yield (Pp, average bark thickness (Bt, number of latex vessel rings (Lv, average distance between consecutive latex vessel rings (Dc, density of latex vessels per 5 mm per ring averaged over all rings (Dd and the diameter of the latex vessels (Di. The joint analysis showed that site effect and progeny x sites interaction were significant for all traits, except Lv. Estimates of individual heritabilities across the three sites were high for Bt; moderate for Lv, Pp and Dc; low for Dd and very low for Di. Genetic correlations in the joint analysis showed high positive correlations between Pp and the other traits. Selecting the best five progenies would result in genetic gains of 24.91% for Pp while selecting best two plants within a progeny would result in a Pp genetic gain of 30.98%.

  3. Depauperate genetic variability detected in the American and European bison using genomic techniques

    Directory of Open Access Journals (Sweden)

    Wilson Gregory A

    2009-12-01

    Full Text Available Abstract A total of 929 polymorphic SNPs in EB (out of 54, 000 SNPs screened using a BovineSNP50 Illumina Genotyping BeadChip, and 1, 524 and 1, 403 polymorphic SNPs in WB and PB, respectively, were analysed. EB, WB and PB have all undergone recent drastic reductions in population size. Accordingly, they exhibited extremely depauperate genomes, deviations from genetic equilibrium and a genome organization consisting of a mosaic of haplotype blocks: regions with low haplotype diversity and high levels of linkage disequilibrium. No evidence for positive or stabilizing selection was found in EB, WB and PB, likely reflecting drift overwhelming selection. We suggest that utilization of genome-wide screening technologies, followed by utilization of less expensive techniques (e.g. VeraCode and Fluidigm EP1, holds large potential for genetic monitoring of populations. Additionally, these techniques will allow radical improvements of breeding practices in captive or managed populations, otherwise hampered by the limited availability of polymorphic markers. This result in improved possibilities for 1 estimating genetic relationships among individuals and 2 designing breeding strategies which attempt to preserve or reduce polymorphism in ecologically relevant genes and/or entire blocks. Reviewers This article was reviewed by: Fyodor Kondrashov and Shamil Sunyaev

  4. Geographic, genetic and life-history variability in a sex-changing fish

    Directory of Open Access Journals (Sweden)

    Chiara Benvenuto

    2015-11-01

    Full Text Available Sequential hermaphroditism, commonly referred to as sex change or sex reversal, is a striking phenomenon in mating-system evolution and the most remarkable example of sexual plasticity. Among vertebrates, it is specific to teleosts. Some fish species reproduce initially as females and then change into males (protogynous hermaphrodites or vice versa (protandrous hermaphrodites. The white sea bream, Diplodus sargus, exhibits a high degree of sexual plasticity: populations have been reported to be gonochoristic, protandrous or digynic (with primary females, derived from intersexual juveniles, and secondary females, derived from males. We analysed populations collected from eight different locations across the species distribution range (between the Mediterranean and the North-Eastern Atlantic. These populations are characterized by different degrees of connectivity, spatial demographics and life histories. Using individual-based analyses, we linked the genetic structure of each specimen with environmental heterogeneity, life-history traits and reproductive modes. Our aim is to gather a better understanding of the variation in reproductive life-history strategies in this sexually plastic species. Diplodus sargus is a valuable candidate organism to investigate sequential hermaphroditism and it also has a commercial value. The application of population genetics tools against the background of life-history theory can bring valuable insights for the management of marine resources. The geographical patterns of sex change (and of age- and size-at-sex change linked with population genetics can be pivotal for both theoretical investigations and conservation and management plans in marine areas.

  5. Multi-objective optimization in systematic conservation planning and the representation of genetic variability among populations.

    Science.gov (United States)

    Schlottfeldt, S; Walter, M E M T; Carvalho, A C P L F; Soares, T N; Telles, M P C; Loyola, R D; Diniz-Filho, J A F

    2015-06-18

    Biodiversity crises have led scientists to develop strategies for achieving conservation goals. The underlying principle of these strategies lies in systematic conservation planning (SCP), in which there are at least 2 conflicting objectives, making it a good candidate for multi-objective optimization. Although SCP is typically applied at the species level (or hierarchically higher), it can be used at lower hierarchical levels, such as using alleles as basic units for analysis, for conservation genetics. Here, we propose a method of SCP using a multi-objective approach. We used non-dominated sorting genetic algorithm II in order to identify the smallest set of local populations of Dipteryx alata (baru) (a Brazilian Cerrado species) for conservation, representing the known genetic diversity and using allele frequency information associated with heterozygosity and Hardy-Weinberg equilibrium. We worked in 3 variations for the problem. First, we reproduced a previous experiment, but using a multi-objective approach. We found that the smallest set of populations needed to represent all alleles under study was 7, corroborating the results of the previous study, but with more distinct solutions. In the 2nd and 3rd variations, we performed simultaneous optimization of 4 and 5 objectives, respectively. We found similar but refined results for 7 populations, and a larger portfolio considering intra-specific diversity and persistence with populations ranging from 8-22. This is the first study to apply multi-objective algorithms to an SCP problem using alleles at the population level as basic units for analysis.

  6. Genetic influences on heart rate variability at rest and during stress

    NARCIS (Netherlands)

    Wang, Xiaoling; Ding, Xiuhua; Su, Shaoyong; Li, Zhibin; Riese, Harriette; Thayer, Julian F.; Treiber, Frank; Snieder, Harold

    2009-01-01

    We tested whether the heritability of heart rate variability (HRV) under stress is different from rest and its dependency on ethnicity or gender. HRV indexed by root mean square of successive differences (RMSSD) and high-frequency (HF) power was measured at rest and during 3 stressors in 427 Europea

  7. Unraveling the genetic expression of the highly variable immune receptors of a killer

    NARCIS (Netherlands)

    Vendelbosch, S.

    2015-01-01

    The Killer Immunoglobulin-like Receptors (KIRs) are a family of highly variable receptors which regulate cytotoxicity of Natural Killer (NK) cells and a subset of T-cells. The KIR genes, clustered on the genome in the KIR locus, are distributed unequally across the population due to variation in gen

  8. The predominantly selfing plant Arabidopsis thaliana experienced a recent reduction in transposable element abundance compared to its outcrossing relative Arabidopsis lyrata

    Directory of Open Access Journals (Sweden)

    de la Chaux Nicole

    2012-02-01

    Full Text Available Abstract Background Transposable elements (TEs are major contributors to genome evolution. One factor that influences their evolutionary dynamics is whether their host reproduces through selfing or through outcrossing. According to the recombinational spreading hypothesis, for instance, TEs can spread more easily in outcrossing species through recombination, and should thus be less abundant in selfing species. We here studied the distribution and evolutionary dynamics of TE families in the predominantly selfing plant Arabidopsis thaliana and its close outcrossing relative Arabidopsis lyrata on a genome-wide scale. We characterized differences in TE abundance between them and asked which, if any, existing hypotheses about TE abundances may explain these differences. Results We identified 1,819 TE families representing all known classes of TEs in both species, and found three times more copies in the outcrossing A. lyrata than in the predominantly selfing A. thaliana, as well as ten times more TE families unique to A. lyrata. On average, elements in A. lyrata are younger than elements in A. thaliana. In particular, A. thaliana shows a marked decrease in element number that occurred during the most recent 10% of the time interval since A. thaliana split from A. lyrata. This most recent period in the evolution of A. thaliana started approximately 500,000 years ago, assuming a splitting time of 5 million years ago, and coincides with the time at which predominant selfing originated. Conclusions Our results indicate that the mating system may be important for determining TE copy number, and that selfing species are likely to have fewer TEs.

  9. Genetic Variability and Phylogenetic Relationships within Trypanosoma cruzi I Isolated in Colombia Based on Miniexon Gene Sequences

    Directory of Open Access Journals (Sweden)

    Claudia Herrera

    2009-01-01

    Full Text Available Phylogenetic studies of Trypanosoma cruzi have identified the existence of two groups: T. cruzi I and T. cruzi II. There are aspects that still remain unknown about the genetic variability within the T. cruzi I group. Given its epidemiological importance, it is necessary to have a better understanding of T. cruzi transmission cycles. Our purpose was to corroborate the existence of haplotypes within the T. cruzi I group and to describe the genetic variability and phylogenetic relationships, based on single nucleotide polymorphisms (SNPs found in the miniexon gene intergenic region, for the isolates from different hosts and epidemiological transmission cycles in Colombian regions. 31 T. cruzi isolates were molecularly characterized. Phylogenetic relationships within T. cruzi I isolates showed four haplotype groups (Ia–Id, associated with their transmission cycle. In previous studies, we reported that haplotype Ia is mainly associated with the domestic cycle and domiciliated Rhodnius prolixus. Haplotype Ib is associated with the domestic cycle and peridomestic cycle, haplotype Ic is closely related with the peridomestic cycle, and haplotype Id is strongly associated with the sylvatic cycle. The phylogenetic methodologies applied in this study are tools that bolster the associations among isolates and thus shed light on Chagas disease epidemiology.

  10. Genetic variability and relationship between MT-1 elephant grass and closely related cultivars assessed by SRAP markers

    Indian Academy of Sciences (India)

    Xin-Ming Xie; Feng Zhou; Xiang-Qian Zhang; Ju-Ming Zhang

    2009-12-01

    Genetic variability and relationships among elephant grass cultivars were estimated by the SRAP (sequence-related amplified polymorphism) assay. A total of 60 individuals collected from five cultivars in China were analysed. Sixty-two selected primer combinations generated 1395 bands, with an average of 22.5 per primer combination. The average value of percentage of polymorphic bands (PPB) was 72.8% at species level. The PPB was from 15.2% to 75%, with an average of 39.6% at cultivar level. $H_{POP}$, within-cultivar Shannon’s index was 1.738 at cultivar level; at species level, the Shannon’s index $(H_{SP})$ was 3.880. An assessment of diversity between cultivars $[(H_{SP} −H_{POP})/H_{SP}]$ indicated that most of the diversity (55.2%) was detected among cultivars, and only 44.8% was within cultivars in total genetic variation. According to UPGMA dendrogram, the five cultivars were clustered into three main groups. One group included MT-1 and Mott with a bootstrap support of 100%, another consisted of Huanan and N51 with a bootstrap support of 81%, and last one was only Guimu-1. The results indicate that the MT-1 and Mott have a closest genetic relationship; Huanan and N51 possess a relatively close relationship, and Guimu-1 is the most distinct from the other four cultivars.

  11. Genetic variability of the serine-rich Entamoeba histolytica protein gene in clinical isolates from the United Arab Emirates.

    Science.gov (United States)

    ElBakri, Ali; Samie, Amidou; Ezzedine, Sinda; Odeh, Ra'ed Abu

    2014-06-01

    The genetic diversity of 20 Entamoeba histolytica isolates from asymptomatic individuals from the UAE was investigated by analyzing polymorphism in the serine-rich E. histolytica gene (SREHP) by nested polymerase chain reaction (PCR) amplification followed by restriction fragment length polymorphism (RFLP) on DNA extracted directly from stool samples. The SREHP gene was successfully amplified in 15 out of 20 E. histolytica-positive samples. Four out of the remaining five isolates did not amplify for the SREHP gene. Despite successful amplification of the SREHP gene in the fifth isolate, AluI digestion of the amplified PCR product revealed no bands. As a result, all five samples were excluded from the study. Twelve different profiles were obtained from the 15 successfully amplified isolates. Thus, demonstrating extensive genetic variability and reinforcing the argument that E. histolytica has an extremely polymorphic genetic structure. Despite the sample size limitation, a finding in the study was the occurrence of one profile common to one Indian isolate while another profile common to one Pakistani isolate; indicating the possibility of clonal infection. Furthermore, we found one isolate from a Bangladeshi expatriate identical to 2 asymptomatic Bangladeshi isolates reported in an earlier study. No clear association between the different genotypes and the study population demographics was noted. The results also indicated the possibility of strains clustering by region.

  12. Genetic variability in residual feed intake in rainbow trout clones and testing of indirect selection criteria (Open Access publication

    Directory of Open Access Journals (Sweden)

    Chatain Béatrice

    2008-11-01

    Full Text Available Abstract Little is known about the genetic basis of residual feed intake (RFI variation in fish, since this trait is highly sensitive to environmental influences, and feed intake of individuals is difficult to measure accurately. The purpose of this work was (i to assess the genetic variability of RFI estimated by an X-ray technique and (ii to develop predictive criteria for RFI. Two predictive criteria were tested: loss of body weight during feed deprivation and compensatory growth during re-feeding. Ten heterozygous rainbow trout clones were used. Individual intake and body weight were measured three times at threeweek intervals. Then, individual body weight was recorded after two cycles of a three-week feed deprivation followed by a three-week re-feeding. The ratio of the genetic variance to the phenotypic variance was found high to moderate for growth, feed intake, and RFI (VG/VP = 0.63 ± 0.11, 0.29 ± 0.11, 0.29 ± 0.09, respectively. The index that integrates performances achieved during deprivation and re-feeding periods explained 59% of RFI variations. These results provide a basis for further studies on the origin of RFI differences and show that indirect criteria are good candidates for future selective breeding programs.

  13. Genetic variability of the fructosamine 3-kinase gene in diabetic patients.

    Science.gov (United States)

    Mosca, Lorena; Penco, Silvana; Patrosso, Maria C; Marocchi, Alessandro; Lapolla, Annunziata; Sartore, Giovanni; Chilelli, Nino C; Paleari, Renata; Mosca, Andrea

    2011-05-01

    Nonenzymatic glycation appears to be an important factor in the pathogenesis of diabetic complications. Fructosamine 3-kinase (FN3K), initially identified in erythrocytes, appears to be responsible for the removal of fructosamine from proteins, suggesting a protective role in nonenzymatic glycation. Recently, genetic variants in the FN3K gene have been studied in diabetic patients. The aim of our study was the molecular characterization of the FN3K gene in a representative group of Italian patients with type 1 (T1DM) and 2 (T2DM) diabetes mellitus and in a cohort of healthy controls. Seventy diabetic subjects (35 type 1 and 35 type 2) with stable glycemic control and 33 healthy control subjects were evaluated using PCR and direct sequencing of the FN3K gene. Denaturing high performance liquid chromatography (DHPLC) was used in controls for screening for the presence of the genetic variants previously found in diabetic patients. Seven different genetic variants were identified, five of them already reported and two new: the p.R187X and p.Y239C mutations identified in two females affected by T2DM. No significant association was found between certain polymorphisms and diabetes conditions. Preliminary haplotype studies are also reported. With respect to genotypes, we noted that some were not present in all the investigated cohort, and some were found related to higher glycated hemoglobin compared to others, although not at a significant level, probably because of the small number of subjects investigated. In conclusion, this study identified two new mutations and additional variants within the FN3K gene. This is the first study on FN3K in Italy. Future work is needed to achieve a better understanding of the FN3K enzyme and its possible clinical utility in the management of diabetic patients.

  14. Analysis of the genetic variability in Parkinson's disease from Southern Spain.

    Science.gov (United States)

    Bandrés-Ciga, Sara; Mencacci, Niccolò Emmanuele; Durán, Raquel; Barrero, Francisco Javier; Escamilla-Sevilla, Francisco; Morgan, Sarah; Hehir, Jason; Vives, Francisco; Hardy, John; Pittman, Alan M

    2016-01-01

    To date, a large spectrum of genetic variants has been related to familial and sporadic Parkinson's disease (PD) in diverse populations worldwide. However, very little is known about the genetic landscape of PD in Southern Spain, despite its particular genetic landscape coming from multiple historical migrations. We included 134 PD patients in this study, of which 97 individuals were diagnosed with late-onset sporadic PD (LOPD), 28 with early-onset sporadic PD (EOPD), and 9 with familial PD (FPD). Genetic analysis was performed through a next-generation sequencing panel to screen 8 PD-related genes (LRRK2, SNCA, PARKIN, PINK1, DJ-1, VPS35, GBA, and GCH1) in EOPD and FPD groups and direct Sanger sequencing of GBA exons 8-11 and LRRK2 exons 31 and 41 in the LOPD group. In the EOPD and FPD groups, we identified 11 known pathogenic mutations among 15 patients (40.5%). GBA (E326K, N370S, D409H, L444P) mutations were identified in 7 patients (18.9%); LRRK2 (p.R1441G and p.G2019S) in 3 patients (8.1%); biallelic PARK2 mutations (p.N52fs, p.V56E, p.C212Y) in 4 cases (10.8%) and PINK1 homozygous p.G309D in 1 patient (2.7%). An EOPD patient carried a single PARK2 heterozygous mutation (p.R402C), and another had a novel heterozygous mutation in VPS35 (p.R32S), both of unknown significance. Moreover, pathogenic mutations in GBA (E326K, T369M, N370S, D409H, L444P) and LRRK2 (p.R1441G and p.G2019S) were identified in 13 patients (13.4%) and 4 patients (4.1%), respectively, in the LOPD group. A large number of known pathogenic mutations related to PD have been identified. In particular, GBA and LRRK2 mutations appear to be considerably frequent in our population, suggesting a strong Jewish influence. Further research is needed to study the contribution of the novel found mutation p.R32S in VPS35 to the pathogenesis of PD.

  15. Depauperate genetic variability detected in the American and European bison using genomic techniques

    DEFF Research Database (Denmark)

    Pertoldi, Cino; Tokarska, Magorzata; Wójcik, Jan M;

    2009-01-01

    A total of 929 polymorphic SNPs in EB (out of 54, 000 SNPs screened using a BovineSNP50 Illumina Genotyping BeadChip), and 1, 524 and 1, 403 polymorphic SNPs in WB and PB, respectively, were analysed. EB, WB and PB have all undergone recent drastic reductions in population size. Accordingly......, likely reflecting drift overwhelming selection. We suggest that utilization of genome-wide screening technologies, followed by utilization of less expensive techniques (e.g. VeraCode and Fluidigm EP1), holds large potential for genetic monitoring of populations. Additionally, these techniques will allow...

  16. Genetic variability of Echinococcus granulosus complex in various geographical populations of Iran inferred by mitochondrial DNA sequences.

    Science.gov (United States)

    Spotin, Adel; Mahami-Oskouei, Mahmoud; Harandi, Majid Fasihi; Baratchian, Mehdi; Bordbar, Ali; Ahmadpour, Ehsan; Ebrahimi, Sahar

    2017-01-01

    To investigate the genetic variability and population structure of Echinococcus granulosus complex, 79 isolates were sequenced from different host species covering human, dog, camel, goat, sheep and cattle as of various geographical sub-populations of Iran (Northwestern, Northern, and Southeastern). In addition, 36 sequences of other geographical populations (Western, Southeastern and Central Iran), were directly retrieved from GenBank database for the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene. The confirmed isolates were grouped as G1 genotype (n=92), G6 genotype (n=14), G3 genotype (n=8) and G2 genotype (n=1). 50 unique haplotypes were identified based on the analyzed sequences of cox1. A parsimonious network of the sequence haplotypes displayed star-like features in the overall population containing IR23 (22: 19.1%) as the most common haplotype. According to the analysis of molecular variance (AMOVA) test, the high value of haplotype diversity of E. granulosus complex was shown the total genetic variability within populations while nucleotide diversity was low in all populations. Neutrality indices of the cox1 (Tajima's D and Fu's Fs tests) were shown negative values in Western-Northwestern, Northern and Southeastern populations which indicating significant divergence from neutrality and positive but not significant in Central isolates. A pairwise fixation index (Fst) as a degree of gene flow was generally low value for all populations (0.00647-0.15198). The statistically Fst values indicate that Echinococcus sensu stricto (genotype G1-G3) populations are not genetically well differentiated in various geographical regions of Iran. To appraise the hypothetical evolutionary scenario, further study is needed to analyze concatenated mitogenomes and as well a panel of single locus nuclear markers should be considered in wider areas of Iran and neighboring countries.

  17. ROS1 rearrangements in lung adenocarcinoma: prognostic impact, therapeutic options and genetic variability

    Science.gov (United States)

    Teixido, Cristina; Michels, Sebastian; Morales-Espinosa, Daniela; Viteri, Santiago; Hartmann, Wolfgang; Merkelbach-Bruse, Sabine; Fischer, Rieke; Schildhaus, Hans-Ulrich; Fassunke, Jana; Sebastian, Martin; Serke, Monika; Kaminsky, Britta; Randerath, Winfried; Gerigk, Ulrich; Ko, Yon-Dschun; Krüger, Stefan; Schnell, Roland; Rothe, Achim; Kropf-Sanchen, Cornelia; Heukamp, Lukas; Rosell, Rafael

    2015-01-01

    Background While recent data show that crizotinib is highly effective in patients with ROS1 rearrangement, few data is available about the prognostic impact, the predictive value for different treatments, and the genetic heterogeneity of ROS1-positive patients. Patients and Methods 1137 patients with adenocarcinoma of the lung were analyzed regarding their ROS1 status. In positive cases, next-generation sequencing (NGS) was performed. Clinical characteristics, treatments and outcome of these patients were assessed. Overall survival (OS) was compared with genetically defined subgroups of ROS1-negative patients. Results 19 patients of 1035 evaluable (1.8%) had ROS1-rearrangement. The median OS has not been reached. Stage IV patients with ROS1-rearrangement had the best OS of all subgroups (36.7 months, p < 0.001). 9 of 14 (64.2%) patients had at least one response to chemotherapy. Estimated mean OS for patients receiving chemotherapy and crizotinib was 5.3 years. Ten patients with ROS1-rearrangement (52.6%) harbored additional aberrations. Conclusion ROS1-rearangement is not only a predictive marker for response to crizotinib, but also seems to be the one of the best prognostic molecular markers in NSCLC reported so far. In stage IV patients, response to chemotherapy was remarkable high and overall survival was significantly better compared to other subgroups including EGFR-mutated and ALK-fusion-positive NSCLC. PMID:25868855

  18. Analysis of genetic variability and relationships among Mentha L. using the limonene synthase gene, LS.

    Science.gov (United States)

    Wang, Hai Tang; Yu, Xu; Liu, Yan; Liang, Cheng-Yuan; Li, Wei-Lin

    2013-07-25

    The genus Mentha comprises a group of aromatic plants with worldwide distribution. Because of frequent interspecific hybridization, the genetic relationships within the genus are not clearly understood. Limonene synthase, which catalyses the first committed step in the essential oil monoterpene biosynthetic pathway, is considered to be a possible rate limiting enzyme. With the homology-based cloning method, primers were designed according to cDNA sequence to amplify full-length DNA sequences in 13 Mentha samples from five species, using Perilla as an outgroup. Analyses of gene structure, length variation, GC-content, Ts/Tv ratio and evolutionary diversity were carried out. Consensus phylogenetic trees were obtained using maximum likelihood, neighbor-joining, and maximum parsimony, respectively, based on the full-length genomic DNA sequences, complete ORF coding sequences and predicted amino acid sequences. The results presented here based on the sequence of MhLS provide the first credibly supported genetic relationships for Mentha, which enables a basis for further mint taxonomy, cultivation and breeding.

  19. Genetic variability among sorghum accessions for seed starch and stalk total sugar content

    Directory of Open Access Journals (Sweden)

    Abe Shegro Gerrano

    2014-12-01

    Full Text Available Sorghum (Sorghum bicolor (L. Moench is a staple food grain in many semi-arid and tropical areas of the world, notably in sub-Saharan Africa because of its adaptation to harsh environments. Among important biochemical components for sorghum for processors are the levels of starch (amylose and amylopectin and total sugar contents. The aim of this study was to determine the genetic variation for total starch in the seed, its components and total sugar in the stalks of the sorghum accessions from Ethiopia and South Africa. Samples of 22 sorghum accessions were evaluated. Significant variations were observed in total starch (31.01 to 64.88 %, amylose (14.05 to 18.91 %, the amylose/amylopectin ratio (0.31 to 0.73 and total stalk sugar content (9.36 to 16.84 %. Multivariate analysis showed a wide genetic variation within and among germplasm accessions which could be used in the selection of parental lines for the improvement of traits of interest through breeding. The variation found among the sorghum accessions shows that an improved total starch and starch components and stalk sugar contents can be achieved through crossing these selected genotypes.

  20. Genetic variability for iron and zinc content in common bean lines and interaction with water availability.

    Science.gov (United States)

    Pereira, H S; Del Peloso, M J; Bassinello, P Z; Guimarães, C M; Melo, L C; Faria, L C

    2014-08-28

    The common bean is an important source of iron and zinc in humans. Increases in the contents of these minerals can combat mineral deficiencies, but these contents are influenced by environmental conditions. Thus, the objectives of this study were to investigate the interaction between common bean lines and water availability on iron and zinc contents (CFe and CZn, respectively), identify superior lines with stable CFe and CZn, and test for a genetic relationship between CFe and CZn. Six crop trials were performed using a randomized block design with three replications. The trials were performed during the winter sowing period for three different combinations of year and site in Brazil. For each combination, 53 lines were evaluated across two parallel trials; one trial was irrigated according to the crop requirements, and the other trial operated under a water deficit. Interaction was detected between lines and environments, and between lines and water availability for CFe and CZn. However, some lines exhibited high CFe and CZn in both conditions. Lines G 6492 and G 6490 exhibited high mean values, stability, and adaptability for both minerals. Other lines exhibited high CFe (Xamego) or CZn (Bambuí and Iapar 65). A moderate genetic correlation (0.62) between CFe and CZn was detected. Water availability during the common bean cycle had an effect on CFe and CZn; however, lines with high CFe and CZn in different conditions of water availability and environment were detected.

  1. Estimation of genetic variability in locally grown pulses (Cajans cajan (L.) Millsp and Vigna unguiculata (L.) Walp): a panacea for sourcing superior genotypes.

    Science.gov (United States)

    Udensi, O; Edu, E A; Umana, E J; Ikpeme, E V

    2011-03-15

    The negligence of breeders and farmers to explore and exploit landraces of pulses is worrisome and urgent measures needed to be set in motion to forestall major future crisis, taking into cognizance the high adaptability and nutritive values accredited to them. This study focused on the estimation of genetic variability and heritability of desirable morphological characters in Fiofio (Cajans cajan) and Olaudi and Akidi (Vigna unguiculata) with the aim of conservation. Three landraces of pulses were sown using randomized complete block design. The field experiment was carried out at the University of Calabar Experimental Farm, University of Calabar, Calabar, during 2008-2010 growing season. Phenotypic and genotypic variances and coefficients of variation and genetic advance were estimated on yield and yield-related traits. The results showed that there were considerable variations among the pulses for the traits studied. The result revealed high genetic variability in the number of leaf per plant, leaf area, number of flowers per plant, number of pods per plant and number of seeds per plant. It also showed that genetic variability in pod length and 100-seed weight was low. Heritability estimates obtained in the result were very high though the magnitude of genetic variability in the yield and yield-related traits was not proportional to the heritability estimates. The traits studied also show high genetic advance. These explicitly showed that there are sufficient genetic variations to warrant conservation and improvement in these extinction-threatened pulses studied.

  2. Genetic variability of wild and captivity populations of Colossoma macropomum (Cuvier, 1818 - doi: 10.4025/actascibiolsci.v34i2.7149

    Directory of Open Access Journals (Sweden)

    Vera Maria Fonseca de Almeida-Val

    2012-03-01

    Full Text Available Tambaqui (Colossoma macropomum is among the most important fish species of the Amazon and one of the most cultivated in Brazil. In the present work we have evaluated the genetic variability of wild and captivity populations of C. macropomum. Enzymatic markers were used to estimate the genetic variability of 41 specimens from a wild group; and 30, 33 and 45 from three captivity groups, which came from Pentecostes (Ceará State, Jaboticabal (São Paulo State and Itacoatiara (Amazonas State, respectively. Nine isoenzymic systems were used to evaluate the genetic variability of these populations. Using zimogram data we obtained the polymorphism level, allele number, allelic frequency, observed and expected heterozigosity, Wright F statistics (FIS, FST, genetic distance, level of similarity and group analysis. The isoenzymic data showed that, from the nine systems, six presented polymorphic loci (Fbp-2, G6pdh-2, G6pdh-3, Pgi-1, Pgi-2 and Pgm-1. The populations from Pentecostes and Jaboticabal presented loss of genetic variability and low heterozigosity, compared to the wild population and to the artificial population acquired at Itacoatiara fish farm. Based on these results and on fish farmer information we could consider the population from Itacoatiara as recently derived from a wild population. Concluding, we suggest that the artificial populations of tambaqui, which contain animals originated from this funding population at Pentecostes, should be renewed with the introduction of a new group of individuals with genetic variability equivalent to the wild population.

  3. The use of race variables in genetic studies of complex traits and the goal of reducing health disparities: a transdisciplinary perspective.

    Science.gov (United States)

    Shields, Alexandra E; Fortun, Michael; Hammonds, Evelynn M; King, Patricia A; Lerman, Caryn; Rapp, Rayna; Sullivan, Patrick F

    2005-01-01

    The use of racial variables in genetic studies has become a matter of intense public debate, with implications for research design and translation into practice. Using research on smoking as a springboard, the authors examine the history of racial categories, current research practices, and arguments for and against using race variables in genetic analyses. The authors argue that the sociopolitical constructs appropriate for monitoring health disparities are not appropriate for use in genetic studies investigating the etiology of complex diseases. More powerful methods for addressing population structure exist, and race variables are unacceptable as gross proxies for numerous social/environmental factors that disproportionately affect minority populations. The authors conclude with recommendations for genetic researchers and policymakers, aimed at facilitating better science and producing new knowledge useful for reducing health disparities.

  4. Genetic variability and differentiation among populations of the Azorean endemic gymnosperm Juniperus brevifolia: baseline information for a conservation and restoration perspective.

    Science.gov (United States)

    Silva, Luís; Elias, Rui B; Moura, Mónica; Meimberg, Harald; Dias, Eduardo

    2011-12-01

    The Azorean endemic gymnosperm Juniperus brevifolia (Seub.) Antoine is a top priority species for conservation in Macaronesia, based on its ecological significance in natural plant communities. To evaluate genetic variability and differentiation among J. brevifolia populations from the Azorean archipelago, we studied 15 ISSR and 15 RAPD markers in 178 individuals from 18 populations. The average number of polymorphic bands per population was 65 for both ISSR and RAPD. The majority of genetic variability was found within populations and among populations within islands, and this partitioning of variability was confirmed by AMOVA. The large majority of population pairwise F(ST) values were above 0.3 and below 0.6. The degree of population genetic differentiation in J. brevifolia was relatively high compared with other species, including Juniperus spp. The genetic differentiation among populations suggests that provenance should be considered when formulating augmentation or reintroduction strategies.

  5. A multiple-alignment based primer design algorithm for genetically highly variable DNA targets.

    Science.gov (United States)

    Brodin, Johanna; Krishnamoorthy, Mohan; Athreya, Gayathri; Fischer, Will; Hraber, Peter; Gleasner, Cheryl; Green, Lance; Korber, Bette; Leitner, Thomas

    2013-08-21

    Primer design for highly variable DNA sequences is difficult, and experimental success requires attention to many interacting constraints. The advent of next-generation sequencing methods allows the investigation of rare variants otherwise hidden deep in large populations, but requires attention to population diversity and primer localization in relatively conserved regions, in addition to recognized constraints typically considered in primer design. Design constraints include degenerate sites to maximize population coverage, matching of melting temperatures, optimizing de novo sequence length, finding optimal bio-barcodes to allow efficient downstream analyses, and minimizing risk of dimerization. To facilitate primer design addressing these and other constraints, we created a novel computer program (PrimerDesign) that automates this complex procedure. We show its powers and limitations and give examples of successful designs for the analysis of HIV-1 populations. PrimerDesign is useful for researchers who want to design DNA primers and probes for analyzing highly variable DNA populations. It can be used to design primers for PCR, RT-PCR, Sanger sequencing, next-generation sequencing, and other experimental protocols targeting highly variable DNA samples.

  6. Intraspecific genetic variability in a population of Moroccan Leishmania infantum revealed by PCR-RFLP of kDNA minicircles.

    Science.gov (United States)

    El Hamouchi, Adil; Ejghal, Rajaa; Hida, Moustapha; Lemrani, Meryem

    2017-05-01

    In Morocco, Leishmania infantum is the main etiologic agent of human and canine visceral leishmaniasis (VL). This species has been proven to be an opportunistic agent in HIV+ patients and is also responsible of sporadic cutaneous leishmaniasis (CL).This work aims to evaluate the genetic variability of Moroccan L. infantum strains based on PCR-RFLP analysis of the kinetoplastid DNA (kDNA) minicircles. A total of 75 DNA samples extracted from positive Giemsa-stained smears (n=32) and from L. infantum cultures (n=43) was studied. The samples have been taken from VL patients infected (n=7) or not (n=56) by HIV, patients with CL (n=2) and finally from infected dogs (n=10). An hypervariable region of kDNA was amplified using the primers MC1 and MC2; the PCR products were digested separately by a panel of nine restriction enzymes. The presence or absence of restriction fragments was scored in a binary matrix and the SplitsTree4 software was used for the construction of a Neighbor-Net network. Moroccan L. infantum population showed an important level of variability with the identification of 6 genotypes. For each genotype a PCR product was sequenced, confirming the presence of all the expected restriction sites. The predominant profile was the genotype B. A new genotype, named Q was detected for the first time, whereas the four other genotypes (G, K, N and O) were reported sporadically in the Mediterranean basin. The Neighbor-Net network segregates our L. infantum population into 3 clusters: Cluster I includes genotype B, cluster II grouping the genotypes O, Q and G and finally the cluster III contains the genotype N. The kDNA-PCR-RFLP assay is suitable for use directly on biological samples; it reveals an important degree of genetic variability among L. infantum strains even those belonging to the same zymodeme what is of great epidemiological interest.

  7. Genetic Variability of Bovine Viral Diarrhea Virus and Evidence for a Possible Genetic Bottleneck during Vertical Transmission in Persistently Infected Cattle.

    Science.gov (United States)

    Dow, Natalie; Chernick, Adam; Orsel, Karin; van Marle, Guido; van der Meer, Frank

    2015-01-01

    Bovine viral diarrhea virus (BVDV), a Pestivirus in the family Flaviviridae, is an economically important pathogen of cattle worldwide. The primary propagators of the virus are immunotolerant persistently infected (PI) cattle, which shed large quantities of virus throughout life. Despite the absence of an acquired immunity against BVDV in these PI cattle there are strong indications of viral variability that are of clinical and epidemiological importance. In this study the variability of E2 and NS5B sequences in multiple body compartments of PI cattle were characterized using clonal sequencing. Phylogenetic analyses revealed that BVDV exists as a quasispecies within PI cattle. Viral variants were clustered by tissue compartment significantly more often than expected by chance alone with the central nervous system appearing to be a particularly important viral reservoir. We also found strong indications for a genetic bottleneck during vertical transmission from PI animals to their offspring. These quasispecies analyses within PI cattle exemplify the role of the PI host in viral propagation and highlight the complex dynamics of BVDV pathogenesis, transmission and evolution.

  8. Genetic Variability of Bovine Viral Diarrhea Virus and Evidence for a Possible Genetic Bottleneck during Vertical Transmission in Persistently Infected Cattle.

    Directory of Open Access Journals (Sweden)

    Natalie Dow

    Full Text Available Bovine viral diarrhea virus (BVDV, a Pestivirus in the family Flaviviridae, is an economically important pathogen of cattle worldwide. The primary propagators of the virus are immunotolerant persistently infected (PI cattle, which shed large quantities of virus throughout life. Despite the absence of an acquired immunity against BVDV in these PI cattle there are strong indications of viral variability that are of clinical and epidemiological importance. In this study the variability of E2 and NS5B sequences in multiple body compartments of PI cattle were characterized using clonal sequencing. Phylogenetic analyses revealed that BVDV exists as a quasispecies within PI cattle. Viral variants were clustered by tissue compartment significantly more often than expected by chance alone with the central nervous system appearing to be a particularly important viral reservoir. We also found strong indications for a genetic bottleneck during vertical transmission from PI animals to their offspring. These quasispecies analyses within PI cattle exemplify the role of the PI host in viral propagation and highlight the complex dynamics of BVDV pathogenesis, transmission and evolution.

  9. The role of protozoa-driven selection in shaping human genetic variability.

    Science.gov (United States)

    Pozzoli, Uberto; Fumagalli, Matteo; Cagliani, Rachele; Comi, Giacomo P; Bresolin, Nereo; Clerici, Mario; Sironi, Manuela

    2010-03-01

    Protozoa exert a strong selective pressure in humans. The selection signatures left by these pathogens can be exploited to identify genetic modulators of infection susceptibility. We show that protozoa diversity in different geographic locations is a good measure of protozoa-driven selective pressure; protozoa diversity captured selection signatures at known malaria resistance loci and identified several selected single nucleotide polymorphisms in immune and hemolytic anemia genes. A genome-wide search enabled us to identify 5180 variants mapping to 1145 genes that are subjected to protozoa-driven selective pressure. We provide a genome-wide estimate of protozoa-driven selective pressure and identify candidate susceptibility genes for protozoa-borne diseases. Copyright 2010 Elsevier Ltd. All rights reserved.

  10. Evaluation of the genetic variability of 13 microsatellite markers in native Indian pigs

    Indian Academy of Sciences (India)

    Rajeev Kaul; Atar Singh; R. K. Vijh; M. S. Tantia; Rahul Behl

    2001-12-01

    We analysed polymorphism of 13 microsatellites in two Indian domesticated pig types (North Indian and Northeast Indian). Heterozygosity, polymorphism information content, and probability of identity of two random individuals were calculated for all microsatellites in both types. The number of alleles observed at a locus varied between five and 12. The evaluated microsatellites exhibited a very high heterozygosity and polymorphism information content. The probability of identity of two random individuals from different populations taking into account all the 13 microsatellites was as low as 3.51 × 10-19. On the basis of these results, we propose that these microsatellite markers may be used with reliability for studying the genetic diversity and for identification of individuals in Indian pig types.

  11. Studies on mutagenic effect on genetic variability in green gram (Vigna radiata (L. ) Wilczek)

    Energy Technology Data Exchange (ETDEWEB)

    Krishnaswami, S.; Rathinam, M. (Tamil Nadu Agricultural Univ. Coimbatore (India). Dept. of Agricultural Botany)

    1982-03-01

    With a view to finding out the effect of mutagenic treatments on heritability in green gram, two cultivars, showing extremes of sensitivity to mutagen, were subjected to two levels each of gamma irradiation and EMS separately and conjointly and the M/sub 2/ generation raised. Families of the higher dose in each treatment were advanced to the M/sub 3/ and the genetic parameters of the various growth and yield attributes, besides seed yield, studied. Barring plant height, heritability of all other traits registered an increase under the mutagen effect. No consistency was evident in the superiority of one mutagen over the other, their behaviour varying with the cultivar and the character studied. Consequent to enhancement in heritability, correlations between the characters underwent alterations under the mutagens.

  12. Multi-variable grey model (MGM (1,n,q)) based on genetic algorithm and its application in urban water consumption

    Institute of Scientific and Technical Information of China (English)

    Yan; Han; Shi; Guoxu

    2007-01-01

    Urban water consumption has some characteristics of grey because it is influenced by economy, population, standard of living and so on. The multi-variable grey model (MGM(1,n)), as the expansion and complement of GM(1,1) model, reveals the relationship between restriction and stimulation among variables, and the genetic algorithm has the whole optimal and parallel characteristics. In this paper, the parameter q of MGM(1,n) model was optimized, and a multi-variable grey model (MGM(1,n,q)) was built by using the genetic algorithm. The model was validated by examining the urban water consumption from 1990 to 2003 in Dalian City. The result indicated that the multi-variable grey model (MGM(1,n,q)) based on genetic algorithm was better than MGM(1,n) model, and the MGM(1,n) model was better than MGM(1,1) model.

  13. Genetic variability and inheritance to aluminum tolerance in nutrient solution in triticale

    Directory of Open Access Journals (Sweden)

    Allan Henrique Silva

    2014-03-01

    Full Text Available Triticale has shown different behavior to aluminum toxicity (A1(3+ when applied nutrient solution. This study had the objective of evaluating 19 triticale lines inserted at International Maize and Wheat Improvement Center (CIMMYT, IAC-5 cultivar and two control cultivars of wheat in the presence of 0, 3, 6, 9, 12 and 15 mg L- 1 of Al3+. Afterwards, four genotypes being two tolerant and two sensitive were chosen to obtain the F1's, F2's, RC1's and RC2's generations, in all possible crossing. The seedlings were submitted to 6 mg L- 1 of Al3+ and analyzed later on (tolerant and sensitive by the chi-square method. The root growth was also obtained to estimate the genetic parameters involved in the character control. The trials were carried out in laboratories, in nutritive solution. The genotypes were tolerant to 15 mg L- 1 of Al3+, exception the line 14 (P3, sensitive to 3 mg L- 1 of Al3+ and the line 13, 17 and the cultivar IAC-5 (P4, sensitive to 6 mg L- 1 of Al3+, the line 15 sensitive to 12 mg L- 1 of Al3+ and the lines 16 and 18 sensitive to 15 mg L- 1 of Al3+. It was concluded that the inheritance to tolerance to aluminum toxicity is dominant and governed by a pair of alleles. The genetic parameters involved in the root growth control in solution containing 6 mg L- 1 of Al3+ also revealed simple inheritance, suggesting a selection in the first segregating generations.

  14. Genetic structure and molecular variability of Cucumber mosaic virus isolates in the United States.

    Directory of Open Access Journals (Sweden)

    Shahideh Nouri

    Full Text Available Cucumber mosaic virus (CMV has a worldwide distribution and the widest host range of any known plant virus. From 2000 to 2012, epidemics of CMV severely affected the production of snap bean (Phaseulos vulgaris L. in the Midwest and Northeastern United States. Virus diversity leading to emergence of new strains is often considered a significant factor in virus epidemics. In addition to epidemics, new disease phenotypes arising from genetic exchanges or mutation can compromise effectiveness of plant disease management strategies. Here, we captured a snapshot of genetic variation of 32 CMV isolates collected from different regions of the U.S including new field as well as historic isolates. Nucleotide diversity (π was low for U.S. CMV isolates. Sequence and phylogenetic analyses revealed that CMV subgroup I is predominant in the US and further showed that the CMV population is a mixture of subgroups IA and IB. Furthermore, phylogenetic analysis suggests likely reassortment between subgroups IA and IB within five CMV isolates. Based on phylogenetic and computational analysis, recombination between subgroups I and II as well as IA and IB in RNA 3 was detected. This is the first report of recombination between CMV subgroups I and II. Neutrality tests illustrated that negative selection was the major force operating upon the CMV genome, although some positively selected sites were detected for all encoded proteins. Together, these data suggest that different regions of the CMV genome are under different evolutionary constraints. These results also delineate composition of the CMV population in the US, and further suggest that recombination and reassortment among strain subgroups does occur but at a low frequency, and point towards CMV genomic regions that differ in types of selection pressure.

  15. Conservation genetics of the endangered Iberian steppe plant Ferula loscosii (Apiaceae).

    Science.gov (United States)

    Pérez-Collazos, E; Catalán, P

    2008-07-01

    Ferula loscosii (Lange) Willk (Apiaceae) is a threatened endemic species native to the Iberian Peninsula. The plant has a narrow and disjunct distribution in three regions, NE, C and SE Spain. Genetic variability within and among 11 populations from its natural distribution was assessed using allozymes. Intermediate levels of genetic diversity were detected in F. loscosii (P(99%) = 36.83; H(E) = 0.125; H(T) = 0.152). However, the highest genetic diversity (58%) corresponded to the threatened populations from SE and C Spain (H(T) = 0.169) rather than the more abundant and larger populations from NE Spain (Ebro valley) (H(T) = 0.122). Low to moderate levels of genetic structure were found among regional ranges (G(ST) = 0.134), and several statistical spatial correlation analyses corroborated substantial genetic differentiation among the three main regional ranges. However, no significant genetic differentiation was found among the NE Spain populations, except for a northernmost population that is geographically isolated. Outcrossing mating and other biological traits of the species could account for the maintenance of the present values of genetic diversity within populations. The existence of an ancestral late Tertiary wider distribution of the species in SE and C Spain, followed by the maintenance of different Quaternary refugia in these warmer areas, together with a more recent and rapid post-glacial expansion towards NE Spain, are arguments that could explain the low genetic variability and structure found in the Ebro valley and the higher levels of diversity in the southern Iberian populations.

  16. A scalable and portable framework for massively parallel variable selection in genetic association studies.

    Science.gov (United States)

    Chen, Gary K

    2012-03-01

    The deluge of data emerging from high-throughput sequencing technologies poses large analytical challenges when testing for association to disease. We introduce a scalable framework for variable selection, implemented in C++ and OpenCL, that fits regularized regression across multiple Graphics Processing Units. Open source code and documentation can be found at a Google Code repository under the URL http://bioinformatics.oxfordjournals.org/content/early/2012/01/10/bioinformatics.bts015.abstract. Supplementary data are available at Bioinformatics online.

  17. Tracing fecal pollution sources in karst groundwater by Bacteroidales genetic biomarkers, bacterial indicators, and environmental variables.

    Science.gov (United States)

    Zhang, Ya; Kelly, Walton R; Panno, Samuel V; Liu, Wen-Tso

    2014-08-15

    Fecal contamination in Midwestern karst regions was evaluated by simultaneously measuring traditional bacterial indicators (coliforms and Escherichia coli), Bacteroidales-based biomarkers, and environmental variables. Water samples from springs and wells were collected from karst regions in Illinois (IL), Wisconsin (WI), Kentucky (KY), and Missouri (MO). Quantitative PCR (Q-PCR) with seven primer sets targeting different members of Bacteroidales was used to determine the origin of fecal contamination (i.e., from human waste, livestock waste, or both). Most samples were contaminated by both human and animal waste, with a few samples showing pollution solely by one or the other. Spring water tended to have higher levels of contamination than well water, and higher concentrations of fecal biomarkers were detected in urban springs compared to rural spring systems. However, there were discrepancies on contamination profile determined by Bacteroidales-based biomarkers and by traditional bacterial indicators. Among all the environmental parameters examined, E. coli, sulfate, total dissolved solids (TDS), and silicon were significantly correlated (pgroundwater systems in Midwestern regions, and the inclusion of traditional bacterial indicators, environmental variables, and Bacteroidales-based MST is an effective approach for identifying fecal contamination in karst regions. Copyright © 2014 Elsevier B.V. All rights reserved.

  18. Genetic variability and phenotypic plasticity of metric thoracic traits in an invasive drosophilid in America.

    Science.gov (United States)

    Bitner-Mathé, Blanche Christine; David, Jean Robert

    2015-08-01

    Thermal phenotypic plasticity of 5 metric thoracic traits (3 related to size and 2 to pigmentation) was investigated in Zaprionus indianus with an isofemale line design. Three of these traits are investigated for the first time in a drosophilid, i.e. thorax width and width of pigmented longitudinal white and black stripes. The reaction norms of white and black stripes were completely different: white stripes were insensitive to growth temperature while the black stripes exhibited a strong linear decrease with increasing temperatures. Thorax width exhibited a concave reaction norm, analogous but not identical to those of wing length and thorax length: the temperatures of maximum value were different, the highest being for thorax width. All traits exhibited a significant heritable variability and a low evolvability. Sexual dimorphism was very variable among traits, being nil for white stripes and thorax width, and around 1.13 for black stripes. The ratio thorax length to thorax width (an elongation index) was always >1, showing that males have a more rounded thorax at all temperatures. Black stripes revealed a significant increase of sexual dimorphism with increasing temperature. Shape indices, i.e. ratios between size traits all exhibited a linear decrease with temperature, the least sensitive being the elongation index. All these results illustrate the complexity of developmental processes but also the analytical strength of biometrical plasticity studies in an eco-devo perspective.

  19. Variability of the Intestinal Uptake of Lipids Is Genetically Determined in Mice

    Science.gov (United States)

    Keelan, M.; Hui, D.Y.; Wild, G.; Clandinin, M.T.

    2008-01-01

    The response of the plasma cholesterol concentration to changes in dietary lipids varies widely in humans and animals. There are variations in the in vivo absorption of cholesterol between different strains of mice. This study was undertaken in three strains of inbred mice to test the hypotheses that: (i) there are strain differences in the in vitro uptake of fatty acids and cholesterol and (ii) the adaptability of the intestine to respond to variations in dietary lipids is genetically determined. An in vitro intestinal ring technique was used to assess the uptake of medium- and long-chain fatty acids and cholesterol into jejunum and ileum of adult DBA/2, C57BL6, and C57L/J mice. The jejunal uptake of cholesterol was similar in C57L/J, DBA/2, or C57BL6 fed ad libitum a low-fat (5.7% fat, no cholesterol) chow diet. This is in contrast to a previous demonstration that in vivo cholesterol absorption was lower in C57L/J than in the other murine strains. The jejunal uptake of several long-chain fatty acids was greater in DBA/2 fed for 4 wk the high-fat (15.8% fat and 1.25% cholesterol) as compared with the low-fat diet. Furthermore, on the high-fat diet, the uptake of many long-chain fatty acids was higher in DBA/2 than in C57BL6 or C57L/J. The differences in cholesterol and fatty acid uptake were not explained by variations in food uptake, body weight gain, or the weight of the intestine. In summary: (i) there are strain differences in the in vitro intestinal uptake of fatty acids but not of cholesterol; (ii) a high-fat diet enhances the uptake of long-chain fatty acids in only one of the three strains examined in this study; and (iii) the pattern of strain- and diet-associated alterations in the in vivo absorption of cholesterol differs from the pattern of changes observed in vitro. We speculate that genetic differences in cholesterol and fatty acid uptake are explained by variations in the expression of protein-mediated components of lipid uptake. PMID:10984106

  20. Using genetic variability available in the breeder's pool to engineer fruit quality.

    Science.gov (United States)

    Orzaez, Diego; Monforte, Antonio J; Granell, Antonio

    2010-01-01

    We substantiate here the opinion that experts in biotechnology and natural biodiversity can work together on the production of successive waves of next-generation GM fruit crops to improve organoleptic and nutritional quality and therefore generate wider public acceptance. In this scenario genetic engineering becomes a faster and more precise way of transferring genes of interest to fruit crop plants from the same or sexually compatible species (intra- or cisgenesis) than more traditional methods, such as MASPB. The availability of complete genome sequences for an increasing number of crop plants, as well as the results from genomics studies, can assist in the identification of gene-to-trait association. The next wave of GM crops will be able to take full advantage of a Synthetic Biology-based strategy in the development of new fruit varieties by using DNA not necessarily present in the breeder's pool for a wide range of applications. There are still a number of challenges which require attention, such as identifying genes and allelic forms associated with traits of interest and improving the precision and stability of the transferred DNA. © 2010 Landes Bioscience

  1. WEDM process variables investigation for HSLA by response surface methodology and genetic algorithm

    Directory of Open Access Journals (Sweden)

    Neeraj Sharma

    2015-06-01

    Full Text Available Wire electric discharge machining (WEDM is a thermo-electric spark erosion non-traditional type manufacturing process. The applications of WEDM have been found in aerospace and die manufacturing industries, where precise dimensions were the prime objective. This process is applied in case of processing difficult to machine material. Brass wire is used as an electrode and High strength low alloy (HSLA steel as a work-piece during experimentation. The present research deals with the effect of process parameters on the overcut while machining the HSLA steel on WEDM. The mathematical model has been developed with the help of Response Surface Methodology (RSM. Further this model is processed with help of Genetic Algorithm (GA to find out the optimum machining parameters. The percentage error between the predicted and experimental values lies in the range of ±10%, which indicates that the developed model can be utilized to predict the overcut values. The experimental plan was executed according to central composite design. The optimal setting of process parameters is pulse on-time-117 μs; pulse off-time-50 μs; spark gap voltage-49 V; peak current-180 A and wire tension-6 g; for minimum overcut, whereas at the optimal setting overcut is 9.9922 μm.

  2. MTNR1B Genetic Variability Is Associated with Gestational Diabetes in Czech Women

    Directory of Open Access Journals (Sweden)

    Daniela Vejrazkova

    2014-01-01

    Full Text Available The gene MTNR1B encodes a receptor for melatonin. Melatonin receptors are expressed in human β-cells, which implies that genetic variants might affect glucose tolerance. Meta-analysis confirmed that the rs10830963 shows the most robust association. The aim of the study was to assess the rs10830963 in Czech GDM patients and controls and to study relations between the SNP and biochemical as well as anthropometric characteristics. Our cohort consisted of 880 women; 458 were diagnosed with GDM, and 422 were normoglycemic controls without history of GDM. Despite similar BMI, the GDM group showed higher WHR, waist circumference, abdominal circumference, and total body fat content. The risk allele G was more frequent in the GDM group (38.3 versus 29.4% in controls, OR 1.49 CI95% [1.22; 1.82]; POR=0.0001. In spite of higher frequency, the G allele in the GDM group was not associated with any markers of glucose metabolism. In contrast, controls showed significant association of the allele G with FPG and with postchallenge glycemia during the oGTT. Frequency analysis indicates that rs10830963 is involved in gestational diabetes in Czech women. However, the association of the SNP with glucose metabolism, which is obvious in controls, is covert in women who have experienced GDM.

  3. Genetic Variability and Association of Quality Characters and Pod Yield in Garden Peas (Pisum sativum L.

    Directory of Open Access Journals (Sweden)

    Firas Mohammad AL-AYSH

    2014-08-01

    Full Text Available Ten garden pea landraces in a randomized complete block design with 3 replications over 2 winter seasons 2011 - 2012 and 2012 - 2013 were evaluated at the experimental field of Dara'a Center of Scientific Agricultural Research, GCSAR, Syria. The study showed high heritability (H with high genotypic coefficient of variation (GCV and genetic gain as percent of mean (GA % for vitamin C, chlorophyll A, chlorophyll B, total carotenoids and pod yield plant-1 indicating good scope for selection. The genotypic (rg and phenotypic associations (rph of pod yield plant-1 were significantly positive with protein content, fiber content and total carotenoids but significantly negative with soluble sugars. Path coefficient analysis confirmed that protein content and total soluble solids registered positive direct effects on pod yield plant-1 and negative indirect effects through each other. Protein content should be considered independently or in combination with total soluble solids and chlorophyll A while imposing selection for amelioration of quality and yield in garden peas.

  4. GENETIC VARIABILITY ASSESSMENT OF FUSARIUM WILT PATHOGEN RACES AFFECTING CHICKPEA USING MOLECULAR MARKERS

    Directory of Open Access Journals (Sweden)

    Jhuma Datta

    2013-06-01

    Full Text Available Genetic diversity in Chickpea wilt pathogen has been characterized using 14 isolates of Fusarium oxysporum f. sp. ciceri (foc collected from major pulse growing regions of India. Out of 247 bands produced by 24 Random Amplified Polymorphic DNA (RAPD primers in Foc isolates, 210 (85% were polymorphic. A maximum of 14 amplicons were generated by primer OPF 05 whereas minimum 7 amplicons were generated by primer K7. A total of 24 alleles were produced by twelve simple sequence repeat (SSR primers with an average of two alleles per marker in foc isolates. The maximum number of 4 alleles was obtained with primer SSR 12. SSR amplicon size ranged from 100 to 400 bp. The Unweighted Pair Group Method with Arithmetic Mean (UPGMA cluster analysis based on RAPD and SSR profiles grouped the fourteen foc isolates into four major clusters. The universal Inter Transcribed Spacer (ITS primer pair amplified 630 bp bands in all fourteen foc isolates while significant length polymorphism was obtained only when analysed by restriction digestion with EcoRI and MspI enzymes. The cluster analysis of ITS-RFLP grouped all 14 Foc isolates into three major clusters. The cluster analysis using RAPD, SSR and ITS-RFLP markers show the grouping of Fusarium isolates strictly according to their cultural characteristics and degree of pathogenicity and not the geographical origin. This information will be helpful for pathologists and plant breeders to design effective resistance breeding programs in chickpea taking into account the diversity in wilt pathogen.

  5. Variable genetic architectures produce virtually identical molecules in bacterial symbionts of fungus-growing ants.

    Science.gov (United States)

    Sit, Clarissa S; Ruzzini, Antonio C; Van Arnam, Ethan B; Ramadhar, Timothy R; Currie, Cameron R; Clardy, Jon

    2015-10-27

    Small molecules produced by Actinobacteria have played a prominent role in both drug discovery and organic chemistry. As part of a larger study of the actinobacterial symbionts of fungus-growing ants, we discovered a small family of three previously unreported piperazic acid-containing cyclic depsipeptides, gerumycins A-C. The gerumycins are slightly smaller versions of dentigerumycin, a cyclic depsipeptide that selectively inhibits a common fungal pathogen, Escovopsis. We had previously identified this molecule from a Pseudonocardia associated with Apterostigma dentigerum, and now we report the molecule from an associate of the more highly derived ant Trachymyrmex cornetzi. The three previously unidentified compounds, gerumycins A-C, have essentially identical structures and were produced by two different symbiotic Pseudonocardia spp. from ants in the genus Apterostigma found in both Panama and Costa Rica. To understand the similarities and differences in the biosynthetic pathways that produced these closely related molecules, the genomes of the three producing Pseudonocardia were sequenced and the biosynthetic gene clusters identified. This analysis revealed that dramatically different biosynthetic architectures, including genomic islands, a plasmid, and the use of spatially separated genetic loci, can lead to molecules with virtually identical core structures. A plausible evolutionary model that unifies these disparate architectures is presented.

  6. ACE genetic variability and response to fluoxetine: lack of association in depressed patients

    Directory of Open Access Journals (Sweden)

    Negar Firouzabadi

    2015-12-01

    Full Text Available Evidences suggest that besides the neurotransmitters contributing to the development of depression, renin-angiotensin system (RAS may also have a substantial role. Certain polymorphisms of RAS are associated with over activity of RAS & depression. Considering that antidepressants reduce the actions of angiotensin II, the main product of RAS, this may come into mind that genetic polymorphisms of the mentioned system may affect the outcome of therapy in depressed patients. In the present study, 100 newly diagnosed depressed patients, according to DSM-IV criteria, were treated with 20 mg of fluoxetine or 8-12 weeks. Patients were categorized into responsive and non-responsive groups according to 50% reduction in symptoms. Genotype frequencies of angiotensin-converting enzyme (ACE gene [ACE (I/D, A-240T and A2350G] were then determined in DNAs extracted from venous blood of the patients using polymerase chain reaction–restriction fragment length polymorphism (PCR– RFLP and PCR. Results indicate that polymorphisms studied and their haplotypes were not associated with better response to fluoxetine. However, a strong association between age and treatment in depressed Iranian patients was observed (P=0.001. In conclusion, unlike previous reports, this study does not support the hypothesis of special genotypes of RAS contributing to a better response to antidepressants in depressed patients.

  7. Molecular characterization of Tunga trimamillata and T. penetrans (Insecta, Siphonaptera, Tungidae: taxonomy and genetic variability

    Directory of Open Access Journals (Sweden)

    Luchetti A.

    2005-06-01

    Full Text Available A new species of the genus Tunga, T. trimamillata has recently been described on the basis of several morphological traits. To explore the taxonomic status of this flea with respect to T. penetrans, we undertook a molecular analysis of cytochrome oxydase II and 16S rDNA mitochondrial genes and of the internal transcribed spacer 2 nuclear marker on samples of both species. Maximum Parsimony evaluations of the three data set indicate a differentiation compatible with a specific rank between the two fleas with very high levels of divergence. Both mitochondrial and nuclear data are in line with a recent bottleneck in the Malagasy population of T. penetrans, possibly due to the recent colonisation of Africa via human transportation. Further, significantly lower mitochondrial variability in the Ecuadorian populations of T. penetrans with respect to the T. trimamillata ones is also evidenced.

  8. Butyrylcholinesterase genetic variability in Guarani Amerindians from the Brazilian state of Mato Grosso do Sul

    Directory of Open Access Journals (Sweden)

    Lupe Furtado

    2006-01-01

    Full Text Available Human butyrylcholinesterase (BChE; EC 3.1.1.8 is a polymorphic enzyme coded by the BCHE gene (3q26.1-q26.2 while the CHE2 gene (2q33-q35 determines a still not characterized substance that forms a complex with BChE (C5, being the CHE2 C5+ and CHE2 C5- phenotypes detected in electrophoresis. The present study investigated BCHE and CHE2 variability and the BChE activity of Brazilian Guarani Amerindians from the Kaiowá and Ñandeva sub-groups living in several indigenous territories in the Brazilian state of Mato Grosso do Sul. The frequency of the BCHE exon 2 D70G (A allele was 0.60% ± 0.35% while that of the BCHE exon 2 G390V (F-2 allele, never before screened in Amerindians, was 8.82% ± 1.35%. This is the first time that the BCHE gene exon 4 A539T (K allele has been surveyed in Brazilian Amerindians where it was found at a frequency of 3.69% ± 0.85%, similar to that found in Chilean Mapuche Amerindians. The BCHE gene variability seen in this survey differs from that of non-isolated populations in respect to both A539T and G390V allele frequency. The CHE2 C5+ phenotype frequency was 14.40% ± 2.22% and falls within the range of that found for other Brazilian Amerindian samples.

  9. IN SITU COMPARISON OF TREE-RING RESPONSES TO CLIMATE AND POPULATION GENETICS: THE NEED TO CONTROL FOR LOCAL CLIMATE AND SITE VARIABLES

    Directory of Open Access Journals (Sweden)

    Johann Mathias Housset

    2016-10-01

    Full Text Available Tree species responses to climate change will be greatly influenced by their evolutionary potential and their phenotypic plasticity. Investigating tree-rings responses to climate and population genetics at the regional scale is therefore crucial in assessing the tree behaviour to climate change. This study combined in situ dendroclimatology and population genetics over a latitudinal gradient and compared the variations between the two at the intra- and inter-population levels. This approach was applied on the northern marginal populations of Thuja occidentalis (eastern white-cedar in the Canadian boreal forest. We aimed first to assess the radial growth variability (response functional trait within populations across the gradient and to compare it with the genetic diversity (microsatellites. Second, we investigated the variability in the growth response to climate at the regional scale through the radial growth-climate relationships, and tested its correlation with environmental variables and population genetic structure. Model selection based on the Akaike Information Criteria revealed that the growth synchronicity between pairs of trees of a population covariates with both the genetic diversity of this population and the amount of precipitation (inverse correlation, although these variables only explained a small fraction of the observed variance. At the regional scale, variance partitioning and partial redundancy analysis indicate that the growth response to climate was greatly modulated by stand environmental variables, suggesting predominant plastic variations in growth-response to climate. Combining in situ dendroclimatology and population genetics is a promising way to investigate species’ response capacity to climate change in natural stands. We stress the need to control for local climate and site conditions effects on dendroclimatic response to climate to avoid misleading conclusions regarding the associations with genetic variables.

  10. [GENETIC VARIABILITY OF MATERNAL PLANTS AND SEED EMBRYOS OF KOCH PINE POPULATIONS (PINUS KOCHIANA KLOTZSCH EX KOCH) IN CRIMEA].

    Science.gov (United States)

    Korshykov, I I; Kalafat, L O; Vynogradova, O M; Podgornyi, D Y

    2016-01-01

    Comparative studies of genetic variability were undertaken for 12 allozyme loci selections of trees and embryos of seed, and also for the crossing systems in five populations of Koch pine of (Pinus kochiana Klotzsch ex Koch) in Crimea. It was shown that in seed embryos the allelic variety peculiar to the maternal plants was restored, however the level of the available (H₀) heterozygosity was considerably lower, 0.286 and 0.189 respectively. For the embryos unlike the trees, in the majority of the analyzed loci the considerable divergence was specific in the actual distribution of genotypes from the theoretically expected according to Hardy- Weinberg law. The proportion of cross pollination at the unilocal (t(s)) estimation varied from 0.384 to 0.673 in the populations, while at the multilocal ones (t(m)) it was 0.639-0.841.

  11. Genetic variability in Astyanax altiparanae Garutti & Britski, 2000 (Teleostei, Characidae from the Upper Paraná River basin, Brazil

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    Maria Dolores Peres

    2005-12-01

    Full Text Available Allozyme data was used to assess the genetic diversity Astyanax altiparanae populations from the floodplain of the Upper Paraná River (PR. Specimens were collected in the southern Brazilian state of Paraná from PR in Porto Rico municipality and Ribeirão Ficha (RF in Ubiratã municipality. The authors used 15% (w/v corn starch gel electrophoresis to identify 21 putative loci for 13 enzymatic systems: Aspartate aminotransferase, 2.6.1.1 (AAT, Acid phosphatase, 3.1.3.2 (ACP, Esterase, 3.1.1.1 (EST, Glycerol-3-phosphate dehydrogenase, 1.1.1.8 (G3PDH, Glucose-6-phosphate dehydrogenase, 1.1.1.49 (G6PDH, Glucose-6-phosphate isomerase, 5.3.1.9 (GPI, Iditol dehydrogenase, 1.1.1.14 (IDDH, Isocitrate dehydrogenase - NADP+, 1.1.1.42 (IDH, L-Lactate dehydrogenase, 1.1.1.27 (LDH, Malate dehydrogenase, 1.1.1.37 (MDH, Malate dehydrogenase - NADP+, 1.1.1.40 (MDHP, Phosphoglucomutase, 5.4.2.2 (PGM, and Superoxide dismutase, 1.15.1.1 (SOD. The proportion of polymorphic loci were estimated as 52.38% in the PR population and 38.10% in the RF population. Expected estimated heterozygosities were 0.1518 ± 0.0493 for the PR population and 0.0905 ± 0.0464 for the RF population. The A. altiparanae heterozygosity data were similar to previous estimates for other PR basin characid species. Allele frequencies were significantly different between the PR and RF populations in respect to some loci (Acp-1, G3pdh-1, Gpi-A, Iddh-1, Mdhp-1 and Mdhp-2. Wright’s statistics for all loci were estimated as Fis = 0.3919, Fit = 0.4804 and Fst = 0.1455. Our results show that the A. altiparanae populations studied are genetically different and have a high degree of genetic variability.

  12. Genetic Structure and Molecular Variability Analysis of Citrus sudden death-associated virus Isolates from Infected Plants Grown in Brazil

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    Emilyn Emy Matsumura

    2016-12-01

    Full Text Available Citrus sudden death-associated virus (CSDaV is a monopartite positive-sense single-stranded RNA virus that was suggested to be associated with citrus sudden death (CSD disease in Brazil. Here, we report the first study of the genetic structure and molecular variability among 31 CSDaV isolates collected from both symptomatic and asymptomatic trees in CSD-affected areas. Analyses of partial nucleotide sequences of five domains of the CSDaV genomic RNA, including those encoding for the methyltransferase, the multi-domain region (MDR, the helicase, the RNA-dependent RNA polymerase and the coat protein, showed that the MDR coding region was the most diverse region assessed here, and a possible association between this region and virus adaption to different host or plant tissues is considered. Overall, the nucleotide diversity (π was low for CSDaV isolates, but the phylogenetic analyses revealed the predominance of two main groups, one of which showed a higher association with CSD-symptomatic plants. Isolates obtained from CSD-symptomatic plants, compared to those obtained from asymptomatic plants, showed higher nucleotide diversity, nonsynonymous and synonymous substitution rates and number of amino acid changes on the coding regions located closer to the 5’ end region of the genomic RNA. This work provides new insights into the genetic diversity of the CSDaV, giving support for further epidemiological studies.

  13. Genetic and Pathogenic Variability of Fusarium oxysporum f. sp. cepae Isolated from Onion and Welsh Onion in Japan.

    Science.gov (United States)

    Sasaki, Kazunori; Nakahara, Katsuya; Tanaka, Shuhei; Shigyo, Masayoshi; Ito, Shin-ichi

    2015-04-01

    Fusarium oxysporum f. sp. cepae causes Fusarium basal rot in onion (common onion) and Fusarium wilt in Welsh onion. Although these diseases have been detected in various areas in Japan, knowledge about the genetic and pathogenic variability of F. oxysporum f. sp. cepae is very limited. In this study, F. oxysporum f. sp. cepae was isolated from onion and Welsh onion grown in 12 locations in Japan, and a total of 55 F. oxysporum f. sp. cepae isolates (27 from onion and 28 from Welsh onion) were characterized based on their rDNA intergenic spacer (IGS) and translation elongation factor-1α (EF-1α) nucleotide sequences, vegetative compatibility groups (VCGs), and the presence of the SIX (secreted in xylem) homologs. Phylogenetic analysis of IGS sequences showed that these isolates were grouped into eight clades (A to H), and 20 onion isolates belonging to clade H were monophyletic and assigned to the same VCG. All the IGS-clade H isolates possessed homologs of SIX3, SIX5, and SIX7. The SIX3 homolog was located on a 4 Mb-sized chromosome in the IGS-clade H isolates. Pathogenicity tests using onion seedlings showed that all the isolates with high virulence were in the IGS-clade H. These results suggest that F. oxysporum f. sp. cepae isolates belonging to the IGS-clade H are genetically and pathogenically different from those belonging to the other IGS clades.

  14. Genetic fusion of single-chain variable fragments to partial spider silk improves target detection in micro- and nanoarrays.

    Science.gov (United States)

    Thatikonda, Naresh; Delfani, Payam; Jansson, Ronnie; Petersson, Linn; Lindberg, Diana; Wingren, Christer; Hedhammar, My

    2016-03-01

    Immobilizing biomolecules with retained functionality and stability on solid supports is crucial for generation of sensitive immunoassays. However, upon use of conventional immobilization strategies, a major portion of the biomolecules (e.g. antibodies) frequently tends to lose their bioactivity. In this study, we describe a procedure to immobilize human single-chain variable fragment (scFv) via genetic fusion to partial spider silk, which have a high tendency to adhere to solid supports. Two scFvs, directed towards serum proteins, were genetically fused to partial spider silk proteins and expressed as silk fusion proteins in E. coli. Antigen binding ability of scFvs attached to a partial silk protein denoted RC was investigated using microarray analysis, whereas scFvs fused to the NC silk variant were examined using nanoarrays. Results from micro- and nanoarrays confirmed the functionality of scFvs attached to both RC and NC silk, and also for binding of targets in crude serum. Furthermore, the same amount of added scFv gives higher signal intensity when immobilized via partial spider silk compared to when immobilized alone. Together, the results suggest that usage of scFv-silk fusion proteins in immunoassays could improve target detection, in the long run enabling novel biomarkers to be detected in crude serum proteomes. Copyright © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. [Genetic history of Aleuts of the Komandor islands from results of analyzing variability of class II HLA genes].

    Science.gov (United States)

    Volod'ko, N V; Derbeneva, O A; Uinuk-ool, T S; Sukernik, R I

    2003-12-01

    Variability of the HLA class II genes (alleles of the DRB1, DQA1, and DQB1 loci) was investigated in a sample of Aleuts of the Commanders (n = 31), whose ancestors inhabited the Commander Islands for many thousand years. Among 19 haplotypes revealed in Aleuts of the Commanders, at most eight were inherited from the native inhabitants of the Commander Islands. Five of these haplotypes (DRB1*0401-DQA1*0301-DQB1*0301, DRB1*1401-DQA1*0101-DQB1*0503, DRB1*0802-DQA1*0401-DQB1*0402, DRB1*1101-DQA1*0501-DQB1*0301, and DRB1*1201-DQA1*0501-DQB1*0301) were typical of Beringian Mongoloids, i.e., Coastal Chukchi and Koryaks, as well as Siberian and Alaskan Eskimos. Genetic contribution of the immigrants to the genetic pool of proper Aleuts constituted about 52%. Phylogenetic analysis based on Transberingian distribution of the DRB1 allele frequencies favored the hypothesis on the common origin of Paleo-Aleuts, Paleo-Eskimos, and the Indians from the northwestern North America, whose direct ancestors survived in Beringian/southwestern Alaskan coastal refugia during the late Ice Age.

  16. Genetic Structure and Molecular Variability Analysis of Citrus sudden death-associated virus Isolates from Infected Plants Grown in Brazil

    Science.gov (United States)

    Matsumura, Emilyn Emy; Coletta Filho, Helvécio Della; de Oliveira Dorta, Silvia; Nouri, Shahideh; Machado, Marcos Antonio

    2016-01-01

    Citrus sudden death-associated virus (CSDaV) is a monopartite positive-sense single-stranded RNA virus that was suggested to be associated with citrus sudden death (CSD) disease in Brazil. Here, we report the first study of the genetic structure and molecular variability among 31 CSDaV isolates collected from both symptomatic and asymptomatic trees in CSD-affected areas. Analyses of partial nucleotide sequences of five domains of the CSDaV genomic RNA, including those encoding for the methyltransferase, the multi-domain region (MDR), the helicase, the RNA-dependent RNA polymerase and the coat protein, showed that the MDR coding region was the most diverse region assessed here, and a possible association between this region and virus adaption to different host or plant tissues is considered. Overall, the nucleotide diversity (π) was low for CSDaV isolates, but the phylogenetic analyses revealed the predominance of two main groups, one of which showed a higher association with CSD-symptomatic plants. Isolates obtained from CSD-symptomatic plants, compared to those obtained from asymptomatic plants, showed higher nucleotide diversity, nonsynonymous and synonymous substitution rates and number of amino acid changes on the coding regions located closer to the 5’ end region of the genomic RNA. This work provides new insights into the genetic diversity of the CSDaV, giving support for further epidemiological studies. PMID:27999249

  17. Phylogenetic and Molecular Variability Studies Reveal a New Genetic Clade of Citrus leprosis virus C.

    Science.gov (United States)

    Ramos-González, Pedro Luis; Chabi-Jesus, Camila; Guerra-Peraza, Orlene; Breton, Michèle Claire; Arena, Gabriella Dias; Nunes, Maria Andreia; Kitajima, Elliot Watanabe; Machado, Marcos Antonio; Freitas-Astúa, Juliana

    2016-06-06

    Citrus leprosis virus C (CiLV-C) causes a severe disease affecting citrus orchards in the Western hemisphere. This study reveals the molecular variability of the virus by analyzing four genomic regions (p29, p15, MP and RNA2-intergenic region) distributed over its two RNAs. Nucleotide diversity (π) values were relatively low but statistically different over the analyzed genes and subpopulations, indicating their distinct evolutionary history. Values of πp29 and πMP were higher than those of πp15 and πRNA2-IR, whereas πMP was increased due to novel discovered isolates phylogenetically clustered in a divergent clade that we called SJP. Isolate BR_SP_SJP_01 RNA1 and RNA2 sequences, clade SJP, showed an identity of 85.6% and 88.4%, respectively, with those corresponding to CiLV-C, the type member of the genus Cilevirus, and its RNA2 5'-proximal region was revealed as a minor donor in a putative inter-clade recombination event. In addition to citrus, BR_SP_SJP_01 naturally infects the weed Commelina benghalensis and is efficiently transmitted by Brevipalpus yothersi mites. Our data demonstrated that negative selection was the major force operating in the evaluated viral coding regions and defined amino acids putatively relevant for the biological function of cilevirus proteins. This work provides molecular tools and sets up a framework for further epidemiological studies.

  18. Genetic engineering of chimeric antigen receptors using lamprey derived variable lymphocyte receptors

    Directory of Open Access Journals (Sweden)

    Robert Moot

    2016-01-01

    Full Text Available Chimeric antigen receptors (CARs are used to redirect effector cell specificity to selected cell surface antigens. Using CARs, antitumor activity can be initiated in patients with no prior tumor specific immunity. Although CARs have shown promising clinical results, the technology remains limited by the availability of specific cognate cell target antigens. To increase the repertoire of targetable tumor cell antigens we utilized the immune system of the sea lamprey to generate directed variable lymphocyte receptors (VLRs. VLRs serve as membrane bound and soluble immune effectors analogous but not homologous to immunoglobulins. They have a fundamentally different structure than immunoglobulin (Ig-based antibodies while still demonstrating high degrees of specificity and affinity. To test the functionality of VLRs as the antigen recognition domain of CARs, two VLR-CARs were created. One contained a VLR specific for a murine B cell leukemia and the other contained a VLR specific for the human T cell surface antigen, CD5. The CAR design consisted of the VLR sequence, myc-epitope tag, CD28 transmembrane domain, and intracellular CD3ζ signaling domain. We demonstrate proof of concept, including gene transfer, biosynthesis, cell surface localization, and effector cell activation for multiple VLR-CAR designs. Therefore, VLRs provide an alternative means of CAR-based cancer recognition.

  19. Genetic variability for mineral concentration of Eruca sativa L. and Diplotaxis tenuifolia L. accessions

    Directory of Open Access Journals (Sweden)

    Mehmet Kadri Bozokalfa

    2009-01-01

    Full Text Available Eruca sativa L. (rocket or arugula and Diplotaxis tenuifolia L. (perennial wall-rocket, are important leafyvegetables and are significant sources of minerals for human nutrition and commonly found in the Mediterranean basin,southern Europe, and Central Asia. The objectives of this study were to determine genotypic variability among and within E.sativa and D. tenuifolia genotypes for NO3, NO2, N, P, K, Ca, Mg, Na, Fe, Cu, Zn, and Mn concentrations; to estimate genotypex environment interaction; and to assess relationships among leaf mineral concentration during two consecutive springseasons. E. sativa and D. tenuifolia leaves contained significant amounts of nutritionally important minerals. In general,genotypic variation was lower than phenotypic variation for all mineral concentrations considered, indicating the influence ofenvironment on the expression of analyzed traits. The variance between genotypes and relative importance within genotypevariation indicates that NO3, NO2, K, Mn, Zn, and Cu concentrations may be improved by selecting among cultivars, if theheritability is adequate.

  20. Genetic variability of CYP2B6 polymorphisms in four southern Chinese populations

    Institute of Scientific and Technical Information of China (English)

    Bing-Ying Xu; Ming-Liang He; Li-Ping Guo; Shui-Shan Lee; Qing-Ming Dong; Yi Tan; Hong Yao; Li-Hua Li; Che-Kit Lin; Hsiang-Fu Kung

    2007-01-01

    AIM: To investigate the genotype and allelic frequencies of Cytochrome P450 2B6 polymorphisms in four southern Chinese populations.METHODS: DNA was obtained from blood samples from Han Chinese from Hong Kong and three minority groups,the Wa, Bulang and Lahu from Yunnan in southern China. Genotyping was performed using real-time PCR and confirmed by direct sequencing.RESULTS: A total of 507 subjects from southern China were studied. Results showed there is a high prevalence of 516G > T (34.5%) in ethnic Chinese compared to literature reports on other Asian populations and Caucasians. The frequency of the 516TT genotype is higher in the Hah majority (23.1%) than in three other ethnic minority groups (i.e., 7.4%, 9.1% and 15.8%) in southern China.CONCLUSION: This was the first study to document the spectrum of CYP2B6 allelic variants and genotypes in a southern Chinese population. The 516G > T allele is associated with a defective metabolism of efavirenz (EFV), which therefore may predispose to drug toxicity.Treatment regimens for human immunodeficiency virus (HIV) and heroin addiction may need to be optimized in different populations because of the marked variability of the key metabolizing enzyme.

  1. Genetic variability and fumonisin production by Fusarium proliferatum isolated from durum wheat grains in Argentina.

    Science.gov (United States)

    Palacios, S A; Susca, A; Haidukowski, M; Stea, G; Cendoya, E; Ramírez, M L; Chulze, S N; Farnochi, M C; Moretti, A; Torres, A M

    2015-05-18

    Fusarium proliferatum is a member of the Fusarium fujikuroi species complex (FFSC) involved in the maize ear rot together with Fusarium verticillioides, which is a very closely related species. Recently, different studies have detected natural fumonisin contamination in wheat kernels and most of them have shown that the main species isolated was F. proliferatum. Fusarium strains obtained from freshly harvested durum wheat samples (2008 to 2011 harvest seasons) from Argentina were characterized through a phylogenetic analysis based on translation elongation factor-1 alpha (EF-1α) and calmodulin (CaM) genes, determination of mating type alleles, and evaluation of fumonisin production capability. The strains were identified as F. proliferatum (72%), F. verticillioides (24%) and other Fusarium species. The ratio of mating type alleles (MAT-1 and MAT-2) obtained for both main populations suggests possible occurrence of sexual reproduction in the wheat fields, although this seems more frequent in F. proliferatum. Phylogenetic analysis revealed greater nucleotide variability in F. proliferatum strains than in F. verticillioides, however this was not related to origin, host or harvest year. The fumonisin-producing ability was detected in 92% of the strains isolated from durum wheat grains. These results indicate that F. proliferatum and F. verticillioides, among the fumonisin producing species, frequently contaminate durum wheat grains in Argentina, presenting a high risk for human and animal health. Copyright © 2015 Elsevier B.V. All rights reserved.

  2. Genetic variability of Scots pine (Pinus sylvestris L. in maternal regions of provenance

    Directory of Open Access Journals (Sweden)

    Przybylski Paweł

    2015-06-01

    Full Text Available The analysis of chosen selected Scots Pine (Pinus sylvestris L., populations representing different seed regions: 107 (Międzyzdroje, 305 (Woziwoda, 206 (Strzałowo, 208 (Białowieża, 504 (Bolesławiec, 606 (Józefów were performed using 10 isoensyme markers: Gdh (E.C.1.4.1.2, Sdh-A, Sdh-B (E.C.1.1.1.25, Pgd-B (E.C.1.1.1.44, Mdh-A, Mdh-C (E.C.1.1.1.37, Got-A, Got-B, Got-C (E.C.2.6.1.1, Dia-C (E.C.1.8.1.4. There were calculated following genetic parameters: allelic frequencies, observed and expected heterozygosities, and Wright’s fixation indexes. In populations, the results of analysis indicated presence of rare alleles. In all study populations, the average effective number of alleles per locus was 1.46 and was lower than expected number of alleles per locus of 1.93. The results for the effective number of alleles of the population per locus were as follows: Strzałowo and Białowieża 1.54, Bolesławiec 1.48, Jozefów 1.44, Świnoujście 1.42, Woziwoda 1.35. Average observed heterozygosity in the studied populations was calculated at the level of 0.26 and it was lower than the expected heterozygosity at 0.28. For populations, the level of heterozygosities were as follow: Strzałowo 0.35, Bolesławiec and Białowieża 0.25, Józefów 0.27, Świnoujście 0.23, Woziwoda 0.26. In particular loci level of heterozygosity was different, as the most heterozygous Mdh-C locus was estimated, while minimum Got-C.

  3. Transcriptome Sequencing of Diverse Peanut (Arachis Wild Species and the Cultivated Species Reveals a Wealth of Untapped Genetic Variability

    Directory of Open Access Journals (Sweden)

    Ratan Chopra

    2016-12-01

    Full Text Available To test the hypothesis that the cultivated peanut species possesses almost no molecular variability, we sequenced a diverse panel of 22 Arachis accessions representing Arachis hypogaea botanical classes, A-, B-, and K- genome diploids, a synthetic amphidiploid, and a tetraploid wild species. RNASeq was performed on pools of three tissues, and de novo assembly was performed. Realignment of individual accession reads to transcripts of the cultivar OLin identified 306,820 biallelic SNPs. Among 10 naturally occurring tetraploid accessions, 40,382 unique homozygous SNPs were identified in 14,719 contigs. In eight diploid accessions, 291,115 unique SNPs were identified in 26,320 contigs. The average SNP rate among the 10 cultivated tetraploids was 0.5, and among eight diploids was 9.2 per 1000 bp. Diversity analysis indicated grouping of diploids according to genome classification, and cultivated tetraploids by subspecies. Cluster analysis of variants indicated that sequences of B genome species were the most similar to the tetraploids, and the next closest diploid accession belonged to the A genome species. A subset of 66 SNPs selected from the dataset was validated; of 782 SNP calls, 636 (81.32% were confirmed using an allele-specific discrimination assay. We conclude that substantial genetic variability exists among wild species. Additionally, significant but lesser variability at the molecular level occurs among accessions of the cultivated species. This survey is the first to report significant SNP level diversity among transcripts, and may explain some of the phenotypic differences observed in germplasm surveys. Understanding SNP variants in the Arachis accessions will benefit in developing markers for selection.

  4. Variabilidade genética em biotipos de leiteiro de Londrina/PR Genetic variability among Euphorbia heterophylla

    Directory of Open Access Journals (Sweden)

    Maria José V. de Vasconcelos

    2000-08-01

    size, which can vary among and within populations. This variability suggested to several authors that E. heterophylla was, in fact, formed by different species. To systematize the study of E. heterophylla and to determine if the phenotypic variability correspond to modifications at the DNA level, we analyzed 10 different plants collected in the soybean field in Londrina (Parana, Brazil. The plants were transplanted to the greenhouse and leaf DNA was extracted for RAPD technique analysis. Twenty-six RAPD "primers" different amplified 102 DNA bands, 38 of them being polymorphic. Genetic distances among the individuals were calculated based on the presence (1 or absence (0 of those bands. Cluster analyses divided the plants into two distinct groups considering an upper limit of 22% relative genetic distance. The genetic distances among the plants were between 1 and 39%, in agreement with the variability obseved at the morphological level.

  5. Microsatellite DNA typing for assessment of genetic variability in Tharparkar breed of Indian zebu (Bos indicus) cattle, a major breed of Rajasthan

    Indian Academy of Sciences (India)

    M. Sodhi; M. Mukesh; B. Prakash; S. P. S. Ahlawat; R. C. Sobti

    2006-12-01

    The present study estimates genetic variability with a set of 25 microsatellite markers in a random sample of 50 animals of Tharparkar breed of Indian zebu (Bos indicus) cattle. Tharparkar is a dual-purpose breed, valued for its milk as well as draught utility, and is adapted to the inhospitable Thar desert conditions of Rajasthan typified by summer temperature hovering above 50°C, sparse rainfall and vegetation, and scarcity of even drinking water. The observed number of alleles ranged from 4 (ETH3, ILSTS030, INRA5, INRA63 and MM8) to 11 (HEL9 and ILSTS034), with allelic diversity (average number of observed alleles per locus) of 6.20. Observed and expected heterozygosity ranged from 0.25 (INRA63) to 0.77 (ETH10), and from 0.51 (HEL5 and HAUT27) to 0.88 (HEL9) respectively. Wide range of genetic variability supported the utility of these microsatellite loci in measurement of genetic diversity indices in other Indian cattle breeds too. Various average genetic variability measures, namely allele diversity (6.20), observed heterozygosity (0.57), expected heterozygosity (0.67) and mean polymorphism information content (0.60) values showed substantial within-breed genetic variability in this major breed of Rajasthan, despite accumulated inbreeding as reflected by high average inbreeding coefficient $(F_{\\text{IS}} = 0.39)$. The Tharparkar population has not experienced a bottleneck in the recent past.

  6. The Use of Genetic Variability Analysis of Fusarium oxysporum f. sp. cubense for Breeding Resistance of Banana against Fusarium Wilting Disease

    Directory of Open Access Journals (Sweden)

    Faria Ruhana

    2015-11-01

    Full Text Available Fusarium wilting on banana crop caused by Fusarium oxysporum f. sp. cubense is one of the important disease in banana plant in Indonesia. This disease can cause plant to wilt and die, therefore bringing loss to the banana farmer and entrepreneur. F. oxysporum f. sp. cubense genetic variability analysis techniques can be done by in vitro or in vivo. One of F.oxysporum f. sp. cubense genetic variability analysis techniques by in vitro is RAPD-PCR. In this research, analysis is continued with pathogen test. Genetic variability analysis by in vivo is needed to determine the level of pathogen and the race. The result of genetic variability techniques by RAPD-PCR done by this writer indicates that there is a big relation/link difference between isolats from different island. Isolat from Mojokerto (East Java is 100% genetically different compared to the one from West Sumatera. Later, result of pathogen test shows that Pisang Ambon Kuning is the most resilient compared to Pisang Raja and William Cavendish. Based on the level of pathogen, there are two race grouping, which are race 1 that attacks Pisang Ambon Kuning and race 4 that attacks Pisang Raja and William Cavendish. Scott-Knott analysis on 26 isolats results in no real difference between isolats tested.

  7. Genetics

    DEFF Research Database (Denmark)

    Christensen, Kaare; McGue, Matt

    2016-01-01

    The sequenced genomes of individuals aged ≥80 years, who were highly educated, self-referred volunteers and with no self-reported chronic diseases were compared to young controls. In these data, healthy ageing is a distinct phenotype from exceptional longevity and genetic factors that protect...

  8. Comparison of genetic variability between Czech and foreign isolates of phytopathogenic bacteria Clavibacter michiganensis subsp. sepedonicus by Rep-PCR technique.

    Science.gov (United States)

    Fousek, J; Mráz, I; Petrzik, K

    2002-01-01

    Repetitive-sequence-based polymerase chain reaction (Rep-PCR) method was used for analysis of genetic variability among bacterial populations from different world locations. Collection of 26 Czech and 13 foreign strains of Clavibacter michiganensis subsp. sepedonicus was amplified using BOX primer targeting to repetitive motif occurring in eubacterial genomes. Genetic fingerprints were visually compared and statistically evaluated by cluster analysis. Genetic similarity was estimated to be approximately 80% among all tested strains. Populations of these bacteria seem to be highly homogeneous; potential influence of geographic origin was not confirmed.

  9. Feasibility study on the FAO chicken microsatellite panel to assess genetic variability in the turkey (Meleagris gallopavo

    Directory of Open Access Journals (Sweden)

    Elena Colombo

    2014-12-01

    Full Text Available The aim of this work was to study the feasibility of the Food and Agriculture Organization (FAO microsatellite panel developed for chickens to assess genetic variability in turkeys. Genomic DNA was extracted from a total of 37 blood samples collected from turkey of different breeds [15 Brianzolo (BR; 12 Colli Euganei (EU; 10 Nero d’Italia (NI], and all 31 chicken microsatellite markers recommended by the FAO were tested. The results show that 22 chicken markers out of 31 suggested by FAO guidelines can be applied to turkey populations. In particular, the multiplex groups confirmed in the turkey were the Multiplex Master Mix 1 (ADL0268, ADL0278, LEI0094, MCW0216, MCW0248 and the Master Mix 2 (MCW0034, MCW0069, MCW0081, MCW0222, MCW0295, whereas 13 microsatellites were amplified only under single polymerase chain reaction (PCR conditions. No PCR products were obtained for 9 markers (LEI0166, MCW0020, MCW0078, MCW0080, MCW0104, MCW0123, MCW0248, MCW0284 and MCW0330, which is 29% of the total markers used. A panel of 22 markers was used to assess genetic diversity in three turkey breeds and a total number of 63 alleles were found. Observed (Ho and expected (He heterozygosity and polymorphism information content (PIC values for each microsatellite and the relative mean values were also calculated. The mean values were 0.210, 0.250, 0.203 for Ho; 0.301, 0.348, 0.228 for He; and 0.265, 0.313, 0.199 for PIC in NI, BR and EU, respectively.

  10. Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe.

    Science.gov (United States)

    Blanquart, François; Wymant, Chris; Cornelissen, Marion; Gall, Astrid; Bakker, Margreet; Bezemer, Daniela; Hall, Matthew; Hillebregt, Mariska; Ong, Swee Hoe; Albert, Jan; Bannert, Norbert; Fellay, Jacques; Fransen, Katrien; Gourlay, Annabelle J; Grabowski, M Kate; Gunsenheimer-Bartmeyer, Barbara; Günthard, Huldrych F; Kivelä, Pia; Kouyos, Roger; Laeyendecker, Oliver; Liitsola, Kirsi; Meyer, Laurence; Porter, Kholoud; Ristola, Matti; van Sighem, Ard; Vanham, Guido; Berkhout, Ben; Kellam, Paul; Reiss, Peter; Fraser, Christophe

    2017-06-01

    HIV-1 set-point viral load-the approximately stable value of viraemia in the first years of chronic infection-is a strong predictor of clinical outcome and is highly variable across infected individuals. To better understand HIV-1 pathogenesis and the evolution of the viral population, we must quantify the heritability of set-point viral load, which is the fraction of variation in this phenotype attributable to viral genetic variation. However, current estimates of heritability vary widely, from 6% to 59%. Here we used a dataset of 2,028 seroconverters infected between 1985 and 2013 from 5 European countries (Belgium, Switzerland, France, the Netherlands and the United Kingdom) and estimated the heritability of set-point viral load at 31% (CI 15%-43%). Specifically, heritability was measured using models of character evolution describing how viral load evolves on the phylogeny of whole-genome viral sequences. In contrast to previous studies, (i) we measured viral loads using standardized assays on a sample collected in a strict time window of 6 to 24 months after infection, from which the viral genome was also sequenced; (ii) we compared 2 models of character evolution, the classical "Brownian motion" model and another model ("Ornstein-Uhlenbeck") that includes stabilising selection on viral load; (iii) we controlled for covariates, including age and sex, which may inflate estimates of heritability; and (iv) we developed a goodness of fit test based on the correlation of viral loads in cherries of the phylogenetic tree, showing that both models of character evolution fit the data well. An overall heritability of 31% (CI 15%-43%) is consistent with other studies based on regression of viral load in donor-recipient pairs. Thus, about a third of variation in HIV-1 virulence is attributable to viral genetic variation.

  11. Genetic variability of the mTOR pathway and prostate cancer risk in the European Prospective Investigation on Cancer (EPIC.

    Directory of Open Access Journals (Sweden)

    Daniele Campa

    Full Text Available The mTOR (mammalian target of rapamycin signal transduction pathway integrates various signals, regulating ribosome biogenesis and protein synthesis as a function of available energy and amino acids, and assuring an appropriate coupling of cellular proliferation with increases in cell size. In addition, recent evidence has pointed to an interplay between the mTOR and p53 pathways. We investigated the genetic variability of 67 key genes in the mTOR pathway and in genes of the p53 pathway which interact with mTOR. We tested the association of 1,084 tagging SNPs with prostate cancer risk in a study of 815 prostate cancer cases and 1,266 controls nested within the European Prospective Investigation into Cancer and Nutrition (EPIC. We chose the SNPs (n = 11 with the strongest association with risk (p<0.01 and sought to replicate their association in an additional series of 838 prostate cancer cases and 943 controls from EPIC. In the joint analysis of first and second phase two SNPs of the PRKCI gene showed an association with risk of prostate cancer (OR(allele = 0.85, 95% CI 0.78-0.94, p = 1.3 x 10⁻³ for rs546950 and OR(allele = 0.84, 95% CI 0.76-0.93, p = 5.6 x 10⁻⁴ for rs4955720. We confirmed this in a meta-analysis using as replication set the data from the second phase of our study jointly with the first phase of the Cancer Genetic Markers of Susceptibility (CGEMS project. In conclusion, we found an association with prostate cancer risk for two SNPs belonging to PRKCI, a gene which is frequently overexpressed in various neoplasms, including prostate cancer.

  12. Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe

    Science.gov (United States)

    Wymant, Chris; Cornelissen, Marion; Gall, Astrid; Bakker, Margreet; Bezemer, Daniela; Hall, Matthew; Hillebregt, Mariska; Ong, Swee Hoe; Albert, Jan; Bannert, Norbert; Fellay, Jacques; Fransen, Katrien; Gourlay, Annabelle J.; Grabowski, M. Kate; Gunsenheimer-Bartmeyer, Barbara; Günthard, Huldrych F.; Kivelä, Pia; Kouyos, Roger; Laeyendecker, Oliver; Liitsola, Kirsi; Meyer, Laurence; Porter, Kholoud; Ristola, Matti; van Sighem, Ard; Vanham, Guido; Berkhout, Ben; Kellam, Paul; Reiss, Peter; Fraser, Christophe

    2017-01-01

    HIV-1 set-point viral load—the approximately stable value of viraemia in the first years of chronic infection—is a strong predictor of clinical outcome and is highly variable across infected individuals. To better understand HIV-1 pathogenesis and the evolution of the viral population, we must quantify the heritability of set-point viral load, which is the fraction of variation in this phenotype attributable to viral genetic variation. However, current estimates of heritability vary widely, from 6% to 59%. Here we used a dataset of 2,028 seroconverters infected between 1985 and 2013 from 5 European countries (Belgium, Switzerland, France, the Netherlands and the United Kingdom) and estimated the heritability of set-point viral load at 31% (CI 15%–43%). Specifically, heritability was measured using models of character evolution describing how viral load evolves on the phylogeny of whole-genome viral sequences. In contrast to previous studies, (i) we measured viral loads using standardized assays on a sample collected in a strict time window of 6 to 24 months after infection, from which the viral genome was also sequenced; (ii) we compared 2 models of character evolution, the classical “Brownian motion” model and another model (“Ornstein–Uhlenbeck”) that includes stabilising selection on viral load; (iii) we controlled for covariates, including age and sex, which may inflate estimates of heritability; and (iv) we developed a goodness of fit test based on the correlation of viral loads in cherries of the phylogenetic tree, showing that both models of character evolution fit the data well. An overall heritability of 31% (CI 15%–43%) is consistent with other studies based on regression of viral load in donor–recipient pairs. Thus, about a third of variation in HIV-1 virulence is attributable to viral genetic variation. PMID:28604782

  13. Breeding Plan to Preserve the Genetic Variability of the Kootenai River White Sturgeon, Final Report, December 1993.

    Energy Technology Data Exchange (ETDEWEB)

    Kincaid, Harold L.

    1993-11-01

    Natural reproduction in the Kootenai River white sturgeon population has not produced a successful year class since 1974, resulting in a declining broodstock and 20 consecutive year classes missing from the age-class structure. This report describes a captive breeding plan designed to preserve the remaining genetic variability and to begin rebuilding the natural age class structure. The captive breeding program will use 3--9 females and an equal number of males captured from the Kootenai River each spring. Fish will be spawned in pairs or in diallel mating designs to produce individual families that will be reared separately to maintain family identity. Fish will be marked to identify family and year class before return to the river. Fish should be returned to the river as fall fingerlings to minimize potential adaptation to the hatchery environment Initially, while tagging methods are tested to ensure positive identification after return to the river, it may be necessary to plant fish as spring yearlings. Number of fish planted will be equalized at 5,000 per family if fall fingerlings or 1,000 per family if spring yearlings. Assuming annual survival rates of 20% during the first winter for fall fingerling plants and 50% for years 1--3, and 85% for years 4--20 of all fish planted, the target numbers would yield 7.9 progeny per family or about 4 breeding pairs at age 20. Natural survival in the river environment during the 19+ years from planting to maturity would result in variability in genetic contribution of families to the next broodstock generation. Fish planted per family would be adjusted in future years when actual survival rate information is known. Broodfish will be tagged when captured to minimize multiple spawning of the same fish. implementation of this breeding plan each year for the 20-year generation interval, using 5 different mating pairs each year, will yield an effective population size of 200, or 22.5% of the estimated 1990 population.

  14. Dalmatian Sage (Salvia officinalis L.: A Review of Biochemical Contents, Medical Properties and Genetic Diversity

    Directory of Open Access Journals (Sweden)

    Martina Grdiša

    2015-11-01

    Full Text Available Dalmatian sage (Salvia officinalis L. represents one of the most significant medicinal autochthonous species in flora of eastern Adriatic coast and islands. It is evergreen outcrossing perennial subshrub with short woody stems that branch extensively and violet flowers. Apart from being native to Mediterranean karst of west Balkan and Apenine peninsula it is cultivated in numerous countries worldwide with Mediterranean and temperate continental climate. From the earliest times it has been used in traditional medicine in healing gingiva, mouth cavity and the sore throat, against bacterial and fungal infections, for wound treatment, memory enhancement, for treating common cold, against sweating, stomach inflammation, ulcer formation, etc. Its essential oil has also been used in preservation of food and as spice as it gives both specific aroma and promotes digestion of food. The essential oil is extremely complex mixture of different active ingredients; however, the thujones and camphor are the dominant compounds and are the parameter by which S. officinalis is distinguished from other Salvia species. The great variability of essential oil composition and yield has been detected depending on various factors such as genotype, environmental conditions, phonological stage, plant parts used for the extraction of essential oil and drying procedure. Molecular genetic analysis of S. officinalis is still limited and comprises the use of RAPD markers, AFLP and SSR markers in assessing mostly the genetic variability and structure of wild S. officinalis populations.

  15. Population Genetics and Genetic Variability ofBulinus globosus (Gastropoda: Planorbidae) From the Two Main River Systems in Zimbabwe

    DEFF Research Database (Denmark)

    Mukaratirwa, S.; Siegismund, Hans Redlef; Kristensen, Thomas K.

    1996-01-01

    Bullnus globosus is the only known vector of Schistosoma haematoblum in Zimbabwe. The population genetic structure of this vector snail from the two main river drainage systems, represented by 27 localities, was determined from starch gel lsoenzyme electrophoretic data. Out of 11 enzyme systems...... of ecological factors (drought/desiccation and floods), genetic drift, and seasonal gene flow as the main factors influencing the genetic structure of these populations....

  16. Impact of strong selection for the PrP major gene on genetic variability of four French sheep breeds (Open Access publication

    Directory of Open Access Journals (Sweden)

    Pantano Thais

    2008-11-01

    Full Text Available Abstract Effective selection on the PrP gene has been implemented since October 2001 in all French sheep breeds. After four years, the ARR "resistant" allele frequency increased by about 35% in young males. The aim of this study was to evaluate the impact of this strong selection on genetic variability. It is focussed on four French sheep breeds and based on the comparison of two groups of 94 animals within each breed: the first group of animals was born before the selection began, and the second, 3–4 years later. Genetic variability was assessed using genealogical and molecular data (29 microsatellite markers. The expected loss of genetic variability on the PrP gene was confirmed. Moreover, among the five markers located in the PrP region, only the three closest ones were affected. The evolution of the number of alleles, heterozygote deficiency within population, expected heterozygosity and the Reynolds distances agreed with the criteria from pedigree and pointed out that neutral genetic variability was not much affected. This trend depended on breed, i.e. on their initial states (population size, PrP frequencies and on the selection strategies for improving scrapie resistance while carrying out selection for production traits.

  17. Algorithm for solving the bi-level decision making problem with continuous variables in the upper level based on genetic algorithm

    Institute of Scientific and Technical Information of China (English)

    XIAO Jian; CHEN Yi-hua

    2005-01-01

    Based on genetic algorithms, a solution algorithm is presented for the bi-level decision making problem with continuous variables in the upper level in accordance with the bi-level decision making principle. The algorithm is compared with Monte Carlo simulated annealing algorithm, and its feasibility and effectiveness are verified with two calculating examples.

  18. Evaluation of genetic effect of NOS3 and G×E interaction on the variability of serum bilirubin in a Han Chinese population.

    Science.gov (United States)

    Yao, Yingshui; Fang, Zhengmei; Yang, Song; Zhao, Hailong; Chen, Yanchun; Jin, Yuelong; Zhao, Xianghai; Zhu, Lijun; Tian, Yuanrui; Shen, Chong

    2017-08-08

    Bilirubin was shown to be related to the generation and functional exertion of endothelial nitric oxide synthase (eNOS) whilst the genetic effect of NOS3 on bilirubin variability was rarely reported. Herein we assessed the associations of three single nucleotide polymorphisms (SNPs) of NOS3 (rs4496877, rs1808593, and rs3918186) with bilirubin elevation in 2077 adults. The results showed that rs1808593 was significantly associated with bilirubin elevation, and odds ratios (ORs) of dominant model for the elevation of total bilirubin (TBIL), direct bilirubin (DBIL), and indirect bilirubin (IDBIL) were 0.837, 0.821 and 0.754, respectively (P NOS3 harbors the genetic susceptibility to the bilirubin elevation. Age, gender, smoking, and drinking could be involved in the genetic modification of NOS3 on the bilirubin variability. Copyright © 2017. Published by Elsevier Inc.

  19. Genetic rearrangements of variable di-residue (RVD)-containing repeat arrays in a baculoviral TALEN system.

    Science.gov (United States)

    Lau, Cia-Hin; Zhu, Haibao; Tay, Johan Chin-Kang; Li, Zhendong; Tay, Felix Chang; Chen, Can; Tan, Wee-Kiat; Du, Shouhui; Sia, Vic-Ki; Phang, Rui-Zhe; Tang, Shin-Yi; Yang, Chiyun; Chi, Zhixia; Liang, Chieh-Ching; Ning, Er; Wang, Shu

    2014-01-01

    Virus-derived gene transfer vectors have been successfully employed to express the transcription activator-like effector nucleases (TALENs) in mammalian cells. Since the DNA-binding domains of TALENs consist of the variable di-residue (RVD)-containing tandem repeat modules and virus genome with repeated sequences is susceptible to genetic recombination, we investigated several factors that might affect TALEN cleavage efficiency of baculoviral vectors. Using a TALEN system designed to target the AAVS1 locus, we observed increased sequence instability of the TALE repeat arrays when a higher multiplicity of infection (MOI) of recombinant viruses was used to produce the baculoviral vectors. We also detected more deleterious mutations in the TALE DNA-binding domains when both left and right TALEN arms were placed into a single expression cassette as compared to the viruses containing one arm only. The DNA sequence changes in the domains included deletion, addition, substitution, and DNA strand exchange between the left and right TALEN arms. Based on these observations, we have developed a protocol using a low MOI to produce baculoviral vectors expressing TALEN left and right arms separately. Cotransduction of the viruses produced by this optimal protocol provided an improved TALEN cleavage efficiency and enabled effective site-specific transgene integration in human cells.

  20. Effect of temperature on the morphological characteristics of Botrytis cinerea and its correlated with the genetic variability

    Institute of Scientific and Technical Information of China (English)

    Jorge G Fernndez; Martn A Fernndez-Baldo; Gabriela Sansone; Viviana Calvente; Delia Benuzzi; Eloy Salinas; Julio Raba; Mara I Sanz

    2014-01-01

    Objective: To study the effect of temperature on the morphological characteristics of Botrytiscinerea (B. cinerea) and its correlated with the genetic variability. B. cinerea is a plant-pathogenic fungus that produces the disease known as grey mould in a wide variety of agriculturally important hosts in many countries.Methods:Six strains from different host collected have been isolated and characterized by several methods as mycelial growth, fungicide resistance, pathogenicity and the effects of the temperature. Also was analyzed by PCR and distinguished by the presence or absence of transposable elements.Results:Results showed that clear morphological differences exist between strains at the temperature of 4, 12 and 28 °C. All strains analyzed molecularly were classified as Group II (transposa-type). Demonstrating a negative correlation between mycelial growth and other characteristics as the fungicide resistance and pathogenicity. Lastly, it is difficult to establish relationships phenotypic and genotypic between strains of B. cinerea.Conclusions:The results indicated that the mycelial growth, resistance at fungicide and pathogenicity are independent of the characteristics molecular, however, are dependent of a factor such as temperature.

  1. Genetic variability of the phloem sap metabolite content of maize (Zea mays L.) during the kernel-filling period.

    Science.gov (United States)

    Yesbergenova-Cuny, Zhazira; Dinant, Sylvie; Martin-Magniette, Marie-Laure; Quilleré, Isabelle; Armengaud, Patrick; Monfalet, Priscilla; Lea, Peter J; Hirel, Bertrand

    2016-11-01

    Using a metabolomic approach, we have quantified the metabolite composition of the phloem sap exudate of seventeen European and American lines of maize that had been previously classified into five main groups on the basis of molecular marker polymorphisms. In addition to sucrose, glutamate and aspartate, which are abundant in the phloem sap of many plant species, large quantities of aconitate and alanine were also found in the phloem sap exudates of maize. Genetic variability of the phloem sap composition was observed in the different maize lines, although there was no obvious relationship between the phloem sap composition and the five previously classified groups. However, following hierarchical clustering analysis there was a clear relationship between two of the subclusters of lines defined on the basis of the composition of the phloem sap exudate and the earliness of silking date. A comparison between the metabolite contents of the ear leaves and the phloem sap exudates of each genotype, revealed that the relative content of most of the carbon- and nitrogen-containing metabolites was similar. Correlation studies performed between the metabolite content of the phloem sap exudates and yield-related traits also revealed that for some carbohydrates such as arabitol and sucrose there was a negative or positive correlation with kernel yield and kernel weight respectively. A posititive correlation was also found between kernel number and soluble histidine. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  2. Molecular characterization and genetic diversity analysis β-glucan content variability in grain of oat (Avena sativa L.

    Directory of Open Access Journals (Sweden)

    Đukić Nevena H.

    2014-01-01

    Full Text Available In grain of ten genetically divergent oat cultivars (Merkur, Minor Abed, Flaming-Kurz, Nuptiele, Prode, Pellerva, Emperor, Astor, Osmo, Simo the variability β-glucan content were investigated. The different value of content of β-glucan was found. Among analyzed oat cultivars, the highest β- glucan contents had Pellerva (6.597%, while the least had Simo (2.971%. The contents of β-glucans were determined by ICC standard Method No 168. The value of β-glucans varied and indicated the differences and similarities between analysed cultivars. The degree of cultivar similarity was determined by dendrogram on which was discriminated two clusters of similar cultivars toward to contents of β-glucan . Within cluster 1, a small group of oats, are five cultivars with small distance (Merkur, Minor Abed, Flamings-Kurz, Nuptiele and Prode. The highest similarity in the range of 88 or the least distance in the range of 12. Within cluster 2 was four oat cultivars (Emperor, Astor, Osmo, Pellerva in which the least differences was between Emperor and Astor with average distance in range 27. Cluster 1 and cluster 2 differed with an average distance of 63. The cultivar Simo expressed the greatest distance to all analysed oat cultivars grouped in two clusters. [Projekat Ministarstva nauke Republike Srbije, br. TR 31092

  3. Effect of temperature on the morphological characteristics of Botrytis cinerea and its correlated with the genetic variability

    Directory of Open Access Journals (Sweden)

    Jorge G Fernández

    2014-07-01

    Full Text Available Objective: To study the effect of temperature on the morphological characteristics of Botrytis cinerea (B. cinerea and its correlated with the genetic variability. B. cinerea is a plant-pathogenic fungus that produces the disease known as grey mould in a wide variety of agriculturally important hosts in many countries. Methods: Six strains from different host collected have been isolated and characterized by several methods as mycelial growth, fungicide resistance, pathogenicity and the effects of the temperature. Also was analyzed by PCR and distinguished by the presence or absence of transposable elements. Results: Results showed that clear morphological differences exist between strains at the temperature of 4, 12 and 28 °C. All strains analyzed molecularly were classified as Group II (transposa-type. Demonstrating a negative correlation between mycelial growth and other characteristics as the fungicide resistance and pathogenicity. Lastly, it is difficult to establish relationships phenotypic and genotypic between strains of B. cinerea. Conclusions: The results indicated that the mycelial growth, resistance at fungicide and pathogenicity are independent of the characteristics molecular, however, are dependent of a factor such as temperature.

  4. Neither protogynous nor obligatory out-crossed: pollination biology and breeding system of the European Red List Fritillaria meleagris L. (Liliaceae).

    Science.gov (United States)

    Zych, M; Stpiczyńska, M

    2012-03-01

    For 4 years we studied pollination biology and breeding system of the critically endangered, Red List plant Fritillaria meleagris L. (Liliaceae), in the larger of the two remaining populations of the plant in SE Poland. Our observations indicated that, contrary to literature data, the species is not dichogamous nor is it obligatorily out-crossing. Selfing, although rare in natural populations, results in fully developed seeds. Flowers are visited by several insect species, mostly social and solitary bees. In spite of extremely low visitation rates to this early spring-flowering plant, the species is not pollen limited. Although the largest pollen loads are transferred by solitary bees, the key pollinators are bumblebees (mostly the most common species, Bombus terrestris and B. lapidarius) due to their seasonal and floral constancy, and tolerance of bad weather conditions. The current decline of the studied population seems not to be related to the species' pollination or breeding systems but to plant habitat loss. It is suggested, however, that in smaller populations, the species' dependence on generally rare pollinators and largely out-crossed breeding system may accelerate local extinction. © 2011 German Botanical Society and The Royal Botanical Society of the Netherlands.

  5. Speech-Language Pathologists' Knowledge of Genetics: Perceived Confidence, Attitudes, Knowledge Acquisition and Practice-Based Variables

    Science.gov (United States)

    Tramontana, G. Michael; Blood, Ingrid M.; Blood, Gordon W.

    2013-01-01

    The purpose of this study was to determine (a) the general knowledge bases demonstrated by school-based speech-language pathologists (SLPs) in the area of genetics, (b) the confidence levels of SLPs in providing services to children and their families with genetic disorders/syndromes, (c) the attitudes of SLPs regarding genetics and communication…

  6. Experimental and genetic analyses reveal that inbreeding depression declines with increased self-fertilization among populations of a coastal dune plant.

    Science.gov (United States)

    Dart, S; Eckert, C G

    2013-03-01

    Theory predicts that inbreeding depression (ID) should decline via purging in self-fertilizing populations. Yet, intraspecific comparisons between selfing and outcrossing populations are few and provide only mixed support for this key evolutionary process. We estimated ID for large-flowered (LF), predominantly outcrossing vs. small-flowered (SF), predominantly selfing populations of the dune endemic Camissoniopsis cheiranthifolia by comparing selfed and crossed progeny in glasshouse environments differing in soil moisture, and by comparing allozyme-based estimates of the proportion of seeds selfed and inbreeding coefficient of mature plants. Based on lifetime measures of dry mass and flower production, ID was stronger in nine LF populations [mean δ = 1-(fitness of selfed seed/fitness of outcrossed seed) = 0.39] than 16 SF populations (mean δ = 0.03). However, predispersal ID during seed maturation was not stronger for LF populations, and ID was not more pronounced under simulated drought, a pervasive stress in sand dune habitat. Genetic estimates of δ were also higher for four LF (δ = 1.23) than five SF (δ = 0.66) populations; however, broad confidence intervals around these estimates overlapped. These results are consistent with purging, but selective interference among loci may be required to maintain strong ID in partially selfing LF populations, and trade-offs between selfed and outcrossed fitness are likely required to maintain outcrossing in SF populations.

  7. A sex-averaged genetic linkage map in coastal Douglas-fir (Pseudotsuga menziesii [Mirb] Franco var menziesii) based on RFLP and RAPD markers

    Science.gov (United States)

    K.D. Jermstad; D.L. Bassoni; N.C. Wheeler; D.B. Neale

    1998-01-01

    We have constructed a sex-averaged genetic linkage map in coastal Douglas-fir ( Pseudotsuga menziesii [Mirb.] Franco var menziesii) using a three-generation outcrossed pedigree and molecular markers. Our research objectives are to learn about genome organization and to identify markers associated with adaptive traits. The map...

  8. Genetic variability in chronic irradiated plant populations - Polymorphism and activity of antioxidant enzymes in chronic irradiated plant populations

    Energy Technology Data Exchange (ETDEWEB)

    Volkova, Polina Y.; Geras' kin, Stanislav A. [Russian Institute of Agricultural Radiology and Agroecology, 249030, Obninsk, Kievskoe shosse 109 km (Russian Federation)

    2014-07-01

    Introduction: The gene pool of natural population is constantly changing in order to provide the greatest fitness at this time. Ability of population to adapt to changing environmental conditions depends on genetic polymorphism of traits which are operates by selection. Chronic stress exposure can change amount or structure intra-population variability. Therefore, it is necessary to analyze the relationships between genetic polymorphism and stress factors, such as radiation exposure. This studies my assist in the development of new bio-indication methods. Materials and methods: Studying sites: Bryansk region is the most contaminated region of Russia as a result of Chernobyl accident. The initial activity by {sup 137}Cs on this territory reached 1 MBq/m{sup 2} above surface. Our study conducted in several districts of Bryansk region, which are characterized the most dose rate. Experimental sites similar to climate characteristics, stand of trees is homogeneous, pine trees take up a significant part of phytocenosis. Heavy metals content in soils and cones be within background. Dose rates vary from 0.14 to 130 mGy/year. Object: Pinus sylvestris L.,the dominant tree species in North European and Asian boreal forests. Scots pine has a long maturation period (18-20 month), which means that significant DNA damage may accumulate in the undifferentiated stem cells, even at low doses (or dose rates) during exposure to low concentrations of contaminants Isozyme analysis: We evaluated isozyme polymorphism of three antioxidant enzymes: superoxide dismutase, glutatione reductase and glutatione peroxidase. Analysis of enzymes activities: We chose key enzymes of antioxidant system for this experiment: superoxide dismutase, catalase and peroxidase. Results and conclusions: We estimated frequency of each allele in reference and experimental populations. based It was showed that frequency of rare alleles increase in chronic irradiated populations, i.e. increase the sampling variance

  9. Genetic variability within the cholesterol lowering pathway and the effectiveness of statins in reducing the risk of MI.

    Science.gov (United States)

    Peters, Bas J M; Pett, Helmi; Klungel, Olaf H; Stricker, Bruno H Ch; Psaty, Bruce M; Glazer, Nicole L; Wiggins, Kerri L; Bis, Josh C; de Boer, Anthonius; Maitland-van der Zee, Anke-Hilse

    2011-08-01

    Genetic variability has been shown to affect statin responsiveness. Participants from the Utrecht Cardiovascular Pharmacogenetics (UCP) studies were enrolled from a population-based registry of pharmacy records linked to hospital discharge records (PHARMO) to investigate tagging SNPs within candidate genes involved in the cholesterol lowering pathway for modification of the effectiveness of statins in reducing the risk of myocardial infarction (MI). Patients who received a prescription for an antihypertensive drug and/or had hypercholesterolemia were selected from the PHARMO database. We designed a nested case-control study in which cases were hospitalized for MI and controls were not. Patients were contacted through their community pharmacies. For this study, only hypercholesterolemic participants were selected. Logistic regression analysis was used to investigate pharmacogenetic interactions. The Heart and Vascular Health Study (HVH) was used to replicate findings from UCP. The study population included 668 cases and 1217 controls. We selected 231 SNPs of which 209 SNPs in 27 genes passed quality control. Ten SNPs in eight genes were found to influence the effectiveness of statins in UCP, of which the most significant interaction was found with SCARB1 rs4765615. Other genes that reached statistical significance (p<0.05) included two SNPs in PCSK9 (rs10888896 and rs505151 (E670G)), two SNPs in ABCG5 (rs4245786 and rs1864815), LIPC rs16940379, ABCA1 rs4149264, PPARG rs2972164, LRP1 rs715948, and SOAT1 rs2493121. None of the total of 5 SNPs that were available for replication in HVH reached statistical significance. In conclusion, ten SNPs were found to modify the effectiveness of statins in reducing the risk of MI in the UCP study. Five were also tested in the HVH study, but no interactions reached statistical significance.

  10. Genetic Variability of Stolbur Phytoplasma in Hyalesthes obsoletus (Hemiptera: Cixiidae) and its Main Host Plants in Vineyard Agroecosystems.

    Science.gov (United States)

    Landi, Lucia; Riolo, Paola; Murolo, Sergio; Romanazzi, Gianfranco; Nardi, Sandro; Isidoro, Nunzio

    2015-08-01

    Bois noir is an economically important grapevine yellows that is induced by 'Candidatus Phytoplasma solani' and principally vectored by the planthopper Hyalesthes obsoletus Signoret (Hemiptera: Cixiidae). This study explores the 'Ca. P. solani' genetic variability associated to the nettle-H. obsoletus and bindweed-H. obsoletus systems in vineyard agroecosystems of the central-eastern Italy. Molecular characterization of 'Ca. P. solani' isolates was carried out using polymerase chain reaction/restriction fragment length polymorphism to investigate the nonribosomal vmp1 gene. Seven phytoplasma vmp-types were detected among the host plants- and insect-associated field-collected samples. The vmp1 gene showed the highest polymorphism in the bindweed-H. obsoletus system, according to restriction fragment length polymorphism analysis, which is in agreement with nucleotide sequence analysis. Five vmp-types were associated with H. obsoletus from bindweed, of which one was solely restricted to planthoppers, with one genotype also in planthoppers from nettle. Type V12 was the most prevalent in both planthoppers and bindweed. H. obsoletus from nettle harbored three vmp-types, of which V3 was predominant. V3 was the only type detected for nettle. Our data demonstrate that planthoppers might have acquired some 'Ca. P. solani' profiles from other plant hosts before landing on nettle or bindweed. Overall, the different vmp1 gene rearrangements observed in these two plant hosts-H. obsoletus systems might represent different adaptations of the pathogen to the two host plants. Molecular information about the complex of vmp-types provides useful data for better understanding of Bois noir epidemiology in vineyard agroecosystem. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  11. Genetic dissection of nitrogen nutrition in pea through a QTL approach of root, nodule, and shoot variability.

    Science.gov (United States)

    Bourion, Virginie; Rizvi, Syed Masood Hasan; Fournier, Sarah; de Larambergue, Henri; Galmiche, Fabien; Marget, Pascal; Duc, Gérard; Burstin, Judith

    2010-06-01

    Pea (Pisum sativum L.) is the third most important grain legume worldwide, and the increasing demand for protein-rich raw material has led to a great interest in this crop as a protein source. Seed yield and protein content in crops are strongly determined by nitrogen (N) nutrition, which in legumes relies on two complementary pathways: absorption by roots of soil mineral nitrogen, and fixation in nodules of atmospheric dinitrogen through the plant-Rhizobium symbiosis. This study assessed the potential of naturally occurring genetic variability of nodulated root structure and functioning traits to improve N nutrition in pea. Glasshouse and field experiments were performed on seven pea genotypes and on the 'Cameor' x 'Ballet' population of recombinant inbred lines selected on the basis of parental contrast for root and nodule traits. Significant variation was observed for most traits, which were obtained from non-destructive kinetic measurements of nodulated root and shoot in pouches, root and shoot image analysis, (15)N quantification, or seed yield and protein content determination. A significant positive relationship was found between nodule establishment and root system growth, both among the seven genotypes and the RIL population. Moreover, several quantitative trait loci for root or nodule traits and seed N accumulation were mapped in similar locations, highlighting the possibility of breeding new pea cultivars with increased root system size, sustained nodule number, and improved N nutrition. The impact on both root or nodule traits and N nutrition of the genomic regions of the major developmental genes Le and Af was also underlined.

  12. Genetic variability of Chlamydophila abortus strains assessed by PCR-RFLP analysis of polymorphic membrane protein-encoding genes.

    Science.gov (United States)

    Sait, Michelle; Clark, Ewan M; Wheelhouse, Nicholas; Spalding, Lucy; Livingstone, Morag; Sachse, Konrad; Markey, Bryan K; Magnino, Simone; Siarkou, Victoria I; Vretou, Evangelia; Caro, María R; Yaga, Raja; Lainson, F Alex; Smith, David G E; Wright, Frank; Longbottom, David

    2011-08-05

    This study used PCR-RFLP to investigate the genetic variability of pmp-encoding genes from fifty-two Chlamydophila abortus (C. abortus) strains originating from abortion cases from various geographical regions and host species. Six primer pairs were used to PCR-amplify DNA fragments encoding eighteen pmps. PCR products were digested using four restriction endonucleases and Bayesian methodologies were used to compare RFLP profiles and assign strains to a RFLP genotype. Strains could be assigned to 2 genotypes in the region encoding pmp18D, 3 genotypes in the regions encoding pmp1A-pmp2B, pmp3E-pmp6H and pmp11G-pmp15G, 4 genotypes in the region encoding pmp7G-pmp10G and 5 genotypes in the region encoding pmp16G-pmp17G. In all regions, the majority of strains (88.4-96.1%) had the same genotype as the reference strain S26/3. No correlation could be made between genotype, host species or geographical origin except for the two variant Greek strains, LLG and POS, which formed a discrete genotype in all pmp-encoding regions except pmp18D. Relative rates of evolution calculated for each pmp-encoding gene locus suggest that differing selective pressures and functional constraints may exist on C. abortus polymorphic membrane proteins. These findings suggest that although intraspecies heterogeneity of pmp-encoding genes in C. abortus is low, the sequence heterogeneity should be an important consideration when using pmps as the basis for novel diagnostics or vaccine development.

  13. Population Genetics and Genetic Variability ofBulinus globosus (Gastropoda: Planorbidae) From the Two Main River Systems in Zimbabwe

    DEFF Research Database (Denmark)

    Mukaratirwa, S.; Siegismund, Hans Redlef; Kristensen, Thomas K.;

    1996-01-01

    Bullnus globosus is the only known vector of Schistosoma haematoblum in Zimbabwe. The population genetic structure of this vector snail from the two main river drainage systems, represented by 27 localities, was determined from starch gel lsoenzyme electrophoretic data. Out of 11 enzyme systems s...... of ecological factors (drought/desiccation and floods), genetic drift, and seasonal gene flow as the main factors influencing the genetic structure of these populations.......Bullnus globosus is the only known vector of Schistosoma haematoblum in Zimbabwe. The population genetic structure of this vector snail from the two main river drainage systems, represented by 27 localities, was determined from starch gel lsoenzyme electrophoretic data. Out of 11 enzyme systems...

  14. Firefly algorithm versus genetic algorithm as powerful variable selection tools and their effect on different multivariate calibration models in spectroscopy: A comparative study

    Science.gov (United States)

    Attia, Khalid A. M.; Nassar, Mohammed W. I.; El-Zeiny, Mohamed B.; Serag, Ahmed

    2017-01-01

    For the first time, a new variable selection method based on swarm intelligence namely firefly algorithm is coupled with three different multivariate calibration models namely, concentration residual augmented classical least squares, artificial neural network and support vector regression in UV spectral data. A comparative study between the firefly algorithm and the well-known genetic algorithm was developed. The discussion revealed the superiority of using this new powerful algorithm over the well-known genetic algorithm. Moreover, different statistical tests were performed and no significant differences were found between all the models regarding their predictabilities. This ensures that simpler and faster models were obtained without any deterioration of the quality of the calibration.

  15. Genetic variability of Passiflora spp. from commercial fields in the Federal District, Brazil Variabilidade genética de Passiflora spp. em plantios comerciais do Distrito Federal, Brasil

    Directory of Open Access Journals (Sweden)

    Ana Paula Gomes de Castro

    2011-06-01

    Full Text Available This study aimed to characterize the genetic variability in commercial accessions of passion fruit from the Federal District, Brazil, by RAPD markers. Genetic analyses were done with leaf samples of 30 accessions. DNA samples were amplified by RAPD technique, and respective markers converted into a binary matrix, from which the genetic distances between the accessions were estimated. Clustering analyis based on genetic distances allowed to detect a wide range of genetic variabillity among the accessions of sour passion fruit, and to separate them from the two sweet passion fruit. The graphical positioning of 'BRS Ouro Vermelho' confirms its potential to improve the genetic variability of commercial varieties of sour passion fruit. Dispersal of genetic distances among commercial accessions of sour passion fruit supports evidence for different genetic origins of the materials planted in the Federal District. The verified genetic variability indicates the potential success of future breeding programs for this region.Este estudo teve como objetivo caracterizar a variabilidade genética de acessos de maracujá comerciais no Distrito Federal por meio de marcadores RAPD. Análises genéticas foram feitas com amostras foliares de 30 acessos. As amostras de DNA foram amplificadas pela técnica de RAPD e os respectivos marcadores convertidos em uma matriz binária, a partir da qual as distâncias genéticas entre os acessos foram estimadas. Análises de agrupamento baseadas em distâncias genéticas permitiram detectar uma ampla gama de variabilidade genética entre os acessos de maracujazeiro-azedo, bem como para separá-los dos dois de maracujazeiro-doce. O posicionamento gráfico de 'BRS Ouro Vermelho' confirma a sua importante contribuição para aumentar a variabilidade genética das atuais variedades comerciais de maracujazeiro-azedo. A dispersão das distâncias genéticas entre os acessos comerciais de maracujazeiro-azedo suportam as evid

  16. Genetic diversity and gene flow in the morphologically variable, rare endemics Begonia dregei and Begonia homonyma (Begoniaceae).

    Science.gov (United States)

    Matolweni, L O; Balkwill, K; McLellan, T

    2000-03-01

    Begonia dregei and B. homonyma (Begoniaceae), rare plants endemic to coastal forests of eastern South Africa, are two closely related species with high levels of variation among populations in the shape of leaves. Distribution of genetic variation and genetic relatedness were investigated in 12 populations of B. dregei and seven of B. homonyma using polyacrylamide gel electrophoresis. Twelve of the 15 enzyme loci examined were polymorphic, but only seven loci were polymorphic within at least one population. Genetic diversity measures indicated that the among-population gene differentiation represents >90% of the total genetic component in both species considered individually or combined. This indicated restricted gene flow, consistent with the limited dispersal abilities of Begonia generally and the ancient separation of isolated forest patches. Genetic distances among populations are much higher than usually found within species. Allozyme data provide no support for the recognition of B. dregei and B. homonyma as distinct species.

  17. Genetic variability among natural populations of Zaprionus indianus (Drosophilidae) in the States of São Paulo and Minas Gerais, Brazil.

    Science.gov (United States)

    Braganholi, D; Bélo, M; Bertoni, B W; Fachin, A L; Beleboni, R O; Zingaretti, S M

    2010-01-01

    Random amplified polymorphic DNA (RAPD) was used to detect polymorphisms among Zaprionus indianus fly populations collected from six municipalities in the States of São Paulo and Minas Gerais, Brazil. This species is an important, recently introduced fruit fly pest of figs and other fruit. Among 21 primers, 16 produced 73 reproducible polymorphic fragments; primer AM-9 produced the greatest number of polymorphic bands (nine), with 52% genetic variability among populations. Genetic divergence analysis of the Z. indianus populations demonstrated two major groups, named Western and Eastern groups. There was greater gene flow within than between groups. The correlation coefficient for genetic and geographic distances (Mantel test) was significant, demonstrating isolation by distance.

  18. Genetic variability and population structure in loci related to milk production traits in native Argentine Creole and commercial Argentine Holstein cattle

    Directory of Open Access Journals (Sweden)

    Golijow C.D.

    1999-01-01

    Full Text Available Many cattle breeds have been subjected to high selection pressure for production traits. Consequently, population genetic structure and allelic distribution could differ in breeds under high selection pressure compared to unselected breeds. Analysis of k-casein, aS1-casein and prolactin gene frequencies was made for Argentine Creole (AC and Argentine Holstein (AH cattle herds. The calculated FST values measured the degree of genetic differentiation of subpopulations, depending on the variances of gene frequencies.The AC breed had considerably more variation among herds at the aS1-casein and k-casein loci. Conservation strategies should consider the entire AC population in order to maintain the genetic variability found in this native breed.

  19. Genetics and consequences of crop domestication.

    Science.gov (United States)

    Flint-Garcia, Sherry A

    2013-09-01

    Phenotypic variation has been manipulated by humans during crop domestication, which occurred primarily between 3000 and 10000 years ago in the various centers of origin around the world. The process of domestication has profound consequences on crops, where the domesticate has moderately reduced genetic diversity relative to the wild ancestor across the genome, and severely reduced diversity for genes targeted by domestication. The question that remains is whether reduction in genetic diversity has affected crop production today. A case study in maize ( Zea mays ) demonstrates the application of understanding relationships between genetic diversity and phenotypic diversity in the wild ancestor and the domesticate. As an outcrossing species, maize has tremendous genetic variation. The complementary combination of genome-wide association mapping (GWAS) approaches, large HapMap data sets, and germplasm resources is leading to important discoveries of the relationship between genetic diversity and phenotypic variation and the impact of domestication on trait variation.

  20. Genetic Variability of Spodoptera frugiperda Smith (Lepidoptera: Noctuidae) Populations from Latin America Is Associated with Variations in Susceptibility to Bacillus thuringiensis Cry Toxins▿

    Science.gov (United States)

    Monnerat, Rose ; Martins, Erica; Queiroz, Paulo; Ordúz, Sergio; Jaramillo, Gabriela; Benintende, Graciela ; Cozzi, Jorge; Real, M. Dolores; Martinez-Ramirez, Amparo; Rausell, Carolina ; Cerón, Jairo; Ibarra, Jorge E.; Del Rincon-Castro, M. Cristina; Espinoza, Ana M. ; Meza-Basso, Luis; Cabrera, Lizbeth; Sánchez, Jorge; Soberon, Mario ; Bravo, Alejandra

    2006-01-01

    Bacillus thuringiensis strains isolated from Latin American soil samples that showed toxicity against three Spodoptera frugiperda populations from different geographical areas (Mexico, Colombia, and Brazil) were characterized on the basis of their insecticidal activity, crystal morphology, sodium dodecyl sulfate-polyacrylamide gel electrophoresis of parasporal crystals, plasmid profiles, and cry gene content. We found that the different S. frugiperda populations display different susceptibilities to the selected B. thuringiensis strains and also to pure preparations of Cry1B, Cry1C, and Cry1D toxins. Binding assays performed with pure toxin demonstrated that the differences in the toxin binding capacities of these insect populations correlated with the observed differences in susceptibility to the three Cry toxins analyzed. Finally, the genetic variability of the three insect populations was analyzed by random amplification of polymorphic DNA-PCR, which showed significant genetic diversity among the three S. frugiperda populations analyzed. The data presented here show that the genetic variability of S. frugiperda populations should be carefully considered in the development of insect pest control strategies, including the deployment of genetically modified maize in different geographical regions. PMID:16936049

  1. Genetic variability of Spodoptera frugiperda Smith (Lepidoptera: Noctuidae) populations from Latin America is associated with variations in susceptibility to Bacillus thuringiensis cry toxins.

    Science.gov (United States)

    Monnerat, Rose; Martins, Erica; Queiroz, Paulo; Ordúz, Sergio; Jaramillo, Gabriela; Benintende, Graciela; Cozzi, Jorge; Real, M Dolores; Martinez-Ramirez, Amparo; Rausell, Carolina; Cerón, Jairo; Ibarra, Jorge E; Del Rincon-Castro, M Cristina; Espinoza, Ana M; Meza-Basso, Luis; Cabrera, Lizbeth; Sánchez, Jorge; Soberon, Mario; Bravo, Alejandra

    2006-11-01

    Bacillus thuringiensis strains isolated from Latin American soil samples that showed toxicity against three Spodoptera frugiperda populations from different geographical areas (Mexico, Colombia, and Brazil) were characterized on the basis of their insecticidal activity, crystal morphology, sodium dodecyl sulfate-polyacrylamide gel electrophoresis of parasporal crystals, plasmid profiles, and cry gene content. We found that the different S. frugiperda populations display different susceptibilities to the selected B. thuringiensis strains and also to pure preparations of Cry1B, Cry1C, and Cry1D toxins. Binding assays performed with pure toxin demonstrated that the differences in the toxin binding capacities of these insect populations correlated with the observed differences in susceptibility to the three Cry toxins analyzed. Finally, the genetic variability of the three insect populations was analyzed by random amplification of polymorphic DNA-PCR, which showed significant genetic diversity among the three S. frugiperda populations analyzed. The data presented here show that the genetic variability of S. frugiperda populations should be carefully considered in the development of insect pest control strategies, including the deployment of genetically modified maize in different geographical regions.

  2. MODEL-ASSISTED ESTIMATION OF THE GENETIC VARIABILITY IN PHYSIOLOGICAL PARAMETERS RELATED TO TOMATO FRUIT GROWTH UNDER CONTRASTED WATER CONDITIONS

    Directory of Open Access Journals (Sweden)

    Dario Constantinescu

    2016-12-01

    Full Text Available Drought stress is a major abiotic stres threatening plant and crop productivity. In case of fleshy fruits, understanding Drought stress is a major abiotic stress threatening plant and crop productivity. In case of fleshy fruits, understanding mechanisms governing water and carbon accumulations and identifying genes, QTLs and phenotypes, that will enable trade-offs between fruit growth and quality under Water Deficit (WD condition is a crucial challenge for breeders and growers. In the present work, 117 recombinant inbred lines of a population of Solanum lycopersicum were phenotyped under control and WD conditions. Plant water status, fruit growth and composition were measured and data were used to calibrate a process-based model describing water and carbon fluxes in a growing fruit as a function of plant and environment. Eight genotype-dependent model parameters were estimated using a multiobjective evolutionary algorithm in order to minimize the prediction errors of fruit dry and fresh mass throughout fruit development. WD increased the fruit dry matter content (up to 85 % and decreased its fresh weight (up to 60 %, big fruit size genotypes being the most sensitive. The mean normalized root mean squared errors of the predictions ranged between 16-18 % in the population. Variability in model genotypic parameters allowed us to explore diverse genetic strategies in response to WD. An interesting group of genotypes could be discriminated in which i the low loss of fresh mass under WD was associated with high active uptake of sugars and low value of the maximum cell wall extensibility, and ii the high dry matter content in control treatment (C was associated with a slow decrease of mass flow. Using 501 SNP markers genotyped across the genome, a QTL analysis of model parameters allowed to detect three main QTLs related to xylem and phloem conductivities, on chromosomes 2, 4 and 8. The model was then applied to design ideotypes with high dry matter

  3. Prevalence and Genetic Variability in Capsid L1 Gene of Rare Human Papillomaviruses (HPV Found in Cervical Lesions of Women from North-East Brazil

    Directory of Open Access Journals (Sweden)

    Ana Pavla Almeida Diniz Gurgel

    2013-01-01

    Full Text Available The aim of this study was to examine the prevalence and genetic variability of the capsid L1 gene of rare HPV genotypes that were found in the cervical lesions of women from North-East Brazil. A total number of 263 patients were included in this study. HPV detection was performed using PCR followed by direct sequencing of MY09/11, as well as type-specific PCR to detect the Alpha-9 species. Epitope prediction was performed to determine whether or not the genetic variants are inserted in B-cell and T-cell epitopes. The prevalence of rare HPV types in cervical lesions was found to be 9.47%. The rare HPV genotypes that were detected were HPV-53, 54, 56, 61, 62, 66, 70, and 81. The genetic variability in the L1 gene of rare HPV types involved thirty nucleotide changes, eight of which were detected for the first time in this study. Moreover, some of these variants are embedded in B-cell or T-cell epitope regions. The results of this research suggest that rare HPV types might be involved in cervical lesions and some of these variants can be found in B-cell and T-cell epitopes. Data on the prevalence and variability of rare HPV types will assist in clarifying the role of these viruses in carcinogenesis.

  4. A unifying study of phenotypic and molecular genetic variability in natural populations of Anadenanthera colubrina var. cebil from Yungas and Paranaense biogeographic provinces in Argentina

    Indian Academy of Sciences (India)

    María Victoria García; Kathleen Prinz; María Eugenia Barrandeguy; Marcos Miretti; Reiner Finkeldey

    2014-04-01

    Anadenanthera colubrina var. cebil is a discontinuously distributed native tree species in South American subtropical forests. Thirteen quantitative traits and eight nuclear microsatellite loci were examined in individuals from two biogeographic provinces of Argentina to determine the number and composition of genetically distinguishable groups of individuals and explore possible spatial patterns of the phenotypic and genetic variability. Means of reproductive traits were higher in the Yungas than in the Paranaense biogeographic province, whereas five out of eight nonreproductive quantitative traits showed higher mean values in the latter. Variance coefficients were moderate, and there were significant differences between and within provinces. Three clusters were defined based on spatial model for cluster membership for quantitative traits. One cluster grouped the individuals from the Paranaense biogeographic province whereas the individuals from the Yungas biogeographic province grouped regarding its population of origin. Parameters of molecular genetic variability showed higher values in the Yungas than in the Paranaense biogeographic province. Observed heterozygosity was lower than expected heterozygosity in both biogeographic provinces, indicating an excess of homozygosity. The homozygosity test by Watterson and the exact test by Slatkin suggested diversifying selection for locus Ac41.1. Bayesian clustering spatial model for microsatellites loci data were performed for both all loci and for all loci excluding locus Ac41.1. In both analyses two clusters were inferred. Analysis of molecular variance revealed similar results for all genotypes and for all genotypes defined excluding locus Ac41.1. Most of the total variance is attributable to genetic variation within clusters. The presence of homogeneous clusters was detected for both the phenotypic and molecular genetic variability. Two Bayesian clustering analyses were performed according to molecular genetic data

  5. HmtDB, a Human Mitochondrial Genomic Resource Based on Variability Studies Supporting Population Genetics and Biomedical Research

    OpenAIRE

    Pappadà Graziano; Scioscia Gaetano; Lascaro Daniela; Santamaria Monica; Accetturo Matteo; Attimonelli Marcella; Russo Luigi; Zanchetta Luigi; Tommaseo-Ponzetta Mila

    2005-01-01

    Abstract Background Population genetics studies based on the analysis of mtDNA and mitochondrial disease studies have produced a huge quantity of sequence data and related information. These data are at present worldwide distributed in differently organised databases and web sites not well integrated among them. Moreover it is not generally possible for the user to submit and contemporarily analyse its own data comparing them with the content of a given database, both for population genetics ...

  6. Marine reserves help preserve genetic diversity after impacts derived from climate variability: Lessons from the pink abalone in Baja California

    Directory of Open Access Journals (Sweden)

    Adrián Munguía-Vega

    2015-07-01

    Full Text Available Genetic diversity is crucial for the adaptation of exploited species like the pink abalone (Haliotis corrugata, faced with threats from climate change, overfishing and impacts associated with aquaculture production. While marine reserves are commonly used to mitigate risks to marine populations, the duration, size, location and larval connectivity needed for a reserve to help conserve genetic resources is still poorly understood. Here, we examine the effects of fishing, reserves, and restocking on the genetic diversity of 10 populations from central Baja California, Mexico, and Southern California, USA. We demonstrate that each population shows characteristic genetic signatures according to recent management decisions. We found high allelic diversity, particularly rare alleles, a larger effective population size and a lack of a recent genetic bottleneck in pink abalones within a small (0.8 km2, recently established (5 years reserve in Baja California, compared to other fished sites after a climatic bottleneck. Higher diversity may result from the presence of older animals in the reserve. Due to its location, the reserve may also act as an important hub connecting distant populations via larval dispersal. In contrast, a population from California showed genetic isolation, loss of allelic diversity and high relatedness, consistent with the collapse of fisheries in the 1990s and their lack of recovery thereafter. In addition, a fished area in Baja California with a history of restocking for over a decade showed an increase in frequency of related individuals and high genetic differentiation from nearby sites that were consistent with the production of larvae from a few adults in the laboratory. A network of strategically placed small marine reserves that considers ocean circulation patterns could help to maintain genetic diversity and connectivity of exploited populations.

  7. Loss of genetic variability in a hatchery strain of Senegalese sole (Solea senegalensis revealed by sequence data of the mitochondrial DNA control region and microsatellite markers

    Directory of Open Access Journals (Sweden)

    Pablo Sánchez

    2012-06-01

    Full Text Available Comparisons of the levels of genetic variation within and between a hatchery F1 (FAR, n=116 of Senegalese sole, Solea senegalensis, and its wild donor population (ATL, n = 26, both native to the SW Atlantic coast of the Iberian peninsula, as well as between the wild donor population and a wild western Mediterranean sample (MED, n=18, were carried out by characterizing 412 base pairs of the nucleotide sequence of the mitochondrial DNA control region I, and six polymorphic microsatellite loci. FAR showed a substantial loss of genetic variability (haplotypic diversity, h=0.49±0.066; nucleotide diversity, π=0.006±0.004; private allelic richness, pAg=0.28 to its donor population ATL (h=0.69±0.114; π=0.009±0.006; pAg=1.21. Pairwise FST values of microsatellite data were highly significant (P < 0.0001 between FAR and ATL (0.053 and FAR and MED (0.055. The comparison of wild samples revealed higher values of genetic variability in MED than in ATL, but only with mtDNA CR-I sequence data (h=0.948±0.033; π=0.030±0.016. However, pairwise ΦST and FST values between ATL and MED were highly significant (P < 0.0001 with mtDNA CR-I (0.228 and with microsatellite data (0.095, respectively. While loss of genetic variability in FAR could be associated with the sampling error when the broodstock was established, the results of parental and sibship inference suggest that most of these losses can be attributed to a high variance in reproductive success among members of the broodstock, particularly among females.

  8. Continuous within-plant variation as a source of intraspecific functional diversity: Patterns, magnitude, and genetic correlates of leaf variability in Helleborus foetidus (Ranunculaceae).

    Science.gov (United States)

    Herrera, Carlos M; Medrano, Mónica; Bazaga, Pilar

    2015-02-01

    Continuous within-plant variation in quantitative traits of reiterated, homologous structures is a component of intraspecific variation, but its contribution to functional diversity remains largely unexplored. For the perennial Helleborus foetidus, we measured functional leaf traits to quantify the contribution of within-plant variation to intraspecific functional variance and evaluate whether within-plant variability itself deserves separate consideration. Within-individual variation in eight leaf traits was quantified for 138 plants sampled from 10 widely spaced locations in the Sierra de Cazorla, southeastern Spain. An amplified fragment length polymorphism (AFLP) technique was used to look for associations between within-plant variability and specific AFLP markers. Leaflets from basal positions in ramets were longer, heavier, had greater surface area and larger stomata, and lower specific area, stomatal index, and stomatal density than those from distal positions. Continuous variation between leaves from the same ramet was the main source of population-wide variance for most traits. Within-plant variability differed among populations. Individuals differed in within-plant variability, which was largely independent of trait means and associated with genetic characteristics. Up to four AFLP markers were associated with the within-plant variability level of a given leaf trait. Subindividual variability in continuous leaf traits was independent of plant means and related to genetic features. The within-individual component generally exceeded the between-individual component of intraspecific variance. Within-plant variation may broaden the ecological breadth and enhance stability and persistence of plant populations and communities and may provide novel insights when incorporated in trait-based community ecology models. © 2015 Botanical Society of America, Inc.

  9. Genetic structure of natural and restored shoalgrass Halodule wrightii populations in the NW Gulf of Mexico

    Science.gov (United States)

    Travis, S.E.; Sheridan, P.

    2006-01-01

    The decline of seagrass communities worldwide has sparked an urgent need for effective restoration strategies, which require a working knowledge of population genetic structure. Halodule wrighti is a common seagrass of the Caribbean region that is being restored to areas of the Gulf of Mexico, yet little is known of its population genetics. This study provides an assessment of individual, clonal and population effects on the genetic structure of 4 natural H. wrightii populations occupying 170 km of coastline in and around Galveston Bay, Texas, for comparison with 7 restored populations ranging in age from 2 to 7 yr. By using molecular markers, in the form of amplified fragment length polymorphisms (AFLPs), we found considerable variation in clonal richness at the population scale (from 0.54 to 0.82), with the restored populations occupying an intermediate to high position within this range. Replicate sampling within individual seagrass beds of 3 to 5m diameter generally revealed higher levels of clonal richness, elevated by 4 to 22% over that at the population scale, suggesting that seed recruitment is more important at the local scale than at distances of >10 m. Genetic diversity was 2 to 3 times less than that expected for a widespread, outcrossing species like H. wrightii, although a 170% increase in the frequency of variable markers relative to the mean for all other populations was noted for a volunteer population that had recruited from a mixture of donor materials planted at a nearby restoration site. Within the spatial extent of this study, natural populations adhered to a model of isolation-by-distance, whereas donor materials from these same natural populations were undergoing a rapid genetic convergence within a restored site where they had been planted together. ?? Inter-Research 2006.

  10. Measuring local genetic variability in populations of codling moth (Lepidoptera: Tortricidae) across an unmanaged and commercial orchard interface.

    Science.gov (United States)

    Fuentes-Contreras, Eduardo; Basoalto, Esteban; Franck, Pierre; Lavandero, Blas; Knight, Alan L; Ramírez, Claudio C

    2014-04-01

    The genetic structure of adult codling moth, Cydia pomonella (L.), populations was characterized both inside a managed apple, Malus domestica Borkdhausen, orchard and in surrounding unmanaged hosts and nonhost trees in central Chile during 2006-2007. Adult males were collected using an array of sex pheromone-baited traps. Five microsatellite genetic markers were used to study the population genetic structure across both spatial (1-100 ha) and temporal (generations within a season) gradients. Analysis of molecular variance (AMOVA) found a significant, but weak, association in both the spatial and temporal genetic structures. Discriminant analysis also found significant differentiation between the first and second generation for traps located either inside or outside the managed orchard. The Bayesian assignment test detected three genetic clusters during each of the two generations, which corresponded to different areas within the unmanaged and managed apple orchard interface. The lack of a strong spatial structure at a local scale was hypothesized to be because of active adult movement between the managed and unmanaged hosts and the asymmetry in the insecticide selection pressure inside and outside the managed habitats. These data highlight the importance of developing area-wide management programs that incorporate management tactics effective at the landscape level for successful codling moth control.

  11. Microsatellite variation reveals high levels of genetic variability and population structure in the gorgonian coral Pseudopterogorgia elisabethae across the Bahamas.

    Science.gov (United States)

    Gutierrez-Rodriguez, Carla; Lasker, Howard R

    2004-08-01

    The primary mechanism of gene flow in marine sessile invertebrates is larval dispersal. In Pseudopterogorgia elisabethae, a commercially important Caribbean gorgonian coral, a proportion of the larvae drop to the substratum within close proximity to the maternal colony, and most matings occur between individuals in close proximity to each other. Such limited dispersal of reproductive propagules suggests that gene flow is limited in this gorgonian. In this study, we characterized the population genetic structure of P. elisabethae across the Bahamas using six microsatellite loci. P. elisabethae was collected from 18 sites across the Bahamas. Significant deviations from Hardy-Weinberg equilibrium due to deficits of heterozygotes within populations were detected for all 18 populations in at least one of the six screened loci. Levels of genetic structure among populations of P. elisabethae were high and significant. A distance analysis placed populations within three groups, one formed by populations located within Exuma Sound, a semi-isolated basin, another consisting of populations located outside the basin and a third group comprising two populations from San Salvador Island. The patterns of genetic variation found in this study are concordant with the life-history traits of the species and in part with the geography of the Bahamas. Conservation and management plans developed for P. elisabethae should considered the high degree of genetic structure observed among populations of the species, as well as the high genetic diversity found in the San Salvador and the Exuma Sound populations. Copyright 2004 Blackwell Publishing Ltd

  12. Do pathogens reduce genetic diversity of their hosts? Variable effects of sylvatic plague in black-tailed prairie dogs.

    Science.gov (United States)

    Sackett, Loren C; Collinge, Sharon K; Martin, Andrew P

    2013-05-01

    Introduced diseases can cause dramatic declines in-and even the loss of-natural populations. Extirpations may be followed by low recolonization rates, leading to inbreeding and a loss of genetic variation, with consequences on population viability. Conversely, extirpations may create vacant habitat patches that individuals from multiple source populations can colonize, potentially leading to an influx of variation. We tested these alternative hypotheses by sampling 15 colonies in a prairie dog metapopulation during 7 years that encompassed an outbreak of sylvatic plague, providing the opportunity to monitor genetic diversity before, during and after the outbreak. Analysis of nine microsatellite loci revealed that within the metapopulation, there was no change in diversity. However, within extirpated colonies, patterns varied: In half of the colonies, allelic richness after recovery was less than the preplague conditions, and in the other half, richness was greater than the preplague conditions. Finally, analysis of variation within individuals revealed that prairie dogs present in recolonized colonies had higher heterozygosity than those present before plague. We confirmed plague survivorship in six founders; these individuals had significantly higher heterozygosity than expected by chance. Collectively, our results suggest that high immigration rates can maintain genetic variation at a regional scale despite simultaneous extirpations in spatially proximate populations. Thus, virulent diseases may increase genetic diversity of host populations by creating vacant habitats that allow an influx of genetic diversity. Furthermore, even highly virulent diseases may not eliminate individuals randomly; rather, they may selectively remove the most inbred individuals. © 2013 Blackwell Publishing Ltd.

  13. The estimation of genetic distance and discriminant variables on breed of duck (Alabio, Bali, Khaki Campbell, Mojosari and Pegagan by morphological analysis

    Directory of Open Access Journals (Sweden)

    B Brahmantiyo

    2003-03-01

    Full Text Available A study on morphological body conformation of Alabio, Bali, Khaki Campbell, Mojosari and Pegagan ducks was carried out to determine the genetic distance and discriminant variables. This research was held in Research Institute for Animal Production, Ciawi, Bogor using 65 Alabio ducks, 40 Bali ducks, 36 Khaki Campbell ducks, 60 Mojosari ducks and 30 Pegagan ducks. Seven different body parts were measured, they were the length of femur, tibia, tarsometatarsus, the circumference of tarsometatarsus, the length of third digits, wing and maxilla. General Linear Models and simple discriminant analysis were used in this observation (SAS package program. Male and female Pegagan ducks had morphological size bigger than Alabio, Bali, Khaki Campbell and Mojosari ducks. Khaki Campbell ducks were mixed with Bali ducks (47.22% and Pegagan ducks from isolated location in South Sumatera were lightly mixed with Alabio and Bali. Mahalanobis genetic distance showed that Bali and Khaki Campbell ducks, also, Alabio and Mojosari ducks had similarity, with genetic distance of 1.420 and 1.548, respectively. Results from canonical analysis showed that the most discriminant variables were obtained from the length of femur, tibia and third digits.

  14. Joint analysis of phenotypic and molecular diversity provides new insights on the genetic variability of the Brazilian physic nut germplasm bank.

    Science.gov (United States)

    Alves, Alexandre Alonso; Bhering, Leonardo Lopes; Rosado, Tatiana Barbosa; Laviola, Bruno Galvêas; Formighieri, Eduardo Fernandes; Cruz, Cosme Damião

    2013-09-01

    The genetic variability of the Brazilian physic nut (Jatropha curcas) germplasm bank (117 accessions) was assessed using a combination of phenotypic and molecular data. The joint dissimilarity matrix showed moderate correlation with the original matrices of phenotypic and molecular data. However, the correlation between the phenotypic dissimilarity matrix and the genotypic dissimilarity matrix was low. This finding indicated that molecular markers (RAPD and SSR) did not adequately sample the genomic regions that were relevant for phenotypic differentiation of the accessions. The dissimilarity values of the joint dissimilarity matrix were used to measure phenotypic + molecular diversity. This diversity varied from 0 to 1.29 among the 117 accessions, with an average dissimilarity among genotypes of 0.51. Joint analysis of phenotypic and molecular diversity indicated that the genetic diversity of the physic nut germplasm was 156% and 64% higher than the diversity estimated from phenotypic and molecular data, respectively. These results show that Jatropha genetic variability in Brazil is not as limited as previously thought.

  15. Naturally occurring genetic variability in expression of Gsta4 is associated with differential survival of axotomized rat motoneurons

    DEFF Research Database (Denmark)

    Mikael, Ström; Al Nimer, Faiez; Lindblom, Rickard

    2012-01-01

    such naturally occurring strain differences is a powerful approach, also known as forward genetics, to gain knowledge of mechanisms relevant for complex diseases, like injury-induced neurodegeneration. Overlapping congenic rat strains were used to fine map a gene region on rat chromosome eight previously shown...

  16. Study of quantitative genetics of gum arabic production complicated by variability in ploidy level of Acacia senegal (L.) Willd

    DEFF Research Database (Denmark)

    Diallo, Adja Madjiguene; Nielsen, Lene Rostgaard; Hansen, Jon Kehlet

    2015-01-01

    Gum arabic is an important international commodity produced by trees of Acacia senegal across Sahelian Africa, but documented results of breeding activities are limited. The objective of this study was to provide reliable estimates of quantitative genetic parameters in order to shed light...

  17. Genetic Determinants of Variable Metabolism Have Little Impact on the Clinical Use of Leading Antipsychotics in the CATIE study

    Science.gov (United States)

    Grossman, Iris; Sullivan, Patrick F.; Walley, Nicole; Liu, Youfang; Dawson, Jeffrey R.; Gumbs, Curtis; Gaedigk, Andrea; Leeder, J. Steven; McEvoy, Joseph P.; Weale, Michael E.; Goldstein, David B.

    2013-01-01

    Purpose To evaluate systematically in real clinical settings whether functional genetic variations in drug metabolizing enzymes influence optimized doses, efficacy, and safety of antipsychotic medications. Methods DNA was collected from 750 patients with chronic schizophrenia treated with five antipsychotic drugs (olanzapine, quetiapine, risperidone, ziprasidone and perphenazine) as part of the Clinical Antipsychotic Trials of Intervention Effectiveness (CATIE) study. Doses for each of the medicines were optimized to 1, 2, 3, or 4x units in identically-appearing capsules in a double blind design. We analyzed 25 known functional genetic variants in the major and minor metabolizing enzymes for each medication. These variants were tested for association with optimized dose and other relevant clinical outcomes. Results None of the tested variants showed a nominally significant main effect in association with any of the tested phenotypes in European-Americans, African-Americans or all patients. Even after accounting for potential covariates no genetic variant was found to be associated with dosing, efficacy, overall tolerability, or tardive dyskinesia. Conclusion There are no strong associations between common functional genetic variants in drug metabolizing enzymes and dosing, safety or efficacy of leading antipsychotics, strongly suggesting merely modest effects on the use of these medicines in most patients in typical clinical settings. PMID:18813134

  18. Reduced Penetrance and Variable Expression of SCN5A Mutations and the Importance of Co-inherited Genetic Variants: Case Report and Review of the Literature

    Directory of Open Access Journals (Sweden)

    T. Robyns, MD.

    2014-05-01

    Full Text Available Mutations in the SCN5A gene are responsible for multiple phenotypical presentations including Brugada syndrome, long QT syndrome, progressive familial heart block, sick sinus syndrome, dilated cardiomyopathy, lone atrial fibrillation and multiple overlap syndromes. These different phenotypic expressions of a mutation in a single gene can be explained by variable expression and reduced penetrance. One of the possible explanations of these phenomena is the co-inheritance of genetic variants. We describe a family where the individuals exhibit a compound heterozygosity in the SCN5A gene including a mutation (R1632H and a new variant (M858L. Individuals with both the mutation and new variant present with a more severe phenotype including spontaneous atrial tachyarrhythmia at young age. We give an overview of the different phenotypes of "SCN5A disease" and discuss the importance of co-inherited genetic variants in the expression of SCN5A disease.

  19. Analysis of a slow-growing line reveals wide genetic variability of carcass and meat quality-related traits

    Directory of Open Access Journals (Sweden)

    Chabault Marie

    2012-10-01

    Full Text Available Abstract Background Slow-growing lines are widely used in France for the production of high quality free-range chickens. While such production is mainly dedicated to the whole carcass market, new prospects are opening up for the development of cuts and processed products. Whether the body composition and meat quality of slow-growing birds can be improved by selection has thus become an important issue. The genetic parameters of growth, body composition and breast meat quality traits were evaluated in relation to behaviour at slaughter in a large pedigree population including 1022 male and female slow-growing birds. Results The heritability coefficients (h2 of body weight and body composition traits varied from 0.3 to 0.5. Abdominal fat percentage was genetically positively correlated with body weight but negatively correlated with breast muscle yield. The characteristics of the breast meat (i.e., post-mortem fall in pH, colour, drip loss, shear-force and lipid content were all heritable, with h2 estimates ranging from 0.18 to 0.48. The rate and extent of the fall in pH were under different genetic control. Strong negative genetic correlations were found between the ultimate pH and the lightness, yellowness and drip loss of the meat. Wing flapping on the shackle line was significantly heritable and exhibited marked genetic correlations with the pH at 15 min post-slaughter and the redness of the meat. The genetic relationships between meat quality traits, body weight and body composition appeared slightly different between males and females. Conclusion This study suggested that there are a number of important criteria for selection on carcass and breast meat quality in slow-growing birds. Selection for reduced abdominal fatness and increased breast muscle yield should be effective as both traits were found to be highly heritable and favourably correlated. Substantial improvement in meat quality could be achieved by selection on ultimate pH which

  20. Mutations in NFKB2 and potential genetic heterogeneity in patients with DAVID syndrome, having variable endocrine and immune deficiencies

    OpenAIRE

    Brue, Thierry; Quentien, Marie-Hélène; Khetchoumian, Konstantin; Bensa, Marco; Capo-Chichi, José-Mario; Delemer, Brigitte; Balsalobre, Aurelio; Nassif, Christina; Papadimitriou, Dimitris T; Pagnier, Anne; Hasselmann, Caroline; Patry, Lysanne; Schwartzentruber, Jeremy; Souchon, Pierre-François; Takayasu, Shinobu

    2014-01-01

    Background DAVID syndrome is a rare condition combining anterior pituitary hormone deficiency with common variable immunodeficiency. NFKB2 mutations have recently been identified in patients with ACTH and variable immunodeficiency. A similar mutation was previously found in Nfkb2 in the immunodeficient Lym1 mouse strain, but the effect of the mutation on endocrine function was not evaluated. Methods We ascertained six unrelated DAVID syndrome families. We performed whole exome and traditional...

  1. Population growth rate and genetic variability of small and large populations of Red flour beetle (Tribolium castaneum) following multigenerational exposure to copper.

    Science.gov (United States)

    Laskowski, Ryszard; Radwan, Jacek; Kuduk, Katarzyna; Mendrok, Magdalena; Kramarz, Paulina

    2015-07-01

    We reared large (1000 individuals) and small (20 individuals) populations of Tribolium castaneum on diet contaminated with copper in order to determine if the size of a population affects its ability to adapt to adverse environmental conditions. After 10 generations, we used microsatellite markers to estimate and subsequently compare the genetic variability of the copper-treated populations with that of the control populations, which were reared on uncontaminated medium. Additionally, we conducted a full cross-factorial experiment which evaluated the effects of 10 generations of "pre-exposure" to copper on a population's fitness in control and copper-contaminated environments. In order to distinguish results potentially arising from genetic adaptation from those due to non-genetic effects associated to parental exposure to copper, we subjected also F11 generation, originating from parents not exposed to copper, to the same cross-factorial experiment. The effects of long-term exposure to copper depended on population size: the growth rates of small populations that were pre-exposed to copper were inhibited compared to those of small populations reared in uncontaminated environments. Large Cu-exposed populations had a higher growth rate in the F10 generation compared to the control groups, while the growth rate of the F11 generation was unaffected by copper exposure history. The only factor that had a significant effect on genetic variability was population size, but this was to be expected given the large difference in the number of individuals between large and small populations. Neither copper contamination nor its interaction with population size affected the number of microsatellite alleles retained in the F10 generation.

  2. Response of CYP1A Gene expression in fish liver of catfish (Ariopsis felis) from Gulf of Mexico and their relationship with the genetic variability.

    Science.gov (United States)

    Zapata-Perez, Omar; Sanchez-Teyer, Lorenzo F; Perez-Nunez, Maria T; Arroyo-Herrera, Ana L; Moreno, Adriana Quiroz; Albores-Medina, Arnulfo

    2010-01-01

    We determined the hepatic Cytochrome P4501A (CYP1A) mRNA and Ethoxyresorufin-O-deethylase (EROD) activities in the fish, Ariopsis felis, from highly polluted to relatively pristine regions in the southwest Gulf of Mexico and their relationship with the genetic polymorphisms of the same fish. We hypothesized that a high genetic variation reflects interindividual variability in levels of CYP1A mRNA underlying the pathway culminating in EROD induction caused by the environmental contaminants. Catfish from Laguna de Mecoacan exhibited marked induction of CYP1A mRNA and high levels of hepatic EROD activities, whereas fish from Laguna de Celestun showed no induction of CYP1A mRNA and moderately low levels of EROD activities. In contrast, the similarity index considering all samples varied from 0.4 to 0.87, showing a wide range of variation. A dendrogram showed a clear grouping of fish collected from the Laguna de Terminos, Rio Coatzacoalcos and Laguna de Celestun, with discrete subgroups according to region. In contrast, fish from Laguna de Mecoacan were grouped together completely separate from the rest of the fish. Despite the low number of fish from Mecoacan (a high bootstrap support was observed in this group), the results indicated a significant genetic variability in comparison with the other ecosystems included. The differential level of expression of CYP1A and the EROD activity observed among the ecosystems analyzed could be due to the high range of genetic variation, with special emphasis on fish collected in Mecoacan where it is possible to find a subspecies of Ariopsis felis.

  3. Genetic variation of the greenhouse whitefly, Trialeurodes vaporariorum (Hemiptera: Aleyrodidae), among populations from Serbia and neighbouring countries, as inferred from COI sequence variability.

    Science.gov (United States)

    Prijović, M; Skaljac, M; Drobnjaković, T; Zanić, K; Perić, P; Marčić, D; Puizina, J

    2014-06-01

    The greenhouse whitefly Trialeurodes vaporariorum Westwood, 1856 (Hemiptera: Aleyrodidae) is an invasive and highly polyphagous phloem-feeding pest of vegetables and ornamentals. Trialeurodes vaporariorum causes serious damage due to direct feeding and transmits several important plant viruses. Excessive use of insecticides has resulted in significantly reduced levels of susceptibility of various T. vaporariorum populations. To determine the genetic variability within and among populations of T. vaporariorum from Serbia and to explore their genetic relatedness with other T. vaporariorum populations, we analysed the mitochondrial cytochrome c oxidase I (COI) sequences of 16 populations from Serbia and six neighbouring countries: Montenegro (three populations), Macedonia (one population) and Croatia (two populations), for a total of 198 analysed specimens. A low overall level of sequence divergence and only five variable nucleotides and six haplotypes were found. The most frequent haplotype, H1, was identified in all Serbian populations and in all specimens from distant localities in Croatia and Macedonia. The COI sequence data that was retrieved from GenBank and the data from our study indicated that H1 is the most globally widespread T. vaporariorum haplotype. A lack of spatial genetic structure among the studied T. vaporariorum populations, as well as two demographic tests that we performed (Tajima's D value and Fu's Fs statistics), indicate a recent colonisation event and population growth. Phylogenetic analyses of the COI haplotypes in this study and other T. vaporariorum haplotypes that were retrieved from GenBank were performed using Bayesian inference and median-joining (MJ) network analysis. Two major haplogroups with only a single unique nucleotide difference were found: haplogroup 1 (containing the five Serbian haplotypes and those previously identified in India, China, the Netherlands, the United Kingdom, Morocco, Reunion and the USA) and haplogroup 3

  4. Effect of genetic algorithm as a variable selection method on different chemometric models applied for the analysis of binary mixture of amoxicillin and flucloxacillin: A comparative study

    Science.gov (United States)

    Attia, Khalid A. M.; Nassar, Mohammed W. I.; El-Zeiny, Mohamed B.; Serag, Ahmed

    2016-03-01

    Different chemometric models were applied for the quantitative analysis of amoxicillin (AMX), and flucloxacillin (FLX) in their binary mixtures, namely, partial least squares (PLS), spectral residual augmented classical least squares (SRACLS), concentration residual augmented classical least squares (CRACLS) and artificial neural networks (ANNs). All methods were applied with and without variable selection procedure (genetic algorithm GA). The methods were used for the quantitative analysis of the drugs in laboratory prepared mixtures and real market sample via handling the UV spectral data. Robust and simpler models were obtained by applying GA. The proposed methods were found to be rapid, simple and required no preliminary separation steps.

  5. THE SIGNIFICANCE OF GENETIC EROSION IN THE PROCESS OF EXTINCTION .4. INBREEDING DEPRESSION AND HETEROSIS EFFECTS CAUSED BY SELFING AND OUTCROSSING IN SCABIOSA-COLUMBARIA

    NARCIS (Netherlands)

    VANTREUREN, R; BIJLSMA, R; OUBORG, NJ; VANDELDEN, W

    1993-01-01

    The effects of self-fertilization, within-population crosses (WPC) and between-population crosses (BPC) on progeny fitness were investigated in the greenhouse for Scabiosa columbaria populations of varying size. Plants grown from field collected seeds were hand pollinated to produce selfed, WPC, and

  6. Study of quantitative genetics of gum arabic production complicated by variability in ploidy level of Acacia senegal (L.) Willd

    DEFF Research Database (Denmark)

    Diallo, Adja Madjiguene; Nielsen, Lene Rostgaard; Hansen, Jon Kehlet;

    2015-01-01

    sibs, while the open-pollinated families of polyploids showed low variation within families. The difference in sibling relationship observed between ploidy levels complicated estimation of genetic parameters. However, based on the diploid trees, we conclude that heritability in gum arabic production......Gum arabic is an important international commodity produced by trees of Acacia senegal across Sahelian Africa, but documented results of breeding activities are limited. The objective of this study was to provide reliable estimates of quantitative genetic parameters in order to shed light...... on the breeding potential for improvement of gum yield and quality. For this purpose, we measured growth on 617 offspring from 60 open-pollinated trees after 18 years, and gum yield and quality based on two seasons, 18 and 19 years after establishment. Genotyping with eight microsatellite markers revealed...

  7. A Genetic Instrumental Variables Analysis of the Effects of Prenatal Smoking on Birth Weight: Evidence from Two Samples

    Science.gov (United States)

    Lehrer, Steven F.; Moreno, Lina M.; Murray, Jeffrey C.; Wilcox, Allen; Lie, Rolv T.

    2011-01-01

    There is a large literature showing the detrimental effects of prenatal smoking on birth and childhood health outcomes. It is somewhat unclear, though, whether these effects are causal or reflect other characteristics and choices by mothers who choose to smoke that may also affect child health outcomes or biased reporting of smoking. In this paper, we use genetic markers that predict smoking behaviors as instruments in order to address the endogeneity of smoking choices in the production of birth and childhood health outcomes. Our results indicate that prenatal smoking produces more dramatic declines in birth weight than estimates that ignore the endogeneity of prenatal smoking, which is consistent with previous studies with non-genetic instruments. We use data from two distinct samples from Norway and the US with different measured instruments and find nearly identical results. The study provides a novel application that can be extended to study several behavioral impacts on health, social and economic outcomes. PMID:21845925

  8. [Genetic variability of the bacterium Ralstonia solanacearum (Burkholderiales: Burholderiaceae) in the banana-growing region of Uraba (Colombia)].

    Science.gov (United States)

    Cardozo, Carolina; Rodríguez, Paola; Cotes, José Miguel; Marín, Mauricio

    2010-03-01

    The banana moko disease, caused by the bacterium Ralstonia solanacearum, is one of the most important phytopathological problems of the banana agribusiness in tropical countries. In Uraba and Magdalena (Colombia), the main exporting regions of banana in Colombia, this disease causes a destruction estimated in 16.5 ha/year. The bacterium presents an extremely high level of genetic variation that affects control measures. This is the first study of its variation in Colombia and was done with AFLP molecular markers on a population of 100 isolates from banana plants, soils and "weeds". The high level of genetic diversity, with Nei and Shannon indexes of h=0.32 and I=0.48, respectively, and the AMOVA, showed that this population is subestructured (Fst=0.66): the host is the main factor of differentiation. Even so, previous tests show that all varieties have pathogenicity on Musa.

  9. Enzyme Polymorphism and Genetic Variability of One Colonized and Several Field Populations of Phlebotomus papatasi (Diptera: Psychodidae)

    Science.gov (United States)

    1993-01-01

    contained one to dIiught. averaginvO(.0072. Gen’ietic identitv ’ ahie. four allomorphs per locus and averagedl 2.35 e- ach >01.97, for the diferent...laborattory popuila. niatural evolutionary processes such as mutation . tion, but their departure fromi Hardy-WeinbeRg migration. drift, an(d...255. Nlunsterman. L. E. 1979. Isozymes of- Aedes ae- irypti. phenotypes. linkage. and use in the genetic References Cited .aiialvsis of svinpatric

  10. Demographics and genetic variability of the new world bollworm (Helicoverpa zea) and the old world bollworm (Helicoverpa armigera) in Brazil.

    Science.gov (United States)

    Leite, Natália A; Alves-Pereira, Alessandro; Corrêa, Alberto S; Zucchi, Maria I; Omoto, Celso

    2014-01-01

    Helicoverpa armigera is one of the primary agricultural pests in the Old World, whereas H. zea is predominant in the New World. However, H. armigera was first documented in Brazil in 2013. Therefore, the geographical distribution, range of hosts, invasion source, and dispersal routes for H. armigera are poorly understood or unknown in Brazil. In this study, we used a phylogeographic analysis of natural H. armigera and H. zea populations to (1) assess the occurrence of both species on different hosts; (2) infer the demographic parameters and genetic structure; (3) determine the potential invasion and dispersal routes for H. armigera within the Brazilian territory; and (4) infer the geographical origin of H. armigera. We analyzed partial sequence data from the cytochrome c oxidase subunit I (COI) gene. We determined that H. armigera individuals were most prevalent on dicotyledonous hosts and that H. zea were most prevalent on maize crops, based on the samples collected between May 2012 and April 2013. The populations of both species showed signs of demographic expansion, and no genetic structure. The high genetic diversity and wide distribution of H. armigera in mid-2012 are consistent with an invasion period prior to the first reports of this species in the literature and/or multiple invasion events within the Brazilian territory. It was not possible to infer the invasion and dispersal routes of H. armigera with this dataset. However, joint analyses using sequences from the Old World indicated the presence of Chinese, Indian, and European lineages within the Brazilian populations of H. armigera. These results suggest that sustainable management plans for the control of H. armigera will be challenging considering the high genetic diversity, polyphagous feeding habits, and great potential mobility of this pest on numerous hosts, which favor the adaptation of this insect to diverse environments and control strategies.

  11. Demographics and genetic variability of the new world bollworm (Helicoverpa zea and the old world bollworm (Helicoverpa armigera in Brazil.

    Directory of Open Access Journals (Sweden)

    Natália A Leite

    Full Text Available Helicoverpa armigera is one of the primary agricultural pests in the Old World, whereas H. zea is predominant in the New World. However, H. armigera was first documented in Brazil in 2013. Therefore, the geographical distribution, range of hosts, invasion source, and dispersal routes for H. armigera are poorly understood or unknown in Brazil. In this study, we used a phylogeographic analysis of natural H. armigera and H. zea populations to (1 assess the occurrence of both species on different hosts; (2 infer the demographic parameters and genetic structure; (3 determine the potential invasion and dispersal routes for H. armigera within the Brazilian territory; and (4 infer the geographical origin of H. armigera. We analyzed partial sequence data from the cytochrome c oxidase subunit I (COI gene. We determined that H. armigera individuals were most prevalent on dicotyledonous hosts and that H. zea were most prevalent on maize crops, based on the samples collected between May 2012 and April 2013. The populations of both species showed signs of demographic expansion, and no genetic structure. The high genetic diversity and wide distribution of H. armigera in mid-2012 are consistent with an invasion period prior to the first reports of this species in the literature and/or multiple invasion events within the Brazilian territory. It was not possible to infer the invasion and dispersal routes of H. armigera with this dataset. However, joint analyses using sequences from the Old World indicated the presence of Chinese, Indian, and European lineages within the Brazilian populations of H. armigera. These results suggest that sustainable management plans for the control of H. armigera will be challenging considering the high genetic diversity, polyphagous feeding habits, and great potential mobility of this pest on numerous hosts, which favor the adaptation of this insect to diverse environments and control strategies.

  12. Genetic modifiers of Lepr{sup fa} associated with variability in insulin production and susceptibility to NIDDM

    Energy Technology Data Exchange (ETDEWEB)

    Chung, W.K.; Zheng, M.; Chua, M. [Rockefeller Univ., New York, NY (United States)] [and others

    1997-05-01

    In an attempt to identify the genetic basis for susceptibility to non-insulin-dependent diabetes mellitus within the context of obesity, we generated 401 genetically obese Lepr{sup fa}/Lepr{sup fa} F2 WKY13M intercross rats that demonstrated wide variation in multiple phenotypic measures related to diabetes, including plasma glucose concentration, percentage of glycosylated hemoglobin, plasma insulin concentration, and pancreatic islet morphology. Using selective genotyping genome scanning approaches, we have identified three quantitative trait loci (QTLs) on Chr. 1 (LOD 7.1 for pancreatic morpholology), Chr. 12 (LOD 5.1 for body mass index and LOD 3.4 for plasma glucose concentration), and Chr. 16 (P < 0.001 for genotype effect on plasma glucose concentration). The obese F2 progeny demonstrated sexual dimorphism for these traits, with increased diabetes susceptibility in the males appearing at approximately 6 weeks of age, as sexual maturation occurred. For each of the QTLs, the linked phenotypes demonstrated sexual dimorphism (more severe affection in males). The QTL on Chr. 1 maps to a region vicinal to that previously linked to adiposity in studies of diabetes susceptibility in the nonobese Goto-Kakizaki rat, which is genetically closely related to the Wistar counterstrain we employed. Several candidate genes, including tubby (tub), multigenic obesity 1 (Mob1), adult obesity and diabetes (Ad), and insulin-like growth factor-2 (Igf2), map to murine regions homologous to the QTL region identified on rat Chr. 1. 60 refs., 5 figs., 4 tabs.

  13. Extremely low genetic variability within and among locations of the greenfish holothurian Stichopus chloronotus Brandt, 1835 in Okinawa, Japan

    Directory of Open Access Journals (Sweden)

    Taha Soliman

    2016-09-01

    Full Text Available The greenfish sea cucumber Stichopus chloronotus is an economically and ecologically important sea cucumber species throughout its range. This species is widely distributed, inhabiting coral reefs of the Indo-Pacific Ocean. Our study evaluated population genetic structure and levels of genetic diversity in southern Japan. A total of 180 individuals were collected from eight locations from Okinawa and Okinoerabu Islands and sequenced using mitochondrial 16S ribosomal DNA (16S and nuclear histone H3 (H3 gene. Only three 16S haplotypes were detected (518 bp with haplotype diversity ranging from 0 to 0.56 and nucleotide diversity from 0 to 0.1%. H3 showed no variation among the studied locations. It is plausible that such results could be due to a shift to asexual reproduction. Additionally, the presence of the species on the east coast of Okinawa could only be detected in one location and all individuals consisted of a single haplotype. Genetic differences between the east and west coasts of Okinawa have been noticed in other coral reef organisms, and attributed to either ecological or biogeographical historical differences between the coasts due to differing levels of isolation during Pleistocene ice ages. Results from the present study should inform management and conservation policies of S. chloronotus in southern Japan.

  14. Extremely low genetic variability within and among locations of the greenfish holothurian Stichopus chloronotus Brandt, 1835 in Okinawa, Japan

    Science.gov (United States)

    Takama, Okuto; Fernandez-Silva, Iria; Reimer, James D.

    2016-01-01

    The greenfish sea cucumber Stichopus chloronotus is an economically and ecologically important sea cucumber species throughout its range. This species is widely distributed, inhabiting coral reefs of the Indo-Pacific Ocean. Our study evaluated population genetic structure and levels of genetic diversity in southern Japan. A total of 180 individuals were collected from eight locations from Okinawa and Okinoerabu Islands and sequenced using mitochondrial 16S ribosomal DNA (16S) and nuclear histone H3 (H3) gene. Only three 16S haplotypes were detected (518 bp) with haplotype diversity ranging from 0 to 0.56 and nucleotide diversity from 0 to 0.1%. H3 showed no variation among the studied locations. It is plausible that such results could be due to a shift to asexual reproduction. Additionally, the presence of the species on the east coast of Okinawa could only be detected in one location and all individuals consisted of a single haplotype. Genetic differences between the east and west coasts of Okinawa have been noticed in other coral reef organisms, and attributed to either ecological or biogeographical historical differences between the coasts due to differing levels of isolation during Pleistocene ice ages. Results from the present study should inform management and conservation policies of S. chloronotus in southern Japan. PMID:27703841

  15. Intraspecific morphological and genetic variability in the European freshwater snail Radix labiata (Rossmaessler, 1835) (Gastropoda: Basommatophora: Lymnaeidae)

    NARCIS (Netherlands)

    Schniebs, K.; Glöer, P.; Vinarski, M.V.; Hundsdoerfer, A.K.

    2013-01-01

    Radix labiata is a widely distributed Palaearctic freshwater snail. This work aims to improve the knowledge of the intraspecific variability in the most important characters used for its determination. To find out which characters are really suitable to distinguish this species from other similar Ra

  16. Sex-specific Tradeoffs With Growth and Fitness Following Life-span Extension by Rapamycin in an Outcrossing Nematode, Caenorhabditis remanei.

    Science.gov (United States)

    Lind, Martin I; Zwoinska, Martyna K; Meurling, Sara; Carlsson, Hanne; Maklakov, Alexei A

    2016-07-01

    Rapamycin inhibits the nutrient-sensing TOR pathway and extends life span in a wide range of organisms. Although life-span extension usually differs between the sexes, the reason for this is poorly understood. Because TOR influences growth, rapamycin likely affects life-history traits such as growth and reproduction. Sexes have different life-history strategies, and theory predicts that they will resolve the tradeoffs between growth, reproduction, and life span differently. Specifically, in taxa with female-biased sexual size dimorphism, reduced growth may have smaller effects on male fitness. We investigated the effects of juvenile, adult, or life-long rapamycin treatment on growth, reproduction, life span, and individual fitness in the outcrossing nematode Caenorhabditis remanei Life-long exposure to rapamycin always resulted in the strongest response, whereas postreproductive exposure did not affect life span. Although rapamycin resulted in longer life span and smaller size in males, male individual fitness was not affected. In contrast, size and fitness were negatively affected in females, whereas life span was only extended under high rapamycin concentrations. Our results support the hypothesis that rapamycin affects key life-history traits in a sex-specific manner. We argue that the fitness cost of life-span extension will be sex specific and propose that the smaller sex generally pay less while enjoying stronger life-span increase.

  17. Analysis of genetic variability in soursop Annona muricata L populations from Central Java and East Java based on random amplified polymorphic DNA RAPD marker

    Directory of Open Access Journals (Sweden)

    Suratman Suratman

    2014-08-01

    Full Text Available The objective of this research was to determine genetic variability of the soursop (Annona muricata L. populations from Central Java and East Java based on RAPD markers. Leaves of 40 individuals were collected from 4 soursop populations in Central Java and East Java, include : Sukoharjo, Karanganyar (Central Java, and Ngawi, Pacitan (East Java. Genomic DNA was extracted from the leaves by the CTAB extraction procedure with some modifications. A total of 15 RAPD primers were purchased from commercial source and tested to find specific diagnostic markers for each individuals by RAPD-PCR. The measurement of soursop population genetic distance was based on similarity coefficient using method of Group Average Clustering and Unweight Pair Group Method Arithmetic (UPGMA of NTSYS program version 2.02i. Results showed that each soursop population collected from different localities seemed have variability in RAPD profiles by using different primers. Four RAPD polymorphic primer was selected from 15 RAPD primers, namely A18, A20, P10 and P11. A total of 58 bands produced, varying from 9 to 20 bands per primer. The selected four RAPD primers produced 57 polymorphic bands, whereas polymorphism for each primer ranged from 95 % to 100 %. Dendrogram indicated that four soursop populations tend to segregate form two separated clade. The sample collected from Sukoharjo formed a separate cluster while the sample collected from Ngawi, Pacitan and Karanganyar grouped together in other cluster and diverged from population Sukoharjo.

  18. Evaluation of genetic variability in the collared peccary Pecari tajacu and the white-lipped peccary Tayassu pecari by microsatellite markers

    Directory of Open Access Journals (Sweden)

    Roxane Wirschum Silva

    2010-01-01

    Full Text Available In this study, the microsatellite technique was used to evaluate the genetic variability in populations of collared and white-lipped peccaries kept in captivity. Six primers developed for domestic pigs were used and amplified in both species. They revealed the presence of five polymorphic loci and one monomorphic locus. The polymorphic loci included 4 of the 16 alleles in collared peccaries, and 3 of the 10 alleles in the white-lipped peccaries. Polymorphic information content (PIC in both species and all the loci was highly informative. The probability of paternity exclusion (PEC, if one of the parents is known, was almost as high in white-lipped peccaries (95.53% as in the collared (99,48%. The Fst values for collared (0.042 and white-lipped (0.1387 peccaries showed that both populations are not structured. The Fis values for all loci, except ACTG2 in white-lipped peccaries (-0.0275 and in both species (0.1985 to 0.9284 in collared peccaries and 0.3621 to 0.4754 in the white-lipped, revealed a high level of homozygosis, probably caused by inbreeding. Data on heterologous amplification and genetic variability in collared and white-lipped peccaries are presented for the first time.

  19. Evaluation of genetic variability in the collared peccary Pecari tajacu and the white-lipped peccary Tayassu pecari by microsatellite markers.

    Science.gov (United States)

    Silva, Roxane Wirschum; de Freitas, Thales R O; Sbalqueiro, Ives José

    2010-01-01

    In this study, the microsatellite technique was used to evaluate the genetic variability in populations of collared and white-lipped peccaries kept in captivity. Six primers developed for domestic pigs were used and amplified in both species. They revealed the presence of five polymorphic loci and one monomorphic locus. The polymorphic loci included 4 of the 16 alleles in collared peccaries, and 3 of the 10 alleles in the white-lipped peccaries. Polymorphic information content (PIC) in both species and all the loci was highly informative. The probability of paternity exclusion (PEC), if one of the parents is known, was almost as high in white-lipped peccaries (95.53%) as in the collared (99,48%). The Fst values for collared (0.042) and white-lipped (0.1387) peccaries showed that both populations are not structured. The Fis values for all loci, except ACTG2 in white-lipped peccaries (-0.0275) and in both species (0.1985 to 0.9284 in collared peccaries and 0.3621 to 0.4754 in the white-lipped), revealed a high level of homozygosis, probably caused by inbreeding. Data on heterologous amplification and genetic variability in collared and white-lipped peccaries are presented for the first time.

  20. Genetic variability and heterogeneity of Venezuelan equine encephalitis virus vector Ochlerotatus taeniorhynchus (Diptera: Culicidae) populations of the Colombian Atlantic coast, based on microsatellite loci.

    Science.gov (United States)

    Bello, F; Becerra, V

    2009-09-29

    In Colombia, the mosquito Ochlerotatus taeniorhynchus has been identified as an efficient vector of the epidemic-epizootic Venezuelan equine encephalitis virus. We evaluated the genetic variability and heterogeneity of this mosquito in Colombian populations using eight microsatellite DNA loci. Two hundred and ten mosquito specimens collected from seven populations of the Colombian Atlantic coast (San Bernardo del Viento, Coveñas, Cartagena, Barranquilla, Ciénaga, Dibulla, and Riohacha) were analyzed. We found five polymorphic microsatellite loci, with 19 alleles giving 62.5% polymorphism; the mean number of alleles per locus was 3.8. The mean expected heterogeneity ranged from 0.568 to 0.660. Most of the polymorphic microsatellite loci were in Hardy-Weinberg disequilibrium, due to both deficit and excess of heterozygotes. The Fst statistic gave a total value of 0.0369, reflecting low genetic differentiation among the populations and, as a consequence, a low degree of structuring among them, while gene flow was high (Nm = 6.52); these findings point to genetic homogeneity among these populations. There was no significant linkage disequilibrium between genotype pairs of the various populations. We concluded that this mosquito is distributed in local populations along the Colombian Atlantic coast; these findings will be useful for developing strategies for controlling this vector.

  1. Evaluation of genetic variability in micropropagated propagules of ornamental pineapple [Ananas comosus var. bracteatus (Lindley) Coppens and Leal] using RAPD markers.

    Science.gov (United States)

    Santos, M D M; Buso, G C S; Torres, A C

    2008-10-21

    The objective of the present study was to evaluate the genetic variability in micropropagated plantlets of ornamental pineapple, after the fourth period of subculture. The basal culture medium consisted of MS salts, vitamins, 3% sucrose, liquid formulation, supplemented with 6-benzylaminopurine (BAP) at concentrations of 0.125, 0.25, 0.5, 1.0, and 2.0 mg/L. The addition of BAP influenced the occurrence of genetic variation revealed using random amplified polymorphic DNA (RAPD) markers. Of a total of 520 primers tested, 44 were selected and amplified; 402 monomorphic bands (97.2%) and 18 polymorphic bands (2.8%) resulted among regenerated plantlets. The polymorphic fragments were produced by 12 primers (OPA-01, OPA-20, OPB-01, OPB-19, OPC-19, OPF-13, OPL-17, OPM-13, OPP-16, OPT-07, OPV-19, and OPX-03). Among the primers that identified polymorphism, OPA-01, OPA-20, OPB-19, OPC-19, OPL-17, OPP-16, and OPX-3 each showed, one polymorphic band and OPF-13 amplified a maximum of three bands. In this study, the RAPD technique was effective in showing the occurrence of somaclonal variations that occur during the micropropagation process of ornamental pineapple cultivation in BAP-supplemented medium, and it is possible to detect the presence of genetic variation in early stages of plant development.

  2. Genetic variability and association pattern among quantitative nutritional traits in Swiss chard (Beta vulgaris subsp. L. var. cicla accessions and its implication for breeding

    Directory of Open Access Journals (Sweden)

    Bozokalfa Kadri M.

    2014-01-01

    Full Text Available In addition to improving agronomic traits, enriched cultivar such as nutritional elements and health promoting compounds are new demands for today's and the future's perspectives of crop breeding. In this respect, among leafy vegetables Swiss chard is a good source of nutritional elements and supplies large amounts of health promoting compounds. The existing knowledge of genetic variability for mineral composition both at the phenotype and genotype level, heritability of characters and also relationships among investigated minerals is fundamental for variety selection in Swiss chard. This also applies for the assurance of desirable agronomic traits with optimum mineral concentrations. This research analysis of variance indicated highly significant differences among Swiss chard accessions for all investigated mineral concentrations and the accessions display higher phenotype coefficient variation than genotype coefficient variation for all traits. The results revealed that phosphorus, magnesium, sodium, iron, copper, zinc, manganese, nitrate and nitrite exhibited high genetic advance accompanied with high heritability (>60%. The remaining mineral content demonstrated high heritability with moderate genetic advance. Genotype correlations were higher than the phenotype correlation for significant mineral concentrations. Genotype and phenotype correlations followed similar trends in all significant cases indicating the high heritable nature of the characters and the results showed that Swiss chard accessions should allow for the selection of individuals for enriched mineral concentration in edible parts of the plant.

  3. The influence of genetic variability and proinflammatory status on the development of bone disease in patients with Gaucher disease.

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    Gervas-Arruga, Javier; Cebolla, Jorge Javier; de Blas, Ignacio; Roca, Mercedes; Pocovi, Miguel; Giraldo, Pilar

    2015-01-01

    Gaucher disease, the most common lysosomal storage disorder, is caused by β-glucocerebrosidase deficiency. Bone complications are the major cause of morbidity in patients with type 1 Gaucher disease (GD1). Genetic components strongly influence bone remodelling. In addition, chronic inflammation produced by Gaucher cells induces the production of several cytokines, which leads to direct changes in the bone remodelling process and can also affect the process indirectly through other immune cells. In this study, we analysed the association between bone mineral density (BMD), bone marrow burden score, and relevant genetic polymorphisms related to bone metabolism, as well as profiles of proinflammatory cytokines in a GD1 cohort. This study included 83 patients distributed according to bone status. BMD was measured with DXA and broadband ultrasound attenuation; bone marrow involvement was evaluated using MRI. We also analysed 26 SNPs located in 14 genes related to bone metabolism. To assess proinflammatory status, we analysed IL-4, IL-6, IL-7, IL-10, IL-13, MIP-1α, MIP-1β, and TNFα in plasma samples from 71 control participants and GD1 patients. SNP genotype proportions and BMD differed significantly between ESRI c.453-397T>C and VDR c.1024+283G>A variants. We also observed significant associations between GD1 genotypes and bone affectation. When patients were stratified by spleen status, we observed significant correlations between non-/splenectomized groups and Spanish MRI (S-MRI) score. Across genotype proportions of non-/splenectomized patients and S-MRI, we observed significant differences in ESRI c.453-397T>C, VDR c.-83-25988G>A, and TNFRSF11B c.9C>G polymorphisms. We observed different significant proinflammatory profiles between control participants, treatment-naïve patients, and patients on enzyme replacement therapy (ERT); between non-/splenectomized patients (between untreated and ERT-treated patients) and among those with differing GBA genotypes. The

  4. [Genetic structure, variability and differentiation of Pinus sylvestris L. populations in the Ukrainian Carpathian Mountains and Rastoch'e].

    Science.gov (United States)

    Pirko, Ia V; Korshikov, I I

    2001-01-01

    On the basis of electrophoretic analysis of 9 enzymous systems encoded by 20 gene loci the level of intra- and inter-population variation of two relict populations of Pinus sylvestris L. in the Ukrainian Carpathians and two ones in Rastochiye was studied. The less allele representation and the lower level of heterozygosity are typical for the Carpathian populations. Fst and Gst, parameters of populations subdivision, were not high--0.020 and 0.022 correspondingly and the coefficient DN was 0.008 in average. The results of the cluster analysis showed that only the populations of Rastochiye were united in one group indicating their genetic affinity.

  5. The influence of genetic variability and proinflammatory status on the development of bone disease in patients with Gaucher disease.

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    Javier Gervas-Arruga

    Full Text Available Gaucher disease, the most common lysosomal storage disorder, is caused by β-glucocerebrosidase deficiency. Bone complications are the major cause of morbidity in patients with type 1 Gaucher disease (GD1. Genetic components strongly influence bone remodelling. In addition, chronic inflammation produced by Gaucher cells induces the production of several cytokines, which leads to direct changes in the bone remodelling process and can also affect the process indirectly through other immune cells. In this study, we analysed the association between bone mineral density (BMD, bone marrow burden score, and relevant genetic polymorphisms related to bone metabolism, as well as profiles of proinflammatory cytokines in a GD1 cohort. This study included 83 patients distributed according to bone status. BMD was measured with DXA and broadband ultrasound attenuation; bone marrow involvement was evaluated using MRI. We also analysed 26 SNPs located in 14 genes related to bone metabolism. To assess proinflammatory status, we analysed IL-4, IL-6, IL-7, IL-10, IL-13, MIP-1α, MIP-1β, and TNFα in plasma samples from 71 control participants and GD1 patients. SNP genotype proportions and BMD differed significantly between ESRI c.453-397T>C and VDR c.1024+283G>A variants. We also observed significant associations between GD1 genotypes and bone affectation. When patients were stratified by spleen status, we observed significant correlations between non-/splenectomized groups and Spanish MRI (S-MRI score. Across genotype proportions of non-/splenectomized patients and S-MRI, we observed significant differences in ESRI c.453-397T>C, VDR c.-83-25988G>A, and TNFRSF11B c.9C>G polymorphisms. We observed different significant proinflammatory profiles between control participants, treatment-naïve patients, and patients on enzyme replacement therapy (ERT; between non-/splenectomized patients (between untreated and ERT-treated patients and among those with differing GBA

  6. Genetic variability of attachment (G and Fusion (F protein genes of human metapneumovirus strains circulating during 2006-2009 in Kolkata, Eastern India

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    Chawla-Sarkar Mamta

    2011-02-01

    Full Text Available Abstract Background Human metapneumovirus (hMPV is associated with the acute respiratory tract infection (ARTI in all the age groups. However, there is limited information on prevalence and genetic diversity of human metapneumovirus (hMPV strains circulating in India. Objective To study prevalence and genomic diversity of hMPV strains among ARTI patients reporting in outpatient departments of hospitals in Kolkata, Eastern India. Methods Nasal and/or throat swabs from 2309 patients during January 2006 to December 2009, were screened for the presence of hMPV by RT-PCR of nucleocapsid (N gene. The G and F genes of representative hMPV positive samples were sequenced. Results 118 of 2309 (5.11% clinical samples were positive for hMPV. The majority (≈80% of the positive cases were detected during July−November all through the study period. Genetic analysis revealed that 77% strains belong to A2 subgroup whereas rest clustered in B1 subgroup. G sequences showed higher diversity at the nucleotide and amino acid level. In contrast, less than 10% variation was observed in F gene of representative strains of all four years. Sequence analysis also revealed changes in the position of stop codon in G protein, which resulted in variable length (217-231 aa polypeptides. Conclusion The study suggests that approximately 5% of ARTI in the region were caused by hMPV. This is the first report on the genetic variability of G and F gene of hMPV strains from India which clearly shows that the G protein of hMPV is continuously evolving. Though the study partially fulfills lacunae of information, further studies from other regions are necessary for better understanding of prevalence, epidemiology and virus evolution in Indian subcontinent.

  7. Genetic variability in sunflower (Helianthus annuus L.) and in the Helianthus genus as assessed by retrotransposon-based molecular markers.

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    Vukich, M; Schulman, A H; Giordani, T; Natali, L; Kalendar, R; Cavallini, A

    2009-10-01

    The inter-retrotransposon amplified polymorphism (IRAP) protocol was applied for the first time within the genus Helianthus to assess intraspecific variability based on retrotransposon sequences among 36 wild accessions and 26 cultivars of Helianthus annuus L., and interspecific variability among 39 species of Helianthus. Two groups of LTRs, one belonging to a Copia-like retroelement and the other to a putative retrotransposon of unknown nature (SURE) have been isolated, sequenced and primers were designed to obtain IRAP fingerprints. The number of polymorphic bands in H. annuus wild accessions is as high as in Helianthus species. If we assume that a polymorphic band can be related to a retrotransposon insertion, this result suggests that retrotransposon activity continued after Helianthus speciation. Calculation of similarity indices from binary matrices (Shannon's and Jaccard's indices) show that variability is reduced among domesticated H. annuus. On the contrary, similarity indices among Helianthus species were as large as those observed among wild H. annuus accessions, probably related to their scattered geographic distribution. Principal component analysis of IRAP fingerprints allows the distinction between perennial and annual Helianthus species especially when the SURE element is concerned.

  8. Blastocystis Isolates from Patients with Irritable Bowel Syndrome and from Asymptomatic Carriers Exhibit Similar Parasitological Loads, but Significantly Different Generation Times and Genetic Variability across Multiple Subtypes.

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    Vargas-Sanchez, Gie-Bele; Romero-Valdovinos, Mirza; Ramirez-Guerrero, Celedonio; Vargas-Hernandez, Ines; Ramirez-Miranda, Maria Elena; Martinez-Ocaña, Joel; Valadez, Alicia; Ximenez, Cecilia; Lopez-Escamilla, Eduardo; Hernandez-Campos, Maria Elena; Villalobos, Guiehdani; Martinez-Hernandez, Fernando; Maravilla, Pablo

    2015-01-01

    Blastocystis spp is a common intestinal parasite of humans and animals that has been associated to the etiology of irritable bowel syndrome (IBS); however, some studies have not found this association. Furthermore, many biological features of Blastocystis are little known. The objective of present study was to assess the generation times of Blastocystis cultures, from IBS patients and from asymptomatic carriers. A total of 100 isolates were obtained from 50 IBS patients and from 50 asymptomatic carriers. Up to 50 mg of feces from each participant were cultured in Barret's and in Pavlova's media during 48 h. Initial and final parasitological load were measured by microscopy and by quantitative PCR. Amplicons were purified, sequenced and submitted to GenBank; sequences were analysed for genetic diversity and a Bayesian inference allowed identifying genetic subtypes (ST). Generation times for Blastocystis isolates in both media, based on microscopic measures and molecular assays, were calculated. The clinical symptoms of IBS patients and distribution of Blastocystis ST 1, 2 and 3 in both groups was comparable to previous reports. Interestingly, the group of cases showed scarce mean nucleotide diversity (π) as compared to the control group (0.011±0.016 and 0.118±0.177, respectively), whilst high gene flow and small genetic differentiation indexes between different ST were found. Besides, Tajima's D test showed negative values for ST1-ST3. No statistical differences regarding parasitological load between cases and controls in both media, as searched by microscopy and by qPCR, were detected except that parasites grew faster in Barret's than in Pavlova's medium. Interestingly, slow growth of isolates recovered from cases in comparison to those of controls was observed (pBlastocystis might be easily affected by intestinal environmental changes due to IBS probably because virulent strains with slow growth may be selected, reducing their genetic variability.

  9. Blastocystis Isolates from Patients with Irritable Bowel Syndrome and from Asymptomatic Carriers Exhibit Similar Parasitological Loads, but Significantly Different Generation Times and Genetic Variability across Multiple Subtypes.

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    Gie-Bele Vargas-Sanchez

    selected, reducing their genetic variability.

  10. Experimental Voltage Stabilization of a Variable Speed Wind Turbine Driving Synchronous Generator using STATCOM based on Genetic Algorithm

    Science.gov (United States)

    El-Zoghby, Helmy M.; Bendary, Ahmed F.

    2016-10-01

    In this paper Static Synchronous Compensator (STATCOM) is used for improving the performance of the power grid with wind turbine that drives synchronous generator. The main feature of the STATCOM is that it has the ability to absorb or inject rapidly reactive power to grid. Therefore the voltage regulation of the power grid with STATCOM device is achieved. STATCOM also improves the stability of the power system after occurring severe disturbance such as faults, or suddenly step change in wind speed. The proposed STATCOM controller is a Proportional-Integral (PI) controller tuned by Genetic Algorithm (GA). An experimental model was built in Helwan University to the proposed system. The system is tested at different operating conditions. The experimental results prove the effectiveness of the proposed STATCOM controller in damping the power system oscillations and restoring the power system voltage and stability.

  11. Conservation priorities for Prunus africana defined with the aid of spatial analysis of genetic data and climatic variables.

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    Barbara Vinceti

    Full Text Available Conservation priorities for Prunus africana, a tree species found across Afromontane regions, which is of great commercial interest internationally and of local value for rural communities, were defined with the aid of spatial analyses applied to a set of georeferenced molecular marker data (chloroplast and nuclear microsatellites from 32 populations in 9 African countries. Two approaches for the selection of priority populations for conservation were used, differing in the way they optimize representation of intra-specific diversity of P. africana across a minimum number of populations. The first method (S1 was aimed at maximizing genetic diversity of the conservation units and their distinctiveness with regard to climatic conditions, the second method (S2 at optimizing representativeness of the genetic diversity found throughout the species' range. Populations in East African countries (especially Kenya and Tanzania were found to be of great conservation value, as suggested by previous findings. These populations are complemented by those in Madagascar and Cameroon. The combination of the two methods for prioritization led to the identification of a set of 6 priority populations. The potential distribution of P. africana was then modeled based on a dataset of 1,500 georeferenced observations. This enabled an assessment of whether the priority populations identified are exposed to threats from agricultural expansion and climate change, and whether they are located within the boundaries of protected areas. The range of the species has been affected by past climate change and the modeled distribution of P. africana indicates that the species is likely to be negatively affected in future, with an expected decrease in distribution by 2050. Based on these insights, further research at the regional and national scale is recommended, in order to strengthen P. africana conservation efforts.

  12. Conservation priorities for Prunus africana defined with the aid of spatial analysis of genetic data and climatic variables.

    Science.gov (United States)

    Vinceti, Barbara; Loo, Judy; Gaisberger, Hannes; van Zonneveld, Maarten J; Schueler, Silvio; Konrad, Heino; Kadu, Caroline A C; Geburek, Thomas

    2013-01-01

    Conservation priorities for Prunus africana, a tree species found across Afromontane regions, which is of great commercial interest internationally and of local value for rural communities, were defined with the aid of spatial analyses applied to a set of georeferenced molecular marker data (chloroplast and nuclear microsatellites) from 32 populations in 9 African countries. Two approaches for the selection of priority populations for conservation were used, differing in the way they optimize representation of intra-specific diversity of P. africana across a minimum number of populations. The first method (S1) was aimed at maximizing genetic diversity of the conservation units and their distinctiveness with regard to climatic conditions, the second method (S2) at optimizing representativeness of the genetic diversity found throughout the species' range. Populations in East African countries (especially Kenya and Tanzania) were found to be of great conservation value, as suggested by previous findings. These populations are complemented by those in Madagascar and Cameroon. The combination of the two methods for prioritization led to the identification of a set of 6 priority populations. The potential distribution of P. africana was then modeled based on a dataset of 1,500 georeferenced observations. This enabled an assessment of whether the priority populations identified are exposed to threats from agricultural expansion and climate change, and whether they are located within the boundaries of protected areas. The range of the species has been affected by past climate change and the modeled distribution of P. africana indicates that the species is likely to be negatively affected in future, with an expected decrease in distribution by 2050. Based on these insights, further research at the regional and national scale is recommended, in order to strengthen P. africana conservation efforts.

  13. Genetic variability in E6 and E7 oncogenes of human papillomavirus Type 16 from Congolese cervical cancer isolates.

    Science.gov (United States)

    Boumba, Luc Magloire Anicet; Assoumou, Samira Zoa; Hilali, Lahoucine; Mambou, Jean Victor; Moukassa, Donatien; Ennaji, Mustapha Moulay

    2015-01-01

    The molecular epidemiological studies showed that some variants of HPV-16, distributed geographically, would present a higher risk of causing cervical cancer. This study aimed to analyze nucleotide changes of HPV-16 E6 and E7 genomic regions from infected Southwestern Congolese women. DNA of twenty HPV-16 isolates was analyzed by amplifying the E6 and E7 genes using type-specific primers PCR and direct sequencing. The sequences obtained were aligned with the HPV-16 GenBank reference sequences. Thirteen (65.0%) out of 20 DNA-samples were successfully amplified. Genetic analysis revealed 18 and 4 nucleotide changes in E6 and E7 genomic regions respectively. The most frequently observed nucleotide variations were the missense C143G, G145T and C335T in E6 (100%), leading to the non-synonymous amino acid variation Q14D and H78Y. E7 genomic region was found to be highly conserved with two most common T789C and T795G (100%) silent variations. All HPV-16 variants identified belonged to the African lineage: 7 (53.8%) belonged to Af-1 lineage and 6 (46.1%) to Af-2 lineage. The missense mutation G622A (D21N) in the E7 region seems to be described for the first time in this study. This study reported for the first time the distribution of HPV-16 E6 and E7 genetic variants in infected women from southwest Congo. The findings confirmed almost ascendancy of the African lineage in our study population.

  14. Genetic predictions of prion disease susceptibility in carnivore species based on variability of the prion gene coding region.

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    Paula Stewart

    Full Text Available Mammalian species vary widely in their apparent susceptibility to prion diseases. For example, several felid species developed prion disease (feline spongiform encephalopathy or FSE during the bovine spongiform encephalopathy (BSE epidemic in the United Kingdom, whereas no canine BSE cases were detected. Whether either of these or other groups of carnivore species can contract other prion diseases (e.g. chronic wasting disease or CWD remains an open question. Variation in the host-encoded prion protein (PrP(C largely explains observed disease susceptibility patterns within ruminant species, and may explain interspecies differences in susceptibility as well. We sequenced and compared the open reading frame of the PRNP gene encoding PrP(C protein from 609 animal samples comprising 29 species from 22 genera of the Order Carnivora; amongst these samples were 15 FSE cases. Our analysis revealed that FSE cases did not encode an identifiable disease-associated PrP polymorphism. However, all canid PrPs contained aspartic acid or glutamic acid at codon 163 which we propose provides a genetic basis for observed susceptibility differences between canids and felids. Among other carnivores studied, wolverine (Gulo gulo and pine marten (Martes martes were the only non-canid species to also express PrP-Asp163, which may impact on their prion diseases susceptibility. Populations of black bear (Ursus americanus and mountain lion (Puma concolor from Colorado showed little genetic variation in the PrP protein and no variants likely to be highly resistant to prions in general, suggesting that strain differences between BSE and CWD prions also may contribute to the limited apparent host range of the latter.

  15. Genetic diversity of staphylocoagulase genes (coa: insight into the evolution of variable chromosomal virulence factors in Staphylococcus aureus.

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    Shinya Watanabe

    Full Text Available BACKGROUND: The production of staphylocoagulase (SC causing the plasma coagulation is one of the important characteristics of Staphylococcus aureus. Although SCs have been classified into 10 serotypes based on the differences in the antigenicity, genetic bases for their diversities and relatedness to chromosome types are poorly understood. METHODOLOGY/PRINCIPAL FINDINGS: We compared the nucleotide sequences of 105 SC genes (coa, 59 of which were determined in this study. D1 regions, which contain prothrombin-activating and -binding domains and are presumed to be the binding site of each type-specific antiserum, were classified into twelve clusters having more than 90% nucleotide identities, resulting to create two novel SC types, XI and XII, in addition to extant 10 types. Nine of the twelve SC types were further subdivided into subtypes based on the differences of the D2 or the central regions. The phylogenetical relations of the D1 regions did not correlate exactly with either one of agr types and multilocus sequence types (STs. In addition, genetic analysis showed that recombination events have occurred in and around coa. So far tested, STs of 126 S. aureus strains correspond to the combination of SC type and agr type except for the cases of CC1 and CC8, which contained two and three different SC types, respectively. CONCLUSION: The data suggested that the evolution of coa was not monophyletic in the species. Chromosomal recombination had occurred at coa and agr loci, resulting in the carriage of the combinations of allotypically different important virulence determinants in staphylococcal chromosome.

  16. Variabilidade genética em búfalos estimada por marcadores RAPD Genetic variability of buffaloes estimated by RAPD markers

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    Maria do Socorro Maués Albuquerque

    2006-04-01

    Full Text Available O objetivo deste trabalho foi caracterizar, por meio de marcadores RAPD, dois grupos genéticos de búfalos, Carabao e tipo Baio, que estão sendo conservados in situ, assim como verificar as relações genéticas entre eles e os outros três grupos genéticos de búfalos existentes no Brasil, Murrah, Jafarabadi e Mediterrâneo, considerados raças comerciais. Foram estudados 48 animais de cada grupo, com exceção dos grupos Murrah e Mediterrâneo, com 47 e 42 animais, respectivamente, compreendendo um total de 233 animais. Os 21 iniciadores polimórficos geraram 98 marcadores. A variabilidade genética entre e dentro dos grupos foi estimada em 26,5 e 73,5%, respectivamente, sugerindo divergência significativa entre os cinco grupos genéticos. Na análise entre pares de grupos, foi verificado que a maior e a menor divergência estavam em torno de 40 e 18%, quando se compararam os grupos Carabao x Mediterrâneo e Murrah x Jafarabadi, respectivamente. Entre os grupos Baio e Murrah, a análise revelou divergência genética de 20,42%, indicando que esses grupos são distintos. Os cinco grupos são geneticamente distintos, o que reforça a necessidade de conservação dos grupos genéticos Carabao e Baio, ameaçados de extinção no Brasil.The objective of this work was to characterize genetically, using RAPD markers, two genetic groups of buffalos, Carabao and Baio, which are being conserved in situ, as well as to verify the genetic relationship among them and the other three genetic groups of buffalos raised in Brazil, considered as commercial breeds: Murrah, Jaffarabadi and Mediterrâneo. Forty eight animals of each group were studied, with the exception of the Murrah and Mediterrâneo, in which 47 and 42 animals, respectively, were sampled, comprising a total of 233 animals. The 21 polymorphic primers produced 98 markers. Genetic variability within and between groups was estimated in 26.5 and 73.5%, respectively, suggesting a significant

  17. Variable Number Tandem Repeat (VNTR) analysis reveals genetic diversity within Mycoplasma mycoides mycoides small colony isolates from Nigeria.

    Science.gov (United States)

    Nwankpa, N D; Manso-silvan, L; Lorenzon, S; Yaya, A; Lombin, L H; Thiaucourt, F

    2010-12-15

    A Variable Number Tandem Repeat (VNTR) analysis was conducted on thirteen (13) M. mycoides mycoides Small Colony isolates from Nigeria using Tandem Repeat (TR) 34 which is a predicted lipoprotein located within the hypothetical protein MAG6170. The analysis revealed diversity within the M. mycoides mycoides Small Colony isolates with five different VNTR types indicated. Some correlation was determined between the VNTR types and their geographical origin. VNTR analysis may represent a useful, rapid first-line test for use in molecular epidemiological analysis of M. mycoides mycoides Small Colony for possible outbreak tracing and disease control.

  18. Variabilidade genética de acessos de maracujá-suspiro com base em marcadores moleculares Genetic variability of wild passion fruit determined by molecular markers

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    Keize Pereira Junqueira

    2007-01-01

    Full Text Available Passiflora nitida é uma espécie silvestre amplamente distribuída pelo território brasileiro, constituindo-se em fonte de resistência a doenças foliares e de raízes. O objetivo deste trabalho foi avaliar a variabilidade genética entre acessos de P. nitida procedentes de diferentes tipos fitofisionômicos de Cerrado e estados brasileiros (Goiás, Distrito Federal, Tocantins, Mato Grosso e Amazonas, usando marcadores moleculares RAPD. O DNA genômico de cada acesso foi extraído, e doze iniciadores decâmeros foram utilizados para a obtençã