Pollen parameters estimates of genetic variability among newly ...

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Pollen parameters estimates of genetic variability among newly selected Nigerian roselle (Hibiscus sabdariffa L.) genotypes. ... Estimates of some pollen parameters where used to assess the genetic diversity among ... HOW TO USE AJOL.

Variability of individual genetic load: consequences for the detection of inbreeding depression.

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Restoux, Gwendal; Huot de Longchamp, Priscille; Fady, Bruno; Klein, Etienne K

2012-03-01

Inbreeding depression is a key factor affecting the persistence of natural populations, particularly when they are fragmented. In species with mixed mating systems, inbreeding depression can be estimated at the population level by regressing the average progeny fitness by the selfing rate of their mothers. We applied this method using simulated populations to investigate how population genetic parameters can affect the detection power of inbreeding depression. We simulated individual selfing rates and genetic loads from which we computed fitness values. The regression method yielded high statistical power, inbreeding depression being detected as significant (5 % level) in 92 % of the simulations. High individual variation in selfing rate and high mean genetic load led to better detection of inbreeding depression while high among-individual variation in genetic load made it more difficult to detect inbreeding depression. For a constant sampling effort, increasing the number of progenies while decreasing the number of individuals per progeny enhanced the detection power of inbreeding depression. We discuss the implication of among-mother variability of genetic load and selfing rate on inbreeding depression studies.

Conspicuous plumage colours are highly variable.

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Delhey, Kaspar; Szecsenyi, Beatrice; Nakagawa, Shinichi; Peters, Anne

2017-01-25

Elaborate ornamental traits are often under directional selection for greater elaboration, which in theory should deplete underlying genetic variation. Despite this, many ornamental traits appear to remain highly variable and how this essential variation is maintained is a key question in evolutionary biology. One way to address this question is to compare differences in intraspecific variability across different types of traits to determine whether high levels of variation are associated with specific trait characteristics. Here we assess intraspecific variation in more than 100 plumage colours across 55 bird species to test whether colour variability is linked to their level of elaboration (indicated by degree of sexual dichromatism and conspicuousness) or their condition dependence (indicated by mechanism of colour production). Conspicuous colours had the highest levels of variation and conspicuousness was the strongest predictor of variability, with high explanatory power. After accounting for this, there were no significant effects of sexual dichromatism or mechanisms of colour production. Conspicuous colours may entail higher production costs or may be more sensitive to disruptions during production. Alternatively, high variability could also be related to increased perceptual difficulties inherent to discriminating highly elaborate colours. Such psychophysical effects may constrain the exaggeration of animal colours. © 2017 The Author(s).

Genetic variability of indigenous cowpea genotypes as determined ...

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Bayesian statistics coupled with the Markov chain Monte Carlo technique was applied to determine population structure, while the genetic variability was established by analysis of molecular variance. UPGMA analysis allowed the separation of the genotypes into three groups, but no relationship between the genetic and ...

Genetic Variants Contribute to Gene Expression Variability in Humans

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Hulse, Amanda M.; Cai, James J.

2013-01-01

Expression quantitative trait loci (eQTL) studies have established convincing relationships between genetic variants and gene expression. Most of these studies focused on the mean of gene expression level, but not the variance of gene expression level (i.e., gene expression variability). In the present study, we systematically explore genome-wide association between genetic variants and gene expression variability in humans. We adapt the double generalized linear model (dglm) to simultaneously fit the means and the variances of gene expression among the three possible genotypes of a biallelic SNP. The genomic loci showing significant association between the variances of gene expression and the genotypes are termed expression variability QTL (evQTL). Using a data set of gene expression in lymphoblastoid cell lines (LCLs) derived from 210 HapMap individuals, we identify cis-acting evQTL involving 218 distinct genes, among which 8 genes, ADCY1, CTNNA2, DAAM2, FERMT2, IL6, PLOD2, SNX7, and TNFRSF11B, are cross-validated using an extra expression data set of the same LCLs. We also identify ∼300 trans-acting evQTL between >13,000 common SNPs and 500 randomly selected representative genes. We employ two distinct scenarios, emphasizing single-SNP and multiple-SNP effects on expression variability, to explain the formation of evQTL. We argue that detecting evQTL may represent a novel method for effectively screening for genetic interactions, especially when the multiple-SNP influence on expression variability is implied. The implication of our results for revealing genetic mechanisms of gene expression variability is discussed. PMID:23150607

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

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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.

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

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Enrique Sáez-Laguna

Full Text Available 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.

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.

Genetic variability of hull-less barley accessions based on molecular and quantitative data

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Ricardo Meneses Sayd

2015-02-01

Full Text Available The objective of this work was to characterize and quantify the genetic, molecular, and agronomic variability of hull-less barley genotypes, for the selection of parents and identification of genotypes adapted to the irrigated production system in the Brazilian Cerrado. Eighteen hull-less barley accessions were evaluated, and three covered barley accessions served as reference. The characterization was based on 157 RAPD molecular markers and ten agronomic traits. Genetic distance matrices were obtained based on molecular markers and quantitative traits. Graphic grouping and dispersion analyses were performed. Genetic, molecular, and agronomic variability was high among genotypes. Ethiopian accessions were genetically more similar, and the Brazilian ones were genetically more distant. For agronomic traits, two more consistent groupings were obtained, one with the most two-rowed materials, and the other with six-rowed materials. The more diverging materials were the two-rowed CI 13453, CN Cerrado 5, CN Cerrado 1, and CN Cerrado 2. The PI 356466, CN Cerrado 1, PI 370799, and CI 13453 genotypes show agronomic traits of interest and, as genetically different genotypes, they are indicated for crossing, in breeding programs.

Molecular evaluation of genetic variability of wheat elite breeding material

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Brbaklić Ljiljana

2009-01-01

Full Text Available Estimation of genetic variability of breeding material is essential for yield improvement in wheat cultivars. Modern techniques based on molecular markers application are more efficient and precise in genetic variability evaluation then conventional methods. Variability of 96 wheat cultivars and lines was analyzed using four microsatellite markers (Gwm11, Gwm428, Psp3200, Psp3071. The markers were chosen according to their potential association with important agronomical traits indicated in the literature. Total of 31 alleles were detected with maximum number of alleles (11 in Xgwm11 locus. The highest polymorphism information content (PIC value (0,831 was found in the locus Xpsp3071. The genotypes were grouped into three subpopulations based on their similarity in the analyzed loci. The results have indicated wide genetic variability of the studied material and possibility of its application in further breeding process after validation of marker-trait association. .

Genetic variability of genital mycoplasmas and its clinical value

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K. I. Plakhova

2015-01-01

Full Text Available The article presents data on genetic variability of genital mycoplasmas. The author presents the results of genetic variability studies for M. hominis, gene vaa, U. parvum, gene mba, and M. genitalium, gene mg192, sampled from women with different clinical manifestations of inflammatory diseases of the urogenital system. Based on the molecular typing results for 138 samples of genital mycoplasmas, the author revealed a relationship between clinical manifestations of inflammatory diseases of the urogenital system caused by U. parvum and different U. parvum serovars as well as different genetic variations of M. hominis.Infection with 6 U. parvum serovar results in the development of inflammatory diseases of the urogenital tract accompanied by subjective manifestations (р < 0.05. Genetic variant II of М. hominis was revealed more often in patients with clinical manifestations of inflammatory diseases while variant I was revealed more often in patients infected with М. hominis without any signs of inflammation (р < 0.05. Genetic variants of M. genitalium were determined; no significant differences in terms of their prevalence in the examined patients were revealed.

Genetic Variability, Correlation Studies and Path Coefficient Analysis in Gladiolus Alatus Cultivars

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Ramzan, A.; Nawab, N. N.; Tariq, M. S.; Ikram, S.; Ahad, A.

2016-01-01

A study was undertaken to find out the estimates of genetic variability, genetic parameters and character association among different flower traits between three gladiolus cultivars viz: Sancerre, Fado and Advanced Red. The experiment was repeated three times by using RCBD (Randomized complete block design) at Department of Horticulture, PMAS-UAAR, Rawalpindi. The highest genotypic coefficient variation (GCV) and phenotypic coefficient variation (PCV) magnitude was observed for spike length (16.00) and number of florets per spike (14.84) followed by number of leaves (10.00). Among the traits studied the highest heritability estimates was recorded in spike length (99.5 percent) followed by number of florets/spike (99.6 percent) and lowest in plant height (98.2 percent). The genetic advance as percent of mean was ranged from 2.8 percent to 24.75 percent. Genetic advance was highest for floret breadth (24.75 percent) and lowest for plant height (2.8 percent). High heritability combined with high genetic advance was noticed for number of florets per spike, spike length and floret breadth indicating additive gene action which suggested that improvement of these traits would be effective for further selection of superior genotypes. Plant height and number of florets per spike showed highly positive and significant association with spike length, number of leaves, leaf area, floret length and floret breadth while, spike length registered positive and significant correlation with number of leaves and floret breadth. The path coefficient analysis based on spike length, as responsible variable exposed that all of the traits exerted direct positive effect except leaf area and floret length. Spike length imparted maximum positive direct effect on the number of florets per spike. Hence, spike length and number of florets per spike may be considered for further improvement. However, Floret length and floret breadth may also be considered as a criterion for selection. (author)

Evaluating Genetic Variability of Sorghum Mutant Lines Tolerant to Acid Soil

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Puspitasari, W.; Human, S.; Wirnas, D.; Trikoesoemaningtyas

2012-01-01

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 (author)

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

African Journals Online (AJOL)

TUOYO

2010-07-26

Jul 26, 2010 ... Full Length Research Paper. Genetic variability in Sudanese Acacia senegal (L.) assessed by random amplified polymorphic DNA. Rami S. Habeballa*, Nada B. Hamza and Eisa I. El Gaali. Commission for Biotechnology and Genetic Engineering, National Centre for Research, Khartoum, Sudan. P. O. Box.

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

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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.

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

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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.

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

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Huby, Marie; Griffon, Laurent; Moureaux, Sophie; De Rochambeau, Hubert; Danchin-Burge, Coralie; Verrier, Etienne

2003-01-01

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.

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

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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.

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.

Variable selection in Logistic regression model with genetic algorithm.

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Zhang, Zhongheng; Trevino, Victor; Hoseini, Sayed Shahabuddin; Belciug, Smaranda; Boopathi, Arumugam Manivanna; Zhang, Ping; Gorunescu, Florin; Subha, Velappan; Dai, Songshi

2018-02-01

Variable or feature selection is one of the most important steps in model specification. Especially in the case of medical-decision making, the direct use of a medical database, without a previous analysis and preprocessing step, is often counterproductive. In this way, the variable selection represents the method of choosing the most relevant attributes from the database in order to build a robust learning models and, thus, to improve the performance of the models used in the decision process. In biomedical research, the purpose of variable selection is to select clinically important and statistically significant variables, while excluding unrelated or noise variables. A variety of methods exist for variable selection, but none of them is without limitations. For example, the stepwise approach, which is highly used, adds the best variable in each cycle generally producing an acceptable set of variables. Nevertheless, it is limited by the fact that it commonly trapped in local optima. The best subset approach can systematically search the entire covariate pattern space, but the solution pool can be extremely large with tens to hundreds of variables, which is the case in nowadays clinical data. Genetic algorithms (GA) are heuristic optimization approaches and can be used for variable selection in multivariable regression models. This tutorial paper aims to provide a step-by-step approach to the use of GA in variable selection. The R code provided in the text can be extended and adapted to other data analysis needs.

Components of genetic variability of ear length of silage maize

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Sečanski Mile

2006-01-01

Full Text Available The objective of this study was to evaluate following parameters of the ear length of silage maize: variability of inbred lines and their diallel hybrids, superior-parent heterosis and genetic components of variability and habitability on the basis of a diallel set. The analysis of genetic variance shows that the additive component (D was lower than the dominant (H1 and H2 genetic variances, while the frequency of dominant genes (u for this trait was greater than the frequency of recessive genes (v Furthermore, this is also confirmed by the dominant to recessive genes ratio in parental inbreeds for the ear length (Kd/Kr> 1, which is greater than unity during both investigation years. The calculated value of the average degree of dominance √H1/D is greater than unity, pointing out to superdominance in inheritance of this trait in both years of investigation, which is also confirmed by the results of Vr/Wr regression analysis of inheritance of the ear length. As a presence of the non-allelic interaction was established it is necessary to study effects of epitasis as it can have a greater significance in certain hybrids. A greater value of dominant than additive variance resulted in high broad-sense habitability for ear length in both investigation years.

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

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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.

Genetic Variability in Glucosinolates in Seed of Brassica juncea: Interest in Mustard Condiment

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Othmane Merah

2015-01-01

Full Text Available Brassica juncea is mostly used for oil production which implies selection of genotypes with low glucosinolates level and high oil content. In contrast, condiment production needs varieties with high level in some glucosinolates including sinigrin. The genetic variability was studied mostly by molecular tools. The objectives were almost the decrease of glucosinolates level in order to use the oilcake for animal feed. The aim of this work is to study the genetic variability for different glucosinolates and their relationships with agronomical traits within a large collection of Brassica juncea genotypes for condiment uses. A collection of 190 genotypes from different origins was studied in Dijon (France. Oil content and total glucosinolates, and sinigrin and gluconapin levels were measured. Flowering and maturation durations, seed yield, and yield components were also measured. Large variability was observed between genotypes for the measured traits within the studied collection. Total glucosinolates varied twofold between extreme genotypes. Values of sinigrin content varied from 0 to more than 134 µmol·g−1. Correlations between glucosinolates traits and both phenological and agronomical characters are presented and discussed for their potential for industrial condiment uses.

Genetic Influence on Slope Variability in a Childhood Reflexive Attention Task.

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Rebecca A Lundwall

Full Text Available Individuals are not perfectly consistent, and interindividual variability is a common feature in all varieties of human behavior. Some individuals respond more variably than others, however, and this difference may be important to understanding how the brain works. In this paper, we explore genetic contributions to response time (RT slope variability on a reflexive attention task. We are interested in such variability because we believe it is an important part of the overall picture of attention that, if understood, has the potential to improve intervention for those with attentional deficits. Genetic association studies are valuable in discovering biological pathways of variability and several studies have found such associations with a sustained attention task. Here, we expand our knowledge to include a reflexive attention task. We ask whether specific candidate genes are associated with interindividual variability on a childhood reflexive attention task in 9-16 year olds. The genetic makers considered are on 11 genes: APOE, BDNF, CHRNA4, COMT, DRD4, HTR4, IGF2, MAOA, SLC5A7, SLC6A3, and SNAP25. We find significant associations with variability with markers on nine and we discuss the results in terms of neurotransmitters associated with each gene and the characteristics of the associated measures from the reflexive attention task.

HIV-1 Genetic Variability in Cuba and Implications for Transmission and Clinical Progression.

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Blanco, Madeline; Machado, Liuber Y; Díaz, Héctor; Ruiz, Nancy; Romay, Dania; Silva, Eladio

2015-10-01

INTRODUCTION Serological and molecular HIV-1 studies in Cuba have shown very low prevalence of seropositivity, but an increasing genetic diversity attributable to introduction of many HIV-1 variants from different areas, exchange of such variants among HIV-positive people with several coinciding routes of infection and other epidemiologic risk factors in the seropositive population. The high HIV-1 genetic variability observed in Cuba has possible implications for transmission and clinical progression. OBJECTIVE Study genetic variability for the HIV-1 env, gag and pol structural genes in Cuba; determine the prevalence of B and non-B subtypes according to epidemiologic and behavioral variables and determine whether a relationship exists between genetic variability and transmissibility, and between genetic variability and clinical disease progression in people living with HIV/AIDS. METHODS Using two molecular assays (heteroduplex mobility assay and nucleic acid sequencing), structural genes were characterized in 590 people with HIV-1 (480 men and 110 women), accounting for 3.4% of seropositive individuals in Cuba as of December 31, 2013. Nonrandom sampling, proportional to HIV prevalence by province, was conducted. Relationships between molecular results and viral factors, host characteristics, and patients' clinical, epidemiologic and behavioral variables were studied for molecular epidemiology, transmission, and progression analyses. RESULTS Molecular analysis of the three HIV-1 structural genes classified 297 samples as subtype B (50.3%), 269 as non-B subtypes (45.6%) and 24 were not typeable. Subtype B prevailed overall and in men, mainly in those who have sex with men. Non-B subtypes were prevalent in women and heterosexual men, showing multiple circulating variants and recombinant forms. Sexual transmission was the predominant form of infection for all. B and non-B subtypes were encountered throughout Cuba. No association was found between subtypes and

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.

Genetic variability assessment in the genus Passiflora by SSR markers

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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.

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.

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.

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.

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 devastating...... outbreaks in disease-free areas. In countries trying to control and eradicate FMD using vaccination strategies, the constantly evolving and wide diversity of field FMDV strains is an obstacle for identifying vaccine strains that are successful in conferring protection against infection with field viruses....... Consequently, quantitative knowledge on the factors that are associated with variability of the FMDV is prerequisite for preventing and controlling FMD in the Indian subcontinent. A hierarchical linear model was used to assess the association between time, space, host species and the genetic variability...

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

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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.

NOTE - Characterization of genetic variability among common bean genotypes by morphological descriptors

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Marilene Santos de Lima

2012-01-01

Full Text Available The purpose of this study was to characterize the genetic variability in 100 genotypes of the Active Germplasm Bank of common bean of the Federal University of Viçosa, by morphological descriptors, classify them in groups of genetic similarity and to identify the degree of relevance of descriptors of genetic divergence. The genotypes were evaluated based on 22 quantitative and qualitative morphological descriptors. The highyielding genotypes V 7936, Gold Gate, LM 95103904, 1829 S 349 Venezuela, and PF 9029975, CNFC 9454 andFe 732015, with upright growth, have potential for use as parents in common bean breeding programs. By genetic divergence analysis, the genotypes were clustered in eight groups of genetic dissimilarity. By methods of principal components, 9 of the 22 descriptors were eliminated, for being redundant or little variable, suggesting that 10-20 morphological descriptors can be used in studies of characterization of genetic variation.

Morphological Characterization and Assessment of Genetic Variability, Character Association, and Divergence in Soybean Mutants

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M. A. Malek

2014-01-01

Full Text Available Genetic diversity is important for crop improvement. An experiment was conducted during 2011 to study genetic variability, character association, and genetic diversity among 27 soybean mutants and four mother genotypes. Analysis of variance revealed significant differences among the mutants and mothers for nine morphological traits. Eighteen mutants performed superiorly to their mothers in respect to seed yield and some morphological traits including yield attributes. Narrow differences between phenotypic and genotypic coefficients of variation (PCV and GCV for most of the characters revealed less environmental influence on their expression. High values of heritability and genetic advance with high GCV for branch number, plant height, pod number, and seed weight can be considered as favorable attributes for soybean improvement through phenotypic selection and high expected genetic gain can be achieved. Pod and seed number and maturity period appeared to be the first order traits for higher yield and priority should be given in selection due to their strong associations and high magnitudes of direct effects on yield. Cluster analysis grouped 31 genotypes into five groups at the coefficient value of 235. The mutants/genotypes from cluster I and cluster II could be used for hybridization program with the mutants of clusters IV and V in order to develop high yielding mutant-derived soybean varieties for further improvement.

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.

Genetic variability of Artemisia capillaris (Wormwood capillary) by ...

African Journals Online (AJOL)

The genetic variability among individuals of Artemisia capillaris from state of Terengganu, Malaysia was examined by using the random amplified polymorphic DNA (RAPD) technique. The samples were collected from differences regional in Terengganu State. The genomic DNA was extracted from the samples leaves.

Estimation of genetic variability and heritability of wheat agronomic traits resulted from some gamma rays irradiation techniques

International Nuclear Information System (INIS)

Wijaya Murti Indriatama; Trikoesoemaningtyas; Syarifah Iis Aisyah; Soeranto Human

2016-01-01

Gamma irradiation techniques have significant effect on frequency and spectrum of macro-mutation but the study of its effect on micro-mutation that related to genetic variability on mutated population is very limited. The aim of this research was to study the effect of gamma irradiation techniques on genetic variability and heritability of wheat agronomic characters at M2 generation. This research was conducted from July to November 2014, at Cibadak experimental station, Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development, Ministry of Agriculture. Three introduced wheat breeding lines (F-44, Kiran-95 & WL-711) were treated by 3 gamma irradiation techniques (acute, fractionated and intermittent). M1 generation of combination treatments were planted and harvested its spike individually per plants. As M2 generation, seeds of 75 M1 spike were planted at the field with one row one spike method and evaluated on the agronomic characters and its genetic components. The used of gamma irradiation techniques decreased mean but increased range values of agronomic traits in M2 populations. Fractionated irradiation induced higher mean and wider range on spike length and number of spike let per spike than other irradiation techniques. Fractionated and intermittent irradiation resulted greater variability of grain weight per plant than acute irradiation. The number of tillers, spike weight, grain weight per spike and grain weight per plant on M2 population resulted from induction of three gamma irradiation techniques have high estimated heritability and broad sense of genetic variability coefficient values. The three gamma irradiation techniques increased genetic variability of agronomic traits on M2 populations, except plant height. (author)

Assessment of genetic variability of maize inbred lines and their ...

African Journals Online (AJOL)

Assessment of genetic variability of maize inbred lines and their hybrids under normal and drought conditions. ... Nigeria Agricultural Journal ... Analysis of variance revealed significant differences for most of the characters under study which indicates the presence of sufficient amount of variability offering ample scope for ...

Genetic variability and inter-character associations in the mutants of Indian mustard

International Nuclear Information System (INIS)

Labana, K.S.; Chaurasia, B.D.; Singh, Balwant

1980-01-01

To study the genetic variability and the inter-character associations in Indian mustard [Brassica juncea (Linn.)Czern. and Coss. subsp. juncea Linn.], 104 radiation-induced mutants (including 'RLM 198') and 'RL 18' were grown during winter season of 1976-77 at the experimental farm of the Punjab Agricultural University. Analysis of variance revealed significant differences between the mutant genotypes for all the characters under study except for the primary branch number and siliqua number of main shoot, which were non-significant. High estimates of phenotypic coefficients of variation (pcv) and genetic coefficients of variation (gcv) were observed for secondary branch number, seed yield/plant, main shoot length and seed number/siliqua. In general, pcv estimates were higher than gcv estimates. The high estimates of both heritability and genetic advance were recorded in similar order for the plant height, seed number/siliqua, main shoot length and seed yield, in which the genetic progress could be achieved through mass selection. Seed yield was positively correlated with the primary branch number, the secondary branch number and the siliqua number of main shoot and negatively with the plant height. Shorter plant height w;.th more number of primary and secondary branches and more siliquae on main shoot were found to be good selection criteria for isolating high-yielding strains. (auth.)

Temporal dynamics of genetic variability in a mountain goat (Oreamnos americanus) population.

Science.gov (United States)

Ortego, Joaquín; Yannic, Glenn; Shafer, Aaron B A; Mainguy, Julien; Festa-Bianchet, Marco; Coltman, David W; Côté, Steeve D

2011-04-01

The association between population dynamics and genetic variability is of fundamental importance for both evolutionary and conservation biology. We combined long-term population monitoring and molecular genetic data from 123 offspring and their parents at 28 microsatellite loci to investigate changes in genetic diversity over 14 cohorts in a small and relatively isolated population of mountain goats (Oreamnos americanus) during a period of demographic increase. Offspring heterozygosity decreased while parental genetic similarity and inbreeding coefficients (F(IS) ) increased over the study period (1995-2008). Immigrants introduced three novel alleles into the population and matings between residents and immigrants produced more heterozygous offspring than local crosses, suggesting that immigration can increase population genetic variability. The population experienced genetic drift over the study period, reflected by a reduced allelic richness over time and an 'isolation-by-time' pattern of genetic structure. The temporal decline of individual genetic diversity despite increasing population size probably resulted from a combination of genetic drift due to small effective population size, inbreeding and insufficient counterbalancing by immigration. This study highlights the importance of long-term genetic monitoring to understand how demographic processes influence temporal changes of genetic diversity in long-lived organisms. © 2011 Blackwell Publishing Ltd.

Genetic variability, trait association and path analysis of yield and yield components in mungbean (vigna radiata (L.) wilczek)

International Nuclear Information System (INIS)

Tabasum, A.; Saleem, M.; Aziz, I.

2010-01-01

Genetic variability, heritability along with genetic advance of traits, their association and direct and indirect effects on yield are essential for crop improvement. Ten mungbean genotypes were studied to assess variability and degree to which various plant traits associate with seed yield. Primary and secondary branches, pods per cluster and pod length showed lesser variability while clusters per plant, 100 seed weight and harvest index exhibited intermediate range of variability. Sufficient genetic variability was observed for plant height, pods per plant, total plant weight and seed yield. Moderate to high heritability estimates were found for all traits. Primary and secondary branches per plant, pod length and 100-seed weight exhibited negative and non significant genotypic and phenotypic correlations with seed yield. Plant height showed positive non-significant and significant genotypic and phenotypic correlation. Pods per cluster correlated significantly negative with seed yield. Clusters per plant, pods per plant, total plant weight and harvest index showed positive significant genotypic and phenotypic correlations with seed yield. Positive direct effects were exerted through secondary branches, pods per plant, pod length, 100 seed weight, total plant weight and harvest index while primary branches, plant height, clusters per plant and pods per cluster had negative direct effects. The present findings could be useful for establishing selection criteria for high seed yield in the mungbean breeding. (author)

INDUCED GENETIC VARIABILITY AND SELECTION FOR HIGH YIELDING MUTANTS IN BREAD WHEAT(TRITICUM AESTIVUM L.)

International Nuclear Information System (INIS)

SOBIEH, S.EL-S.S.

2007-01-01

This study was conducted during the two winter seasons of 2004/2005 and 2005/2006 at the experimental farm belonging to Plant Research Department, Nuclear Research Centre, AEA, Egypt.The aim of this study is to determine the effect of gamma rays(150, 200 and 250 Gy) on means of yield and its attributes for exotic wheat variety (vir-25) and induction of genetic variability that permits to perform visual selection through the irradiated populations, as well as to determine difference in seed protein patterns between vir-25 parent variety and some selectants in M2 generation.The results showed that the different doses of gamma rays had non-significant effect on mean value of yield/plant and significant effect on mean values of it's attributes. 0n the other hand, the considered genetic variability was generated as result of applying gamma irradiation. The highest amount of induced genetic variability was detected for number of grains/ spike, spike length and number of spikes/plant. Additionally, these three traits exhibited strong association with grain yield/plant, hence, they were used as a criterion for selection.Some variant plants were selected from radiation treatment 250 Gy, with 2-10 spikes per plant.These variant plants exhibited increasing in spike length and number of gains/spike.The results also revealed that protein electrophoresis were varied in the number and position of bands from genotype to another and various genotypes share bands with molecular weights 31.4 and 3.2 KD.Many bands were found to be specific for the genotype and the nine wheat mutants were characterized by the presence of bands of molecular weights: 151.9, 125.7, 14.1 and 5.7 KD at M-167.4, 21.7 and 8.2 at M-299.7 KD at M-3136.1, 97.6, 49.8, 27.9 and 20.6 KD at M-4 135.2, 95.3 and 28.1 KD at M-5 135.5, 67.7, 47.1, 32.3, 21.9 and 9.6 KD at M-6 126.1, 112.1, 103.3, 58.8, 20.9 and 12.1 KD at M-7 127.7, 116.6, 93.9, 55.0 and 47.4 KD at M-8 141.7, 96.1, 79.8, 68.9, 42.1, 32.7, 22.0 and 13

genetic variability among landraces of sesame in ethiopia abstract

African Journals Online (AJOL)

journal

Modified Rogers' Distances (MRD) and a principal coordinate analysis based on a ... Moreover, existence of great genetic variability between the landraces is a good starting point of sesame ...... among and within CIMMYT wheat landrace.

ABCB1 genetic variability and methadone dosage requirements in opioid-dependent individuals.

Science.gov (United States)

Coller, Janet K; Barratt, Daniel T; Dahlen, Karianne; Loennechen, Morten H; Somogyi, Andrew A

2006-12-01

The most common treatment for opioid dependence is substitution therapy with another opioid such as methadone. The methadone dosage is individualized but highly variable, and program retention rates are low due in part to nonoptimal dosing resulting in withdrawal symptoms and further heroin craving and use. Methadone is a substrate for the P-glycoprotein transporter, encoded by the ABCB1 gene, which regulates central nervous system exposure. This retrospective study aimed to investigate the influence of ABCB1 genetic variability on methadone dose requirements. Genomic deoxyribonucleic acid was isolated from opioid-dependent subjects (n = 60) and non-opioid-dependent control subjects (n = 60), and polymerase chain reaction-restriction fragment length polymorphism and allele-specific polymerase chain reaction were used to determine the presence of single nucleotide polymorphisms at positions 61, 1199, 1236, 2677, and 3435. ABCB1 haplotypes were inferred with PHASE software (version 2.1). There were no significant differences in the allele or genotype frequencies of the individual single nucleotide polymorphisms or haplotypes between the 2 populations. ABCB1 genetic variability influenced daily methadone dose requirements, such that subjects carrying 2 copies of the wild-type haplotype required higher doses compared with those with 1 copy and those with no copies (98.3 +/- 10.4, 58.6 +/- 20.9, and 55.4 +/- 26.1 mg/d, respectively; P = .029). In addition, carriers of the AGCTT haplotype required significantly lower doses than noncarriers (38.0 +/- 16.8 and 61.3 +/- 24.6 mg/d, respectively; P = .04). Although ABCB1 genetic variability is not related to the development of opioid dependence, identification of variant haplotypes may, after larger prospective studies have been performed, provide clinicians with a tool for methadone dosage individualization.

Resolving the Complex Genetic Basis of Phenotypic Variation and Variability of Cellular Growth.

Science.gov (United States)

Ziv, Naomi; Shuster, Bentley M; Siegal, Mark L; Gresham, David

2017-07-01

In all organisms, the majority of traits vary continuously between individuals. Explaining the genetic basis of quantitative trait variation requires comprehensively accounting for genetic and nongenetic factors as well as their interactions. The growth of microbial cells can be characterized by a lag duration, an exponential growth phase, and a stationary phase. Parameters that characterize these growth phases can vary among genotypes (phenotypic variation), environmental conditions (phenotypic plasticity), and among isogenic cells in a given environment (phenotypic variability). We used a high-throughput microscopy assay to map genetic loci determining variation in lag duration and exponential growth rate in growth rate-limiting and nonlimiting glucose concentrations, using segregants from a cross of two natural isolates of the budding yeast, Saccharomyces cerevisiae We find that some quantitative trait loci (QTL) are common between traits and environments whereas some are unique, exhibiting gene-by-environment interactions. Furthermore, whereas variation in the central tendency of growth rate or lag duration is explained by many additive loci, differences in phenotypic variability are primarily the result of genetic interactions. We used bulk segregant mapping to increase QTL resolution by performing whole-genome sequencing of complex mixtures of an advanced intercross mapping population grown in selective conditions using glucose-limited chemostats. We find that sequence variation in the high-affinity glucose transporter HXT7 contributes to variation in growth rate and lag duration. Allele replacements of the entire locus, as well as of a single polymorphic amino acid, reveal that the effect of variation in HXT7 depends on genetic, and allelic, background. Amplifications of HXT7 are frequently selected in experimental evolution in glucose-limited environments, but we find that HXT7 amplifications result in antagonistic pleiotropy that is absent in naturally

Hookworm infection, anaemia and genetic variability of the New Zealand sea lion.

Science.gov (United States)

Acevedo-Whitehouse, Karina; Petetti, Laura; Duignan, Padraig; Castinel, Aurelie

2009-10-07

Hookworms are intestinal blood-feeding nematodes that parasitize and cause high levels of mortality in a wide range of mammals, including otariid pinnipeds. Recently, an empirical study showed that inbreeding (assessed by individual measures of multi-locus heterozygosity) is associated with hookworm-related mortality of California sea lions. If inbreeding increases susceptibility to hookworms, effects would expectedly be stronger in small, fragmented populations. We tested this assumption in the New Zealand sea lion, a threatened otariid that has low levels of genetic variability and high hookworm infection rates. Using a panel of 22 microsatellites, we found that average allelic diversity (5.9) and mean heterozygosity (0.72) were higher than expected for a small population with restricted breeding, and we found no evidence of an association between genetic variability and hookworm resistance. However, similar to what was observed for the California sea lion, homozygosity at a single locus explained the occurrence of anaemia and thrombocytopenia in hookworm-infected pups (generalized linear model, F = 11.81, p < 0.001) and the effect was apparently driven by a particular allele (odds ratio = 34.95%; CI: 7.12-162.41; p < 0.00001). Our study offers further evidence that these haematophagus parasites exert selective pressure on otariid blood-clotting processes.

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

African Journals Online (AJOL)

segregating progenies with maximum genetic variability for selection. .... cultivar Clipper applied in slots of the first two, the tenth, and the last ... solution (50 ml glacial acetic acid, 200 ml methanol and 250 ml distilled water) ...... Adelaide, South.

Environmental and geographic variables are effective surrogates for genetic variation in conservation planning.

Science.gov (United States)

Hanson, Jeffrey O; Rhodes, Jonathan R; Riginos, Cynthia; Fuller, Richard A

2017-11-28

Protected areas buffer species from anthropogenic threats and provide places for the processes that generate and maintain biodiversity to continue. However, genetic variation, the raw material for evolution, is difficult to capture in conservation planning, not least because genetic data require considerable resources to obtain and analyze. Here we show that freely available environmental and geographic distance variables can be highly effective surrogates in conservation planning for representing adaptive and neutral intraspecific genetic variation. We obtained occurrence and genetic data from the IntraBioDiv project for 27 plant species collected over the European Alps using a gridded sampling scheme. For each species, we identified loci that were potentially under selection using outlier loci methods, and mapped their main gradients of adaptive and neutral genetic variation across the grid cells. We then used the cells as planning units to prioritize protected area acquisitions. First, we verified that the spatial patterns of environmental and geographic variation were correlated, respectively, with adaptive and neutral genetic variation. Second, we showed that these surrogates can predict the proportion of genetic variation secured in randomly generated solutions. Finally, we discovered that solutions based only on surrogate information secured substantial amounts of adaptive and neutral genetic variation. Our work paves the way for widespread integration of surrogates for genetic variation into conservation planning.

Mycoplasma hyopneumoniae genetic variability within a swine operation.

Science.gov (United States)

Pantoja, Lucina Galina; Pettit, Kalie; Dos Santos, Lucas F; Tubbs, Rick; Pieters, Maria

2016-03-01

The objective of our study was to characterize the Mycoplasma hyopneumoniae genetic diversity within a swine operation comingling weaned pigs. Bronchial swabs and tracheal aspirates were collected from 3 nursery-to-finish farms. During the finishing production stages, samples were obtained from mortalities and from live coughing pigs in rooms where mortality was not observed. A total of 105 samples were examined by a M. hyopneumoniae real-time polymerase chain reaction and subjected to genetic typing using a multilocus variable number tandem repeat analysis (MLVA) assay. The MLVA was used to identify genetic variants based on the number of repeats in 2 variable number tandem repeats loci, namely P97 and P146, thought to mediate adherence of M. hyopneumoniae to swine cilia. Four distinguishable M. hyopneumoniae variants were identified: MVLA variants 9-15, 11-21, 9-21, and 7-15. Variant 9-15 was the most prevalent, observed in 79% of rooms, and detected on all 3 farms. Variant 11-21 was present in 37% of the rooms on 2 of the 3 farms. Only one 9-21 variant was identified in 1 farm, and all samples of variant 7-15 were recovered from another farm. Based on the low prevalence and limited geographic distribution of the last 2 variants, it is hypothesized that they might be the result of in-situ recombination. All variants detected in this investigation appeared to belong to 3 clusters. Overall, a limited number of variants and clusters were identified in a system that comingles pigs from different sources, suggesting limited M. hyopneumoniae genetic variation within commercial swine production environments. © 2016 The Author(s).

Genetic variability, correlation and path analysis in sponge gourd ...

African Journals Online (AJOL)

Windows-7

2013-02-06

Feb 6, 2013 ... fiber used in industries for filter and cleaning the motor car, glass wares, kitchen ... The fibrous vascular system inside the fruit after been separated from the skin, ... was carried out to gather information on genetic variability ...

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. Copyright © 2015 by the Genetics Society of America.

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. Copyright © 2013 Elsevier B.V. All rights reserved.

Genetic variability assessment of accessions of Corchorus olitorius L ...

African Journals Online (AJOL)

SAM

2014-05-14

May 14, 2014 ... genetic variabilities among 14 accessions of the species using sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE). Seven polypeptide bands were obtained ranging from. 9.73 to 88.79 KDa thus depicting variations in the banding patterns of the accessions. The unweighted.

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.

Genetic variability in elite barley genotypes based on the agro-morphological characteristics evaluated under irrigated system

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Renato Fernando Amabile

Full Text Available ABSTRACT Recently, researches have shown that the Brazilian savannah has a great potential to supply the demand for barley grains. The purpose of this study was to assess the genetic variability in 39 elite barley (Hordeum vulgare L. genotypes based on the agro-morphological traits of a crop irrigated in the savannah system. An irrigation experiment in the design of complete randomized block with four replicates was conducted at Federal District - Brazil. The evaluated traits were: distance from the last knot to the rachis, distance from the flag leaf to rachis, spike length, number of grains by ear, flag leaf area, plant height, silking, lodging, grain yield, thousand-seed weight, protein content and grain commercial classification. After using analysis of variance the means were used to estimate the genetic dissimilarity among all genotypes pairs based on the Mahalanobis’ generalized distance. Cluster analysis using genetic distance matrix was performed having Unweighted Pair Group Method using Arithmetic Means method (UPGMA as the criteria. Highly significant differences were found among the genotypes for all traits evaluated. The high coefficient of genetic variation indicates the possibility of having genetic gains for all traits. The traits that most contributed to the variability were the flag leaf area and silking, while the protein content and lodging were the traits that contributed the least. Based on the cluster analysis, at least three major groups of similarity were found. There was a clustering trend of two and six-rowed materials. The most divergent genotypes were PFC 2005123, Antártica-1, Nandi and FM 404.

Genetic variability for different quantitative traits in M2 generations of opium poppy (Papaver somniferum L.)

International Nuclear Information System (INIS)

Chatterjee, A.; Shukla, S.; Singh, S.P.

2004-01-01

An experiment on induced mutation in two varieties of opium poppy was laid out to create new genetic variability for isolation of high yielding genotypes. Varieties NBRI-1 and NBRI-5 were subjected to irradiation for five doses of gamma rays and NBRI-5 was also treated with four doses of EMS and 20 mixed doses of EMS plus gamma rays. The data were recorded on 15 plants/treatment for 10 polygenic characters as pooled in M1 and M2 generations separately as well as in each dose-wise in M2 population. The results indicated that GCV, heritability and genetic advance were higher in M1 than M2 in both the varieties for all the traits except for opium and seed yield. The genetic advance was consistently high for opium yield, seed yield and capsule weight in all the doses for both the varieties with some exception. The dose level of kR10 and kR30 in NBRI-1 revealed high GCV, heritability and genetic advance for seed weight. These treatment levels also had high values of all these three genetic parameters for capsules per plant, capsule size and capsule weight. The values of these three parameters were also high for all the doses in M2 generations of both the varieties for opium yield, seed weight, capsule weight and capsule size in comparison to control. The GCV, heritability and genetic advance were consistently high for all the mixed doses in NBRI-5 for opium yield, seed weight and capsule weight, with some exception [it

Genetic distance estimates and variable factors distinguishing between goat Kacang, Muara and Samosir

Science.gov (United States)

Hamdan; Saputra, H.; Mirwandhono, E.; Hasnudi; Sembiring, I.; Umar, S.; Ginting, N.; Alwiyah

2018-02-01

The purpose of this research was to look the genetic distance and factors distinguishing variable betwen types of goats in North Sumatera. This research have been conducted in PayaBakung, Hamparan Perak and Klambir Lima village, Deli Serdang district, Batu Binumbun, Aritonang, HutaGinjang village, Muarasubdistrict, North Tapanuli district and ParbabaDolok, Siopat Sosor, Sinabulan village, Ronggur Nihuta Pangururan village, Sitonggi-tonggi village in the subdistrict RonggurNihuta, Samosir district of the month of July 2016. The data was analyzed using descriptive, discriminants, canonical, Principal Component Analysis, Distance genetic and Tree Phylogenetic. The result showed that the nearest genetic distance goat found in Kacang and Samosir (1.973), and the farthest genetic distnace find in Samosir and Muara (8.671). The variables made it difference was goat race Base Rim Horn (0.856) and Long Horn (0.878). Genetic distance values most far between Muaragoat with Samosir goat was (8.671). The conclude that the crossing superior result, must be cross between two goat types with value genetics most distance. It will have a better chance heterosis in cross result.

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

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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.

Analysis of genetic variability in the Czech Dachshund population using microsatellite markers

Czech Academy of Sciences Publication Activity Database

Přibáňová, M.; Horák, Pavel; Schröffelová, D.; Urban, T.; Bechyňová, Renata; Musilová, L.

2009-01-01

Roč. 126, - (2009), s. 311-318 ISSN 0931-2668 R&D Projects: GA AV ČR 1QS500450578; GA ČR GD523/03/H076 Institutional research plan: CEZ:AV0Z50450515 Keywords : dachshund * dog * genetic variability * microsatellite Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.706, year: 2009

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.

Optimized design on condensing tubes high-speed TIG welding technology magnetic control based on genetic algorithm

Science.gov (United States)

Lu, Lin; Chang, Yunlong; Li, Yingmin; Lu, Ming

2013-05-01

An orthogonal experiment was conducted by the means of multivariate nonlinear regression equation to adjust the influence of external transverse magnetic field and Ar flow rate on welding quality in the process of welding condenser pipe by high-speed argon tungsten-arc welding (TIG for short). The magnetic induction and flow rate of Ar gas were used as optimum variables, and tensile strength of weld was set to objective function on the base of genetic algorithm theory, and then an optimal design was conducted. According to the request of physical production, the optimum variables were restrained. The genetic algorithm in the MATLAB was used for computing. A comparison between optimum results and experiment parameters was made. The results showed that the optimum technologic parameters could be chosen by the means of genetic algorithm with the conditions of excessive optimum variables in the process of high-speed welding. And optimum technologic parameters of welding coincided with experiment results.

Genetic consequences of forest fragmentation for a highly specialized arboreal mammal--the edible dormouse.

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Joanna Fietz

Full Text Available Habitat loss and fragmentation represent the most serious extinction threats for many species and have been demonstrated to be especially detrimental for mammals. Particularly, highly specialized species with low dispersal abilities will encounter a high risk of extinction in fragmented landscapes. Here we studied the edible dormouse (Glis glis, a small arboreal mammal that is distributed throughout Central Europe, where forests are mostly fragmented at different spatial scales. The aim of this study was to investigate the effect of habitat fragmentation on genetic population structures using the example of edible dormouse populations inhabiting forest fragments in south western Germany. We genotyped 380 adult individuals captured between 2001 and 2009 in four different forest fragments and one large continuous forest using 14 species-specific microsatellites. We hypothesised, that populations in small forest patches have a lower genetic diversity and are more isolated compared to populations living in continuous forests. In accordance with our expectations we found that dormice inhabiting forest fragments were isolated from each other. Furthermore, their genetic population structure was more unstable over the study period than in the large continuous forest. Even though we could not detect lower genetic variability within individuals inhabiting forest fragments, strong genetic isolation and an overall high risk to mate with close relatives might be precursors to a reduced genetic variability and the onset of inbreeding depression. Results of this study highlight that connectivity among habitat fragments can already be strongly hampered before genetic erosion within small and isolated populations becomes evident.

Estimates of genetic variability in mutated population of triticum aestivum

International Nuclear Information System (INIS)

Larik, A.S.; Siddiqui, K.A.; Soomoro, A.H.

1980-01-01

M 2 populations of four cultivars of Mexican origin (Mexipak-65, Nayab, Pak-70 and 6134 x C-271) and two locally bred cultivars (H-68 and C-591) of bread wheat, triticum aestivum (2n = 6x = AA BB DD) derived from six irradiation treatments (gamma rays 60sub(Co); 10, 15 and 20 kR and fast neutrons; 300, 600 and 900 RADS) were critically examined for spike length, spikelets per spike, grains per spike and grain yield. Genotypes varied significantly (p>=0.01) for all the characters. Irradiation treatment were instrumental in creating significant variability for all the characters, indicating that varieties did not perform uniformly across different gamma rays as well as fast neutron treatments. In the M 2 generation there was a considerable increase in variance for all the four metrical traits. Comparisons were made between controls and treated populations. Mutagenic treatments shifted the mean values mostly towards the negative direction, but the shift was not unidirectional nor equally effective for all the characters. The differences in mean values and the nature of variability observed in M 2 indicated a possible preference of selection M 3 generation. In general, estimates of genetic variability and heritability (b.s) increased with increasing doses of gamma rays and fast neutrons. Genetic advance also exhibited similar trend. The observed variability can be utilized in the evolution of new varieties. (authors)

Genetic variability in five species of Anostomidae (Ostariophysi - Characiformes

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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.

Variability, heritability and genetic advance in F2 populations of aromatic rice involving induced mutants and Basmati varieties

International Nuclear Information System (INIS)

Hasib, K.M.; Ganguli, P.K.; Kole, P.C.

2000-01-01

The F 2 generation of five cross-combinations of aromatic rice involving two induced mutants 124-17-4 and 21-6-1 of aromatic tall Indica cultivar Gobindabhog and three basmati varieties was studied for mean performance, variability, heritability and genetic advance. The cross 21-6-1/Pakistan Basmati showed higher mean values for grain yield plant, and several yield components. Wide variability was observed for panicle number plant, filled grains panicle, test weight, dry matter production plant, harvest index and grain yield plant. Among the traits, filled grains panicle and test weight in all the crosses, grain yield plant, in five crosses and harvest index in two crosses had high heritability coupled with high genetic advance indicating predominant role of additive gene action. The crosses 21-6-1/Pakistan Basmati and 124-17-4/Pusa Basmati I could be exploited for isolation of promising aromatic recombinants. (author)

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

Genetic variability of Indonesian local chili pepper: The facts

Science.gov (United States)

Arumingtyas, Estri Laras; Kusnadi, Joni; Sari, Dewi Ratih Tirto; Ratih, Nursita

2017-11-01

Chili pepper (Capsicum frutescens) is one species of Solanaceae family that is very popular in Indonesia and some other tropical countries because of its pungency. Chili pepper is an important spice in Indonesia and is also eaten fresh as a pickle to increase appetite. In Indonesia, there are various local names for chili pepper includingcabai, cengek, lombok, pedesan etc. These varied local names represent the various morphological shapes of the chili pepper fruit. We have investigated the variability of some chili cultivars based on morphological characteristics, molecular markers, pungency, and capsaicin content. Some biological facts, such as the tendency of chili pepper to outbreed, have also been found. In this paper, the source of variability and the possible mechanism of increasing genetic variability of Indonesian local chili pepper are also discussed.

Clinical Characteristics and Genetic Variability of Human Rhinovirus in Mexico

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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.

Genetic variability in Asparagus racemosus (Willd.) from Madhya ...

African Journals Online (AJOL)

Random amplified polymorphic DNA (RAPD) markers were used to assess genetic diversity in Asparagus racemosus (Willd.) an important medicinal plant collected from 7 different locations covering Madhya Pradesh. High level of genetic similarity was observed in the collected accessions. 4 random primers generated a ...

Variability in seed traits, oil content and genetic diversity in local and ...

African Journals Online (AJOL)

Variability in seed traits, oil content and genetic diversity of Jatropha curcas L. according to rainfall gradient in Senegal are hereby reported and discussed. Seed oil variability ranged from 58.61% in Sudanian zone to 46.94% in Sahelian zone. Seed oil content and seed thickness were correlated to rainfall with a correlation ...

Radiation induced mutants in elite genetic background for the augmentation of genetic diversity

International Nuclear Information System (INIS)

Kumar, V.; Bhagwat, S.G.

2011-01-01

Rice (Oryza sativa L.), an important food crop for India, shows large genetic diversity. However, despite the large genetic resource, high genetic similarity is reported in cultivated varieties indicating genetic erosion. Radiation induced mutations provide genetic variability in elite background. In the present study, twenty gamma ray induced mutants of rice variety WL112 (carrying sd-1 semi-dwarfing gene) were analysed for genetic diversity using microsatellite markers. The high range of genetic diversity among mutants indicated that the mutants possess potential for enhancing variability in rice. Cluster analysis showed presence of five clusters having small sub-clusters. Earliness, semi-dwarf stature or resistance to blast disease observed among the mutants showed that these will be useful in breeding programmes. (author)

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)

Genetic variability of tissue cultured Sorghum bicolor (L) Moench as ...

African Journals Online (AJOL)

To evaluate their performance for seedling traits at seedling stage (under hydroponics), plant water relations under water stress and ultimately grain yield, and to estimate the genetic variability of the regenerates, the parent plants of local sorghum cultivars in Kenya using simple sequence repeats (SSR) markers were ...

Can the reproductive system of a rare and narrowly endemic plant species explain its high genetic diversity?

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Daniele M. Rodrigues

2018-01-01

Full Text Available ABSTRACT The reproductive system of flowering plants can be highly variable, affecting their biology, gene flow and genetic variability among populations. Petunia secreta is a rare annual endemic species of Pedra do Segredo, located in the municipality of Caçapava do Sul, state of Rio Grande do Sul, Brazil. Although rare, the species possesses a high level of genetic variability. We investigated the reproductive system of P. secreta, including fruit production and seed germinability, in order to determine if its reproductive system can explain its genetic diversity. We sampled five populations and conducted five greenhouse hand-pollination treatments: 1 autonomous apomixis; 2 self-pollination; 3 hand self-pollination; 4 geitonogamy; and 5 cross-pollination. We analysed a total of 40 plants, 468 flowers, and 6,500 seeds. Only autonomous apomixis and self-pollination did not produce fruit. No differences in fruit weight were observed among pollination treatments (P > 0.05. Seeds of two colours were produced, with no differences in germinability. Considering all plants, populations, and treatments, the average germinability was 73 % (range 9 % to 100 %. These results, along with other previous studies, indicate that the reproductive systems of P. secreta, and its large effective population size, can explain its high genetic diversity.

Temporal stability of genetic variability and differentiation in the three-spined stickleback (Gasterosteus aculeatus).

Science.gov (United States)

DeFaveri, Jacquelin; Merilä, Juha

2015-01-01

Temporal variation in allele frequencies, whether caused by deterministic or stochastic forces, can inform us about interesting demographic and evolutionary phenomena occurring in wild populations. In spite of the continued surge of interest in the genetics of three-spined stickleback (Gasterosteus aculeatus) populations, little attention has been paid towards the temporal stability of allele frequency distributions, and whether there are consistent differences in effective size (Ne) of local populations. We investigated temporal stability of genetic variability and differentiation in 15 microsatellite loci within and among eight collection sites of varying habitat type, surveyed twice over a six-year time period. In addition, Nes were estimated with the expectation that they would be lowest in isolated ponds, intermediate in larger lakes and largest in open marine sites. In spite of the marked differences in genetic variability and differentiation among the study sites, the temporal differences in allele frequencies, as well as measures of genetic diversity and differentiation, were negligible. Accordingly, the Ne estimates were temporally stable, but tended to be lower in ponds than in lake or marine habitats. Hence, we conclude that allele frequencies in putatively neutral markers in three-spined sticklebacks seem to be temporally stable - at least over periods of few generations - across a wide range of habitat types differing markedly in levels of genetic variability, effective population size and gene flow.

Temporal stability of genetic variability and differentiation in the three-spined stickleback (Gasterosteus aculeatus.

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Jacquelin DeFaveri

Full Text Available Temporal variation in allele frequencies, whether caused by deterministic or stochastic forces, can inform us about interesting demographic and evolutionary phenomena occurring in wild populations. In spite of the continued surge of interest in the genetics of three-spined stickleback (Gasterosteus aculeatus populations, little attention has been paid towards the temporal stability of allele frequency distributions, and whether there are consistent differences in effective size (Ne of local populations. We investigated temporal stability of genetic variability and differentiation in 15 microsatellite loci within and among eight collection sites of varying habitat type, surveyed twice over a six-year time period. In addition, Nes were estimated with the expectation that they would be lowest in isolated ponds, intermediate in larger lakes and largest in open marine sites. In spite of the marked differences in genetic variability and differentiation among the study sites, the temporal differences in allele frequencies, as well as measures of genetic diversity and differentiation, were negligible. Accordingly, the Ne estimates were temporally stable, but tended to be lower in ponds than in lake or marine habitats. Hence, we conclude that allele frequencies in putatively neutral markers in three-spined sticklebacks seem to be temporally stable - at least over periods of few generations - across a wide range of habitat types differing markedly in levels of genetic variability, effective population size and gene flow.

High genetic diversity in the coat protein and 3' untranslated regions

Indian Academy of Sciences (India)

The 3′ terminal region consisting of the coat protein (CP) coding sequence and 3′ untranslated region (3′UTR) was cloned and sequenced from seven isolates. Sequence comparisons revealed considerable genetic diversity among the isolates in their CP and 3′UTR, making CdMV one of the highly variable members ...

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.

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

DEFF Research Database (Denmark)

Burgess, Stephen; Thompson, Simon G; Thompson, Grahame

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...

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

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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.

Environmental interaction, additive and non-additive genetic variability is involved in the expression of tissue and whole-plant heat tolerance in upland cotton (Gossypium hirsutum. L

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Hafeez-ur-Rahman

2006-01-01

Full Text Available Heat tolerance is measured at tissue level by cellular membrane thermostability (CMT and at the whole plant level by the heat tolerance index (HTI. Eight upland cotton cultivars and 15 crosses were used to determine the type and extent of genetic variability associated with the expression of these traits between and within environments. Heat stress and non-stress conditions were used as the CMT environments and years for HTI. The wide variation in heterotic expression and combining ability effects observed for CMT and HTI suggest multigenic inheritance of these traits. Significant genetic variability across environments was evident but the traits were not highly heritable because of substantial environmental interaction. The available genetic variability included both additive and non-additive components, but the proportion of additive genetic variability was high for HTI. The parental cultivars CRIS-19 and CIM-448 were good donor parents for high CMT under heat-stressed conditions, and MNH-552 and N-Karishma under non-stressed conditions. Cultivar FH-634 was a good donor parent for HTI. The results show two types of general combining ability (GCA inheritance among high CMT parents: positive GCA inheritance expressed by CRIS-19 in the presence of heat stress and MNH-552 and N-Karishma in the absence of heat stress; and negative GCA inheritance expressed by FH-900 in the presence of heat stress. It was also evident that genes controlling high CMT in cultivar CRIS-19 were different from those present in the MNH-552, N-Karishma and FH-900 cultivars. Similarly, among high HTI parents, FH-634 showed positive and CIM-443 negative GCA inheritance. No significant relationship due to genetic causes existed between tissue and whole plant heat tolerance, diminishing the likelihood of simultaneous improvement and selection of the two traits.

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

effects of genetic homogeneity on variability of cloned minipigs compared with non-cloned controls regarding behavioural variables in a cognitive test, namely the spontaneous object recognition test. Significant differences in the variability between the cloned and control pigs were found in five out...... was numerically greater for the control group compared to the cloned group, indicating that variation may be less in cloned animals, but not demonstrable with the small group size of the present study (n = 6 for each of the two groups tested). Overall, this study failed to show unambiguously that variability......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...

Detection genetic variability of secale cereale L. by scot markers

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Lenka Petrovičová

2017-01-01

Full Text Available Rye (Secale cereale L. is our traditional cereal used for baking. The genetic variability of grown rye has been reduced by modern agronomic practices, which subsequently prompted the importance of search for species that could be useful as a gene pool for the improving of flour quality for human consumption or for other industrial uses. Therefore, the aim of this study was to detect genetic variability among the set of 45 rye genotypes using 8 SCoT markers. Amplification of genomic DNA of 45 genotypes, using SCoT analysis, yielded 114 fragments, with an average of 14.25 polymorphic fragments per primer. The most polymorphic primer was SCoT 36, where 21 polymorphic amplification products were detected. In contract the lowest polymorphic primer was SCoT 45 with 5 polymorphic products. Genetic polymorphism was characterized based on diversity index (DI, probability of identity (PI and polymorphic information content (PIC. The hierarchical cluster analysis showed that the rye genotypes were divided into 2 main clusters. One rye genotype Motto, origin from Poland formed a separate subcluster (1b. Subscluster 2a included only genotype Valtické (CSK. In this experiment, SCoT proved to be a rapid, reliable and practicable method for revealing of polymorphism in the rye cultivars. Normal 0 21 false false false EN-GB X-NONE X-NONE

Agrobiodiversity Genetic Variability Utilization in Organic Food Production

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Dimitrijević Miodrag

2018-03-01

Full Text Available The food production at the global level is about to meet its border. Industrialization of agriculture correlates with an explosive enlargement of human population, during XX and at the beginning of XXI centuries. An ongoing process of environmental erosion has been speeding up during that period, not only in our physical surrounding, but also in biodiversity. A new direction in agricultural food production is in demand. Organic food production has been recognized as the way of providing safety and quality food, preserving the environment in the same time. In the other hand new land areas have to be explored for agricultural use, in order to enhance food quantity to meeting the increasing demand for food. These targets set new requirements in plant breeding. To fulfill these requirements the genetic variability harbored in genetic resources has to be preserved, examined and put to good use.

Genetic variability in uptake of nitrogen at various growth stages of barley and wheat under dryland conditions

International Nuclear Information System (INIS)

Della, A.; Hadjichristodoulou, A.

1976-01-01

Protein and dry matter in a number of high protein and commercial varieties of barley and wheat were tested at various growth stages and at two locations. Large genetic variability was found in uptake of nitrogen, which was taken up generally before heading. High protein yields were not associated with high protein content but with higher dry matter yields. Nitrogen fertilization increased protein content and protein yield at a low protein location only. It was concluded that it is possible to breed for both high grain and high straw protein varieties. (author)

Highly structured genetic diversity of the Mycobacterium tuberculosis population in Djibouti.

Science.gov (United States)

Godreuil, S; Renaud, F; Choisy, M; Depina, J J; Garnotel, E; Morillon, M; Van de Perre, P; Bañuls, A L

2010-07-01

Djibouti is an East African country with a high tuberculosis incidence. This study was conducted over a 2-month period in Djibouti, during which 62 consecutive patients with pulmonary tuberculosis (TB) were included. Genetic characterization of Mycobacterium tuberculosis, using mycobacterial interspersed repetitive-unit variable-number tandem-repeat typing and spoligotyping, was performed. The genetic and phylogenetic analysis revealed only three major families (Central Asian, East African Indian and T). The high diversity and linkage disequilibrium within each family suggest a long period of clonal evolution. A Bayesian approach shows that the phylogenetic structure observed in our sample of 62 isolates is very likely to be representative of the phylogenetic structure of the M. tuberculosis population in the total number of TB cases.

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.

Genetic variability among advanced lines of brassica

International Nuclear Information System (INIS)

Ullah, N.; Farhatullah, A.; Rahman, H.U.; Fayyaz, L.

2015-01-01

Genetic variability for morphological and biochemical traits among six advanced lines (F10:11) of brassica was studied at The University of Agriculture Peshawar during crop season of 2012-13. These lines were developed through interspecific hybridization. Significant differences at (p=0.01) for plant height, main, pods main raceme-1, pod length, seed yield plant-1 and protein content at (p=0.05) for 100-seed weight, oil content were recorded. The advanced line, AUP-05 produced the maximum seed yield plant-1 (19.73 g), protein content (24.56%), 100-seed weight (0.64 g). Advanced line AUP-04 had the highest erucic acid (50.31%), linolenic acid (10.60%) and was late maturing (179.33). Advanced line AUP-06 produced the high oil content (48.82%). Advanced line AUP-03 produced comparatively longer main raceme (69.32 cm). Environmental variance was smaller than genotypic variance for majority of the traits. Genotypic and phenotypic coefficients of variation ranged from 2.45 to 25.67% and 2.50 to 27.68%, respectively. Heritability was high for majority of the traits. The maximum heritability was recorded for plant height (0.61), main raceme length (0.81), pods main raceme-1 (0.74), seed yield plant-1 (0.86) and protein content (0.77). Moderate heritability was observed for oil (0.58) contents. Heritability for 100-seed weight (0.30) was the lowest. These lines may be released as new improved varieties for specific parameters. (author)

Genetic variability and population structure in loci related to milk production traits in native Argentine Creole and commercial Argentine Holstein cattle

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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.

Comparative assessment of genetic variability in cryptolepis buchananii, tylophora hirsuta and wattakaka volubilis

International Nuclear Information System (INIS)

Mahmood, T.; Azir, N.; Abbasi, B.H.; Naqvi, S.

2011-01-01

Asclepiadaceae is an economically important family with great medicinal value. However, very little work has been carried out on the genetic variability of Asclepiadaceae members especially on some medicinally important species like Tylophora hirsuta, Wattakaka volubilis and Cryptolepis buchananii. Keeping in view the importance of these species, a study was designed to explore the genetic diversity of these 3 species of Asclepiadaceae and the plant material was collected from Quaid-i-Azam university campus, Islamabad. To assess the genetic variability and polymorphism among these species, randomly amplified polymorphic DNA (RAPD) markers were used. Sixty RAPD primers from OPA, OPC, OPF and OPG series were used; only 8 primers of OPC series gave amplification. Maximum polymorphism at interspecific and intraspecific levels was shown by OPC9 and minimum polymorphism was observed in OPC5. The data was analyzed using NTSYS software pc version 2.02. Low genetic diversification was observed at intraspecific and interspecific level. Moreover, during cluster analysis Tylophora hirsuta and Wattakaka volubilis were found to be present in the same cluster showing a close relationship whereas Cryptolepis buchananii appeared in a separate cluster. (author)

Genetic variability of Pantaneiro horse using RAPD-PCR markers

OpenAIRE

Egito,Andréa Alves do; Fuck,Beatriz Helena; McManus,Concepta; Paiva,Samuel Rezende; Albuquerque,Maria do Socorro Maués; Santos,Sandra Aparecida; Abreu,Urbano Gomes Pinto de; Silva,Joaquim Augusto da; Sereno,Fabiana Tavares Pires de Souza; Mariante,Arthur da Silva

2007-01-01

Blood samples were collected from Pantaneiro Horses in five regions of Mato Grosso do Sul and Mato Grosso States. Arabian, Mangalarga Marchador and Thoroughbred were also included to estimate genetic distances and the existing variability among and within these breeds by RAPD-PCR (Random Amplified Polymorphic DNA - Polymerase Chain Reaction) molecular markers. From 146 primers, 13 were chosen for amplification and 44 polymorphic bands were generated. The analysis of molecular variance (AMOVA)...

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.

Genetic variability of European honey bee, Apis mellifera in mid hills ...

African Journals Online (AJOL)

To observe the genetic variability in European honey bee, A. mellifera, PCR was run separately with five primers and analysis of the banding pattern was worked out to investigate the molecular profile of honey bee genotypes collected from different locations having random amplified polymorphic DNA (RAPD) primers.

Genetic variability of wild populations of Leporinus elongatus in the São Domingos River - MS Brazil: a preliminary view on the construction of the hydroelectric plant

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Ricardo Pereira Ribeiro

2016-09-01

Full Text Available Most of the electricity used in Brazil comes from hydroelectric plants, mainly due to the great availability of its water resources. However, the construction of these plants denotes serious problems related to migration of native fish and the genetic conservation of stocks. Current study evaluates two wild population of Leporinus elongatus (piapara located downstream (Population A - PopA and upstream (Population B - PopB of the Cachoeira Branca before the construction of the São Domingos hydroelectric plant (HPP in the Mato Grosso do Sul State, Brazil. Thirty samples from caudal fins were collected and analyzed for each population. Eighty-nine fragments, including 72 polymorphic ones (80.9%, were analyzed. Low fragments (less than 0.100 in both populations (PopA = 2 and PopB = 3 were identified. Nine fixed fragments (frequency 1.000 (PopA = 3 and PopB = 6, and four exclusive fragments (PopA = 3 and PopB = 1 were also reported. The genetic variability within populations, calculated by Shannon Index and by percentage of polymorphic fragments, indicated high rates of intrapopulation variability (PopA = 0.309 and 61.80% and PopB = 0.392 and 71.90%, respectively. Genetic distance and identity rates (0.089 and 0.915, respectively were different between populations, whilst AMOVA showed that most variations lie within the populations and not between them. Fst and Nm rates showed moderate genetic differentiation with low numbers of migrants. Results reveal populations with high intra-population genetic variability and genetic differentiation, with low gene flow. The passage ladders of São Domingos HPP should control fish transposition to preserve genetic variability.

Genetic variability in the population of the endemic bee Anthophora ...

African Journals Online (AJOL)

The genetic diversity and spatial genetic population structure of the solitary bee Anthophora pauperata Walker 1871, a species endemic to St Katherine Protectorate, were studied by RAPD markers in seven wadis in the St Katherine Protectorate, South Sinai, Egypt. High levels of genetic diversity were found, mostly within ...

Variable-number-of-tandem-repeats analysis of genetic diversity in Pasteuria ramosa.

Science.gov (United States)

Mouton, L; Ebert, D

2008-05-01

Variable-number-of-tandem-repeats (VNTR) markers are increasingly being used in population genetic studies of bacteria. They were recently developed for Pasteuria ramosa, an endobacterium that infects Daphnia species. In the present study, we genotyped P. ramosa in 18 infected hosts from the United Kingdom, Belgium, and two lakes in the United States using seven VNTR markers. Two Daphnia species were collected: D. magna and D. dentifera. Six loci showed length polymorphism, with as many as five alleles identified for a single locus. Similarity coefficient calculations showed that the extent of genetic variation between pairs of isolates within populations differed according to the population, but it was always less than the genetic distances among populations. Analysis of the genetic distances performed using principal component analysis revealed strong clustering by location of origin, but not by host Daphnia species. Our study demonstrated that the VNTR markers available for P. ramosa are informative in revealing genetic differences within and among populations and may therefore become an important tool for providing detailed analysis of population genetics and epidemiology.

Population structure and genetic variability of mainland and insular populations of the Neotropical water rat, Nectomys squamipes (Rodentia, Sigmodontinae

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Francisca C. Almeida

2005-12-01

Full Text Available Seven microsatellite loci were used to investigate the genetic variability and structure of six mainland and two island populations of the Neotropical water rat Nectomys squamipes, a South American semi-aquatic rodent species with a wide distribution. High levels of variability were found within mainland populations while island populations were less variable but the more differentiated in respect to allele number and frequency. The time of biological divergence between mainland and island populations coincided with geological data. A significant geographic structure was found in mainland populations (theta = 0.099; rho = 0.086 although the degree of differentiation was relatively low in respect to the distance between surveyed localities (24 to 740 km. Genetic and geographic distances were not positively correlated as previously found with random amplified polymorphic DNA (RAPD markers. Significant but low genetic differentiation in the mainland and lack of isolation by distance can be explained by large population size and/or recent population expansion. Additionally, the agreement between the age of geologic events (sea level fluctuations and divergence times for insular populations points to a good reference for molecular clock calibration to associate recent environmental changes and the distribution pattern of small mammals in the Brazilian Atlantic Forest.

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.

Genetic variability of South African fiscal shrikes ( Lanius collaris ...

African Journals Online (AJOL)

Rogers' (1972) mean genetic distance (D) was 0.094, and Nei's (1978) mean unbiased genetic distance was 0.019. A phenogram (unweighted pair group method) and a phylogenetic tree (distance Wagner network), both based on Rogers' (1972) distance, showed some degree of geographical subgrouping. The high ...

High genetic diversity and low population structure in Porter's sunflower (Helianthus porteri).

Science.gov (United States)

Gevaert, Scott D; Mandel, Jennifer R; Burke, John M; Donovan, Lisa A

2013-01-01

Granite outcrops in the southeastern United States are rare and isolated habitats that support edaphically controlled communities dominated by herbaceous plants. They harbor rare and endemic species that are expected to have low genetic variability and high population structure due to small population sizes and their disjunct habitat. We test this expectation for an annual outcrop endemic, Helianthus porteri (Porter's sunflower). Contrary to expectation, H. porteri has relatively high genetic diversity (H e = 0.681) and relatively low genetic structure among the native populations (F ST = 0.077) when compared to 5 other Helianthus species (N = 288; 18 expressed sequence tag-SSR markers). These findings suggest greater gene flow than expected. The potential for gene flow is supported by the analysis of transplant populations established with propagules from a common source in 1959. One population established close to a native population (1.5 km) at the edge of the natural range is genetically similar to and shares rare alleles with the adjacent native population and is distinct from the central source population. In contrast, a transplant population established north of the native range has remained similar to the source population. The relatively high genetic diversity and low population structure of this species, combined with the long-term success of transplanted populations, bode well for its persistence as long as the habitat persists.

Genetic variability, heritability, character association and path analysis in F/sub 1/ hybrids of tomato

International Nuclear Information System (INIS)

Saleem, M.Y.; Iqbal, Q.; Asghar, M.

2013-01-01

Twenty-five F/sub 1/ hybrids generated from 5*5 diallel crosses were evaluated to study the quantitative genetics of yield and some yield related traits during 2009-10. Worth of room was realized for improvement due to highly significant genetic variations among all traits studied. The highest estimates of genotypic and phenotypic coefficients of variability were recorded for number of fruits per plant while fruit width was the most heritable trait. Plant height, number of fruits per plant and fruit weight revealed significant positive genotypic and phenotypic association along with direct positive effect on fruit yield per plant. It is therefore, recommended that fruit weight, number of fruits per plant and plant height should be given due importance in selection of promising crosses to develop commercial hybrid variety in tomato. (author)

Assessment of genetic variability in somaclonal population of sugarcane

International Nuclear Information System (INIS)

Seema, N.; Raza, S.; Yasmeen, S.; Bibi, S.; Nizamani, G.S.

2014-01-01

In the present study plant tissue culture technique was used to create the genetic variability in three sugarcane clones NIA98, BL4 and AEC82-1026. Callus induced in these clones in media containing MS + 2, 4 D (2mg 1it-1) and Dicamba (1mg1it-1). The embryogenic calli then regenerated in media containing MS basal media + Kinetin (2mg1it-1) + IBA (2mg1it-1) + IAA (2mglit-1). After shooting and rooting, plants were exposed to green house and acclimatization of the somaclones in the field condition. RAPD markers were used to evaluate the genetic variation at DNA level between parents and somaclones of NIA98, BL4 and AEC82-1026 developed through callus culture. Fourteen RAPD primer chosen randomly were used to amplify DNA from plant material to assess the genetic variation between parents and regenerated somaclones. The highest similarity was obtained between BL4 parent and BL4 somaclone (96%). While minimum similarity found between NIA-98 parent and AEC82-1026 somaclone (69%). In this study, we used RAPD to investigate the somaclonal variation in sugarcane clones derived from callus cultures. (author)

High degree of genetic differentiation in marine three-spined sticklebacks (Gasterosteus aculeatus).

Science.gov (United States)

Defaveri, Jacquelin; Shikano, Takahito; Shimada, Yukinori; Merilä, Juha

2013-09-01

Populations of widespread marine organisms are typically characterized by a low degree of genetic differentiation in neutral genetic markers, but much less is known about differentiation in genes whose functional roles are associated with specific selection regimes. To uncover possible adaptive population divergence and heterogeneous genomic differentiation in marine three-spined sticklebacks (Gasterosteus aculeatus), we used a candidate gene-based genome-scan approach to analyse variability in 138 microsatellite loci located within/close to (<6 kb) functionally important genes in samples collected from ten geographic locations. The degree of genetic differentiation in markers classified as neutral or under balancing selection-as determined with several outlier detection methods-was low (F(ST) = 0.033 or 0.011, respectively), whereas average FST for directionally selected markers was significantly higher (F(ST) = 0.097). Clustering analyses provided support for genomic and geographic heterogeneity in selection: six genetic clusters were identified based on allele frequency differences in the directionally selected loci, whereas four were identified with the neutral loci. Allelic variation in several loci exhibited significant associations with environmental variables, supporting the conjecture that temperature and salinity, but not optic conditions, are important drivers of adaptive divergence among populations. In general, these results suggest that in spite of the high degree of physical connectivity and gene flow as inferred from neutral marker genes, marine stickleback populations are strongly genetically structured in loci associated with functionally relevant genes. © 2013 John Wiley & Sons Ltd.

Estimation of genetic variability level in inbred CF1 mouse lines ...

Indian Academy of Sciences (India)

To estimate the genetic variability levels maintained by inbred lines selected for body weight and to compare them with a nonselected population from which the lines were derived, we calculated the per cent polymorphic loci (P) and marker diversity (MD) index from data on 43 putative loci of inter simple sequence repeats ...

Genetic Variability of Beauveria bassiana and a DNA Marker for Environmental Monitoring of a Highly Virulent Isolate Against Cosmopolites sordidus.

Science.gov (United States)

Ferri, D V; Munhoz, C F; Neves, P M O; Ferracin, L M; Sartori, D; Vieira, M L C; Fungaro, M H P

2012-12-01

The banana weevil Cosmopolites sordidus (Germar) is one of a number of pests that attack banana crops. The use of the entomopathogenic fungus Beauveria bassiana as a biological control agent for this pest may contribute towards reducing the application of chemical insecticides on banana crops. In this study, the genetic variability of a collection of Brazilian isolates of B. bassiana was evaluated. Samples were obtained from various geographic regions of Brazil, and from different hosts of the Curculionidae family. Based on the DNA fingerprints generated by RAPD and AFLP, we found that 92 and 88 % of the loci were polymorphic, respectively. The B. bassiana isolates were attributed to two genotypic clusters based on the RAPD data, and to three genotypic clusters, when analyzed with AFLP. The nucleotide sequences of nuclear ribosomal DNA intergenic spacers confirmed that all isolates are in fact B. bassiana. Analysis of molecular variance showed that variability among the isolates was not correlated with geographic origin or hosts. A RAPD-specific marker for isolate CG 1024, which is highly virulent to C. sordidus, was cloned and sequenced. Based on the sequences obtained, specific PCR primers BbasCG1024F (5'-TGC GGC TGA GGA GGA CT-3') and BbasCG1024R (5'-TGC GGC TGA GTG TAG AAC-3') were designed for detecting and monitoring this isolate in the field.

Dietary differentiation and the evolution of population genetic structure in a highly mobile carnivore.

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Małgorzata Pilot

Full Text Available Recent studies on highly mobile carnivores revealed cryptic population genetic structures correlated to transitions in habitat types and prey species composition. This led to the hypothesis that natal-habitat-biased dispersal may be responsible for generating population genetic structure. However, direct evidence for the concordant ecological and genetic differentiation between populations of highly mobile mammals is rare. To address this we analyzed stable isotope profiles (δ(13C and δ(15N values for Eastern European wolves (Canis lupus as a quantifiable proxy measure of diet for individuals that had been genotyped in an earlier study (showing cryptic genetic structure, to provide a quantitative assessment of the relationship between individual foraging behavior and genotype. We found a significant correlation between genetic distances and dietary differentiation (explaining 46% of the variation in both the marginal test and crucially, when geographic distance was accounted for as a co-variable. These results, interpreted in the context of other possible mechanisms such as allopatry and isolation by distance, reinforce earlier studies suggesting that diet and associated habitat choice are influencing the structuring of populations in highly mobile carnivores.

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

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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.

Heterozygosity level and its relationship with genetic variability mechanisms in beans

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Rita Carolina de Melo

Full Text Available ABSTRACT Heterozygosity is an extremely important resource in early breeding programs using autogamous plants because it is usually associated with the presence of genetic variability. Induced mutation and artificial hybridization can increase distinctly the proportion of loci in heterozygosis. This study aimed to compare segregating and mutant populations and relate the mechanisms used to generate variability with their respective heterozygosity levels tested. The treatments mutant populations (M2, M3, M4, M5, M6 and M7, segregating populations (F4, F5 and F6 and lines (BRS Pérola and IPR Uirapuru were evaluated by multivariate analysis and compared by orthogonal contrasts. The canonical discriminant analysis revealed which response variables contributed to differentiate the treatments assessed. All orthogonal contrasts involving the mutant populations showed significant differences, except the contrast between M2 vs. M3, M4, M5, M6, M7. The orthogonal contrast between the mutant and segregating populations denotes a significant variation in the interest in genetic breeding. The traits stem diameter (1.41 and number of legumes per plant (2.72 showed the highest canonical weight in this contrast. Conversely, number of grains per plant (-3.58 approached the mutant and segregating populations. No significant difference was observed in the linear comparison of means F5 vs. F6. The traits are fixed early in the segregant populations, unlike the mutant populations. Comparatively, induced mutation provides more loci in heterozygosis than artificial hybridization. Selection pressure should vary according to the variability creation mechanism used at the beginning of the breeding program.

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

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Sibeli B S Cembranelli

Full Text Available 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

Landscape attributes and life history variability shape genetic structure of trout populations in a stream network

Science.gov (United States)

Neville, H.M.; Dunham, J.B.; Peacock, M.M.

2006-01-01

Spatial and temporal landscape patterns have long been recognized to influence biological processes, but these processes often operate at scales that are difficult to study by conventional means. Inferences from genetic markers can overcome some of these limitations. We used a landscape genetics approach to test hypotheses concerning landscape processes influencing the demography of Lahontan cutthroat trout in a complex stream network in the Great Basin desert of the western US. Predictions were tested with population- and individual-based analyses of microsatellite DNA variation, reflecting patterns of dispersal, population stability, and local effective population sizes. Complementary genetic inferences suggested samples from migratory corridors housed a mixture of fish from tributaries, as predicted based on assumed migratory life histories in those habitats. Also as predicted, populations presumed to have greater proportions of migratory fish or from physically connected, large, or high quality habitats had higher genetic variability and reduced genetic differentiation from other populations. Populations thought to contain largely non-migratory individuals generally showed the opposite pattern, suggesting behavioral isolation. Estimated effective sizes were small, and we identified significant and severe genetic bottlenecks in several populations that were isolated, recently founded, or that inhabit streams that desiccate frequently. Overall, this work suggested that Lahontan cutthroat trout populations in stream networks are affected by a combination of landscape and metapopulation processes. Results also demonstrated that genetic patterns can reveal unexpected processes, even within a system that is well studied from a conventional ecological perspective. ?? Springer 2006.

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.

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.

Detecting high-order interactions of single nucleotide polymorphisms using genetic programming.

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Nunkesser, Robin; Bernholt, Thorsten; Schwender, Holger; Ickstadt, Katja; Wegener, Ingo

2007-12-15

Not individual single nucleotide polymorphisms (SNPs), but high-order interactions of SNPs are assumed to be responsible for complex diseases such as cancer. Therefore, one of the major goals of genetic association studies concerned with such genotype data is the identification of these high-order interactions. This search is additionally impeded by the fact that these interactions often are only explanatory for a relatively small subgroup of patients. Most of the feature selection methods proposed in the literature, unfortunately, fail at this task, since they can either only identify individual variables or interactions of a low order, or try to find rules that are explanatory for a high percentage of the observations. In this article, we present a procedure based on genetic programming and multi-valued logic that enables the identification of high-order interactions of categorical variables such as SNPs. This method called GPAS cannot only be used for feature selection, but can also be employed for discrimination. In an application to the genotype data from the GENICA study, an association study concerned with sporadic breast cancer, GPAS is able to identify high-order interactions of SNPs leading to a considerably increased breast cancer risk for different subsets of patients that are not found by other feature selection methods. As an application to a subset of the HapMap data shows, GPAS is not restricted to association studies comprising several 10 SNPs, but can also be employed to analyze whole-genome data. Software can be downloaded from http://ls2-www.cs.uni-dortmund.de/~nunkesser/#Software

[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.

Morphology and genetic variability within Taenia multiceps in ruminants from Italy.

Science.gov (United States)

Varcasia, Antonio; Pipia, Anna Paola; Dessì, Giorgia; Zidda, Antonella; Tamponi, Claudia; Pau, Marco; Scala, Antonio; Boufana, Belgees

2016-06-15

The aim of this study was to investigate the genetic variability and population structure of Taenia multiceps, and to correlate morphological features of individual coenuri with haplotypes. A total of 92 animals (86 sheep; 4 goats; 1 cattle; 1 mouflon, Ovis musimon) aged between 6-36 months showing clinical symptoms of cerebral coenurosis were included in this study. T. multiceps coenuri (n=118) sampled from live animals during routine surgery procedures or at post-mortem inspections were examined morphologically and molecularly identified. Morphological features of the 52 coenuri selected for this study (number and size of large and small hooks) were within the range reported in the literature. Fifty-two of the molecularly confirmed T. multiceps coenuri harboured by 47 animals (sheep=41; cattle=1; goats=4; mouflon=1) were used to determine gene genealogies and population genetic indices and were compared to the 3 T. multiceps genetic variants, Tm1-Tm3 previously described from Sardinia, Italy. For the 379 bp cox1 dataset we identified 11 polymorphic sites of which 8 were parsimony informative. A high haplotype diversity (0.664±0.067) was recorded for the cox1 sequences defining 10 haplotypes (TM01-TM10). The comparison of haplotypes generated in this study with published T. multiceps Tm1 variant pointed to the possible existence of a common lineage for T. multiceps. No correlation was detected between the size of the small and large hooks and the cox 1 haplotypes. Polycystic infestation (2-9 coenuri) was recorded in 27.7% of animals (13/47). No statistical correlation between polycystic T. multiceps infection and haplotypes was detected. Copyright © 2016 Elsevier B.V. All rights reserved.

Prevalence and genetic variability of Plesiomonas shigelloides in temperate climate surface waters of the Pannonian Plain

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Petrušić Milivoje

2018-01-01

Full Text Available Plesiomonas shigelloides, a Gram-negative bacterium and the causative agent of intestinal diseases and extraintestinal infections in humans and animals, is most frequently found in aquatic environments in tropical or subtropical areas. The present study was designed to establish the prevalence and genetic variability of P. shigelloides in surface waters (lakes, rivers, ponds, inlets and canals located in a temperate climate zone, namely the Pannonian Plain of the northern part of Serbia and southern part of Hungary. The strains were isolated directly by plating samples on inositol-brilliant green-bile agar with neutral red or phenol red as indicators. Our results indicate that phenol red effectively facilitates differentiation of P. shigelloides from other bacteria. A number of samples were enriched using alkaline peptone water broth, peptone inositolbile broth and tetrathionate broth. The recovery of the isolates was more successful with the first medium. Out of a total of 51 water samples collected from 28 different locations, 22 samples (43.1% were found positive for P. shigelloides. Among the 37 isolated strains, 34 were from lakes (Šatrinci, Ludaš, Panonija, Krivaja, Pecs, Kapetanski rit, Pavlovci, Kovacsszenaja, Dobrodol, Vranjaš, Borkovac, Hermann Otto, Sot, Šelevrenac, Zobnatica, Palić, Orfui, Jarkovci, Čonoplja and 3 were from rivers (Danube, Sava. The strains were identified by phenotypic characteristic or by the VITEK2 system and confirmed by PCR using 23S rRNA species-specific oligos. The strains showed a high genetic variability, displaying a variety of RAPD profiles. Our results reveal for the first time a high prevalence of genetically diverse P. shigelloides populations in surface waters located in the temperate climate of central and southeastern Europe. [Project of the Serbian Ministry of Education, Science and Technological Development, Grant no. OI 172058

Thinking positively: The genetics of high intelligence

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Shakeshaft, Nicholas G.; Trzaskowski, Maciej; McMillan, Andrew; Krapohl, Eva; Simpson, Michael A.; Reichenberg, Avi; Cederlöf, Martin; Larsson, Henrik; Lichtenstein, Paul; Plomin, Robert

2015-01-01

High intelligence (general cognitive ability) is fundamental to the human capital that drives societies in the information age. Understanding the origins of this intellectual capital is important for government policy, for neuroscience, and for genetics. For genetics, a key question is whether the genetic causes of high intelligence are qualitatively or quantitatively different from the normal distribution of intelligence. We report results from a sibling and twin study of high intelligence and its links with the normal distribution. We identified 360,000 sibling pairs and 9000 twin pairs from 3 million 18-year-old males with cognitive assessments administered as part of conscription to military service in Sweden between 1968 and 2010. We found that high intelligence is familial, heritable, and caused by the same genetic and environmental factors responsible for the normal distribution of intelligence. High intelligence is a good candidate for “positive genetics” — going beyond the negative effects of DNA sequence variation on disease and disorders to consider the positive end of the distribution of genetic effects. PMID:25593376

Genetic variability and heritability estimates of some polygenic traits in upland cotton

International Nuclear Information System (INIS)

Baloch, M.J.

2004-01-01

Plant breeders are more interested in genetic variance rather than phenotypic variance because it is amenable to selection and bring further improvement in the character. Twenty-eight F/sub 2/ progenies were tested in two environments so as to predict genetic variances, heritability estimates and genetic gains. Mean squares for locations were significant for all the five traits suggesting that genotypes performed differently under varying environments. Genetic variances, in most cases, however, were about equal to that of phenotypic variances consequently giving high heritability estimates and significant genetic gains. The broad sense heritability estimates were; 94.2, 92.9, 33.6, 81.9 and 86.9% and genetic gains were; 30.19, 10.55,0.20,0.89 and 1.76 in seed cotton yield, bolls per plant, lint %, fibre length and fibre uniformity ratio, respectively. Substantial genetic variances and high heritability estimates implied that these characters could be improved through selection from segregating populations. (author)

Genetic variability of the length of postpartum anoestrus in Charolais cows and its relationship with age at puberty

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Ménissier François

2000-07-01

Full Text Available Abstract Fertility records (n = 1 802 were collected from 615 Charolais primiparous and multiparous cows managed in an experimental herd over an 11-year period. The objectives of the study were to describe the genetic variability of the re-establishment of postpartum reproductive activity and the relationship with body weight (BW and body condition score (BCS at calving and age at puberty. The length of postpartum anoestrus was estimated based on weekly blood progesterone assays and on twice daily detection of oestrus behaviour. The first oestrus behaviour was observed 69 days (± 25 days s.d. post-calving and the first positive progesterone measurement (≥ 1 ng mL-1 was observed at 66 days (± 22 days s.d. for the group of easy-calving multiparous suckling cows. Estimates of heritability and repeatability were h2 = 0.12 and r = 0.38 respectively, for the interval from calving to first oestrus (ICO. Corresponding values were h2 = 0.35 and r = 0.60 for the interval from calving to the first positive progesterone test (ICP. The genetic correlation between both criteria was high (rg = 0.98. The genetic relationships between postpartum intervals and BW and BCS of the female at calving were negative: the genetic aptitude to be heavier at calving and to have high body reserves was related to shorter postpartum intervals. A favourable genetic correlation between age at puberty and postpartum intervals was found (rg between 0.45 and 0.70. The heifers which were genetically younger at puberty also had shorter postpartum intervals.

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

African Journals Online (AJOL)

Some cultivars e.g. Munyeera, New Kawogo, Silk and Sowola which showed high flowering ability failed to fertilise and set seed when crossed to specific cultivars. Preliminary genetic analysis for yield and quality following crossing elite 7 female and 6 male cultivars in a North Carolina 2 mating design showed wide genetic ...

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

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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.

The use of random amplified polymorphic DNA to evaluate the genetic variability of Ponkan mandarin (Citrus reticulata Blanco accessions

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Coletta Filho Helvécio Della

2000-01-01

Full Text Available RAPD analysis of 19 Ponkan mandarin accessions was performed using 25 random primers. Of 112 amplification products selected, only 32 were polymorphic across five accessions. The absence of genetic variability among the other 14 accessions suggested that they were either clonal propagations with different local names, or that they had undetectable genetic variability, such as point mutations which cannot be detected by RAPD.

Association of genetic and phenotypic variability with geography and climate in three southern California oaks.

Science.gov (United States)

Riordan, Erin C; Gugger, Paul F; Ortego, Joaquín; Smith, Carrie; Gaddis, Keith; Thompson, Pam; Sork, Victoria L

2016-01-01

Geography and climate shape the distribution of organisms, their genotypes, and their phenotypes. To understand historical and future evolutionary and ecological responses to climate, we compared the association of geography and climate of three oak species (Quercus engelmannii, Quercus berberidifolia, and Quercus cornelius-mulleri) in an environmentally heterogeneous region of southern California at three organizational levels: regional species distributions, genetic variation, and phenotypic variation. We identified climatic variables influencing regional distribution patterns using species distribution models (SDMs), and then tested whether those individual variables are important in shaping genetic (microsatellite) and phenotypic (leaf morphology) variation. We estimated the relative contributions of geography and climate using multivariate redundancy analyses (RDA) with variance partitioning. The modeled distribution of each species was influenced by climate differently. Our analysis of genetic variation using RDA identified small but significant associations between genetic variation with climate and geography in Q. engelmannii and Q. cornelius-mulleri, but not in Q. berberidifolia, and climate explained more of the variation. Our analysis of phenotypic variation in Q. engelmannii indicated that climate had more impact than geography, but not in Q. berberidifolia. Throughout our analyses, we did not find a consistent pattern in effects of individual climatic variables. Our comparative analysis illustrates that climate influences tree response at all organizational levels, but the important climate factors vary depending on the level and on the species. Because of these species-specific and level-specific responses, today's sympatric species are unlikely to have similar distributions in the future. © 2016 Botanical Society of America.

Genetic analysis of glucosinolate variability in broccoli florets using genome-anchored single nucleotide polymorphisms.

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Brown, Allan F; Yousef, Gad G; Reid, Robert W; Chebrolu, Kranthi K; Thomas, Aswathy; Krueger, Christopher; Jeffery, Elizabeth; Jackson, Eric; Juvik, John A

2015-07-01

The identification of genetic factors influencing the accumulation of individual glucosinolates in broccoli florets provides novel insight into the regulation of glucosinolate levels in Brassica vegetables and will accelerate the development of vegetables with glucosinolate profiles tailored to promote human health. Quantitative trait loci analysis of glucosinolate (GSL) variability was conducted with a B. oleracea (broccoli) mapping population, saturated with single nucleotide polymorphism markers from a high-density array designed for rapeseed (Brassica napus). In 4 years of analysis, 14 QTLs were associated with the accumulation of aliphatic, indolic, or aromatic GSLs in floret tissue. The accumulation of 3-carbon aliphatic GSLs (2-propenyl and 3-methylsulfinylpropyl) was primarily associated with a single QTL on C05, but common regulation of 4-carbon aliphatic GSLs was not observed. A single locus on C09, associated with up to 40 % of the phenotypic variability of 2-hydroxy-3-butenyl GSL over multiple years, was not associated with the variability of precursor compounds. Similarly, QTLs on C02, C04, and C09 were associated with 4-methylsulfinylbutyl GSL concentration over multiple years but were not significantly associated with downstream compounds. Genome-specific SNP markers were used to identify candidate genes that co-localized to marker intervals and previously sequenced Brassica oleracea BAC clones containing known GSL genes (GSL-ALK, GSL-PRO, and GSL-ELONG) were aligned to the genomic sequence, providing support that at least three of our 14 QTLs likely correspond to previously identified GSL loci. The results demonstrate that previously identified loci do not fully explain GSL variation in broccoli. The identification of additional genetic factors influencing the accumulation of GSL in broccoli florets provides novel insight into the regulation of GSL levels in Brassicaceae and will accelerate development of vegetables with modified or enhanced GSL

CRISPR/Cas9 gene drives in genetically variable and nonrandomly mating wild populations.

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Drury, Douglas W; Dapper, Amy L; Siniard, Dylan J; Zentner, Gabriel E; Wade, Michael J

2017-05-01

Synthetic gene drives based on CRISPR/Cas9 have the potential to control, alter, or suppress populations of crop pests and disease vectors, but it is unclear how they will function in wild populations. Using genetic data from four populations of the flour beetle Tribolium castaneum , we show that most populations harbor genetic variants in Cas9 target sites, some of which would render them immune to drive (ITD). We show that even a rare ITD allele can reduce or eliminate the efficacy of a CRISPR/Cas9-based synthetic gene drive. This effect is equivalent to and accentuated by mild inbreeding, which is a characteristic of many disease-vectoring arthropods. We conclude that designing such drives will require characterization of genetic variability and the mating system within and among targeted populations.

Genetic variability in Brazilian wheat cultivars assessed by microsatellite markers

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Ivan Schuster

2009-01-01

Full Text Available Wheat (Triticum aestivum is one of the most important food staples in the south of Brazil. Understanding genetic variability among the assortment of Brazilian wheat is important for breeding. The aim of this work was to molecularly characterize the thirty-six wheat cultivars recommended for various regions of Brazil, and to assess mutual genetic distances, through the use of microsatellite markers. Twenty three polymorphic microsatellite markers (PMM delineated all 36 of the samples, revealing a total of 74 simple sequence repeat (SSR alleles, i.e. an average of 3.2 alleles per locus. Polymorphic information content (PIC value calculated to assess the informativeness of each marker ranged from 0.20 to 0.79, with a mean of 0.49. Genetic distances among the 36 cultivars ranged from 0.10 (between cultivars Ocepar 18 and BRS 207 to 0.88 (between cultivars CD 101 and Fudancep 46, the mean distance being 0.48. Twelve groups were obtained by using the unweighted pair-group method with arithmetic means analysis (UPGMA, and thirteen through the Tocher method. Both methods produced similar clusters, with one to thirteen cultivars per group. The results indicate that these tools may be used to protect intellectual property and for breeding and selection programs.

Genetic Variability of Macrophomina phaseolina Isolates from Dry Beans in Turkey

OpenAIRE

Serkan Yeşil; Kubilay Kurtuluş Baştaş

2016-01-01

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 ...

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; pKenya 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 © 2015. Published by Elsevier B.V.

Assessment of genetic variability in Trigonella foenum-graecum L. germplasm by SDS-page analysis

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Qadir Abdul

2017-01-01

Full Text Available The 96 genotypes of Trigonella foenum-graecum L. (Fenugreek were estimated by using Sodium Dodecyl Sulphate Poly Acrylamide Gel Electrophoresis (SDS-PAGE. The accessions were maintained from diverse ecological areas of the world. Total seed storage proteins were electrophoresis on 12.5% polyacrylamide gels. A total of 17 protein bands were detected, of which seven were highly polymorphic and six were moderate polymorphic and four were low polymorphic with molecular weight extending from of ~15 to ~180 kDa. The dendrogram based on similarity matrix using Unweighted Pair Group Method with Arithmetic Mean (UPGMA divided all the genotypes into four major clusters i.e., I, II, III and IV comprising 51, 24, 10 and 11 accessions, respectively. Although limited genetic diversity was detected amongst known germplasm but the presence/absence of polymorphic bands revealed a significant variances among different Trigonella genotypes. The differences exposed in this project work should be oppressed for the future breeding prospective of Trigonella genotypes by using other advanced molecular techniques. The SDS-PAGE per se seems inadequate tool for such kind of analysis, and may be integrated with other genetic and sequence based approaches for more precise estimation of the genetic variability within closely related accessions. Our results provide baseline for obtaining locally adapted and improved cultivars of fenugreek in Pakistan.

Evolution of the genetic variability of eight French dairy cattle breeds assessed by pedigree analysis.

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Danchin-Burge, C; Leroy, G; Brochard, M; Moureaux, S; Verrier, E

2012-06-01

A pedigree analysis was performed on eight French dairy cattle breeds to assess their change in genetic variability since a first analysis completed in 1996. The Holstein, Normande and Montbéliarde breeds are selected internationally with over hundreds of thousands cows registered in the performance recording system. Three breeds are internationally selected but with limited numbers of cows in France (Brown Swiss, French Simmental and French Red Pied). The last two remaining breeds (Abondance and Tarentaise) are raised at regional level. The effective numbers of ancestors of cows born between 2004 and 2007 varied between 15 (Abondance and Tarentaise) and 51 (French Red Pied). The effective population sizes (classical approach) varied between 53 (Abondance) and 197 (French Red Pied). This article also compares the genetic variability of the ex situ (collections of the French National Cryobank) and in situ populations. The results were commented in regard to the recent history of gene flows in the different breeds as well as the existence of more or less stringent bottlenecks. Our results showed that whatever the size of the breeds, their genetic diversity impoverished quite rapidly since 1996 and they all could be considered as quite poor from a genetic diversity point of view. It shows the need for setting up cryobanks as gene reservoirs as well as sustainable breeding programmes that include loss of genetic diversity as an integrated control parameter. © 2011 Blackwell Verlag GmbH.

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

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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.

Genetic parameters and estimated genetic gains in young rubber tree progenies

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Cecília Khusala Verardi

2013-04-01

Full Text Available The objective of this work was to assess the genetic parameters and to estimate genetic gains in young rubber tree progenies. The experiments were carried out during three years, in a randomized block design, with six replicates and ten plants per plot, in three representative Hevea crop regions of the state of São Paulo, Brazil. Twenty-two progenies were evaluated, from three to five years old, for rubber yield and annual girth growth. Genetic gain was estimated with the multi-effect index (MEI. Selection by progenies means provided greater estimated genetic gain than selection based on individuals, since heritability values of progeny means were greater than the ones of individual heritability, for both evaluated variables, in all the assessment years. The selection of the three best progenies for rubber yield provided a selection gain of 1.28 g per plant. The genetic gains estimated with MEI using data from early assessments (from 3 to 5-year-old were generally high for annual girth growth and rubber yield. The high genetic gains for annual girth growth in the first year of assessment indicate that progenies can be selected at the beginning of the breeding program. Population effective size was consistent with the three progenies selected, showing that they were not related and that the population genetic variability is ensured. Early selection with the genetic gains estimated by MEI can be made on rubber tree progenies.

IN SITU COMPARISON OF TREE-RING RESPONSES TO CLIMATE AND POPULATION GENETICS: THE NEED TO CONTROL FOR LOCAL CLIMATE AND SITE VARIABLES

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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.

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

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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.

Genetic Variability of 27 Traits in a Core Collection of Flax (Linum usitatissimum L.).

Science.gov (United States)

You, Frank M; Jia, Gaofeng; Xiao, Jin; Duguid, Scott D; Rashid, Khalid Y; Booker, Helen M; Cloutier, Sylvie

2017-01-01

Assessment of genetic variability of plant core germplasm is needed for efficient germplasm utilization in breeding improvement. A total of 391 accessions of a flax core collection, which preserves the variation present in the world collection of 3,378 accessions maintained by Plant Gene Resources of Canada (PGRC) and represents a broad range of geographical origins, different improvement statuses and two morphotypes, was evaluated in field trials in up to 8 year-location environments for 10 agronomic, eight seed quality, six fiber and three disease resistance traits. The large phenotypic variation in this subset was explained by morphotypes (22%), geographical origins (11%), and other variance components (67%). Both divergence and similarity between two basic morphotypes, namely oil or linseed and fiber types, were observed, whereby linseed accessions had greater thousand seed weight, seeds m -2 , oil content, branching capability and resistance to powdery mildew while fiber accessions had greater straw weight, plant height, protein content and resistance to pasmo and fusarium wilt diseases, but they had similar performance in many traits and some of them shared common characteristics of fiber and linseed types. Weak geographical patterns within either fiber or linseed accessions were confirmed, but specific trait performance was identified in East Asia for fiber type, and South Asia and North America for linseed type. Relatively high broad-sense heritability was obtained for seed quality traits, followed by agronomic traits and resistance to powdery mildew and fusarium wilt. Diverse phenotypic and genetic variability in the flax core collection constitutes a useful resource for breeding.

Genetic Variability of Show Jumping Attributes in Young Horses Commencing Competing

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Tomasz Próchniak

2015-08-01

Full Text Available The aim of the study was to select traits that may constitute a prospective criterion for breeding value prediction of young horses. The results of 1,232 starts of 894 four-, five-, six-, and seven-year-old horses, obtained during jumping championships for young horses which had not been evaluated in, alternative to championships, training centres were analyed. Nine traits were chosen of those recorded: ranking in the championship, elimination (y/n, conformation, rating of style on day one, two, and three, and penalty points on day one, two, and three of a championship. (Covariance components were estimated via the Gibbs sampling procedure and adequate (covariance component ratios were calculated. Statistical classifications were trait dependent but all fitted random additive genetic and permanent environment effects. It was found that such characteristics as penalty points and jumping style are potential indicators of jumping ability, and the genetic variability of the traits was within the range of 14% to 27%. Given the low genetic correlations between the conformation and other results achieved on the parkour, the relevance of assessment of conformation in four-years-old horses has been questioned.

Genetic Variability of Macrophomina phaseolina Isolates from Dry Beans in Turkey

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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.

Rapid and inexpensive analysis of genetic variability in Arapaima gigas by PCR multiplex panel of eight microsatellites.

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Hamoy, I G; Santos, E J M; Santos, S E B

2008-01-22

The aim of the present study was the development of a multiplex genotyping panel of eight microsatellite markers of Arapaima gigas, previously described. Specific primer pairs were developed, each one of them marked with either FAM-6, HEX or NED. The amplification conditions using the new primers were standardized for a single reaction. The results obtained demonstrate high heterozygosity (average of 0.69) in a Lower Amazon population. The multiplex system described can thus be considered a fast, efficient and inexpensive method for the investigation of genetic variability in Arapaima populations.

GENETIC VARIABILITY OF THREE POPULATIONS OF FLYING FISH, Hirundichthy oxycephalus FROM MAKASSAR STRAIT

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Andi Parenrengi

2016-03-01

Full Text Available Flying fish, Hirundichthy oxycephalus is one of economically important marine species to Indonesia, particularly in Makassar Strait and Flores Sea. However, there is a limited published data on genetic variation in molecular marker level of this species. Random Amplified Polymorphic DNA (RAPD was employed in this study to determine the genetic variability of three populations of flying fish collected from Takalar, Pare-Pare, and Majene in Makassar Strait. Genomic DNA was isolated from preserved muscle tissue using phenol-chloroform technique. Two selected arbitrary primers (CA-01 and P-40 were performed to generate RAPD finger printing of flying fish populations. The two primers generated a total of 81 fragments (loci and 50 polymorphic fragments with size ranging from 125 to 1,250 bp. There were no significant differences in number of fragment and number of polymorphic fragment among populations. The high polymorphism (63.5±7.4% was obtained from Takalar population followed by Pare-Pare (58.3±19.6% and Majene population (57.7±0.8%. Similarity index of individuals was 0.60±0.17 for Takalar, 0.63±0.17 for Majene and 0.75±0.21 for Pare-Pare population. Seven fragments were identified as species-specific markers of H. oxycephalus. The UPGMA cluster analysis showed that the Takalar population was genetically closer to Pare-Pare population (D= 0.0812 than to Majene population (D= 0.1873.

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.

Recent habitat fragmentation caused by major roads leads to reduction of gene flow and loss of genetic variability in ground beetles.

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Keller, Irene; Largiadèr, Carlo R

2003-02-22

Although habitat fragmentation is suspected to jeopardize the long-term survival of many species, few data are available on its impact on the genetic variability of invertebrates. We assess the genetic population structure of the flightless ground beetle Carabus violaceus L., 1758 in a Swiss forest, which is divided into several fragments by a highway and two main roads. Eight samples were collected from different forest fragments and analysed at six microsatellite loci. The largest genetic differentiation was observed between samples separated by roads and in particular by the highway. The number of roads between sites explained 44% of the variance in pairwise F(ST) estimates, whereas the age of the road and the geographical distance between locations were not significant factors. Furthermore, a comparison of allelic richness showed that the genetic variability in a small forest fragment isolated by the highway was significantly lower than in the rest of the study area. These findings strongly support the hypothesis that large roads are absolute barriers to gene flow in C. violaceus, which may lead to a loss of genetic variability in fragmented populations.

Genetical variability of Gladioli as the result of gamma-radiation

International Nuclear Information System (INIS)

Jakota, L.I.; Murin, A.V.

1994-01-01

In the starting material of Gladioli, got in the result of Y-radiation, the forms with white spots on the petals were observed. The Gladioli form 165-81 is distinguished by low growth and middle early flowering. The flower form is triangular. Basic pigmentation is red. White spots of different size on the petals were observed. The investigation was made in 1992 in the field of genetical variability of Gladioli. The Gladioli form 165-81 was irradiated with gamma-radiation dose 30 Gr. As a result the depression of biometric indicators was observed. Consequently, 30 Gr is a mutant dose for Gladioli

Genetic variability in Melipona scutellaris from Recôncavo, Bahia, Brazil.

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Viana, J L; Francisco, A K; Carvalho, C A L; Waldschmidt, A M

2013-09-10

Bees play a key role in pollination and thereby help maintain plant diversity. The stingless bee Melipona scutellaris is an important pollinator in northeastern Brazil because it is endemic to this region. Both deforestation and timber harvesting have reduced the nesting sites for this species, thus reducing its population and range. Genetic studies may help reverse this process by providing important tools for their proper management with a view to conservation of this species. Microsatellite markers have proven to be ideal for mapping genes and population genetic studies. Our aim was to study, using microsatellite markers, the interpopulation genetic variability of M. scutellaris in different parts of the Recôncavo region in Bahia State, Brazil. In all, 95 adult workers from 11 localities in Recôncavo Baiano (Amargosa, Cabaceiras do Paraguaçu, Conceição da Feira, Conceição do Almeida, Domingos Macedo Costa, Governador Mangabeira, Jaguaripe, Jiquiriça, Maragojipe, São Felipe, and Vera Cruz) were analyzed using 10 pairs of microsatellite primers developed for different Meliponini species. The total number of alleles, allele richness, and genetic diversity ranged from 2 to 7 per locus (average = 4.4), 1.00 to 4.88, and 0.0 to 0.850, respectively. The expected and observed heterozygosities varied from 0.0 to 0.76 and 0.0 to 0.84, respectively. No locus showed deviation from the expected frequencies in the chi-square test or linkage disequilibrium. The fixation index, analysis of molecular variance, and unweighted pair-group method using the arithmetic average revealed the effects of human activities on the populations of M. scutellaris, as little genetic structure was detected.

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

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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.

Infection dynamics and genetic variability of Mycoplasma hyopneumoniae in self-replacement gilts.

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Takeuti, Karine L; de Barcellos, David E S N; de Andrade, Caroline P; de Almeida, Laura L; Pieters, Maria

2017-09-01

The aim of this study was to assess the longitudinal pattern of M. hyopneumoniae detection in self-replacement gilts at various farms and to characterize the genetic diversity among samples. A total of 298 gilts from three M. hyopneumoniae positive farms were selected at 150days of age (doa). Gilts were tested for M. hyopneumoniae antibodies by ELISA, once in serum at 150 doa and for M. hyopneumoniae detection in laryngeal swabs by real time PCR two or three times. Also, 425 piglets were tested for M. hyopneumoniae detection in laryngeal swabs. A total of 103 samples were characterized by Multiple Locus Variable-number tandem repeats Analysis. Multiple comparison tests were performed and adjusted using Bonferroni correction to compare prevalences of positive gilts by ELISA and real time PCR. Moderate to high prevalence of M. hyopneumoniae in gilts was detected at 150 doa, which decreased over time, and different detection patterns were observed among farms. Dam-to-piglet transmission of M. hyopneumoniae was not detected. The characterization of M. hyopneumoniae showed 17 different variants in all farms, with two identical variants detected in two of the farms. ELISA testing showed high prevalence of seropositive gilts at 150 doa in all farms. Results of this study showed that circulation of M. hyopneumoniae in self-replacement gilts varied among farms, even under similar production and management conditions. In addition, the molecular variability of M. hyopneumoniae detected within farms suggests that in cases of minimal replacement gilt introduction bacterial diversity maybe farm specific. Copyright © 2017 Elsevier B.V. All rights reserved.

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.

Genetic variability in Cynara cardunculus L. domestic and wild types for grain oil production and fatty acids composition

International Nuclear Information System (INIS)

Raccuia, Salvatore Antonino; Piscioneri, Ilario; Sharma, Neeta; Melilli, Maria Grazia

2011-01-01

This paper aimed to study the genetic variability within different types of Cynara cardunculus L., domestic and wild types, for their grain oil amount and oil fatty acid composition. The grain oils were extracted from 8 domestic cardoons and 4 wild cardoons, by Soxhlet method, and obtained oils were characterized for palmitic, stearic, oleic and linoleic acids by gas chromatography. The oil amount, resulted on average of accessions 216 g kg -1 DM with a good range of variability (CV = 11.7%). Unsaturated acids (oleic and linoleic) predominated over saturated ones (stearic and palmitic acids), the chemical characterization of extracted oil, showed the main compound (as % of analysed fatty acids), averaged for all populations, was linoleic acid (44.5%), followed by oleic acid (42.6%), palmitic acid (9.8%) and stearic acid (3.1%). In particular referring the oleic acid wild cardoon populations showed a mean value of 289 g kg -1 oil, against a mean value of 472 g kg -1 oil showed by domestic cardoon accessions. Three of the studied domestic cardoon ('DC1', 'DC3' and 'DC7') showed values higher than 795 g kg -1 oil, while all the other accessions had concentration lower than 370 g kg -1 oil. The three types of domestic cardoon 'DC1', 'DC3' and 'DC7' showed a fatty acids profile similar to genetic modified sunflower oil, representing new genetic material that potentially could be used for high quality biodiesel production, characterised by a low Iodine Number. -- Highlights: → The grain oils from 12 cardoons were characterized for fatty acids composition. → The oil amount, resulted on average of accessions 216 g kg -1 DM. → Oleic and linoleic acids predominated over stearic and palmitic acids. → Three domestic cardoons grain oil showed high oleic acid content (795 g kg -1 oil). → This oil could be used for high quality biodiesel production, with a low IN.

High genetic diversity among and within bitter manioc varieties cultivated in different soil types in Central Amazonia

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Alessandro Alves-Pereira

2017-04-01

Full Text Available Abstract Although manioc is well adapted to nutrient-poor Oxisols of Amazonia, ethnobotanical observations show that bitter manioc is also frequently cultivated in the highly fertile soils of the floodplains and Amazonian dark earths (ADE along the middle Madeira River. Because different sets of varieties are grown in each soil type, and there are agronomic similarities between ADE and floodplain varieties, it was hypothesized that varieties grown in ADE and floodplain were more closely related to each other than either is to varieties grown in Oxisols. We tested this hypothesis evaluating the intra-varietal genetic diversity and the genetic relationships among manioc varieties commonly cultivated in Oxisols, ADE and floodplain soils. Genetic results did not agree with ethnobotanical expectation, since the relationships between varieties were variable and most individuals of varieties with the same vernacular name, but grown in ADE and floodplain, were distinct. Although the same vernacular name could not always be associated with genetic similarities, there is still a great amount of variation among the varieties. Many ecological and genetic processes may explain the high genetic diversity and differentiation found for bitter manioc varieties, but all contribute to the maintenance and amplification of genetic diversity within the manioc in Central Amazonia.

AFLP polymorphisms allow high resolution genetic analysis of American Tegumentary Leishmaniasis agents circulating in Panama and other members of the Leishmania genus.

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Carlos M Restrepo

Full Text Available American Tegumentary Leishmaniasis is caused by parasites of the genus Leishmania, and causes significant health problems throughout the Americas. In Panama, Leishmania parasites are endemic, causing thousands of new cases every year, mostly of the cutaneous form. In the last years, the burden of the disease has increased, coincident with increasing disturbances in its natural sylvatic environments. The study of genetic variation in parasites is important for a better understanding of the biology, population genetics, and ultimately the evolution and epidemiology of these organisms. Very few attempts have been made to characterize genetic polymorphisms of parasites isolated from Panamanian patients of cutaneous leishmaniasis. Here we present data on the genetic variability of local isolates of Leishmania, as well as specimens from several other species, by means of Amplified Fragment Length Polymorphisms (AFLP, a technique seldom used to study genetic makeup of parasites. We demonstrate that this technique allows detection of very high levels of genetic variability in local isolates of Leishmania panamensis in a highly reproducible manner. The analysis of AFLP fingerprints generated by unique selective primer combinations in L. panamensis suggests a predominant clonal mode of reproduction. Using fluorescently labeled primers, many taxon-specific fragments were identified which may show potential as species diagnostic fragments. The AFLP permitted a high resolution genetic analysis of the Leishmania genus, clearly separating certain groups among L. panamensis specimens and highly related species such as L. panamensis and L. guyanensis. The phylogenetic networks reconstructed from our AFLP data are congruent with established taxonomy for the genus Leishmania, even when using single selective primer combinations. Results of this study demonstrate that AFLP polymorphisms can be informative for genetic characterization in Leishmania parasites, at

Genetic Diversity Studies Based on Morphological Variability, Pathogenicity and Molecular Phylogeny of the Sclerotinia sclerotiorum Population From Indian Mustard (Brassica juncea

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Pankaj Sharma

2018-06-01

Full Text Available White mold or stem rot disease are ubiquitously distributed throughout the world and the causal organism of this disease Sclerotinia sclerotiorum (Lib. de Bary, is known to infect over 400 plant species. Sclerotinia stem rot is one of the most devastating fungal diseases and poses a serious threat to the worldwide cultivation of oilseed Brassica including India. S. sclerotiorum pathogen usually infects the stem but in severe cases leaves and pods also affected at different developmental stages that deteriorate not only the oil quality but also causing the seed and oil yield losses up to 90% depending on the severity of the disease infestation. This study investigated the morphological and molecular characterization of pathogenic S. sclerotiorum (Lib de Bary geographical isolates from oilseed Brassica including Brassica juncea (Indian mustard. The aim of this study was to compare isolates of S. sclerotiorum originated from different agro-climatic conditions and to analyse similarity or differences between them as well as to examine the virulence of this pathogen specifically in Brassica for the first time. The collection of S. sclerotiorum isolates from symptomatic Brassica plants was done and analyzed for morphological features, and molecular characterization. The virulence evaluation test of 65 isolates on four Brassica cultivars has shown 5 of them were highly virulent, 46 were virulent and 14 were moderately virulent. Phylogenetic analysis encompassing all the morphological features, SSR polymorphism, and ITS sequencing has shown the existence of high genetic diversity among the isolates that categorized all the isolates in three evolutionary lineages in the derived dendrogram. Further, genetic variability analysis based on sequences variation in ITS region of all the isolates has shown the existence of either insertions or deletions of the nucleotides in the ITS region has led to the interspecies variability and observed the variation were

Genetic Variability in DNA Repair Proteins in Age-Related Macular Degeneration

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Janusz Blasiak

2012-10-01

Full Text Available The pathogenesis of age-related macular degeneration (AMD is complex and involves interactions between environmental and genetic factors, with oxidative stress playing an important role inducing damage in biomolecules, including DNA. Therefore, genetic variability in the components of DNA repair systems may influence the ability of the cell to cope with oxidative stress and in this way contribute to the pathogenesis of AMD. However, few reports have been published on this subject so far. We demonstrated that the c.977C>G polymorphism (rs1052133 in the hOGG1 gene and the c.972G>C polymorphism (rs3219489 in the MUTYH gene, the products of which play important roles in the repair of oxidatively damaged DNA, might be associated with the risk of AMD. Oxidative stress may promote misincorporation of uracil into DNA, where it is targeted by several DNA glycosylases. We observed that the g.4235T>C (rs2337395 and c.−32A>G (rs3087404 polymorphisms in two genes encoding such glycosylases, UNG and SMUG1, respectively, could be associated with the occurrence of AMD. Polymorphisms in some other DNA repair genes, including XPD (ERCC2, XRCC1 and ERCC6 (CSB have also been reported to be associated with AMD. These data confirm the importance of the cellular reaction to DNA damage, and this may be influenced by variability in DNA repair genes, in AMD pathogenesis.

GSTM1, GSTP1, and GSTT1 genetic variability in Turkish and worldwide populations.

Science.gov (United States)

Karaca, Sefayet; Karaca, Mehmet; Cesuroglu, Tomris; Erge, Sema; Polimanti, Renato

2015-01-01

Glutathione S-transferase (GST) variants have been widely investigated to better understand their role in several pathologic conditions. To our knowledge, no data about these genetic polymorphisms within the Turkish population are currently available. The aim of this study was to analyze GSTM1 positive/null, GSTT1 positive/null, GSTP1*I105V (rs1695), and GSTP1*A114V (rs1138272) variants in the general Turkish population, to provide information about its genetic diversity, and predisposition to GST-related diseases. Genotyping was performed in 500 Turkish individuals using the Sequenom MassARRAY platform. A comparative analysis was executed using the data from the HapMap and Human Genome Diversity Projects (HGDP). Sequence variation was deeply explored using the Phase 1 data of the 1,000 Genomes Project. The variability of GSTM1, GSTT1, and GSTP1 polymorphisms in the Turkish population was similar to that observed in Central Asian, European, and Middle Eastern populations. The high linkage disequilibrium between GSTP1*I105V and GSTP1*A114V in these populations may have a confounding effect on GSTP1 genetic association studies. In analyzing GSTM1, GSTT1, and GSTP1 sequence variation, we observed other common functional variants that may be candidates for associated studies of diseases related to GST genes (e.g., cancer, cardiovascular disease, and allergy). This study provides novel data about GSTM1 positive/null, GSTT1 positive/null, GSTP1*I105V, and GSTP1*A114V variants in the Turkish population, and other functional variants that may affect GSTM1, GSTT1, and GSTP1 functions among worldwide populations. This information can assist in the design of future genetic association studies investigating oxidative stress-related diseases. © 2014 Wiley Periodicals, Inc.

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

African Journals Online (AJOL)

ONOS

2010-05-10

May 10, 2010 ... coefficient of variation; h2, heritability; GA, genetic advance;. EMS, ethyl methane ... The analysis of variance (ANOVA) revealed the significance degree among the ... fullest extent. The estimates of range, phenotypic and.

Human genetics studies in areas of high natural radiation. VII. Genetic load

Energy Technology Data Exchange (ETDEWEB)

Freire-Maia, A [Faculdade de Ciencias Medicas e Biologicas de Botucatu (Brazil). Departamento de Genetica

1975-01-01

Two methods to estimate the inbreeding load, employed in our analysis, are reviewed. Besides the total population, a sample constituted of individuals with no alien ancesters is also analyzed. The measurements by genetic load models show a clear effect of natural radioactivity (especially for abortions, pre-natal mortality, anomalies, and abnormalities in general). The results on stillbirths and post-natal and total mortalities are discussed and it is concluded that uncontrolled concomitant variables (if not chance alone) cause the differences.

Study of the genetic variability of isolated belonging to the group B of the Respiratory Virus Human Sincicial

International Nuclear Information System (INIS)

Delfraro, A.

1998-07-01

The study allows analyzing the genetic variability of stumps belonging to the group B of the Breathing Virus Sincicial (Vrs), isolated in Uruguay among the years 1990 and 1996. They were evidenced by sequence the nucleotides changes and the changes were determined that take place at level of amino acids, the following ones were used technical: enzyme immunoassay, of extraction of viral RNA, of reverse transcription and Pcr, of purification of DNA and electrophoresis of nucleic acids. The result proven in the entirety of the isolated virus the genetic variability, enlarging and confirming the evolution pattern proposed by Sullender and collaborators, (1991) for the group B of Vrs [es

Impact of strong selection for the PrP major gene on genetic variability of four French sheep breeds (Open Access publication

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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.

Genetic variability of Cordia alliodora (R. and P.) Oken progenies

International Nuclear Information System (INIS)

Marulanda, Marta Leonor; Lopez, Ana Maria; Uribe, Marcela; Ospina, Carlos Mario

2011-01-01

Cordia alliodora is a well-known wood producer tree of tropical areas of Latin America and the Caribbean characterized for producing valuable wood and by its fast growth rate. In Colombia, it is frequent on agro-forestall systems with coffee. This species, like most forest species have biological problems for genetic improvement programs, such as long regeneration periods and high costs for supporting a population in a long term. The molecular assisted markers in plant breeding programs have had a great impact on genetic improvement, due to the fact they minimize their intervals of regeneration, increase the genetic gain by generation and allow the evaluation of the genetic information essential for the species. In this work, 60 genotypes of C. alliodora were characterized, belonging to the provenance and progenies tests established by the program of genetic improvement of Cenicafe. The characterization was carried out through micro satellite markers, after developing a genomic library enriched with micro satellites of the species. Finally, 24 specific micro satellites were evaluated, 20 of which allowed the detection of 28 polymorphic and multiallelic loci. These results provide a guide for orienting the policies of sustainable production and conservation of this valuable species; also, it provides a useful tool for the identification of clones with commercial interest.

Hybrid Model Based on Genetic Algorithms and SVM Applied to Variable Selection within Fruit Juice Classification

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C. Fernandez-Lozano

2013-01-01

Full Text Available 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.

Environmental carcinogenesis and genetic variability

International Nuclear Information System (INIS)

Knudsen, A.G. Jr

1977-01-01

It was found that carcinogenesis in man may involve the interaction of genetic and environmental forces, and that mutation, whether germinal or somatic, seems to be involved in the origin of many, perhaps all cancers. The cancers of man may be visualized as occurring in four groups of individuals according to whether (1) neither genetic nor environmental factors are dominant, i.e. 'background' or 'spontaneous' cancer, (2) heredity alone is dominant, (3) environment alone is important, or (4) both are operating (Knudsen, 1977). The last two groups together are widely thought to contribute 70-80% of cancer cases in the United States; the relative contribution of each group is a major question to be answered

Genetic diversity of dispersed seeds is highly variable among leks of the long-wattled umbrellabird

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Ottewell, Kym; Browne, Luke; Cabrera, Domingo; Olivo, Jorge; Karubian, Jordan

2018-01-01

Frugivorous animals frequently generate clumped distributions of seeds away from source trees, but genetic consequences of this phenomenon remain poorly resolved. Seed dispersal of the palm Oenocarpus bataua by long-wattled umbrellabirds Cephalopterus penduliger generates high seed densities in leks (i.e., multi-male display sites), providing a suitable venue to investigate how dispersal by this frugivore may influence seed source diversity and genetic structure at local and landscape levels. We found moderate levels of maternal seed source diversity in primary seed rain across five leks in northwest Ecuador (unweighted mean alpha diversity α = 9.52, weighted mean αr = 3.52), with considerable variation among leks (αr range: 1.81-24.55). Qualitatively similar findings were obtained for allelic diversity and heterozygosity. Higher densities of O. bataua adults around leks were associated with higher values of αr and heterozygosity (non-significant trends) and allelic diversity (significant correlation). Seed source overlap between different leks was not common but did occur at low frequency, providing evidence for long-distance seed dispersal by umbrellabirds into leks. Our findings are consistent with the idea that seed pool diversity within leks may be shaped by the interaction between density of local trees, which can vary considerably between leks, and umbrellabird foraging ecology, particularly a lack of territorial defense of fruiting trees. Taken as a whole, this work adds to our growing appreciation of the ways resource distribution and associated frugivore foraging behaviors mechanistically shape seed dispersal outcomes and the distribution of plant genotypes across the landscape.

Bayesian inference for the genetic control of water deficit tolerance in spring wheat by stochastic search variable selection.

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Safari, Parviz; Danyali, Syyedeh Fatemeh; Rahimi, Mehdi

2018-06-02

Drought is the main abiotic stress seriously influencing wheat production. Information about the inheritance of drought tolerance is necessary to determine the most appropriate strategy to develop tolerant cultivars and populations. In this study, generation means analysis to identify the genetic effects controlling grain yield inheritance in water deficit and normal conditions was considered as a model selection problem in a Bayesian framework. Stochastic search variable selection (SSVS) was applied to identify the most important genetic effects and the best fitted models using different generations obtained from two crosses applying two water regimes in two growing seasons. The SSVS is used to evaluate the effect of each variable on the dependent variable via posterior variable inclusion probabilities. The model with the highest posterior probability is selected as the best model. In this study, the grain yield was controlled by the main effects (additive and non-additive effects) and epistatic. The results demonstrate that breeding methods such as recurrent selection and subsequent pedigree method and hybrid production can be useful to improve grain yield.

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

Genetic variability of Echinococcus granulosus complex in various geographical populations of Iran inferred by mitochondrial DNA sequences.

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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. Copyright © 2016 Elsevier B.V. All rights reserved.

Genetic variability of concentration of microelements in wild sunflower species and hybrids

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Kastori Rudolf R.

2010-01-01

Full Text Available The aim of this work was to investigate genetic specificity of sunflower nutrition with microelements. Therefore, concentrations of essential (Zn, B, Mn, Cu, Fe and Ni and non-essential (Cr, Al, Cd, As, Pb and Ba micronutrients were analyzed. Five sunflower hybrids the most grown in Serbia and different populations of wild sunflower species originating from North America: Helianthus neglectus Heiser (3, Helianthus agrophyllus T&G (3, Helianthus petiolaris Nutt. (2, Helianthus annuus L. (4 were included in the experiment. Populations of wild sunflower species and hybrids differed significantly with respect to the concentration of analyzed elements. Manganese concentration was significantly higher in hybrids than in wild species. In all genotypes Fe, B and Mn had the highest concentration. Coefficient of variation of microelement concentration depended on genotype and particular element. In wild populations, for essential microelements, it was between 3.7 and 59.5, whereas in hybrids it varied from 10.0 to 48.8. Coefficient of variation of concentration of non-essential microelements in wild populations varied from 7.7 to 73.8, and in hybrids from 15.1 to 48.8. Average coefficient of variation in both wild species and hybrids was the lowest for Mn and Pb. It was the highest for Cr, Ni, and Zn in hybrids and for Cd, Ni, and Cr in wild species. The results suggest that genetic specificity with respect to uptake of microelements in wild species and hybrids is highly expressed. Broad genetic variability of concentrations of microelements in wild species and hybrids indicate that their reactions to deficiency and/or excess of those elements probably are not the same either. This finding may be used in breeding process aimed specifically at improvement of tolerance and capacity to accumulate microelements in sunflower. Phytoremediation technology designed to reduce the amount of microelements in the soil could thus be advanced by utilization of such

Evaluating the Genetics of Common Variable Immunodeficiency: Monogenetic Model and Beyond

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Guillem de Valles-Ibáñez

2018-05-01

Full Text Available Common variable immunodeficiency (CVID is the most frequent symptomatic primary immunodeficiency characterized by recurrent infections, hypogammaglobulinemia and poor response to vaccines. Its diagnosis is made based on clinical and immunological criteria, after exclusion of other diseases that can cause similar phenotypes. Currently, less than 20% of cases of CVID have a known underlying genetic cause. We have analyzed whole-exome sequencing and copy number variants data of 36 children and adolescents diagnosed with CVID and healthy relatives to estimate the proportion of monogenic cases. We have replicated an association of CVID to p.C104R in TNFRSF13B and reported the second case of homozygous patient to date. Our results also identify five causative genetic variants in LRBA, CTLA4, NFKB1, and PIK3R1, as well as other very likely causative variants in PRKCD, MAPK8, or DOCK8 among others. We experimentally validate the effect of the LRBA stop-gain mutation which abolishes protein production and downregulates the expression of CTLA4, and of the frameshift indel in CTLA4 producing expression downregulation of the protein. Our results indicate a monogenic origin of at least 15–24% of the CVID cases included in the study. The proportion of monogenic patients seems to be lower in CVID than in other PID that have also been analyzed by whole exome or targeted gene panels sequencing. Regardless of the exact proportion of CVID monogenic cases, other genetic models have to be considered for CVID. We propose that because of its prevalence and other features as intermediate penetrancies and phenotypic variation within families, CVID could fit with other more complex genetic scenarios. In particular, in this work, we explore the possibility of CVID being originated by an oligogenic model with the presence of heterozygous mutations in interacting proteins or by the accumulation of detrimental variants in particular immunological pathways, as well as

Joint High-Dimensional Bayesian Variable and Covariance Selection with an Application to eQTL Analysis

KAUST Repository

Bhadra, Anindya

2013-04-22

We describe a Bayesian technique to (a) perform a sparse joint selection of significant predictor variables and significant inverse covariance matrix elements of the response variables in a high-dimensional linear Gaussian sparse seemingly unrelated regression (SSUR) setting and (b) perform an association analysis between the high-dimensional sets of predictors and responses in such a setting. To search the high-dimensional model space, where both the number of predictors and the number of possibly correlated responses can be larger than the sample size, we demonstrate that a marginalization-based collapsed Gibbs sampler, in combination with spike and slab type of priors, offers a computationally feasible and efficient solution. As an example, we apply our method to an expression quantitative trait loci (eQTL) analysis on publicly available single nucleotide polymorphism (SNP) and gene expression data for humans where the primary interest lies in finding the significant associations between the sets of SNPs and possibly correlated genetic transcripts. Our method also allows for inference on the sparse interaction network of the transcripts (response variables) after accounting for the effect of the SNPs (predictor variables). We exploit properties of Gaussian graphical models to make statements concerning conditional independence of the responses. Our method compares favorably to existing Bayesian approaches developed for this purpose. © 2013, The International Biometric Society.

Population structure, fluctuating asymmetry and genetic variability in an endemic and highly isolated Astyanax fish population (Characidae

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Maria Claudia Gross

2004-01-01

Full Text Available Morphological and chromosomal markers were used to infer the structure and genetic variability of a population of fish of the genus Astyanax, geographically isolated at sinkhole 2 of Vila Velha State Park, Paraná, Brazil. Two morphotypes types were observed, the standard phenotype I and phenotype II which showed an anatomical alteration probably due to an inbreeding process. Fluctuating asymmetry (FA analysis of different characters showed low levels of morphological variation among the population from sinkhole 2 and in another population from the Tibagi river (Paraná, Brazil. The Astyanax karyotype was characterized in terms of chromosomal morphology, constitutive heterochromatin and nucleolar organizer regions. Males and females presented similar karyotypes (2n=48, 6M+18SM+14ST+10A with no evidence of a sex chromosome system. One female from sinkhole 2 was a natural triploid with 2n=3x=72 chromosomes (9M+27SM+21ST+15A. The data are discussed regarding the maintenance of population structure and their evolutionary importance, our data suggesting that Astyanax from the Vila Velha State Park sinkhole 2 is a recently isolated population.

Genetic determination of high productivity in experimental hybrid combinations of sugar beet (Beta vulgaris L.

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М. О. Корнєєва

2016-05-01

Full Text Available Purpose. Creation of experimental sugar beet hybrid combinations of high sugar yield values and defining gene­tic determination of their heterotic effect. Methods. Diallel crossing and topcrossing, genetic analysis of quantitative traits. Results. The authors have studied the frequency of occurrence of sugar beet heterotic hybrid combinations for «sugar yield» trait created on the basis of two pollinator lines to be genetically valuable for productivity elements, CMS lines and single-cross sterile hybrids with the use of diallel and topcrossing system of controlled hybridization. The share of parental components’ effect and their interaction in CMS hybrids variability for productivity was determined. Expediency of heterotic forecasting based on high combining ability lines was substabtiated. Promising high-yielding sugar beet combinations were selected that exceeded the group standard by 4.1–16.3%. Conclusions. The theory of genetic balance by M. V. Turbin was confirmed. Such hybrids as [CMS 5OT 4]MGP 1 (116.3%, [CMS 1OT 2]MGP 1 (112.5% and [CMS 3OT 5]MGP 1 (113.2% were recognized as the best for their productivity, MGP 1 and MGP 2 lines – as the best for their combining ability.

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

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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.

Detecting Major Genetic Loci Controlling Phenotypic Variability in Experimental Crosses

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Rönnegård, Lars; Valdar, William

2011-01-01

Traditional methods for detecting genes that affect complex diseases in humans or animal models, milk production in livestock, or other traits of interest, have asked whether variation in genotype produces a change in that trait’s average value. But focusing on differences in the mean ignores differences in variability about that mean. The robustness, or uniformity, of an individual’s character is not only of great practical importance in medical genetics and food production but is also of scientific and evolutionary interest (e.g., blood pressure in animal models of heart disease, litter size in pigs, flowering time in plants). We describe a method for detecting major genes controlling the phenotypic variance, referring to these as vQTL. Our method uses a double generalized linear model with linear predictors based on probabilities of line origin. We evaluate our method on simulated F2 and collaborative cross data, and on a real F2 intercross, demonstrating its accuracy and robustness to the presence of ordinary mean-controlling QTL. We also illustrate the connection between vQTL and QTL involved in epistasis, explaining how these concepts overlap. Our method can be applied to a wide range of commonly used experimental crosses and may be extended to genetic association more generally. PMID:21467569

Genetic diversity and phylogeography of highly zoonotic Echinococcus granulosus genotype G1 in the Americas (Argentina, Brazil, Chile and Mexico) based on 8279bp of mtDNA.

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Laurimäe, Teivi; Kinkar, Liina; Andresiuk, Vanessa; Haag, Karen Luisa; Ponce-Gordo, Francisco; Acosta-Jamett, Gerardo; Garate, Teresa; Gonzàlez, Luis Miguel; Saarma, Urmas

2016-11-01

Echinococcus granulosus is a taeniid cestode and the etiological agent of an infectious zoonotic disease known as cystic echinococcosis (CE) or hydatid disease. CE is a serious public health concern in many parts of the world, including the Americas, where it is highly endemic in many regions. Echinococcus granulosus displays high intraspecific genetic variability and is divided into multiple genotypes (G1-G8, G10) with differences in their biology and etiology. Of these, genotype G1 is responsible for the majority of human and livestock infections and has the broadest host spectrum. However, despite the high significance to the public and livestock health, the data on genetic variability and regional genetic differences of genotype G1 in America are scarce. The aim of this study was to evaluate the genetic variability and phylogeography of G1 in several countries in America by sequencing a large portion of the mitochondrial genome. We analysed 8279bp of mtDNA for 52 E. granulosus G1 samples from sheep, cattle and pigs collected in Argentina, Brazil, Chile and Mexico, covering majority of countries in the Americas where G1 has been reported. The phylogenetic network revealed 29 haplotypes and a high haplotype diversity (Hd=0.903). The absence of phylogeographic segregation between different regions in America suggests the importance of animal transportation in shaping the genetic structure of E. granulosus G1. In addition, our study revealed many highly divergent haplotypes, indicating a long and complex evolutionary history of E. granulosus G1 in the Americas. Copyright © 2016 Elsevier B.V. All rights reserved.

Phylogeography, genetic variability and structure of Acanthamoeba metapopulations in Iran inferred by 18S ribosomal RNA sequences: A systematic review and meta-analysis.

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Spotin, Adel; Moslemzadeh, Hamid Reza; Mahami-Oskouei, Mahmoud; Ahmadpour, Ehsan; Niyyati, Maryam; Hejazi, Seyed Hossein; Memari, Fatemeh; Noori, Jafar

2017-09-01

To verify phylogeography and genetic structure of Acanthamoeba populations among the Iranian clinical isolates and natural/artificial environments distributed in various regions of the country. We searched electronic databases including Medline, PubMed, Science Direct, Scopus and Google Scholar from 2005 to 2016. To explore the genetic variability of Acanthamoeba sp, 205 sequences were retrieved from keratitis patients, immunosuppressed cases and environmental sources as of various geographies of Iran. T4 genotype was the predominant strain in Iran, and the rare genotypes belonged to T2, T3, T5 (Acanthamoeba lenticulata), T6, T9, T11, T13 and T15 (Acanthamoeba jacobsi). A total of 47 unique haplotypes of T4 were identified. A parsimonious network of the sequence haplotypes demonstrated star-like feature containing haplogroups IR6 (34.1%) and IR7 (31.2%) as the most common haplotypes. In accordance with the analysis of molecular variance, the high value of haplotype diversity (0.612-0.848) of Acanthamoeba T4 represented genetic variability within populations. Neutrality indices of the 18S ribosomal RNA demonstrated negative values in all populations which represented a considerable divergence from neutrality. The majority of genetic diversity belonged to the infected contact lens and dust samples in immunodeficiency and ophthalmology wards, which indicated potential routes for exposure to a pathogenic Acanthamoeba sp. in at-risk individuals. A pairwise fixation index (F ST ) was from low to high values (0.02433-0.41892). The statistically F ST points out that T4 is genetically differentiated between north-west, north-south and central-south metapopulations, but not differentiated between west-central, west-south, central-south, and north-central isolates. An occurrence of IR6 and IR7 displays that possibly a gene flow of Acanthamoeba T4 occurred after the founder effect or bottleneck experience through ecological changes or host mobility. This is the first

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

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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.

Radiation induced genetic variability studies in M2 and F2M2 generation in chilli (Capsicum annum L.)

International Nuclear Information System (INIS)

Rangaiah, S.; Manjunath, A.; Naik, Puttarama; Gangappa, E.

2002-01-01

Chilli (Capsicum annum L.) is an important commercial crop in India. Mutation breeding is one of the effective tool to create new variability. Since, yield and its component characters show polygenic inheritance, information on amount of heritable portion of variability created through mutation for these characters is needed to use the induced variability for crop improvement. To harness more variability mutation has been superimposed on hybridization in several crops. The present study is undertaken to estimate the genetic variability induced through gamma irradiation for the polygenically inherited productive traits of chilli in M 2 and F 2 M 2 generation

EVALUATION OF GENETIC VARIABILITY OF FRESHWATER PRAWN COLLECTED FROM MAKASSAR-SULAWESI, PANGKALANBUNKALIMANTAN, JAMBI-SUMATRA, SUKABUMI-JAVA, AND GIMacro USING mtDNA CO-I MARKERS

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Estu Nugroho

2009-06-01

Full Text Available The objective of this research is to evaluate the genetic variability of freshwater prawn, Macrobrachium rosenbergii. The genetic variability of freshwater prawn collected from Makassar-Sulawesi, Pangkalanbun-Kalimantan, Jambi-Sumatra, Sukabumi-Java, and GIMacro strain was examined using polymorphism of the mitochondria DNA (mtDNA markers. Twelve composite haplotypes were detected following digestion of CO1 sequences with four endonucleases: Hae III, Rsa I, Mbo I, and Taq I. The average haplotype diversity was 0.217. Significant genetic difference was observed among freshwater prawn populations, especially among Makassar-Sulawesi population and others. Makassar-Sulawesi strain has future prospect for genetic resources in breeding program.

Variability and genetic differentiation among Anopheles (Ano. intermedius Chagas, 1908 and Anopheles (Ano. mattogrossensis Lutz & Neiva, 1911 (Diptera: Culicidae from the Brazilian Amazon

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Joselita Maria Mendes dos Santos

2005-10-01

Full Text Available Anopheles (Anopheles intermedius and Anopheles (Ano. mattogrossensis are Brazilian anopheline species belonging to the scarcely studied Anopheles subgenus. Few studies have been done on the genetic differentiation of these species. Both species have been found infected by Plasmodium and are sympatric with other anopheline species from the Nyssorhynchus subgenus. Eighteen enzymatic loci were analyzed in larval specimens of An. intermedius and An. mattogrossensis aiming to estimate the variability and genetic differentiation between these species. An. mattogrossensis population showed higher genetic variability (P = 44.4 and Ho = 0.081 ± 0.031 than that of An. intermedius (P = 33.3 and Ho = 0.048 ± 0.021. Most analyzed loci showed genotypic frequencies according to Hardy-Weinberg equilibrium, except for LAP1 and LAP2 in An. intermedius, and EST1 and PGM loci in An. mattogrossensis. The genetic distance between these species (D = 0.683 was consistent with the inter-specific values reported for Anopheles subgenus. We verified that the polymorphism and heterozygosity percentile values found in both species and compared to those in the literature, showed no relation between the level of isozyme variability and geographical distribution. The low variability found in these two species is probably more related to the niche they occupy than to their geographic distribution.

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.

Genetic and Environmental Control of Neurodevelopmental Robustness in Drosophila.

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David J Mellert

Full Text Available Interindividual differences in neuronal wiring may contribute to behavioral individuality and affect susceptibility to neurological disorders. To investigate the causes and potential consequences of wiring variation in Drosophila melanogaster, we focused on a hemilineage of ventral nerve cord interneurons that exhibits morphological variability. We find that late-born subclasses of the 12A hemilineage are highly sensitive to genetic and environmental variation. Neurons in the second thoracic segment are particularly variable with regard to two developmental decisions, whereas its segmental homologs are more robust. This variability "hotspot" depends on Ultrabithorax expression in the 12A neurons, indicating variability is cell-intrinsic and under genetic control. 12A development is more variable and sensitive to temperature in long-established laboratory strains than in strains recently derived from the wild. Strains with a high frequency of one of the 12A variants also showed a high frequency of animals with delayed spontaneous flight initiation, whereas other wing-related behaviors did not show such a correlation and were thus not overtly affected by 12A variation. These results show that neurodevelopmental robustness is variable and under genetic control in Drosophila and suggest that the fly may serve as a model for identifying conserved gene pathways that stabilize wiring in stressful developmental environments. Moreover, some neuronal lineages are variation hotspots and thus may be more amenable to evolutionary change.

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

Science.gov (United States)

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

2011-11-17

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

Genetic variability, correlation and path coefficients of yield and its components analysis in pumpkin (Cucurbita moschata Duch Ex Poir

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GM Mohsin

2017-06-01

Full Text Available Genetic variability, correlation and path coefficient were studied for yield and yield component traits in twenty one diverse genotypes of pumpkin. Highest genotypic coefficient of variation was recorded for fruit length (cm, single fruit weight (kg, Brix (% and yield per plant (kg. Heritability estimates in broad sense were higher for almost all the characters. The characters namely, fruit length, single fruit weight, yield per plant and brix% had high genotypic coefficient of variation coupled with heritability gave high genetic advance expressed as percentage of mean ranged from 76.84 to 96.06 which indicated that these characters were less influenced by environment confirming additive gene action, and therefore, selection of these characters would be more effective for yield improvement of pumpkins. Total six traits likely fruit length, fruit diameter, flesh thickness, single fruit weight and number of fruits per plant were positively and significantly associated with yield per plant. Path coefficient analysis also revealed maximum contribution of single fruit weight (0.869 to yield and this was followed by the contribution of number of fruit per plant (0.527 at genotypic level.

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

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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.

Demographic variability and heterogeneity among individuals within and among clonal bacteria strains

DEFF Research Database (Denmark)

Jouvet, Lionel; Rodriguez-Rojas, Alexandro; Steiner, Ulrich

2018-01-01

to accurately decompose the drivers of heterogeneity among individuals as genetically fixed or selectively neutral. Rather than working on wild populations we present here data from a simple bacterial system in the lab, Escherichia coli. Our system, based on cutting-edge microfluidic techniques, provides high...... control over the genotype and the environment. It therefore allows to unambiguously decompose and quantify fixed genetic variability and dynamic stochastic variability among individuals. We show that within clonal individual variability (dynamic heterogeneity) in lifespan and lifetime reproduction...

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

Genetic variability of Taenia solium cysticerci recovered from experimentally infected pigs and from naturally infected pigs using microsatellite markers.

Science.gov (United States)

Pajuelo, Mónica J; Eguiluz, María; Roncal, Elisa; Quiñones-García, Stefany; Clipman, Steven J; Calcina, Juan; Gavidia, Cesar M; Sheen, Patricia; Garcia, Hector H; Gilman, Robert H; Gonzalez, Armando E; Zimic, Mirko

2017-12-01

The adult Taenia solium, the pork tapeworm, usually lives as a single worm in the small intestine of humans, its only known definitive host. Mechanisms of genetic variation in T. solium are poorly understood. Using three microsatellite markers previously reported [1], this study explored the genetic variability of T. solium from cysts recovered from experimentally infected pigs. It then explored the genetic epidemiology and transmission in naturally infected pigs and adult tapeworms recovered from human carriers from an endemic rural community in Peru. In an initial study on experimental infection, two groups of three piglets were each infected with proglottids from one of two genetically different tapeworms for each of the microsatellites. After 7 weeks, pigs were slaughtered and necropsy performed. Thirty-six (92.3%) out of 39 cysts originated from one tapeworm, and 27 (100%) out of 27 cysts from the other had exactly the same genotype as the parental tapeworm. This suggests that the microsatellite markers may be a useful tool for studying the transmission of T. solium. In the second study, we analyzed the genetic variation of T. solium in cysts recovered from eight naturally infected pigs, and from adult tapeworms recovered from four human carriers; they showed genetic variability. Four pigs had cysts with only one genotype, and four pigs had cysts with two different genotypes, suggesting that multiple infections of genetically distinct parental tapeworms are possible. Six pigs harbored cysts with a genotype corresponding to one of the identified tapeworms from the human carriers. In the dendrogram, cysts appeared to cluster within the corresponding pigs as well as with the geographical origin, but this association was not statistically significant. We conclude that genotyping of microsatellite size polymorphisms is a potentially important tool to trace the spread of infection and pinpoint sources of infection as pigs spread cysts with a shared parental genotype.

Genetic variability of Taenia solium cysticerci recovered from experimentally infected pigs and from naturally infected pigs using microsatellite markers.

Directory of Open Access Journals (Sweden)

Mónica J Pajuelo

2017-12-01

Full Text Available The adult Taenia solium, the pork tapeworm, usually lives as a single worm in the small intestine of humans, its only known definitive host. Mechanisms of genetic variation in T. solium are poorly understood. Using three microsatellite markers previously reported [1], this study explored the genetic variability of T. solium from cysts recovered from experimentally infected pigs. It then explored the genetic epidemiology and transmission in naturally infected pigs and adult tapeworms recovered from human carriers from an endemic rural community in Peru. In an initial study on experimental infection, two groups of three piglets were each infected with proglottids from one of two genetically different tapeworms for each of the microsatellites. After 7 weeks, pigs were slaughtered and necropsy performed. Thirty-six (92.3% out of 39 cysts originated from one tapeworm, and 27 (100% out of 27 cysts from the other had exactly the same genotype as the parental tapeworm. This suggests that the microsatellite markers may be a useful tool for studying the transmission of T. solium. In the second study, we analyzed the genetic variation of T. solium in cysts recovered from eight naturally infected pigs, and from adult tapeworms recovered from four human carriers; they showed genetic variability. Four pigs had cysts with only one genotype, and four pigs had cysts with two different genotypes, suggesting that multiple infections of genetically distinct parental tapeworms are possible. Six pigs harbored cysts with a genotype corresponding to one of the identified tapeworms from the human carriers. In the dendrogram, cysts appeared to cluster within the corresponding pigs as well as with the geographical origin, but this association was not statistically significant. We conclude that genotyping of microsatellite size polymorphisms is a potentially important tool to trace the spread of infection and pinpoint sources of infection as pigs spread cysts with a shared

Genetic variability in arbuscular mycorrhizal fungi compatibility supports the selection of durum wheat genotypes for enhancing soil ecological services and cropping systems in Canada.

Science.gov (United States)

Singh, A K; Hamel, C; Depauw, R M; Knox, R E

2012-03-01

Crop nutrient- and water-use efficiency could be improved by using crop varieties highly compatible with arbuscular mycorrhizal fungi (AMF). Two greenhouse experiments demonstrated the presence of genetic variability for this trait in modern durum wheat ( Triticum turgidum L. var. durum Desf.) germplasm. Among the five cultivars tested, 'AC Morse' had consistently low levels of AM root colonization and DT710 had consistently high levels of AM root colonization, whereas 'Commander', which had the highest colonization levels under low soil fertility conditions, developed poor colonization levels under medium fertility level. The presence of genetic variability in durum wheat compatibility with AMF was further evidenced by significant genotype × inoculation interaction effects in grain and straw biomass production; grain P, straw P, and straw K concentrations under medium soil fertility level; and straw K and grain Fe concentrations at low soil fertility. Mycorrhizal dependency was an undesirable trait of 'Mongibello', which showed poor growth and nutrient balance in the absence of AMF. An AMF-mediated reduction in grain Cd under low soil fertility indicated that breeding durum wheat for compatibility with AMF could help reduce grain Cd concentration in durum wheat. Durum wheat genotypes should be selected for compatibility with AMF rather than for mycorrhizal dependency.

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

Science.gov (United States)

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

2017-08-01

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

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

Detailed genetic structure of European bitterling populations in Central Europe

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Veronika Bartáková

2015-11-01

Full Text Available The European bitterling (Rhodeus amarus is a small cyprinid fish whose populations declined markedly between 1950 and 1980. However, its range currently expands, partly due to human-assisted introductions. We determined the genetic variability and detailed spatial structure among bitterling populations in Central Europe and tested alternative hypotheses about colonization of this area. Twelve polymorphic microsatellite loci on a large sample of 688 individuals had been used to analyse genetic variability and population structure. Samples originated from 27 localities with emphasis on area of the Czech Republic where three major sea drainages (Black, Baltic, and Northern Sea meet. Highly variable level of intrapopulation genetic variability had generally been detected and a recent decrease in numbers (“bottleneck” had been indicated by genetic data among six populations. High level of interpopulation differentiation was identified even within the basins. There was a significant role of genetic drift and indications of low dispersal ability of R. amarus. Surprisingly, the Odra River was inhabited by two distinct populations without any genetic signatures of a secondary contact. Czech part of the Odra (Baltic basin was colonized from the Danubian refugium (similarly to adjacent Danubian basin rivers including the Morava, while Polish part of the Odra was genetically similar to the populations in the Vistula River (Baltic basin, that has been colonized by a different (Eastern phylogeographic lineage of R. amarus. Most Czech R. amarus populations were colonized from the Danubian refugium, suggesting potential for a human-mediated colonization of the Odra or Elbe Rivers by R. amarus. One Elbe basin population was genetically mixed from the two (Danubian and Eastern phylogeographic lineages. In general the Czech populations of R. amarus were genetically stable except for a single population which has probably been recently introduced. This research

T-cell receptor variable genes and genetic susceptibility to celiac disease: an association and linkage study.

Science.gov (United States)

Roschmann, E; Wienker, T F; Gerok, W; Volk, B A

1993-12-01

Genetic susceptibility of celiac disease is primarily associated with a particular combination of and HLA-DQA1/DQB1 gene; however, this does not fully account for the genetic predisposition. Therefore, the aim of this study was to examine whether T-cell receptor (TCR) genes may be susceptibility genes in celiac disease. HLA class II typing was performed by polymerase chain reaction amplification in combination with sequence-specific oligonucleotide hybridization. TCR alpha (TCRA), TCR gamma (TCRG), and TCR beta (TCRB) loci were investigated by restriction fragment length polymorphism analysis. Allelic frequencies of TCRA, TCRG, and TCRB variable genes were compared between patients with celiac disease (n = 53) and control patients (n = 67), and relative risk (RR) estimates were calculated. The RR was 1.67 for allele C1 at TCRA1, 3.35 for allele D2 at TCRA2, 1.66 for allele B2 at TCRG, and 1.35 for allele B at TCRB, showing no significant association. Additionally, linkage analysis was performed in 23 families. The logarithm of odd scores for celiac disease vs. the TCR variable genes at TCRA, TCRG, and TCRB showed no significant linkage. These data suggest that the analyzed TCR variable gene segments V alpha 1.2, V gamma 11, and V beta 8 do not play a major role in susceptibility to celiac disease.

Genetic analysis of the Venezuelan Criollo horse.

Science.gov (United States)

Cothran, E G; Canelon, J L; Luis, C; Conant, E; Juras, R

2011-10-07

Various horse populations in the Americas have an origin in Spain; they are remnants of the first livestock introduced to the continent early in the colonial period (16th and 17th centuries). We evaluated genetic variability within the Venezuelan Criollo horse and its relationship with other horse breeds. We observed high levels of genetic diversity within the Criollo breed. Significant population differentiation was observed between all South American breeds. The Venezuelan Criollo horse showed high levels of genetic diversity, and from a conservation standpoint, there is no immediate danger of losing variation unless there is a large drop in population size.

Genetic variability and cadmium metabolism and toxicity

OpenAIRE

Rentschler, Gerda

2014-01-01

Abstract: Cadmium (Cd) is ubiquitous in the environment. Human exposure in non-smokers occurs mainly via intake of healthy food like vegetables, cereals, and shellfish. Adverse health effects on kidney and bone at low-level environmental Cd exposure are well-documented in adults. There is considerable inter-individual variation in both metabolism (toxicokinetics) and toxicity (toxicodynamics) of Cd. This may be due to genetic factors. The aim of this thesis was to identify genetic fact...

Microsatellite DNA analysis of northern pike ( Esox lucius L.) populations: insights into the genetic structure and demographic history of a genetically depauperate species

DEFF Research Database (Denmark)

Jacobsen, B. H.; Hansen, Michael Møller; Loeschcke, V.

2005-01-01

The northern pike Esox lucius L. is a freshwater fish exhibiting pronounced population subdivision and low genetic variability. However, there is limited knowledge on phylogeographical patterns within the species, and it is not known whether the low genetic variability reflects primarily current...... low effective population sizes or historical bottlenecks. We analysed six microsatellite loci in ten populations from Europe and North America. Genetic variation was low, with the average number of alleles within populations ranging from 2.3 to 4.0 per locus. Genetic differentiation among populations...... was high (overall theta(ST) = 0.51; overall rho(ST) = 0.50). Multidimensional scaling analysis of genetic distances between populations and spatial analysis of molecular variance suggested a single phylogeographical race within the sampled populations from northern Europe, whereas North American...

High genetic diversity and fine-scale spatial structure in the marine flagellate Oxyrrhis marina (Dinophyceae uncovered by microsatellite loci.

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Chris D Lowe

2010-12-01

Full Text Available Free-living marine protists are often assumed to be broadly distributed and genetically homogeneous on large spatial scales. However, an increasing application of highly polymorphic genetic markers (e.g., microsatellites has provided evidence for high genetic diversity and population structuring on small spatial scales in many free-living protists. Here we characterise a panel of new microsatellite markers for the common marine flagellate Oxyrrhis marina. Nine microsatellite loci were used to assess genotypic diversity at two spatial scales by genotyping 200 isolates of O. marina from 6 broad geographic regions around Great Britain and Ireland; in one region, a single 2 km shore line was sampled intensively to assess fine-scale genetic diversity. Microsatellite loci resolved between 1-6 and 7-23 distinct alleles per region in the least and most variable loci respectively, with corresponding variation in expected heterozygosities (H(e of 0.00-0.30 and 0.81-0.93. Across the dataset, genotypic diversity was high with 183 genotypes detected from 200 isolates. Bayesian analysis of population structure supported two model populations. One population was distributed across all sampled regions; the other was confined to the intensively sampled shore, and thus two distinct populations co-occurred at this site. Whilst model-based analysis inferred a single UK-wide population, pairwise regional F(ST values indicated weak to moderate population sub-division (0.01-0.12, but no clear correlation between spatial and genetic distance was evident. Data presented in this study highlight extensive genetic diversity for O. marina; however, it remains a substantial challenge to uncover the mechanisms that drive genetic diversity in free-living microorganisms.

Living in Heterogeneous Woodlands - Are Habitat Continuity or Quality Drivers of Genetic Variability in a Flightless Ground Beetle?

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Tamar Marcus

Full Text Available Although genetic diversity is one of the key components of biodiversity, its drivers are still not fully understood. While it is known that genetic diversity is affected both by environmental parameters as well as habitat history, these factors are not often tested together. Therefore, we analyzed 14 microsatellite loci in Abax parallelepipedus, a flightless, forest dwelling ground beetle, from 88 plots in two study regions in Germany. We modeled the effects of historical and environmental variables on allelic richness, and found for one of the regions, the Schorfheide-Chorin, a significant effect of the depth of the litter layer, which is a main component of habitat quality, and of the sampling effort, which serves as an inverse proxy for local population size. For the other region, the Schwäbische Alb, none of the potential drivers showed a significant effect on allelic richness. We conclude that the genetic diversity in our study species is being driven by current local population sizes via environmental variables and not by historical processes in the studied regions. This is also supported by lack of genetic differentiation between local populations sampled from ancient and from recent woodlands. We suggest that the potential effects of former fragmentation and recolonization processes have been mitigated by the large and stable local populations of Abax parallelepipedus in combination with the proximity of the ancient and recent woodlands in the studied landscapes.

Variabilidade genética em biotipos de leiteiro de Londrina/PR Genetic variability among Euphorbia heterophylla

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Maria José V. de Vasconcelos

2000-08-01

Full Text Available Euphorbia heterophylla, também conhecida como amendoim-bravo ou leiteira, é considerada planta invasora importante em mais de 56 países, inclusive no Brasil, tendo acarretado perdas de até 33 % na cultura da soja. Fenotipicamente, é uma espécie de características variáveis, especialmente em relação ao formato do limbo foliar. Esta variabilidade fenotípica tem sido utilizada para diferenciar e classificar as plantas, sugerindo a vários autores que a leiteira seria, de fato, constituída por diferentes espécies. Para estudar a variabilidade genética a nível de DNA entre plantas de Euphorbia heterophylla, que apresentam folhas morfologicamente diferentes, foram analisadas dez plantas diferentes coletadas em campos de soja, em Londrina/PR. As plantas foram transplantadas para casa-devegetação e o DNA das folhas foi extraído para análise pela técnica de RAPD. Vinte seis diferentes "primers", de dez nucleotídeos de sequência aleatória, geraram total de 102 bandas de DNA, sendo 38 delas polimórficas. A distância genética entre os indivíduos foi calculada em função da presença e da ausência das bandas, variando de 1 a 39% entre plantas. A análise de agrupamento dividiu as plantas em dois grupos, considerando limite de distância relativa de 22%. Os grupos gerados separaram nitidamente as plantas quanto ao formato do limbo foliar (estreito ou arredondado e quanto á ramificação (densa ou normal.Euphorbia heterophylla is an important weed affecting the performance of annual and perennial crops. It is native from tropical and subtropical regions in the American continent, and has been detected at high densities in 20 different countries worldwide, and at low densities in other 40 countries. In Brazil, it has been inclued among the ten most important weeds affecting different crops, causing yield losses up to 33% in soybean fields. Phenotypically, this species is extremely variable, especially in relation to leaf shape and

Genetic studies on two soybean cultivars irradiated with gamma rays

International Nuclear Information System (INIS)

El-Demerdash, H.M.

2007-01-01

In the present study, the effect of gamma irradiation was used in two Egyptian soybean cultivars; Giza-22 and Giza-82, to induce genetic variability with doses of 100, 150 and 200 Gy. Some agronomic characters were tested in M1 and M2 generations single plants. Oil and protein contents were measured from the resulted mutants of the two soybean cultivars at M2 generation. Some genetic parameters were estimated on the mean values of M2 generation. The results showed significant differences induced by gamma ray doses in all studied characters, particularly for 200 Gy in M1 generation. Gamma irradiation increased the genetic variability in M2 generation, which helped in selecting some high yielding mutants and some mutants with high oil and protein contents from the two cultivars. The estimated coefficients of phenotypic variance as well as coefficient of genotypic variance were high for seeds weight/plant, pod weight/plant, number of seeds/plant, number of pods/plant and number of nods/plant which showed better scope in genetic improvement. Heritability in the broad sense was high in most of the studied characters. The expected genetic advance (G.A) from selection was high for number of seeds, for number of pods, for pods weight and for mature plant height

Genetic risk factors for nonsyndromic cleft lip with or without cleft palate in a Brazilian population with high African ancestry.

Science.gov (United States)

do Rego Borges, Andrea; Sá, Jamile; Hoshi, Ryuichi; Viena, Camila Sane; Mariano, Lorena C; de Castro Veiga, Patricia; Medrado, Alena Peixoto; Machado, Renato Assis; de Aquino, Sibele Nascimento; Messetti, Ana Camila; Spritz, Richard A; Coletta, Ricardo D; Reis, Silvia R A

2015-10-01

Nonsyndromic cleft lip with or without cleft palate (NSCL ± P) is the most common orofacial birth defect, exhibiting variable prevalence around the world, often attributed to ethnic and environmental differences. Linkage analyses and genome-wide association studies have identified several genomic susceptibility regions for NSCL ± P, mostly in European-derived or Asian populations. Genetic predisposition to NSCL ± P is ethnicity-dependent, and the genetic basis of susceptibility to NSCL ± P likely varies among populations. The population of Brazil is highly admixed, with highly variable ancestry; thus, the genetic determinants of NSCL ± P susceptibility may be quite different. This study tested association of 8 single-nucleotide polymorphisms (SNPs), previously identified by genome-wide studies in other populations, with NSCL ± P in a Brazilian population with high African ancestry. SNPs rs560426, rs642961, rs1530300, rs987525, rs3758249, rs7078160, rs17085106, and rs13041247 were genotyped in 293 Brazilian patients with NSCL ± P and 352 unaffected Brazilian controls. Each sample was also genotyped for 40 biallelic short insertion/deletion polymorphic markers to characterize genetic ancestry. The average African ancestry background was 31.1% for the NSCL ± P group and 36.7% for the control group. After adjustment for ancestry and multiple testing, the minor alleles of rs3758249 (OR: 1.58, 95% CI: 1.25-2.01, P = 0.0001) and rs7078160 (OR: 1.59, 95% CI: 1.21-2.07, P = 0.0002) were significantly associated with risk of NSCL ± P. Polymorphisms located in IRF6 (rs642961) and 8q24 (rs1530300 and rs987525) showed marginal associations in this Brazilian population with high African ancestry. These results indicate that rs3758249 at 9q22 and rs7078160 at 10q25.3 represent risk loci for NSCL ± P in the Brazilian population with high African ancestry. © 2015 Wiley Periodicals, Inc.

Genome-wide prediction of traits with different genetic architecture through efficient variable selection.

Science.gov (United States)

Wimmer, Valentin; Lehermeier, Christina; Albrecht, Theresa; Auinger, Hans-Jürgen; Wang, Yu; Schön, Chris-Carolin

2013-10-01

In genome-based prediction there is considerable uncertainty about the statistical model and method required to maximize prediction accuracy. For traits influenced by a small number of quantitative trait loci (QTL), predictions are expected to benefit from methods performing variable selection [e.g., BayesB or the least absolute shrinkage and selection operator (LASSO)] compared to methods distributing effects across the genome [ridge regression best linear unbiased prediction (RR-BLUP)]. We investigate the assumptions underlying successful variable selection by combining computer simulations with large-scale experimental data sets from rice (Oryza sativa L.), wheat (Triticum aestivum L.), and Arabidopsis thaliana (L.). We demonstrate that variable selection can be successful when the number of phenotyped individuals is much larger than the number of causal mutations contributing to the trait. We show that the sample size required for efficient variable selection increases dramatically with decreasing trait heritabilities and increasing extent of linkage disequilibrium (LD). We contrast and discuss contradictory results from simulation and experimental studies with respect to superiority of variable selection methods over RR-BLUP. Our results demonstrate that due to long-range LD, medium heritabilities, and small sample sizes, superiority of variable selection methods cannot be expected in plant breeding populations even for traits like FRIGIDA gene expression in Arabidopsis and flowering time in rice, assumed to be influenced by a few major QTL. We extend our conclusions to the analysis of whole-genome sequence data and infer upper bounds for the number of causal mutations which can be identified by LASSO. Our results have major impact on the choice of statistical method needed to make credible inferences about genetic architecture and prediction accuracy of complex traits.

Little genetic variability in resilience among cattle exists for a range of performance traits across herds in Ireland differing in Fasciola hepatica prevalence.

Science.gov (United States)

Twomey, Alan J; Graham, David A; Doherty, Michael L; Blom, Astrid; Berry, Donagh P

2018-06-04

It is anticipated that in the future, livestock will be exposed to a greater risk of infection from parasitic diseases. Therefore, future breeding strategies for livestock, which are generally long-term strategies for change, should target animals adaptable to environments with a high parasitic load. Covariance components were estimated in the present study for a selection of dairy and beef performance traits over herd-years differing in Fasciola hepatica load using random regression sire models. Herd-year prevalence of F. hepatica was determined by using F. hepatica-damaged liver phenotypes which were recorded in abattoirs nationally. The data analyzed consisted up to 83,821 lactation records from dairy cows for a range of milk production and fertility traits, as well as 105,054 young animals with carcass-related information obtained at slaughter. Reaction norms for individual sires were derived from the random regression coefficients. The heritability and additive genetic standard deviations for all traits analyzed remained relatively constant as herd-year F. hepatica prevalence gradient increased up to a prevalence level of 0.7; although there was a large increase in heritability and additive genetic standard deviation for milk and fertility traits in the observed F. hepatica prevalence levels >0.7, only 5% of the data existed in herd-year prevalence levels >0.7. Very little rescaling, therefore, exists across differing herd-year F. hepatica prevalence levels. Within-trait genetic correlations among the performance traits across different herd-year F. hepatica prevalence levels were less than unity for all traits. Nevertheless, within-trait genetic correlations for milk production and carcass traits were all >0.8 for F. hepatica prevalence levels between 0.2 and 0.8. The lowest estimate of within-trait genetic correlations for the different fertility traits ranged from -0.03 (SE = 1.09) in age of first calving to 0.54 (SE = 0.22) for calving to first service

Studies of genetic variability of the glucose transporter 2 promoter in patients with type 2 diabetes mellitus

DEFF Research Database (Denmark)

Møller, A M; Jensen, N M; Pildal, J

2001-01-01

This study was performed to test the hypothesis that genetic variation in the promoter of the glucose transporter 2 (GLUT2) might predispose to prediabetic phenotypes or type 2 diabetes. A total of 1611 bp comprising the minimal promoter region of the GLUT2 gene were examined by combined single-s......-tolerant subjects. In conclusion, we found no evidence supporting the hypothesis that genetic variability in the minimal promoter of the GLUT2 is associated with type 2 diabetes or prediabetic phenotypes in the Danish population.......This study was performed to test the hypothesis that genetic variation in the promoter of the glucose transporter 2 (GLUT2) might predispose to prediabetic phenotypes or type 2 diabetes. A total of 1611 bp comprising the minimal promoter region of the GLUT2 gene were examined by combined single...

Global issues of genetic diversity.

Science.gov (United States)

Vida, G

1994-01-01

Genetic diversity within species is highly significant during their adaptation to environmental changes and, consequently, for their long-term survival. The genetic variability of species is also the basis for the evolution of higher levels of biodiversity, the evolution of species, and it might be an indispensible prerequisite for the functioning of our biosphere. Studies which promote understanding of the maintenance and the functional aspects of biodiversity at any level are therefore essential for the future welfare of mankind.

Biological pathways and genetic variables involved in pain

NARCIS (Netherlands)

Shi, Qiuling; Cleeland, Charles S.; Klepstad, Pål; Miaskowski, Christine; Pedersen, Nancy L.; Abernethy, Amy P.; Baas, Frank; Barsevick, Andrea M.; Bartels, Meike; Boomsma, Dorret I.; Chauhan, Cynthia; Dueck, Amylou C.; Frost, Marlene H.; Hall, Per; Halyard, Michele Y.; Martin, Nicholas G.; Mosing, Miriam; Movsas, Benjamin; van Noorden, Cornelis J. F.; Patrick, Donald L.; Ropka, Mary E.; Shinozaki, Gen; Singh, Jasvinder A.; Sloan, Jeff A.; Sprangers, Mirjam A. G.; Veenhoven, Ruut; Yang, Ping; Zwinderman, Ailko H.

2010-01-01

Purpose This paper summarizes current knowledge of pain-related and analgesic-related pathways as well as genetic variations involved in pain perception and management. Methods The pain group of the GENEQOL Consortium was given the task of summarizing the current status of research on genetic

Inter- and intra-population genetic variability of introduced silkworm (Bombyx mori L. strains raised in Bulgaria

Directory of Open Access Journals (Sweden)

Teodora Staykova

2013-01-01

Full Text Available The genetic variability of four populations belonging to two introduced silkworm strains (Bombyx mori L. of various origins has been studied using isoenzymic analysis of six enzyme systems. Nonspecific esterases, phosphoglucomutase, malate dehydrogenase, acid phosphatase, alkaline phosphatase and hexokinase from different tissue of larvae 5th instar have been analysed using PAGE. Polymorphism in six from a total of nine loci has been found. Inter- and intra-population differences have been ascertained expressed in different allele composition of the gene pool and different frequencies of alleles. A higher degree of inter-population variability has been reported on the acid phosphatase and a lower one – on the phosphoglucomutase.

Genetic variability and heritability for resistance to black stem (Phoma macdonaldii) in sunflower (Helianthus annuus L.)

International Nuclear Information System (INIS)

Abou Al Fadil, T.; Dechamp-Guillaume, G.; Poormohammad Kiani, S.; Sarrafi, A.

2004-01-01

Black stem, caused by Phoma macdonaldii, is one of the most important diseases of sunflower in many Countries. In order to study the genetic control of the disease, seeds of the inbred line AS-613 were exposed to 75 Grays of gamma rays and M1 and M2 plants were self-pollinated to obtain the M3 generation. Among M3 mutants, M3-8, a relatively resistant line to black stem, was crossed with AS-613. Seeds from this cross were grown and F1 plants were self-pollinated to produce F2 seeds from which the F3 generation was produced. Eighty-eight F3 families and two parents were used to determine the genetic variability of partial resistance to black stem in sunflower. Twelve-day-old seedlings were inoculated at the junction of the cotyledon petiole and hypocotyl with 20 micronl of pycniospore suspension. Seven days after inoculation, both cotyledon petioles of the seedling were scored according to the percentage of petiole area exhibiting symptoms (necrosis). Significant difference in resistance between the two parents, M3-8 and AS-613, indicates that mutagenesis can be considered as important tool to produce genetic variation for resistance to Phoma in sunflower. Results showed that F3 families included extreme genotypes with a relatively high resistance rate compared with the parents. Ten percent of F3 families showed a resistance rate higher than the one of the best parent, indicating transgressive segregation for resistance to black stem among families. The percentage of heritability was 69.6, which indicates that progeny selection for resistance to the disease is possible [it

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.

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

Directory of Open Access Journals (Sweden)

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.

Genetic diversity of six populations of red hybrid tilapia, using microsatellites genetic markers

Directory of Open Access Journals (Sweden)

Boris Briñez R.

2011-05-01

Full Text Available Objective. To determine and evaluate the genetic diversity of six populations of red hybrid tilapia, with the purpose to assess the potential benefit of a future breeding program conducted at the Research Center for Aquaculture (Ceniacua, Colombia. Material and methods. A total of 300 individuals, representing a wide genetic variability, were genotyped using a fluorescent microsatellite marker set of 5 gene-based SSRs in 6 different farms belonging to 4 States of Colombia. Results. The result showed that the mean number of alleles per locus per population was 8.367. The population 5 had the highest mean number of alleles with 9.6 alleles, followed by population 4 with 9.4 alleles, population 2 with 9.2, population 3 with 8.0, population 1 with 7.2 and population 6 with 6.8 alleles. The analysis of the distribution of genetic variation was (17.32% among population, while among individuals within populations was (28.55% and within individuals was high (54.12%. The standard diversity indices showed that population 4 was the more variable (mean He=0.837 followed by population 1 (mean He=0.728, population 3 (mean He=0.721, population 5 (mean He=0.705, population 2 (mean He=0.690, population 6 (mean He=0.586. Highly significant deviations from Hardy–Weinberg, exhibited all of the populations, mostly due to deficits of heterozygotes. Genotype frequencies at loci UNH 106 of population 5 and loci UNH 172 of population 6 were Hardy-Weinberg equilibrium (HWE. Conclusions. The results of this study, contribute to the genetic breeding program of Tilapia, conduced by the Research Center for Aquaculture. The Fst distance showed that the samples are differentiated genetically and it is possible to use at the beginning of the genetic program. However, it is recommended to introduce others individuals to the crossbreeding program.

Extreme genetic structure in a social bird species despite high dispersal capacity.

Science.gov (United States)

Morinha, Francisco; Dávila, José A; Bastos, Estela; Cabral, João A; Frías, Óscar; González, José L; Travassos, Paulo; Carvalho, Diogo; Milá, Borja; Blanco, Guillermo

2017-05-01

Social barriers have been shown to reduce gene flow and contribute to genetic structure among populations in species with high cognitive capacity and complex societies, such as cetaceans, apes and humans. In birds, high dispersal capacity is thought to prevent population divergence unless major geographical or habitat barriers induce isolation patterns by dispersal, colonization or adaptation limitation. We report that Iberian populations of the red-billed chough, a social, gregarious corvid with high dispersal capacity, show a striking degree of genetic structure composed of at least 15 distinct genetic units. Monitoring of marked individuals over 30 years revealed that long-distance movements over hundreds of kilometres are common, yet recruitment into breeding populations is infrequent and highly philopatric. Genetic differentiation is weakly related to geographical distance, and habitat types used are overall qualitatively similar among regions and regularly shared by individuals of different populations, so that genetic structure is unlikely to be due solely to isolation by distance or isolation by adaptation. Moreover, most population nuclei showed relatively high levels of genetic diversity, suggesting a limited role for genetic drift in significantly differentiating populations. We propose that social mechanisms may underlie this unprecedented level of genetic structure in birds through a pattern of isolation by social barriers not yet described, which may have driven this remarkable population divergence in the absence of geographical and environmental barriers. © 2017 John Wiley & Sons Ltd.

High-p{sub T} B-tagging and top-tagging with variable-R jets in ATLAS

Energy Technology Data Exchange (ETDEWEB)

Behr, Katharina [Sub-department of Particle Physics, University of Oxford, Denys-Wilkinson Building, Keble Road, Oxford OX1 3RH (United Kingdom)

2015-07-01

Variable-R jets, whose effective size is inversely proportional to their transverse momentum, are a versatile tool for object reconstruction across the large transverse momentum regime accessible during Run 2 of the LHC. I discuss the performance of Variable-R jets in two different contexts: (1) Boosted top-tagging. The separation between the decay products of highly energetic top quarks decreases with p{sub T}{sup top} causing them to overlap and merge into a single jet. Taggers relying on large fixed-R jets overestimate the real size of the top jet in the highly boosted regime and are more susceptible to the effects of pile-up. Variable-R jets are studied as the basis for more natural taggers which may not even require grooming. (2) B-tagging. The b-tagging performance in boosted topologies suffers in the presence of close-by jets. This limits the sensitivity of many searches such as those in boosted hh → 4b final states. New b-taggers relying on track jets with smaller sizes than the traditional R=0.4 to better isolate the b-hadron decay show significant improvements in highly boosted scenarios but perform worse at low transverse momenta where they fail to capture the full b-jet. Variable-R track jets provide a unified approach to b-tagging in both p{sub T} regimes.

Genetic divergence of rubber tree estimated by multivariate techniques and microsatellite markers

Directory of Open Access Journals (Sweden)

Lígia Regina Lima Gouvêa

2010-01-01

Full Text Available Genetic diversity of 60 Hevea genotypes, consisting of Asiatic, Amazonian, African and IAC clones, and pertaining to the genetic breeding program of the Agronomic Institute (IAC, Brazil, was estimated. Analyses were based on phenotypic multivariate parameters and microsatellites. Five agronomic descriptors were employed in multivariate procedures, such as Standard Euclidian Distance, Tocher clustering and principal component analysis. Genetic variability among the genotypes was estimated with 68 selected polymorphic SSRs, by way of Modified Rogers Genetic Distance and UPGMA clustering. Structure software in a Bayesian approach was used in discriminating among groups. Genetic diversity was estimated through Nei's statistics. The genotypes were clustered into 12 groups according to the Tocher method, while the molecular analysis identified six groups. In the phenotypic and microsatellite analyses, the Amazonian and IAC genotypes were distributed in several groups, whereas the Asiatic were in only a few. Observed heterozygosity ranged from 0.05 to 0.96. Both high total diversity (H T' = 0.58 and high gene differentiation (Gst' = 0.61 were observed, and indicated high genetic variation among the 60 genotypes, which may be useful for breeding programs. The analyzed agronomic parameters and SSRs markers were effective in assessing genetic diversity among Hevea genotypes, besides proving to be useful for characterizing genetic variability.

Genetic and Nongenetic Determinants of Cell Growth Variation Assessed by High-Throughput Microscopy

Science.gov (United States)

Ziv, Naomi; Siegal, Mark L.; Gresham, David

2013-01-01

In microbial populations, growth initiation and proliferation rates are major components of fitness and therefore likely targets of selection. We used a high-throughput microscopy assay, which enables simultaneous analysis of tens of thousands of microcolonies, to determine the sources and extent of growth rate variation in the budding yeast (Saccharomyces cerevisiae) in different glucose environments. We find that cell growth rates are regulated by the extracellular concentration of glucose as proposed by Monod (1949), but that significant heterogeneity in growth rates is observed among genetically identical individuals within an environment. Yeast strains isolated from different geographic locations and habitats differ in their growth rate responses to different glucose concentrations. Inheritance patterns suggest that the genetic determinants of growth rates in different glucose concentrations are distinct. In addition, we identified genotypes that differ in the extent of variation in growth rate within an environment despite nearly identical mean growth rates, providing evidence that alleles controlling phenotypic variability segregate in yeast populations. We find that the time to reinitiation of growth (lag) is negatively correlated with growth rate, yet this relationship is strain-dependent. Between environments, the respirative activity of individual cells negatively correlates with glucose abundance and growth rate, but within an environment respirative activity and growth rate show a positive correlation, which we propose reflects differences in protein expression capacity. Our study quantifies the sources of genetic and nongenetic variation in cell growth rates in different glucose environments with unprecedented precision, facilitating their molecular genetic dissection. PMID:23938868

Using variable combination population analysis for variable selection in multivariate calibration.

Science.gov (United States)

Yun, Yong-Huan; Wang, Wei-Ting; Deng, Bai-Chuan; Lai, Guang-Bi; Liu, Xin-bo; Ren, Da-Bing; Liang, Yi-Zeng; Fan, Wei; Xu, Qing-Song

2015-03-03

Variable (wavelength or feature) selection techniques have become a critical step for the analysis of datasets with high number of variables and relatively few samples. In this study, a novel variable selection strategy, variable combination population analysis (VCPA), was proposed. This strategy consists of two crucial procedures. First, the exponentially decreasing function (EDF), which is the simple and effective principle of 'survival of the fittest' from Darwin's natural evolution theory, is employed to determine the number of variables to keep and continuously shrink the variable space. Second, in each EDF run, binary matrix sampling (BMS) strategy that gives each variable the same chance to be selected and generates different variable combinations, is used to produce a population of subsets to construct a population of sub-models. Then, model population analysis (MPA) is employed to find the variable subsets with the lower root mean squares error of cross validation (RMSECV). The frequency of each variable appearing in the best 10% sub-models is computed. The higher the frequency is, the more important the variable is. The performance of the proposed procedure was investigated using three real NIR datasets. The results indicate that VCPA is a good variable selection strategy when compared with four high performing variable selection methods: genetic algorithm-partial least squares (GA-PLS), Monte Carlo uninformative variable elimination by PLS (MC-UVE-PLS), competitive adaptive reweighted sampling (CARS) and iteratively retains informative variables (IRIV). The MATLAB source code of VCPA is available for academic research on the website: http://www.mathworks.com/matlabcentral/fileexchange/authors/498750. Copyright © 2015 Elsevier B.V. All rights reserved.

Genetic variability of a Brazilian Capsicum frutescens germplasm collection using morphological characteristics and SSR markers.

Science.gov (United States)

Carvalho, S I C; Bianchetti, L B; Ragassi, C F; Ribeiro, C S C; Reifschneider, F J B; Buso, G S C; Faleiro, F G

2017-07-06

Characterization studies provide essential information for the conservation and use of germplasm in plant breeding programs. In this study, 103 Capsicum frutescens L. accessions from the Active Germplasm Bank of Embrapa Hortaliças, representative of all five Brazilian geographic regions, were characterized based on morphological characteristics and microsatellite (or simple sequence repeat - SSR) molecular markers. Morphological characterization was carried out using 57 descriptors, and molecular characterization was based on 239 alleles from 24 microsatellite loci. From the estimates of genetic distances among accessions, based on molecular characterization, a cluster analysis was carried out, and a dendrogram was established. Correlations between morphological and molecular variables were also estimated. Twelve morphological descriptors were monomorphic for the set of C. frutescens accessions, and those with the highest degree of polymorphism were stem length (14.0 to 62.0 cm), stem diameter (1.0 to 4.2 cm), days to flowering (90 to 129), days to fruiting (100 to 140), fruit weight (0.1 to 1.4 g), fruit length (0.6 to 4.6 cm), and fruit wall thickness (0.25 to 1.5 mm). The polymorphism information content for the SSR loci varied from 0.36 (EPMS 417) to 0.75 (CA49), with an overall mean of 0.57. The correlation value between morphological and molecular characterization data was 0.6604, which was statistically significant. Fourteen accessions were described as belonging to the morphological type tabasco, 85 were described as malagueta, and four were malaguetinha, a morphological type confirmed in this study. The typical morphological pattern of malagueta was described. Six similarity groups were established for C. frutescens based on the dendrogram and are discussed individually. The genetic variability analyzed in the study highlights the importance of characterizing genetic resources available for the development of new C. frutescens cultivars with the potential

Comparison of genetic variability between Czech and foreign isolates of phytopathogenic bacteria Clavibacter michiganensis subsp. sepedonicus by Rep-PCR technique

Czech Academy of Sciences Publication Activity Database

Fousek, Jan; Mráz, Ivan; Petrzik, Karel

2002-01-01

Roč. 47, - (2002), s. 450-454 ISSN 0015-5632 R&D Projects: GA ČR GA522/00/0887 Keywords : Clavibacter michiganensis * genetic variability Subject RIV: EE - Microbiology, Virology Impact factor: 0.979, year: 2002

High genetic diversity of Jatropha curcas assessed by ISSR.

Science.gov (United States)

Díaz, B G; Argollo, D M; Franco, M C; Nucci, S M; Siqueira, W J; de Laat, D M; Colombo, C A

2017-05-31

Jatropha curcas L. is a highly promising oilseed for sustainable production of biofuels and bio-kerosene due to its high oil content and excellent quality. However, it is a perennial and incipiently domesticated species with none stable cultivar created until now despite genetic breeding programs in progress in several countries. Knowledge of the genetic structure and diversity of the species is a necessary step for breeding programs. The molecular marker can be used as a tool for speed up the process. This study was carried out to assess genetic diversity of a germplasm bank represented by J. curcas accessions from different provenance beside interspecific hybrid and backcrosses generated by IAC breeding programs using inter-simple sequence repeat markers. The molecular study revealed 271 bands of which 98.9% were polymorphic with an average of 22.7 polymorphic bands per primer. Genetic diversity of the germplasm evaluated was slightly higher than other germplasm around the world and ranged from 0.55 to 0.86 with an average of 0.59 (Jaccard index). Cluster analysis (UPGMA) revealed no clear grouping as to the geographical origin of accessions, consistent with genetic structure analysis using the Structure software. For diversity analysis between groups, accessions were divided into eight groups by origin. Nei's genetic distance between groups was 0.14. The results showed the importance of Mexican accessions, congeneric wild species, and interspecific hybrids for conservation and development of new genotypes in breeding programs.

Seedling vigor and genetic variability for rice seed, seedling emergence and seedling traits

International Nuclear Information System (INIS)

Ali, S.S.; Jafri, S.J.H.; Jamil, M.; Ijaz, M.

1994-01-01

Eleven local rice cultivars including Basmati 370 were evaluated for seedling vigor. Three groups of traits were evaluated viz; seed traits (Seed density, seed volume see weight, paddy length and grain length), seed emergence traits (emergence %, emergence index and emergence rate index), and seedling traits (fresh root length, dry root weight, emergence percentage, root length, dry root weight, seed weight and relative root weight were observed significant, respectively. Seed density, relative root weight, emergence rate index and root to shoot ratio were relatively more amenable to improvement. Relative expected genetic advance was the function of heritability and coefficient of phenotypic variability, latter being more important. (author)

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.

Genetic analysis of seed proteins contents in cowpea ( Vigna ...

African Journals Online (AJOL)

In order to select cowpea genotypes with high food value, 10 varieties were genetically screened in Ngaoundéré (Cameroon) for seed crude protein and its soluble fractions contents. Five divergent lines were studied through a 5 x 5 half diallel cross mating. The genotypes presented a significant genetic variability for these ...

Genetic variability in MCF-7 sublines: evidence of rapid genomic and RNA expression profile modifications

International Nuclear Information System (INIS)

Nugoli, Mélanie; Theillet, Charles; Chuchana, Paul; Vendrell, Julie; Orsetti, Béatrice; Ursule, Lisa; Nguyen, Catherine; Birnbaum, Daniel; Douzery, Emmanuel JP; Cohen, Pascale

2003-01-01

Both phenotypic and cytogenetic variability have been reported for clones of breast carcinoma cell lines but have not been comprehensively studied. Despite this, cell lines such as MCF-7 cells are extensively used as model systems. In this work we documented, using CGH and RNA expression profiles, the genetic variability at the genomic and RNA expression levels of MCF-7 cells of different origins. Eight MCF-7 sublines collected from different sources were studied as well as 3 subclones isolated from one of the sublines by limit dilution. MCF-7 sublines showed important differences in copy number alteration (CNA) profiles. Overall numbers of events ranged from 28 to 41. Involved chromosomal regions varied greatly from a subline to another. A total of 62 chromosomal regions were affected by either gains or losses in the 11 sublines studied. We performed a phylogenetic analysis of CGH profiles using maximum parsimony in order to reconstruct the putative filiation of the 11 MCF-7 sublines. The phylogenetic tree obtained showed that the MCF-7 clade was characterized by a restricted set of 8 CNAs and that the most divergent subline occupied the position closest to the common ancestor. Expression profiles of 8 MCF-7 sublines were analyzed along with those of 19 unrelated breast cancer cell lines using home made cDNA arrays comprising 720 genes. Hierarchical clustering analysis of the expression data showed that 7/8 MCF-7 sublines were grouped forming a cluster while the remaining subline clustered with unrelated breast cancer cell lines. These data thus showed that MCF-7 sublines differed at both the genomic and phenotypic levels. The analysis of CGH profiles of the parent subline and its three subclones supported the heteroclonal nature of MCF-7 cells. This strongly suggested that the genetic plasticity of MCF-7 cells was related to their intrinsic capacity to generate clonal heterogeneity. We propose that MCF-7, and possibly the breast tumor it was derived from, evolved

Genetic and geochemical signatures to prevent frauds and counterfeit of high-quality asparagus and pistachio.

Science.gov (United States)

Zannella, Carmela; Carucci, Francesca; Aversano, Riccardo; Prohaska, Thomas; Vingiani, Simona; Carputo, Domenico; Adamo, Paola

2017-12-15

A fingerprinting strategy based on genetic (simple sequence repeat) and geochemical (multielement and 87 Sr/ 86 Sr ratio) analysis was tested to prove the geographical origin of high-quality Italian products "White Asparagus from Bassano del Grappa" and "Green Pistachio from Bronte". Genetic analysis generated many polymorphic alleles and different specific amplified fragments in both agriproducts. In addition, a core set of markers was defined. According to variability within production soils and products, potential candidate elements linking asparagus (Zn, P, Cr, Mg, B, K) and pistachio (Mn, P, Cr, Mg, Ti, B, K, Sc, S) to the production areas were identified. The Sr isotopic signature was an excellent marker when Italian asparagus was compared with literature data for Hungarian and Peruvian asparagus. This work reinforces the use of Sr isotope composition in the soil bioavailable fraction, as assessed by 1mol/L NH 4 NO 3 , to distinguish white asparagus and pistachio originating from different geographical areas. Copyright © 2017 Elsevier Ltd. All rights reserved.

Awareness of Societal Issues among High School Biology Teachers Teaching Genetics

Science.gov (United States)

Lazarowitz, Reuven; Bloch, Ilit

2005-01-01

The purpose of this study was to investigate how aware high school biology teachers are of societal issues (values, moral, ethic, and legal issues) while teaching genetics, genetics engineering, molecular genetics, human heredity, and evolution. The study includes a short historical review of World War II atrocities during the Holocaust when…

Expression patterns of the aquaporin gene family during renal development: influence of genetic variability.

Science.gov (United States)

Parreira, Kleber S; Debaix, Huguette; Cnops, Yvette; Geffers, Lars; Devuyst, Olivier

2009-08-01

High-throughput analyses have shown that aquaporins (AQPs) belong to a cluster of genes that are differentially expressed during kidney organogenesis. However, the spatiotemporal expression patterns of the AQP gene family during tubular maturation and the potential influence of genetic variation on these patterns and on water handling remain unknown. We investigated the expression patterns of all AQP isoforms in fetal (E13.5 to E18.5), postnatal (P1 to P28), and adult (9 weeks) kidneys of inbred (C57BL/6J) and outbred (CD-1) mice. Using quantitative polymerase chain reaction (PCR), we evidenced two mRNA patterns during tubular maturation in C57 mice. The AQPs 1-7-11 showed an early (from E14.5) and progressive increase to adult levels, similar to the mRNA pattern observed for proximal tubule markers (Megalin, NaPi-IIa, OAT1) and reflecting the continuous increase in renal cortical structures during development. By contrast, AQPs 2-3-4 showed a later (E15.5) and more abrupt increase, with transient postnatal overexpression. Most AQP genes were expressed earlier and/or stronger in maturing CD-1 kidneys. Furthermore, adult CD-1 kidneys expressed more AQP2 in the collecting ducts, which was reflected by a significant delay in excreting a water load. The expression patterns of proximal vs. distal AQPs and the earlier expression in the CD-1 strain were confirmed by immunoblotting and immunostaining. These data (1) substantiate the clustering of important genes during tubular maturation and (2) demonstrate that genetic variability influences the regulation of the AQP gene family during tubular maturation and water handling by the mature kidney.

High efficiency, variable geometry, centrifugal cryogenic pump

International Nuclear Information System (INIS)

Forsha, M.D.; Nichols, K.E.; Beale, C.A.

1994-01-01

A centrifugal cryogenic pump has been developed which has a basic design that is rugged and reliable with variable speed and variable geometry features that achieve high pump efficiency over a wide range of head-flow conditions. The pump uses a sealless design and rolling element bearings to achieve high reliability and the ruggedness to withstand liquid-vapor slugging. The pump can meet a wide range of variable head, off-design flow requirements and maintain design point efficiency by adjusting the pump speed. The pump also has features that allow the impeller and diffuser blade heights to be adjusted. The adjustable height blades were intended to enhance the pump efficiency when it is operating at constant head, off-design flow rates. For small pumps, the adjustable height blades are not recommended. For larger pumps, they could provide off-design efficiency improvements. This pump was developed for supercritical helium service, but the design is well suited to any cryogenic application where high efficiency is required over a wide range of head-flow conditions

[Genetic Variability and Structure of SNP Haplotypes in the DMPK Gene in Yakuts and Other Ethnic Groups of Northern Eurasia in Relation to Myotonic Dystrophy].

Science.gov (United States)

Swarovskaya, M G; Stepanova, S K; Marussin, A V; Sukhomyasova, A L; Maximova, N R; Stepanov, V A

2015-06-01

The genetic variability of the DMPK locus has been studied in relation to six SNP markers (rs2070736, rs572634, rs1799894, rs527221, rs915915, and rs10415988) in Yakuts with myotonic dystrophy (MD) in the Yakut population and in populations of northern Eurasia. Significant differences were observed in the allele frequencies between patients and a population sample of Yakuts for three SNP loci (rs915915, rs1799894, and rs10415988) associated with a high chance of disease manifestation. The odds ratios (OR) of MD development in representatives of the Yakut population for these three loci were 2.59 (95% CI, p = 0,004), 4.99 (95% CI, p = 0.000), and 3.15 (95% CI, p = 0.01), respectively. Haplotype TTTCTC, which is associated with MD, and haplotype GTCCTT, which was observed only in Yakut MD patients (never in MD patients of non-Yakut origin), were revealed. A low level of variability in the locus of DMRK gene in Yakuts (H(e) = 0.283) compared with other examined populations was noted. An analysis of pairwise genetic relationships between populations revealed their significant differentiation for all the examined loci. In addition, a low level of differentiation in territorial groups of Yakut populations (F(ST) = 0.79%), which was related to the high subdivision of the northern Eurasian population (F(ST) = 11.83%), was observed.

Genetic variability in Sambucus nigra L. clones : a preliminary ...

Indian Academy of Sciences (India)

c Indian Academy of Sciences. ONLINE ... yield and production evaluations revealed that clones from ..... Population genetic software for teaching and research. Mol. Ecol. ... and genetic evaluation of interspecific hybrids within the genus.

Bivariate analysis of the genetic variability among some accessions of African Yam Bean (Sphenostylis stenocarpa (Hochst ex A. RichHarms

Directory of Open Access Journals (Sweden)

Solomon Tayo AKINYOSOYE

2017-12-01

Full Text Available Variability is an important factor to consider in crop improvement programmes. This study was conducted in two years to assess genetic variability and determine relationship between seed yield, its components and tuber production characters among twelve accessions of African yam bean. Data collected were subjected to combined analysis of variance (ANOVA, Principal Component Analysis (PCA, hierarchical and K-means clustering analyses. Results obtained revealed that genotype by year (G × Y interaction had significant effects on some of variables measured (days to first flowering, days to 50 % flowering, number of pod per plant, pod length, seed yield and tuber yield per plant in this study.The first five principal components (PC with Eigen values greater than 1.0 accounted for about 66.70 % of the total variation, where PC1 and PC 2 accounted for 39.48 % of variation and were associated with seed and tuber yield variables. Three heterotic groups were clearly delineated among genotypes with accessions AY03 and AY10 identified for high seed yield and tuber yield respectively. Non-significant relationship that existed between tuber and seed yield per plant of these accessions was recommended for further test in various agro-ecologies for their suitability, adaptability and possible exploitation of heterosis to further improve the accessions.

Genetic variability and health of Norway spruce stands in the Regional Directorate of the State Forests in Krosno

Directory of Open Access Journals (Sweden)

Gutkowska Justyna

2017-03-01

Full Text Available The study was conducted in 2015 in six spruce stands situated in different forest districts administratively belonging to the Regional Directorate of State Forests in Krosno. Each spruce population was represented by 30 trees and assessed in terms of their current health status. Genetic analyses were performed on shoot samples from each tree using nine nuclear DNA markers and one mitochondrial DNA marker (nad1. The health status of the trees was described according to the classification developed by Szczepkowski and Tarasiuk (2005 and the correlation between health classes and the level of genetic variability was computed with STATISTICA (α = 0.05.

Inter- and intra-population genetic variability of introduced silkworm (Bombyx mori L.) strains raised in Bulgaria

OpenAIRE

Teodora Staykova

2013-01-01

The genetic variability of four populations belonging to two introduced silkworm strains (Bombyx mori L.) of various origins has been studied using isoenzymic analysis of six enzyme systems. Nonspecific esterases, phosphoglucomutase, malate dehydrogenase, acid phosphatase, alkaline phosphatase and hexokinase from different tissue of larvae 5th instar have been analysed using PAGE. Polymorphism in six from a total of nine loci has been found. Inter- and intra-population differences have been a...

Rapid Recombination Mapping for High-Throughput Genetic Screens in Drosophila

OpenAIRE

Sapiro, Anne L.; Ihry, Robert J.; Buhr, Derek L.; Konieczko, Kevin M.; Ives, Sarah M.; Engstrom, Anna K.; Wleklinski, Nicholas P.; Kopish, Kristin J.; Bashirullah, Arash

2013-01-01

Mutagenesis screens are a staple of classical genetics. Chemical-induced mutations, however, are often difficult and time-consuming to identify. Here, we report that recombination analysis with pairs of dominant visible markers provides a rapid and reliable strategy to map mutations in Drosophila melanogaster. This method requires only two generations and a total of six crosses in vials to estimate the genetic map position of the responsible lesion with high accuracy. This genetic map positio...

Relationship between heavy metals pollution and genetic diversity in Mediterranean populations of the sandhopper Talitrus saltator (Montagu) (Crustacea, Amphipoda)

International Nuclear Information System (INIS)

Ungherese, G.; Mengoni, A.; Somigli, S.; Baroni, D.; Focardi, S.; Ugolini, A.

2010-01-01

Trace metals are one of the groups of pollutants that reduce genetic variability in natural populations, causing the phenomenon known as 'genetic erosion'. In this study we evaluate the relationship between trace metals contamination (Hg, Cd and Cu) and genetic variability, assessed using fluorescent Inter-Simple Sequence Repeats (fISSRs). We used eight populations of a well-established biomonitor of trace metals on sandy beaches: the amphipod Talitrus saltator. The trace metals analysis confirmed the ability of sandhoppers to accumulate Hg, Cd and Cu. Moreover, populations from sites with high Hg availability had the lowest values of genetic diversity. Our results validate the use of fISSR markers in genetic studies in sandhoppers and support the 'genetic erosion' hypothesis by showing the negative influence of Hg contamination on sandhopper genetic diversity. Therefore, genetic variability assessed with fISSR markers could be successfully employed as a biomarker of Hg exposure. - Genetic variability of sandhoppers is affected by heavy metals contamination.

Variabilidade genética e ecológica de Stylosanthes macrocephala determinadas por RAPD e SIG Genetic and ecological variability of Stylosanthes macrocephaladetermined by RAPD markers and GIS

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Ana Maria Barros

2005-09-01

accessions were collected from different ecogeographical areas in seven Brazilian States, five hydrographic regions, seven vegetation types and seven soil types. Collecting sites ranged from 1 to 1,298 m above sea level with annual rainfall from 550 to 2,870 mm. Accession distribution along those diverse ecosystems indicate high adaptive diversity. Using 161 RAPD markers, genetic distances between accessions ranged from 0.02 to 0.42. These genetic distances allowed the establishment of ten genetic groups. Accessions collected in specific hydrographic region tended to be grouped in the same genetic group. Accessions collected in Bahia and Minas Gerais States showed high genetic variability. The high genetic variability observed in the accessions showed the importance of this S. macrocephala collection for breeding programs.

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

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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.

The molecular genetic architecture of self-employment.

Science.gov (United States)

van der Loos, Matthijs J H M; Rietveld, Cornelius A; Eklund, Niina; Koellinger, Philipp D; Rivadeneira, Fernando; Abecasis, Gonçalo R; Ankra-Badu, Georgina A; Baumeister, Sebastian E; Benjamin, Daniel J; Biffar, Reiner; Blankenberg, Stefan; Boomsma, Dorret I; Cesarini, David; Cucca, Francesco; de Geus, Eco J C; Dedoussis, George; Deloukas, Panos; Dimitriou, Maria; Eiriksdottir, Guðny; Eriksson, Johan; Gieger, Christian; Gudnason, Vilmundur; Höhne, Birgit; Holle, Rolf; Hottenga, Jouke-Jan; Isaacs, Aaron; Järvelin, Marjo-Riitta; Johannesson, Magnus; Kaakinen, Marika; Kähönen, Mika; Kanoni, Stavroula; Laaksonen, Maarit A; Lahti, Jari; Launer, Lenore J; Lehtimäki, Terho; Loitfelder, Marisa; Magnusson, Patrik K E; Naitza, Silvia; Oostra, Ben A; Perola, Markus; Petrovic, Katja; Quaye, Lydia; Raitakari, Olli; Ripatti, Samuli; Scheet, Paul; Schlessinger, David; Schmidt, Carsten O; Schmidt, Helena; Schmidt, Reinhold; Senft, Andrea; Smith, Albert V; Spector, Timothy D; Surakka, Ida; Svento, Rauli; Terracciano, Antonio; Tikkanen, Emmi; van Duijn, Cornelia M; Viikari, Jorma; Völzke, Henry; Wichmann, H-Erich; Wild, Philipp S; Willems, Sara M; Willemsen, Gonneke; van Rooij, Frank J A; Groenen, Patrick J F; Uitterlinden, André G; Hofman, Albert; Thurik, A Roy

2013-01-01

Economic variables such as income, education, and occupation are known to affect mortality and morbidity, such as cardiovascular disease, and have also been shown to be partly heritable. However, very little is known about which genes influence economic variables, although these genes may have both a direct and an indirect effect on health. We report results from the first large-scale collaboration that studies the molecular genetic architecture of an economic variable-entrepreneurship-that was operationalized using self-employment, a widely-available proxy. Our results suggest that common SNPs when considered jointly explain about half of the narrow-sense heritability of self-employment estimated in twin data (σ(g)(2)/σ(P)(2) = 25%, h(2) = 55%). However, a meta-analysis of genome-wide association studies across sixteen studies comprising 50,627 participants did not identify genome-wide significant SNPs. 58 SNPs with pself-employment in an independent sample (p≥0.039). Our results are consistent with a highly polygenic molecular genetic architecture of self-employment, with many genetic variants of small effect. Although self-employment is a multi-faceted, heavily environmentally influenced, and biologically distal trait, our results are similar to those for other genetically complex and biologically more proximate outcomes, such as height, intelligence, personality, and several diseases.

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.

Multilocus genotypic data reveal high genetic diversity and low population genetic structure of Iranian indigenous sheep

International Nuclear Information System (INIS)

Vahidi, S.M.F.; Faruque, M.O.; Falahati Anbaran, M.; Afraz, F.; Mousavi, S.M.; Boettcher, P.; Joost, S.; Han, J.L.; Colli, L.; Periasamy, K.; Negrini, R.; Ajmone-Marsan, P.

2016-01-01

Full text: Iranian livestock diversity is still largely unexplored, in spite of the interest in the populations historically reared in this country located near the Fertile Crescent, a major livestock domestication centre. In this investigation, the genetic diversity and differentiation of 10 Iranian indigenous fat-tailed sheep breeds were investigated using 18 microsatellite markers. Iranian breeds were found to host a high level of diversity. This conclusion is substantiated by the large number of alleles observed across loci (average 13.83, range 7–22) and by the high within-breed expected heterozygosity (average 0.75, range 0.72–0.76). Iranian sheep have a low level of genetic differentiation, as indicated by the analysis of molecular variance, which allocated a very small proportion (1.67%) of total variation to the between-population component, and by the small fixation index (FST = 0.02). Both Bayesian clustering and principal coordinates analysis revealed the absence of a detectable genetic structure. Also, no isolation by distance was observed through comparison of genetic and geographical distances. In spite of high within-breed variation, signatures of inbreeding were detected by the FIS indices, which were positive in all and statistically significant in three breeds. Possible factors explaining the patterns observed, such as considerable gene flow and inbreeding probably due to anthropogenic activities in the light of population management and conservation programmes are discussed. (author)

Distribution of the Most Common Genetic Variants Associated with a Variable Drug Response in the Population of the Republic of Macedonia

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Nestorovska Kapedanovska A.

2014-12-01

Full Text Available Genetic variation in the regulation, expression and activity of genes coding for Phase I, Phase II drug metabolizing enzymes (DMEs and drug targets, can be defining factors for the variability in both the effectiveness and occurrence of drug therapy side effects. Information regarding the geographic structure and multi-ethnic distribution of clinically relevant genetic variations is becoming increasingly useful for improving drug therapy and explaining inter-individual and inter-ethnic differences in drug response.

TMTI Task 1.6 Genetic Engineering Methods and Detection

Energy Technology Data Exchange (ETDEWEB)

Slezak, T; Lenhoff, R; Allen, J; Borucki, M; Vitalis, E; Gardner, S

2009-12-04

A large number of GE techniques can be adapted from other microorganisms to biothreat bacteria and viruses. Detection of GE in a microorganism increases in difficulty as the size of the genetic change decreases. In addition to the size of the engineered change, the consensus genomic sequence of the microorganism can impact the difficulty of detecting an engineered change in genomes that are highly variable from strain to strain. This problem will require comprehensive databases of whole genome sequences for more genetically variable biothreat bacteria and viruses. Preliminary work with microarrays for detecting synthetic elements or virulence genes and analytic bioinformatic approaches for whole genome sequence comparison to detect genetic engineering show promise for attacking this difficult problem but a large amount of future work remains.

Therapeutic Vaccine Against HIV, Viral Variability, Cytotoxic T Lymphocyte Epitopes, and Genetics of Patients.

Science.gov (United States)

Fleury, Herve; Tumiotto, Camille; Bellecave, Pantxika; Recordon-Pinson, Patricia

2018-01-01

The scientific and medical community is seeking to cure HIV. Several pathways have been or are being explored including therapeutic vaccination. Viroimmunological studies on primary infection as well as on elite controllers have demonstrated the importance of the cytotoxic CD8 response and have mainly oriented research on vaccine constructs toward this type of response. The results of these trials are clearly not commensurate with the hope placed in them. Might there be one or more uncontrolled variables? The genetics of patients need to be taken into consideration, especially their human lymphocyte antigen (HLA) alleles. There is a need to find a balance between the conservation of cytotoxic T lymphocyte (CTL) epitopes and presentation by HLA alleles. The pathway is a narrow one between adaptation of the virus to HLA I restriction and the definition of conserved proviral CTL epitopes presentable by HLA I alleles. It is likely that the genetics of patients will need to be considered for HIV-1 vaccine studies and that multidisciplinary collaboration will be essential in this field of infectious diseases.

Microsatellite DNA typing for assessment of genetic variability in ...

Indian Academy of Sciences (India)

these microsatellite loci in measurement of genetic diversity indices in other Indian cattle breeds too. Various .... enced a recent reduction in the effective population size or a genetic ... by using the m p val.exe program (Garza and Williamson.

A DNA fingerprinting procedure for ultra high-throughput genetic analysis of insects.

Science.gov (United States)

Schlipalius, D I; Waldron, J; Carroll, B J; Collins, P J; Ebert, P R

2001-12-01

Existing procedures for the generation of polymorphic DNA markers are not optimal for insect studies in which the organisms are often tiny and background molecular information is often non-existent. We have used a new high throughput DNA marker generation protocol called randomly amplified DNA fingerprints (RAF) to analyse the genetic variability in three separate strains of the stored grain pest, Rhyzopertha dominica. This protocol is quick, robust and reliable even though it requires minimal sample preparation, minute amounts of DNA and no prior molecular analysis of the organism. Arbitrarily selected oligonucleotide primers routinely produced approximately 50 scoreable polymorphic DNA markers, between individuals of three independent field isolates of R. dominica. Multivariate cluster analysis using forty-nine arbitrarily selected polymorphisms generated from a single primer reliably separated individuals into three clades corresponding to their geographical origin. The resulting clades were quite distinct, with an average genetic difference of 37.5 +/- 6.0% between clades and of 21.0 +/- 7.1% between individuals within clades. As a prelude to future gene mapping efforts, we have also assessed the performance of RAF under conditions commonly used in gene mapping. In this analysis, fingerprints from pooled DNA samples accurately and reproducibly reflected RAF profiles obtained from individual DNA samples that had been combined to create the bulked samples.

STUDY OF GENETIC VARIABILITY OF TRITICALE VARIETIES BY SSR MARKERS

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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.

Evaluation of genetic variability in potato cv. 'Parda-Pastusa' obtained through the physical mutagenic agents

International Nuclear Information System (INIS)

Angarita-Zerda, A.; Mosquera, T.; Nustez, C.

1997-01-01

'Parda-Pastusa' is probably the most important variety of potato in Colombia. Its susceptibility to frost and Phytophthora infestans can cause important losses in the crop. In order to induce genetic variability to select clones resistant to frost and late blight, disease-free micropropagated plantlets, obtained from meristem culture of indexed tubers were irradiated with gamma rays from a 60 Co source. Virus-free mericlones were initially irradiated with 0,25, 50, 75 and 100 Gy or with 0, 10, 20 and 30 Gy. The optimal radiation dose was found to be 20 Gy. A mass propagation was carried out, and plantlets were irradiated with the optimal radiation dose. Clones derived from irradiated material were propagated for selection under simulated frost conditions (-7 deg. C for 360 minutes) and co-cultured with extracts of fungus, Phytophthora infestans. The selected clones will be transferred to field conditions for evaluation of agronomic and genetic characteristics. (author). 1 ref

Evaluation of genetic variability in potato cv. `Parda-Pastusa` obtained through the physical mutagenic agents

Energy Technology Data Exchange (ETDEWEB)

Angarita-Zerda, A; Mosquera, T; Nustez, C [Tissue Culture Lab., Agronomy School, National Univ. of Colombia, Santafe de Bogota (Colombia)

1997-07-01

`Parda-Pastusa` is probably the most important variety of potato in Colombia. Its susceptibility to frost and Phytophthora infestans can cause important losses in the crop. In order to induce genetic variability to select clones resistant to frost and late blight, disease-free micropropagated plantlets, obtained from meristem culture of indexed tubers were irradiated with gamma rays from a {sup 60}Co source. Virus-free mericlones were initially irradiated with 0,25, 50, 75 and 100 Gy or with 0, 10, 20 and 30 Gy. The optimal radiation dose was found to be 20 Gy. A mass propagation was carried out, and plantlets were irradiated with the optimal radiation dose. Clones derived from irradiated material were propagated for selection under simulated frost conditions (-7 deg. C for 360 minutes) and co-cultured with extracts of fungus, Phytophthora infestans. The selected clones will be transferred to field conditions for evaluation of agronomic and genetic characteristics. (author). 1 ref.

High Variability in Outcome Reporting Patterns in High-Impact ACL Literature.

Science.gov (United States)

Makhni, Eric C; Padaki, Ajay S; Petridis, Petros D; Steinhaus, Michael E; Ahmad, Christopher S; Cole, Brian J; Bach, Bernard R

2015-09-16

ACL (anterior cruciate ligament) reconstruction is one of the most commonly performed and studied procedures in modern sports medicine. A multitude of objective and subjective patient outcome measures exists; however, nonstandardized reporting patterns of these metrics may create challenges in objectively analyzing pooled results from different studies. The goal of this study was to document the variability in outcome reporting patterns in high-impact orthopaedic studies of ACL reconstruction. All clinical studies pertaining to ACL reconstruction in four high-impact-factor orthopaedic journals over a five-year period were reviewed. Biomechanical, basic science, and imaging studies were excluded, as were studies with fewer than fifty patients, yielding 119 studies for review. Incorporation of various objective and subjective outcomes was noted for each study. Substantial variability in reporting of both objective and subjective measures was noted in the study cohort. Although a majority of studies reported instrumented laxity findings, there was substantial variability in the type and method of laxity reporting. Most other objective outcomes, including range of motion, strength, and complications, were reported in <50% of all studies. Return to pre-injury level of activity was infrequently reported (24% of studies), as were patient satisfaction and pain assessment following surgery (8% and 13%, respectively). Of the patient-reported outcomes, the International Knee Documentation Committee (IKDC), Lysholm, and Tegner scores were most often reported (71%, 63%, and 42%, respectively). Substantial variability in outcome reporting patterns exists among high-impact studies of ACL reconstruction. Such variability may create challenges in interpreting results and pooling them across different studies. Copyright © 2015 by The Journal of Bone and Joint Surgery, Incorporated.

The Escherichia coli argW-dsdCXA genetic island is highly variable, and E. coli K1 strains commonly possess two copies of dsdCXA.

Science.gov (United States)

Moritz, Rebecca L; Welch, Rodney A

2006-11-01

The genome sequences of Escherichia coli pathotypes reveal extensive genetic variability in the argW-dsdCXA island. Interestingly, the archetype E. coli K1 neonatal meningitis strain, strain RS218, has two copies of the dsdCXA genes for d-serine utilization at the argW and leuX islands. Because the human brain contains d-serine, an epidemiological study emphasizing K1 isolates surveyed the dsdCXA copy number and function. Forty of 41 (97.5%) independent E. coli K1 isolates could utilize d-serine. Southern blot hybridization revealed physical variability within the argW-dsdC region, even among 22 E. coli O18:K1:H7 isolates. In addition, 30 of 41 K1 strains, including 21 of 22 O18:K1:H7 isolates, had two dsdCXA loci. Mutational analysis indicated that each of the dsdA genes is functional in a rifampin-resistant mutant of RS218, mutant E44. The high percentage of K1 strains that can use d-serine is in striking contrast to our previous observation that only 4 of 74 (5%) isolates in the diarrheagenic E. coli (DEC) collection have this activity. The genome sequence of diarrheagenic E. coli isolates indicates that the csrRAKB genes for sucrose utilization are often substituted for dsdC and a portion of dsdX present at the argW-dsdCXA island of extraintestinal isolates. Among DEC isolates there is a reciprocal pattern of sucrose fermentation versus d-serine utilization. The ability to use d-serine is a trait strongly selected for among E. coli K1 strains, which have the ability to infect a wide range of extraintestinal sites. Conversely, diarrheagenic E. coli pathotypes appear to have substituted sucrose for d-serine as a potential nutrient.

Human genetics studies in areas of high natural radiation, 7

International Nuclear Information System (INIS)

Freire-Maia, A.

1975-01-01

Two methods to estimate the inbreeding load, employed in our analysis, are reviewed. Besides the total population, a sample constituted of individuals with no alien ancestral is also analysed. The measurements by genetic load models show any clear effect of natural radioactivity (especially for abortions, pre-natal mortality, anomalies, and abnormalities in general). The results on stillbirths and post-natal and total mortalities are discussed and it is concluded that uncontrolled concomitant variables (if not chance alone) cause the differences [pt

Individual Differences in Scotopic Visual Acuity and Contrast Sensitivity: Genetic and Non-Genetic Influences.

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Alex J Bartholomew

Full Text Available Despite the large amount of variation found in the night (scotopic vision capabilities of healthy volunteers, little effort has been made to characterize this variation and factors, genetic and non-genetic, that influence it. In the largest population of healthy observers measured for scotopic visual acuity (VA and contrast sensitivity (CS to date, we quantified the effect of a range of variables on visual performance. We found that young volunteers with excellent photopic vision exhibit great variation in their scotopic VA and CS, and this variation is reliable from one testing session to the next. We additionally identified that factors such as Circadian preference, iris color, astigmatism, depression, sex and education have no significant impact on scotopic visual function. We confirmed previous work showing that the amount of time spent on the vision test influences performance and that laser eye surgery results in worse scotopic vision. We also showed a significant effect of intelligence and photopic visual performance on scotopic VA and CS, but all of these variables collectively explain <30% of the variation in scotopic vision. The wide variation seen in young healthy volunteers with excellent photopic vision, the high test-retest agreement, and the vast majority of the variation in scotopic vision remaining unexplained by obvious non-genetic factors suggests a strong genetic component. Our preliminary genome-wide association study (GWAS of 106 participants ruled out any common genetic variants of very large effect and paves the way for future, larger genetic studies of scotopic vision.

Is the Experience of Thermal Pain Genetics Dependent?

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Emilia Horjales-Araujo

2015-01-01

Full Text Available It is suggested that genetic variations explain a significant portion of the variability in pain perception; therefore, increased understanding of pain-related genetic influences may identify new targets for therapies and treatments. The relative contribution of the different genes to the variance in clinical and experimental pain responses remains unknown. It is suggested that the genetic contributions to pain perception vary across pain modalities. For example, it has been suggested that more than 60% of the variance in cold pressor responses can be explained by genetic factors; in comparison, only 26% of the variance in heat pain responses is explained by these variations. Thus, the selection of pain model might markedly influence the magnitude of the association between the pain phenotype and genetic variability. Thermal pain sensation is complex with multiple molecular and cellular mechanisms operating alone and in combination within the peripheral and central nervous system. It is thus highly probable that the thermal pain experience is affected by genetic variants in one or more of the pathways involved in the thermal pain signaling. This review aims to present and discuss some of the genetic variations that have previously been associated with different experimental thermal pain models.

Exploring the Role of Genetic Variability and Lifestyle in Oxidative Stress Response for Healthy Aging and Longevity

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Giuseppe Passarino

2013-08-01

Full Text Available 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.

Genetic variability and divergence studies in seed traits and oil content of Jatropha (Jatropha curcas L.) accessions

Energy Technology Data Exchange (ETDEWEB)

Kaushik, N.; Kumar, Krishan; Kumar, Sushil [CCS HAU, Regional Research Station, Bawal (Rewari) (India); Kaushik, Nutan; Roy, S. [The Energy Resource Institute, New Delhi (India)

2007-07-15

Variability in seed traits and oil content of 24 accessions of Jatropha curcas collected from different agroclimatic zones of Haryana state, India were assessed. There were significant differences (P<0.05) in seed size, 100-seed weight and oil content between accessions. Maximum seed weight was recorded in seeds collected from IC-520602 and the least weight was recorded in IC-520587. Oil variability ranged from 28.00% in IC-520589 to 38.80% in IC-520601. In general phenotypic coefficient of variation was higher than the genotypic coefficient of variation indicating the predominant role of environment. High heritability and genetic gain were recorded for oil content (99.00% and 18.90%) and seed weight (96.00% and 18.00%), respectively, indicating the additive gene action. Seed weight had positive correlation with seed length, breadth, thickness and oil content. On the basis of non-hierarchical Euclidian cluster analysis, six clusters were obtained with highest number of accession falling under cluster III. Maximum and minimum intra cluster distance was observed for cluster VI (2.499) and for cluster III (2.252), respectively. Whereas maximum inter-cluster distance was observed between cluster VI and IV (5.129) and minimum between cluster III and II (2.472). Among the six clusters formed cluster IV showed maximum cluster value for seed size whereas, cluster VI showed maximum value for oil content and seed weight. Thus on the basis of present finding it is suggested that the crossing between accessions of cluster IV and VI will result in wide spectrum of variability in subsequent generations. (author)

Divergence and genetic variability among superior rubber tree genotypes Divergência e variabilidade genética de genótipos superiores de seringueira

Directory of Open Access Journals (Sweden)

Lígia Regina Lima Gouvêa

2010-02-01

Full Text Available The objective of this work was to estimate the genetic variability and divergence among 22 superior rubber tree (Hevea sp. genotypes of the IAC 400 series. Univariate and multivariate analyses were performed using eight quantitative traits (descriptors, including yield. In the univariate analyses, the estimated parameters were: genetic and environmental variances; genetic and environmental coefficients of variation; and the variation index. The Mahalanobis generalized distance, the Tocher agglomerative method and canonical variables were used for the multivariate analyses. In the univariate analyses, variability was verified among the genotypes for all the variables evaluated. The Tocher method grouped the genotypes into 11 clusters of dissimilarity. The first four canonical variables explained 87.93% of the cumulative variation. The highest genetic variability was found in rubber yield-related traits, which contributed the most to the genetic divergence. The most divergent pairs of genotypes are suggested for crossbreeding. The genotypes evaluated are suitable for breeding and may be used to continue the IAC rubber tree breeding program.O objetivo deste trabalho foi estimar a divergência e a variabilidade genética entre 22 genótipos superiores de seringueira (Hevea sp. da série IAC 400. Análises univariadas e multivariadas foram realizadas com oito caracteres quantitativos (descritores, incluindo produtividade. Na análise univariada, os parâmetros estimados foram: variâncias genética e ambiental, coeficientes de variação genética e ambiental, e índice de variação. A distância generalizada de Mahalanobis, o método aglomerativo de Tocher e variáveis canônicas foram utilizados nas análises multivariadas. Nas análises univariadas, verificou-se variabilidade entre os genótipos para todas as variáveis avaliadas. O método de Tocher agrupou os genótipos em 11 grupos de dissimilaridade. As quatro primeiras variáveis can

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....

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.

Experimental Population Genetics in the Introductory Genetics Laboratory Using "Drosophila" as a Model Organism

Science.gov (United States)

Johnson, Ronald; Kennon, Tillman

2009-01-01

Hypotheses of population genetics are derived and tested by students in the introductory genetics laboratory classroom as they explore the effects of biotic variables (physical traits of fruit flies) and abiotic variables (island size and distance) on fruit fly populations. In addition to this hypothesis-driven experiment, the development of…

High-voltage variable-duration pulse generator

International Nuclear Information System (INIS)

Anisimova, T.E.; Akkuratov, E.V.; Gromovenko, V.M.; Nikonov, Yu.P.; Malinin, A.N.

1988-01-01

A high-voltage generator is described that allows pulse duration tau to be varied within wide limits and has high efficiency (at least 50% for tau = 0.5 tau/sub max/) and an amplitude of up to 5 kV, a repetition frequency of up to 200 Hz,and a variable duration of 0-30 μsec. The generator is used in the controller of an electron accelerator

Morphological and agronomical characterization and estimates of genetic parameters of sesbania Scop. (Leguminosae accessions

Directory of Open Access Journals (Sweden)

Veasey E.A.

1999-01-01

Full Text Available Twenty-two accessions of seven Sesbania (Leguminosae species: S. emerus, S. rostrata, S. tetraptera, S. exasperata (annuals, S. grandiflora, S. sesban and S. virgata (perennials, used for ruminant fodder, firewood, wood products, soil improvement, and human food, were investigated, with the aim of characterizing both inter- and intraspecific genetic variability, estimating genetic parameters for the characters evaluated and appraising the forage potential of the accessions. These were planted at the Instituto de Zootecnia, Nova Odessa, SP, Brazil, in a randomized complete block design with 22 treatments and four replications. Seventeen morphological and 17 agronomic characters were evaluated. Genetic parameters coefficient of intraspecific genetic diversity (bi and coefficient of intraspecific genetic variation (CVgi were obtained for the species represented by more than one accession. Highly significant differences were observed among as well as within species for most characters, showing considerable genetic variability. S. exasperata showed intraspecific genetic variability for the largest number of morphological characters. The same was observed for S. sesban for the agronomic characters. Most of the characters gave high bi values, above 0.80, indicating the possibility of selecting superior genotypes. The CVgi values, on the other hand, which indicate the magnitude of the existing genetic variability relative to the character mean, varied according to the species and character evaluated. Differences between annual and perennial species were observed, with higher biomass yields presented by the annuals at the first cut and by the perennials after the second cut, reaching the highest yield at the third cut. The annual species had higher seed production. Accession NO 934 of S. sesban gave the highest biomass yields and regrowth vigor, showing promise as a forage legume plant.

Induction of mutation: Improvement of genetic variability of wheat (Triticum sp.)

International Nuclear Information System (INIS)

Parodi, P.C.P.

1984-01-01

The malnutrition problem in developing countries can be solved by increased production of foods with high proteic content. This paper discusses the application of mutagenesis by radiation in the development of an improved wheat variability with high content of proteins and amino acids. Wheat is the staple food of developing countries

Genetic diversity in Trichomonas vaginalis.

Science.gov (United States)

Meade, John C; Carlton, Jane M

2013-09-01

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

Genetic variability within french race and riding horse breeds from genealogical data and blood marker polymorphisms

OpenAIRE

Moureaux, Sophie; Verrier, Etienne; Ricard, Anne; Meriaux, J-Claude

1996-01-01

The genetic variability of five horse breeds raised in France was analysed: Thoroughbred, Trotteur Français, Arab, Anglo-Arab and Selle Français. Genealogical data and genotypes at seven blood group and nine protein loci were used. Paternal family sizes were found to be unbalanced, especially in Trotteur français, Selle Franqais and Thoroughbred. Average coefficients of inbreeding for offspring born from 1989 to 1992 were 1.02 (Thoroughbred), 1.86 (Trotteur Français), 3.08 (Arab), 1.17 (...

Genetic variability induction in the size of the size of rice plantules by combined irradiation and temperature treatments

International Nuclear Information System (INIS)

Garcia, D.; Gonzalez, L.M.; Gumberra, R.

1993-01-01

Induced variability in the size of rice plantules was determined using the heritability calculation in a narrow sense, by means of the progenitor-descendant regression. Progenitor stands for the original variety, whereas descendant stands for plant population from CO6 0 gamma-rays irradiated seeds (at 100-600 Gy doses), treated at different temperatures. Results obtained: show the possibility to increase efficiency in variability induction by a combined course of action of both factors. In this experience, the best combination turned out to be 300 Gy-0 celsius grated, which of all the changes that it caused, some 75 percent was of a genetic nature

Genetic variability of cultivated cowpea in Benin assessed by ...

African Journals Online (AJOL)

STORAGESEVER

2008-12-17

Dec 17, 2008 ... Res. Crop Evol. 48: 559-566. Mignouna HD, Ng NQ, Ikea J, Thottapilly G (1998). Genetic diversity in cowpea as revealed by random amplified polymorphic DNA. J. Gen. Breed. 52: 151-159. Nei M, Li WH (1979). Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc.

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.

Genetic variability, correlation and path analysis of yield contributing characters in sweet potato (ipomoea batatas lam.)

International Nuclear Information System (INIS)

Hossain, M.D.; Rabbani, M.G.; Mollah, M.L.R.

2000-01-01

Evaluation of 30 sweet potato (Ipomoea batatas Lam.) genotypes for yield contributing characters and tuber yield per plant revealed high phenotypic and genotypic coefficient of variation (PCV and GCV, respectively) for number of tubers per plant, average tuber weight and tuber yield per plant. The heritability and genetic advance were higher for tuber yield per plant, average tuber weight and number of tubers per plant. These three characters also reflected high heritability as well as high genetic advance. As high positive significant correlation, as well as positive direct effect of average tuber weight and number of tubers per plant on tuber yield per plant were found, these characters should be given prime importance for selecting high yielding sweet potato genotypes. (author)

Genetic stability evaluation of quercus suber l. somatic embryogenesis by rapd analysis

International Nuclear Information System (INIS)

Fernandes, P.; Costa, A.; Rocha, A.C.C.; Santos, C.

2011-01-01

A reliable protocol for adult Quercus suber L. somatic embryogenesis (SE) was developed recently. To evaluate the potential use of this protocol in cork oak forest breeding programs, it is essential to guarantee somatic embryos/emblings genetic stability. Random Amplification of Polymorphic DNA (RAPD) is currently used to assess somaclonal variation providing information on genetic variability of the micropropagation process. In this work, SE was induced from adult trees by growing leaf explants on MS medium supplemented with 2,4-D and zeatin. Embling conversion took place on MS medium without growth regulators. DNA from donor tree, somatic embryos and emblings was used to assess genetic variability by RAPD fingerprinting. Fourteen primers produced 165 genetic loci with high quality and reproducibility. Despite somatic embryos originated some poor quality PCR-profiles, replicable and excellent fingerprints were obtained for both donor plant and embling. Results presented no differences among regenerated emblings and donor plant. Hence, the SE protocol used did not induce, up to moment, any genetic variability, confirming data previously obtained with other molecular/genetic techniques, supporting that this protocol may be used to provide true-to-type plants from important forestry species. (author)

Heritability of high sugar consumption through drinks and the genetic correlation with substance use.

Science.gov (United States)

Treur, Jorien L; Boomsma, Dorret I; Ligthart, Lannie; Willemsen, Gonneke; Vink, Jacqueline M

2016-10-01

High sugar consumption contributes to the rising prevalence of obesity. Sugar can have rewarding effects that are similar to, but less strong than, the effects of addictive substances. People who consume large amounts of sugar also tend to use more addictive substances, but it is unclear whether this is due to shared genetic or environmental risk factors. We examined whether there are genetic influences on the consumption of sugar-containing drinks and whether genetic factors can explain the association with substance use. The frequency of consumption of sugar-containing drinks (e.g., cola, soft drinks, and energy drinks) and addictive substances (nicotine, caffeine, alcohol, cannabis, and illicit drugs) was obtained for 8586 twins who were registered at the Netherlands Twin Register (women: 68.7%; mean ± SD age: 33.5 ± 15.3 y). Participants were categorized as high or low sugar consumers (>1 compared with ≤1 SD above daily consumption in grams) and as high or low substance users (≥2 compared with <2 substances). Through bivariate genetic modeling, genetic and environmental influences on sugar consumption, substance use, and their association were estimated. Genetic factors explained 48% of the variation in high sugar consumption, whereas unique environmental factors explained 52%. For high substance use, these values were 62% and 38%, respectively. There was a moderate phenotypic association between high sugar consumption and high substance use (r = 0.2), which was explained by genetic factors (59%) and unique environmental factors (41%). The positive association between high sugar consumption and high substance use was partly due to unique environmental factors (e.g., social situations). Genetic factors were also of influence, suggesting that neuronal circuits underlying the development of addiction and obesity are related. Further research is needed to identify genes that influence sugar consumption and those that overlap with substance use. © 2016

The influence of gamma rays irradiation on chlorophyll mutation and genetic variability of agronomic characters in soybean plant

International Nuclear Information System (INIS)

Ratma, Rivaie; Sumargono, A.M. Riyanti

1998-01-01

Seeds of soybean mutant line No. 13/PsJ with 12% moisture content were irradiated by 0,10;0,20;0.30 and 0.40 kGy of gamma rays treatment. Number of irradiated seed for each treatment was 1500 seeds. Irradiated of seeds were planted in the 4m X 5m plot size with 0,20m x 0,40m spacing and two seed each hole and were planted as M-1 plants in the wet season of 1996/1997 at PAIR field experiment in Pasar Jumat, Jakarta. The experiment was designed Randomized Block Design with three replication Plans of M-1 generation were harvested individuality and were planted as known M2 plants in the next generation in dry season of 1997 at PAIR field experiment. Seven days planting the chlorophyll mutation of plants were recorded by Frydenberg method and the genetic variability of plant height, number of fertile pods and nodes were calculated by Singh and Chaudhary formula. Results of the experiment showed that chlorophyll mutation and genetic variability of plant height and number of fertile pods could be improved be 0.10 and 0,20 kGy of gamma rays treatment. (authors)

Variability, heritability, character association, path analysis and morphological diversity in snake gourd

Directory of Open Access Journals (Sweden)

A.S.M. Mahbubur Rahman Khan

2016-11-01

Full Text Available Genetic variability, heritability and path coefficient analysis were studied in 21 genotypes of snake gourd. The phenotypic coefficient of variations was found slightly higher than the genotypic coefficient of variations for all characters studied, indicating that the apparent variation is not only genetic but also influenced by the growing environment in the expression of the traits. The genotypic coefficient of variation was high for the fruit yield, number of fruits per vine, length of fruit and single fruit weight. High heritability coupled with high-to-moderate genetic advance was estimated for all characters studied. Correlation studies revealed that the fruit yield had a significant, positive correlation with the number of fruits per vine, length of fruit and single fruit weight. Importantly, more than 90% of the genotypic total variation was contributed by the characters included in the path analysis. The highest, direct, positive effect was recorded for the number of fruits per vine. The divergence value for cluster analysis indicated that the genotypes from clusters II and III had the highest inter-cluster distance and were expected to provide high heterosis in hybridization and to show wide variability in genetic architecture. The selection of high yielding genotypes should give emphasis to the number of fruits per vine, length of fruit and single fruit weight.

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

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)

1996-12-31

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

Genetic variability of the equine casein genes.

Science.gov (United States)

Brinkmann, J; Jagannathan, V; Drögemüller, C; Rieder, S; Leeb, T; Thaller, G; Tetens, J

2016-07-01

The casein genes are known to be highly variable in typical dairy species, such as cattle and goat, but the knowledge about equine casein genes is limited. Nevertheless, mare milk production and consumption is gaining importance because of its high nutritive value, use in naturopathy, and hypoallergenic properties with respect to cow milk protein allergies. In the current study, the open reading frames of the 4 casein genes CSN1S1 (αS1-casein), CSN2 (β-casein), CSN1S2 (αS2-casein), and CSN3 (κ-casein) were resequenced in 253 horses of 14 breeds. The analysis revealed 21 nonsynonymous nucleotide exchanges, as well as 11 synonymous nucleotide exchanges, leading to a total of 31 putative protein isoforms predicted at the DNA level, 26 of which considered novel. Although the majority of the alleles need to be confirmed at the transcript and protein level, a preliminary nomenclature was established for the equine casein alleles. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

use of genetic variability estimates and interrelationships

African Journals Online (AJOL)

Prof. Adipala Ekwamu

of 11 agronomic and biochemical traits to water stress based on estimation of genetic ... of primary branches and 100 seed weight under W0, and number of primary ... selection of superior drought-tolerant genotype (LR1) with good yield ...

Genetic parameters for longevity in Holteins cows

Directory of Open Access Journals (Sweden)

Elisa Junqueira Oliveira

2012-12-01

Full Text Available The milk yield has been the most selected trait in dairy cattle breeding programs. However various studies have shown a decline in adaptive and longevity traits in herds that are under selection for improving production, especially in taurine breeds, as the Holstein, who was highly selected for milk production. The aim of this study was to estimate genetic parameters for first lactation 305-day milk yield (Y305 and for longevity traits and to verify the association among them, in high production Holstein cows. The data sets used were from Agrindus Farm, with calving occurring between 1989 and 2005. The traits analyzed were Y305, productive life (PL, calculated as the length of lactation days from the first day of lactation until the culling, and age at culling (AC. Variance components were estimated by Restricted Maximum Likelihood, applying multi-trait animal model. Heritability estimates for Y305, PL and AC were, respectively, 0.35, 0.07 and 0.10. Heritability estimates for PL and AC suggest small genetic variability to get genetic gains by direct selection for these traits, because they are influenced by decisions of voluntary and involuntary culling, being largely affected by factors related to the environment. It is difficult to measure these traits because it is necessary to evaluate culling of animals and causes of culling. The magnitude of the heritability estimate for Y305 evidences the existence of reasonable additive genetic variability, which allows efficiency by selecting for this trait. The genetic correlations between Y305 and PL was 0.02 and between Y305 and AC was 0.01, suggesting small genetic association between Y305 and longevity traits. In this case, the selection for Y305 is viable due to high heritability estimate and the favorable and almost null genetic correlation between Y305 and the longevity traits. Some studies have used to analyze longevity traits as threshold and since this trait has great economic importance, it

Genetic characterization of the Bardigiano horse using microsatellite markers

Directory of Open Access Journals (Sweden)

Claudio Lisa

2010-01-01

Full Text Available The study was aimed at investigating the genetic structure of the Bardigiano horse and its relationships with the Haflinger, Maremmano and Arabian breeds using 11 microsatellite markers. A total of 94 alleles were detected across the breeds, with a mean of 8.5 alleles per locus and a mean observed heterozygosity of 0.69. Compared to the other breeds, the Bardigiano horse showed quite a high genetic variability, as indicated by the mean number of alleles (7.0 vs 6.1÷7.6 and by the observed heterozygosity (0.72 vs 0.66÷0.71. Moreover, the genotype distributions in the Bardigiano groups of different sex and age were not significantly different. The overall FST value showed that the genetic differences among breeds accounted for 7.8% (P=0.001 of the total variation, and the pairwise FST values were all significant. The assignment test allocated between 96.8 and 98.9% of the individuals to the population they were collected from, with a mean probability of assignment of about 97% for all breeds, except for the Arabian, where it approached 100%. The results have highlighted that the Bardigiano breed has a high within and between breed variability, which is considerably more than could be expected by looking at its evolution history. This justifies the need for the development of additional breeding strategies to preserve the existing genetic variability.

[Genetic variability and differentiation of three Russian populations of yellow potato cyst nematode Globodera rostochiensis as revealed by nuclear markers].

Science.gov (United States)

Khrisanfova, G G; Kharchevnikov, D A; Popov, I O; Zinov'eva, S V; Semenova, S K

2008-05-01

Genetic variability of yellow potato cyst nematode G. rostochiensis from three Russian populations (Karelia, Vladimir oblast, and Moscow oblast) was investigated using two types of nuclear markers. Using RAPD markers identified with the help of six random primers (P-29, OPA-10, OPT-14, OPA-11, OPB-11, and OPH-20), it was possible to distinguish Karelian population from the group consisting of the populations from two adjacent regions (Moscow oblast and Vladimir oblast). Based on the combined matrix, containing 294 RAPD fragments, dendrogram of genetic differences was constructed, and the indices of genetic divergence and partition (P, H, and G(st)), as well as the gene flow indices N(m) between the nematode samples examined, were calculated. The dendrogram structure, genetic diversity indices, and variations of genetic distances between single individuals in each population from Karelia and Central Russia pointed to genetic isolation and higher genetic diversity of the nematodes from Karelia. Based on polymorphism of rDNA first intergenic spacer ITS1, attribution of all populations examined to the species G. rostochiensis was proved. Small variations of the ITS1 sequence in different geographic populations of nematodes from different regions of the species world range did not allow isolation of separate groups within the species. Possible factors (including interregional transportations of seed potato) affecting nematode population structure in Russia are discussed.

Bayesian Multiresolution Variable Selection for Ultra-High Dimensional Neuroimaging Data.

Science.gov (United States)

Zhao, Yize; Kang, Jian; Long, Qi

2018-01-01

Ultra-high dimensional variable selection has become increasingly important in analysis of neuroimaging data. For example, in the Autism Brain Imaging Data Exchange (ABIDE) study, neuroscientists are interested in identifying important biomarkers for early detection of the autism spectrum disorder (ASD) using high resolution brain images that include hundreds of thousands voxels. However, most existing methods are not feasible for solving this problem due to their extensive computational costs. In this work, we propose a novel multiresolution variable selection procedure under a Bayesian probit regression framework. It recursively uses posterior samples for coarser-scale variable selection to guide the posterior inference on finer-scale variable selection, leading to very efficient Markov chain Monte Carlo (MCMC) algorithms. The proposed algorithms are computationally feasible for ultra-high dimensional data. Also, our model incorporates two levels of structural information into variable selection using Ising priors: the spatial dependence between voxels and the functional connectivity between anatomical brain regions. Applied to the resting state functional magnetic resonance imaging (R-fMRI) data in the ABIDE study, our methods identify voxel-level imaging biomarkers highly predictive of the ASD, which are biologically meaningful and interpretable. Extensive simulations also show that our methods achieve better performance in variable selection compared to existing methods.

Antigenic and genetic variability of human metapneumoviruses

NARCIS (Netherlands)

S. Herfst (Sander); L. Sprong; P.A. Cane; E. Forleo-Neto; A.D.M.E. Osterhaus (Albert); R.A.M. Fouchier (Ron); R.L. de Swart (Rik); B.G. van den Hoogen (Bernadette)

2004-01-01

textabstractHuman metapneumovirus (HMPV) is a member of the subfamily Pneumovirinae within the family Paramyxo- viridae. Other members of this subfamily, respiratory syncytial virus and avian pneumovirus, can be divided into subgroups on the basis of genetic or antigenic differences or both. For

Brucella Genetic Variability in Wildlife Marine Mammals Populations Relates to Host Preference and Ocean Distribution.

Science.gov (United States)

Suárez-Esquivel, Marcela; Baker, Kate S; Ruiz-Villalobos, Nazareth; Hernández-Mora, Gabriela; Barquero-Calvo, Elías; González-Barrientos, Rocío; Castillo-Zeledón, Amanda; Jiménez-Rojas, César; Chacón-Díaz, Carlos; Cloeckaert, Axel; Chaves-Olarte, Esteban; Thomson, Nicholas R; Moreno, Edgardo; Guzmán-Verri, Caterina

2017-07-01

Intracellular bacterial pathogens probably arose when their ancestor adapted from a free-living environment to an intracellular one, leading to clonal bacteria with smaller genomes and less sources of genetic plasticity. Still, this plasticity is needed to respond to the challenges posed by the host. Members of the Brucella genus are facultative-extracellular intracellular bacteria responsible for causing brucellosis in a variety of mammals. The various species keep different host preferences, virulence, and zoonotic potential despite having 97-99% similarity at genome level. Here, we describe elements of genetic variation in Brucella ceti isolated from wildlife dolphins inhabiting the Pacific Ocean and the Mediterranean Sea. Comparison with isolates obtained from marine mammals from the Atlantic Ocean and the broader Brucella genus showed distinctive traits according to oceanic distribution and preferred host. Marine mammal isolates display genetic variability, represented by an important number of IS711 elements as well as specific IS711 and SNPs genomic distribution clustering patterns. Extensive pseudogenization was found among isolates from marine mammals as compared with terrestrial ones, causing degradation in pathways related to energy, transport of metabolites, and regulation/transcription. Brucella ceti isolates infecting particularly dolphin hosts, showed further degradation of metabolite transport pathways as well as pathways related to cell wall/membrane/envelope biogenesis and motility. Thus, gene loss through pseudogenization is a source of genetic variation in Brucella, which in turn, relates to adaptation to different hosts. This is relevant to understand the natural history of bacterial diseases, their zoonotic potential, and the impact of human interventions such as domestication. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

High genetic diversity in a potentially vulnerable tropical tree species despite extreme habitat loss.

Directory of Open Access Journals (Sweden)

Annika M E Noreen

Full Text Available Over the last 150 years, Singapore's primary forest has been reduced to less than 0.2% of its previous area, resulting in extinctions of native flora and fauna. Remaining species may be threatened by genetic erosion and inbreeding. We surveyed >95% of the remaining primary forest in Singapore and used eight highly polymorphic microsatellite loci to assess genetic diversity indices of 179 adults (>30 cm stem diameter, 193 saplings (>1 yr, and 1,822 seedlings (<1 yr of the canopy tree Koompassia malaccensis (Fabaceae. We tested hypotheses relevant to the genetic consequences of habitat loss: (1 that the K. malaccensis population in Singapore experienced a genetic bottleneck and a reduction in effective population size, and (2 K. malaccensis recruits would exhibit genetic erosion and inbreeding compared to adults. Contrary to expectations, we detected neither a population bottleneck nor a reduction in effective population size, and high genetic diversity in all age classes. Genetic diversity indices among age classes were not significantly different: we detected overall high expected heterozygosity (He = 0.843-0.854, high allelic richness (R = 16.7-19.5, low inbreeding co-efficients (FIS = 0.013-0.076, and a large proportion (30.1% of rare alleles (i.e. frequency <1%. However, spatial genetic structure (SGS analyses showed significant differences between the adults and the recruits. We detected significantly greater SGS intensity, as well as higher relatedness in the 0-10 m distance class, for seedlings and saplings compared to the adults. Demographic factors for this population (i.e. <200 adult trees are a cause for concern, as rare alleles could be lost due to stochastic factors. The high outcrossing rate (tm = 0.961, calculated from seedlings, may be instrumental in maintaining genetic diversity and suggests that pollination by highly mobile bee species in the genus Apis may provide resilience to acute habitat loss.

Could refuge theory and rivers acting as barriers explain the genetic variability distribution in the Atlantic Forest?

Science.gov (United States)

Cazé, Ana Luiza R; Mäder, Geraldo; Nunes, Teonildes S; Queiroz, Luciano P; de Oliveira, Guilherme; Diniz-Filho, José Alexandre F; Bonatto, Sandro L; Freitas, Loreta B

2016-08-01

The Atlantic Forest is one of the most species-rich ecoregions in the world. The historical origins of this richness and the evolutionary processes that produced diversification and promoted speciation in this ecosystem remain poorly understood. In this context, focusing on Passiflora contracta, an endemic species from the Atlantic Forest distributed exclusively at sea level along forest edges, this study aimed to characterize the patterns of genetic variability and explore two hypotheses that attempt to explain the possible causes of the genetic diversity in this region: the refuge and riverine barrier theories. We employed Bayesian methods combined with niche modeling to identify genetically homogeneous groups, to determine the diversification age, and identify long-term climate stability areas to species survival. The analyses were performed using molecular markers from nuclear and plastid genomes, with samples collected throughout the entire geographic distribution of the species, and comparisons with congeners species. The results indicated that populations were genetically structured and provided evidence of demographic stability. The molecular markers indicated the existence of a clear structure and the presence of five homogeneous groups. Interestingly, the separation of the groups coincides with the geographical locations of local rivers, corroborating the hypothesis of rivers acting as barriers to gene flow in this species. The highest levels of genetic diversity and the areas identified as having long-term climate stability were found in the same region reported for other species as a possible refuge area during the climatic changes of the Quaternary. Copyright © 2016 Elsevier Inc. All rights reserved.

Beta activity measurements in high, variable gamma backgrounds

International Nuclear Information System (INIS)

Stanga, D.; Sandu, E.; Craciun, L.

1997-01-01

In many cases beta activity measurements must be performed in high and variable gamma backgrounds. In such instances it is necessary to use well-shielded detectors but this technique is limited to laboratory equipment and frequently insufficient. In order to perform in a simple manner beta activity measurements in high and variable backgrounds a software-aided counting technique have been developed and a counting system have been constructed. This technique combines the different counting techniques with traditional method of successive measurement of the sample and background. The counting system is based on a programmable multi-scaler which is endowed with appropriate software and allow all operations to be performed via keyboard in an interactive fashion. Two large - area proportional detectors were selected in order to have the same background and the same gamma response within 5%. A program has been developed for the counting data analysis and beta activity computing. The software-aided counting technique has been implemented for beta activity measurement in high and variable backgrounds. (authors)

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.

Induction and selection of superior genetic variables of oil seed rape (brassica napus L.)

International Nuclear Information System (INIS)

Shah, S.S.; Ali, I.; Rehman, K.

1990-01-01

Dry and uniform seeds of two rape seed varieties, Ganyou-5 and Tower, were subjected to different doses of gamma rays. Genetic variation in yield and yield components generated in M1 was studied in M2 and 30 useful variants were isolated from a large magnetized population. The selected mutants were progeny tested for stability of the characters in M3. Only five out of 30 progenies were identified to be uniform and stable. Further selection was made in the segregating m3 progenies. Results on some of the promising mutants are reported. The effect of irradiation treatment was highly pronounced on pod length, seeds per pod and 1000-seed weight. The genetic changes thus induced would help to evolve high yielding versions of different rape seed varieties under local environmental conditions. (author)

Comparison of maternal omentin-1 levels and genetic variability between spontaneous term and preterm births.

Science.gov (United States)

Šplíchal, Zbyněk; Zlámal, Filip; Máchal, Jan; Lipková, Jolana; Pavlová, Tereza; Hodická, Zuzana; Ventruba, Pavel; Vašků, Anna; Bienertová-Vašků, Julie

2018-07-01

To determine maternal omentin-1 levels and genetic variability in the omentin-1 gene in women with spontaneous term and preterm births (PTBs). Maternal serum omentin-1 levels and the role of the omentin-1 Val109Asp (rs2274907) polymorphism were evaluated in 32 women with spontaneous term birth (sTB) and 30 women with spontaneous preterm birth (sPTB) including women with (n = 16) and without (n = 14) preterm premature rupture of membranes (PPROM). Maternal omentin-1 levels were significantly lower in women with sPTBs compared to term births during the hospitalization period (p = .015). However, maternal omentin-1 levels were similar in women with sPTBs with and without PPROM (p = .990). Furthermore, the omentin-1 Val109Asp polymorphism was found to have no significant effect on omentin-1 serum levels. In addition, no significant differences in genotype distributions and allelic frequencies between sTB and sPTB were established. High omentin-1 levels in normal sTBs compared to PTBs without significant differences between cases with and without PPROM suggest that omentin-1 plays a potential role in the pathophysiology of PTB but not in the PPROM mechanism itself.

Studies of genetic variability of the glucose transporter 2 promoter in patients with type 2 diabetes mellitus

DEFF Research Database (Denmark)

Møller, A M; Jensen, N M; Pildal, J

2001-01-01

This study was performed to test the hypothesis that genetic variation in the promoter of the glucose transporter 2 (GLUT2) might predispose to prediabetic phenotypes or type 2 diabetes. A total of 1611 bp comprising the minimal promoter region of the GLUT2 gene were examined by combined single......-tolerant subjects. In conclusion, we found no evidence supporting the hypothesis that genetic variability in the minimal promoter of the GLUT2 is associated with type 2 diabetes or prediabetic phenotypes in the Danish population.......-strand conformational polymorphism and heteroduplex analysis followed by direct sequencing of identified variants on genomic DNA from 96 randomly recruited Danish type 2 diabetic patients. We identified 4 nucleotide variants, -447g-->a, -149c-->a, -122t-->c, and -44g-->a. None of the variants were positioned in known...

Minimal approaches to genetic improvement of growth rates in white spruce

Science.gov (United States)

D.T. Lester

1973-01-01

Several features of central importance to genetic improvement of white spruce have been demonstrated by tree breeders. First, white spruce is genetically a highly variable species and much of the existent variation can be readily incorporated in planting stock (Jeffers 1969, Holst and Teich 1969). Second, local seed often is not the best for rapid growth (Nienstaedt...

Genetic structure and gene flow among Komodo dragon populations inferred by microsatellite loci analysis.

Science.gov (United States)

Ciofi, C; Bruford, M W

1999-12-01

A general concern for the conservation of endangered species is the maintenance of genetic variation within populations, particularly when they become isolated and reduced in size. Estimates of gene flow and effective population size are therefore important for any conservation initiative directed to the long-term persistence of a species in its natural habitat. In the present study, 10 microsatellite loci were used to assess the level of genetic variability among populations of the Komodo dragon Varanus komodoensis. Effective population size was calculated and gene flow estimates were compared with palaeogeographic data in order to assess the degree of vulnerability of four island populations. Rinca and Flores, currently separated by an isthmus of about 200 m, retained a high level of genetic diversity and showed a high degree of genetic similarity, with gene flow values close to one migrant per generation. The island of Komodo showed by far the highest levels of genetic divergence, and its allelic distinctiveness was considered of great importance in the maintenance of genetic variability within the species. A lack of distinct alleles and low levels of gene flow and genetic variability were found for the small population of Gili Motang island, which was identified as vulnerable to stochastic threats. Our results are potentially important for both the short- and long-term management of the Komodo dragon, and are critical in view of future re-introduction or augmentation in areas where the species is now extinct or depleted.

Phenotypic variability in a population of globe artichoke

Directory of Open Access Journals (Sweden)

Angélica Reolon da Costa

2014-11-01

Full Text Available The existence of variability is a prerequisite for genetic improvement in plants. Globe artichoke is a high nutritious vegetable with medical value, representing a profitable alternative for rural producers. This research was conducted with the aim of evaluating the phenotypic variability in a commercial cultivar of artichoke (Cynara cardunculus var. scolymus L established from seeds. Field plants were assessed when primary head reached commercial stage. An amount of 21 quantitative and 5 multicategoric characters were assessed. The quantitative data were submitted to multivariate analysis. For quantitative characters the distance between individuals varied from 3.0 to 50.9, revealing high intrapopulation variability. The greater relative contribution characters for genetic divergence were the primary head fresh mass (79.88% and bottom fresh mass (8.43%. This indicates the possibility of plant selection for head quality in this population. The clustering analysis through UPGMA method, based on quantitative characters, allowed the formation of five groups. For multicategoric traits, the similarity among individuals varied from 1.22% to 100%. Within the existing population variability, it was possible to select plants with superior quantitative traits desirable for in natura consumption, as primary head fresh weight and length, bottom fresh mass, bract basis length and width, as well as non-quantitative traits as round head shape, absence of thorn and presence of violet color in the head.

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.

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.

GENETIC, PATHOGENIC AND TOXIGENIC VARIABILITY OF F

African Journals Online (AJOL)

Vesna Krnjaja

2012-03-08

Mar 8, 2012 ... The same authors concluded that natural populations of F. proliferatum in Iran were probably genetically divergent and included isolates representing a potential risk for disease development. Elmer (1991) and Elmer et al. (1999) collected 110 and. 77 isolates of F. proliferatum from asparagus originating.

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.

Complex spatial dynamics maintain northern leopard frog (Lithobates pipiens) genetic diversity in a temporally varying landscape

Science.gov (United States)

Mushet, David M.; Euliss, Ned H.; Chen, Yongjiu; Stockwell, Craig A.

2013-01-01

In contrast to most local amphibian populations, northeastern populations of the Northern Leopard Frog (Lithobates pipiens) have displayed uncharacteristically high levels of genetic diversity that have been attributed to large, stable populations. However, this widely distributed species also occurs in areas known for great climatic fluctuations that should be reflected in corresponding fluctuations in population sizes and reduced genetic diversity. To test our hypothesis that Northern Leopard Frog genetic diversity would be reduced in areas subjected to significant climate variability, we examined the genetic diversity of L. pipiens collected from 12 sites within the Prairie Pothole Region of North Dakota. Despite the region's fluctuating climate that includes periods of recurring drought and deluge, we found unexpectedly high levels of genetic diversity approaching that of northeastern populations. Further, genetic structure at a landscape scale was strikingly homogeneous; genetic differentiation estimates (Dest) averaged 0.10 (SD = 0.036) across the six microsatellite loci we studied, and two Bayesian assignment tests (STRUCTURE and BAPS) failed to reveal the development of significant population structure across the 68 km breadth of our study area. These results suggest that L. pipiens in the Prairie Pothole Region consists of a large, panmictic population capable of maintaining high genetic diversity in the face of marked climate variability.

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

KAUST Repository

Ragab, Alaa I.

2013-05-01

The whitefly Bemisia tabaci species complex has been well documented as one of the most economically important emergent plant virus vectors, through serious feeding damage to its broad range of plant hosts and transmission of plant viruses to important agricultural crops. It has been shown to have associations with endosymbionts which have significant effects on the insect fitness. The purpose of this study was to provide information for the biotype and secondary endosymbiont distribution for B. tabaci populations in the relatively unstudied Arabian peninsula. The geographical localization and variation in endosymbiont populations across the region were identified using a sequence-driven analysis of the population genetics of the secondary endosymbiont. Live field specimens were collected from 22 different locations in the region and preserved in 70% ethanol for genetic studies. Previously established procedures were used to extract and purify total insect DNA from 24-30 individual whiteflies for each location (Frohlich et al., 1999; Chiel et al., 2007). Specimens were subjected to PCR amplification using the respective 16S rDNAprimers for the Rickettsia, Hamiltonella, and Wolbachia to amplify endosymbiont DNA. PCR was run with primers for the highly conserved whitefly mitochondrial cytochrome oxidase subunit I (COI) gene for biotyping. Samples were sequenced using the Sanger method and the data analyzed to correlate the presence, prevalence and geographical distribution of endosymbionts in B. tabaci. Phylogenies 5 were constructed to track evolutionary differences amongst the endosymbionts and insects and how they have influenced the evolution of the regional populations. Samples were characterized by differences in the genomes and endosymbionts of common whitefly ‘biotypes’ that have different host plant preferences, vector capacities and insecticide resistance characteristics. It was found that the B biotype is the predominant haplotype, with no evidence of

A High-Level Petri Net Framework for Genetic Regulatory Networks

Directory of Open Access Journals (Sweden)

Banks Richard

2007-12-01

Full Text Available To understand the function of genetic regulatory networks in the development of cellular systems, we must not only realise the individual network entities, but also the manner by which they interact. Multi-valued networks are a promising qualitative approach for modelling such genetic regulatory networks, however, at present they have limited formal analysis techniques and tools. We present a flexible formal framework for modelling and analysing multi-valued genetic regulatory networks using high-level Petri nets and logic minimization techniques. We demonstrate our approach with a detailed case study in which part of the genetic regulatory network responsible for the carbon starvation stress response in Escherichia coli is modelled and analysed. We then compare and contrast this multivalued model to a corresponding Boolean model and consider their formal relationship.

Morphological and genetics analysis of Stachys sylvatica (Lamiaceae coenopopulations in the mountains of South Siberia

Directory of Open Access Journals (Sweden)

I. E. Yamskikh

2016-03-01

Full Text Available Stachys sylvatica is Tertiary nemoral relict from the Sout Siberian mountains. Modification and genetic variability of 11 Stachys sylvatica populations from South Siberian mountains were studied. Investigations revealed that S. sylvatica grew in coniferous (spruce, pine, Siberian stone pine, fir, and mixed forests, aspen, linden forests and floodplain habitats. Climatic area of the species is limited to an annual precipitation of 500–1250 mm, effective heat sum 1600–2050 ºC and altitude from 150 to 700 m a.s.l. In the study of the state of the S. sylvatica coenopopulations we determined the population size, projective cover, evaluated the morphological variability of vegetative and genera­tive characteristics. To establish the significance of differences between the average values of the same characters we used ANOVA. It was revealed that most of the morphometric characters had medium and high level of variability. The genetic variability of species we detected by RAF-PCR method (Randomly Amplified DNA Fingerprinting. The analysis of genetic variation of the S. sylvatica coenopopulations showed that the studied species was characterized by a very high level of intra-population polymorphism. The maximum level of genetic variability was observed in the population growing on the border of the species area. Gene pools of all studied coenopopulations have a satisfactory condition and can be reproduced by itself. All studied coenopopulations of Stachys sylvatica are poorly differenti­ated and do not show the tendency to the formation of new taxa. Moreover, a similar genetic structure we have seen in the coenopopulations growing not only in different parts of the area, but also in communities radically different in environmental and phytocenotic conditions. With increasing of anthropogenic impact on coenopopulations we have observed an increase of the size of the generative organs of Stachys sylvatica. The separation of individuals on a

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

Science.gov (United States)

Nóbrega de Sousa, Taís; Carvalho, Luzia Helena; Alves de Brito, Cristiana Ferreira

2011-01-01

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.

Rangewide Genetic Variation in Coast Redwood Populations at a Chloroplast Microsatellite Locus

Science.gov (United States)

Chris Brinegar

2012-01-01

Old growth and second growth populations of coast redwood (Sequoia sempervirens) were sampled at 10 locations throughout its range and analyzed at a highly variable chloroplast microsatellite locus. Very low FST values indicated that there was no significant genetic differentiation between adjacent old growth and second growth populations at each location. Genetic...

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

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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.

Genetic variability in the human cannabinoid receptor 1 is associated with resting state EEG theta power in humans.

Science.gov (United States)

Heitland, I; Kenemans, J L; Böcker, K B E; Baas, J M P

2014-11-01

It has long been postulated that exogenous cannabinoids have a profound effect on human cognitive functioning. These cannabinoid effects are thought to depend, at least in parts, on alterations of phase-locking of local field potential neuronal firing. The latter can be measured as activity in the theta frequency band (4-7Hz) by electroencephalogram. Theta oscillations are supposed to serve as a mechanism in neural representations of behaviorally relevant information. However, it remains unknown whether variability in endogenous cannabinoid activity is involved in theta rhythms and therefore, may serve as an individual differences index of human cognitive functioning. To clarify this issue, we recorded resting state EEG activity in 164 healthy human subjects and extracted EEG power across frequency bands (δ, θ, α, and β). To assess variability in the endocannabinoid system, two genetic polymorphisms (rs1049353, rs2180619) within the cannabinoid receptor 1 (CB1) were determined in all participants. As expected, we observed significant effects of rs1049353 on EEG power in the theta band at frontal, central and parietal electrode regions. Crucially, these effects were specific for the theta band, with no effects on activity in the other frequency bands. Rs2180619 showed no significant associations with theta power after Bonferroni correction. Taken together, we provide novel evidence in humans showing that genetic variability in the cannabinoid receptor 1 is associated with resting state EEG power in the theta frequency band. This extends prior findings of exogenous cannabinoid effects on theta power to the endogenous cannabinoid system. Copyright © 2014 Elsevier B.V. All rights reserved.

High Turndown Ratio, High Delta-Emittance, Variable Emissivity Electrochromics, Phase I

Data.gov (United States)

National Aeronautics and Space Administration — Variable-emittance materials are in high demand for applications ranging from manned and unmanned space platforms (e.g. in radiators at the Moon's poles where damage...

Air temperature variability in a high-elevation Himalayan catchment

NARCIS (Netherlands)

Heynen, Martin; Miles, Evan; Ragettli, Silvan; Buri, Pascal; Immerzeel, Walter W.; Pellicciotti, Francesca

2016-01-01

Air temperature is a key control of processes affecting snow and glaciers in high-elevation catchments, including melt, snowfall and sublimation. It is therefore a key input variable to models of land-surface-atmosphere interaction. Despite this importance, its spatial variability is poorly

Isoenzymatic variability in tropical maize populations under reciprocal recurrent selection

Directory of Open Access Journals (Sweden)

Pinto Luciana Rossini

2003-01-01

Full Text Available Maize (Zea mays L. is one of the crops in which the genetic variability has been extensively studied at isoenzymatic loci. The genetic variability of the maize populations BR-105 and BR-106, and the synthetics IG-3 and IG-4, obtained after one cycle of a high-intensity reciprocal recurrent selection (RRS, was investigated at seven isoenzymatic loci. A total of twenty alleles were identified, and most of the private alleles were found in the BR-106 population. One cycle of reciprocal recurrent selection (RRS caused reductions of 12% in the number of alleles in both populations. Changes in allele frequencies were also observed between populations and synthetics, mainly for the Est 2 locus. Populations presented similar values for the number of alleles per locus, percentage of polymorphic loci, and observed and expected heterozygosities. A decrease of the genetic variation values was observed for the synthetics as a consequence of genetic drift effects and reduction of the effective population sizes. The distribution of the genetic diversity within and between populations revealed that most of the diversity was maintained within them, i.e. BR-105 x BR-106 (G ST = 3.5% and IG-3 x IG-4 (G ST = 4.0%. The genetic distances between populations and synthetics increased approximately 21%. An increase in the genetic divergence between the populations occurred without limiting new selection procedures.

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.

Prediction of composite fatigue life under variable amplitude loading using artificial neural network trained by genetic algorithm

Science.gov (United States)

Rohman, Muhamad Nur; Hidayat, Mas Irfan P.; Purniawan, Agung

2018-04-01

Neural networks (NN) have been widely used in application of fatigue life prediction. In the use of fatigue life prediction for polymeric-base composite, development of NN model is necessary with respect to the limited fatigue data and applicable to be used to predict the fatigue life under varying stress amplitudes in the different stress ratios. In the present paper, Multilayer-Perceptrons (MLP) model of neural network is developed, and Genetic Algorithm was employed to optimize the respective weights of NN for prediction of polymeric-base composite materials under variable amplitude loading. From the simulation result obtained with two different composite systems, named E-glass fabrics/epoxy (layups [(±45)/(0)2]S), and E-glass/polyester (layups [90/0/±45/0]S), NN model were trained with fatigue data from two different stress ratios, which represent limited fatigue data, can be used to predict another four and seven stress ratios respectively, with high accuracy of fatigue life prediction. The accuracy of NN prediction were quantified with the small value of mean square error (MSE). When using 33% from the total fatigue data for training, the NN model able to produce high accuracy for all stress ratios. When using less fatigue data during training (22% from the total fatigue data), the NN model still able to produce high coefficient of determination between the prediction result compared with obtained by experiment.

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

Science.gov (United States)

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

2017-09-21

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

Genetic influences on level and stability of self-esteem

OpenAIRE

Neiss, Michelle; Sedikides, Constantine; Stevenson, Jim

2006-01-01

We attempted to clarify the relation between self-esteem level (high vs. low) and perceived self-esteem stability (within-person variability) by using a behavioral genetics approach. We tested whether the same or independent genetic and environmental influences impact on level and stability. Adolescent twin siblings (n = 183 pairs) completed level and stability scales at two time points. Heritability for both was substantial. The remaining variance in each was attributable to non-shared envir...

Microsatellite markers suggest high genetic diversity in an urban ...

Indian Academy of Sciences (India)

FRANCISCO MORINHA

diversity in an urban population of Cooper's hawks (Accipiter cooperii). J. Genet. 95, e19–e24. ... high quality habitat for this species (Boggie and Mannan. 2014) and the rapid ... The high densities of birds in urban populations can result in the ..... comparing urban and rural Cooper's hawk populations are mandatory to ...

Use of genetic algorithms for high hydrostatic pressure inactivation ...

African Journals Online (AJOL)

) for high hydrostatic pressure (HHP) inactivation of Bacillus cereus spores, Bacillus subtilis spores and cells, Staphylococcus aureus and Listeria monocytogenes, all in milk buffer, were used to demonstrate the utility of genetic algorithms ...

Genetic Alterations and Their Clinical Implications in High-Recurrence Risk Papillary Thyroid Cancer.

Science.gov (United States)

Lee, Min-Young; Ku, Bo Mi; Kim, Hae Su; Lee, Ji Yun; Lim, Sung Hee; Sun, Jong-Mu; Lee, Se-Hoon; Park, Keunchil; Oh, Young Lyun; Hong, Mineui; Jeong, Han-Sin; Son, Young-Ik; Baek, Chung-Hwan; Ahn, Myung-Ju

2017-10-01

Papillary thyroid carcinomas (PTCs) frequently involve genetic alterations. The objective of this study was to investigate genetic alterations and further explore the relationships between these genetic alterations and clinicopathological characteristics in a high-recurrence risk (node positive, N1) PTC group. Tumor tissue blocks were obtained from 240 surgically resected patients with histologically confirmed stage III/IV (pT3/4 or N1) PTCs. We screened gene fusions using NanoString's nCounter technology and mutational analysis was performed by direct DNA sequencing. Data describing the clinicopathological characteristics and clinical courses were retrospectively collected. Of the 240 PTC patients, 207 (86.3%) had at least one genetic alteration, including BRAF mutation in 190 patients (79.2%), PIK3CA mutation in 25 patients (10.4%), NTRK1/3 fusion in six patients (2.5%), and RET fusion in 24 patients (10.0%). Concomitant presence of more than two genetic alterations was seen in 36 patients (15%). PTCs harboring BRAF mutation were associated with RET wild-type expression (p=0.001). RET fusion genes have been found to occur with significantly higher frequency in N1b stage patients (p=0.003) or groups of patients aged 45 years or older (p=0.031); however, no significant correlation was found between other genetic alterations. There was no trend toward favorable recurrence-free survival or overall survival among patients lacking genetic alterations. In the selected high-recurrence risk PTC group, most patients had more than one genetic alteration. However, these known alterations could not entirely account for clinicopathological features of high-recurrence risk PTC.

Plasmodium vivax merozoite surface protein-3 alpha: a high-resolution marker for genetic diversity studies.

Science.gov (United States)

Prajapati, Surendra Kumar; Joshi, Hema; Valecha, Neena

2010-06-01

Malaria, an ancient human infectious disease caused by five species of Plasmodium, among them Plasmodium vivax is the most widespread human malaria species and causes huge morbidity to its host. Identification of genetic marker to resolve higher genetic diversity for an ancient origin organism is a crucial task. We have analyzed genetic diversity of P. vivax field isolates using highly polymorphic antigen gene merozoite surface protein-3 alpha (msp-3 alpha) and assessed its suitability as high-resolution genetic marker for population genetic studies. 27 P. vivax field isolates collected during chloroquine therapeutic efficacy study at Chennai were analyzed for genetic diversity. PCR-RFLP was employed to assess the genetic variations using highly polymorphic antigen gene msp-3 alpha. We observed three distinct PCR alleles at msp-3 alpha, and among them allele A showed significantly high frequency (53%, chi2 = 8.22, p = 0.001). PCR-RFLP analysis revealed 14 and 17 distinct RFLP patterns for Hha1 and Alu1 enzymes respectively. Further, RFLP analysis revealed that allele A at msp-3 alpha is more diverse in the population compared with allele B and C. Combining Hha1 and Alu1 RFLP patterns revealed 21 distinct genotypes among 22 isolates reflects higher diversity resolution power of msp-3 alpha in the field isolates. P. vivax isolates from Chennai region revealed substantial amount of genetic diversity and comparison of allelic diversity with other antigen genes and microsatellites suggesting that msp-3 alpha could be a high-resolution marker for genetic diversity studies among P. vivax field isolates.

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.

Olfactory map formation in the Drosophila brain: genetic specificity and neuronal variability.

Science.gov (United States)

Brochtrup, Anna; Hummel, Thomas

2011-02-01

The development of the Drosophila olfactory system is a striking example of how genetic programs specify a large number of different neuron types and assemble them into functional circuits. To ensure precise odorant perception, each sensory neuron has to not only select a single olfactory receptor (OR) type out of a large genomic repertoire but also segregate its synaptic connections in the brain according to the OR class identity. Specification and patterning of second-order interneurons in the olfactory brain center occur largely independent of sensory input, followed by a precise point-to-point matching of sensory and relay neurons. Here we describe recent progress in the understanding of how cell-intrinsic differentiation programs and context-dependent cellular interactions generate a stereotyped sensory map in the Drosophila brain. Recent findings revealed an astonishing morphological diversity among members of the same interneuron class, suggesting an unexpected variability in local microcircuits involved in insect sensory processing. Copyright © 2010 Elsevier Ltd. All rights reserved.

High-Speed Photo-Polarimetry of Magnetic Cataclysmic Variables

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S. B. Potter

2015-02-01

Full Text Available I review recent highlights of the SAAO High-speed Photo-POlarimeter (HIPPO on the study of magnetic Cataclysmic Variables. Its high-speed capabilities are demonstrated with example observations made of the intermediate polar NY Lup and the polar IGRJ14536-5522.

Genetic and non-genetic correlates of vitamins K and D.

Science.gov (United States)

Shea, M K; Benjamin, E J; Dupuis, J; Massaro, J M; Jacques, P F; D'Agostino, R B; Ordovas, J M; O'Donnell, C J; Dawson-Hughes, B; Vasan, R S; Booth, S L

2009-04-01

To assess the genetic and nongenetic correlates of circulating measures of vitamins K and D status in a community-based sample of men and women. A cross-sectional study of 1762 participants of the Framingham Offspring Study (919 women; mean age 59 years). Vitamin K status was measured as plasma phylloquinone and serum percent undercarboxylated osteocalcin (ucOC), and vitamin D was measured using plasma 25-hydroxyvitamin D (25(OH)D). Associations between vitamin K status and vitamin D status with biologically plausible nongenetic factors were assessed using stepwise regression. Heritability and linkage were determined using Sequential Oligogenic Linkage Analysis Routines (SOLAR). Nongenetic factors accounted for 20.1 and 12.3% of the variability in plasma phylloquinone in men and women respectively, with triglycerides and phylloquinone intake being the primary correlates. In men 12.2% and in women 14.6% of the variability in %ucOC was explained by nongenetic factors in our models. Heritability estimates for these vitamin K status biomarkers were nonsignificant. Season, vitamin D intake, high-density lipoprotein (HDL) cholesterol and waist circumference explained 24.7% (men) and 24.2% (women) of the variability in plasma 25(OH)D. Of the three vitamins examined, only 25(OH)D was significantly heritable (heritability estimate=28.8%, Pvitamin K status was attributed to nongenetic factors, whereas plasma 25(OH)D was found to be significantly heritable. Further studies are warranted to investigate genetic loci influencing vitamin D status.

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.

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

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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

Variability induced by spaceflight environment on high oil and normal maize lines

International Nuclear Information System (INIS)

Xu Xiaowei; Xu Li; Dong Xin; Jin Weiwei; Chen Shaojiang

2011-01-01

High oil inbred line BY815 and two normal inbred lines 1145 and F349 treated with spaceflight were used for variability analysis. Results showed that the mutation rate of BY815 was 21.61% in SP 1 , while the mutation rates of 1145 and F349 were 2.57% and 3.13% respectively. Only six mutants were found from these three materials in SP 2 , of which two mutants, HT-3 from BY815 exhibiting albino leaf color and HT-5 from 1145 exhibiting stripe-like spots leaves, were worthy of further study. Genetic analysis of the two mutants showed that the segregation ratio of normal and mutant phenotypes was 3 : 1, which was in accordance with Mendel's single gene inheritance law. Cytological observation of all the six mutants showed no chromosome abnormalities. By using SSR (simple sequence repeat) method, 130 pairs of primers were employed and only one mutant originated from inbred line 1145 showed polymorphic and the mutated loci rate of the genome in this mutant was 8.46%. (authors)

The Information Content of Discrete Functions and Their Application in Genetic Data Analysis.

Science.gov (United States)

Sakhanenko, Nikita A; Kunert-Graf, James; Galas, David J

2017-12-01

The complex of central problems in data analysis consists of three components: (1) detecting the dependence of variables using quantitative measures, (2) defining the significance of these dependence measures, and (3) inferring the functional relationships among dependent variables. We have argued previously that an information theory approach allows separation of the detection problem from the inference of functional form problem. We approach here the third component of inferring functional forms based on information encoded in the functions. We present here a direct method for classifying the functional forms of discrete functions of three variables represented in data sets. Discrete variables are frequently encountered in data analysis, both as the result of inherently categorical variables and from the binning of continuous numerical variables into discrete alphabets of values. The fundamental question of how much information is contained in a given function is answered for these discrete functions, and their surprisingly complex relationships are illustrated. The all-important effect of noise on the inference of function classes is found to be highly heterogeneous and reveals some unexpected patterns. We apply this classification approach to an important area of biological data analysis-that of inference of genetic interactions. Genetic analysis provides a rich source of real and complex biological data analysis problems, and our general methods provide an analytical basis and tools for characterizing genetic problems and for analyzing genetic data. We illustrate the functional description and the classes of a number of common genetic interaction modes and also show how different modes vary widely in their sensitivity to noise.

Variability of Cutaneous Leishmaniasis Lesions Is Not Associated with Genetic Diversity of Leishmania tropica in Khyber Pakhtunkhwa Province of Pakistan.

Science.gov (United States)

Khan, Nazma Habib; Llewellyn, Martin S; Schönian, Gabriele; Sutherland, Colin J

2017-11-01

Leishmania tropica is the causative agent of cutaneous leishmaniasis in Pakistan. Here, intraspecific diversity of L. tropica from northern Pakistan was investigated using multilocus microsatellite typing. Fourteen polymorphic microsatellite markers were typed in 34 recently collected L. tropica isolates from Pakistan along with 158 archival strains of diverse Afro-Eurasian origins. Previously published profiles for 145 strains of L. tropica originating from different regions of Africa, Central Asia, Iran, and Middle East were included for comparison. Six consistently well-supported genetic groups were resolved: 1) Asia, 2) Morroco A, 3) Namibia and Kenya A, 4) Kenya B/Tunisia and Galilee, 5) Morocco B, and 6) Middle East. Strains from northern Pakistan were assigned to Asian cluster except for three that were placed in a geographically distant genetic group; Morocco A. Lesion variability among these Pakistani strains was not associated with specific L. tropica genetic profile. Pakistani strains showed little genetic differentiation from strains of Iraq, Afghanistan, and Syria (F ST = 0.00-0.06); displayed evidence of modest genetic flow with India (F ST = 0.14). Furthermore, genetic structuring within these isolates was not geographically defined. Pak-Afghan cluster was in significant linkage disequilibrium (I A = 1.43), had low genetic diversity, and displayed comparatively higher heterozygosity (F IS = -0.62). Patterns of genetic diversity observed suggest dominance of a minimally diverse clonal lineage within northern Pakistan. This is surprising as a wide clinical spectrum was observed in patients, suggesting the importance of host and other factors. Further genotyping studies of L. tropica isolates displaying different clinical phenotypes are required to validate this potentially important observation.

A Massively Parallel Sequencing Approach Uncovers Ancient Origins and High Genetic Variability of Endangered Przewalski's Horses

OpenAIRE

Goto, Hiroki; Ryder, Oliver A.; Fisher, Allison R.; Schultz, Bryant; Kosakovsky Pond, Sergei L.; Nekrutenko, Anton; Makova, Kateryna D.

2011-01-01

The endangered Przewalski's horse is the closest relative of the domestic horse and is the only true wild horse species surviving today. The question of whether Przewalski's horse is the direct progenitor of domestic horse has been hotly debated. Studies of DNA diversity within Przewalski's horses have been sparse but are urgently needed to ensure their successful reintroduction to the wild. In an attempt to resolve the controversy surrounding the phylogenetic position and genetic diversity o...

High and distinct range-edge genetic diversity despite local bottlenecks.

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Jorge Assis

Full Text Available The genetic consequences of living on the edge of distributional ranges have been the subject of a largely unresolved debate. Populations occurring along persistent low latitude ranges (rear-edge are expected to retain high and unique genetic diversity. In contrast, currently less favourable environmental conditions limiting population size at such range-edges may have caused genetic erosion that prevails over past historical effects, with potential consequences on reducing future adaptive capacity. The present study provides an empirical test of whether population declines towards a peripheral range might be reflected on decreasing diversity and increasing population isolation and differentiation. We compare population genetic differentiation and diversity with trends in abundance along a latitudinal gradient towards the peripheral distribution range of Saccorhiza polyschides, a large brown seaweed that is the main structural species of kelp forests in SW Europe. Signatures of recent bottleneck events were also evaluated to determine whether the recently recorded distributional shifts had a negative influence on effective population size. Our findings show decreasing population density and increasing spatial fragmentation and local extinctions towards the southern edge. Genetic data revealed two well supported groups with a central contact zone. As predicted, higher differentiation and signs of bottlenecks were found at the southern edge region. However, a decrease in genetic diversity associated with this pattern was not verified. Surprisingly, genetic diversity increased towards the edge despite bottlenecks and much lower densities, suggesting that extinctions and recolonizations have not strongly reduced diversity or that diversity might have been even higher there in the past, a process of shifting genetic baselines.

Mitochondrial DNA variability among eight Tikúna villages: evidence for an intratribal genetic heterogeneity pattern.

Science.gov (United States)

Mendes-Junior, Celso Teixeira; Simões, Aguinaldo Luiz

2009-11-01

To study the genetic structure of the Tikúna tribe, four major Native American mitochondrial DNA (mtDNA) founder haplogroups were analyzed in 187 Amerindians from eight Tikúna villages located in the Brazilian Amazon. The central position of these villages in the continent makes them relevant for attempts to reconstruct population movements in South America. In this geographic region, there is particular concern regarding the genetic structure of the Tikúna tribe, formerly designated "enigmatic" due to its remarkable degree of intratribal homogeneity and the scarcity of private protein variants. In spite of its large population size and geographic distribution, the Tikúna tribe presents marked genetic and linguistic isolation. All individuals presented indigenous mtDNA haplogroups. An intratribal genetic heterogeneity pattern characterized by two highly homogeneous Tikúna groups that differ considerably from each other was observed. Such a finding was unexpected, since the Tikúna tribe is characterized by a social system that favors intratribal exogamy and patrilocality that would lead to a higher female migration rate and homogenization of the mtDNA gene pool. Demographic explosions and religious events, which significantly changed the sizes and compositions of many Tikúna villages, may be reflected in the genetic results presented here.

Spatial heterogeneity as a genetic mixing mechanism in highly philopatric colonial seabirds.

Science.gov (United States)

Cristofari, Robin; Trucchi, Emiliano; Whittington, Jason D; Vigetta, Stéphanie; Gachot-Neveu, Hélène; Stenseth, Nils Christian; Le Maho, Yvon; Le Bohec, Céline

2015-01-01

How genetic diversity is maintained in philopatric colonial systems remains unclear, and understanding the dynamic balance of philopatry and dispersal at all spatial scales is essential to the study of the evolution of coloniality. In the King penguin, Aptenodytes patagonicus, return rates of post-fledging chicks to their natal sub-colony are remarkably high. Empirical studies have shown that adults return year after year to their previous breeding territories within a radius of a few meters. Yet, little reliable data are available on intra- and inter-colonial dispersal in this species. Here, we present the first fine-scale study of the genetic structure in a king penguin colony in the Crozet Archipelago. Samples were collected from individual chicks and analysed at 8 microsatellite loci. Precise geolocation data of hatching sites and selective pressures associated with habitat features were recorded for all sampling locations. We found that despite strong natal and breeding site fidelity, king penguins retain a high degree of panmixia and genetic diversity. Yet, genetic structure appears markedly heterogeneous across the colony, with higher-than-expected inbreeding levels, and local inbreeding and relatedness hotspots that overlap predicted higher-quality nesting locations. This points towards heterogeneous population structure at the sub-colony level, in which fine-scale environmental features drive local philopatric behaviour, while lower-quality patches may act as genetic mixing mechanisms at the colony level. These findings show how a lack of global genetic structuring can emerge from small-scale heterogeneity in ecological parameters, as opposed to the classical model of homogeneous dispersal. Our results also emphasize the importance of sampling design for estimation of population parameters in colonial seabirds, as at high spatial resolution, basic genetic features are shown to be location-dependent. Finally, this study stresses the importance of

Spatial heterogeneity as a genetic mixing mechanism in highly philopatric colonial seabirds.

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Robin Cristofari

Full Text Available How genetic diversity is maintained in philopatric colonial systems remains unclear, and understanding the dynamic balance of philopatry and dispersal at all spatial scales is essential to the study of the evolution of coloniality. In the King penguin, Aptenodytes patagonicus, return rates of post-fledging chicks to their natal sub-colony are remarkably high. Empirical studies have shown that adults return year after year to their previous breeding territories within a radius of a few meters. Yet, little reliable data are available on intra- and inter-colonial dispersal in this species. Here, we present the first fine-scale study of the genetic structure in a king penguin colony in the Crozet Archipelago. Samples were collected from individual chicks and analysed at 8 microsatellite loci. Precise geolocation data of hatching sites and selective pressures associated with habitat features were recorded for all sampling locations. We found that despite strong natal and breeding site fidelity, king penguins retain a high degree of panmixia and genetic diversity. Yet, genetic structure appears markedly heterogeneous across the colony, with higher-than-expected inbreeding levels, and local inbreeding and relatedness hotspots that overlap predicted higher-quality nesting locations. This points towards heterogeneous population structure at the sub-colony level, in which fine-scale environmental features drive local philopatric behaviour, while lower-quality patches may act as genetic mixing mechanisms at the colony level. These findings show how a lack of global genetic structuring can emerge from small-scale heterogeneity in ecological parameters, as opposed to the classical model of homogeneous dispersal. Our results also emphasize the importance of sampling design for estimation of population parameters in colonial seabirds, as at high spatial resolution, basic genetic features are shown to be location-dependent. Finally, this study stresses the

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

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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.

Hopes and Expectations Regarding Genetic Testing for Schizophrenia Among Young Adults at Clinical High-Risk for Psychosis.

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Friesen, Phoebe; Lawrence, Ryan E; Brucato, Gary; Girgis, Ragy R; Dixon, Lisa

2016-11-01

Genetic tests for schizophrenia could introduce both risks and benefits. Little is known about the hopes and expectations of young adults at clinical high-risk for psychosis concerning genetic testing for schizophrenia, despite the fact that these youth could be among those highly affected by such tests. We conducted semistructured interviews with 15 young adults at clinical high-risk for psychosis to ask about their interest, expectations, and hopes regarding genetic testing for schizophrenia. Most participants reported a high level of interest in genetic testing for schizophrenia, and the majority said they would take such a test immediately if it were available. Some expressed far-reaching expectations for a genetic test, such as predicting symptom severity and the timing of symptom onset. Several assumed that genetic testing would be accompanied by interventions to prevent schizophrenia. Participants anticipated mixed reactions on finding out they had a genetic risk for schizophrenia, suggesting that they might feel both a sense of relief and a sense of hopelessness. We suggest that genetic counseling could play an important role in counteracting a culture of genetic over-optimism and helping young adults at clinical high-risk for psychosis understand the limitations of genetic testing. Counseling sessions could also invite individuals to explore how receiving genetic risk information might impact their well-being, as early evidence suggests that some psychological factors help individuals cope, whereas others heighten distress related to genetic test results.

Mitochondrial DNA control region variability in wild boars from west Balkans

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Đan Mihajla

2013-01-01

Full Text Available The wild boar (Sus scrofa is one of most abundant game species in hunting areas of Balkan region. The large fraction of pre-glacial genetic diversity in wild boar populations from the Balkans was addressed due to high proportion of unique mtDNA haplotypes found in Greece, indicating Balkan as main refugial area for wild boars. The aim of the present study is to characterize mitochondrial DNA control region variability in wild boars from different areas in the West Balkan region, in order to evaluate level of genetic variability, to detect unique haplotypes and to infer possible structuring. The total number of 163 individuals from different sampling localities were included in the study. A fragment of the mtDNA control region was amplified and sequenced by standard procedures. Population genetic analyses were performed using several computer packages: BioEdit, ARLEQUIN 3.5.1.2., Network 4.6.0.0 and MEGA5. Eleven different haplotypes were identified and haplotype diversity was 0.676, nucleotide diversity 0.0026, and the average number of nucleotide differences (k 1.169. The mismatch distribution and neutrality tests indicated the expansion of the all populations. It is shown that high level of genetic diversity is present in the wild boars from the West Balkan region and we have managed to detect regional unique haplotypes in high frequency. Genetic diversity differences have been found in regional wild boar groups, clustering them in two main clusters, but further speculations on the reasons for the observed clustering are prevented due to restricted informativness of the single locus marker. Obtained knowledge of genetic variation in the wild boar may be relevant for improving knowledge of the phylogeny and phylogeography of the wild boars, but as well as for hunting societies and responsible authorities for the effective control of wild boar populations.

Estimates of genetic parameters and path analysis in lentil (lens culinaris medik)

International Nuclear Information System (INIS)

Younis, N.; Hanif, M.; Sadiq, S.; Abbas, G.; Asghar, M.J.; Haq, M.A.

2008-01-01

These studies were conducted to determine the genetic parameters and character association in elite lines 0 lentil (Lens culinaris Medik).Genetic parameters like genotypic and phenotypic variances, coefficients of variation heritability, genetic advance, correlation coefficients and path coefficients were estimated. Significant variation was noted for all the traits. High heritability estimates were observed for all the traits except number of primary branches per plant. In general phenotypic coefficients of variability were greater than their corresponding genotypic coefficient of variability. Higher estimates of heritability and genetic advance were observed for seed yield (97.10%, 90.71%), harvest index (96.20%, 63.29%) and maturity days (95.90%, 63.39%) indicating the these characters are mainly controlled by additive genes and selection of such traits might be effective for the improvement of seed yield. Days to flower, plant height, number of primary branches, biological yield, harvest index and hundred seed weight had positive direct effect on seed yield. Biological yield, hundred seed weight and harvest index also had positive and highly significant genotypic and phenotypic correlation with seed yield. Hence these traits could be used for the improvement of seed yield resulting in the evolution of high yielding varieties 0 lentil. (author)

Past climate-driven range shifts and population genetic diversity in arctic plants

DEFF Research Database (Denmark)

Pellissier, Loïc; Eidesen, Pernille Bronken; Ehrich, Dorothee

2016-01-01

High intra-specific genetic diversity is necessary for species adaptation to novel environments under climate change, but species tracking suitable conditions are losing alleles through successive founder events during range shift. Here, we investigated the relationship between range shift since ...... the Last Glacial Maximum (LGM) and extant population genetic diversity across multiple plant species to understand variability in species responses...

Variabilidad genética de poblaciones en cautiverio de Crocodylus moreletii (Crocodylia: Crocodylidae mediante el uso de marcadores microsatelitales Genetic variability in captive populations of Crocodylus moreletii (Crocodylia: Crocodylidae using microsatellites markers

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Ricardo Serna-Lagunes

2012-03-01

characterize and compare the genetic variability of four populations of C. moreletii (two wild versus two born ex situ. Through PCR were amplified seven microsatellite polymorphic loci, however a heterozygote deficit, diminished by the presence of null alleles, was found in the populations (average H O=0.02. The AMOVA indicated that the highest proportion of genetic variability is within populations, and a limited genetic differentiation among populations (average F ST=0.03, probably due to high inbreeding index (average F IS=0.97. When comparing the genetic variability between and within other crocodilian species, we found that in C. moreletii is well below those reported. We concluded that the limited genetic variability in ex situ born populations is probably due to a founder effect derived from the social structure of their progenitors, and by the bottleneck effect, inferred by the limited effective population size, that historically characterizes their natural distribution in wild populations.

Wolbachia and genetic variability in the birdnest blowfly Protocalliphora sialia.

Science.gov (United States)

Baudry, E; Bartos, J; Emerson, K; Whitworth, T; Werren, J H

2003-07-01

Wolbachia are widespread cytoplasmically inherited bacteria that induce various reproductive alterations in host arthropods, including cytoplasmic incompatibility (CI), an incompatibility between sperm and egg that typically results in embryonic death. CI has been invoked as a possible mechanism for reproductive isolation and speciation in arthropods, by restricting gene flow and promoting maintenance (and evolution) of genetic divergence between populations. Here we investigate patterns of Wolbachia infection and nuclear and mitochondrial differentiation in geographical populations of the birdnest blowfly Protocalliphora sialia. Blowflies in western North America are infected with two A-group Wolbachia, with some individuals singly and others doubly infected. Individuals in eastern North America mostly show single infections with a B-group Wolbachia. Populations in the Midwest are polymorphic for infections and show A- or B-group infection. There is a low level of mitochondrial divergence and perfect concordance of mitochondrial haplotype with infection type, suggesting that two Wolbachia-associated selective sweeps of the mitochondrion have occurred in this species. Amplified fragment length polymorphism analysis of nuclear genetic variation shows genetic differentiation between the eastern-Midwestern and western populations. Both Midwestern and eastern flies infected with A-Wolbachia show eastern nuclear genetic profiles. Current results therefore suggest that Wolbachia has not acted as a major barrier to gene flow between western and eastern-Midwestern populations, although some genetic differentiation between A-Wolbachia infected and B-Wolbachia infected individuals in eastern-Midwestern populations cannot be ruled out.

Why Are High Altitude Natives So Strong at High Altitude? Nature vs. Nurture: Genetic Factors vs. Growth and Development.

Science.gov (United States)

Brutsaert, Tom

Among high-altitude natives there is evidence of a general hypoxia tolerance leading to enhanced performance and/or increased capacity in several important domains. These domains likely include an enhanced physical work capacity, an enhanced reproductive capacity, and an ability to resist several common pathologies of chronic high-altitude exposure. The "strength" of the high-altitude native in this regard may have both a developmental and a genetic basis, although there is better evidence for the former (developmental effects) than for the latter. For example, early-life hypoxia exposure clearly results in lung growth and remodeling leading to an increased O2 diffusing capacity in adulthood. Genetic research has yet to reveal a population genetic basis for enhanced capacity in high-altitude natives, but several traits are clearly under genetic control in Andean and Tibetan populations e.g., resting and exercise arterial O2 saturation (SaO2). This chapter reviews the effects of nature and nurture on traits that are relevant to the process of gas exchange, including pulmonary volumes and diffusion capacity, the maximal oxygen consumption (VO2max), the SaO2, and the alveolar-arterial oxygen partial pressure difference (A-aDO2) during exercise.

Genetic divergence of common bean cultivars.

Science.gov (United States)

Veloso, J S; Silva, W; Pinheiro, L R; Dos Santos, J B; Fonseca, N S; Euzebio, M P

2015-09-22

The aim of this study was to evaluate genetic divergence in the 'Carioca' (beige with brown stripes) common bean cultivar used by different institutions and in 16 other common bean cultivars used in the Rede Cooperativa de Pesquisa de Feijão (Cooperative Network of Common Bean Research), by using simple sequence repeats associated with agronomic traits that are highly distributed in the common bean genome. We evaluated 22 polymorphic loci using bulks containing DNA from 30 plants. There was genetic divergence among the Carioca cultivar provided by the institutions. Nevertheless, there was lower divergence among them than among the other cultivars. The cultivar used by Instituto Agronômico do Paraná was the most divergent in relation to the Carioca samples. The least divergence was observed among the samples used by Universidade Federal de Lavras and by Embrapa Arroz e Feijão. Of all the cultivars, 'CNFP 10104' and 'BRSMG Realce' showed the greatest dissimilarity. The cultivars were separated in two groups of greatest similarity using the Structure software. Genetic variation among cultivars was greater than the variation within or between the groups formed. This fact, together with the high estimate of heterozygosity observed and the genetic divergence of the samples of the Carioca cultivar in relation to the original provided by Instituto Agronômico de Campinas, indicates a mixture of cultivars. The high divergence among cultivars provides potential for the utilization of this genetic variability in plant breeding.

Genetic parameters of eventing horse competition in France

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Chanu Isabelle

2001-03-01

Full Text Available Abstract Genetic parameters of eventing horse competitions were estimated. About 13 000 horses, 30 000 annual results during 17 years and 110 000 starts in eventing competitions during 8 years were recorded. The measures of performance were logarithmic transformations of annual earnings, annual earnings per start, and annual earnings per place, and underlying variables responsible for ranks in each competition. Heritabilities were low (0.11/0.17 for annual results, 0.07 for ranks. Genetic correlations between criteria were high (greater than 0.90 except between ranks and earnings per place (0.58 or per start (0.67. Genetic correlations between ages (from 5 to 10 years old were also high (more than 0.85 and allow selection on early performances. The genetic correlation between the results in different levels of competition (high/international and low/amateur was near 1. Genetic correlations of eventing with other disciplines, which included partial aptitude needed for eventing, were very low for steeplechase races (0.18 and moderate with sport: jumping (0.45, dressage (0.58. The results suggest that selection on jumping performance will lead to some positive correlated response for eventing performance, but much more response could be obtained if a specific breeding objective and selection criteria were developed for eventing.

Phenotypic plasticity and genetic adaptation to high-altitude hypoxia in vertebrates.

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Storz, Jay F; Scott, Graham R; Cheviron, Zachary A

2010-12-15

High-altitude environments provide ideal testing grounds for investigations of mechanism and process in physiological adaptation. In vertebrates, much of our understanding of the acclimatization response to high-altitude hypoxia derives from studies of animal species that are native to lowland environments. Such studies can indicate whether phenotypic plasticity will generally facilitate or impede adaptation to high altitude. Here, we review general mechanisms of physiological acclimatization and genetic adaptation to high-altitude hypoxia in birds and mammals. We evaluate whether the acclimatization response to environmental hypoxia can be regarded generally as a mechanism of adaptive phenotypic plasticity, or whether it might sometimes represent a misdirected response that acts as a hindrance to genetic adaptation. In cases in which the acclimatization response to hypoxia is maladaptive, selection will favor an attenuation of the induced phenotypic change. This can result in a form of cryptic adaptive evolution in which phenotypic similarity between high- and low-altitude populations is attributable to directional selection on genetically based trait variation that offsets environmentally induced changes. The blunted erythropoietic and pulmonary vasoconstriction responses to hypoxia in Tibetan humans and numerous high-altitude birds and mammals provide possible examples of this phenomenon. When lowland animals colonize high-altitude environments, adaptive phenotypic plasticity can mitigate the costs of selection, thereby enhancing prospects for population establishment and persistence. By contrast, maladaptive plasticity has the opposite effect. Thus, insights into the acclimatization response of lowland animals to high-altitude hypoxia can provide a basis for predicting how altitudinal range limits might shift in response to climate change.

Find the weakest link. A comparison between demographic, genetic and demo-genetic metapopulation extinction times

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Robert Alexandre

2011-09-01

Full Text Available Abstract Background While the ultimate causes of most species extinctions are environmental, environmental constraints have various secondary consequences on evolutionary and ecological processes. The roles of demographic, genetic mechanisms and their interactions in limiting the viabilities of species or populations have stirred much debate and remain difficult to evaluate in the absence of demography-genetics conceptual and technical framework. Here, I computed projected times to metapopulation extinction using (1 a model focusing on the effects of species properties, habitat quality, quantity and temporal variability on the time to demographic extinction; (2 a genetic model focusing on the dynamics of the drift and inbreeding loads under the same species and habitat constraints; (3 a demo-genetic model accounting for demographic-genetic processes and feedbacks. Results Results indicate that a given population may have a high demographic, but low genetic viability or vice versa; and whether genetic or demographic aspects will be the most limiting to overall viability depends on the constraints faced by the species (e.g., reduction of habitat quantity or quality. As a consequence, depending on metapopulation or species characteristics, incorporating genetic considerations to demographically-based viability assessments may either moderately or severely reduce the persistence time. On the other hand, purely genetically-based estimates of species viability may either underestimate (by neglecting demo-genetic interactions or overestimate (by neglecting the demographic resilience true viability. Conclusion Unbiased assessments of the viabilities of species may only be obtained by identifying and considering the most limiting processes (i.e., demography or genetics, or, preferentially, by integrating them.

The calculated genetic barrier for antiretroviral drug resistance substitutions is largely similar for different HIV-1 subtypes

NARCIS (Netherlands)

Vijver, D.A. van de; Wensing, A.M.J.; Angarano, G.; Asjo, B.; Balotta, C.; Camacho, R.; Chaix, M.; Costagliola, D.; De Luca, A.; Derdelinckx, I.; Grossman, Z.; Hamouda, O.; Hatzakis, A.; Hemmer, R.; Hoepelman, A.I.M.; Horban, A.; Korn, K.; Kücherer, C.; Leitner, T.; Loveday, C.; MacRae, E.; Maljkovic, I.; Mendoza, C. de; Meyer, L.; Nielsen, C.; Op de Coul, E.L.M.; Omaasen, V.; Paraskevis, D.; Perrin, L.; Puchhammer-Stöckl, E.; Salminen, M.; Schmit, J.; Scheider, F.; Schuurman, R.; Soriano, V.; Stanczak, G.; Stanojevic, M.; Vandamme, A.; Laethem, K. van; Violin, M.; Wilde, K.; Yerly, S.; Zazzi, M.; Boucher, C.A.B.

The genetic barrier, defined as the number of mutations required to overcome drug-selective pressure, is an important factor for the development of HIV drug resistance. Because of high variability between subtypes, particular HIV-1 subtypes could have different genetic barriers for drug

Assessment of Genetic Variability in Sorghum Accessions (Sorghum ...

African Journals Online (AJOL)

ADOWIE PERE

The polymorphic information content (PIC) of individual primer ranged from 0.34 to 0.70 with a mean value of 0.54 indicating enough ... Keywords: Sorghum; Simple Sequence Repeat markers; Genetic variation; Polymorphic Information Content;. Coefficient of ... based techniques include Restriction Fragment Length.

Genetic mutations in Gorlin-Goltz syndrome

OpenAIRE

Daneswari, Muthumula; Reddy, Mutjumula Swamy Ranga

2013-01-01

Gorlin-Goltz syndrome is a rare multisystemic disease inherited in a dominant autosomal at a high level of penetrance and variable expressiveness. It is mainly characterized by basal cell carcinoma, odontogenic keratocyst and skeletal anomalies. Diagnosis is based upon established major and minor clinical and radiographic criteria and gene mutation analysis. This article presents a case of Gorlin-Goltz syndrome, its genetic predisposition, diagnosis and management.

Genetic mutations in Gorlin-Goltz syndrome.

Science.gov (United States)

Daneswari, Muthumula; Reddy, Mutjumula Swamy Ranga

2013-07-01

Gorlin-Goltz syndrome is a rare multisystemic disease inherited in a dominant autosomal at a high level of penetrance and variable expressiveness. It is mainly characterized by basal cell carcinoma, odontogenic keratocyst and skeletal anomalies. Diagnosis is based upon established major and minor clinical and radiographic criteria and gene mutation analysis. This article presents a case of Gorlin-Goltz syndrome, its genetic predisposition, diagnosis and management.

Impact of ecological diversity on genetic and phytochemical variation injuniperus excelsa from high elevation zones of quetta valley, pakistan

International Nuclear Information System (INIS)

Seed, S.; Barozai, M.Y.K.; Ahmed, A.; Tareen, R.B.

2017-01-01

Juniperusexcelsa (Cupressaceae) is an evergreen tree and the second most diverse group of the conifers distributed abundantly in high elevation zones of Balochistan. Genetic and phytochemical variations in three naturally occurring populations of J.excelsa were analysed. Genetic variability was assessed by different molecular markers (RAPD, ISSR and URP) with an objective to use genetic diversity as a key to conserve the taxon which is also known as living fossil as dominated in Mesozoic era. Genetic diversity was assessed by polymorphic bands to generate a dendrogram based on UPGMA. Using tested markers, 116 bands were amplified out of which 67 bands were polymorphic with an average value of 8.37 (57%) bands per primer. Based on data, a cluster dendrogram was prepared that exhibited the mean genetic similarity matrix as 0.57 and two major clusters diverge at 0.49. The genetic similarity coefficient among all accessions ranged from 0.35 to 0.90. In phytochemical analysis, total phenolic and flavonoid contents were estimated and compared among all accessions. Ecological characteristics of the study sites were measured to check their impact on genetic and chemical variation. Soil properties were analyzed for Principal Component Analysis. Chemical variation of J. excelsa of three sites revealed by dissimilarity matrix exhibiting genetic distance based on TPC and Flavonoids. Cluster analysis represent two major groups. Mean concentration of TPC and flavonoids were 56+-9.15 and 150+-27.9 mg/g respectively. PCA of soil considered three factors had Eigen values >1 and explain cumulatively 4.60 %, 26.02% and 10.36 % of the variance. First factor was positively correlated with second and fifth, but negatively correlated with other factors. In conclusion, molecular marker profiling together with phytochemical variation of total phenolic and flavonoid content in all accessions of Juniperusexcelsa and impact of ecological diversity on Genetic and chemical variation can be used

[Genetic polymorphism of Gentiana lutea L. (Gentianaceae) populations from Chornohora Ridge of Ukrainian Carpathians].

Science.gov (United States)

Mosula, M Z; Konvaliuk, I I; Mel'nyk, V M; Drobyk, N M; Tsaryk, I V; Nesteruk, Iu I; Kunakh, V A

2014-01-01

The features of genetic structure and level of diversity were investigated for G. lutea populations from Chornohora Ridge of Ukrainian Carpathians using RAPD- and ISSR-PCR. We have shown a high level of genetic diversity for investigated populations. The differences between populations account for 59-72% of the total genetic variation, whereas intrapopulation polymorphism makes up 28-41%. The relationships among genetic variability level and ecological-geographical conditions as well as biological features of the species were assumed to be possible. The obtained results indicate the genetic isolation of G. lutea Chornohora populations from Ukrainian Carpathians. Pozhyzhevska agropopulation was characterized by a high level of polymorphism that means the possibility to use artificial plantings of the investigated species for its conservation.

The Molecular Genetic Architecture of Self-Employment

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van der Loos, Matthijs J. H. M.; Rietveld, Cornelius A.; Eklund, Niina; Koellinger, Philipp D.; Rivadeneira, Fernando; Abecasis, Gonçalo R.; Ankra-Badu, Georgina A.; Baumeister, Sebastian E.; Benjamin, Daniel J.; Biffar, Reiner; Blankenberg, Stefan; Boomsma, Dorret I.; Cesarini, David; Cucca, Francesco; de Geus, Eco J. C.; Dedoussis, George; Deloukas, Panos; Dimitriou, Maria; Eiriksdottir, Guðny; Eriksson, Johan; Gieger, Christian; Gudnason, Vilmundur; Höhne, Birgit; Holle, Rolf; Hottenga, Jouke-Jan; Isaacs, Aaron; Järvelin, Marjo-Riitta; Johannesson, Magnus; Kaakinen, Marika; Kähönen, Mika; Kanoni, Stavroula; Laaksonen, Maarit A.; Lahti, Jari; Launer, Lenore J.; Lehtimäki, Terho; Loitfelder, Marisa; Magnusson, Patrik K. E.; Naitza, Silvia; Oostra, Ben A.; Perola, Markus; Petrovic, Katja; Quaye, Lydia; Raitakari, Olli; Ripatti, Samuli; Scheet, Paul; Schlessinger, David; Schmidt, Carsten O.; Schmidt, Helena; Schmidt, Reinhold; Senft, Andrea; Smith, Albert V.; Spector, Timothy D.; Surakka, Ida; Svento, Rauli; Terracciano, Antonio; Tikkanen, Emmi; van Duijn, Cornelia M.; Viikari, Jorma; Völzke, Henry; Wichmann, H. -Erich; Wild, Philipp S.; Willems, Sara M.; Willemsen, Gonneke; van Rooij, Frank J. A.; Groenen, Patrick J. F.; Uitterlinden, André G.; Hofman, Albert; Thurik, A. Roy

2013-01-01

Economic variables such as income, education, and occupation are known to affect mortality and morbidity, such as cardiovascular disease, and have also been shown to be partly heritable. However, very little is known about which genes influence economic variables, although these genes may have both a direct and an indirect effect on health. We report results from the first large-scale collaboration that studies the molecular genetic architecture of an economic variable–entrepreneurship–that was operationalized using self-employment, a widely-available proxy. Our results suggest that common SNPs when considered jointly explain about half of the narrow-sense heritability of self-employment estimated in twin data (σg 2/σP 2 = 25%, h 2 = 55%). However, a meta-analysis of genome-wide association studies across sixteen studies comprising 50,627 participants did not identify genome-wide significant SNPs. 58 SNPs with pentrepreneurship reveal significant associations. Finally, SNP-based genetic scores that use results from the meta-analysis capture less than 0.2% of the variance in self-employment in an independent sample (p≥0.039). Our results are consistent with a highly polygenic molecular genetic architecture of self-employment, with many genetic variants of small effect. Although self-employment is a multi-faceted, heavily environmentally influenced, and biologically distal trait, our results are similar to those for other genetically complex and biologically more proximate outcomes, such as height, intelligence, personality, and several diseases. PMID:23593239

Behavioral Variability and Somatic Mosaicism: A Cytogenomic Hypothesis.

Science.gov (United States)

Vorsanova, Svetlana G; Zelenova, Maria A; Yurov, Yuri B; Iourov, Ivan Y

2018-04-01

Behavioral sciences are inseparably related to genetics. A variety of neurobehavioral phenotypes are suggested to result from genomic variations. However, the contribution of genetic factors to common behavioral disorders (i.e. autism, schizophrenia, intellectual disability) remains to be understood when an attempt to link behavioral variability to a specific genomic change is made. Probably, the least appreciated genetic mechanism of debilitating neurobehavioral disorders is somatic mosaicism or the occurrence of genetically diverse (neuronal) cells in an individual's brain. Somatic mosaicism is assumed to affect directly the brain being associated with specific behavioral patterns. As shown in studies of chromosome abnormalities (syndromes), genetic mosaicism is able to change dynamically the phenotype due to inconsistency of abnormal cell proportions. Here, we hypothesize that brain-specific postzygotic changes of mosaicism levels are able to modulate variability of behavioral phenotypes. More precisely, behavioral phenotype variability in individuals exhibiting somatic mosaicism might correlate with changes in the amount of genetically abnormal cells throughout the lifespan. If proven, the hypothesis can be used as a basis for therapeutic interventions through regulating levels of somatic mosaicism to increase functioning and to improve overall condition of individuals with behavioral problems.

Dissecting high-dimensional phenotypes with bayesian sparse factor analysis of genetic covariance matrices.

Science.gov (United States)

Runcie, Daniel E; Mukherjee, Sayan

2013-07-01

Quantitative genetic studies that model complex, multivariate phenotypes are important for both evolutionary prediction and artificial selection. For example, changes in gene expression can provide insight into developmental and physiological mechanisms that link genotype and phenotype. However, classical analytical techniques are poorly suited to quantitative genetic studies of gene expression where the number of traits assayed per individual can reach many thousand. Here, we derive a Bayesian genetic sparse factor model for estimating the genetic covariance matrix (G-matrix) of high-dimensional traits, such as gene expression, in a mixed-effects model. The key idea of our model is that we need consider only G-matrices that are biologically plausible. An organism's entire phenotype is the result of processes that are modular and have limited complexity. This implies that the G-matrix will be highly structured. In particular, we assume that a limited number of intermediate traits (or factors, e.g., variations in development or physiology) control the variation in the high-dimensional phenotype, and that each of these intermediate traits is sparse - affecting only a few observed traits. The advantages of this approach are twofold. First, sparse factors are interpretable and provide biological insight into mechanisms underlying the genetic architecture. Second, enforcing sparsity helps prevent sampling errors from swamping out the true signal in high-dimensional data. We demonstrate the advantages of our model on simulated data and in an analysis of a published Drosophila melanogaster gene expression data set.

Implementation and utilization of genetic testing in personalized medicine

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Abul-Husn NS

2014-08-01

Full Text Available Noura S Abul-Husn,1,* Aniwaa Owusu Obeng,2,3,* Saskia C Sanderson,1 Omri Gottesman,2 Stuart A Scott11Department of Genetics and Genomic Sciences, 2The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, 3Department of Pharmacy, Mount Sinai Hospital, New York, NY, USA*These authors contributed equally to this manuscriptAbstract: Clinical genetic testing began over 30 years ago with the availability of mutation detection for sickle cell disease diagnosis. Since then, the field has dramatically transformed to include gene sequencing, high-throughput targeted genotyping, prenatal mutation detection, preimplantation genetic diagnosis, population-based carrier screening, and now genome-wide analyses using microarrays and next-generation sequencing. Despite these significant advances in molecular technologies and testing capabilities, clinical genetics laboratories historically have been centered on mutation detection for Mendelian disorders. However, the ongoing identification of deoxyribonucleic acid (DNA sequence variants associated with common diseases prompted the availability of testing for personal disease risk estimation, and created commercial opportunities for direct-to-consumer genetic testing companies that assay these variants. This germline genetic risk, in conjunction with other clinical, family, and demographic variables, are the key components of the personalized medicine paradigm, which aims to apply personal genomic and other relevant data into a patient's clinical assessment to more precisely guide medical management. However, genetic testing for disease risk estimation is an ongoing topic of debate, largely due to inconsistencies in the results, concerns over clinical validity and utility, and the variable mode of delivery when returning genetic results to patients in the absence of traditional counseling. A related class of genetic testing with analogous issues of clinical utility and

Genetic parameters of body weight and prolificacy in pigeons

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Beaumont Catherine

2000-07-01

Full Text Available Abstract Genetic parameters of body weight at weaning and of prolificacy were estimated in three commercial lines of pigeons selected by BLUP (Best Linear Unbiased Prediction on both traits. The model of analysis took into account the direct genetic effects for both traits and the effect of parental permanent environment for body weight. Depending on the line considered, body weight varied from 556.7 g to 647.6 g and prolificacy ranged from 12.5 to 16.8 pigeons weaned per couple of parents per year. Heritability of body weight was high, varying between 0.46 and 0.60, and permanent environment was responsible for 6% to 9% of the total variability. On the contrary, prolificacy was poorly heritable (0.04 to 0.12. They were highly and negatively correlated (-0.77 to -0.82. Body weight showed significant genetic trends in lines B and C. No significant genetic difference could be observed between males and females for both traits.

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

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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.

Genetic diversity and structure of Brazilian ginger germplasm (Zingiber officinale) revealed by AFLP markers.

Science.gov (United States)

Blanco, Eleonora Zambrano; Bajay, Miklos Maximiliano; Siqueira, Marcos Vinícius Bohrer Monteiro; Zucchi, Maria Imaculada; Pinheiro, José Baldin

2016-12-01

Ginger is a vegetable with medicinal and culinary properties widely cultivated in the Southern and Southeastern Brazil. The knowledge of ginger species' genetic variability is essential to direct correctly future studies of conservation and genetic improvement, but in Brazil, little is known about this species' genetic variability. In this study, we analyzed the genetic diversity and structure of 55 Brazilian accessions and 6 Colombian accessions of ginger, using AFLP (Amplified Fragment Length Polymorphism) molecular markers. The molecular characterization was based on 13 primers combinations, which generated an average of 113.5 polymorphic loci. The genetic diversity estimates of Nei (Hj), Shannon-Weiner index (I) and an effective number of alleles (n e ) were greater in the Colombian accessions in relation to the Brazilian accessions. The analysis of molecular variance showed that most of the genetic variation occurred between the two countries while in the Brazilian populations there is no genetic structure and probably each region harbors 100 % of genetic variation found in the samples. The bayesian model-based clustering and the dendrogram using the dissimilarity's coefficient of Jaccard were congruent with each other and showed that the Brazilian accessions are highly similar between themselves, regardless of the geographic region of origin. We suggested that the exploration of the interspecific variability and the introduction of new varieties of Z.officinale are viable alternatives for generating diversity in breeding programs in Brazil. The introduction of new genetic materials will certainly contribute to a higher genetic basis of such crop.

Analysis of Genetic Parameters on Ethiopian Mustard (Brassica Carinata A. Braun Genotypes in Northwestern Ethiopia

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Walle Tesfaye

2014-12-01

Full Text Available This study was carried out with the objective to estimate the genotypic variability and other yield related traits of Ethiopian mustard in North West Ethiopia. A total of 36 genotypes of Ethiopian mustard were considered for this study. Analysis of variance was computed to contrast the variability within the collected genotypes based on yield and other yield related traits. The results revealed highly significant values(p<0.01 for days to 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<0.05 were noted for days to flowering, plant height, primary branch per plant, biomass per plot, oil yield per plot differences among the genotypes. Genotypic coefficient of variation (GCV % was lower than phenotypic coefficient of variation (PCV % for all the traits studied. High genetic advance with heritability was observed in the following characters; plant height, biomass of the plant, number of secondary branch per plant and grain filling period. There are variations in the extent of genetic variability, heritability and genetic advance of traits which can facilitate selection for further improvement of important traits of Ethiopian mustard. Therefore, it can be concluded that the variability within Ethiopian mustard genotypes collected from different areas of northern Ethiopia is high and vital for better crop improvement.

Temperature-dependent behaviours are genetically variable in the nematode Caenorhabditis briggsae.

Science.gov (United States)

Stegeman, Gregory W; de Mesquita, Matthew Bueno; Ryu, William S; Cutter, Asher D

2013-03-01

Temperature-dependent behaviours in Caenorhabditis elegans, such as thermotaxis and isothermal tracking, are complex behavioural responses that integrate sensation, foraging and learning, and have driven investigations to discover many essential genetic and neural pathways. The ease of manipulation of the Caenorhabditis model system also has encouraged its application to comparative analyses of phenotypic evolution, particularly contrasts of the classic model C. elegans with C. briggsae. And yet few studies have investigated natural genetic variation in behaviour in any nematode. Here we measure thermotaxis and isothermal tracking behaviour in genetically distinct strains of C. briggsae, further motivated by the latitudinal differentiation in C. briggsae that is associated with temperature-dependent fitness differences in this species. We demonstrate that C. briggsae performs thermotaxis and isothermal tracking largely similar to that of C. elegans, with a tendency to prefer its rearing temperature. Comparisons of these behaviours among strains reveal substantial heritable natural variation within each species that corresponds to three general patterns of behavioural response. However, intraspecific genetic differences in thermal behaviour often exceed interspecific differences. These patterns of temperature-dependent behaviour motivate further development of C. briggsae as a model system for dissecting the genetic underpinnings of complex behavioural traits.

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

OpenAIRE

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

2015-01-01

Burkholderia pseudomallei is a soil dwelling Gram-negative bacteria predominates in Southeast Asia zone and the tropical part of Australia. Genetic diversity has been explored among various populations and environments worldwide. To date, little data is available on MLST profiling of clinical B. pseudomallei isolates in peninsular Malaysia. In this brief report, thirteen culture positive B. pseudomallei cases collected from a single population of Terengganu state in the Western Peninsular Mal...

Virulence factors and genetic variability of Staphylococcus aureus strains isolated from raw sheep's milk cheese.

Science.gov (United States)

Spanu, Vincenzo; Spanu, Carlo; Virdis, Salvatore; Cossu, Francesca; Scarano, Christian; De Santis, Enrico Pietro Luigi

2012-02-01

Contamination of dairy products with Staphylococcus aureus can be of animal or human origin. The host pathogen relationship is an important factor determining genetic polymorphism of the strains and their potential virulence. The aim of the present study was to carry out an extensive characterization of virulence factors and to study the genetic variability of S. aureus strains isolated from raw ewe's milk cheese. A total of 100 S. aureus strains isolated from cheese samples produced in 10 artisan cheese factories were analyzed for the presence of enterotoxins (sea-see) and enterotoxins-like genes (seh, sek, sel, sem, seo, sep), leukocidins, exfoliatins, haemolysins, toxic shock syndrome toxin 1 (TSST-1) and the accessory gene regulator alleles (agr). Strains were also typed using pulsed-field gel electrophoresis (PFGE). AMOVA analysis carried out on PFGE and PCR data showed that the major component explaining genetic distance between strains was the dairy of origin. Of the total isolates 81% had a pathogenicity profile ascribable to "animal" biovar while 16% could be related to "human" biovar. The biovar allowed to estimate the most likely origin of the contamination. Minimum inhibitory concentrations (MICs) of nine antimicrobial agents and the presence of the corresponding genes coding for antibiotic resistance was also investigated. 18 strains carrying blaZ gene showed resistance to ampicillin and penicillin and 6 strains carrying tetM gene were resistant to tetracycline. The presence of mecA gene and methicillin resistance, typical of strains of human origin, was never detected. The results obtained in the present study confirm that S. aureus contamination in artisan cheese production is mainly of animal origin. Copyright © 2011. Published by Elsevier B.V.

Genetic Variability among Lucerne Cultivars Based on Biochemical (SDS-PAGE) and Morphological Markers

Science.gov (United States)

Farshadfar, M.; Farshadfar, E.

The present research was conducted to determine the genetic variability of 18 Lucerne cultivars, based on morphological and biochemical markers. The traits studied were plant height, tiller number, biomass, dry yield, dry yield/biomass, dry leaf/dry yield, macro and micro elements, crude protein, dry matter, crude fiber and ash percentage and SDS- PAGE in seed and leaf samples. Field experiments included 18 plots of two meter rows. Data based on morphological, chemical and SDS-PAGE markers were analyzed using SPSSWIN soft ware and the multivariate statistical procedures: cluster analysis (UPGMA), principal component. Analysis of analysis of variance and mean comparison for morphological traits reflected significant differences among genotypes. Genotype 13 and 15 had the greatest values for most traits. The Genotypic Coefficient of Variation (GCV), Phenotypic Coefficient of Variation (PCV) and Heritability (Hb) parameters for different characters raged from 12.49 to 26.58% for PCV, hence the GCV ranged from 6.84 to 18.84%. The greatest value of Hb was 0.94 for stem number. Lucerne genotypes could be classified, based on morphological traits, into four clusters and 94% of the variance among the genotypes was explained by two PCAs: Based on chemical traits they were classified into five groups and 73.492% of variance was explained by four principal components: Dry matter, protein, fiber, P, K, Na, Mg and Zn had higher variance. Genotypes based on the SDS-PAGE patterns all genotypes were classified into three clusters. The greatest genetic distance was between cultivar 10 and others, therefore they would be suitable parent in a breeding program.

POPULATION GENETICS OF Atta sexdens rubropilosa (HYMENOPTERA: FORMICIDAE

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Liriana Belizário Cantagalli

2013-01-01

Full Text Available The genetic variability of Atta sexdens rubropilosa leaf-cutting ants collected from five brazilian localities was evaluated with PCR-RAPD technique. We used 15 primers producing 148 fragments of which 123 (83,11 % contained polymorphisms. The estimated Shannon index was 0.3836 ± 0.2335 showing that these ants possess high genetic diversity. The GST value was 0,2372 and PT = 0,184, indicating that the analyzed populations are moderately differentiated and 82 % of the variation obtained occur within populations. Although Mantel’s test had shown correlation between genetic distances and geographic was observed that Ivatuba and Itambé (33,8 km have the small geographical distance and the largest genetic distance. The lower genetic distance was estimated for Maringá and Ivatuba but this localities have a small geographic distance (42,3 km, indicating that there are no barriers for mating among reproducers in these populations. The high degree of polymorphism (83,11 % and the ability to cross among the populations in the studied regions indicate that this species of leaf-cutting ant is well adapted to the region; therefore, integrated control programs can be developed.

Population genetics of Atta sexdens rubropilosa (Hymenoptera: Formicidae)

International Nuclear Information System (INIS)

Belizario Cantagalli, Liriana; Aparecida Mangolin, Claudete; Colla Ruvolo Takasusuki, Maria Claudia

2013-01-01

The genetic variability of Atta sexdens rubropilosa leaf-cutting ants collected from five Brazilian localities was evaluated with PCR-RAPD technique. we used 15 primers producing 148 fragments of which 123 (83.11 %) contained polymorphisms. the estimated Shannon index was 0.3836 ± 0.2335 showing that these ants possess high genetic diversity. the G S T value was 0.2372 and Φ p t = 0.184, indicating that the analyzed populations are moderately differentiated and 82 % of the variation obtained occur within populations. although mantel's test had shown correlation between genetic distances and geographic was observed that Ivatuba and Itambe (33.8 km) have the small geographical distance and the largest genetic distance. the lower genetic distance was estimated for Maringa and Ivatuba but this localities have a small geographic distance (42.3 km), indicating that there are no barriers for mating among reproducers in these populations. the high degree of polymorphism (83.11 %) and the ability to cross among the populations in the studied regions indicate that this species of leaf-cutting ant is well adapted to the region; therefore, integrated control programs can be developed.

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.

Market Designs for High Levels of Variable Generation: Preprint

Energy Technology Data Exchange (ETDEWEB)

Milligan, M.; Holttinen, H.; Kiviluoma, J.; Orths, A.; Lynch, M.; Soder, L.

2014-10-01

Variable renewable generation is increasing in penetration in modern power systems, leading to higher variability in the supply and price of electricity as well as lower average spot prices. This raises new challenges, particularly in ensuring sufficient capacity and flexibility from conventional technologies. Because the fixed costs and lifetimes of electricity generation investments are significant, designing markets and regulations that ensure the efficient integration of renewable generation is a significant challenge. This papers reviews the state of play of market designs for high levels of variable generation in the United States and Europe and considers new developments in both regions.

STUDY OF PHENOTYPIC CHARACTERS VARIABILITY OF THE SILKMOTH COCOON FROM THE NATIVE GENETIC STOCK OF BOMBYX MORI L. SP.

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ALEXANDRA MATEI

2008-10-01

Full Text Available This study had aims the analysis of phenotypic characters variability of silkmoth cocoon within the native genetic stock of Bombyx mori L. sp. The biological material was represented by 72 races consisting of the gene stock of Bombyx mori sp., grouped by their origin. The main phenotypical ad quantitative parameters of the races that represent the gene stock of Bombyx mori sp., present the following values: raw cocoon weight (1.445-2.361 g, cocoon shell weight (0.240-0.520 g, fiber length (746-1356 m, metric number of fiber (2917-3764 m/g. Depending on the quantitative parameters value, the silkworm races are being used differently, entire genetic stock being destined for various technological levels, as follows: 4 active races (parents of hybrids, 4 candidate races for parents of hybrids, 64 races in preservation.

A massively parallel sequencing approach uncovers ancient origins and high genetic variability of endangered Przewalski's horses.

Science.gov (United States)

Goto, Hiroki; Ryder, Oliver A; Fisher, Allison R; Schultz, Bryant; Kosakovsky Pond, Sergei L; Nekrutenko, Anton; Makova, Kateryna D

2011-01-01

The endangered Przewalski's horse is the closest relative of the domestic horse and is the only true wild horse species surviving today. The question of whether Przewalski's horse is the direct progenitor of domestic horse has been hotly debated. Studies of DNA diversity within Przewalski's horses have been sparse but are urgently needed to ensure their successful reintroduction to the wild. In an attempt to resolve the controversy surrounding the phylogenetic position and genetic diversity of Przewalski's horses, we used massively parallel sequencing technology to decipher the complete mitochondrial and partial nuclear genomes for all four surviving maternal lineages of Przewalski's horses. Unlike single-nucleotide polymorphism (SNP) typing usually affected by ascertainment bias, the present method is expected to be largely unbiased. Three mitochondrial haplotypes were discovered-two similar ones, haplotypes I/II, and one substantially divergent from the other two, haplotype III. Haplotypes I/II versus III did not cluster together on a phylogenetic tree, rejecting the monophyly of Przewalski's horse maternal lineages, and were estimated to split 0.117-0.186 Ma, significantly preceding horse domestication. In the phylogeny based on autosomal sequences, Przewalski's horses formed a monophyletic clade, separate from the Thoroughbred domestic horse lineage. Our results suggest that Przewalski's horses have ancient origins and are not the direct progenitors of domestic horses. The analysis of the vast amount of sequence data presented here suggests that Przewalski's and domestic horse lineages diverged at least 0.117 Ma but since then have retained ancestral genetic polymorphism and/or experienced gene flow.

Genetic Diversity Analysis of South and East Asian Duck Populations Using Highly Polymorphic Microsatellite Markers

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Dongwon Seo

2016-04-01

Full Text Available Native duck populations have lower productivity, and have not been developed as much as commercials duck breeds. However, native ducks have more importance in terms of genetic diversity and potentially valuable economic traits. For this reason, population discriminable genetic markers are needed for conservation and development of native ducks. In this study, 24 highly polymorphic microsatellite (MS markers were investigated using commercial ducks and native East and South Asian ducks. The average polymorphic information content (PIC value for all MS markers was 0.584, indicating high discrimination power. All populations were discriminated using 14 highly polymorphic MS markers by genetic distance and phylogenetic analysis. The results indicated that there were close genetic relationships among populations. In the structure analysis, East Asian ducks shared more haplotypes with commercial ducks than South Asian ducks, and they had more independent haplotypes than others did. These results will provide useful information for genetic diversity studies in ducks and for the development of duck traceability systems in the market.

Marine reserves help preserve genetic diversity after impacts derived from climate variability: Lessons from the pink abalone in Baja California

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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.

Highly variable penetrance of abnormal phenotypes in embryonic lethal knockout mice

Science.gov (United States)

Wilson, Robert; Geyer, Stefan H.; Reissig, Lukas; Rose, Julia; Szumska, Dorota; Hardman, Emily; Prin, Fabrice; McGuire, Christina; Ramirez-Solis, Ramiro; White, Jacqui; Galli, Antonella; Tudor, Catherine; Tuck, Elizabeth; Mazzeo, Cecilia Icoresi; Smith, James C.; Robertson, Elizabeth; Adams, David J.; Mohun, Timothy; Weninger, Wolfgang J.

2017-01-01

Background: Identifying genes that are essential for mouse embryonic development and survival through term is a powerful and unbiased way to discover possible genetic determinants of human developmental disorders. Characterising the changes in mouse embryos that result from ablation of lethal genes is a necessary first step towards uncovering their role in normal embryonic development and establishing any correlates amongst human congenital abnormalities. Methods: Here we present results gathered to date in the Deciphering the Mechanisms of Developmental Disorders (DMDD) programme, cataloguing the morphological defects identified from comprehensive imaging of 220 homozygous mutant and 114 wild type embryos from 42 lethal and subviable lines, analysed at E14.5. Results: Virtually all mutant embryos show multiple abnormal phenotypes and amongst the 42 lines these affect most organ systems. Within each mutant line, the phenotypes of individual embryos form distinct but overlapping sets. Subcutaneous edema, malformations of the heart or great vessels, abnormalities in forebrain morphology and the musculature of the eyes are all prevalent phenotypes, as is loss or abnormal size of the hypoglossal nerve. Conclusions: Overall, the most striking finding is that no matter how profound the malformation, each phenotype shows highly variable penetrance within a mutant line. These findings have challenging implications for efforts to identify human disease correlates. PMID:27996060

Assessing Extinction Risk: Integrating Genetic Information

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Jason Dunham

1999-06-01

Full Text Available Risks of population extinction have been estimated using a variety of methods incorporating information from different spatial and temporal scales. We briefly consider how several broad classes of extinction risk assessments, including population viability analysis, incidence functions, and ranking methods integrate information on different temporal and spatial scales. In many circumstances, data from surveys of neutral genetic variability within, and among, populations can provide information useful for assessing extinction risk. Patterns of genetic variability resulting from past and present ecological and demographic events, can indicate risks of extinction that are otherwise difficult to infer from ecological and demographic analyses alone. We provide examples of how patterns of neutral genetic variability, both within, and among populations, can be used to corroborate and complement extinction risk assessments.

Genetics and variation

Science.gov (United States)

John R. Jones; Norbert V. DeByle

1985-01-01

The broad genotypic variability in quaking aspen (Populus tremuloides Michx.), that results in equally broad phenotypic variability among clones is important to the ecology and management of this species. This chapter considers principles of aspen genetics and variation, variation in aspen over its range, and local variation among clones. For a more...

Variabilidade genética para teor de proteína bruta em grãos de aveia Genetic variability for total grain protein in oat

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Rodrigo Rodrigues Matiello

1997-06-01

Full Text Available O aumento da utilização dos grãos de aveia na alimentação humana tem estimulado os melhoristas a selecionar genótipos com alta qualidade de grãos. O presente trabalho foi realizado com o objetivo de identificar e caracterizar a variabilidade genética para o caráter teor de proteína bruta de grãos em genótipos cultivados de aveia, introduções silvestres de A. fatua L., A. sterilis L. e em populações híbridas de A. sativa L. x A. sterilis L. Os resultados revelaram uma ampla variabilidade genética para o caráter dentro dos grupos estudados. As diferenças observadas entre os genótipos cultivados parecem ocorrer devido a constituição genotípica diferenciada. O grupo silvestre de A. sterilis L. foi, em média, superior aos demais, sendo que a introdução I-325 se destacou pelo alto teor de proteína. O comportamento similar entre as introduções de A. fatua L. pode ser atribuído a coleta de introduções de apenas uma região, o que reduziu a variabilidade genética. Foram encontrados híbridos artificiais entre A. sativa L. x A. sterilis L. com alto teor de proteína e características desejáveis do grupo cultivado.The increased use of oat grains as human food has stimulated plant breeders to select genotypes with high grain quality. This work aimed to identify and characterize genetic variability for total grain protein in cultivated oat and introductions of A. fatua L., A. sterilis L. and hybrid populations from A. sativa L. x A. sterilis L.. The results showed a large genetic variability for the trait in the studied groups. Differences among cultivated oat genotypes may be attributed to different genetic constitution. A. sterilis L. group showed high protein content specially with the introduction of I-325. Genotypes from A. fatua L. showed similar low levels of protein probably because the narrow range of regions sampled in this study. Some hybrids from A. sativa L. x A. sterilis L. showed high protein content and

Genetic diversity in Kenyan populations of Acacia senegal (L.) willd ...

African Journals Online (AJOL)

Acacia senegal belongs to the subgenus, Aculeiferum. It is an African arid and semi arid zone multipurpose tree species, highly valued for gum arabic production, agroforestry and desertification control besides other multiple uses. Genetic variation and resulting variable groupings were assessed using combined ...

Scrub typhus in South India: clinical and laboratory manifestations, genetic variability, and outcome.

Science.gov (United States)

Varghese, George M; Janardhanan, Jeshina; Trowbridge, Paul; Peter, John V; Prakash, John A J; Sathyendra, Sowmya; Thomas, Kurien; David, Thambu S; Kavitha, M L; Abraham, Ooriapadickal C; Mathai, Dilip

2013-11-01

This study sought to document the clinical and laboratory manifestations, genetic variability, and outcomes of scrub typhus, an often severe infection caused by Orientia tsutsugamushi, in South India. Patients admitted to a large teaching hospital with IgM ELISA-confirmed scrub typhus were evaluated. Clinical examination with a thorough search for an eschar, laboratory testing, chest X-ray, and outcome were documented and analyzed. Additionally, a 410-bp region of the 56-kDa type-specific antigen gene of O. tsutsugamushi was sequenced and compared with isolates from other regions of Asia. Most of the 154 patients evaluated presented with fever and non-specific symptoms. An eschar was found in 86 (55%) patients. Mild hepatic involvement was seen in most, with other organ involvement including respiratory, cardiovascular, and renal. Multi-organ dysfunction was noted in 59 (38.3%), and the fatality rate was 7.8%. Hypotension requiring vasoactive agents was found to be an independent predictor of mortality (p<0.001). The phylogeny of 26 samples showed 17 (65%) clustering with the Kato-like group and eight (31%) with the Karp-like group. The presentation of scrub typhus can be variable, often non-specific, but with potentially severe multi-organ dysfunction. Prompt recognition is key to specific treatment and good outcomes. Further study of the circulating strains is essential for the development of a successful vaccine and sensitive point-of-care testing. Copyright © 2013 International Society for Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Foundations of genetic algorithms 1991

CERN Document Server

1991-01-01

Foundations of Genetic Algorithms 1991 (FOGA 1) discusses the theoretical foundations of genetic algorithms (GA) and classifier systems.This book compiles research papers on selection and convergence, coding and representation, problem hardness, deception, classifier system design, variation and recombination, parallelization, and population divergence. Other topics include the non-uniform Walsh-schema transform; spurious correlations and premature convergence in genetic algorithms; and variable default hierarchy separation in a classifier system. The grammar-based genetic algorithm; condition

Caracterização molecular e variabilidade genética de acessos elite de mandioca para fins industriais Molecular characterization and genetic variability of elite cassava accessions for industrial purpose

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Eduardo Alano Vieira

2010-12-01

laboratory conditions, the accessions were evaluated though RAPD markers, being afterwards estimated by the matrix of genetic similarity among the accessions, through the Jaccard index. The analyses through 11 primers generated a total of 120 RAPD markers, among which 74 (62% were polymorphic, revealing the presence of high genetic variability within the group of evaluated accessions. The clustering analyses revealed the formation of a single strong group, comprised of the accessions BGMC 1130, BGMC 788, BGMC 1270 and BGMC 1107, which indicates that the cassava genetic breeding hybridizations among these accessions should not be prioritized, upon risk of endogamy effects. The accession BGMC 436 was the most divergent as compared to the others and, as it expresses high productive potential within the Central Brazil Cerrado, it represents a good option as parent for the cassava breeding in this region. The study confirmed that the RAPD markers are efficient for the determination of genetic variability among evaluated accessions and that within the group there is high genetic variability useful for the plant breeding.

Genetic characterization of canine parvovirus from dogs in Pakistan.

Science.gov (United States)

Shabbir, M Z; Sohail, M U; Chaudhary, U N; Yaqub, W; Rashid, I; Saleem, M H; Munir, M

Canine parvoviruses (CPV) exist as antigenic variants with varying frequencies and genetic variabilities across the globe. Given the endemicity and high prevalence in Pakistan, we characterized the CPVs originating from dogs-population to elucidate viral diversity and evolution. Fecal samples from clinically diseased pups (n = 17) of different breeds and age (2-6 months) were processed for hemagglutination assay (HA), and later for partial amplification of VP2 gene sequence and amino acid analysis. A total of 11 samples (64.71%) were found positive both in hemagglutination and PCR assays. Phylogenetic and evolutionary analysis demonstrated higher genetic heterogeneity in studied strains and constituted seven clusters within the CPV-2a group, however, they shared high level of identity with Chinese strains. Further studies are necessary to elucidate genetic analysis and epidemiology of CPV variants across a wide geographical area of the country.

Functional genetic divergence in high CO2 adapted Emiliania huxleyi populations.

Science.gov (United States)

Lohbeck, Kai T; Riebesell, Ulf; Collins, Sinéad; Reusch, Thorsten B H

2013-07-01

Predicting the impacts of environmental change on marine organisms, food webs, and biogeochemical cycles presently relies almost exclusively on short-term physiological studies, while the possibility of adaptive evolution is often ignored. Here, we assess adaptive evolution in the coccolithophore Emiliania huxleyi, a well-established model species in biological oceanography, in response to ocean acidification. We previously demonstrated that this globally important marine phytoplankton species adapts within 500 generations to elevated CO2 . After 750 and 1000 generations, no further fitness increase occurred, and we observed phenotypic convergence between replicate populations. We then exposed adapted populations to two novel environments to investigate whether or not the underlying basis for high CO2 -adaptation involves functional genetic divergence, assuming that different novel mutations become apparent via divergent pleiotropic effects. The novel environment "high light" did not reveal such genetic divergence whereas growth in a low-salinity environment revealed strong pleiotropic effects in high CO2 adapted populations, indicating divergent genetic bases for adaptation to high CO2 . This suggests that pleiotropy plays an important role in adaptation of natural E. huxleyi populations to ocean acidification. Our study highlights the potential mutual benefits for oceanography and evolutionary biology of using ecologically important marine phytoplankton for microbial evolution experiments. © 2012 The Author(s). Evolution © 2012 The Society for the Study of Evolution.

Facial emotion perception differs in young persons at genetic and clinical high-risk for psychosis.

Science.gov (United States)

Kohler, Christian G; Richard, Jan A; Brensinger, Colleen M; Borgmann-Winter, Karin E; Conroy, Catherine G; Moberg, Paul J; Gur, Ruben C; Gur, Raquel E; Calkins, Monica E

2014-05-15

A large body of literature has documented facial emotion perception impairments in schizophrenia. More recently, emotion perception has been investigated in persons at genetic and clinical high-risk for psychosis. This study compared emotion perception abilities in groups of young persons with schizophrenia, clinical high-risk, genetic risk and healthy controls. Groups, ages 13-25, included 24 persons at clinical high-risk, 52 first-degree relatives at genetic risk, 91 persons with schizophrenia and 90 low risk persons who completed computerized testing of emotion recognition and differentiation. Groups differed by overall emotion recognition abilities and recognition of happy, sad, anger and fear expressions. Pairwise comparisons revealed comparable impairments in recognition of happy, angry, and fearful expressions for persons at clinical high-risk and schizophrenia, while genetic risk participants were less impaired, showing reduced recognition of fearful expressions. Groups also differed for differentiation of happy and sad expressions, but differences were mainly between schizophrenia and control groups. Emotion perception impairments are observable in young persons at-risk for psychosis. Preliminary results with clinical high-risk participants, when considered along findings in genetic risk relatives, suggest social cognition abilities to reflect pathophysiological processes involved in risk of schizophrenia. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Selection of common bean lines with high grain yield and high grain calcium and iron concentrations

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Nerinéia Dalfollo Ribeiro

2014-02-01

Full Text Available Genetic improvement of common bean nutritional quality has advantages in marketing and can contribute to society as a food source. The objective of this study was to evaluate the genetic variability for grain yield, calcium and iron concentrations in grains of inbred common bean lines obtained by different breeding methods. For this, 136 F7 inbred lines were obtained using the Pedigree method and 136 F7 inbred lines were obtained using the Single-Seed Descent (SSD method. The lines showed genetic variability for grain yield, and concentrations of calcium and iron independently of the method of advancing segregating populations. The Pedigree method allows obtaining a greater number of lines with high grain yield. Selection using the SSD method allows the identification of a larger number of lines with high concentrations of calcium and iron in grains. Weak negative correlations were found between grain yield and calcium concentration (r = -0.0994 and grain yield and iron concentration (r = -0.3926. Several lines show genetic superiority for grain yield and concentrations of calcium and iron in grains and their selection can result in new common bean cultivars with high nutritional quality.

Mutation Scanning in a Single and a Stacked Genetically Modified (GM) Event by Real-Time PCR and High Resolution Melting (HRM) Analysis

Science.gov (United States)

Ben Ali, Sina-Elisabeth; Madi, Zita Erika; Hochegger, Rupert; Quist, David; Prewein, Bernhard; Haslberger, Alexander G.; Brandes, Christian

2014-01-01

Genetic mutations must be avoided during the production and use of seeds. In the European Union (EU), Directive 2001/18/EC requires any DNA construct introduced via transformation to be stable. Establishing genetic stability is critical for the approval of genetically modified organisms (GMOs). In this study, genetic stability of two GMOs was examined using high resolution melting (HRM) analysis and real-time polymerase chain reaction (PCR) employing Scorpion primers for amplification. The genetic variability of the transgenic insert and that of the flanking regions in a single oilseed rape variety (GT73) and a stacked maize (MON88017 × MON810) was studied. The GT73 and the 5' region of MON810 showed no instabilities in the examined regions. However; two out of 100 analyzed samples carried a heterozygous point mutation in the 3' region of MON810 in the stacked variety. These results were verified by direct sequencing of the amplified PCR products as well as by sequencing of cloned PCR fragments. The occurrence of the mutation suggests that the 5' region is more suitable than the 3' region for the quantification of MON810. The identification of the single nucleotide polymorphism (SNP) in a stacked event is in contrast to the results of earlier studies of the same MON810 region in a single event where no DNA polymorphism was found. PMID:25365178

Effect of oligonucleotide primers in determining viral variability within hosts

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Moya Andrés

2004-12-01

Full Text Available Abstract Background Genetic variability in viral populations is usually estimated by means of polymerase chain reaction (PCR based methods in which the relative abundance of each amplicon is assumed to be proportional to the frequency of the corresponding template in the initial sample. Although bias in template-to-product ratios has been described before, its relevance in describing viral genetic variability at the intrapatient level has not been fully assessed yet. Results To investigate the role of oligonucleotide design in estimating viral variability within hosts, genetic diversity in hepatitis C virus (HCV populations from eight infected patients was characterised by two parallel PCR amplifications performed with two slightly different sets of primers, followed by cloning and sequencing (mean = 89 cloned sequences per patient. Population genetics analyses of viral populations recovered by pairs of amplifications revealed that in seven patients statistically significant differences were detected between populations sampled with different set of primers. Conclusions Genetic variability analyses demonstrates that PCR selection due to the choice of primers, differing in their degeneracy degree at some nucleotide positions, can eclipse totally or partially viral variants, hence yielding significant different estimates of viral variability within a single patient and therefore eventually producing quite different qualitative and quantitative descriptions of viral populations within each host.

Effect of oligonucleotide primers in determining viral variability within hosts.

Science.gov (United States)

Bracho, Maria Alma; García-Robles, Inmaculada; Jiménez, Nuria; Torres-Puente, Manuela; Moya, Andrés; González-Candelas, Fernando

2004-12-09

Genetic variability in viral populations is usually estimated by means of polymerase chain reaction (PCR) based methods in which the relative abundance of each amplicon is assumed to be proportional to the frequency of the corresponding template in the initial sample. Although bias in template-to-product ratios has been described before, its relevance in describing viral genetic variability at the intrapatient level has not been fully assessed yet. To investigate the role of oligonucleotide design in estimating viral variability within hosts, genetic diversity in hepatitis C virus (HCV) populations from eight infected patients was characterised by two parallel PCR amplifications performed with two slightly different sets of primers, followed by cloning and sequencing (mean = 89 cloned sequences per patient). Population genetics analyses of viral populations recovered by pairs of amplifications revealed that in seven patients statistically significant differences were detected between populations sampled with different set of primers. Genetic variability analyses demonstrates that PCR selection due to the choice of primers, differing in their degeneracy degree at some nucleotide positions, can eclipse totally or partially viral variants, hence yielding significant different estimates of viral variability within a single patient and therefore eventually producing quite different qualitative and quantitative descriptions of viral populations within each host.

Genetic variability in Oligosarcus paranensis (Teleostei: Characiformes from the São Francisco river, Ivaí river basin – Paraná State, Brazil - doi: 10.4025/actascibiolsci.v35i3.14179

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Michele Rocha dos Santos

2013-08-01

Full Text Available The genetic variability of Oligosarcus paranensis was estimated from a population collected in São Francisco river, Prudentópolis county in Paraná State (Brazil using the electrophoresis in starch gel technique. Eleven enzymatic systems were analyzed: Aspartate aminotransaminase (AAT; E. C. 2.6.1, Alcohol dehydrogenase (ADH; E. C. 1.1.1.1, Esterase (EST; E. C. 3.1.1.1, Glucose-6-phosphate isomerase (GPI; E. C. 5.3.1.9, Glycerol-3-Phosphate dehydrogenase (G3PDH; E. C. 1.1.1, Isocitrate dehydrogenase (IDH; E. C. 1.1.1.42, L-lactate dehydrogenase (LDH; E. C. 1.1.1.27, Malate dehydrogenase (MDH; E. C. 1.1.1.37 , Malate dehydrogenase NADP (ME; E. C. 1.1.1.40, Phosphoglucomutase (PGM; E. C. 5.4.2.2 and Sorbitol dehydrogenase (SORB; E.C. 1.1.1.14. Twenty loci were identified through 15% corn starch gel electrophoresis of which nine (45% were polymorphic. The average expected heterozygosity was estimated as 0.1229 ± 0.1728, and the observed was 0.0586 ± 0.1069, indicating high genetic variability. The average value of FIS = 0.5145 indicates homozygote excess.  

Non-native Listeners’ Recognition of High-Variability Speech Using PRESTO

Science.gov (United States)

Tamati, Terrin N.; Pisoni, David B.

2015-01-01

Background Natural variability in speech is a significant challenge to robust successful spoken word recognition. In everyday listening environments, listeners must quickly adapt and adjust to multiple sources of variability in both the signal and listening environments. High-variability speech may be particularly difficult to understand for non-native listeners, who have less experience with the second language (L2) phonological system and less detailed knowledge of sociolinguistic variation of the L2. Purpose The purpose of this study was to investigate the effects of high-variability sentences on non-native speech recognition and to explore the underlying sources of individual differences in speech recognition abilities of non-native listeners. Research Design Participants completed two sentence recognition tasks involving high-variability and low-variability sentences. They also completed a battery of behavioral tasks and self-report questionnaires designed to assess their indexical processing skills, vocabulary knowledge, and several core neurocognitive abilities. Study Sample Native speakers of Mandarin (n = 25) living in the United States recruited from the Indiana University community participated in the current study. A native comparison group consisted of scores obtained from native speakers of English (n = 21) in the Indiana University community taken from an earlier study. Data Collection and Analysis Speech recognition in high-variability listening conditions was assessed with a sentence recognition task using sentences from PRESTO (Perceptually Robust English Sentence Test Open-Set) mixed in 6-talker multitalker babble. Speech recognition in low-variability listening conditions was assessed using sentences from HINT (Hearing In Noise Test) mixed in 6-talker multitalker babble. Indexical processing skills were measured using a talker discrimination task, a gender discrimination task, and a forced-choice regional dialect categorization task. Vocabulary

Genetic diversity and germplasm conservation of three minor Andean tuber crop species

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Malice M.

2009-01-01

Full Text Available In traditional Andean agrosystems, three minor tuber crop species are of regional or local importance: oca (Oxalis tuberosa Molina, ulluco (Ullucus tuberosus Caldas and mashua (Tropaeolum tuberosum Ruiz and Pav.. Genetic diversity within these species is very large and could result from the high ecological and cultural variability that characterizes the Andean area. Nowadays, many anthropic or ecological factors cause the loss of diversity and contribute to genetic erosion. The development of conservation strategies for genetic resources of Andean tubers, in situ as well as ex situ, includes a better knowledge of diversity in addition to the study of Andean farming strategies linked to this genetic diversity.

Building high resolution genetic variation map for Mongolians

DEFF Research Database (Denmark)

Guo, Xiaosen

the paternal or maternal transmission, or carrying out the genetic disease studies based on the data of a small number of variants or partial genomic regions. In the study plan, first, we collected the genomic DNA of a representative Mongolian male individual, performed high coverage whole genome sequencing...... the pigmentation gene OCA2 play an important role in the convergent skin lightening of East Asians during recent human evolution. However, the genomics research on Mongolians, which attract strong research interests, still remains the levels of using the data of Y chromosome or Mitochondrial genome to explore...... the individual possesses a risk allele that may cause carnitine deficiency. Y haplogroup analysis located the paternal inheritance to the clade D3a, which is the one of oldest lineage in East Asians and present the most common in Tibeto- Burman populations. Through final population genetics analyses, we roughly...

The genetics of speciation by reinforcement.

Directory of Open Access Journals (Sweden)

Daniel Ortiz-Barrientos

2004-12-01

Full Text Available Reinforcement occurs when natural selection strengthens behavioral discrimination to prevent costly interspecies matings, such as when matings produce sterile hybrids. This evolutionary process can complete speciation, thereby providing a direct link between Darwin's theory of natural selection and the origin of new species. Here, by examining a case of speciation by reinforcement in Drosophila,we present the first high-resolution genetic study of variation within species for female mating discrimination that is enhanced by natural selection. We show that reinforced mating discrimination is inherited as a dominant trait, exhibits variability within species, and may be influenced by a known set of candidate genes involved in olfaction. Our results show that the genetics of reinforced mating discrimination is different from the genetics of mating discrimination between species, suggesting that overall mating discrimination might be a composite phenomenon, which in Drosophila could involve both auditory and olfactory cues. Examining the genetics of reinforcement provides a unique opportunity for both understanding the origin of new species in the face of gene flow and identifying the genetic basis of adaptive female species preferences, two major gaps in our understanding of speciation.

GENETIC DIVERSITY OF WINTER BREAD WHEAT (Triticum aestivum L. ssp. vulgare

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Sonja Petrović

2011-06-01

Full Text Available Diversity was analyzed based on agronomic and morphologic traits and molecular data. The main objectives of this study were: 1. to estimate genetic diversity of wheat germplasm using agronomic and morphologic traits and molecular markers, 2. to investigate the existence of genetic erosion within tested wheat germplasm, 3. to explore potential utilization of combination of agronomic, morphologic and molecular markers in plant breeding. Forty winter bread wheat varieties were used originating from Croatia, Austria, France, Italy and Russia. Field trial was conducted during two vegetation years (2007/2008, 2008/2009 in three replications according to randomized block design. Ten traits were included in agronomic and morphologic analysis. Composition of high molecular weight glutenin subunits (HMW GS was evaluated for 16 varieties, whereas literature data are used for the rest. Starch composition analysis was based on amylose and amylopectin isolation, their quantity and ratio. For the SSR analysis 26 microsatellite primers were used, and for the AFLP analysis four primer combinations. Statistical analysis was performed using SAS Software 9.1.3, NTSYS ver.2.2., Arlequin ver2.0. and Powermarker ver.3.25. Analyzed varieties displayed highly significant differences (p<0,001 for all agronomic traits and for amylose/amylopectin ratio. High variability of HMW GS was found among varieties. Estimation of genetic diversity based on morphologic and molecular data were used to construct dendograms. AMOVA was used to evaluate variability based on molecular data. Genetic diversity was estimated among and within morphologic and molecular data. SSR and AFLP markers showed efficient discrimination power between highly related genotypes. Significant correlation was found out between two molecular methods which showed more accurate estimate of genetic diversity than by agronomic and morphologic data.

North Atlantic Origin of Interdecadal variability of Siberian High

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Kim, Seon-Hwa; Sung, Mi-Kyung; Kim, Baek-Min

2017-04-01

We suggest that the changes in the mean atmospheric circulation structure in the North Atlantic Ocean upstream region of Eurasian continent play an important role in the interdecadal variability of Siberian High (SH) through the modulation of Ural blocking frequency. Previous studies suggested that the interdecadal variability of SH is partly explained by the Arctic Oscillation. However, in this study, we emphasize the role of 'Warm Arctic and Cold Eurasia (WACE)', which is the second mode of winter surface air temperature variability over Eurasia. We show that the correlation between SH and WACE is high in general compared to that between SH and AO. However, the correlation between SH and WACE does not always exhibit high constant value. It shows a distinctive interdecadal fluctuation in the correlation. We found that this fluctuation in the correlation is due to the interdecadal fluctuation of the continental trough over the North Atlantic and the resultant strengthening of in-situ atmospheric baroclinicity. This accompanies changes in the transient vorticity flux divergence which leads to the downstream wave development and anomalous anticyclonic flow near Ural region. Obviously, the existence of anticyclonic flow over Ural region helps more frequent occurrence of Ural blocking and it is shown that this condition favors positive WACE event, which links to an intensified SH.

Genetic Divergence and Chemotype Diversity in the Fusarium Head Blight Pathogen Fusarium poae.

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Vanheule, Adriaan; De Boevre, Marthe; Moretti, Antonio; Scauflaire, Jonathan; Munaut, Françoise; De Saeger, Sarah; Bekaert, Boris; Haesaert, Geert; Waalwijk, Cees; van der Lee, Theo; Audenaert, Kris

2017-08-23

Fusarium head blight is a disease caused by a complex of Fusarium species. F. poae is omnipresent throughout Europe in spite of its low virulence. In this study, we assessed a geographically diverse collection of F. poae isolates for its genetic diversity using AFLP (Amplified Fragment Length Polymorphism). Furthermore, studying the mating type locus and chromosomal insertions, we identified hallmarks of both sexual recombination and clonal spread of successful genotypes in the population. Despite the large genetic variation found, all F. poae isolates possess the nivalenol chemotype based on Tri7 sequence analysis. Nevertheless, Tri gene clusters showed two layers of genetic variability. Firstly, the Tri1 locus was highly variable with mostly synonymous mutations and mutations in introns pointing to a strong purifying selection pressure. Secondly, in a subset of isolates, the main trichothecene gene cluster was invaded by a transposable element between Tri5 and Tri6 . To investigate the impact of these variations on the phenotypic chemotype, mycotoxin production was assessed on artificial medium. Complex blends of type A and type B trichothecenes were produced but neither genetic variability in the Tri genes nor variability in the genome or geography accounted for the divergence in trichothecene production. In view of its complex chemotype, it will be of utmost interest to uncover the role of trichothecenes in virulence, spread and survival of F. poae .

Rapid genetic diversification within dog breeds as evidenced by a case study on Schnauzers.

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Streitberger, K; Schweizer, M; Kropatsch, R; Dekomien, G; Distl, O; Fischer, M S; Epplen, J T; Hertwig, S T

2012-10-01

As a result of strong artificial selection, the domesticated dog has arguably become one of the most morphologically diverse vertebrate species, which is mirrored in the classification of around 400 different breeds. To test the influence of breeding history on the genetic structure and variability of today's dog breeds, we investigated 12 dog breeds using a set of 19 microsatellite markers from a total of 597 individuals with about 50 individuals analysed per breed. High genetic diversity was noted over all breeds, with the ancient Asian breeds (Akita, Chow Chow, Shar Pei) exhibiting the highest variability, as was indicated chiefly by an extraordinarily high number of rare and private alleles. Using a Bayesian clustering method, we detected significant genetic stratification within the closely related Schnauzer breeds. The individuals of these three recently differentiated breeds (Miniature, Standard and Giant Schnauzer) could not be assigned to a single cluster each. This hidden genetic structure was probably caused by assortative mating owing to breeders' preferences regarding coat colour types and the underlying practice of breeding in separate lineages. Such processes of strong artificial disruptive selection for different morphological traits in isolated and relatively small lineages can result in the rapid creation of new dog types and potentially new breeds and represent a unique opportunity to study the evolution of genetic and morphological differences in recently diverged populations. © 2011 The Authors, Animal Genetics © 2011 Stichting International Foundation for Animal Genetics.

Low vagally-mediated heart rate variability and increased susceptibility to ventricular arrhythmias in rats bred for high anxiety.

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Carnevali, Luca; Trombini, Mimosa; Graiani, Gallia; Madeddu, Denise; Quaini, Federico; Landgraf, Rainer; Neumann, Inga D; Nalivaiko, Eugene; Sgoifo, Andrea

2014-04-10

In humans, there is a documented association between anxiety disorders and cardiovascular disease. Putative underlying mechanisms may include an impairment of the autonomic nervous system control of cardiac function. The primary objective of the present study was to characterize cardiac autonomic modulation and susceptibility to arrhythmias in genetic lines of rats that differ largely in their anxiety level. To reach this goal, electrocardiographic recordings were performed in high-anxiety behavior (HAB, n=10) and low-anxiety behavior (LAB, n=10) rats at rest, during stressful stimuli and under autonomic pharmacological manipulations, and analyzed by means of time- and frequency-domain indexes of heart rate variability. During resting conditions, HAB rats displayed a reduced heart rate variability, mostly in terms of lower parasympathetic (vagal) modulation compared to LAB rats. In HAB rats, this relatively low cardiac vagal control was associated with smaller heart rate responsiveness to acute stressors compared to LAB counterparts. In addition, beta-adrenergic pharmacological stimulation induced a larger incidence of ventricular tachyarrhythmias in HABs compared to LABs. At sacrifice, a moderate increase in heart-body weight ratio was observed in HAB rats. We conclude that high levels of anxiety-related behavior in rats are associated with signs of i) impaired autonomic modulation of heart rate (low vagally-mediated heart rate variability), ii) poor adaptive heart rate responsiveness to stressful stimuli, iii) increased arrhythmia susceptibility, and iv) cardiac hypertrophy. These results highlight the utility of the HAB/LAB model for investigating the mechanistic basis of the comorbidity between anxiety disorders and cardiovascular disease. Copyright © 2014 Elsevier Inc. All rights reserved.

Effects of Amerindian Genetic Ancestry on Clinical Variables and Therapy in Patients with Rheumatoid Arthritis.

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Sánchez, Elena; García de la Torre, Ignacio; Sacnún, Mónica; Goñi, Mario; Berbotto, Guillermo; Paira, Sergio; Musuruana, Jorge Luis; Graf, César; Alvarellos, Alejandro; Messina, Osvaldo D; Babini, Alejandra; Strusberg, Ingrid; Marcos, Juan Carlos; Scherbarth, Hugo; Spindler, Alberto; Quinteros, Ana; Toloza, Sergio; Moreno, José Luis C; Catoggio, Luis J; Tate, Guillermo; Eimon, Alicia; Citera, Gustavo; Pellet, Antonio Catalán; Nasswetter, Gustavo; Cardiel, Mario H; Miranda, Pedro; Ballesteros, Francisco; Esquivel-Valerio, Jorge A; Maradiaga-Ceceña, Marco A; Acevedo-Vásquez, Eduardo M; García, Conrado García; Tusié-Luna, Teresa; Pons-Estel, Bernardo A; Alarcón-Riquelme, Marta E

2017-12-01

To define whether Amerindian genetic ancestry correlates with clinical and therapeutic variables in admixed individuals with rheumatoid arthritis (RA) from Latin America. Patients with RA (n = 1347) and healthy controls (n = 1012) from Argentina, Mexico, Chile, and Peru were included. Samples were genotyped for the Immunochip v1 using the Illumina platform. Clinical data were obtained through interviews or the clinical history. Percentage of Amerindian ancestry was comparable between cases and controls. Morning stiffness (p ancestry after Bonferroni correction. Higher Amerindian ancestry correlated only with weight loss (p Bonferroni ancestry correlated with higher doses of azathioprine (p ancestry protects against most major clinical criteria of RA, but regarding the association of RF with increased European ancestry, age, sex, and smoking are modifiers. Ancestry also correlates with the therapeutic profiles.

Genetic high throughput screening in Retinitis Pigmentosa based on high resolution melting (HRM) analysis.

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Anasagasti, Ander; Barandika, Olatz; Irigoyen, Cristina; Benitez, Bruno A; Cooper, Breanna; Cruchaga, Carlos; López de Munain, Adolfo; Ruiz-Ederra, Javier

2013-11-01

Retinitis Pigmentosa (RP) involves a group of genetically determined retinal diseases caused by a large number of mutations that result in rod photoreceptor cell death followed by gradual death of cone cells. Most cases of RP are monogenic, with more than 80 associated genes identified so far. The high number of genes and variants involved in RP, among other factors, is making the molecular characterization of RP a real challenge for many patients. Although HRM has been used for the analysis of isolated variants or single RP genes, as far as we are concerned, this is the first study that uses HRM analysis for a high-throughput screening of several RP genes. Our main goal was to test the suitability of HRM analysis as a genetic screening technique in RP, and to compare its performance with two of the most widely used NGS platforms, Illumina and PGM-Ion Torrent technologies. RP patients (n = 96) were clinically diagnosed at the Ophthalmology Department of Donostia University Hospital, Spain. We analyzed a total of 16 RP genes that meet the following inclusion criteria: 1) size: genes with transcripts of less than 4 kb; 2) number of exons: genes with up to 22 exons; and 3) prevalence: genes reported to account for, at least, 0.4% of total RP cases worldwide. For comparison purposes, RHO gene was also sequenced with Illumina (GAII; Illumina), Ion semiconductor technologies (PGM; Life Technologies) and Sanger sequencing (ABI 3130xl platform; Applied Biosystems). Detected variants were confirmed in all cases by Sanger sequencing and tested for co-segregation in the family of affected probands. We identified a total of 65 genetic variants, 15 of which (23%) were novel, in 49 out of 96 patients. Among them, 14 (4 novel) are probable disease-causing genetic variants in 7 RP genes, affecting 15 patients. Our HRM analysis-based study, proved to be a cost-effective and rapid method that provides an accurate identification of genetic RP variants. This approach is effective for