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1

Copper tolerance and genetic diversity of Porcellionides sexfasciatus (ISOPODA) in a highly contaminated mine habitat.  

Science.gov (United States)

Organisms inhabiting metal-contaminated areas may develop metal tolerance, with either phenotypic adjustments or genetic changes (adaptation) or with both. In the present study, three populations of the terrestrial isopod Porcellionides sexfasciatus, collected at an abandoned mine area, were compared to assess the effects of metal contamination on tolerance to lethal and sublethal levels of copper, through comparison of survival, avoidance, and feeding. The effects of metal contamination on genetic diversity were considered using random amplified polymorphic DNA (RAPD) markers. No evidence of increased metal tolerance of the population inhabiting the contaminated site was found. There was no correlation between metal exposure and within-population genetic variance, but the three populations were clearly separated from each other. In conclusion, the populations of P. sexfasciatus in the mine landscape live rather isolated from each other and show no differential tolerance to Cu or indications of genetic erosion. Their phenotypic plasticity provides a means to survive despite exposure to extremely high metal concentrations in the soil. PMID:23322508

Costa, Dalila; Bouchon, Didier; van Straalen, Nico M; Sousa, José Paulo; Ribeiro, Rui

2013-02-21

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Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background The Direct Repeat locus of the Mycobacterium tuberculosis complex (MTC) is a member of the CRISPR (Clustered regularly interspaced short palindromic repeats) sequences family. Spoligotyping is the widely used PCR-based reverse-hybridization blotting technique that assays the genetic diversity of this locus and is useful both for clinical laboratory, molecular epidemiology, evolutionary and population genetics. It is easy, robust, cheap, and produces highly diverse portable numerical results, as the result of the combination of (1) Unique Events Polymorphism (UEP) (2) Insertion-Sequence-mediated genetic recombination. Genetic convergence, although rare, was also previously demonstrated. Three previous international spoligotype databases had partly revealed the global and local geographical structures of MTC bacilli populations, however, there was a need for the release of a new, more representative and extended, international spoligotyping database. Results The fourth international spoligotyping database, SpolDB4, describes 1939 shared-types (STs) representative of a total of 39,295 strains from 122 countries, which are tentatively classified into 62 clades/lineages using a mixed expert-based and bioinformatical approach. The SpolDB4 update adds 26 new potentially phylogeographically-specific MTC genotype families. It provides a clearer picture of the current MTC genomes diversity as well as on the relationships between the genetic attributes investigated (spoligotypes) and the infra-species classification and evolutionary history of the species. Indeed, an independent Naïve-Bayes mixture-model analysis has validated main of the previous supervised SpolDB3 classification results, confirming the usefulness of both supervised and unsupervised models as an approach to understand MTC population structure. Updated results on the epidemiological status of spoligotypes, as well as genetic prevalence maps on six main lineages are also shown. Our results suggests the existence of fine geographical genetic clines within MTC populations, that could mirror the passed and present Homo sapiens sapiens demographical and mycobacterial co-evolutionary history whose structure could be further reconstructed and modelled, thereby providing a large-scale conceptual framework of the global TB Epidemiologic Network. Conclusion Our results broaden the knowledge of the global phylogeography of the MTC complex. SpolDB4 should be a very useful tool to better define the identity of a given MTC clinical isolate, and to better analyze the links between its current spreading and previous evolutionary history. The building and mining of extended MTC polymorphic genetic databases is in progress.

Brudey Karine; Driscoll Jeffrey R; Rigouts Leen; Prodinger Wolfgang M; Gori Andrea; Al-Hajoj Sahal A; Allix Caroline; Aristimuño Liselotte; Arora Jyoti; Baumanis Viesturs; Binder Lothar; Cafrune Patricia; Cataldi Angel; Cheong Soonfatt; Diel Roland; Ellermeier Christopher; Evans Jason T; Fauville-Dufaux Maryse; Ferdinand Séverine; de Viedma Dario; Garzelli Carlo; Gazzola Lidia; Gomes Harrison M; Guttierez M Cristina; Hawkey Peter M; van Helden Paul D; Kadival Gurujaj V; Kreiswirth Barry N; Kremer Kristin; Kubin Milan; Kulkarni Savita P; Liens Benjamin; Lillebaek Troels; Ly Ho; Martin Carlos; Martin Christian; Mokrousov Igor; Narvskaïa Olga; Ngeow Yun; Naumann Ludmilla; Niemann Stefan; Parwati Ida; Rahim Zeaur; Rasolofo-Razanamparany Voahangy; Rasolonavalona Tiana; Rossetti M Lucia; Rüsch-Gerdes Sabine; Sajduda Anna; Samper Sofia; Shemyakin Igor G; Singh Urvashi B; Somoskovi Akos; Skuce Robin A; van Soolingen Dick; Streicher Elisabeth M; Suffys Philip N; Tortoli Enrico; Tracevska Tatjana; Vincent Véronique; Victor Tommie C; Warren Robin M; Yap Sook; Zaman Khadiza; Portaels Françoise; Rastogi Nalin; Sola Christophe

2006-01-01

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Recombination and Genetic Diversity  

Scientific Electronic Library Online (English)

Full Text Available Abstract in english In this paper we present a spatial stochastic model for genetic recombination, that answers if diversity is preserved in an infinite population of recombinat-ing individuals distributed spatially. We show that, for finite times, recombination may maintain all the various potential different types, but when time grows infinitely, the diversity of individuals extinguishes off. So under the model premisses, recombination and spatial localization alone are not enough to expla (more) in diversity in a population. Further we discuss an application of the model to a controversy regarding the diversity of "Major Histocompatibility Complex" (MHC).

Coutinho, T. C.; Silva, T.T.da; Toledo, G.L.

2012-12-01

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Genetic Diversity and Human Equality.  

Science.gov (United States)

The idea of equality often, if not frequently, bogs down in confusion and apparent contradictions; equality is confused with identity, and diversity with inequality. It would seem that the easiest way to discredit the idea of equality is to show that people are innately, genetically, and, therefore, irremediably diverse and unlike. The snare is,…

Dobzhansky, Theodosius

5

Bacterial Diversity at an Acid Mine Drainage Site in Maine  

Science.gov (United States)

Bacterial diversity in acidic mine drainage at a historic Maine iron mining site was investigated by isolation of environmental DNA, PCR amplification of the V3 region of the 16S rRNA gene, denaturing gradient gel electrophoresis, and DNA sequencing.

Gaynor, J.; Sawyer, T.; Riley, F. E.; Moulton, K. D.; Rothschild, L. J.; Duboise, S. M.

2010-04-01

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Mining Frequent Itemsets Using Genetic Algorithm  

CERN Document Server

In general frequent itemsets are generated from large data sets by applying association rule mining algorithms like Apriori, Partition, Pincer-Search, Incremental, Border algorithm etc., which take too much computer time to compute all the frequent itemsets. By using Genetic Algorithm (GA) we can improve the scenario. The major advantage of using GA in the discovery of frequent itemsets is that they perform global search and its time complexity is less compared to other algorithms as the genetic algorithm is based on the greedy approach. The main aim of this paper is to find all the frequent itemsets from given data sets using genetic algorithm.

Ghosh, Soumadip; Sarkar, Debasree; Sarkar, Partha Pratim; 10.5121/ijaia.2010.1411

2010-01-01

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Genetic Diversity in Irrigated Rice  

Directory of Open Access Journals (Sweden)

Full Text Available Genetic diversity of 62 genotypes of irrigated rice originating from BRRI, IRRI and China were studied through Mahalanobis D2statistic. The genotypes were grouped into five clusters. The cluster II and IV contained the highest number of genotypes (16) and the cluster I contained the lowest (7). The highest intra cluster distance was noticed for the cluster I and the lowest for cluster III. The highest inter cluster distance was observed between cluster I and cluster IV followed by cluster I and cluster V, cluster I and cluster III, cluster III and cluster IV and lowest between cluster IV and cluster V. The highest cluster means for yield and other three yield contributing characters are obtained from cluster I, six highest and two second highest means for yield contributing characters are found in cluster III but the lowest cluster mean for yield. Therefore more emphasis should be given on cluster I for selecting genotypes as parents for crossing with the genotypes of cluster III, which may produce new recombinants with desired traits.

M.R. Islam; M.A.B. Faruquei; M.A.R. Bhuiyan; P.S. Biswas; M.A. Salam

2004-01-01

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Microbial Diversity in Uranium Mine Waste Heaps  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Two different uranium mine waste heaps near Ronneburg, Thuringia, Germany, which contain the remains of the activity of the former uranium-mining Soviet-East German company Wismut AG, were analyzed for the occurrence of lithotrophic and chemoorganotropic leach bacteria. A total of 162 ore samples we...

Schippers, A.; Hallmann, R.; Wentzien, S.; Sand, W.

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Mining Frequent Itemsets Using Genetic Algorithm  

Directory of Open Access Journals (Sweden)

Full Text Available In general frequent itemsets are generated from large data sets by applyingassociation rule mining algorithms like Apriori, Partition, Pincer-Search, Incremental, Borderalgorithm etc., which take too much computer time to compute all the frequent itemsets. By usingGenetic Algorithm (GA) we can improve the scenario. The major advantage of using GA in thediscovery of frequent itemsets is that they perform global search and its time complexity is lesscompared to other algorithms as the genetic algorithm is based on the greedy approach. Themain aim of this paper is to find all the frequent itemsets from given data sets using geneticalgorithm.

Soumadip Ghosh; Sushanta Biswas; Debasree Sarkar; Partha Pratim Sarkar

2010-01-01

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Association Rules Mining using Modified Genetic Algorithm  

Directory of Open Access Journals (Sweden)

Full Text Available the association rules are generally used to find out the relations between different data entities in given data set. Practically the data set can contain a large number of data entities which forms a large number of rules set but for the understanding of efficient relation it is needed that rules should be kept as minimum as possible without losing the useful information this is a difficult task and can be seen as optimization problem. In this paper we are presenting an improved genetic algorithm based association rule mining & the results shows that the proposed algorithm outperforms the genetic algorithm in terms of time and quality.

Prof. Shailendra Shrivastava

2012-01-01

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Does genetic diversity reduce sibling competition?  

UK PubMed Central (United Kingdom)

An enduring hypothesis for the proximal benefits of sex is that recombination increases the genetic variation among offspring and that this genetic variation increases offspring performance. A corollary of this hypothesis is that mothers that mate multiply increase genetic variation within a clutch and gain benefits due to genetic diversity alone. Many studies have demonstrated that multiple mating can increase offspring performance, but most attribute this increase to sexual selection and the role of genetic diversity has received less attention. Here, we used a breeding design to generate populations of full-siblings, half-siblings, and unrelated individuals of the solitary ascidian Ciona intestinalis. Importantly, we preclude the potentially confounding influences of maternal effects and sexual selection. We found that individuals in populations with greater genetic diversity had greater performance (metamorphic success, postmetamorphic survival, and postmetamorphic size) than individuals in populations with lower genetic diversity. Furthermore, we show that by mating with multiple males and thereby increasing genetic variation within a single clutch of offspring, females gain indirect fitness benefits in the absence of mate-choice. Our results show that when siblings are likely to interact, genetic variation among individuals can decrease competition for resources and generate substantial fitness benefits within a single generation.

Aguirre JD; Marshall DJ

2012-01-01

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Optimized association rule mining using genetic algorithm  

Directory of Open Access Journals (Sweden)

Full Text Available In general the rule generated by association rule mining algorithms like priori, partition,pincer-search, incremental, border algorithm etc, does not consider negation occurrence of the attributein them and also these rules have only one attribute in the consequent part. By using Genetic Algorithm(GAs) the system can predict the rules which contain negative attributes in the generated rules alongwith more than one attribute in consequent part. The major advantage of using GAs in the discovery ofprediction rules is that they perform global search and its complexity is less compared to otheralgorithms as the genetic algorithm is based on the greedy approach. The main aim of this paper is tofind all the possible optimized rules from given data set using genetic algorithm.

Anandhavalli M.; Suraj Kumar Sudhanshu; Ayush Kumar; Ghose M.K.

2009-01-01

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Genetic diversity of eleven European pig breeds  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract A set of eleven pig breeds originating from six European countries, and including a small sample of wild pigs, was chosen for this study of genetic diversity. Diversity was evaluated on the basis of 18 microsatellite markers typed over a total of 483 DNA samples collected. Average breed heterozygosity varied from 0.35 to 0.60. Genotypic frequencies generally agreed with Hardy-Weinberg expectations, apart from the German Landrace and Schwäbisch-Hällisches breeds, which showed significantly reduced heterozygosity. Breed differentiation was significant as shown by the high among-breed fixation index (overall FST = 0.27), and confirmed by the clustering based on the genetic distances between individuals, which grouped essentially all individuals in 11 clusters corresponding to the 11 breeds. The genetic distances between breeds were first used to construct phylogenetic trees. The trees indicated that a genetic drift model might explain the divergence of the two German breeds, but no reliable phylogeny could be inferred among the remaining breeds. The same distances were also used to measure the global diversity of the set of breeds considered, and to evaluate the marginal loss of diversity attached to each breed. In that respect, the French Basque breed appeared to be the most "unique" in the set considered. This study, which remains to be extended to a larger set of European breeds, indicates that using genetic distances between breeds of farm animals in a classical taxonomic approach may not give clear resolution, but points to their usefulness in a prospective evaluation of diversity.

Laval Guillaume; Iannuccelli Nathalie; Legault Christian; Milan Denis; Groenen Martien AM; Giuffra Elisabetta; Andersson Leif; Nissen Peter H; Jørgensen Claus B; Beeckmann Petra; Geldermann Hermann; Foulley Jean-Louis; Chevalet Claude; Ollivier Louis

2000-01-01

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Design and impact analysis for diversion at Coal Creek mine  

Energy Technology Data Exchange (ETDEWEB)

A diversion system has been designed to carry the flow from East Fork of Coal Creek around the area proposed for mining at Thunder Basin Coal Company's (TBCC) Coal Creek mine in Campbell County, Wyoming. This paper describes the field and analysis procedures necessary to prepare the diversion design and impact evaluation, and the innovative concepts developed for the diversion system design to minimize impacts on downstream channel stability. Under the proposed diversion system design, water from the East Basin of Coal Creek will be diverted at two locations. At one location, flow will be impounded by a small dam and decanted by a pump through a pipeline into East Fork at the location of the second diversion. At this location, a training dike will be placed across the stream channel to divert flows into a diversion channel. Gravity flow along the diversion channel will deliver water to a playa area which will be converted into a detention basin by placing a small dam across its southern end. Flows up to the magnitude of the 24-hour 2-year peak flow will be passed directly through the detention basin into Middle Fork with negligible attenuation of flow rates. For less frequent events, water will be stored in the detention basin in order to prevent velocities in Lower Middle Fork from exceeding the maximum permissible velocity above which scouring may occur. Evaporation and seepage losses from the diversion system were estimated to be small and should be more than offset by the addition of water from the playa drainage basin into the Coal Creek drainage. Velocities predicted for the Lower Middle Fork after the diversion is constructed are expected to be low enough that significant erosion of the channel is not expected to occur.

Bowles, D.S.; Grant, J.L.; Humphries, W.E.; O' Hayre, A.P.

1985-12-01

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Genetic diversity of Kensington mango in Australia.  

UK PubMed Central (United Kingdom)

The genetic diversity of Kensington mangoes (Mangifera indica L.) was investigated using random amplified polymorphic DNA (RAPD) analysis. DNA was extracted from leaves of 27 'Kensington Pride', 2 'R2E2' and 1 seedling. RAPD analysis with 10 oligonucleotide primers allowed the scoring of 107 markers. The R2E2 trees (20% dissimilarity) and the seedling (10% dissimilarity) were distinct from the Kensington Pride. However, there was very little evidence of significant genetic variation within Kensington Pride selections. Fifteen of the selections were identical in all 107 markers. Only 2 selections, WEAN2 and ML2N1, differed by more than 5%. These plants provide the best options for use in genetic improvement of the Kensington Pride mango. Many of the differences found in Kensington mango orchards may be due to environmental factors not genetic variations.

Bally ISE; Graham GC; Henry RJ

1996-01-01

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Mapping human genetic diversity in Asia.  

UK PubMed Central (United Kingdom)

Asia harbors substantial cultural and linguistic diversity, but the geographic structure of genetic variation across the continent remains enigmatic. Here we report a large-scale survey of autosomal variation from a broad geographic sample of Asian human populations. Our results show that genetic ancestry is strongly correlated with linguistic affiliations as well as geography. Most populations show relatedness within ethnic/linguistic groups, despite prevalent gene flow among populations. More than 90% of East Asian (EA) haplotypes could be found in either Southeast Asian (SEA) or Central-South Asian (CSA) populations and show clinal structure with haplotype diversity decreasing from south to north. Furthermore, 50% of EA haplotypes were found in SEA only and 5% were found in CSA only, indicating that SEA was a major geographic source of EA populations.

Abdulla MA; Ahmed I; Assawamakin A; Bhak J; Brahmachari SK; Calacal GC; Chaurasia A; Chen CH; Chen J; Chen YT; Chu J; Cutiongco-de la Paz EM; De Ungria MC; Delfin FC; Edo J; Fuchareon S; Ghang H; Gojobori T; Han J; Ho SF; Hoh BP; Huang W; Inoko H; Jha P; Jinam TA; Jin L; Jung J; Kangwanpong D; Kampuansai J; Kennedy GC; Khurana P; Kim HL; Kim K; Kim S; Kim WY; Kimm K; Kimura R; Koike T; Kulawonganunchai S; Kumar V; Lai PS; Lee JY; Lee S; Liu ET; Majumder PP; Mandapati KK; Marzuki S; Mitchell W; Mukerji M; Naritomi K; Ngamphiw C; Niikawa N; Nishida N; Oh B; Oh S; Ohashi J; Oka A; Ong R; Padilla CD; Palittapongarnpim P; Perdigon HB; Phipps ME; Png E; Sakaki Y; Salvador JM; Sandraling Y; Scaria V; Seielstad M; Sidek MR; Sinha A; Srikummool M; Sudoyo H; Sugano S; Suryadi H; Suzuki Y; Tabbada KA; Tan A; Tokunaga K; Tongsima S; Villamor LP; Wang E; Wang Y; Wang H; Wu JY; Xiao H; Xu S; Yang JO; Shugart YY; Yoo HS; Yuan W; Zhao G; Zilfalil BA

2009-12-01

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Genetic diversity of Coccidioides posadasii from Brazil.  

Science.gov (United States)

Studies of the genetic variation within populations of Coccidioides posadasii are scarce, especially for those recovered from South America. Understanding the distribution of genotypes among populations is important for epidemiological surveillance. This study evaluated the genetic diversity of 18 Brazilian strains of C. posadasii through the sequencing of the 18-28S region of nuclear rDNA, as well as through RAPD and M13-PCR fingerprinting techniques. The sequences obtained were compared to Coccidioides spp. previously deposited in GenBank. The MEGA5 program was used to perform phylogenetic analyses. Within the C. posadasii clade, a single cluster was observed, containing seven isolates from Ceará, which presented a single nucleotide polymorphism. These isolates were from the same geographical area. The strains of C. posadasii showed a lower rate of genetic diversity in the ITS1 and ITS2 regions. The results of M13 and RAPD-PCR fingerprinting indicated a similar electrophoretic profile. No differences between clinical and environmental isolates were detected. This was the first study assessing the genetic variability of a larger number of C. posadasii isolates from Brazil. PMID:23167705

Brilhante, Raimunda Sâmia Nogueira; de Lima, Rita Amanda Chaves; Ribeiro, Joyce Fonteles; de Camargo, Zoilo Pires; Castelo-Branco, Débora de Souza Collares Maia; Grangeiro, Thalles Barbosa; Cordeiro, Rossana de Aguiar; Gadelha Rocha, Marcos Fábio; Sidrim, José Júlio Costa

2012-11-21

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Managing genetic diversity and society needs  

Directory of Open Access Journals (Sweden)

Full Text Available Most livestock are not indigenous to Brazil. Several animal species were considered domesticated in the pre-colonial period, since the indigenous people manage them as would be typical of European livestock production. For over 500 years there have been periodic introductions resulting in the wide range of genetic diversity that for centuries supported domestic animal production in the country. Even though these naturalized breeds have acquired adaptive traits after centuries of natural selection, they have been gradually replaced by exotic breeds, to such an extent, that today they are in danger of extinction To avoid further loss of this important genetic material, in 1983 Embrapa Genetic Resources and Biotechnology decided to include conservation of animal genetic resources among its priorities. In this paper we describe the effort to genetically characterize these populations, as a tool to ensure their genetic variability. To effectively save the threatened local breeds of livestock it is important to find a niche market for each one, reinserting them in production systems. They have to be utilized in order to be conserved. And there is no doubt that due to their adaptive traits, the Brazilian local breeds of livestock can play an important role in animal production, to meet society needs.

Arthur da Silva Mariante; Andréa Alves Egito; Maria do Socorro Maués Albuquerque; Samuel Rezende Paiva; Alexandre Floriani Ramos

2008-01-01

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Genetic diversity of American wild rice species  

Scientific Electronic Library Online (English)

Full Text Available Abstract in english Studies on genetic diversity and genetic structure of natural populations are important in order to define strategies for in situ and ex situ conservation actions and for plant pre-breeding programs. Aiming to assess the genetic diversity and genetic structure of three wild American Oryza species with isozyme markers, 14 populations of the diploid O. glumaepatula (AglAgl), 11 populations of the tetraploid O. grandiglumis (CCDD) and five populations of the also tetraploid (more) O. latifolia (CCDD) were studied. They were all originated from Rio Paraguay hydrographic basin and the Amazon. Four enzymes were used and they gave 40 polymorphic bands. The most polymorphic species was O. glumaepatula, followed by O. latifolia and O. grandiglumis. A cluster analysis with the Jaccard similarity coefficient separated the diploid from the two tetraploid species, and also the two tetraploid species. This separation was also evident on a scatter plot from a principal component analysis, suggesting that they should be treated as two separate species, although further studies are necessary to provide support for this affirmative. The AMOVA analyses showed a high intrapopulational variability for O. latifolia (67.6%) and O. grandiglumis (52.2%), when compared to their interpopulational variability (32.4% and 47.8%, respectively), which suggests the hypothesis of a higher degree of outcrossing events within these species. When studying the correlation between the Jaccard dissimilarity coefficient and geographic distances, a spatial genetic structure was observed for O. glumaepatula only. These results are important for defining strategies of both in situ and ex situ conservation.

Veasey, Elizabeth Ann; Bressan, Eduardo de Andrade; Zucchi, Maria Imaculada; Vencovsky, Roland; Cardim, Daruska Cavalcante; Silva, Rainério Meireles da

2011-08-01

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Genetic diversity of American wild rice species  

Directory of Open Access Journals (Sweden)

Full Text Available Studies on genetic diversity and genetic structure of natural populations are important in order to define strategies for in situ and ex situ conservation actions and for plant pre-breeding programs. Aiming to assess the genetic diversity and genetic structure of three wild American Oryza species with isozyme markers, 14 populations of the diploid O. glumaepatula (AglAgl), 11 populations of the tetraploid O. grandiglumis (CCDD) and five populations of the also tetraploid O. latifolia (CCDD) were studied. They were all originated from Rio Paraguay hydrographic basin and the Amazon. Four enzymes were used and they gave 40 polymorphic bands. The most polymorphic species was O. glumaepatula, followed by O. latifolia and O. grandiglumis. A cluster analysis with the Jaccard similarity coefficient separated the diploid from the two tetraploid species, and also the two tetraploid species. This separation was also evident on a scatter plot from a principal component analysis, suggesting that they should be treated as two separate species, although further studies are necessary to provide support for this affirmative. The AMOVA analyses showed a high intrapopulational variability for O. latifolia (67.6%) and O. grandiglumis (52.2%), when compared to their interpopulational variability (32.4% and 47.8%, respectively), which suggests the hypothesis of a higher degree of outcrossing events within these species. When studying the correlation between the Jaccard dissimilarity coefficient and geographic distances, a spatial genetic structure was observed for O. glumaepatula only. These results are important for defining strategies of both in situ and ex situ conservation.

Elizabeth Ann Veasey; Eduardo de Andrade Bressan; Maria Imaculada Zucchi; Roland Vencovsky; Daruska Cavalcante Cardim; Rainério Meireles da Silva

2011-01-01

 
 
 
 
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Great ape genetic diversity and population history.  

UK PubMed Central (United Kingdom)

Most great ape genetic variation remains uncharacterized; however, its study is critical for understanding population history, recombination, selection and susceptibility to disease. Here we sequence to high coverage a total of 79 wild- and captive-born individuals representing all six great ape species and seven subspecies and report 88.8?million single nucleotide polymorphisms. Our analysis provides support for genetically distinct populations within each species, signals of gene flow, and the split of common chimpanzees into two distinct groups: Nigeria-Cameroon/western and central/eastern populations. We find extensive inbreeding in almost all wild populations, with eastern gorillas being the most extreme. Inferred effective population sizes have varied radically over time in different lineages and this appears to have a profound effect on the genetic diversity at, or close to, genes in almost all species. We discover and assign 1,982 loss-of-function variants throughout the human and great ape lineages, determining that the rate of gene loss has not been different in the human branch compared to other internal branches in the great ape phylogeny. This comprehensive catalogue of great ape genome diversity provides a framework for understanding evolution and a resource for more effective management of wild and captive great ape populations.

Prado-Martinez J; Sudmant PH; Kidd JM; Li H; Kelley JL; Lorente-Galdos B; Veeramah KR; Woerner AE; O'Connor TD; Santpere G; Cagan A; Theunert C; Casals F; Laayouni H; Munch K; Hobolth A; Halager AE; Malig M; Hernandez-Rodriguez J; Hernando-Herraez I; Prüfer K; Pybus M; Johnstone L; Lachmann M; Alkan C; Twigg D; Petit N; Baker C; Hormozdiari F; Fernandez-Callejo M; Dabad M; Wilson ML; Stevison L; Camprubí C; Carvalho T; Ruiz-Herrera A; Vives L; Mele M; Abello T; Kondova I; Bontrop RE; Pusey A; Lankester F; Kiyang JA; Bergl RA; Lonsdorf E; Myers S; Ventura M; Gagneux P; Comas D; Siegismund H; Blanc J; Agueda-Calpena L; Gut M; Fulton L; Tishkoff SA; Mullikin JC; Wilson RK; Gut IG; Gonder MK; Ryder OA; Hahn BH; Navarro A; Akey JM; Bertranpetit J; Reich D; Mailund T; Schierup MH; Hvilsom C; Andrés AM; Wall JD; Bustamante CD; Hammer MF; Eichler EE; Marques-Bonet T

2013-07-01

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Great ape genetic diversity and population history  

DEFF Research Database (Denmark)

Most great ape genetic variation remains uncharacterized; however, its study is critical for understanding population history, recombination, selection and susceptibility to disease. Here we sequence to high coverage a total of 79 wild- and captive-born individuals representing all six great ape species and seven subspecies and report 88.8?million single nucleotide polymorphisms. Our analysis provides support for genetically distinct populations within each species, signals of gene flow, and the split of common chimpanzees into two distinct groups: Nigeria-Cameroon/western and central/eastern populations. We find extensive inbreeding in almost all wild populations, with eastern gorillas being the most extreme. Inferred effective population sizes have varied radically over time in different lineages and this appears to have a profound effect on the genetic diversity at, or close to, genes in almost all species. We discover and assign 1,982 loss-of-function variants throughout the human and great ape lineages, determining that the rate of gene loss has not been different in the human branch compared to other internal branches in the great ape phylogeny. This comprehensive catalogue of great ape genome diversity provides a framework for understanding evolution and a resource for more effective management of wild and captive great ape populations.

Prado-Martinez, Javier; Sudmant, Peter H

2013-01-01

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A Survey of Association Rule Mining Using Genetic Algorithm  

Directory of Open Access Journals (Sweden)

Full Text Available Data mining is the analysis step of the "Knowledge Discovery in Databases" process, or KDD. It is the process that results in the discovery of new patterns in large data sets. It utilizes methods at the intersection of artificial intelligence, machine learning, statistics, and database systems. The overall goal of the data mining process is to extract knowledge from an existing data set and transform it into a human-understandable structure. In data mining, association rule learning is a popular and well researched method for discovering interesting relations between variables in large databases. Association rules are usually required to satisfy a user-specified minimum support and a user-specified minimum confidence at the same time. Genetic algorithm (GA) is a search heuristic that mimics the process of natural evolution. This heuristic is routinely used to generate useful solutions to optimization and search problems. Genetic algorithms belong to the larger class of evolutionary algorithms, which generate solutions to optimization problems using techniques inspired by natural evolution, such as inheritance, mutation, selection, and crossover. In previous, many researchers have proposed Genetic Algorithms for mining interesting association rules from quantitative data. In this paper we represent a survey of Association Rule Mining Using Genetic Algorithm. The techniques are categorized based upon different approaches. This paper provides the major advancement in the approaches for association rule mining using genetic algorithms.

Anubha Sharma

2012-01-01

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Genetic erosion of diversity in cereals  

Directory of Open Access Journals (Sweden)

Full Text Available Cereals play an important role in human nutrition. Consequently, one of the main goals in breeding is to obtain varieties with high genetic potential for yield. Modern agricultural production includes the expansion of intensive varieties over large areas that lead to narrow selection criteria in breeding programs. The consequence is a drastic reduction in the number of species and genotypes (genetic erosion), or harming biological diversity of local populations, and spontaneous relatives (biodiversity) in cereals. Based on detailed inventories of the territory of Montenegro and to some extent in Eastern Serbia, a endangerment of gene pool in cereals could be denoted. The reason for this is a transition to another type of agricultural production, changing land purposes, the presence of nursing homes, and use of intensive varieties. Old varieties and local populations represent the original genetic variability that could be used in breeding programs and organic production. It is therefore essential to take measures to preserve the genetic resources of cereals.

Petrovi? Sofija; Dimitrijevi? Miodrag

2012-01-01

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A Survey: Web Log Mining using Genetic Algorithm .  

Directory of Open Access Journals (Sweden)

Full Text Available Web mining has become a vast area of Research in last few years. Web Mining Which deals with the extraction of interesting knowledge from logging information produced by web server. In this paper we present a survey generate clusters using a multi objective genetic algorithm. Genetic algorithm is also a very hot area of research. In this paper we will compare the error value between FCM(Fuzzy c-means) and FCM-MOGA(Fuzzy CMeans multi objective Genetic algorithm). Genetic algorithm follows some steps and produce optimize solution. In using GA standard deviation and iteration value also affected. In this paper we have survey various paper based on Web log mining and FCM and GA.

Ranu Singhal; NirupamaTiwari

2013-01-01

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GENETIC DIVERSITY IN CROP IMPROVEMENT: THE SOYBEAN EXPERIENCE  

Science.gov (United States)

Crop diversity is essential to sustainable food production. Japan is a historical center of diversity for soybean (possibly introduced ca. 0 A.D.) but diversity of modern Japanese cultivars is not well characterized. The objectives of this study were to quantify genetic diversity of Japanese culti...

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Rarity and genetic diversity in Indo-Pacific Acropora corals.  

UK PubMed Central (United Kingdom)

Among various potential consequences of rarity is genetic erosion. Neutral genetic theory predicts that rare species will have lower genetic diversity than common species. To examine the association between genetic diversity and rarity, variation at eight DNA microsatellite markers was documented for 14 Acropora species that display different patterns of distribution and abundance in the Indo-Pacific Ocean. Our results show that the relationship between rarity and genetic diversity is not a positive linear association because, contrary to expectations, some rare species are genetically diverse and some populations of common species are genetically depleted. Our data suggest that inbreeding is the most likely mechanism of genetic depletion in both rare and common corals, and that hybridization is the most likely explanation for higher than expected levels of genetic diversity in rare species. A significant hypothesis generated from our study with direct conservation implications is that as a group, Acropora corals have lower genetic diversity at neutral microsatellite loci than may be expected from their taxonomic diversity, and this may suggest a heightened susceptibility to environmental change. This hypothesis requires validation based on genetic diversity estimates derived from a large portion of the genome.

Richards ZT; Oppen MJ

2012-08-01

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Rarity and genetic diversity in Indo-Pacific Acropora corals.  

Science.gov (United States)

Among various potential consequences of rarity is genetic erosion. Neutral genetic theory predicts that rare species will have lower genetic diversity than common species. To examine the association between genetic diversity and rarity, variation at eight DNA microsatellite markers was documented for 14 Acropora species that display different patterns of distribution and abundance in the Indo-Pacific Ocean. Our results show that the relationship between rarity and genetic diversity is not a positive linear association because, contrary to expectations, some rare species are genetically diverse and some populations of common species are genetically depleted. Our data suggest that inbreeding is the most likely mechanism of genetic depletion in both rare and common corals, and that hybridization is the most likely explanation for higher than expected levels of genetic diversity in rare species. A significant hypothesis generated from our study with direct conservation implications is that as a group, Acropora corals have lower genetic diversity at neutral microsatellite loci than may be expected from their taxonomic diversity, and this may suggest a heightened susceptibility to environmental change. This hypothesis requires validation based on genetic diversity estimates derived from a large portion of the genome. PMID:22957189

Richards, Zoe T; Oppen, Madeleine J H

2012-07-06

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Conservation of Genetic Diversity in Culture Plants  

Directory of Open Access Journals (Sweden)

Full Text Available The most important international document relating to the conservation of biodiversity is one adopted by theUN in Rio de Janeiro (1992) that "Convention on Biodiversity". Based on this agreement, the EU has taken a series ofmeasures to reduce genetic erosion in agriculture, which grew with the expansion of industrialized agriculture.Throughout its existence, mankind has used some 10,000 growing plant species. According to FAO statistics, today,90% of food production is ensured by some 120 growing plant species. In addition to drastic reduction in specificdiversity, the advent of industrialized agriculture has generated a process of strong genetic erosion. Old varieties andlocal varieties of crops have mostly been affected, in favour of "modern" varieties. Landraces are characterized by highheterogenity. They have the advantage of being much better adapted to biotic and abiotic stress conditions (diseases,pests, drought, low in nutrients, etc.) and have excellent taste qualities, which can justify a higher price recovery thancommercial varieties. Thanks to these features, these crops need small inputs, which correspond to the concept ofsustainable development. Landraces are an invaluable genetic potential for obtaining new varieties of plants and are bestsuited for crop cultivation in ecological systems, becoming more common. Also, for long term food security in thecontext of global warming, rich genetic diversity will be require. “In situ” and “ex situ” conservation are the two majorstrategies used in the conservation of plant genetic resources. There is a fundamental difference between these twostrategies: “ex situ” conservation involves sampling, transfer and storage of a particular species population away fromthe original location, while “in situ” conservation (in their natural habitat) implies that the varieties of interest,management and monitoring their place of origin takes place in the community to which they belong. These twostrategies should not be viewed as alternatives or in opposition, but a complementary approach is required. Obviously,only the on farm preservation, with traditional technologies, allows a sustainable management of the varieties, becausethese, in their natural habitat, can continue their evolutionary processes under the pressures of the environment, man,and technology. Romania, with an agricultural area of 14,722 millions Ha, still has a very rich diversity of conservationvarieties in plants growing, but they risk losing if appropriate action is taken.

MAXIM A.

2010-01-01

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A genetic algorithm-based approach to data mining  

Energy Technology Data Exchange (ETDEWEB)

Most data mining systems to date have used variants of traditional machine-learning algorithms to tackle the task of directed knowledge discovery. This paper presents an approach which, as well as being useful for such directed data mining, can also be applied to the further tasks of undirected data mining and hypothesis refinement. This approach exploits parallel genetic algorithms as the search mechanism and seeks to evolve explicit {open_quotes}rules{close_quotes} for maximum comprehensibility. Example rules found in real commercial datasets are presented.

Flockhart, I.W.; Radcliffe, N.J. [Univ. of Edinburgh (United Kingdom)

1996-12-31

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Crop genetic diversity benefits farmland biodiversity in cultivated fields  

Digital Repository Infrastructure Vision for European Research (DRIVER)

This study tested whether increasing crop genetic diversity benefited farmland biodiversity in bread wheat (Triticum aestivum) fields, using an experimental approach in which arthropod and wild plant diversity were compared in a genetically homogeneous wheat variety vs. a variety mixture. The divers...

Chateil, Carole; Goldringer, Isabelle; Tarallo, Léa; Kerbiriou, Christian; Le Viol, Isabelle; Ponge, Jean-François

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Genetic diversity enhances restoration success by augmenting ecosystem services.  

UK PubMed Central (United Kingdom)

Disturbance and habitat destruction due to human activities is a pervasive problem in near-shore marine ecosystems, and restoration is often used to mitigate losses. A common metric used to evaluate the success of restoration is the return of ecosystem services. Previous research has shown that biodiversity, including genetic diversity, is positively associated with the provision of ecosystem services. We conducted a restoration experiment using sources, techniques, and sites similar to actual large-scale seagrass restoration projects and demonstrated that a small increase in genetic diversity enhanced ecosystem services (invertebrate habitat, increased primary productivity, and nutrient retention). In our experiment, plots with elevated genetic diversity had plants that survived longer, increased in density more quickly, and provided more ecosystem services (invertebrate habitat, increased primary productivity, and nutrient retention). We used the number of alleles per locus as a measure of genetic diversity, which, unlike clonal diversity used in earlier research, can be applied to any organism. Additionally, unlike previous studies where positive impacts of diversity occurred only after a large disturbance, this study assessed the importance of diversity in response to potential environmental stresses (high temperature, low light) along a water-depth gradient. We found a positive impact of diversity along the entire depth gradient. Taken together, these results suggest that ecosystem restoration will significantly benefit from obtaining sources (transplants or seeds) with high genetic diversity and from restoration techniques that can maintain that genetic diversity.

Reynolds LK; McGlathery KJ; Waycott M

2012-01-01

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Islands as refugia of Trifolium repens genetic diversity  

UK PubMed Central (United Kingdom)

Island populations are often thought to be more susceptible to the loss of genetic diversity as a consequence of limited population size and genetic drift, greater susceptibility to detrimental stochastic events and low levels of immigration. However the geographic isolation of islands may create refuges for native crop species whose genetic diversity is threatened from the genetic erosion occurring in mainland areas as a result of crop-wild gene flow and genetic swamping. Many UK islands remain uncharacterised in terms of plant genetic diversity. In this study we compared the genetic diversity of mainland populations and landraces of Trifolium repens with wild populations collected from the islands surrounding the UK, including the island of Hirta in the St Kildan archipelago. Individuals from St Kilda represent a unique conservation resource, with populations both highly differentiated from UK mainland populations and genetically distinct from cultivated varieties, whilst able to retain diversity through limited human influence on the islands. In contrast, there is relative genetic similarity of wild UK populations to cultivated forms highlighted in mainland populations, but with geographic barriers preventing complete homogenisation of the mainland UK genepool. We underline the need for conservation priorities to include common species that are threatened by gene flow from cultivation, and draw attention to the potential of islands to preserve natural levels of genetic diversity.

Hargreaves Serene; Maxted Nigel; Hirano Ryoko; Abberton Michael; Skøt Leif; Ford-Lloyd BrianV

2010-06-01

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Genetic Landscapes GIS Toolbox: tools to map patterns of genetic divergence and diversity.  

UK PubMed Central (United Kingdom)

The Landscape Genetics GIS Toolbox contains tools that run in the Geographic Information System software, ArcGIS(®), to map genetic landscapes and to summarize multiple genetic landscapes as average and variance surfaces. These tools can be used to visualize the distribution of genetic diversity across geographic space and to study associations between patterns of genetic diversity and geographic features or other geo-referenced environmental data sets. Together, these tools create genetic landscape surfaces directly from tables containing genetic distance or diversity data and sample location coordinates, greatly reducing the complexity of building and analyzing these raster surfaces in a Geographic Information System.

Vandergast AG; Perry WM; Lugo RV; Hathaway SA

2011-01-01

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Genetic diversity of HCV in Brazil.  

UK PubMed Central (United Kingdom)

BACKGROUND: Many studies have documented the molecular epidemiological scenario of HCV within individual Brazilian states, but we still have an incomplete understanding of the dispersion dynamics of the virus in different regions throughout the country. METHODS: A total of 676 HCV NS5B gene sequences of subtypes 1a (n=321), 1b (n=170) and 3a (n=185), isolated from seven different Brazilian states covering four out of five regions were analysed in the present study. We also analysed 22 HCV NS5B gene sequences of minor genetic variants including genotype 2 (n=13), genotype 4 (n=6) and subtype 5a (n=3). Brazilian HCV sequences were aligned with sequences of non-Brazilian origin and subjected to maximum likelihood phylogenetic analyses. RESULTS: These analyses revealed that the Brazilian HCV epidemic resulted from multiple introductions and autochthonous transmission of subtypes 1a, 1b, 3a and genotypes 2, 4 and 5. Brazilian HCV subtype 1a epidemic is dominated by the dissemination of one major clade; while Brazilian HCV subtypes 1b and 3a epidemics are characterized by concurrent dissemination of several independent HCV lineages. Some HCV Brazilian lineages of subtypes 1a, 1b, 2b and 3a were successful in becoming established and disseminated through several regions in the country. Despite significant phylogenetic intermixing of Brazilian sequences, the distribution of HCV strains from different states across lineages was not completely homogeneous. CONCLUSIONS: These results demonstrate the existence of multiple introductions and local propagation of both prevalent and uncommon HCV genetic variants in Brazil and identify some major Brazilian HCV clades with nationwide dissemination. This study also suggests that the observed HCV diversity in Brazil has been shaped by both frequent viral migration among regions and in situ viral dissemination.

Lampe E; Lewis-Ximenez L; Espírito-Santo MP; Delvaux NM; Pereira SA; Peres-da-Silva A; Martins RM; Soares MA; Santos AF; Vidal LL; Germano FN; de Martinez AM; Basso R; Pinho JR; Malta FM; Gomes-Gouvêa M; Moliterno RA; Bertolini DA; Fujishima MA; Bello G

2013-01-01

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Genetic Diversity of Escherichia Coli from Sanandaj  

Directory of Open Access Journals (Sweden)

Full Text Available Background and Objectives: The Escherichia coli strains are greatly important in nosocomial and community acquired infections. The aim of this study was to determine the transmission of bacterial infections using genetic analysis. Materials and Methods: Two hundred and thirty Escherichia coli strains, isolated from different clinical samples, were characterized by enterobacterial repetitive intergenic consensus (ERIC)–PCR technique. The results and the similarity between the strains were determined on the basis of Jaccard similarity coefficient in the SAHN program of the NTSYS-pc software.Results:The ERIC–PCR profiles allowed typing of the 230 isolates into 205 ERIC-types which were grouped into twenty main clusters (C01–C20).The first group makes up 4.34% of the total isolates. Out of the 230 isolates, 34.2% belonged to D phylogenic group which were associated with extra-intestinal samples.Conclusion: Our results showed high diversity in E. coli isolates indicating low rate of hospital infection in our university hospitals. The majority of the isolates belonged to the D phylogenic group.

Rashid Ramazanzadeh; Serveh Zamani; Saman Zamani

2013-01-01

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Genetic diversity of Echinococcus spp. in Russia.  

UK PubMed Central (United Kingdom)

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

Konyaev SV; Yanagida T; Nakao M; Ingovatova GM; Shoykhet YN; Bondarev AY; Odnokurtsev VA; Loskutova KS; Lukmanova GI; Dokuchaev NE; Spiridonov S; Alshinecky MV; Sivkova TN; Andreyanov ON; Abramov SA; Krivopalov AV; Karpenko SV; Lopatina NV; Dupal TA; Sako Y; Ito A

2013-08-01

38

GENETIC RESOURCES AND DIVERSITY IN PAKISTANI CATTLE  

Directory of Open Access Journals (Sweden)

Full Text Available Cattle in Pakistan have traditionally been raised for producing bullocks except breeds such as Sahiwal and Red Sindhi which are established milch breeds. General production system is low-input extensive system with crossbreds mainly raised under intensive high input system in the cattle/buffalo colonies to sustain the demand of milk especially during summer, the slump period in buffalo milk. Although, draft breeds are losing utility yet, it will take many generations before they are replaced due to mechanization. Efforts, however, are needed for their in situ conservation and directional selection towards beef. Institutional records indicate weak genetic control for most of the economic traits but accurate recording of performance and pedigrees can improve these estimates. Breeding policy guidelines need adoption in letter and sprit to conserve various breeds. Institutions established for breed improvement need to be restructured for achieving the goals. Adequate diversity in performance and adaptability can be exploited for actual improvement accruing to conservation and development of indigenous cattle resources.

M. SAJJAD KHAN, ZIA-UR REHMAN1 , MUQARRAB A. KHAN2 AND SOHAIL AHMAD3

2008-01-01

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Beauveria bassiana: Quercetinase production and genetic diversity.  

Science.gov (United States)

Beauveria bassiana genetic diversity and ability to synthesize quercetin 2,3-dioxygenase (quercetinase) were analyzed. B. bassiana isolates, obtained from Brazilian soil samples, produced quercetinase after induction using 0.5 g/L quercetin. B. bassiana ATCC 7159 (29.6 nmol/mL/min) and isolate IP 11 (27.5 nmol/ml/min) showed the best performances and IP 3a (9.5 nmol/mL/min) presented the lowest level of quercetinase activity in the culture supernatant. A high level of polymorphism was detected by random amplified polymorphic DNA (RAPD) analysis. The use of internal-transcribed-spacer ribosomal region restriction fragment length polymorphism (ITS-RFLP) did not reveal characteristic markers to differentiate isolates. However, the ITS1-5.8S-ITS2 region sequence analysis provided more information on polymorphism among the isolates, allowing them to be clustered by relative similarity into three large groups. Correlation was tested according to the Person's correlation. Data of our studies showed, that lower associations among groups, level of quercetinase production, or geographical origin could be observed. This study presents the production of a novel biocatalyst by B. bassiana and suggests the possible industrial application of this fungal species in large-scale biotechnological manufacture of quercetinase. PMID:24031599

Eula Maria de M B, Costa; Fabiana Cristina, Pimenta; Christian, Luz; Valéria de, Oliveira; Marília, Oliveira; Elda, Bueno; Silvana, Petrofeza

2011-03-01

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Beauveria bassiana: quercetinase production and genetic diversity  

Scientific Electronic Library Online (English)

Full Text Available Abstract in english Beauveria bassiana genetic diversity and ability to synthesize quercetin 2,3-dioxygenase (quercetinase) were analyzed. B. bassiana isolates, obtained from Brazilian soil samples, produced quercetinase after induction using 0.5 g/L quercetin. B. bassiana ATCC 7159 (29.6 nmol/mL/min) and isolate IP 11 (27.5 nmol/ml/min) showed the best performances and IP 3a (9.5 nmol/mL/min) presented the lowest level of quercetinase activity in the culture supernatant. A high level of pol (more) ymorphism was detected by random amplified polymorphic DNA (RAPD) analysis. The use of internal-transcribed-spacer ribosomal region restriction fragment length polymorphism (ITS-RFLP) did not reveal characteristic markers to differentiate isolates. However, the ITS1-5.8S-ITS2 region sequence analysis provided more information on polymorphism among the isolates, allowing them to be clustered by relative similarity into three large groups. Correlation was tested according to the Person's correlation. Data of our studies showed, that lower associations among groups, level of quercetinase production, or geographical origin could be observed. This study presents the production of a novel biocatalyst by B. bassiana and suggests the possible industrial application of this fungal species in large-scale biotechnological manufacture of quercetinase.

Costa, Eula Maria de M. B; Pimenta, Fabiana Cristina; Luz, Christian; Oliveira, Valéria de; Oliveira, Marília; Bueno, Elda; Petrofeza, Silvana

2011-03-01

 
 
 
 
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Beauveria bassiana: quercetinase production and genetic diversity  

Directory of Open Access Journals (Sweden)

Full Text Available Beauveria bassiana genetic diversity and ability to synthesize quercetin 2,3-dioxygenase (quercetinase) were analyzed. B. bassiana isolates, obtained from Brazilian soil samples, produced quercetinase after induction using 0.5 g/L quercetin. B. bassiana ATCC 7159 (29.6 nmol/mL/min) and isolate IP 11 (27.5 nmol/ml/min) showed the best performances and IP 3a (9.5 nmol/mL/min) presented the lowest level of quercetinase activity in the culture supernatant. A high level of polymorphism was detected by random amplified polymorphic DNA (RAPD) analysis. The use of internal-transcribed-spacer ribosomal region restriction fragment length polymorphism (ITS-RFLP) did not reveal characteristic markers to differentiate isolates. However, the ITS1-5.8S-ITS2 region sequence analysis provided more information on polymorphism among the isolates, allowing them to be clustered by relative similarity into three large groups. Correlation was tested according to the Person's correlation. Data of our studies showed, that lower associations among groups, level of quercetinase production, or geographical origin could be observed. This study presents the production of a novel biocatalyst by B. bassiana and suggests the possible industrial application of this fungal species in large-scale biotechnological manufacture of quercetinase.

Eula Maria de M. B Costa; Fabiana Cristina Pimenta; Christian Luz; Valéria de Oliveira; Marília Oliveira; Elda Bueno; Silvana Petrofeza

2011-01-01

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Genome mining expands the chemical diversity of the cyanobactin family to include highly modified linear peptides.  

UK PubMed Central (United Kingdom)

Ribosomal peptides are produced through the posttranslational modification of short precursor peptides. Cyanobactins are a growing family of cyclic ribosomal peptides produced by cyanobacteria. However, a broad systematic survey of the genetic capacity to produce cyanobactins is lacking. Here we report the identification of 31 cyanobactin gene clusters from 126 genomes of cyanobacteria. Genome mining suggested a complex evolutionary history defined by horizontal gene transfer and rapid diversification of precursor genes. Extensive chemical analyses demonstrated that some cyanobacteria produce short linear cyanobactins with a chain length ranging from three to five amino acids. The linear peptides were N-prenylated and O-methylated on the N and C termini, respectively, and named aeruginosamide and viridisamide. These findings broaden the structural diversity of the cyanobactin family to include highly modified linear peptides with rare posttranslational modifications.

Leikoski N; Liu L; Jokela J; Wahlsten M; Gugger M; Calteau A; Permi P; Kerfeld CA; Sivonen K; Fewer DP

2013-08-01

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A REVIEW ON GENETIC DIVERSITY OF WILD PLANTS BY USING DIFFERENT GENETIC MARKERS  

Directory of Open Access Journals (Sweden)

Full Text Available Biodiversity is the variation of life at all levels of biological organization. One of the important components of biological diversity is the genetic diversity. Genetic diversity refers to the variation of genes or entire genome within and between populations of organisms. Keeping in view the significance of genetic diversity in wild plants, some research articles based on important wild plant genera and species of angiosperms including few rare, threatened, endemic, medicinal and economically important from different regions of the world are reviewed. The genetic diversity of plant species depends on different factors i.e. ecological, geographical, breeding system & anthropogenic effects. High genetic diversity is observed at species level even in small sized population by using AFLP, SSR, & ISSR genetic markers.

Muhammad Younas Khan Barozai, Sazia Saeed

2012-01-01

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Genetic diversity in soybean genotypes with resistance to Heterodera glycines  

Directory of Open Access Journals (Sweden)

Full Text Available The purpose of this study was to analyze the genetic diversity among soybean genotypes inoculated with Heteroderaglycines race 3. The experiments were conducted in a greenhouse. In two performance tests of morphological characteristics andresistance to the pathogen, 27 soybean genotypes were assessed. The coefficient of genotypic determination was estimated by themethod of analysis of variance and the genetic diversity analyzed based on dendrograms and optimization method. The estimatedcoefficients of determination indicated a predominantly genetic origin of the genotypic differences in the traits. The genetic variabilitywas maintained in the superior genotypes, which can be used in breeding programs for resistance to soybean cyst nematode

Éder Matsuo; Tuneo Sediyama; Cosme Damião Cruz; Rosângela D’Arc de Lima Oliveira; Rita de Cássia Teixeira Oliveira; Ana Paula Oliveira Nogueira

2011-01-01

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Limited intra-genetic diversity in Dientamoeba fragilis housekeeping genes.  

UK PubMed Central (United Kingdom)

Dientamoeba fragilis is a common intestinal parasite of unsettled clinical significance. Differences in clinical outcome of parasitic infections may reflect parasite genetic diversity, and so tools to study intra-genetic diversity that could potentially reflect differences in clinical phenotypes are warranted. Here, we show that genetic analysis of three D. fragilis housekeeping genes enables clear distinction between the two known genotypes, but that integration of housekeeping genes in multi-locus sequencing tools for D. fragilis may have limited epidemiological and clinical value due to no further added genetic resolution.

Stensvold CR; Clark CG; Röser D

2013-08-01

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Limited intra-genetic diversity in Dientamoeba fragilis housekeeping genes.  

Science.gov (United States)

Dientamoeba fragilis is a common intestinal parasite of unsettled clinical significance. Differences in clinical outcome of parasitic infections may reflect parasite genetic diversity, and so tools to study intra-genetic diversity that could potentially reflect differences in clinical phenotypes are warranted. Here, we show that genetic analysis of three D. fragilis housekeeping genes enables clear distinction between the two known genotypes, but that integration of housekeeping genes in multi-locus sequencing tools for D. fragilis may have limited epidemiological and clinical value due to no further added genetic resolution. PMID:23681023

Stensvold, Christen Rune; Clark, C Graham; Röser, Dennis

2013-05-13

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Genetic diversity of Actinobacillus lignieresii isolates from different hosts  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Abstract Genetic diversity detected by analysis of amplified fragment length polymorphisms (AFLPs) of 54 Actinobacilus lignieresii isolates from different hosts and geographic localities is described. On the basis of variances in AFLP profiles, the strains were grouped in two majo...

Kokotovic Branko; Angen Øystein; Bisgaard Magne

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Genetic diversity among varieties of chia (Salvia hispanica L.).  

UK PubMed Central (United Kingdom)

Chia, Salvia hispanica L., was a staple crop in pre-Columbian Mesoamerica. Despite the great potential of the species as an oilseed crop, little research related to domesticated and wild varieties exists. A study was undertaken to assess genetic diversity among 38 wild and domesticated accessions of S. hispanica collected throughout Mesoamerica by using RAPD markers. Genetic diversity was higher among wild varieties (H(G) = 0.15) than all domesticated varieties (H(G) = 0.10) and modern commercial domesticated varieties (H(G) = 0.02), suggesting a slight loss of diversity accompanying domestication and a near lack of diversity in modern commercial varieties. In addition, the preliminary results indicate that the center of genetic diversity is in the highlands of western Mexico.

Cahill JP

2004-11-01

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Genetic diversity among fourteen different Fusarium species using RAPD marker  

Directory of Open Access Journals (Sweden)

Full Text Available Bonde SR, Gade AK, Rai MK. 2012. Genetic diversity among fourteen different Fusarium species using RAPD marker. Biodiversitas 13: 55-60. We report genetic diversity of total fourteen different Fusarium species by RAPD-PCR analysis using 25 random primers. The genus Fusarium is food borne pathogen responsible for T-2 toxin production which affects human and animal health. In the present study, total 14-different species of Fusarium were analyzed on the basis of genetic diversity using RAPD method. A dendrogram was developed by UPGMA method. RAPD analysis was carried out by using 25 different universal primers each of them consisted of 10 bases. Genetic similarity coefficients between pair wise varied from 0.00 to 0.9 based on an unweighted paired group method of arithmetic average (UPGMA) cluster analysis. RAPD-PCR technique can be used as an important tool for the genetic differentiation Fusarium species.

SHITAL R. BONDE; ANIKET K. GADE; MAHENDRA K. RAI

2013-01-01

50

Keel A Data Mining Tool: Analysis With Genetic  

Directory of Open Access Journals (Sweden)

Full Text Available This work is related to the KEEL (Knowledge Extraction basedon Evolutionary Learning) tool, an open source software thatsupports data management and provides a platform for theanalysis of evolutionary learning for Data Mining problems ofdifferent kinds including as regression, classification,unsupervised learning. It includes a big collection of evolutionarylearning algorithms based on different approaches: Pittsburgh,Michigan. It empowers the user to perform complete analysis ofany genetic fuzzy system in comparison to existing ones, with astatistical test module for comparison.

Ms. Pooja Mittal; Manju Narwal

2012-01-01

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The diversity of culturable airborne fungi in an active South African gold mine  

Scientific Electronic Library Online (English)

Full Text Available Abstract in english Several studies have been conducted on the presence and diversity of airborne fungal spores in residential and occupational areas. This is the first investigation on this topic in the mining environment. The impact of fungi-especially as opportunistic pathogens-on their health and productivity needs to be assessed, considering the compromised health of a large number of HIV-infected miners in South Africa. Accordingly, the aim of this study was to determine the abundance (more) of fungal spores as well as the diversity of culturable airborne fungi in an active gold mine. The results indicate that three of the sampled sites in the mine contain abundant numbers of culturable airborne fungi. The first site was next to an auxiliary extraction fan, which could act as an accumulator for airborne fungal spores from the rest of the mine. The two other sites had high human activity, disturbances from which may contribute to an elevated fungal load in the air. The presence of timber supports at one site may serve as a growth substrate for several fungal genera. The diversity of filamentous fungal genera increased from outside the mine to deeper into the mine, whereas the diversity of yeast genera followed an opposite trend, with no yeasts detected deep in the mine. Although most of the isolates identified are not pathogens, they could still have a negative impact (either as opportunistic pathogens or allergens) on workers, especially immunocompromised persons if exposed to them for prolonged periods.

Pohl, C.H.; Kriel, W.; Venter, P.; Van Heerden, E.; Albertyn, J.

2007-08-01

52

Positive relationships between genetic diversity and abundance in fishes.  

Science.gov (United States)

Molecular markers, such as mitochondrial DNA and microsatellite loci, are widely studied to assess population genetics and phylogeography; however, the selective neutrality of these markers is increasingly being questioned. Given the importance of molecular markers in fisheries science and conservation, we evaluated the neutrality of both mtDNA and microsatellite loci through their associations with population size. We surveyed mtDNA and microsatellite data from the primary literature and determined whether genetic diversity increased with abundance across a total of 105 marine and freshwater fishes, with both global fisheries catch data and body size as proxies for abundance (with an additional 57 species for which only body size data were assessed). We found that microsatellite data generally yielded higher associations with abundance than mtDNA data, and within mtDNA analyses, number of haplotypes and haplotype diversity were more strongly associated with abundance than nucleotide diversity, particularly for freshwater fishes. We compared genetic diversity between freshwater and marine fishes and found that marine fishes had higher values of all measures of genetic diversity than freshwater fishes. Results for both mtDNA and microsatellites generally conformed to neutral expectations, although weaker relationships were often found between mtDNA nucleotide diversity and 'abundance' compared to any other genetic statistic. We speculate that this is because of historical events unrelated to natural selection, although a role for selection cannot be ruled out. PMID:20849560

McCusker, Megan R; Bentzen, Paul

2010-09-17

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Promiscuity, sexual selection, and genetic diversity: a reply to spurgin.  

UK PubMed Central (United Kingdom)

We recently reported a positive association between female promiscuity and genetic diversity across passerine birds, and launched the hypothesis that female promiscuity acts as a balancing selection, pressure maintaining genetic diversity in populations (Gohli et al. ). Spurgin () questions both our analyses and interpretations. While we agree that the hypothesis needs more comprehensive empirical testing, we find his specific points of criticism unjustified. In a more general perspective, we call for a more explicit recognition of female mating preferences as mechanisms of selection in population genetics theory.

Lifjeld JT; Gohli J; Johnsen A

2013-10-01

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Genetic Diversity of Neisseria gonorrhoeae Housekeeping Genes  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Molecular typing of Neisseria gonorrhoeae strains is an important tool for epidemiological studies of gonococcal infection and transmission. The recently developed multilocus sequence typing (MLST) method is based on the genetic variation among housekeeping genes. As a preliminary investigation for ...

Viscidi, Raphael P.; Demma, James C.

55

[Evolutionary process unveiled by the maximum genetic diversity hypothesis].  

UK PubMed Central (United Kingdom)

As two major popular theories to explain evolutionary facts, the neutral theory and Neo-Darwinism, despite their proven virtues in certain areas, still fail to offer comprehensive explanations to such fundamental evolutionary phenomena as the genetic equidistance result, abundant overlap sites, increase in complexity over time, incomplete understanding of genetic diversity, and inconsistencies with fossil and archaeological records. Maximum genetic diversity hypothesis (MGD), however, constructs a more complete evolutionary genetics theory that incorporates all of the proven virtues of existing theories and adds to them the novel concept of a maximum or optimum limit on genetic distance or diversity. It has yet to meet a contradiction and explained for the first time the half-century old Genetic Equidistance phenomenon as well as most other major evolutionary facts. It provides practical and quantitative ways of studying complexity. Molecular interpretation using MGD-based methods reveal novel insights on the origins of humans and other primates that are consistent with fossil evidence and common sense, and reestablished the important role of China in the evolution of humans. MGD theory has also uncovered an important genetic mechanism in the construction of complex traits and the pathogenesis of complex diseases. We here made a series of sequence comparisons among yeasts, fishes and primates to illustrate the concept of limit on genetic distance. The idea of limit or optimum is in line with the yin-yang paradigm in the traditional Chinese view of the universal creative law in nature.

Huang YM; Xia MY; Huang S

2013-05-01

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

International Nuclear Information System (INIS)

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)

2011-01-01

57

[Analysis of genetic diversity and genetic relationships of Lonicera macranthoides cultivars].  

UK PubMed Central (United Kingdom)

OBJECTIVE: To study genetic diversity and genetic relationships among Lonicera macranthoides cultivars. METHOD: Five cultivars were estimated by ISSR and SRAP. The data of amplified bands were analyzed by Treeconw software. The system diagram of genetic relationship was built by UPGMA. RESULT: Twenty ISSR primers amplified 186 bands with 103 (54.63%) polymorphic bands and 58 SRAP primer combinations amplified 591 bands with 347(55.46%) polymorphic bands. Genetic distance ranges were 0.058 4-0.230 8 (by ISSRs) and 0.1071-0.2611 (by SRAPs). Both ISSR and SRAP analyses revealed a middle level of genetic diversity in L. macranthoides cultivars. The dendrograms based on SRAP and ISSR markers were not all the same. CONCLUSION: The genetic diversity of L. macranthoides cultivars is middle. ISSR and SRAP markers can be effectively applied to genetic analysis in L. macranthoides cultivars.

Chen D; Zhang X; Li L

2012-07-01

58

Clonal structure and genetic diversity of three desert phreatophytes.  

Science.gov (United States)

The objective of this paper was to assess clone sizes of three perennial desert plant species with AFLP markers and to relate them to clonal and genetic diversity and to hydroecology. The study was carried out at the southern rim of the Taklamakan Desert, where sexual regeneration is only possible shortly after rare flooding events, resulting in rarely established cohorts with subsequent extensive vertical growth and horizontal clonal spread. In this environment, repeated seedling establishment is excluded. We expected decreasing clonal and genetic diversity with increasing clone size and increasing distance to the groundwater table and a common response pattern among all study species. Maximum sizes of Populus euphratica and Alhagi sparsifolia clones were 121 ha and 6.1 ha, respectively, while Tamarix ramosissima clones reached a maximum size of only 38 m(2). In P. euphratica and A. sparsifolia, clonal diversity declined with increasing clone size and increasing distance to the groundwater table, while genetic diversity remained unaffected. Tamarix ramosissima differed from the other species because of a much smaller clonality. Clone size and clonal diversity were found to be good proxy variables for clone age. Despite the considerable age of the clones, genetic diversity is maintained in the populations. PMID:21622383

Vonlanthen, Beatrix; Zhang, Ximing; Bruelheide, Helge

2010-01-15

59

Clonal structure and genetic diversity of three desert phreatophytes.  

UK PubMed Central (United Kingdom)

The objective of this paper was to assess clone sizes of three perennial desert plant species with AFLP markers and to relate them to clonal and genetic diversity and to hydroecology. The study was carried out at the southern rim of the Taklamakan Desert, where sexual regeneration is only possible shortly after rare flooding events, resulting in rarely established cohorts with subsequent extensive vertical growth and horizontal clonal spread. In this environment, repeated seedling establishment is excluded. We expected decreasing clonal and genetic diversity with increasing clone size and increasing distance to the groundwater table and a common response pattern among all study species. Maximum sizes of Populus euphratica and Alhagi sparsifolia clones were 121 ha and 6.1 ha, respectively, while Tamarix ramosissima clones reached a maximum size of only 38 m². In P. euphratica and A. sparsifolia, clonal diversity declined with increasing clone size and increasing distance to the groundwater table, while genetic diversity remained unaffected. Tamarix ramosissima differed from the other species because of a much smaller clonality. Clone size and clonal diversity were found to be good proxy variables for clone age. Despite the considerable age of the clones, genetic diversity is maintained in the populations.

Vonlanthen B; Zhang X; Bruelheide H

2010-02-01

60

Clonal structure and genetic diversity of three desert phreatophytes.  

UK PubMed Central (United Kingdom)

The objective of this paper was to assess clone sizes of three perennial desert plant species with AFLP markers and to relate them to clonal and genetic diversity and to hydroecology. The study was carried out at the southern rim of the Taklamakan Desert, where sexual regeneration is only possible shortly after rare flooding events, resulting in rarely established cohorts with subsequent extensive vertical growth and horizontal clonal spread. In this environment, repeated seedling establishment is excluded. We expected decreasing clonal and genetic diversity with increasing clone size and increasing distance to the groundwater table and a common response pattern among all study species. Maximum sizes of Populus euphratica and Alhagi sparsifolia clones were 121 ha and 6.1 ha, respectively, while Tamarix ramosissima clones reached a maximum size of only 38 m(2). In P. euphratica and A. sparsifolia, clonal diversity declined with increasing clone size and increasing distance to the groundwater table, while genetic diversity remained unaffected. Tamarix ramosissima differed from the other species because of a much smaller clonality. Clone size and clonal diversity were found to be good proxy variables for clone age. Despite the considerable age of the clones, genetic diversity is maintained in the populations.

Vonlanthen B; Zhang X; Bruelheide H

2010-02-01

 
 
 
 
61

Polishing the craft of genetic diversity creation in directed evolution.  

UK PubMed Central (United Kingdom)

Genetic diversity creation is a core technology in directed evolution where a high quality mutant library is crucial to its success. Owing to its importance, the technology in genetic diversity creation has seen rapid development over the years and its application has diversified into other fields of scientific research. The advances in molecular cloning and mutagenesis since 2008 were reviewed. Specifically, new cloning techniques were classified based on their principles of complementary overhangs, homologous sequences, overlapping PCR and megaprimers and the advantages, drawbacks and performances of these methods were highlighted. New mutagenesis methods developed for random mutagenesis, focused mutagenesis and DNA recombination were surveyed. The technical requirements of these methods and the mutational spectra were compared and discussed with references to commonly used techniques. The trends of mutant libraries preparation were summarized. Challenges in genetic diversity creation were discussed with emphases on creating "smart" libraries, controlling the mutagenesis spectrum and specific challenges in each group of mutagenesis methods. An outlined of the wider applications of genetic diversity creation includes genome engineering, viral evolution, metagenomics and study of protein functions. The review ends with an outlook for genetic diversity creation and the prospective developments that can have future impact in this field.

Tee KL; Wong TS

2013-09-01

62

Rapid range expansion increases genetic differentiation while causing limited reduction in genetic diversity in a damselfly.  

UK PubMed Central (United Kingdom)

Many ectothermic species are currently expanding their geographic range due to global warming. This can modify the population genetic diversity and structure of these species because of genetic drift during the colonization of new areas. Although the genetic signatures of historical range expansions have been investigated in an array of species, the genetic consequences of natural, contemporary range expansions have received little attention, with the only studies available focusing on range expansions along a narrow front. We investigate the genetic consequences of a natural range expansion in the Mediterranean damselfly Coenagrion scitulum, which is currently rapidly expanding along a broad front in different directions. We assessed genetic diversity and genetic structure using 12 microsatellite markers in five centrally located populations and five recently established populations at the edge of the geographic distribution. Our results suggest that, although a marginal significant decrease in the allelic richness was found in the edge populations, genetic diversity has been preserved during the range expansion of this species. Nevertheless, edge populations were genetically more differentiated compared with core populations, suggesting genetic drift during the range expansion. The smaller effective population sizes of the edge populations compared with central populations also suggest a contribution of genetic drift after colonization. We argue and document that range expansion along multiple axes of a broad expansion front generates little reduction in genetic diversity, yet stronger differentiation of the edge populations.Heredity advance online publication, 3 July 2013; doi:10.1038/hdy.2013.64.

Swaegers J; Mergeay J; Therry L; Larmuseau MH; Bonte D; Stoks R

2013-07-01

63

Evaluation of genetic and functional diversity of Stenotrophomonas isolates from diverse effluent treatment plants.  

Science.gov (United States)

In this study, the samples were collected from nine ETPs and soil contaminated with petroleum products. The genetic diversity of 30 Stenotrophomonas isolates was demonstrated by phylogenetic analysis of their 16S rRNA gene nucleotide sequences, and randomly amplified polymorphic DNA (RAPD) analysis supplemented with in silico signature and restriction enzyme (REs--AluI, BfaI, DpnII, HaeIII, RsaI and Tru9I) digestion analyses. Genetic diversity based on nucleotide sequence data revealed distinct clusters. Functional diversity was analysed on the basis of the abilities of these isolates to degrade phenol, p-cresol, catechol, 4-methylcatechol and hydroquinone. Based on the environmental, genetic and functional diversities, a consortium of mixed defined microbes has been proposed for bioremediation programs. PMID:20554196

Verma, Vinita; Raju, Sajan C; Kapley, Atya; Kalia, Vipin Chandra; Daginawala, Hatim F; Purohit, Hemant J

2010-10-01

64

Evaluation of genetic and functional diversity of Stenotrophomonas isolates from diverse effluent treatment plants.  

UK PubMed Central (United Kingdom)

In this study, the samples were collected from nine ETPs and soil contaminated with petroleum products. The genetic diversity of 30 Stenotrophomonas isolates was demonstrated by phylogenetic analysis of their 16S rRNA gene nucleotide sequences, and randomly amplified polymorphic DNA (RAPD) analysis supplemented with in silico signature and restriction enzyme (REs--AluI, BfaI, DpnII, HaeIII, RsaI and Tru9I) digestion analyses. Genetic diversity based on nucleotide sequence data revealed distinct clusters. Functional diversity was analysed on the basis of the abilities of these isolates to degrade phenol, p-cresol, catechol, 4-methylcatechol and hydroquinone. Based on the environmental, genetic and functional diversities, a consortium of mixed defined microbes has been proposed for bioremediation programs.

Verma V; Raju SC; Kapley A; Kalia VC; Daginawala HF; Purohit HJ

2010-10-01

65

Genetic diversity analysis of common beans based on molecular markers.  

UK PubMed Central (United Kingdom)

A core collection of the common bean (Phaseolus vulgaris L.), representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico) Germplasm Bank. After evaluation, the genetic structure of this collection (200 accessions) was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each), as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP) +3/+3 primer combinations and seven simple sequence repeats (SSR) loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA) and molecular variance (AMOVA) analyses. AFLP analysis produced 530 bands (88.5% polymorphic) while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus). AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation.

Gill-Langarica HR; Muruaga-Martínez JS; Vargas-Vázquez ML; Rosales-Serna R; Mayek-Pérez N

2011-10-01

66

Genetic diversity analysis of common beans based on molecular markers.  

Science.gov (United States)

A core collection of the common bean (Phaseolus vulgaris L.), representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico) Germplasm Bank. After evaluation, the genetic structure of this collection (200 accessions) was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each), as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP) +3/+3 primer combinations and seven simple sequence repeats (SSR) loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA) and molecular variance (AMOVA) analyses. AFLP analysis produced 530 bands (88.5% polymorphic) while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus). AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation. PMID:22215964

Gill-Langarica, Homar R; Muruaga-Martínez, José S; Vargas-Vázquez, M L Patricia; Rosales-Serna, Rigoberto; Mayek-Pérez, Netzahualcoyotl

2011-10-01

67

Genetic diversity analysis of common beans based on molecular markers  

Directory of Open Access Journals (Sweden)

Full Text Available A core collection of the common bean (Phaseolus vulgaris L.), representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico) Germplasm Bank. After evaluation, the genetic structure of this collection (200 accessions) was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each), as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP) +3/+3 primer combinations and seven simple sequence repeats (SSR) loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA) and molecular variance (AMOVA) analyses. AFLP analysis produced 530 bands (88.5% polymorphic) while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus). AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation.

Homar R. Gill-Langarica; José S. Muruaga-Martínez; M.L. Patricia Vargas-Vázquez; Rigoberto Rosales-Serna; Netzahualcoyotl Mayek-Pérez

2011-01-01

68

Vietnamese chickens: a gate towards Asian genetic diversity  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Chickens represent an important animal genetic resource and the conservation of local breeds is an issue for the preservation of this resource. The genetic diversity of a breed is mainly evaluated through its nuclear diversity. However, nuclear genetic diversity does not provide the same information as mitochondrial genetic diversity. For the species Gallus gallus, at least 8 maternal lineages have been identified. While breeds distributed westward from the Indian subcontinent usually share haplotypes from 1 to 2 haplogroups, Southeast Asian breeds exhibit all the haplogroups. The Vietnamese Ha Giang (HG) chicken has been shown to exhibit a very high nuclear diversity but also important rates of admixture with wild relatives. Its geographical position, within one of the chicken domestication centres ranging from Thailand to the Chinese Yunnan province, increases the probability of observing a very high genetic diversity for maternal lineages, and in a way, improving our understanding of the chicken domestication process. Results A total of 106 sequences from Vietnamese HG chickens were first compared to the sequences of published Chinese breeds. The 25 haplotypes observed in the Vietnamese HG population belonged to six previously published haplogroups which are: A, B, C, D, F and G. On average, breeds from the Chinese Yunnan province carried haplotypes from 4.3 haplogroups. For the HG population, haplogroup diversity is found at both the province and the village level (0.69). The AMOVA results show that genetic diversity occurred within the breeds rather than between breeds or provinces. Regarding the global structure of the mtDNA diversity per population, a characteristic of the HG population was the occurrence of similar pattern distribution as compared to G. gallus spadiceus. However, there was no geographical evidence of gene flow between wild and domestic populations as observed when microsatellites were used. Conclusions In contrast to other chicken populations, the HG chicken population showed very high genetic diversity at both the nuclear and mitochondrial levels. Due to its past and recent history, this population accumulates a specific and rich gene pool highlighting its interest and the need for conservation.

Berthouly-Salazar C; Rognon X; Nhu Van T; Gély M; Vu Chi C; Tixier-Boichard M; Bed'Hom B; Bruneau N; Verrier E; Maillard JC; Michaux JR

2010-01-01

69

[Analysis of genetic diversity of wheat using genetic resources information system GRIS  

UK PubMed Central (United Kingdom)

The possibilities of using the Genetic Resources Information and Analysis System (GRIS) 3.2, a database and software package, in studies of various aspects of genetic diversity in wheat are demonstrated. A model of genetic diversity was analyzed; diversity levels were estimated in wheat from various regions at different times. The genetic basis of Russian winter and spring common wheat cultivars was investigated. Transmission of powdery mildew resistance genes was traced in cultivars with identified Pm genes. For some genes, patterns of geographical distribution were characterized. Description of GRIS 3.2 is given: the package consists of a database on the global gene pool of wheat and software on genealogical and statistic analyses of genetic diversity.

Martynov SP; Dobrotvorskaia TV

2000-02-01

70

[Analysis of genetic diversity of wheat using genetic resources information system GRIS].  

Science.gov (United States)

The possibilities of using the Genetic Resources Information and Analysis System (GRIS) 3.2, a database and software package, in studies of various aspects of genetic diversity in wheat are demonstrated. A model of genetic diversity was analyzed; diversity levels were estimated in wheat from various regions at different times. The genetic basis of Russian winter and spring common wheat cultivars was investigated. Transmission of powdery mildew resistance genes was traced in cultivars with identified Pm genes. For some genes, patterns of geographical distribution were characterized. Description of GRIS 3.2 is given: the package consists of a database on the global gene pool of wheat and software on genealogical and statistic analyses of genetic diversity. PMID:10752032

Martynov, S P; Dobrotvorskaia, T V

2000-02-01

71

Genetic erosion of diversity in cereals  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Cereals play an important role in human nutrition. Consequently, one of the main goals in breeding is to obtain varieties with high genetic potential for yield. Modern agricultural production includes the expansion of intensive varieties over large areas that lead to narrow selection criteria in ...

Petrovi? Sofija; Dimitrijevi? Miodrag

72

Analysis of Genetic Diversity in Bangladeshi Chicken using RAPD Markers  

Directory of Open Access Journals (Sweden)

Full Text Available Understanding the genetic diversity at molecular level is a prerequisite in developing strategies for effective conservation and utilization of chicken genetic resources. We studied the genetic variation within and between Bangladeshi native (Naked Neck, Frizzle and Non-descriptive indigenous) and exotic (White Leghorn, Rhode Island Red, Commercial layer and broiler) chicken populations by Random Amplified Polymorphic DNA (RAPD). Four out of the 20 random primers exhibited sufficient variability for studied populations. The four primers yielded a total of 39 distinct bands, 25 of which were polymorphic. Estimation of polymorphic loci, intra-population similarity indices and Nei’s gene diversity suggested that genetic diversities within a population were high in non-descriptive, Frizzle, Naked Neck, Rhode Island Red and White Leghorn chicken populations compared to the commercial layer and broiler populations. The coefficient of gene differentiation (GST = 0.34) and gene flow (Nm = 0.98) values reflected a high level of population differences. UPGMA dendrogram segregated the chicken populations in various degree based on their genetic distance. The overall genetic distance among native chicken was relatively low comparison to the exotic populations. The results of present study might have significant impact on the breeding and conservation of native chicken genetic resources in Bangladesh.

M.B.R. Mollah; F.B. Islam; M.S. Islam; M.A. Ali; M.S. Alam

2009-01-01

73

Genetic diversity of Plasmodium vivax and Plasmodium falciparum in Honduras.  

UK PubMed Central (United Kingdom)

BACKGROUND: Understanding the population structure of Plasmodium species through genetic diversity studies can assist in the design of more effective malaria control strategies, particularly in vaccine development. Central America is an area where malaria is a public health problem, but little is known about the genetic diversity of the parasite's circulating species. This study aimed to investigate the allelic frequency and molecular diversity of five surface antigens in field isolates from Honduras. METHODS: Five molecular markers were analysed to determine the genotypes of Plasmodium vivax and Plasmodium falciparum from endemic areas in Honduras. Genetic diversity of ama-1, msp-1 and csp was investigated for P. vivax, and msp-1 and msp-2 for P. falciparum. Allelic frequencies were calculated and sequence analysis performed. RESULTS AND CONCLUSION: A high genetic diversity was observed within Plasmodium isolates from Honduras. A different number of genotypes were elucidated: 41 (n?=?77) for pvama-1; 23 (n?=?84) for pvcsp; and 23 (n?=?35) for pfmsp-1. Pvcsp sequences showed VK210 as the only subtype present in Honduran isolates. Pvmsp-1 (F2) was the most polymorphic marker for P. vivax isolates while pvama-1 was least variable. All three allelic families described for pfmsp-1 (n?=?30) block 2 (K1, MAD20, and RO33), and both allelic families described for the central domain of pfmsp-2 (n?=?11) (3D7 and FC27) were detected. However, K1 and 3D7 allelic families were predominant. All markers were randomly distributed across the country and no geographic correlation was found. To date, this is the most complete report on molecular characterization of P. vivax and P. falciparum field isolates in Honduras with regards to genetic diversity. These results indicate that P. vivax and P. falciparum parasite populations are highly diverse in Honduras despite the low level of transmission.

Lopez AC; Ortiz A; Coello J; Sosa-Ochoa W; Torres RE; Banegas EI; Jovel I; Fontecha GA

2012-01-01

74

Genetic diversity of Plasmodium vivax and Plasmodium falciparum in Honduras  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Understanding the population structure of Plasmodium species through genetic diversity studies can assist in the design of more effective malaria control strategies, particularly in vaccine development. Central America is an area where malaria is a public health problem, but little is known about the genetic diversity of the parasite’s circulating species. This study aimed to investigate the allelic frequency and molecular diversity of five surface antigens in field isolates from Honduras. Methods Five molecular markers were analysed to determine the genotypes of Plasmodium vivax and Plasmodium falciparum from endemic areas in Honduras. Genetic diversity of ama-1, msp-1 and csp was investigated for P. vivax, and msp-1 and msp-2 for P. falciparum. Allelic frequencies were calculated and sequence analysis performed. Results and conclusion A high genetic diversity was observed within Plasmodium isolates from Honduras. A different number of genotypes were elucidated: 41 (n?=?77) for pvama-1; 23 (n?=?84) for pvcsp; and 23 (n?=?35) for pfmsp-1. Pvcsp sequences showed VK210 as the only subtype present in Honduran isolates. Pvmsp-1 (F2) was the most polymorphic marker for P. vivax isolates while pvama-1 was least variable. All three allelic families described for pfmsp-1 (n?=?30) block 2 (K1, MAD20, and RO33), and both allelic families described for the central domain of pfmsp-2 (n?=?11) (3D7 and FC27) were detected. However, K1 and 3D7 allelic families were predominant. All markers were randomly distributed across the country and no geographic correlation was found. To date, this is the most complete report on molecular characterization of P. vivax and P. falciparum field isolates in Honduras with regards to genetic diversity. These results indicate that P. vivax and P. falciparum parasite populations are highly diverse in Honduras despite the low level of transmission.

Lopez Ana; Ortiz Andres; Coello Jorge; Sosa-Ochoa Wilfredo; Torres Rosa E; Banegas Engels I; Jovel Irina; Fontecha Gustavo A

2012-01-01

75

Genetic diversity affects colony survivorship in commercial honey bee colonies.  

UK PubMed Central (United Kingdom)

Honey bee (Apis mellifera) queens mate with unusually high numbers of males (average of approximately 12 drones), although there is much variation among queens. One main consequence of such extreme polyandry is an increased diversity of worker genotypes within a colony, which has been shown empirically to confer significant adaptive advantages that result in higher colony productivity and survival. Moreover, honey bees are the primary insect pollinators used in modern commercial production agriculture, and their populations have been in decline worldwide. Here, we compare the mating frequencies of queens, and therefore, intracolony genetic diversity, in three commercial beekeeping operations to determine how they correlate with various measures of colony health and productivity, particularly the likelihood of queen supersedure and colony survival in functional, intensively managed beehives. We found the average effective paternity frequency (m e ) of this population of honey bee queens to be 13.6?±?6.76, which was not significantly different between colonies that superseded their queen and those that did not. However, colonies that were less genetically diverse (headed by queens with m e ???7.0) were 2.86 times more likely to die by the end of the study when compared to colonies that were more genetically diverse (headed by queens with m e ?>?7.0). The stark contrast in colony survival based on increased genetic diversity suggests that there are important tangible benefits of increased queen mating number in managed honey bees, although the exact mechanism(s) that govern these benefits have not been fully elucidated.

Tarpy DR; Vanengelsdorp D; Pettis JS

2013-08-01

76

Genetic diversity and relationships of Vietnamese and European pig breeds  

International Nuclear Information System (INIS)

Indigenous resources of the Asian pig population are less defined and only rarely compared with European breeds. In this study, five indigenous pig breeds from Viet Nam (Mong Cai, Muong Khuong, Co, Meo, Tap Na), two exotic breeds kept in Viet Nam (Large White, Landrace), three European commercial breeds (Pietrain, Landrace, Large White), and European Wild Boar were chosen for evaluation and comparison of genetic diversity. Samples and data from 317 animals were collected and ten polymorphic microsatellite loci were selected according to the recommendations of the FAO Domestic Animal Diversity Information System (DAD-IS; http://www.fao.org/dad-is/). Effective number of alleles, Polymorphism Information Content (PIC), within-breed diversity, estimated heterozygosities and tests for Hardy-Weinberg equilibrium were determined. Breed differentiation was evaluated using the fixation indices of Wright (1951). Genetic distances between breeds were estimated according to Nei (1972) and used for the construction of UPGMA dendrograms which were evaluated by bootstrapping. Heterozygosity was higher in indigenous Vietnamese breeds than in the other breeds. The Vietnamese indigenous breeds also showed higher genetic diversity than the European breeds and all genetic distances had a strong bootstrap support. The European commercial breeds, in contrast, were closely related and bootstrapping values for genetic distances among them were below 60%. European Wild Boar displayed closer relation with commercial breeds of European origin than with the native breeds from Viet Nam. This study is one of the first to contribute to a genetic characterization of autochthonous Vietnamese pig breeds and it clearly demonstrates that these breeds harbour a rich reservoir of genetic diversity. (author)

2005-01-01

77

The genetic diversity of Plasmodium vivax: a review  

Directory of Open Access Journals (Sweden)

Full Text Available The genetic diversity of Plasmodium vivax has been investigated in several malaria-endemic areas, including the Brazilian Amazon region, where this is currently the most prevalent species causing malaria in humans. This review summarizes current views on the use of molecular markers to examine P. vivax populations, with a focus on studies performed in Brazilian research laboratories. We emphasize the importance of phylogenetic studies on this parasite and discuss the perspectives created by our increasing understanding of genetic diversity and population structure of this parasite for the development of new control strategies, including vaccines, and more effective drugs for the treatment of P. vivax malaria.

Wanessa Christina de Souza-Neiras; Luciane Moreno Storti de Melo; Ricardo Luiz Dantas Machado

2007-01-01

78

[Study on genetic diversity of herba Cistanches by RAPD].  

UK PubMed Central (United Kingdom)

OBJECTIVE: To determine the genetic diversity of Cistanche species. METHOD: Two populations of Cistanche deserticola and four populations of C. tubulosa were analyzed by random amplified polymorphic DNA (RAPD) markers. RESULT: A total of 76 and 87 loci were amplified using 10 random primers each other. The average percentage of polymorphic loci of C. deserticola was 47.37%. The PPL were 39.47% and 35.53% for two populations. Average Nei's gene diversity was 0.1358, Shannon' s genetic diversity was 0.2072, and Gst was 0.2546. The average PPL of C. tubulosa was 27.59%. It was 19.54% to 25.29% in different populations and Andi'er population had the highest. Average Nei's gene diversity was 0.0823, and Shannon' s genetic diversity was 0.125 8, Cst was 0.175 5. CONCLUSION: The diversity of Cistanche deserticola is higher than that of C. tubulosa, but both has differentiation among populations, C. deserticola has already separated itself into two different ecotypes.

Cui GH; Chen M; Huang LQ; Xiao SP; Li D

2004-08-01

79

Landscape, population structure and genetic diversity of Stomoxys calcitrans.  

Science.gov (United States)

To investigate whether different landscapes could affect genetic diversity and structure of the cosmopolitan diptera Stomoxys calcitrans, populations from Gabon and southern France were studied using dominant amplified fragment length polymorphism (AFLP) markers. Gabon is characterized by a forested closed landscape, and southern France by an open Mediterranean landscape. The genetic diversity between Gabon and France populations did not differ significantly (P > 0.05). Contrary to our expectation, this study shows a moderate level of genetic differentiation between these two distant countries (Fst = 0.0979) and a low genetic structure among Gabonese and French populations (Fst = 0.0291 and 0.0275 respectively). This result could indicate the capacities of S. calcitrans populations to sustain a high level of gene flow, despite geographic distance and isolation. PMID:19353950

Dsouli Aymes, N; Mavoungou, J F; De Stordeur, E; Duvallet, G

2009-03-01

80

Landscape, population structure and genetic diversity of Stomoxys calcitrans.  

UK PubMed Central (United Kingdom)

To investigate whether different landscapes could affect genetic diversity and structure of the cosmopolitan diptera Stomoxys calcitrans, populations from Gabon and southern France were studied using dominant amplified fragment length polymorphism (AFLP) markers. Gabon is characterized by a forested closed landscape, and southern France by an open Mediterranean landscape. The genetic diversity between Gabon and France populations did not differ significantly (P > 0.05). Contrary to our expectation, this study shows a moderate level of genetic differentiation between these two distant countries (Fst = 0.0979) and a low genetic structure among Gabonese and French populations (Fst = 0.0291 and 0.0275 respectively). This result could indicate the capacities of S. calcitrans populations to sustain a high level of gene flow, despite geographic distance and isolation.

Dsouli Aymes N; Mavoungou JF; De Stordeur E; Duvallet G

2009-03-01

 
 
 
 
81

Genetic diversity of Actinobacillus lignieresii isolates from different hosts  

DEFF Research Database (Denmark)

Genetic diversity detected by analysis of amplified fragment length polymorphisms (AFLPs) of 54 Actinobacilus lignieresii isolates from different hosts and geographic localities is described. On the basis of variances in AFLP profiles, the strains were grouped in two major clusters; one comprising strains isolated from horses and infected wounds of humans bitten by horses and another consisting of strains isolated from bovine and ovine hosts. The present data indicate a comparatively higher degree of genetic diversity among strains isolated from equine hosts and confirm the existence of a separate genomospecies for A. lignieresi-like isolates from horses. Among the isolates from bovine and ovine hosts some clonal lines appear to be genetically stable over time and could be detected at very distant geographic localities. Although all ovine strains investigated grouped in a single cluster, the existence of distinct genetic lineages that have evolved specificity for ovine hosts is not obvious and needs to be confirmed in other studies.

Kokotovic, Branko; Angen, Øystein

2011-01-01

82

Genetic diversity of Actinobacillus lignieresii isolates from different hosts  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Genetic diversity detected by analysis of amplified fragment length polymorphisms (AFLPs) of 54 Actinobacilus lignieresii isolates from different hosts and geographic localities is described. On the basis of variances in AFLP profiles, the strains were grouped in two major clusters; one comprising strains isolated from horses and infected wounds of humans bitten by horses and another consisting of strains isolated from bovine and ovine hosts. The present data indicate a comparatively higher degree of genetic diversity among strains isolated from equine hosts and confirm the existence of a separate genomospecies for A. lignieresi-like isolates from horses. Among the isolates from bovine and ovine hosts some clonal lines appear to be genetically stable over time and could be detected at very distant geographic localities. Although all ovine strains investigated grouped in a single cluster, the existence of distinct genetic lineages that have evolved specificity for ovine hosts is not obvious and needs to be confirmed in other studies.

Kokotovic Branko; Angen Øystein; Bisgaard Magne

2011-01-01

83

Genetic diversity of Actinobacillus lignieresii isolates from different hosts.  

Science.gov (United States)

Genetic diversity detected by analysis of amplified fragment length polymorphisms (AFLPs) of 54 Actinobacillus lignieresii isolates from different hosts and geographic localities is described. On the basis of variances in AFLP profiles, the strains were grouped in two major clusters; one comprising strains isolated from horses and infected wounds of humans bitten by horses and another consisting of strains isolated from bovine and ovine hosts. The present data indicate a comparatively higher degree of genetic diversity among strains isolated from equine hosts and confirm the existence of a separate genomospecies for A. lignieresi-like isolates from horses. Among the isolates from bovine and ovine hosts some clonal lines appear to be genetically stable over time and could be detected at very distant geographic localities. Although all ovine strains investigated grouped in a single cluster, the existence of distinct genetic lineages that have evolved specificity for ovine hosts is not obvious and needs to be confirmed in other studies. PMID:21303512

Kokotovic, Branko; Angen, Øystein; Bisgaard, Magne

2011-02-08

84

Genetic diversity of Actinobacillus lignieresii isolates from different hosts.  

UK PubMed Central (United Kingdom)

Genetic diversity detected by analysis of amplified fragment length polymorphisms (AFLPs) of 54 Actinobacillus lignieresii isolates from different hosts and geographic localities is described. On the basis of variances in AFLP profiles, the strains were grouped in two major clusters; one comprising strains isolated from horses and infected wounds of humans bitten by horses and another consisting of strains isolated from bovine and ovine hosts. The present data indicate a comparatively higher degree of genetic diversity among strains isolated from equine hosts and confirm the existence of a separate genomospecies for A. lignieresi-like isolates from horses. Among the isolates from bovine and ovine hosts some clonal lines appear to be genetically stable over time and could be detected at very distant geographic localities. Although all ovine strains investigated grouped in a single cluster, the existence of distinct genetic lineages that have evolved specificity for ovine hosts is not obvious and needs to be confirmed in other studies.

Kokotovic B; Angen Ø; Bisgaard M

2011-01-01

85

Frequent coinfection reduces RNA virus population genetic diversity.  

UK PubMed Central (United Kingdom)

The masking of deleterious mutations by complementation and the reassortment of virus segments (virus sex) are expected to increase population genetic diversity among coinfecting viruses. Conversely, clonally reproducing or noncoinfecting virus populations may experience clonal interference where viral clones compete with one another, preventing selective sweeps. This dynamic reduces the efficiency of selection and increases the genetic diversity. To determine the relative influences of these forces on population genetic diversity, we evolved 6 populations of bacteriophage ?6 under conditions promoting or preventing coinfection. Following 300 generations, we isolated and partially sequenced 10 clones from each population. We found greater diversity among asexual populations than sexual populations. Moreover, sexual populations did not show greater relative fitnesses than asexual populations, implying that reduced genetic variation did not result from purifying selection. However, sexual populations were less genetically robust than asexual populations and likely more prone to the deleterious epistatic effects of mutations. As such, a neutral mutation on the asexually evolved (robust) background could be profoundly deleterious on the sexually evolved (brittle) background. This could facilitate sexual populations undergoing greater purifying selection to remove deleterious mutations, but this selection is not reflected by increases in average population fitness. Our results bolster a growing literature suggesting that RNA virus segmentation is probably not a mechanism that evolved because it provides a generalized benefit of sex.

Dennehy JJ; Duffy S; O'Keefe KJ; Edwards SV; Turner PE

2013-09-01

86

Pheochromocytomas: from genetic diversity to new paradigms.  

Science.gov (United States)

Pheochromocytomas and paragangliomas are catecholamine-secreting tumors of neural crest origin caused by germline mutations in at least six distinct genes. This genetic heterogeneity has provided a rich source for both the discovery and functional characterization of new tumor-related genes. However, the genetic repertoire of these tumors is still not fully known, and current evidence points to the existence of additional pheochromocytoma susceptibility genes. Here, the unique contributions of three hereditary models of pheochromocytoma that can advance our knowledge of the disease pathogenesis are presented. The first model, loss of succinate dehydrogenase (SDH) function, illustrates how SDHB, C, or D mutations, components of the energy metabolism pathway, serve as a unique system to explore the pervasive metabolic shift of cancer cells towards glycolysis as a source of energy (also known as the Warburg effect) in contrast to the characteristic oxidative phosphorylation of normal cells. In the second model, mechanisms of tumorigenesis distinct from classical pheochromocytoma susceptibility genes are discussed in the context of a novel putative suppressor of neural crest-derived tumors, the KIF1B beta gene. Finally, NF1 loss is highlighted as a valuable study model to investigate the cell lineage selectivity of the Egln3-mediated developmental apoptotic defect of chromaffin precursor cells. Results from these studies may offer clues to understand the tissue specificity of hereditary pheochromocytoma syndromes. These distinct hereditary disease models illustrate how genetic-driven progress has the potential to narrow current gaps in our knowledge of pheochromocytoma and paraganglioma pathogenesis. PMID:19391076

Qin, Y; Buddavarapu, K; Dahia, P L M

2009-04-23

87

Pheochromocytomas: from genetic diversity to new paradigms.  

UK PubMed Central (United Kingdom)

Pheochromocytomas and paragangliomas are catecholamine-secreting tumors of neural crest origin caused by germline mutations in at least six distinct genes. This genetic heterogeneity has provided a rich source for both the discovery and functional characterization of new tumor-related genes. However, the genetic repertoire of these tumors is still not fully known, and current evidence points to the existence of additional pheochromocytoma susceptibility genes. Here, the unique contributions of three hereditary models of pheochromocytoma that can advance our knowledge of the disease pathogenesis are presented. The first model, loss of succinate dehydrogenase (SDH) function, illustrates how SDHB, C, or D mutations, components of the energy metabolism pathway, serve as a unique system to explore the pervasive metabolic shift of cancer cells towards glycolysis as a source of energy (also known as the Warburg effect) in contrast to the characteristic oxidative phosphorylation of normal cells. In the second model, mechanisms of tumorigenesis distinct from classical pheochromocytoma susceptibility genes are discussed in the context of a novel putative suppressor of neural crest-derived tumors, the KIF1B beta gene. Finally, NF1 loss is highlighted as a valuable study model to investigate the cell lineage selectivity of the Egln3-mediated developmental apoptotic defect of chromaffin precursor cells. Results from these studies may offer clues to understand the tissue specificity of hereditary pheochromocytoma syndromes. These distinct hereditary disease models illustrate how genetic-driven progress has the potential to narrow current gaps in our knowledge of pheochromocytoma and paraganglioma pathogenesis.

Qin Y; Buddavarapu K; Dahia PL

2009-09-01

88

Roads, Interrupted Dispersal, and Genetic Diversity in Timber Rattlesnakes  

UK PubMed Central (United Kingdom)

Anthropogenic habitat modification often creates barriers to animal movement, transforming formerly contiguous habitat into a patchwork of habitat islands with low connectivity. Roadways are a feature of most landscapes that can act as barriers or filters to migration among local populations. Even small and recently constructed roads can have a significant impact on population genetic structure of some species, but not others. We developed a research approach that combines fine-scale molecular genetics with behavioral and ecological data to understand the impacts of roads on population structure and connectivity. We used microsatellite markers to characterize genetic variation within and among populations of timber rattlesnakes (Crotalus horridus) occupying communal hibernacula (dens) in regions bisected by roadways. We examined the impact of roads on seasonal migration, genetic diversity, and gene flow among populations. Snakes in hibernacula isolated by roads had significantly lower genetic diversity and higher genetic differentiation than snakes in hibernacula in contiguous habitat. Genetic-assignment analyses revealed that interruption to seasonal migration was the mechanism underlying these patterns. Our results underscore the sizeable impact of roads on this species, despite their relatively recent construction at our study sites (7 to 10 generations of rattlesnakes), the utility of population genetics for studies of road ecology, and the need for mitigating effects of roads.

CLARK RULONW; BROWN WILLIAMS; STECHERT RANDY; ZAMUDIO KELLYR

2010-08-01

89

Roads, interrupted dispersal, and genetic diversity in timber rattlesnakes.  

UK PubMed Central (United Kingdom)

Anthropogenic habitat modification often creates barriers to animal movement, transforming formerly contiguous habitat into a patchwork of habitat islands with low connectivity. Roadways are a feature of most landscapes that can act as barriers or filters to migration among local populations. Even small and recently constructed roads can have a significant impact on population genetic structure of some species, but not others. We developed a research approach that combines fine-scale molecular genetics with behavioral and ecological data to understand the impacts of roads on population structure and connectivity. We used microsatellite markers to characterize genetic variation within and among populations of timber rattlesnakes (Crotalus horridus) occupying communal hibernacula (dens) in regions bisected by roadways. We examined the impact of roads on seasonal migration, genetic diversity, and gene flow among populations. Snakes in hibernacula isolated by roads had significantly lower genetic diversity and higher genetic differentiation than snakes in hibernacula in contiguous habitat. Genetic-assignment analyses revealed that interruption to seasonal migration was the mechanism underlying these patterns. Our results underscore the sizeable impact of roads on this species, despite their relatively recent construction at our study sites (7 to 10 generations of rattlesnakes), the utility of population genetics for studies of road ecology, and the need for mitigating effects of roads.

Clark RW; Brown WS; Stechert R; Zamudio KR

2010-08-01

90

Genetic diversity in natural populations of Sorbus pohuashanensis  

Directory of Open Access Journals (Sweden)

Full Text Available Sorbus pohuashanensis is a tree species native to northern China with high potential for ornamental use. The genetic structure and diversity of eight natural populations of Sorbus pohuashanensis were studied at ten loci encoding four isozymes using horizontal starch gel electrophoresis. Genetic diversity was high at the species level with the mean number of alleles per locus Na = 2.2000, the percentage of polymorphic loci P = 100%, and the mean expected heterozygosity He = 0.4240. Values of the three parameters of He, Ne,and Shannon?s information index indicated a random pattern of genetic diversity among the eight populations. A low level of genetic differentiation among populations (Fst = 0.0758) and a high estimate of gene flow (Nm = 3.0472) were detected together with a high level of genetic identity (I) among the populations (from 0.8585 to 0.9872). Wright’s F-statistics analysis indicated an excess of heterozygotes both at the individual population level (Fis = –0.4180) and at the total population level (Fit = –0.3105). ?2-tests (P?0.05) indicated that 73.62% of the assayed loci departed from the Hardy-Weinberg equilibrium. The UPGMA cluster analysis suggested that the genetic distances among populations were weakly correlated with their geographic distances.

Jian Zheng; Yongqi Zheng; Chuanhong Zhang; Yichen Zong; Bojing Li; Chao Wu

2008-01-01

91

Regional genetic diversity patterns in Antarctic hairgrass (Deschampsia antarctica Desv.)  

UK PubMed Central (United Kingdom)

To determine patterns in diversity of a major Antarctic plant species, including relationships of Antarctic populations with those outside the Antarctic zone. Antarctic Peninsula, Maritime Antarctica, sub-Antarctic islands, Falkland Islands and South America. Amplified fragment length polymorphisms (AFLPs) and chloroplast sequences were used to study patterns of genetic diversity in Antarctic hairgrass (Deschampsia antarctica Desv.) and the genetic relationships between populations over its distribution range. Thirty-eight populations were sampled from a large part of the distribution of D. antarctica, and additionally, herbarium specimens were included for areas from which we could not obtain fresh samples. A gradient in AFLP diversity was observed going from the Falklands southwards into the Antarctic. This gradient in diversity was also observed within the Antarctic Peninsula: diversity was lower further south. Diversity in the chloroplast genome of D. antarctica was low. Only three chloroplast haplotypes were found, each with a strong regional distribution. The phylogenetic construction of AFLP marker frequencies in meta-populations of D. antarctica supports a stepping-stone model of colonization, whereby gene flow mainly occurs between neighbouring populations. It is concluded that long-distance gene flow is very limited in D. antarctica. A very low diversity was found in the sub-Antarctic islands in the Indian Ocean, indicating that these populations have experienced a recent evolutionary bottleneck.

Wouw Markvande; Dijk Petervan; Huiskes AdHL

2008-02-01

92

Assessment of genetic diversity in the sorghum reference set using EST-SSR markers.  

Science.gov (United States)

Selection and use of genetically diverse genotypes are key factors in any crop breeding program to develop cultivars with a broad genetic base. Molecular markers play a major role in selecting diverse genotypes. In the present study, a reference set representing a wide range of sorghum genetic diversity was screened with 40 EST-SSR markers to validate both the use of these markers for genetic structure analyses and the population structure of this set. Grouping of accessions is identical in distance-based and model-based clustering methods. Genotypes were grouped primarily based on race within the geographic origins. Accessions derived from the African continent contributed 88.6 % of alleles confirming the African origin of sorghum. In total, 360 alleles were detected in the reference set with an average of 9 alleles per marker. The average PIC value was 0.5230 with a range of 0.1379-0.9483. Sub-race, guinea margaritiferum (Gma) from West Africa formed a separate cluster in close proximity to wild accessions suggesting that the Gma group represents an independent domestication event. Guineas from India and Western Africa formed two distinct clusters. Accessions belongs to the kafir race formed the most homogeneous group as observed in earlier studies. This analysis suggests that the EST-SSR markers used in the present study have greater discriminating power than the genomic SSRs. Genetic variance within the subpopulations was very high (71.7 %) suggesting that the germplasm lines included in the set are more diverse. Thus, this reference set representing the global germplasm is an ideal material for the breeding community, serving as a community resource for trait-specific allele mining as well as genome-wide association mapping. PMID:23708149

Ramu, P; Billot, C; Rami, J-F; Senthilvel, S; Upadhyaya, H D; Ananda Reddy, L; Hash, C T

2013-05-25

93

Surface-mining water-diversion design manual. Technical report  

Energy Technology Data Exchange (ETDEWEB)

The manual provides basic information and procedures for hydrologic analysis and the design and implementation of an adequate drainage system before, during, and after surface mining operations to minimize adverse environmental impacts. It is a comprehensive design manual for use by experienced engineers and hydrologists.

Anderson, S.A.; Fullerton, W.T.; Li, R.M.; Peterson, M.R.; Schall, J.D.

1982-09-01

94

Microbial diversity in uranium mining-impacted soils as revealed by high-density 16S microarray and clone library.  

Science.gov (United States)

Microbial diversity was characterized in mining-impacted soils collected from two abandoned uranium mine sites, the Edgemont and the North Cave Hills, South Dakota, using a high-density 16S microarray (PhyloChip) and clone libraries. Characterization of the elemental compositions of soils by X-ray fluorescence spectroscopy revealed higher metal contamination including uranium at the Edgemont than at the North Cave Hills mine site. Microarray data demonstrated extensive phylogenetic diversity in soils and confirmed nearly all clone-detected taxonomic levels. Additionally, the microarray exhibited greater diversity than clone libraries at each taxonomic level at both the mine sites. Interestingly, the PhyloChip detected the largest number of taxa in Proteobacteria phylum for both the mine sites. However, clone libraries detected Acidobacteria and Bacteroidetes as the most numerically abundant phyla in the Edgemont and North Cave Hills mine sites, respectively. Several 16S rDNA signatures found in both the microarrays and clone libraries displayed sequence similarities with yet-uncultured bacteria representing a hitherto unidentified diversity. Results from this study demonstrated that highly diverse microbial populations were present in these uranium mine sites. Diversity indices indicated that microbial communities at the North Cave Hills mine site were much more diverse than those at the Edgemont mine site. PMID:19888627

Rastogi, Gurdeep; Osman, Shariff; Vaishampayan, Parag A; Andersen, Gary L; Stetler, Larry D; Sani, Rajesh K

2010-01-01

95

Microbial diversity in uranium mining-impacted soils as revealed by high-density 16S microarray and clone library.  

UK PubMed Central (United Kingdom)

Microbial diversity was characterized in mining-impacted soils collected from two abandoned uranium mine sites, the Edgemont and the North Cave Hills, South Dakota, using a high-density 16S microarray (PhyloChip) and clone libraries. Characterization of the elemental compositions of soils by X-ray fluorescence spectroscopy revealed higher metal contamination including uranium at the Edgemont than at the North Cave Hills mine site. Microarray data demonstrated extensive phylogenetic diversity in soils and confirmed nearly all clone-detected taxonomic levels. Additionally, the microarray exhibited greater diversity than clone libraries at each taxonomic level at both the mine sites. Interestingly, the PhyloChip detected the largest number of taxa in Proteobacteria phylum for both the mine sites. However, clone libraries detected Acidobacteria and Bacteroidetes as the most numerically abundant phyla in the Edgemont and North Cave Hills mine sites, respectively. Several 16S rDNA signatures found in both the microarrays and clone libraries displayed sequence similarities with yet-uncultured bacteria representing a hitherto unidentified diversity. Results from this study demonstrated that highly diverse microbial populations were present in these uranium mine sites. Diversity indices indicated that microbial communities at the North Cave Hills mine site were much more diverse than those at the Edgemont mine site.

Rastogi G; Osman S; Vaishampayan PA; Andersen GL; Stetler LD; Sani RK

2010-01-01

96

Genetic diversity in rhizosphere soil microbes detected with SRAP markers  

Directory of Open Access Journals (Sweden)

Full Text Available We have attempted to use the SRAP (sequence-related amplified polymorphism) markers, a new molecular technology, to study genetic diversity in soil microbes. We sampled rhizosphere soil microbes from 20 plant species and employed 22 SRAP primer combinations. A total of 237 scorable fragments were identi-fied, of which 221 (93.2%) were polymorphic loci. The average percentage of polymorphic loci (PPL), po-lymorphism information content (PIC), allele haplotype (Ah), and expected heterozygosity (He) for each primer combination were 93.78%, 0.94, 18.05 and 0.92, respectively. Our results revealed rich genetic diver-sity in rhizosphere soil microbes and the high ability of SRAP to resolve samples based on their genetic basis. Differences in genetic distance for rice rhizosphere microbes between two locations, and that among four different developmental stages were both significant at 0.01 level, but the difference was not significant be-tween two varieties. Shannon diversity indices indicated that the genetic diversity of rhizosphere soil mi-crobes was lowest in rice and highest in lettuce. The rhizosphere soil microbes from 20 plant species could be clustered into three groups at the 0.454 (GD) level based on UPGMA, in which the first group was from rice, while the second group was from celery planted in plastic green house, and the third group was from 18 other plant species cultivated in dry lands. Our results suggest that SRAP is an efficient method for analyzing the genetic diversity in rhizosphere soil microbes.

Chunnan Li; Hairui Cui; Weibo Wang

2011-01-01

97

Genetic diversity of noroviruses in Brazil  

Directory of Open Access Journals (Sweden)

Full Text Available Norovirus (NoV) infections are a major cause of acute gastroenteritis outbreaks around the world. In Brazil, the surveillance system for acute diarrhoea does not include the diagnosis of NoV, precluding the ability to assess its impact on public health. The present study assessed the circulation of NoV genotypes in different Brazilian states by partial nucleotide sequencing analysis of the genomic region coding for the major capsid viral protein. NoV genogroup II genotype 4 (GII.4) was the prevalent (78%) followed by GII.6, GII.7, GII.12, GII.16 and GII.17, demonstrating the great diversity of NoV genotypes circulating in Brazil. Thus, this paper highlights the importance of a virological surveillance system to detect and characterize emerging strains of NoV and their spreading potential.

Julia Monassa Fioretti; Mônica Simões Rocha Ferreira; Matias Victoria; Carmen Baur Vieira; Maria da Penha Trindade Pinheiro Xavier; José Paulo Gagliardi Leite; Marize Pereira Miagostovich

2011-01-01

98

Genetic diversity of noroviruses in Brazil  

Scientific Electronic Library Online (English)

Full Text Available Abstract in english Norovirus (NoV) infections are a major cause of acute gastroenteritis outbreaks around the world. In Brazil, the surveillance system for acute diarrhoea does not include the diagnosis of NoV, precluding the ability to assess its impact on public health. The present study assessed the circulation of NoV genotypes in different Brazilian states by partial nucleotide sequencing analysis of the genomic region coding for the major capsid viral protein. NoV genogroup II genotype (more) 4 (GII.4) was the prevalent (78%) followed by GII.6, GII.7, GII.12, GII.16 and GII.17, demonstrating the great diversity of NoV genotypes circulating in Brazil. Thus, this paper highlights the importance of a virological surveillance system to detect and characterize emerging strains of NoV and their spreading potential.

Fioretti, Julia Monassa; Ferreira, Mônica Simões Rocha; Victoria, Matias; Vieira, Carmen Baur; Xavier, Maria da Penha Trindade Pinheiro; Leite, José Paulo Gagliardi; Miagostovich, Marize Pereira

2011-12-01

99

metabolicMine: an integrated genomics, genetics and proteomics data warehouse for common metabolic disease research.  

UK PubMed Central (United Kingdom)

Common metabolic and endocrine diseases such as diabetes affect millions of people worldwide and have a major health impact, frequently leading to complications and mortality. In a search for better prevention and treatment, there is ongoing research into the underlying molecular and genetic bases of these complex human diseases, as well as into the links with risk factors such as obesity. Although an increasing number of relevant genomic and proteomic data sets have become available, the quantity and diversity of the data make their efficient exploitation challenging. Here, we present metabolicMine, a data warehouse with a specific focus on the genomics, genetics and proteomics of common metabolic diseases. Developed in collaboration with leading UK metabolic disease groups, metabolicMine integrates data sets from a range of experiments and model organisms alongside tools for exploring them. The current version brings together information covering genes, proteins, orthologues, interactions, gene expression, pathways, ontologies, diseases, genome-wide association studies and single nucleotide polymorphisms. Although the emphasis is on human data, key data sets from mouse and rat are included. These are complemented by interoperation with the RatMine rat genomics database, with a corresponding mouse version under development by the Mouse Genome Informatics (MGI) group. The web interface contains a number of features including keyword search, a library of Search Forms, the QueryBuilder and list analysis tools. This provides researchers with many different ways to analyse, view and flexibly export data. Programming interfaces and automatic code generation in several languages are supported, and many of the features of the web interface are available through web services. The combination of diverse data sets integrated with analysis tools and a powerful query system makes metabolicMine a valuable research resource. The web interface makes it accessible to first-time users, whereas the Application Programming Interface (API) and web services provide convenient data access and tools for bioinformaticians. metabolicMine is freely available online at http://www.metabolicmine.org Database URL: http://www.metabolicmine.org.

Lyne M; Smith RN; Lyne R; Aleksic J; Hu F; Kalderimis A; Stepan R; Micklem G

2013-01-01

100

metabolicMine: an integrated genomics, genetics and proteomics data warehouse for common metabolic disease research.  

Science.gov (United States)

Common metabolic and endocrine diseases such as diabetes affect millions of people worldwide and have a major health impact, frequently leading to complications and mortality. In a search for better prevention and treatment, there is ongoing research into the underlying molecular and genetic bases of these complex human diseases, as well as into the links with risk factors such as obesity. Although an increasing number of relevant genomic and proteomic data sets have become available, the quantity and diversity of the data make their efficient exploitation challenging. Here, we present metabolicMine, a data warehouse with a specific focus on the genomics, genetics and proteomics of common metabolic diseases. Developed in collaboration with leading UK metabolic disease groups, metabolicMine integrates data sets from a range of experiments and model organisms alongside tools for exploring them. The current version brings together information covering genes, proteins, orthologues, interactions, gene expression, pathways, ontologies, diseases, genome-wide association studies and single nucleotide polymorphisms. Although the emphasis is on human data, key data sets from mouse and rat are included. These are complemented by interoperation with the RatMine rat genomics database, with a corresponding mouse version under development by the Mouse Genome Informatics (MGI) group. The web interface contains a number of features including keyword search, a library of Search Forms, the QueryBuilder and list analysis tools. This provides researchers with many different ways to analyse, view and flexibly export data. Programming interfaces and automatic code generation in several languages are supported, and many of the features of the web interface are available through web services. The combination of diverse data sets integrated with analysis tools and a powerful query system makes metabolicMine a valuable research resource. The web interface makes it accessible to first-time users, whereas the Application Programming Interface (API) and web services provide convenient data access and tools for bioinformaticians. metabolicMine is freely available online at http://www.metabolicmine.org Database URL: http://www.metabolicmine.org. PMID:23935057

Lyne, Mike; Smith, Richard N; Lyne, Rachel; Aleksic, Jelena; Hu, Fengyuan; Kalderimis, Alex; Stepan, Radek; Micklem, Gos

2013-08-09

 
 
 
 
101

Genetic diversity and conservation in a small endangered horse population.  

UK PubMed Central (United Kingdom)

The Old Kladruber horses arose in the 17th century as a breed used for ceremonial purposes. Currently, grey and black coat colour varieties exist as two sub-populations with different recent breeding history. As the population underwent historical bottlenecks and intensive inbreeding, loss of genetic variation is considered as the major threat. Therefore, genetic diversity in neutral and non-neutral molecular markers was examined in the current nucleus population. Fifty microsatellites, 13 single nucleotide polymorphisms (SNPs) in immunity-related genes, three mutations in coat colour genes and one major histocompatibility (MHC-DRA) gene were studied for assessing genetic diversity after 15 years of conservation. The results were compared to values obtained in a similar study 13 years ago. The extent of genetic diversity of the current population was comparable to other breeds, despite its small size and isolation. The comparison between 1997 and 2010 did not show differences in the extent of genetic diversity and no loss of allele richness and/or heterozygosity was observed. Genetic differences identified between the black and grey sub-populations observed 13 years ago persisted. Deviations from the Hardy-Weinberg equilibrium found in 19 microsatellite loci and in five SNP loci are probably due to selective breeding. No differences between neutral and immunity-related markers were found. No changes in the frequencies of markers associated with two diseases, melanoma and insect bite hypersensitivity, were observed, due probably to the short interval of time between comparisons. It, thus, seems that, despite its small size, previous bottlenecks and inbreeding, the molecular variation of Old Kladruber horses is comparable to other horse breeds and that the current breeding policy does not compromise genetic variation of this endangered population.

Janova E; Futas J; Klumplerova M; Putnova L; Vrtkova I; Vyskocil M; Frolkova P; Horin P

2013-08-01

102

Assessment of Genetic Diversity in Tea Genotypes Through RAPD Primers  

Directory of Open Access Journals (Sweden)

Full Text Available This study communicates the result of 24 promising tea genotypes evaluated through 11 Randomly Amplified Polymorphic DNA primers. High level of genetic diversity was observed on DNA level among the genotypes. The results of cluster analysis based on RAPDs revealed that four major groups could be recognized in tea grown in Mansehra District.

Habib Ahmad; Sahib Gul; Imtiaz Ali Khan; Mukhtar Alam

2007-01-01

103

Genetic diversity in Spanish donkey breeds using microsatellite DNA markers  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Genetic diversity at 13 equine microsatellite loci was compared in five endangered Spanish donkey breeds: Andaluza, Catalana, Mallorquina, Encartaciones and Zamorano-Leonesa. All of the equine microsatellites used in this study were amplified and were polymorphic in the domestic donkey breeds with t...

Aranguren-Méndez, José; Jordana, Jordi; Gomez, Mariano

104

Genetic diversity of Ralstonia solanacearum strains from China  

UK PubMed Central (United Kingdom)

A survey of bacterial wilt in China collected 286 strains of Ralstonia solanacearum from 17 plant species in 13 Chinese provinces to investigate genetic diversity using the biovar (bv.) and phylotype classification schemes. A phylotype-specific multiplex-PCR showed that 198 isolates belonged to phylotype I (bv. 3, 4 and 5) and 68 to phylotype II (bv. 2 and bv. 1). A phylogenetic analysis examined the partial sequence of the egl and hrpB gene of all strains and the genetic diversity of 95 representatives was reported, demonstrating that Chinese strains are partitioned into phylotype I (Asia) and II (Americas). Phylotype I strains (historically typed bv. 3, 4 and 5), had considerable phylogenetic diversity, including 10 different sequevars: seven previously described sequevars 12 to 18 and three new sequevars: 34, 44 and 48. Chinese strains Z1, Z2, Z3, Z7, Pe74 and Tm82 were not genetically distinguishable from the edible ginger reference strain ACH92 (r4-bv. 4) for sequevar 16. This is believed to be the first report of this ginger group in China. All Chinese bv. 2 strains falling into the genetically and phenotypically diverse phylotype II were placed into phylotype IIB sequevar 1 (historically the Andean race3-bv. 2 potato brown rot agent). In both the egl and hrpB sequence-based trees, strains isolated from mulberry were present in two distinct branches found in sequevars 12 and 48 (reference strains R292 and M2, respectively).

Xu J; Pan ZC; Prior P; Xu JS; Zhang Z; Zhang H; Zhang LQ; He LY; Feng J

2009-12-01

105

Genetic diversity in the SIR model of pathogen evolution  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We introduce a model for assessing the levels and patterns of genetic diversity in pathogen populations, whose epidemiology follows a susceptible-infected-recovered model (SIR). We model the population of pathogens as a metapopulation composed of subpopulations (infected hosts), where pathogens repl...

Gordo, I.; Gomes, M.G.M.; Reis, D.G.; Campos, P.R.A.

106

Genetic diversity of Actinobacillus lignieresii isolates from different hosts  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Genetic diversity detected by analysis of amplified fragment length polymorphisms (AFLPs) of 54 Actinobacilus lignieresii isolates from different hosts and geographic localities is described. On the basis of variances in AFLP profiles, the strains were grouped in two major clusters; one comprising s...

Kokotovic, Branko; Angen, Øystein; Bisgaard, Magne

107

Genetic Diversity within Cryptosporidium parvum and Related Cryptosporidium Species  

Digital Repository Infrastructure Vision for European Research (DRIVER)

To assess the genetic diversity in Cryptosporidium parvum, we have sequenced the small subunit (SSU) rRNA gene of seven Cryptosporidium spp., various isolates of C. parvum from eight hosts, and a Cryptosporidium isolate from a desert monitor. Phylogenetic analysis of the SSU rRNA sequences confirmed...

Xiao, Lihua; Morgan, Una M.; Limor, Josef; Escalante, Ananias; Arrowood, Michael; Shulaw, William; Thompson, R. C. A.

108

Genetic Diversity of Tunisian Barley Accessions Based on Microsatellite Markers  

Directory of Open Access Journals (Sweden)

Full Text Available Genetic diversity can be measured by several criteria, including phenotype, pedigree, allelic diversity at marker loci and allelic diversity at loci controlling phenotypes of interest. Abundance, high level of polymorphism and ease of genotyping make simple sequence repeats (SSRs) an excellent molecular marker system for genetics diversity analyses. In this study, we used a three of mapped SSRs to examine the genetic diversity of Tunisian barley accessions and to establish phylogenetic relationships among them. These primers produce a total of 9 bands witch 7 loci polymorphic, the percentage of polymorphism ranged from 14.28 to 42.85%. The clustering grouped the studied accessions into 3 clusters with no correlation to geographical origins. The CFA permit to group the various populations by projected them in a plan formed by two axes (F1, F2), present 3 groups which are similar with those obtained by hierarchical classification. Present results demonstrate that this SSR marker was highly informative and was useful in generating a meaningful classification of barley germplasm.

F. Guasmi; L. Touil; K. Feres; W. Elfelah; T. Triki; A. Ferchichi

2008-01-01

109

Soybean parent selection based on genetic diversity  

Directory of Open Access Journals (Sweden)

Full Text Available Thirty-four soybean lines were assessed for twelve traits. The genetic distances were estimates using multivariate techniques, to identify parents to be included in breeding programs for hybridization. Grouping by the Tocher method, from generalized Mahalanobis distances, divided the 34 lines into four groups. The most important agronomic traits, weight of seeds per plot, plant height, height of first pod and days to maturity were considered when recommending for crossing. The following crosses were recommended based on the genetic divergence and the key agronomic traits: lines 23, 10, 2, 27 and 25 (group I) with genotype 6 (group II) and genotype 16 (group III). Thus only ten crosses would be made, representing only 2% of the total crosses which could be made in the partial diallel among the 34 lines assessed, which would allow up to 561 combinations.Trinta e quatro linhagens de soja foram avaliadas para doze características. As distâncias genéticas foram estimadas utilizando técnicas multivariadas com objetivo de identificar parentais a serem incluidos em um programa de melhoramento envolvendo hibridação. O agrupamento pelo método de Tocher, a partir das distâncias generalizadas de Mahalanobis, dividiu as 34 linhagens em 4 grupos. As caracterísiticas agronômicas mais importantes, peso de sementes por parcela, altura de planta, altura da primeira vagem e dias para maturação foram consideradas para a recomendação dos cruzamentos. Os seguintes cruzamentos foram recomendados baseado na divergência genética e nas características agronômicas chave: linhagens 23, 10, 2, 27 e 25 (grupo I) com genótipo 6 (grupoII) e com o genótipo 16 (grupo III). Portanto somente 10 cruzamentos poderiam ser realizados representando somente 2% do total de cruzamentos qu poderiam ser realizados em um dialelo parcial entre as 34 linhagens avaliadas as quais admitiriam até 561 combinações.

Valéria Carpentieri-Pípolo; Antônio Eduardo Pípolo; Flávio André Martins da Silva; Marcos Rafael Petek

2000-01-01

110

Maintenance of genetic diversity through plant-herbivore interactions.  

UK PubMed Central (United Kingdom)

Identifying the factors governing the maintenance of genetic variation is a central challenge in evolutionary biology. New genomic data, methods and conceptual advances provide increasing evidence that balancing selection, mediated by antagonistic species interactions, maintains genome-wide functionally important genetic variation within species and natural populations. Because diverse interactions between plants and herbivorous insects dominate terrestrial communities, they provide excellent systems to address this hypothesis. Population genomic studies of Arabidopsis thaliana and its relatives suggest spatial variation in herbivory maintains adaptive genetic variation controlling defense phenotypes, both within and among populations. Conversely, inter-species variation in plant defenses promotes adaptive genetic variation in herbivores. Emerging genomic model herbivores of Arabidopsis could illuminate how genetic variation in herbivores and plants interact simultaneously.

Gloss AD; Nelson Dittrich AC; Goldman-Huertas B; Whiteman NK

2013-08-01

111

Assessment of genetic diversity in Cattleya intermedia Lindl. (Orchidaceae)  

Directory of Open Access Journals (Sweden)

Full Text Available Orchids are valuable pot plants and Cattleya intermedia is a promising species underused in breeding programs. Recently, breeding work with this species produced superior plants that are believed to be not the true species owing to the morphological differences from wild plants. The aim of this study was to estimate the level of genetic diversity and interrelationships between wild and bred Cattleya intermedia collected at three different Brazilian states and from commercial breeders with RAPD markers. A total of 65 polymorphic bands were used to generate a genetic distance matrix. No specific groupings were revealed by the cluster analysis as bred materials were not different from wild plants. The genetic differentiation (F ST = 0.01626) was very low indicating a high gene flow in C. intermedia due to artificial crosses and a high differentiation between populations. The genetic variability available within this species is high enough to allow genetic progress in flower shape and size.

Nelson Barbosa Machado Neto; Luiz Gonzaga Esteves Vieira

2011-01-01

112

Inferring recent historic abundance from current genetic diversity.  

UK PubMed Central (United Kingdom)

Recent historic abundance is an elusive parameter of great importance for conserving endangered species and understanding the pre-anthropogenic state of the biosphere. The number of studies that have used population genetic theory to estimate recent historic abundance from contemporary levels of genetic diversity has grown rapidly over the last two decades. Such assessments often yield unexpectedly large estimates of historic abundance. We review the underlying theory and common practices of estimating recent historic abundance from contemporary genetic diversity, and critically evaluate the potential issues at various estimation steps. A general issue of mismatched spatio-temporal scales between the estimation itself and the objective of the estimation emerged from our assessment; genetic diversity-based estimates of recent historic abundance represent long-term averages, whereas the objective typically is an estimate of recent abundance for a specific population. Currently, the most promising approach to estimate the difference between recent historic and contemporary abundance requires that genetic data be collected from samples of similar spatial and temporal duration. Novel genome-enabled inference methods may be able to utilize additional information of dense genome-wide distributions of markers, such as of identity-by-descent tracts, to infer recent historic abundance from contemporary samples only.

Palsbøll PJ; Zachariah Peery M; Olsen MT; Beissinger SR; Bérubé M

2013-01-01

113

Genetic diversity and molecular genealogy of local silkworm varieties  

Directory of Open Access Journals (Sweden)

Full Text Available In order to explore the genetic diversity and systematic differentiation pattern among silkworm varieties, aiming to guide hybridization breeding, we sequenced a total of 72 Bmamy2 gene fragments from local silkworm varieties. The analysis of nucleotide sequence diversity and systematic differentiation indicated that there was rich genovariation in the sequencing region of Bmamy2 gene, and the base mutation rate is 5.6–8.2%, the haplotype diversity is 0.8294, and the nucleotide diversity is 0.0236±0.00122, suggesting Bmamy2 being a better marking gene with rich nucleotide sequence diversity, based on which the genetic diversity among different local silkworm varieties can be identified. The same heredity population structure is proclaimed by several analysis methods that every clade consisting of varieties from different geosystems and ecological types, while the varieties from the same geosystem and ecotype belong to different clades in the phylogeny. There is no population structure pattern that different varieties claded together according to geosystem or ecotype. It can be speculated that the silkworm origins from mixture of kinds of several voltinism mulberry silkworm, Bombyx mandarina, while the domestication events took place in several regions, from which the domesticated mulberry silkworms are all devoting to the domesticated silkworm population of today.

Zhouhe Du; Junfeng Liu; Binbin Liu; Yanchun Zuo; Jianmei Wu; Yi-an Chen; Jianfei Zhang; Cheng Lu

2013-01-01

114

Community genetics: resource addition has opposing effects on genetic and species diversity in a 150-year experiment.  

UK PubMed Central (United Kingdom)

We used the Park Grass Experiment, begun in 1856, to test alternative hypotheses about the relationship between genetic diversity and plant species diversity. The niche variation hypothesis predicts that populations with few interspecific competitors and hence broader niches are expected to contain greater genetic diversity. The coexistence hypothesis predicts that genetic diversity within species favours coexistence among species and therefore species and genetic diversity should be positively correlated. Amplified Fragment Length Polymorphism (AFLP) markers were used to measure the genetic diversity of populations of Anthoxanthum odoratum growing in 10 plots of differing species richness that lie along resource and soil pH gradients. Genetic diversity in A. odoratum was positively correlated with the number of resources added to a plot, but not correlated with species richness. However, separate analyses have shown a negative correlation between resource addition and species richness at Park Grass and elsewhere, so genetic and species diversity appear to respond in opposite directions.

Silvertown J; Biss PM; Freeland J

2009-02-01

115

Community genetics: resource addition has opposing effects on genetic and species diversity in a 150-year experiment.  

Science.gov (United States)

We used the Park Grass Experiment, begun in 1856, to test alternative hypotheses about the relationship between genetic diversity and plant species diversity. The niche variation hypothesis predicts that populations with few interspecific competitors and hence broader niches are expected to contain greater genetic diversity. The coexistence hypothesis predicts that genetic diversity within species favours coexistence among species and therefore species and genetic diversity should be positively correlated. Amplified Fragment Length Polymorphism (AFLP) markers were used to measure the genetic diversity of populations of Anthoxanthum odoratum growing in 10 plots of differing species richness that lie along resource and soil pH gradients. Genetic diversity in A. odoratum was positively correlated with the number of resources added to a plot, but not correlated with species richness. However, separate analyses have shown a negative correlation between resource addition and species richness at Park Grass and elsewhere, so genetic and species diversity appear to respond in opposite directions. PMID:19143828

Silvertown, Jonathan; Biss, Pamela M; Freeland, Joanna

2009-02-01

116

Surface-mining water-diversion design manual, September 1982  

Energy Technology Data Exchange (ETDEWEB)

The design manual provides basic information and procedures for hydrologic analysis and design for water channels and diversions including design examples. It is a comprehensive design manual for use by experienced engineers and hydrologists.

Anderson, S.A.; Fullerton, W.T.; Li, R.M.; Peterson, M.R.; Schall, J.D.

1989-01-01

117

Population connectivity buffers genetic diversity loss in a seabird.  

UK PubMed Central (United Kingdom)

BACKGROUND: Ancient DNA has revolutionized conservation genetic studies as it allows monitoring of the genetic variability of species through time and predicting the impact of ecosystems' threats on future population dynamics and viability. Meanwhile, the consequences of anthropogenic activities and climate change to island faunas, particularly seabirds, remain largely unknown. In this study, we examined temporal changes in the genetic diversity of a threatened seabird, the Cory's shearwater (Calonectris borealis). FINDINGS: We analysed the mitochondrial DNA control region of ancient bone samples from the late-Holocene retrieved from the Canary archipelago (NE Atlantic) together with modern DNA sequences representative of the entire breeding range of the species. Our results show high levels of ancient genetic diversity in the Canaries comparable to that of the extant population. The temporal haplotype network further revealed rare but recurrent long-distance dispersal between ocean basins. The Bayesian demographic analyses reveal both regional and local population size expansion events, and this is in spite of the demographic decline experienced by the species over the last millennia. CONCLUSIONS: Our findings suggest that population connectivity of the species has acted as a buffer of genetic losses and illustrate the use of ancient DNA to uncover such cryptic genetic events.

Ramírez O; Gómez-Díaz E; Olalde I; Illera JC; Rando JC; González-Solís J; Lalueza-Fox C

2013-01-01

118

Thai pigs and cattle production, genetic diversity of livestock and strategies for preserving animal genetic resources  

Directory of Open Access Journals (Sweden)

Full Text Available This paper reviews the current situation of livestock production in Thailand, genetic diversity and evaluation, as well as management strategies for animal genetic resources focusing on pigs and cattle. Sustainable conservation of indigenous livestock as a genetic resource and vital components within the agricultural biodiversity domain is a great challenge as well as an asset for the future development of livestock production in Thailand.

Kesinee Gatphayak

2013-01-01

119

[Genetic diversity and population genetic structure of Beauveria bassiana in northern China].  

Science.gov (United States)

A total of 622 isolates of Beauveria bassiana collected from 13 provinces in northern China were divided into 13 provincial subpopulations, and 568 of the 622 isolates belonging to 8 insect orders and Araneida, whose hosts could be indentified to order level, were divided into 9 host order subpopulations, with the genetic diversity and population genetic structure of the B. bassiana in northern China analyzed by using ISSR (inter-simple sequence repeat) technique. All the diversity indices showed that the B. bassiana in northern China had higher genetic diversity and population heterogeneity. Among the B. bassiana subpopulations, Inner Mongolia subpopulation and Lepidoptera subpopulation showed the highest genetic diversity and population heterogeneity, while Henan subpopulation and Araneida subpopulation showed the lowest ones. The genetic differentiation index and genetic distance between Henan and Liaoning subpopulations and between Araneida and Mantodea subpopulations were the highest, while those between Ningxia and Shaanxi subpopulations and between Coleoptera and Hymenoptera subpopulations were the lowest. The mean genetic differentiation index and mean genetic distance between the host order subpopulations were lower than those between the provincial subpopulations. These results and the subpopulation clustering analysis based on the genetic distance of subpopulations all demonstrated that the genetic lineage of B. bassiana isolates in northern China was associated with neither their geographic origin nor their host origin. The variation of B. bassiana in northern China was mainly caused by the variation between families and between genera of different host orders, and also, caused by the diversity between different collection sites and between different microhabitats within the collection sites. PMID:23431795

He, Ling-Min; Hu, Xiao-Lei; Chen, Xue; Zhang, Sheng-Li; Luan, Feng-Gang; Li, Zeng-Zhi

2012-11-01

120

Microbialite genetic diversity and composition relate to environmental variables.  

UK PubMed Central (United Kingdom)

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

Centeno CM; Legendre P; Beltrán Y; Alcántara-Hernández RJ; Lidström UE; Ashby MN; Falcón LI

2012-12-01

 
 
 
 
121

Analysis of genetic diversity of sweetpotato landraces in China  

UK PubMed Central (United Kingdom)

Genetic diversity of 48 sweetpotato landraces, randomly sampled from 4 regions (Anhui, Fujian, Henan and Guangdong) in China, was analyzed using RAPD, ISSR and AFLP markers. Both 30 RAPD and 14 ISSR primers and 9 AFLP primer combinations generated 227, 249 and 260 polymorphic bands, respectively. AFLPs were better than RAPDs and ISSRs in terms of the number of polymorphic bands detected and the experimental stability. These three molecular markers revealed the similar results that Chinese landraces possess high genetic diversity, and the genetic variation of Guangdong landraces was significantly (at 0.01 level) higher than that of the landraces from other three regions. These results support the hypothesis that China was the secondary center of sweetpotato diversity and also showed that Guangdong was the earliest region where sweetpotato was introduced to China. In this study, the combined RAPDs, ISSRs and AFLPs dataset appeared to be appropriate in resolving the sweetpotato varietal relationships. These landraces can be divided into two groups by UPGMA cluster based on genetic distances, one mainly includes 8 landraces from Guangdong, and another consists of the remaining landraces from Guangdong and landraces from the other three regions. Thus, the utilization of Guangdong landraces should be specially considered in sweetpotato breeding.

He Xueqin; Liu Qingchang; Wang Yuping; Zhai Hong

2005-01-01

122

Genetic diversity of Ascaris in southwestern Uganda  

DEFF Research Database (Denmark)

Despite the common occurrence of ascariasis in southwestern Uganda, helminth control in the region has been limited. To gain further insights into the genetic diversity of Ascaris in this area, a parasitological survey in mothers (n=41) and children (n=74) living in two villages, Habutobere and Musezero, was carried out. Adult Ascaris worms were collected from infected individuals by chemo-expulsion using pyrantel pamoate treatment. Genetic diversity within these worms was assessed by inspection of DNA sequence variation in a mitochondrial marker and length polymorphism at microsatellite loci. Overall prevalence of ascariasis was 42.5% in mothers and 30.4% in their children and a total of 98 worms was examined from 18 hosts. Sequence analysis of a portion of the mitochondrial cytochrome c oxidase subunit 1 gene revealed 19 different haplotypes, 13 of which had not been previously encountered. Microsatellite analysis using eight loci provided evidence for high gene flow between worm populations from the two villages but comparing these worms with others obtained in a prior study on Unguja, Zanzibar, confirmed little genetic exchange and mixing of worm populations between the two areas. By adding to our understanding of the genetic diversity of Ascaris in Africa, this study provides useful information for monitoring changes in parasite population structure in the face of ongoing and future control.

Betson, Martha; Nejsum, Peter

2012-01-01

123

Analysis of genetic diversity in Bolivian llama populations using microsatellites.  

UK PubMed Central (United Kingdom)

South American camelids (SACs) have a major role in the maintenance and potential future of rural Andean human populations. More than 60% of the 3.7 million llamas living worldwide are found in Bolivia. Due to the lack of studies focusing on genetic diversity in Bolivian llamas, this analysis investigates both the genetic diversity and structure of 12 regional groups of llamas that span the greater part of the range of distribution for this species in Bolivia. The analysis of 42 microsatellite markers in the considered regional groups showed that, in general, there were high levels of polymorphism (a total of 506 detected alleles; average PIC across per marker: 0.66), which are comparable with those reported for other populations of domestic SACs. The estimated diversity parameters indicated that there was high intrapopulational genetic variation (average number of alleles and average expected heterozygosity per marker: 12.04 and 0.68, respectively) and weak genetic differentiation among populations (FST range: 0.003-0.052). In agreement with these estimates, Bolivian llamas showed a weak genetic structure and an intense gene flow between all the studied regional groups, which is due to the exchange of reproductive males between the different flocks. Interestingly, the groups for which the largest pairwise FST estimates were observed, Sud Lípez and Nor Lípez, showed a certain level of genetic differentiation that is probably due to the pattern of geographic isolation and limited communication infrastructures of these southern localities. Overall, the population parameters reported here may serve as a reference when establishing conservation policies that address Bolivian llama populations.

Barreta J; Gutiérrez-Gil B; Iñiguez V; Romero F; Saavedra V; Chiri R; Rodríguez T; Arranz JJ

2013-08-01

124

Genetic Diversity of Tunisian Date Palm Germplasm Using ISSR Markers  

Directory of Open Access Journals (Sweden)

Full Text Available Aim of the study is the analysis of the genetic diversity among a set of Tunisian date palm varieties. We used different genetic markers generated from selected ISSR primers. Inter Simple Sequence Repeat (ISSR) markers involve Polymerase Chain Reaction (PCR) amplification of DNA using a single primer composed of a microsatellite sequence. ISSR technology rapidly reveals high polymorphic fingerprints and determines genetic diversity. Seven primers were used to cluster 10 date palm varieties and 82 polymorphic markers were sufficient to identify all of the studied varieties. These discrete molecular markers were used to estimate genetic distances among the 10 accessions and to examine their genetic relationships. Data analysis identified phenetic groups that were in agreement with those obtained according to agronomic traits and random amplified polymorphic DNA (RAPD) markers. Among the 12 Simple Sequence Repeat (SSR) motifs tested, the most abundant were AG. Present result provides evidence of divergence between Tunisian varieties that are organized in clusters. However, we are unable to identify all tested genotypes as mono varietal groups.

K. Karim; B. Chokri; S. Amel; H. Wafa; H. Richid; D. Nouredine

2010-01-01

125

Genetic diversity of the narrow endemic Astragalus oniciformis (Fabaceae).  

Science.gov (United States)

Astragalus oniciformis Barneby is a narrow endemic xerophyte of the upper Snake River Plain of central Idaho, USA, where it inhabits stabilized, aeolian sand deposits and previously burned, sandy sites over Quaternary basalt flows. The objective of this study was to determine the levels and distribution of genetic differentiation within and among populations of A. oniciformis. Fifteen individuals from each of eight populations, chosen from throughout the range of the species, were selected based on accessibility, density of individuals, and large population size. Inter-simple sequence repeats were chosen as the marker to assess genetic differentiation. The two primers selected yielded 40 polymorphic loci in A. oniciformis. In an analysis of molecular variance, 88.69% of the variation was significantly attributed to variation within populations. High gene flow (N(m) = 3.91-3.93; SD = 0.01) and a low percentage deviation from Hardy-Weinberg equilibrium due to population subdivision (G(ST) = 0.113-0.1134; SD = 0.0002) were found among sampled populations. These results suggest that current threats to this species, including changing fire patterns and habitat loss from grazing disturbance, have not yet affected the genetic diversity of this species. Preservation of large populations and smaller, intervening, dispersed patches will help preserve the genetic integrity and the genetic diversity found in A. oniciformis. PMID:21652349

Alexander, J Andrew; Liston, Aaron; Popovich, Steve J

2004-12-01

126

Genetic diversity of the narrow endemic Astragalus oniciformis (Fabaceae).  

UK PubMed Central (United Kingdom)

Astragalus oniciformis Barneby is a narrow endemic xerophyte of the upper Snake River Plain of central Idaho, USA, where it inhabits stabilized, aeolian sand deposits and previously burned, sandy sites over Quaternary basalt flows. The objective of this study was to determine the levels and distribution of genetic differentiation within and among populations of A. oniciformis. Fifteen individuals from each of eight populations, chosen from throughout the range of the species, were selected based on accessibility, density of individuals, and large population size. Inter-simple sequence repeats were chosen as the marker to assess genetic differentiation. The two primers selected yielded 40 polymorphic loci in A. oniciformis. In an analysis of molecular variance, 88.69% of the variation was significantly attributed to variation within populations. High gene flow (N(m) = 3.91-3.93; SD = 0.01) and a low percentage deviation from Hardy-Weinberg equilibrium due to population subdivision (G(ST) = 0.113-0.1134; SD = 0.0002) were found among sampled populations. These results suggest that current threats to this species, including changing fire patterns and habitat loss from grazing disturbance, have not yet affected the genetic diversity of this species. Preservation of large populations and smaller, intervening, dispersed patches will help preserve the genetic integrity and the genetic diversity found in A. oniciformis.

Alexander JA; Liston A; Popovich SJ

2004-12-01

127

Genetic diversity of the narrow endemic Astragalus oniciformis (fabaceae)  

UK PubMed Central (United Kingdom)

Astragalus oniciformis Barneby is a narrow endemic xerophyte of the upper Snake River Plain of central Idaho, USA, where it inhabits stabilized, aeolian sand deposits and previously burned, sandy sites over Quaternary basalt flows. The objective of this study was to determine the levels and distribution of genetic differentiation within and among populations of A. oniciformis. Fifteen individuals from each of eight populations, chosen from throughout the range of the species, were selected based on accessibility, density of individuals, and large population size. Inter-simple sequence repeats were chosen as the marker to assess genetic differentiation. The two primers selected yielded 40 polymorphic loci in A. oniciformis. In an analysis of molecular variance, 88.69% of the variation was significantly attributed to variation within populations. High gene flow (N(m) = 3.91-3.93; SD = 0.01) and a low percentage deviation from Hardy-Weinberg equilibrium due to population subdivision (G(ST) = 0.113-0.1134; SD = 0.0002) were found among sampled populations. These results suggest that current threats to this species, including changing fire patterns and habitat loss from grazing disturbance, have not yet affected the genetic diversity of this species. Preservation of large populations and smaller, intervening, dispersed patches will help preserve the genetic integrity and the genetic diversity found in A. oniciformis.

Alexander JA; Liston A; Popovich SJ

2004-12-01

128

The flavonoid biosynthetic pathway in Arabidopsis: Structural and genetic diversity.  

UK PubMed Central (United Kingdom)

Flavonoids are representative plant secondary products. In the model plant Arabidopsis thaliana, at least 54 flavonoid molecules (35 flavonols, 11 anthocyanins and 8 proanthocyanidins) are found. Scaffold structures of flavonoids in Arabidopsis are relatively simple. These include kaempferol, quercetin and isorhamnetin for flavonols, cyanidin for anthocyanins and epicatechin for proanthocyanidins. The chemical diversity of flavonoids increases enormously by tailoring reactions which modify these scaffolds, including glycosylation, methylation and acylation. Genes responsible for the formation of flavonoid aglycone structures and their subsequent modification reactions have been extensively characterized by functional genomic efforts - mostly the integration of transcriptomics and metabolic profiling followed by reverse genetic experimentation. This review describes the state-of-art of flavonoid biosynthetic pathway in Arabidopsis regarding both structural and genetic diversity, focusing on the genes encoding enzymes for the biosynthetic reactions and vacuole translocation.

Saito K; Yonekura-Sakakibara K; Nakabayashi R; Higashi Y; Yamazaki M; Tohge T; Fernie AR

2013-02-01

129

RAPD analysis for genetic diversity of germplasm resources of Strobilanthes  

Directory of Open Access Journals (Sweden)

Full Text Available The 18 samples representing 18 populations of Strobilanthes cusia (Nees) O. Ktze in Fujian Province of China were analyzed with RAPD markers. Eleven primers were used, a total of 106 bands were scored and 88 of them were polymorphic. The percentage of polymorphic loci was 77.36%, Nei’s gene diversity was 0.2420, and Shannon’s index was 0.3700. The 18 populations were classified into 2 groups based on the RAPD data by the method of hierarchical cluster analysis. Most of the populations from Fujian were clustered into a group, other populations were clustered into the other group. There was a high level of genetic diversity among the populations, and the genetic differentiation was obvious among the populations from Fujian.

Shuju Ning; Yingjiao Zhang; Renlei Zhu; Lanfang Zhu; Jianyong Lin; Daozhi Wei

2012-01-01

130

The genetic diversity of Plasmodium vivax: a review  

Scientific Electronic Library Online (English)

Full Text Available Abstract in english The genetic diversity of Plasmodium vivax has been investigated in several malaria-endemic areas, including the Brazilian Amazon region, where this is currently the most prevalent species causing malaria in humans. This review summarizes current views on the use of molecular markers to examine P. vivax populations, with a focus on studies performed in Brazilian research laboratories. We emphasize the importance of phylogenetic studies on this parasite and discuss the pers (more) pectives created by our increasing understanding of genetic diversity and population structure of this parasite for the development of new control strategies, including vaccines, and more effective drugs for the treatment of P. vivax malaria.

Souza-Neiras, Wanessa Christina de; Melo, Luciane Moreno Storti de; Machado, Ricardo Luiz Dantas

2007-06-01

131

Genetic diversity and maternal origin of Bangladeshi chicken.  

UK PubMed Central (United Kingdom)

Local domestic chicken populations are of paramount importance as a source of protein in developing countries. Bangladesh possesses a large number of native chicken populations which display a broad range of phenotypes well adapted to the extreme wet and hot environments of this region. This and the fact that wild jungle fowls (JFs) are still available in some regions of the country, it urges to study the present genetic diversity and relationships between Bangladeshi autochthonous chicken populations. Here, we report the results of the mitochondrial DNA (mtDNA) sequence polymorphisms analyses to assess the genetic diversity and possible maternal origin of Bangladeshi indigenous chickens. A 648-bp fragment of mtDNA control region (D-loop) was analyzed in 96 samples from four different chicken populations and one red JF population. Sequence analysis revealed 39 variable sites that defined 25 haplotypes. Estimates of haplotype and nucleotide diversities ranged from 0.745 to 0.901 and from 0.011 to 0.016, respectively. The pairwise differences between populations ranged from 0.091 to 1.459 while most of the PhiST (?ST) values were significant. Furthermore, AMOVA analysis revealed 89.16 % of the total genetic diversity was accounted for within population variation, indicating little genetic differentiation among the studied populations. The median network analysis from haplotypes of Bangladeshi chickens illustrated five distinct mitochondrial haplogroups (A, D, E, F and I). Individuals from all Bangladeshi chicken populations were represented in the major clades D and E; those maternal origins are presumed to be from Indian Subcontinent and Southeast Asian countries, more particularly from South China, Vietnam, Myanmar and Thailand. Further, phylogenetic analysis between indigenous chicken populations and sub-species of red JFs showed G. g. gallus and G. g. spadiceus shared with almost all haplogroups and had major influence than G. g. murghi in the origin of indigenous chicken of Bangladesh. These results suggest that Bangladeshi indigenous chickens still have abundant genetic diversity and have originated from multiple maternal lineages, and further conservation efforts are warranted to maintain the diversity.

Bhuiyan MS; Chen S; Faruque S; Bhuiyan AK; Beja-Pereira A

2013-06-01

132

Mini core germplasm collections for infusing genetic diversity in plant breeding programs  

Directory of Open Access Journals (Sweden)

Full Text Available Plant genetic resources are essential components to meet future food security needs of world. Crop germplasm diversitycontributes to developing improved crop cultivars aimed at increasing crop productivity. The large size of germplasmcollections, coupled with unavailability of detailed data and information, has resulted in low use (<1%) of germplasmleading to a narrow genetic base in many crops. The miniaturization of crop collections with almost full representation ofgenetic diversity in the form of mini core (~1% of the entire collection) approach is an effective methodology to enrichand enhance crop improvement programs. The concept and process of developing mini core at The International CropsResearch Institute for the Semi-Arid Tropics (ICRISAT) has been recognized worldwide as an “International PublicGood” (IPG). The mini core provides a means for accessing the larger collections for further exploration and also helps inproper assessment of genetic diversity and population structure and for association mapping and targeted gene mining.Use of mini core approach will lead to greater utilization of diverse germplasm for developing broad-based cultivars,especially in the context of climate change. Many national programs have shown immense interest in evaluating minicore as reflected by the supply of 114 sets of mini core of chickpea, groundnut, pigeonpea, sorghum, pearl millet, foxtailmillet and finger millet to researchers in 14 countries. Scientists have been able to identify new and diverse sources ofvariation for morpho-agronomic, quality, biotic, and abiotic stress resistance traits in various crops. The molecularcharacterization of the mini core will further enhance its use in plant breeding programs.

Hari D Upadhyaya*, Devvart Yadav, Naresh Dronavalli, CLL Gowda, and Sube Singh

2010-01-01

133

Could contaminant induced mutations lead to a genetic diversity overestimation?  

UK PubMed Central (United Kingdom)

Contaminant driven genetic erosion reported through the inspection of selectable traits can be underestimated using neutral markers. This divergence was previously reported in the aquatic system of an abandoned pyrite mine. The most sensitive genotypes of the microcrustacean cladoceran Daphnia longispina were found to be lacking in the impacted reservoir near the entrance of the metal rich acid mine drainage (AMD). Since that divergence could be, at least partially, accounted for by mutagenicity and genotoxicity of the AMD, the present study aimed at providing such a characterization. The Allium cepa chromosomal aberration assay, using root meristematic cells, was carried out, by exposing seeds to 100, 10, 1, and 0.1 % of the local AMD. Chromosomal aberrations, cell division phases and cell death were quantified after the AMD exposure and after 24 and 48 h recovery periods. The AMD revealed to be mutagenic and genotoxic, even after diluting it to 1 and 0.1 %. Dilutions within this range were previously found to be below the lethality threshold and to elicit sublethal effects on reproduction of locally collected D. longispina clonal lineages Significant mutagenic effects (micronuclei and chromosomal breaks) were also found at 0.1 % AMD, supporting that exposure may induce permanent genetic alterations. Recovery tests showed that AMD genotoxic effects persisted after the exposure.

Sobral O; Marin-Morales MA; Ribeiro R

2013-07-01

134

Could contaminant induced mutations lead to a genetic diversity overestimation?  

Science.gov (United States)

Contaminant driven genetic erosion reported through the inspection of selectable traits can be underestimated using neutral markers. This divergence was previously reported in the aquatic system of an abandoned pyrite mine. The most sensitive genotypes of the microcrustacean cladoceran Daphnia longispina were found to be lacking in the impacted reservoir near the entrance of the metal rich acid mine drainage (AMD). Since that divergence could be, at least partially, accounted for by mutagenicity and genotoxicity of the AMD, the present study aimed at providing such a characterization. The Allium cepa chromosomal aberration assay, using root meristematic cells, was carried out, by exposing seeds to 100, 10, 1, and 0.1 % of the local AMD. Chromosomal aberrations, cell division phases and cell death were quantified after the AMD exposure and after 24 and 48 h recovery periods. The AMD revealed to be mutagenic and genotoxic, even after diluting it to 1 and 0.1 %. Dilutions within this range were previously found to be below the lethality threshold and to elicit sublethal effects on reproduction of locally collected D. longispina clonal lineages Significant mutagenic effects (micronuclei and chromosomal breaks) were also found at 0.1 % AMD, supporting that exposure may induce permanent genetic alterations. Recovery tests showed that AMD genotoxic effects persisted after the exposure. PMID:23686739

Sobral, Olímpia; Marin-Morales, Maria Aparecida; Ribeiro, Rui

2013-05-18

135

Probing genetic diversity to characterize red rot resistance in sugarcane  

International Nuclear Information System (INIS)

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

2011-01-01

136

Genetic diversity of Plasmodium vivax in Kolkata, India  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Plasmodium vivax malaria accounts for approximately 60% of malaria cases in Kolkata, India. There has been limited information on the genotypic polymorphism of P. vivax in this malaria endemic area. Three highly polymorphic and single copy genes were selected for a study of genetic diversity in Kolkata strains. Methods Blood from 151 patients with P. vivax infection diagnosed in Kolkata between April 2003 and September 2004 was genotyped at three polymorphic loci: the P. vivax circumsporozoite protein (pvcs), the merozoite surface protein 1 (pvmsp1) and the merozoite surface protein 3-alpha (pvmsp3-alpha). Results Analysis of these three genetic markers revealed that P. vivax populations in Kolkata are highly diverse. A large number of distinguishable alleles were found from three genetic markers: 11 for pvcs, 35 for pvmsp1 and 37 for pvmsp3-alpha. These were, in general, randomly distributed amongst the isolates. Among the 151 isolates, 142 unique genotypes were detected the commonest genotype at a frequency of less than 2% (3/151). The overall rate of mixed genotype infections was 10.6%. Conclusion These results indicate that the P. vivax parasite population is highly diverse in Kolkata, despite the low level of transmission. The genotyping protocols used in this study may be useful for differentiating re-infection from relapse and recrudescence in studies assessing of malarial drug efficacy in vivax malaria.

Kim Jung-Ryong; Imwong Mallika; Nandy Amitabha; Chotivanich Kesinee; Nontprasert Apichart; Tonomsing Naowarat; Maji Ardhendu; Addy Manjulika; Day Nick PJ; White Nicholas J; Pukrittayakamee Sasithon

2006-01-01

137

Genetic diversity and recombination analysis of sweepoviruses from Brazil  

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Full Text Available Abstract Background Monopartite begomoviruses (genus Begomovirus, family Geminiviridae) that infect sweet potato (Ipomoea batatas) around the world are known as sweepoviruses. Because sweet potato plants are vegetatively propagated, the accumulation of viruses can become a major constraint for root production. Mixed infections of sweepovirus species and strains can lead to recombination, which may contribute to the generation of new recombinant sweepoviruses. Results This study reports the full genome sequence of 34 sweepoviruses sampled from a sweet potato germplasm bank and commercial fields in Brazil. These sequences were compared with others from public nucleotide sequence databases to provide a comprehensive overview of the genetic diversity and patterns of genetic exchange in sweepoviruses isolated from Brazil, as well as to review the classification and nomenclature of sweepoviruses in accordance with the current guidelines proposed by the Geminiviridae Study Group of the International Committee on Taxonomy of Viruses (ICTV). Co-infections and extensive recombination events were identified in Brazilian sweepoviruses. Analysis of the recombination breakpoints detected within the sweepovirus dataset revealed that most recombination events occurred in the intergenic region (IR) and in the middle of the C1 open reading frame (ORF). Conclusions The genetic diversity of sweepoviruses was considerably greater than previously described in Brazil. Moreover, recombination analysis revealed that a genomic exchange is responsible for the emergence of sweepovirus species and strains and provided valuable new information for understanding the diversity and evolution of sweepoviruses.

Albuquerque Leonardo C; Inoue-Nagata Alice K; Pinheiro Bruna; Resende Renato O; Moriones Enrique; Navas-Castillo Jesús

2012-01-01

138

DETECTION OF GENETIC DIVERSITY OF TRITICALE BY MICROSATELLITE MARKERS  

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Full Text Available The aim of our work was to detect genetic variability in the set of 59 winter and spring triticale (x Triticosecale Witt.) varieties using 5 wheat SSR markers. Totally, 35 alleles with an average number of 7 alleles per locus were detected. The highest number of alleles showed out Xbarc 004 (9). Based on the number and frequencies of alleles, the diversity index (DI), the probability of identity (PI) and the polymorphic information content (PIC) of SSR markers were calculated. The polymorphic information content (PIC) ranged from 0.264 to 0.920 with an average of 0.654, which is generally considered sufficient for this purpose. For the assessment of genetic diversity the dendrogram, based on the hierarchical cluster analysis using UPGMA algorithm was prepared. Fifty nine triticale cultivars were grouped into three major clusters. The cultivar Terelland 22 (USA) separated as unique one, second subcluster contained 3 cultivars and third one 55 cultivars. It was not possible to differentiate 15 genotypes between each other. For better differentiation it is necessary to use more polymorphic microsatellite markers. Results showed the utility of microsatellite markers for estimation of genetic diversity of triticale genotypes leading to genotype identification.

Andrej Trebichalský; Želmíra Balážová; Zdenka Gálová; Milan Ch?apek; Marián Tomka

2013-01-01

139

A genetic algorithm approach to recognition and data mining  

Energy Technology Data Exchange (ETDEWEB)

We review here our use of genetic algorithm (GA) and genetic programming (GP) techniques to perform {open_quotes}data mining,{close_quotes} the discovery of particular/important data within large datasets, by finding optimal data classifications using known examples. Our first experiments concentrated on the use of a K-nearest neighbor algorithm in combination with a GA. The GA selected weights for each feature so as to optimize knn classification based on a linear combination of features. This combined GA-knn approach was successfully applied to both generated and real-world data. We later extended this work by substituting a GP for the GA. The GP-knn could not only optimize data classification via linear combinations of features but also determine functional relationships among the features. This allowed for improved performance and new information on important relationships among features. We review the effectiveness of the overall approach on examples from biology and compare the effectiveness of the GA and GP.

Punch, W.F.; Goodman, E.D.; Min, Pei [Michigan State Univ., East Lansing, MI (United States)] [and others

1996-12-31

140

Genetic Diversity in Natural Populations of New World Leishmania  

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Full Text Available Our results have shown the wide diversity of parasites within New World Leishmania. Biochemical and molecular characterization of species within the genus has revealed that much of the population heterogeneity has a genetic basis. The source of genetic diversity among Leishmania appears to arise from predominantly asexual, clonal reproduction, although occasional bouts of sexual reproduction can not be ruled out. Genetic variation is extensive with some clones widely distributed and others seemingly unique and localized to a particular endemic focus. Epidemiological studies of leishmaniasis has been directed to the ecology and dynamics of transmission of Leishmania species/variants, particularly in localized areas. Future research using molecular techniques should aim to identify and follow Leishmania types in nature and correlate genetic typing with important clinical characteristics such as virulence, pathogenicity, drug resistance and antigenic variation. The epidemiological significance of such variation not only has important implications for the control of the leishmaniases, but would also help to elucidate the evolutionary biology of the causative agents.

Cupolillo Elisa; Momen Hooman; Grimaldi Jr Gabriel

1998-01-01

 
 
 
 
141

Genetic Diversity in Natural Populations of New World Leishmania  

Scientific Electronic Library Online (English)

Full Text Available Abstract in english Our results have shown the wide diversity of parasites within New World Leishmania. Biochemical and molecular characterization of species within the genus has revealed that much of the population heterogeneity has a genetic basis. The source of genetic diversity among Leishmania appears to arise from predominantly asexual, clonal reproduction, although occasional bouts of sexual reproduction can not be ruled out. Genetic variation is extensive with some clones widely dist (more) ributed and others seemingly unique and localized to a particular endemic focus. Epidemiological studies of leishmaniasis has been directed to the ecology and dynamics of transmission of Leishmania species/variants, particularly in localized areas. Future research using molecular techniques should aim to identify and follow Leishmania types in nature and correlate genetic typing with important clinical characteristics such as virulence, pathogenicity, drug resistance and antigenic variation. The epidemiological significance of such variation not only has important implications for the control of the leishmaniases, but would also help to elucidate the evolutionary biology of the causative agents.

Cupolillo, Elisa; Momen, Hooman; Grimaldi Jr, Gabriel

1998-09-01

142

Genetic Diversity in Tunisian Ceratonia siliqua L. (Caesalpinioideae) Natural Populations  

UK PubMed Central (United Kingdom)

The last two centuries witnessed the human-caused fragmentation of Tunisian Ceratonia siliqua L. (Caesalpinoideae) populations which were often represented by scattered individuals. Seventeen populations growing in four bioclimatic zones: sub-humid, upper semi-arid, mean semi-arid and lower semi-arid zones, were sampled for allozyme diversity to assess their genetic diversity and structuration using eight isozymes revealed by starch gel electrophoresis. The species showed high diversity within populations. The average number of alleles per polymorphic locus was 1.98, the percentage of polymorphic loci was 83.4% and the mean observed heterozygosity (Ho) and expected heterozygosity (He) under Hardy-Weinberg equilibrium were respectively 0.247 and 0.316. A substantial level of inbreeding within populations induced by Wahlund effect, was observed (F IS = 0.231). High diversity resulted from the great number of genotypes in the ancestral population before fragmentation, favoured by the outbreeding of the species. High differentiation and low gene flow were detected among populations (F ST = 0.200) and among pairs of ecological zones (0.113< F ST <0.198). However, the differentiation coefficient of the four zones was low (F ST = 0.085) and similar to the average F ST for forest trees. Population structuration depends on geographic distance between sites rather than bioclimate, indicating that structuration has occurred slowly and that climatic conditions have had little effect. Nei's genetic distances (D) between populations were low and ranged from 0.004 to 0.201. Mean D value for all population was 0.087. The UPGMA clustering established for all populations through Nei's genetic distances did not clearly show that, for the majority of populations, grouping had resulted from ecological factors or geographic location. The substantial differentiation and the high genetic similarities between populations indicate that populations have been recently isolated as a result of anthropic pressure. In-situ conservation strategies must first focus on populations with a high level of genetic diversity and rare alleles. Appropriate conservation action should take account of bioclimatic zones. Ex-situ preservation should be based on a maximum number of individuals collected within populations in each ecological group and their propagation in different bioclimates by means of cuttings.

Makrem Afif; Najeh BenFadhel; Laarbi KhoudjaMohamed; Mohamed Boussaïd

2006-11-01

143

Diversity of bacterial communities in acid mine drainage from the Shen-bu copper mine, Gansu province, China  

Scientific Electronic Library Online (English)

Full Text Available Abstract in english This study presents bacterial population analyses of microbial communities inhabiting three sites of acid mine drainage (AMD) in the Shen-bu copper mine, Gansu Province, China. These sites were located next to acid-leached chalcopyrite slagheaps that had been abandoned since 1995. The pH values of these samples with high concentrations of metals ranged from 2.0 to 3.5. Amplified ribosomal DNA restriction analysis (ARDRA) was used to characterize the bacterial population b (more) y amplifying the 16S rRNA gene of microorganisms. A total of 39 operational taxonomic units (OTUs) were obtained from the three samples and sequenced from 384 clones. Sequence data and phylogenetic analyses showed that two dominant clones (JYC-1B, JYC-1D) in sample JYC-1 represented 69.5% of the total clones affiliated with Acidithiobacillus ferrooxidans (?-Proteobacteria), and the most dominant clones of JYC-2 and JYC-3 were affiliated with Caulobacter crescentus (?-Protebacteria). At the level of bacterial divisions, differences in the relative incidence of particular phylogenetic groups among the three samples and discrepancies in physicochemical characteristics suggested that the physico-chemical characteristics had an influence on phylogenetic diversity. Furthermore, the relationships between the discrepancies of physicochemical characteristics and the diversity of the bacteria communities in the three samples suggested that the biogeochemical properties, pH and concentration of soluble metal, could be key factors in controlling the structure of the bacterial population

Yang, Yu; Shi, Wuyang; Wan, Minxi; Zhang, Yanfei; Zou, Lihong; Huang, Jufang; Qiu, Guanzhou; Liu, Xueduan

2008-01-01

144

Assessment of genetic diversity within and between pearl millet landraces.  

Science.gov (United States)

A minimum core subset of pearl millet [ Pennisetum glaucum (L.) R. Br.], which comprised 504 landrace accessions, was recently established from the global pearl millet germplasm collection of ICRISAT. The accessions for this core were selected by a random proportional sampling strategy following stratification of the entire landrace collection (about 16,000 accessions) according to their geographic origin and morpho-agronomic traits. In this study RFLP probes were used to quantify the genetic diversity within and between landrace accessions of this minimum core using a subset comprising ten accessions of Indian origin. Twenty five plants per accession were assayed with EcoRI, EcoRV, HindIII and DraI restriction enzymes, and 16 highly polymorphic RFLP probes, nine associated with a quantitative trait loci (QTLs) for downy mildew resistance, and five associated with a QTL for drought tolerance. A total of 51 alleles were detected using 16 different probe-enzyme combinations. The partitioning of variance components based on the analysis of molecular variance (AMOVA) for diversity analysis revealed high within-accession variability (30.9%), but the variability between accessions was significantly higher (69.1%) than that within the accessions. A dendrogram based on the dissimilarity matrix obtained using Ward's algorithm further delineated the 250 plants into ten major clusters, each comprised of plants from a single accession (with the exception of two single plants). A similar result was found in an earlier study using morpho-agronomic traits and geographic origin. This study demonstrated the utility of RFLP markers in detecting polymorphism and estimating genetic diversity in a highly cross-pollinated species such as pearl millet. When less-tedious marker systems are available, this method could be further extended to assess the genetic diversity between and within the remaining accessions in the pearl millet core subset. PMID:12582479

Bhattacharjee, Ranjana; Bramel, J.; Hash, T.; Kolesnikova-Allen, A.; Khairwal, S.

2002-08-01

145

Assessment of genetic diversity within and between pearl millet landraces.  

UK PubMed Central (United Kingdom)

A minimum core subset of pearl millet [ Pennisetum glaucum (L.) R. Br.], which comprised 504 landrace accessions, was recently established from the global pearl millet germplasm collection of ICRISAT. The accessions for this core were selected by a random proportional sampling strategy following stratification of the entire landrace collection (about 16,000 accessions) according to their geographic origin and morpho-agronomic traits. In this study RFLP probes were used to quantify the genetic diversity within and between landrace accessions of this minimum core using a subset comprising ten accessions of Indian origin. Twenty five plants per accession were assayed with EcoRI, EcoRV, HindIII and DraI restriction enzymes, and 16 highly polymorphic RFLP probes, nine associated with a quantitative trait loci (QTLs) for downy mildew resistance, and five associated with a QTL for drought tolerance. A total of 51 alleles were detected using 16 different probe-enzyme combinations. The partitioning of variance components based on the analysis of molecular variance (AMOVA) for diversity analysis revealed high within-accession variability (30.9%), but the variability between accessions was significantly higher (69.1%) than that within the accessions. A dendrogram based on the dissimilarity matrix obtained using Ward's algorithm further delineated the 250 plants into ten major clusters, each comprised of plants from a single accession (with the exception of two single plants). A similar result was found in an earlier study using morpho-agronomic traits and geographic origin. This study demonstrated the utility of RFLP markers in detecting polymorphism and estimating genetic diversity in a highly cross-pollinated species such as pearl millet. When less-tedious marker systems are available, this method could be further extended to assess the genetic diversity between and within the remaining accessions in the pearl millet core subset.

Bhattacharjee R; Bramel J; Hash T; Kolesnikova-Allen A; Khairwal S

2002-10-01

146

Characterisation of the genetic diversity of Brucella by multilocus sequencing  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Brucella species include economically important zoonotic pathogens that can infect a wide range of animals. There are currently six classically recognised species of Brucella although, as yet unnamed, isolates from various marine mammal species have been reported. In order to investigate genetic relationships within the group and identify potential diagnostic markers we have sequenced multiple genetic loci from a large sample of Brucella isolates representing the known diversity of the genus. Results Nine discrete genomic loci corresponding to 4,396 bp of sequence were examined from 160 Brucella isolates. By assigning each distinct allele at a locus an arbitrary numerical designation the population was found to represent 27 distinct sequence types (STs). Diversity at each locus ranged from 1.03–2.45% while overall genetic diversity equated to 1.5%. Most loci examined represent housekeeping gene loci and, in all but one case, the ratio of non-synonymous to synonymous change was substantially Brucella species, B. abortus, B. melitensis, B. ovis and B. neotomae correspond to well-separated clusters. With the exception of biovar 5, B. suis isolates cluster together, although they form a more diverse group than other classical species with a number of distinct STs corresponding to the remaining four biovars. B. canis isolates are located on the same branch very closely related to, but distinguishable from, B. suis biovar 3 and 4 isolates. Marine mammal isolates represent a distinct, though rather weakly supported, cluster within which individual STs display one of three clear host preferences. Conclusion The sequence database provides a powerful dataset for addressing ongoing controversies in Brucella taxonomy and a tool for unambiguously placing atypical, phenotypically discordant or newly emerging Brucella isolates. Furthermore, by using the phylogenetic backbone described here, robust and rationally selected markers for use in diagnostic assay development can be identified.

Whatmore Adrian M; Perrett Lorraine L; MacMillan Alastair P

2007-01-01

147

Genetic diversity among Indian Aloe accessions based on RAPD analysis  

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Full Text Available Forty six accessions of Aloe, which were collected from different part of India and maintained at Issapur farm of National Bureau of Plant Genetic Resources (NBPGR), New Delhi were studied for molecular diversity using RAPD markers. RAPD is an efficient marker for genetic diversity study because it doesn’t require prior genomic information. In the present study 32 RAPD primers were screened consisting of OPL, OPM, OPC and OPE series from Operon technologies, USA. Out of 32 primers, ten primers could amplify good and reproducible amplicons across all the 46 accessions. Ten RAPD primers amplified total 56 bands across 46 accessions out of which 54 (96.4%) were polymorphic. The number of bands generated by RAPD primers across 46 accessions varied from 2 (OPL-03) to 9 (OPM-11 and OPM-14) bands with an average of 5.6 bands per primer. Polymorphic information content (PIC) was calculated for all 10 primers and PIC values varied from 0.13 to 0.44. Based on PIC value maximum accessions were separated by primer OPC-17 (PIC-0.44). Pair wise genetic similarities among the accessions were determined using Jaccard’s similarity coefficient (0.31 to 1.0) and cluster analysis was performed by employing UPGMA method for all 56 RAPD bands generated. All the 46 accessions were grouped into five separate clusters except IC527342, IC524197, IC436191, IC112521 and IC520361 which were ungrouped. The grouping of samples doesn’t show any geographical isolation except in cluster5 where out of five accessions from Delhi, four were grouping together. Principal component analysis (PCA) was also performed and samples were getting distributed in all the axis which confirmed that the accessions studied had good genetic diversity and can be used in future breeding programme.

B.S. PANWAR; Rakesh SINGH; V.K. DWIVEDI; Ashok KUMAR; Pummy KUMARI

2013-01-01

148

Hidden genetic diversity in the green alga Spirogyra (Zygnematophyceae, Streptophyta)  

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Full Text Available Abstract Background The unbranched filamentous green alga Spirogyra (Streptophyta, Zygnemataceae) is easily recognizable based on its vegetative morphology, which shows one to several spiral chloroplasts. This simple structure falsely points to a low genetic diversity: Spirogyra is commonly excluded from phylogenetic analyses because the genus is known as a long-branch taxon caused by a high evolutionary rate. Results We focused on this genetic diversity and sequenced 130 Spirogyra small subunit nuclear ribosomal DNA (SSU rDNA) strands of different origin. The resulting SSU rDNA sequences were used for phylogenetic analyses using complex evolutionary models (posterior probability, maximum likelihood, neighbor joining, and maximum parsimony methods). The sequences were between 1672 and 1779 nucleotides long. Sequence comparisons revealed 53 individual clones, but our results still support monophyly of the genus. Our data set did not contain a single slow-evolving taxon that would have been placed on a shorter branch compared to the remaining sequences. Out of 130 accessions analyzed, 72 showed a secondary loss of the 1506 group I intron, which formed a long-branched group within the genus. The phylogenetic relationship to the genus Spirotaenia was not resolved satisfactorily. The genetic distance within the genus Spirogyra exceeded the distances measured within any other genus of the remaining Zygnemataceae included in this study. Conclusion Overall, we define eight distinct clades of Spirogyra, one of them including the genus Sirogonium. A large number of non-homoplasious synapomorphies (NHS; 114 NHS in total) was found for Spirogyra (41 NHS) and for each clade (totaling 73 NHS). This emphasizes the high genetic diversity of this genus and the distance to the remaining Zygnematophyceae.

Chen Charlotte; Barfuss Michael HJ; Pröschold Thomas; Schagerl Michael

2012-01-01

149

Peach genetic resources: diversity, population structure and linkage disequilibrium.  

UK PubMed Central (United Kingdom)

BACKGROUND: Peach (Prunus persica (L.) Batsch) is one of the most important model fruits in the Rosaceae family. Native to the west of China, where peach has been domesticated for more than 4,000 years, its cultivation spread from China to Persia, Mediterranean countries and to America. Chinese peach has had a major impact on international peach breeding programs due to its high genetic diversity. In this research, we used 48 highly polymorphic SSRs, distributed over the peach genome, to investigate the difference in genetic diversity, and linkage disequilibrium (LD) among Chinese cultivars, and North American and European cultivars, and the evolution of current peach cultivars. RESULTS: In total, 588 alleles were obtained with 48 SSRs on 653 peach accessions, giving an average of 12.25 alleles per locus. In general, the average value of observed heterozygosity (0.47) was lower than the expected heterozygosity (0.60). The separate analysis of groups of accessions according to their origin or reproductive strategies showed greater variability in Oriental cultivars, mainly due to the high level of heterozygosity in Chinese landraces. Genetic distance analysis clustered the cultivars into two main groups: one included four wild related Prunus, and the other included most of the Oriental and Occidental landraces and breeding cultivars. STRUCTURE analysis assigned 469 accessions to three subpopulations: Oriental (234), Occidental (174), and Landraces (61). Nested STRUCTURE analysis divided the Oriental subpopulation into two different subpopulations: 'Yu Lu' and 'Hakuho'. The Occidental breeding subpopulation was also subdivided into nectarine and peach subpopulations. Linkage disequilibrium (LD) analysis in each of these subpopulations showed that the percentage of linked (r2 > 0.1) intra-chromosome comparisons ranged between 14% and 47%. LD decayed faster in Oriental (1,196 Kbp) than in Occidental (2,687 Kbp) samples. In the 'Yu Lu' subpopulation there was considerable LD extension while no variation of LD with physical distance was observed in the landraces. From the first STRUCTURE result, LG1 had the greatest proportion of alleles in LD within all three subpopulations. CONCLUSIONS: Our study demonstrates a high level of genetic diversity and relatively fast decay of LD in the Oriental peach breeding program. Inclusion of Chinese landraces will have a greater effect on increasing genetic diversity in Occidental breeding programs. Fingerprinting with genotype data for all 658 cultivars will be used for accession management in different germplasms. A higher density of markers are needed for association mapping in Oriental germplasm due to the low extension of LD. Population structure and evaluation of LD provides valuable information for GWAS experiment design in peach.

Li XW; Meng XQ; Jia HJ; Yu ML; Ma RJ; Wang LR; Cao K; Shen ZJ; Niu L; Tian JB; Chen MJ; Xie M; Arus P; Gao ZS; Aranzana MJ

2013-09-01

150

Limited genetic diversity preceded extinction of the Tasmanian tiger.  

UK PubMed Central (United Kingdom)

The Tasmanian tiger or thylacine was the largest carnivorous marsupial when Europeans first reached Australia. Sadly, the last known thylacine died in captivity in 1936. A recent analysis of the genome of the closely related and extant Tasmanian devil demonstrated limited genetic diversity between individuals. While a similar lack of diversity has been reported for the thylacine, this analysis was based on just two individuals. Here we report the sequencing of an additional 12 museum-archived specimens collected between 102 and 159 years ago. We examined a portion of the mitochondrial DNA hyper-variable control region and determined that all sequences were on average 99.5% identical at the nucleotide level. As a measure of accuracy we also sequenced mitochondrial DNA from a mother and two offspring. As expected, these samples were found to be 100% identical, validating our methods. We also used 454 sequencing to reconstruct 2.1 kilobases of the mitochondrial genome, which shared 99.91% identity with the two complete thylacine mitochondrial genomes published previously. Our thylacine genomic data also contained three highly divergent putative nuclear mitochondrial sequences, which grouped phylogenetically with the published thylacine mitochondrial homologs but contained 100-fold more polymorphisms than the conserved fragments. Together, our data suggest that the thylacine population in Tasmania had limited genetic diversity prior to its extinction, possibly as a result of their geographic isolation from mainland Australia approximately 10,000 years ago.

Menzies BR; Renfree MB; Heider T; Mayer F; Hildebrandt TB; Pask AJ

2012-01-01

151

Limited genetic diversity preceded extinction of the Tasmanian tiger.  

Science.gov (United States)

The Tasmanian tiger or thylacine was the largest carnivorous marsupial when Europeans first reached Australia. Sadly, the last known thylacine died in captivity in 1936. A recent analysis of the genome of the closely related and extant Tasmanian devil demonstrated limited genetic diversity between individuals. While a similar lack of diversity has been reported for the thylacine, this analysis was based on just two individuals. Here we report the sequencing of an additional 12 museum-archived specimens collected between 102 and 159 years ago. We examined a portion of the mitochondrial DNA hyper-variable control region and determined that all sequences were on average 99.5% identical at the nucleotide level. As a measure of accuracy we also sequenced mitochondrial DNA from a mother and two offspring. As expected, these samples were found to be 100% identical, validating our methods. We also used 454 sequencing to reconstruct 2.1 kilobases of the mitochondrial genome, which shared 99.91% identity with the two complete thylacine mitochondrial genomes published previously. Our thylacine genomic data also contained three highly divergent putative nuclear mitochondrial sequences, which grouped phylogenetically with the published thylacine mitochondrial homologs but contained 100-fold more polymorphisms than the conserved fragments. Together, our data suggest that the thylacine population in Tasmania had limited genetic diversity prior to its extinction, possibly as a result of their geographic isolation from mainland Australia approximately 10,000 years ago. PMID:22530022

Menzies, Brandon R; Renfree, Marilyn B; Heider, Thomas; Mayer, Frieder; Hildebrandt, Thomas B; Pask, Andrew J

2012-04-18

152

Genetic diversity of polysporic isolates of Moniliophthora perniciosa (Tricholomataceae).  

UK PubMed Central (United Kingdom)

The causal agent of witches' broom disease, Moniliophthora perniciosa is a hemibiotrophic and endemic fungus of the Amazon basin and the most important cocoa disease in Brazil. The purpose of this study was to analyze the genetic diversity of polysporic isolates of M. perniciosa to evaluate the adaptation of the pathogen from different Brazilian regions and its association with different hosts. Polysporic isolates obtained previously in potato dextrose agar cultures of M. perniciosa from different Brazilian states and different hosts (Theobroma cacao, Solanum cernuum, S. paniculatum, S. lycocarpum, Solanum sp, and others) were analyzed by somatic compatibility grouping where the mycelium interactions were distinguished after 4-8 weeks of confrontation between the different isolates of M. perniciosa based on the precipitation line in the transition zone and by protein electrophoresis through SDS-PAGE. The diversity of polysporic isolates of M. perniciosa was grouped according to geographic proximity and respective hosts. The great genetic diversity of M. perniciosa strains from different Brazilian states and hosts favored adaptation in unusual environments and dissemination at long distances generating new biotypes.

Ferreira LF; Duarte KM; Gomes LH; Carvalho RS; Leal Junior GA; Aguiar MM; Armas RD; Tavares FC

2012-01-01

153

Genetic diversity and molecular evolution of chinese waxy maize germplasm.  

UK PubMed Central (United Kingdom)

Waxy maize (Zea mays L. var. certaina Kulesh), with many excellent characters in terms of starch composition and economic value, has grown in China for a long history and its production has increased dramatically in recent decades. However, the evolution and origin of waxy maize still remains unclear. We studied the genetic diversity of Chinese waxy maize including typical landraces and inbred lines by SSR analysis and the results showed a wide genetic diversity in the Chinese waxy maize germplasm. We analyzed the origin and evolution of waxy maize by sequencing 108 samples, and downloading 52 sequences from GenBank for the waxy locus in a number of accessions from genus Zea. A sharp reduction of nucleotide diversity and significant neutrality tests (Tajima's D and Fu and Li's F*) were observed at the waxy locus in Chinese waxy maize but not in nonglutinous maize. Phylogenetic analysis indicated that Chinese waxy maize originated from the cultivated flint maize and most of the modern waxy maize inbred lines showed a distinct independent origin and evolution process compared with the germplasm from Southwest China. The results indicated that an agronomic trait can be quickly improved to meet production demand by selection.

Zheng H; Wang H; Yang H; Wu J; Shi B; Cai R; Xu Y; Wu A; Luo L

2013-01-01

154

Genetic diversity of breeding popcorn lines determined by SSR markers  

Scientific Electronic Library Online (English)

Full Text Available Abstract in english Information about genetic dissimilarity is very important to corroborate genealogical relationships and to predict the most heterozygotic hybrid combinations. Eight popcorn S6 lines of diverse germplasm types were evaluated using simple sequence repeats (SSR) markers. Of a total of 51 evaluated polymorphic primers, 15 were used for polymerase chain reaction (PCR) amplification. The genetic distance was estimated by Rogers’ modified distance. The different popcorn br (more) eeding programs in Brazil are possibly using highly similar base-populations. The genetic similarity of lines P1-3 and P8-1 was lowest, while P3-3 and P8-2 were genetically more similar. The cophenetic correlation showed that the Unweighted Pair-Group Method Using Arithmetic Averages (UPGMA) was reliable to discriminate the genotypes in five groups. The clusters were consistent with the estimates of genetic identity. There was a moderate coincidence degree between the groups and genealogy of lines. Higher levels of heterozygosity are expected from crosses between the group containing lines P3-3 and P7-3 with that of P1-3 and P7-4. Crosses between lines P1-3 and P8-1 are also promising.

Ribeiro Trindade, Ana Paula; Barth Pinto, Ronald José; Amaral Júnior, Antonio Teixeira do; Mangolin, Claudete Aparecida; Silva Machado, Maria de Fátima Pires da; Scapim, Carlos Alberto

2010-01-01

155

Assessment of genetic diversity in Cattleya intermedia Lindl. (Orchidaceae)  

Scientific Electronic Library Online (English)

Full Text Available Abstract in english Orchids are valuable pot plants and Cattleya intermedia is a promising species underused in breeding programs. Recently, breeding work with this species produced superior plants that are believed to be not the true species owing to the morphological differences from wild plants. The aim of this study was to estimate the level of genetic diversity and interrelationships between wild and bred Cattleya intermedia collected at three different Brazilian states and from commerc (more) ial breeders with RAPD markers. A total of 65 polymorphic bands were used to generate a genetic distance matrix. No specific groupings were revealed by the cluster analysis as bred materials were not different from wild plants. The genetic differentiation (F ST = 0.01626) was very low indicating a high gene flow in C. intermedia due to artificial crosses and a high differentiation between populations. The genetic variability available within this species is high enough to allow genetic progress in flower shape and size.

Machado Neto, Nelson Barbosa; Vieira, Luiz Gonzaga Esteves

2011-10-01

156

Indigenous cattle in Sri Lanka: production systems and genetic diversity  

International Nuclear Information System (INIS)

[en] Production status, farming systems and genetic diversity of indigenous cattle in Sri Lanka were evaluated using six geographically distinct populations. The indigenous cattle population of the country is considered as a nondescript mixture of genotypes, and represents more than half of the total cattle population of 1.2 million heads. Five distinct indigenous populations were investigated for morphological analysis, and four were included in evaluating genetic differences. Farming systems were analysed using a pre-tested structured questionnaire. The genetic variation was assessed within and between populations using 15 autosomal and two Y-specific microsatellite markers, and compared with two indigenous populations from the African region. Farming system analysis revealed that indigenous cattle rearing was based on traditional mixed-crop integration practices and operates under limited or no input basis. The contribution of indigenous cattle to total tangible income ranged from zero to 90% reflecting the high variation in the purpose of keeping. Morphometric measurements explained specific phenotypic characteristics arising from geographical isolation and selective breeding. Though varying according to the region, the compact body, narrow face, small horns and humps with shades of brown and black coat colour described the indigenous cattle phenotype in general. Genetic analysis indicated that indigenous cattle in Sri Lanka have high diversity with average number of alleles per locus ranging from 7.9 to 8.5. Average heterozygosity of different regions varied within a narrow range (0.72 ± 0.04 to 0.76 ± 0.03). Genetic distances between regions were low (0.085 and 0.066) suggesting a similar mixture of genotypes across regions. Y-specific analysis indicated a possible introgression of Taurine cattle in one of the cattle populations. (author)

2010-01-01

157

Comparative molecular analysis of the prokaryotic diversity of two salt mine soils in southwest China.  

UK PubMed Central (United Kingdom)

While much is known about the microbial diversity in some hypersaline environments, little is known about those of salt mine tunnel soils. The objective of this study was to conduct a comprehensive phylogenetic comparison of the archaeal and bacterial communities present in Yipinglang salt mine (YPL) and Qiaohou salt mine (QH) tunnels differing in salinity and salt composition using 16S rRNA gene clone libraries. Two hundred twenty-eight sequences for QH and 182 sequences for YPL were analyzed by amplified ribosomal DNA-restriction analysis. Libraries revealed 44 bacterial and 57 archaeal different operational taxonomic units belonging to at least 8 bacterial and 3 archaeal divisions, but not all divisions were observed in both salt mines. The bacterial community affiliated with the Bacteroidetes was the most abundant (60% of clones) in QH, while the community in YPL was dominated by ?-Proteobacteria (45% of clones). All archaeal clones from QH were affiliated with Halobacteriaceae. In contrast, in the YPL library, 49% of clones belonged to Halobacteriaceae, 31% of clones related to unclassified archaea, and 21% of clones belonged to Crenarchaeota. Bioinformatic analysis and comparisons showed that the clone libraries were significantly different between two salt mines.

Xiao W; Wang ZG; Wang YX; Schneegurt MA; Li ZY; Lai YH; Zhang SY; Wen ML; Cui XL

2013-03-01

158

Genetic variation in biomass traits among 20 diverse rice varieties.  

UK PubMed Central (United Kingdom)

Biofuels provide a promising route of producing energy while reducing reliance on petroleum. Developing sustainable liquid fuel production from cellulosic feedstock is a major challenge and will require significant breeding efforts to maximize plant biomass production. Our approach to elucidating genes and genetic pathways that can be targeted for improving biomass production is to exploit the combination of genomic tools and genetic diversity in rice (Oryza sativa). In this study, we analyzed a diverse set of 20 recently resequenced rice varieties for variation in biomass traits at several different developmental stages. The traits included plant size and architecture, aboveground biomass, and underlying physiological processes. We found significant genetic variation among the 20 lines in all morphological and physiological traits. Although heritability estimates were significant for all traits, heritabilities were higher in traits relating to plant size and architecture than for physiological traits. Trait variation was largely explained by variety and breeding history (advanced versus landrace) but not by varietal groupings (indica, japonica, and aus). In the context of cellulosic biofuels development, cell wall composition varied significantly among varieties. Surprisingly, photosynthetic rates among the varieties were inversely correlated with biomass accumulation. Examining these data in an evolutionary context reveals that rice varieties have achieved high biomass production via independent developmental and physiological pathways, suggesting that there are multiple targets for biomass improvement. Future efforts to identify loci and networks underlying this functional variation will facilitate the improvement of biomass traits in other grasses being developed as energy crops.

Jahn CE; Mckay JK; Mauleon R; Stephens J; McNally KL; Bush DR; Leung H; Leach JE

2011-01-01

159

Genetic variation in biomass traits among 20 diverse rice varieties.  

Science.gov (United States)

Biofuels provide a promising route of producing energy while reducing reliance on petroleum. Developing sustainable liquid fuel production from cellulosic feedstock is a major challenge and will require significant breeding efforts to maximize plant biomass production. Our approach to elucidating genes and genetic pathways that can be targeted for improving biomass production is to exploit the combination of genomic tools and genetic diversity in rice (Oryza sativa). In this study, we analyzed a diverse set of 20 recently resequenced rice varieties for variation in biomass traits at several different developmental stages. The traits included plant size and architecture, aboveground biomass, and underlying physiological processes. We found significant genetic variation among the 20 lines in all morphological and physiological traits. Although heritability estimates were significant for all traits, heritabilities were higher in traits relating to plant size and architecture than for physiological traits. Trait variation was largely explained by variety and breeding history (advanced versus landrace) but not by varietal groupings (indica, japonica, and aus). In the context of cellulosic biofuels development, cell wall composition varied significantly among varieties. Surprisingly, photosynthetic rates among the varieties were inversely correlated with biomass accumulation. Examining these data in an evolutionary context reveals that rice varieties have achieved high biomass production via independent developmental and physiological pathways, suggesting that there are multiple targets for biomass improvement. Future efforts to identify loci and networks underlying this functional variation will facilitate the improvement of biomass traits in other grasses being developed as energy crops. PMID:21062890

Jahn, Courtney E; Mckay, John K; Mauleon, Ramil; Stephens, Janice; McNally, Kenneth L; Bush, Daniel R; Leung, Hei; Leach, Jan E

2010-11-09

160

Analysis of genetic diversity of Lactarius hatsudake in south China.  

UK PubMed Central (United Kingdom)

Lactarius hatsudake is a type of ectomycorrhizal fungus that significantly influences the growth of pine trees. It is widely prevalent in Asian countries and has a high economic value. Artificial cultivation of this fungus has not been achieved as yet; therefore, excessive manual harvesting may cause serious damages to the site of its production. In this study, we analyzed 41 samples of L. hatsudake from south China using internal transcribed spacer (ITS) sequences. By comparing the differences among ITS sequences to identify the haplotype diversity within each population, the relationships among local populations, the relationship between the level of genetic differentiation and geographical separation, and the contributions of local and regional geographical separations to the overall ITS haplotype variation were analyzed. Genetic analysis indicates that ITS sequences obtained from these 41 L. hatsudake samples could be identified as 18 haplotypes, of which 13 haplotypes were contained in only a single sample, whereas the remaining sequence types all were contained in two or more samples. The most common sequence type, haplotype 6, was found in 16 samples and was distributed across nearly every region. The Mantel test demonstrated that there is no significant linear relationship between geographical distance and the F(ST) value of genetic difference. Results of this research illustrates that there exists a certain degree of genetic intermixing among natural populations of L. hatsudake. From the group genetic analysis, it appears that there exists genetic differentiation of lower frequencies in natural populations of L. hatsudake; however, the linear relationship between the degree of genetic differentiation and geographical distance is not distinctly apparent.

He L; Liang G; Guoying Z; Jun-ang L

2011-08-01

 
 
 
 
161

Analysis of genetic diversity of Lactarius hatsudake in south China.  

Science.gov (United States)

Lactarius hatsudake is a type of ectomycorrhizal fungus that significantly influences the growth of pine trees. It is widely prevalent in Asian countries and has a high economic value. Artificial cultivation of this fungus has not been achieved as yet; therefore, excessive manual harvesting may cause serious damages to the site of its production. In this study, we analyzed 41 samples of L. hatsudake from south China using internal transcribed spacer (ITS) sequences. By comparing the differences among ITS sequences to identify the haplotype diversity within each population, the relationships among local populations, the relationship between the level of genetic differentiation and geographical separation, and the contributions of local and regional geographical separations to the overall ITS haplotype variation were analyzed. Genetic analysis indicates that ITS sequences obtained from these 41 L. hatsudake samples could be identified as 18 haplotypes, of which 13 haplotypes were contained in only a single sample, whereas the remaining sequence types all were contained in two or more samples. The most common sequence type, haplotype 6, was found in 16 samples and was distributed across nearly every region. The Mantel test demonstrated that there is no significant linear relationship between geographical distance and the F(ST) value of genetic difference. Results of this research illustrates that there exists a certain degree of genetic intermixing among natural populations of L. hatsudake. From the group genetic analysis, it appears that there exists genetic differentiation of lower frequencies in natural populations of L. hatsudake; however, the linear relationship between the degree of genetic differentiation and geographical distance is not distinctly apparent. PMID:21815833

He, Li; Liang, Guo; Guoying, Zhou; Jun-ang, Liu

2011-08-04

162

Population genetic estimation of the loss of genetic diversity during horizontal transmission of HIV-1  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Genetic diversity of the human immunodeficiency virus type 1 (HIV-1) population within an individual is lost during transmission to a new host. The demography of transmission is an important determinant of evolutionary dynamics, particularly the relative impact of natural selection and genetic drift immediately following HIV-1 infection. Despite this, the magnitude of this population bottleneck is unclear. Results We use coalescent methods to quantify the bottleneck in a single case of homosexual transmission and find that over 99% of the env and gag diversity present in the donor is lost. This was consistent with the diversity present at seroconversion in nine other horizontally infected individuals. Furthermore, we estimated viral diversity at birth in 27 infants infected through vertical transmission and found there to be no difference between the two modes of transmission. Conclusion Assuming the bottleneck at transmission is selectively neutral, such a severe reduction in genetic diversity has important implications for adaptation in HIV-1, since beneficial mutations have a reduced chance of transmission.

Edwards Charles TT; Holmes Edward C; Wilson Daniel J; Viscidi Raphael P; Abrams Elaine J; Phillips Rodney E; Drummond Alexei J

2006-01-01

163

[Genetic diversity and phylogeny of bradyrhizobia associated with Desmodium spp].  

UK PubMed Central (United Kingdom)

OBJECTIVE: Genetic diversity and phylogeny of bradyrhizobial strains associated with Desmodium spp. in subtropic and temperate regions of China were analyzed. METHODS: We studied 29 desmodia isolates from different regions with BOX-PCR fingerprinting and multilocus sequence analysis (nifH, nodC and recA gene) to describe the genotypic characteristics and phylogenetic relationships. RESULTS: We achieved 25 genotypes with BOX-PCR genomic fingerprinting analysis, indicating that the tested strains had a great diversity at genomic level. The representative bradyrhizobial strains were located in three phylogenic branches with multilocus sequence analysis (niffH, nodC and recA gene), that was closely related to Bradyrhizobium elkanii, Bradyrhizobium japonicum and Bradyrhizobium yuanmingense, respectively. CONCLUSION: The desmodia bradyrhizobia had abundantly diversity. Diverse symbiotic genes including nifH and nodC genes were also found in these strains that indicated that the symbiotic genes were mainly maintained by vertical transfer in these bradyrhizobial populations and coevolved with housekeeping genes.

Gu J; Zhang J; Jia R; Chen W

2011-10-01

164

Improved Genetic Algorithm Based on Simulated Annealing and Quantum Computing Strategy for Mining Association Rules  

Directory of Open Access Journals (Sweden)

Full Text Available Association rules mining is an important content in data mining. It can discover the relations of different attributes by analyzing and disposing data which is in database. This paper proposes a novel data mining algorithm to enhance the capability of exploring valuable information from databases with continuous values. The algorithm combines with quantum-inspired genetic algorithm and simulated annealing to find interesting association rules. The final best sets of membership functions in all the populations are then gathered together to be used for mining association rules. The experiment result demonstrates that the proposed approach could generate more association rules than other algorithms.

Dongsheng Liu

2010-01-01

165

RAPD analysis of molecular genetic diversity and genetic relationship of four grouper species  

UK PubMed Central (United Kingdom)

The RAPD ?randomly amplified polymorphic DNA? technology was applied to studying the genetic diversity and genetic relationship of four grouper species, including two raised population?Epinephelus malabaricus from Hainan,China and E. coioides from Guangdong, China? and two wild populations?E. firio and E. merra captured from the South China Sea. 25 random primers were used to be analyzed , and the genetic relationship of these grouper species was analyzed by UPGMA. The results indicated that? first, the percentages of polymorphic loci of the wild populations of E. frio and E. merra were 58.07% and 55.65%, and the mean heterozygositys of the wild populations of E. frio and E. merra were 0.1793 and 0.1622,respectively, the level of genetic diversity of them was high and the genetic status was good. However, that of the raised populations of E. malabaricus and E. coioides was low. The percentages of polymorphic loci were 49.70% and 40.38%, and the mean heterozygositys were 0.1349 and 0.1135 respectively, which indicated the level of genetic diversity of the raised grouper populations was declined, and it should be taken some remedial measures. Second, the interspecies genetic distance and clustering analysis showed that? among four grouper species, the genetic distance between E. malabaricus and E. coioides was minimum?0.2570?, E. frio and E. merra took second palace?0.5146?, E. coioides and E. firio was maximum?0.5810?. Finally, among the fragments generated by 8 primers, some specific fragments which can be used to identify these groupers, were found.

Yin Shaowu; Huang Hai; Liao Jingqiu; Zhang Ben; Chen Guohua

2006-01-01

166

Genetic diversity in populations of Gentoo penguins (Pygoscelis papua).  

UK PubMed Central (United Kingdom)

RAPD analysis was used to examine the extent of genetic polymorphism in two populations of Gentoo penguin (Pygoscelis papua) from Antarctic Islands (Petermann and Livingston). The chosen two of three 10 mer oligonucleotide primers accordingly to preliminary results showed different levels of polymorphism in Gentoo penguins at Petermann Island (from 23.53 to 42.86%) and Livingston Island (from 52.94 to 57.14%). Nei's similarity coefficients were in range from 0.5606 (when Gentoo genome profiles were compared with RAPD profiles of two related penguin species: Pygoscelis adeliae (Adelie) and Pygoscelis antarctica (Chinstrep)) to 0.9281 among observed Gentoo penguin populations. Nei's distances values ranged from 0.0746 to 0.5787 among the populations and species. The obtained results will be used for further estimation of genetic diversity of Gentoo penguins and determination of their taxonomic status.

Dranitsina AS; Telegeev GD; Maliuta SS; Bezrukov VF

2006-03-01

167

Genetic diversity of subgroup 1 ilarviruses from eastern Australia.  

Science.gov (United States)

This is the first report of the genetic diversity within ilarvirus subgroup 1 from eastern Australia. It supports the separation of tobacco streak virus (TSV) strains from parthenium (Parthenium hysterophorus) and crownbeard (Verbescina encelioides) based on serology and host specificity. It has confirmed one previously described strain of TSV as a member of the species Strawberry necrotic shock virus and another as a new subgroup 1 ilarvirus, ageratum latent virus (AgLV), from Ageratum houstonianum. A multiplex RT-PCR showed that the genetically distinct strains of TSV and AgLV were commonly found in symptomless infections in virus-specific alternative weed hosts growing over a wide geographical range in eastern Australia. TSV has been one of the most damaging viruses in Australian oilseed and pulse crops in recent years, and this study has provided the taxonomic knowledge essential for the development of control programs for these viruses. PMID:23474983

Sharman, M; Thomas, J E

2013-03-09

168

The impact of recent events on human genetic diversity.  

UK PubMed Central (United Kingdom)

The historical record tells us stories of migrations, population expansions and colonization events in the last few thousand years, but what was their demographic impact? Genetics can throw light on this issue, and has mostly done so through the maternally inherited mitochondrial DNA (mtDNA) and the male-specific Y chromosome. However, there are a number of problems, including marker ascertainment bias, possible influences of natural selection, and the obscuring layers of the palimpsest of historical and prehistorical events. Y-chromosomal lineages are particularly affected by genetic drift, which can be accentuated by recent social selection. A diversity of approaches to expansions in Europe is yielding insights into the histories of Phoenicians, Roma, Anglo-Saxons and Vikings, and new methods for producing and analysing genome-wide data hold much promise. The field would benefit from more consensus on appropriate methods, and better communication between geneticists and experts in other disciplines, such as history, archaeology and linguistics.

Jobling MA

2012-03-01

169

Diversity and genetic structure among subpopulations of Gossypium mustelinum (Malvaceae).  

UK PubMed Central (United Kingdom)

Gossypium mustelinum is the only cotton species native to Brazil; it is endemic to the semi-arid region of the northeast. The populations are found near perennial and semi-perennial sources of water, such as ponds or pools in intermittent streams. Problems with in situ conservation derive from human interference in its habitat, mainly because of excessive cattle grazing and deforestation. Establishing efficient strategies for in situ conservation requires knowledge of the genetic structure of the populations. We evaluated the structure and genetic variability of populations of G. mustelinum in the Tocó and Capivara Rivers (State of Bahia). Two hundred and eighteen mature G. mustelinum plants were genotyped with SSR markers. The molecular data were used to estimate the allelic frequencies, the heterozygosity, the F statistics, and the genetic distance among the populations and among individuals. We found high genetic diversity among the populations. The FST indexes for each population were also high and strongly correlated with physical distance. The high estimated level of endogamy and the low observed heterozygosity are indicative that the populations reproduce mainly by self-fertilization and crosses between related individuals. Consequently, strategies for in situ preservation should include at least three occurrence sites of G. mustelinum from each population. For ex situ conservation, the collections should include as many sites as possible.

Alves MF; Barroso PA; Ciampi AY; Hoffmann LV; Azevedo VC; Cavalcante U

2013-01-01

170

Genetic diversity in tetraploid switchgrass revealed by AFLP marker polymorphisms.  

UK PubMed Central (United Kingdom)

Switchgrass (Panicum virgatum) is a perennial warm-season grass native to North America that has been identified as a dedicated cellulosic biofuel crop. We quantified genetic diversity in tetraploid switchgrass germplasm collected at Oklahoma State University and characterized genetic relatedness among the collections from distinct regions. Fifty-six tetraploid accessions, including seven upland and 49 lowland genotypes from throughout the US, were examined. The amplified fragment length polymorphism (AFLP) procedure was utilized to generate DNA profiling patterns that were scored visually. Sixteen selective AFLP primer combinations were used to amplify 452 polymorphic bands. The accessions' genetic similarity coefficients, UPGMA (unweighted pair-group method with arithmetic averaging) cluster analysis and principle coordinate analysis, were performed. The upland and lowland accessions clustered according to ecotypes, with one exception (TN104). Genetic similarity coefficients among the accessions ranged from 0.73 to 0.95. Analysis of molecular variance (AMOVA) was performed, showing significant differences between the upland and lowland genotypes. The trnL marker confirmed that TN104 was a lowland genotype, but the trnL marker identification of upland and lowland genotypes was not consistent with the AFLP analysis in two germplasms (Miami and AR4).

Todd J; Wu YQ; Wang Z; Samuels T

2011-01-01

171

Evaluation of genetic diversity and conservation priorities for Egyptian chickens  

Directory of Open Access Journals (Sweden)

Full Text Available In this study, 21 microsatellite markers were used to genotype 196 Egyptian local chickens obtained from Fayoumi (n = 35), Dandarawy (n = 30), Baladi (n = 29), Sinai (n = 30), El-Salam (n = 36), and Golden Montazah (n = 36) strains. The results were compared to two pure commercial chicken populations reared in Japan-White Leghorn (n = 42) and Rhode Island Red (n = 43). A total of 162 alleles were observed, with an average of 7.7 alleles per locus. The average expected heterozygosity for the Egyptian chickens was 0.595. The closest pairwise Nei’s genetic distance was recorded between Sinai and Golden Montazah (0.038) and the smallest pairwise FST value (0.006) was observed between Baladi and Sinai. The most probable structure clustering of the eight studied populations was at K = 6. Baladi, Sinai and Golden Montazah strains were clustered together forming admixed mosaic cluster. Dandarawy ranked firstly and contributed the most to aggregate genetic diversity based on two prioritization methods. The information resulting from this study may be used as an initial guide to design further investigations for development of sustainable genetic improvement and conservation programs for the Egyptian chicken genetic resources.

Sherif Ramadan; Boniface B. Kayang; Eiji Inoue; Keijiro Nirasawa; Hiroshi Hayakawa; Shin’ichi Ito; Miho Inoue-Murayama

2012-01-01

172

Mining cation (CAX) transporter diversity for nutrition-enhanced crops and phytoremediation  

Directory of Open Access Journals (Sweden)

Full Text Available Plant CAX (cation/proton exchangers) have been demonstrated to be versatile tools for nutritional enhancement of crops and phytoremediation. However, the extent of sequence diversity of plant CAXs has not been fully understood. Therefore, we isolated new CAXs from several local plants that occur in the Gujarat State in India to explore the diversity. We have identified a novel element in two Asteraceae species that is absent from any CAX in the public databases. The sequence diversity and the new element discovered in this investigation will be further studied biochemically for future applications in genetically modified plants.

Neeraj Jain; Toshiro Shigaki; Rajani S Nadgauda

2009-01-01

173

Genetic Diversity in Bread Wheat (Triticum aestivum L.) Genotypes  

Directory of Open Access Journals (Sweden)

Full Text Available Wheat is one most important cereal crops grown in Ethiopia. Yet, keeping in view insufficient information on exotic bread wheat genotypes is limiting the access to useful traits present among the genotypes in the Somali region of Ethiopia. The aim of the study was to assess the extent of genetic diversity among bread wheat genotypes. Twenty six bread wheat (Triticum aestivum L.) genotypes obtained from ICARDA-CIMMYT were tested at Gode and Kelafo research sites at three cropping seasons (2009/10, 2010/11 and 2011/12) under irrigation. The experiment was conducted in randomized complete block design with three replications. Ten agronomic traits were included in the study. The mean values, ranges and the coefficient of variation of the 10 characters indicated the existence of sufficient variability among genotypes. Multivariate techniques were used to classify 26 bread wheat genotypes. Principal component analysis showed that the first six principal components explained about 91.87% of the total variation. D2 analysis showed the 26 bread wheat genotypes grouped into six clusters. This made to become moderate diversity among the genotypes. The crosses between genotypes selected from cluster-III with cluster-VI and cluster V with cluster VI are expected to produce better genetic recombination and segregation in their progenies. Therefore, these bread wheat genotypes need to be crossed and selected to develop high yielding pure line variety.

A. Degewione; S. Alamerew

2013-01-01

174

Genetic diversity of Mycobacterium tuberculosis isolates from Inner Mongolia, China.  

UK PubMed Central (United Kingdom)

BACKGROUND: Tuberculosis (TB) is a serious public health problem in China, and within China, Inner Mongolia has a high prevalence area of TB. Though studies on the genetic diversity of Mycobacterium tuberculosis (MTB) have been reported in many provinces, there are no such studies to date in Inner Mongolia. In this study, we investigated the genetic diversity of MTB in Inner Mongolia. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we analyzed 372 clinical MTB isolates with 22-loci mycobacterial interspersed repetitive unit and variable-number tandem repeats (MIRU-VNTR), spoligotyping, large sequence polymorphism (LSP), and NTF region analysis to understand the TB genotypes prevalent in Inner Mongolia. We found that the Beijing family was the most prevalent genotype (85.48%, 318/372), and the "modern" sublineage accounted for 76.73% (244/318) of the isolates. Our data also showed that there was no statistically significant association between the two major nationalities and the Beijing genotype (?(2)?=?3.612, P?=?0.057; P>0.05). CONCLUSION/SIGNIFICANCE: The Beijing genotype is the most prevalent family of M. tuberculosis in Inner Mongolia, and we do not find any correlation between the Beijing genotype and the major nationalities.

Yu Q; Su Y; Lu B; Ma Y; Zhao X; Yang X; Dong H; Liu Y; Lian L; Wan L; Wu Y; Wan K

2013-01-01

175

Genetic diversity in Spanish donkey breeds using microsatellite DNA markers  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Genetic diversity at 13 equine microsatellite loci was compared in five endangered Spanish donkey breeds: Andaluza, Catalana, Mallorquina, Encartaciones and Zamorano-Leonesa. All of the equine microsatellites used in this study were amplified and were polymorphic in the domestic donkey breeds with the exception of HMS1, which was monomorphic, and ASB2, which failed to amplify. Allele number, frequency distributions and mean heterozygosities were very similar among the Spanish donkey breeds. The unbiased expected heterozygosity (HE) over all the populations varied between 0.637 and 0.684 in this study. The low GST value showed that only 3.6% of the diversity was between breeds (P A distance matrix showed little differentiation between Spanish breeds, but great differentiation between them and the Moroccan ass and also with the horse, used as an outgroup. These results confirm the potential use of equine microsatellite loci as a tool for genetic studies in domestic donkey populations, which could also be useful for conservation plans.

Aranguren-Méndez José; Jordana Jordi; Gomez Mariano

2001-01-01

176

Genetic diversity in a world germplasm collection of tall fescue.  

Science.gov (United States)

Festuca arundinacea Schreb., commonly known as tall fescue, is a major forage crop in temperate regions. Recently, a molecular analysis of different accessions of a world germplasm collection of tall fescue has demonstrated that it contains different species from the genus Festuca and allowed their rapid classification into the three major morphotypes (Continental, Mediterranean and Rhizomatous). In this study, we explored the genetic diversity of 161 accessions of Festuca species from 29 countries, including 28 accessions of INTA (Argentina), by analyzing 15 polymorphic SSR markers by capillary electrophoresis. These molecular markers allowed us to detect a total of 214 alleles. The number of alleles per locus varied between 5 and 24, and the values of polymorphic information content ranged from 0.627 to 0.840. In addition, the accessions analyzed by flow cytometry showed different ploidy levels (diploid, tetraploid, hexaploid and octaploid), placing in evidence that the world germplasm collection consisted of multiple species, as previously suggested. Interestingly, almost all accessions of INTA germplasm collection were true hexaploid tall fescue, belonging to two eco-geographic races (Continental and Mediterranean). Finally, the data presented revealed an ample genetic diversity of tall fescue showing the importance of preserving the INTA collection for future breeding programs. PMID:23885206

Cuyeu, Romina; Rosso, Beatriz; Pagano, Elba; Soto, Gabriela; Fox, Romina; Ayub, Nicolás Daniel

2013-05-17

177

Genetic diversity in a world germplasm collection of tall fescue.  

UK PubMed Central (United Kingdom)

Festuca arundinacea Schreb., commonly known as tall fescue, is a major forage crop in temperate regions. Recently, a molecular analysis of different accessions of a world germplasm collection of tall fescue has demonstrated that it contains different species from the genus Festuca and allowed their rapid classification into the three major morphotypes (Continental, Mediterranean and Rhizomatous). In this study, we explored the genetic diversity of 161 accessions of Festuca species from 29 countries, including 28 accessions of INTA (Argentina), by analyzing 15 polymorphic SSR markers by capillary electrophoresis. These molecular markers allowed us to detect a total of 214 alleles. The number of alleles per locus varied between 5 and 24, and the values of polymorphic information content ranged from 0.627 to 0.840. In addition, the accessions analyzed by flow cytometry showed different ploidy levels (diploid, tetraploid, hexaploid and octaploid), placing in evidence that the world germplasm collection consisted of multiple species, as previously suggested. Interestingly, almost all accessions of INTA germplasm collection were true hexaploid tall fescue, belonging to two eco-geographic races (Continental and Mediterranean). Finally, the data presented revealed an ample genetic diversity of tall fescue showing the importance of preserving the INTA collection for future breeding programs.

Cuyeu R; Rosso B; Pagano E; Soto G; Fox R; Ayub ND

2013-07-01

178

Genetic diversity in a world germplasm collection of tall fescue  

Scientific Electronic Library Online (English)

Full Text Available Abstract in english Festuca arundinacea Schreb., commonly known as tall fescue, is a major forage crop in temperate regions. Recently, a molecular analysis of different accessions of a world germplasm collection of tall fescue has demonstrated that it contains different species from the genus Festuca and allowed their rapid classification into the three major morphotypes (Continental, Mediterranean and Rhizomatous). In this study, we explored the genetic diversity of 161 accessions of Festuc (more) a species from 29 countries, including 28 accessions of INTA (Argentina), by analyzing 15 polymorphic SSR markers by capillary electrophoresis. These molecular markers allowed us to detect a total of 214 alleles. The number of alleles per locus varied between 5 and 24, and the values of polymorphic information content ranged from 0.627 to 0.840. In addition, the accessions analyzed by flow cytometry showed different ploidy levels (diploid, tetraploid, hexaploid and octaploid), placing in evidence that the world germplasm collection consisted of multiple species, as previously suggested. Interestingly, almost all accessions of INTA germplasm collection were true hexaploid tall fescue, belonging to two eco-geographic races (Continental and Mediterranean). Finally, the data presented revealed an ample genetic diversity of tall fescue showing the importance of preserving the INTA collection for future breeding programs.

Cuyeu, Romina; Rosso, Beatriz; Pagano, Elba; Soto, Gabriela; Fox, Romina; Ayub, Nicolás Daniel

2013-01-01

179

Genetic diversity of caprine Blastocystis from Peninsular Malaysia.  

UK PubMed Central (United Kingdom)

Blastocystis sp. is a common intestinal parasite found in humans and animals. The possibility of zoonotic transmission to humans from livestock especially goats led us to investigate the genetic diversity of caprine Blastocystis sp. obtained from five different farms in Peninsular Malaysia. Moreover, there is a lack of information on the prevalence as well as genetic diversity of Blastocystis sp. in goat worldwide. Results showed that 73/236 (30.9 %) of the goats were found to be positive for Blastocystis infection. The most predominant Blastocystis sp. subtype was ST1 (60.3 %) followed by ST7 (41.1 %), ST6 (41.1 %), and ST3 (11.0 %) when amplified by PCR using sequenced-tagged site (STS) primers. Four farms had goats infected only with ST1 whereas the fifth showed mixed infections with multiple STs. The proximity of the fifth farm to human dwellings, nearby domesticated animals and grass land as opposed to a sterile captive environment in the first four farms may account for the multiple STs seen in the fifth farm. Since ST1, ST3, ST6 and ST 7 were previously reported in human infection worldwide in particular Malaysia, the potential of the zoonotic transmission of blastocystosis should not be disregarded. The implications of different farm management systems on the distribution of Blastocystis sp. STs are discussed.

Tan TC; Tan PC; Sharma R; Sugnaseelan S; Suresh KG

2013-01-01

180

Genetic diversity of caprine Blastocystis from Peninsular Malaysia.  

Science.gov (United States)

Blastocystis sp. is a common intestinal parasite found in humans and animals. The possibility of zoonotic transmission to humans from livestock especially goats led us to investigate the genetic diversity of caprine Blastocystis sp. obtained from five different farms in Peninsular Malaysia. Moreover, there is a lack of information on the prevalence as well as genetic diversity of Blastocystis sp. in goat worldwide. Results showed that 73/236 (30.9 %) of the goats were found to be positive for Blastocystis infection. The most predominant Blastocystis sp. subtype was ST1 (60.3 %) followed by ST7 (41.1 %), ST6 (41.1 %), and ST3 (11.0 %) when amplified by PCR using sequenced-tagged site (STS) primers. Four farms had goats infected only with ST1 whereas the fifth showed mixed infections with multiple STs. The proximity of the fifth farm to human dwellings, nearby domesticated animals and grass land as opposed to a sterile captive environment in the first four farms may account for the multiple STs seen in the fifth farm. Since ST1, ST3, ST6 and ST 7 were previously reported in human infection worldwide in particular Malaysia, the potential of the zoonotic transmission of blastocystosis should not be disregarded. The implications of different farm management systems on the distribution of Blastocystis sp. STs are discussed. PMID:22961236

Tan, Tian Chye; Tan, Peng Chiang; Sharma, Reuben; Sugnaseelan, Sumita; Suresh, Kumar Govind

2012-09-08

 
 
 
 
181

Genetic diversity among five T4-like bacteriophages  

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Full Text Available Abstract Background Bacteriophages are an important repository of genetic diversity. As one of the major constituents of terrestrial biomass, they exert profound effects on the earth's ecology and microbial evolution by mediating horizontal gene transfer between bacteria and controlling their growth. Only limited genomic sequence data are currently available for phages but even this reveals an overwhelming diversity in their gene sequences and genomes. The contribution of the T4-like phages to this overall phage diversity is difficult to assess, since only a few examples of complete genome sequence exist for these phages. Our analysis of five T4-like genomes represents half of the known T4-like genomes in GenBank. Results Here, we have examined in detail the genetic diversity of the genomes of five relatives of bacteriophage T4: the Escherichia coli phages RB43, RB49 and RB69, the Aeromonas salmonicida phage 44RR2.8t (or 44RR) and the Aeromonas hydrophila phage Aeh1. Our data define a core set of conserved genes common to these genomes as well as hundreds of additional open reading frames (ORFs) that are nonconserved. Although some of these ORFs resemble known genes from bacterial hosts or other phages, most show no significant similarity to any known sequence in the databases. The five genomes analyzed here all have similarities in gene regulation to T4. Sequence motifs resembling T4 early and late consensus promoters were observed in all five genomes. In contrast, only two of these genomes, RB69 and 44RR, showed similarities to T4 middle-mode promoter sequences and to the T4 motA gene product required for their recognition. In addition, we observed that each phage differed in the number and assortment of putative genes encoding host-like metabolic enzymes, tRNA species, and homing endonucleases. Conclusion Our observations suggest that evolution of the T4-like phages has drawn on a highly diverged pool of genes in the microbial world. The T4-like phages harbour a wealth of genetic material that has not been identified previously. The mechanisms by which these genes may have arisen may differ from those previously proposed for the evolution of other bacteriophage genomes.

Nolan James M; Petrov Vasiliy; Bertrand Claire; Krisch Henry M; Karam Jim D

2006-01-01

182

Genetic variation in the Sorbs of eastern Germany in the context of broader European genetic diversity.  

Science.gov (United States)

Population isolates have long been of interest to genetic epidemiologists because of their potential to increase power to detect disease-causing genetic variants. The Sorbs of Germany are considered as cultural and linguistic isolates and have recently been the focus of disease association mapping efforts. They are thought to have settled in their present location in eastern Germany after a westward migration from a largely Slavic-speaking territory during the Middle Ages. To examine Sorbian genetic diversity within the context of other European populations, we analyzed genotype data for over 30?000 autosomal single-nucleotide polymorphisms from over 200 Sorbs individuals. We compare the Sorbs with other European individuals, including samples from population isolates. Despite their geographical proximity to German speakers, the Sorbs showed greatest genetic similarity to Polish and Czech individuals, consistent with the linguistic proximity of Sorbian to other West Slavic languages. The Sorbs also showed evidence of subtle levels of genetic isolation in comparison with samples from non-isolated European populations. The level of genetic isolation was less than that observed for the Sardinians and French Basque, who were clear outliers on multiple measures of isolation. The finding of the Sorbs as only a minor genetic isolate demonstrates the need to genetically characterize putative population isolates, as they possess a wide range of levels of isolation because of their different demographic histories. PMID:21559053

Veeramah, Krishna R; Tönjes, Anke; Kovacs, Peter; Gross, Arnd; Wegmann, Daniel; Geary, Patrick; Gasperikova, Daniela; Klimes, Iwar; Scholz, Markus; Novembre, John; Stumvoll, Michael

2011-05-11

183

Genetic variation in the Sorbs of eastern Germany in the context of broader European genetic diversity.  

UK PubMed Central (United Kingdom)

Population isolates have long been of interest to genetic epidemiologists because of their potential to increase power to detect disease-causing genetic variants. The Sorbs of Germany are considered as cultural and linguistic isolates and have recently been the focus of disease association mapping efforts. They are thought to have settled in their present location in eastern Germany after a westward migration from a largely Slavic-speaking territory during the Middle Ages. To examine Sorbian genetic diversity within the context of other European populations, we analyzed genotype data for over 30?000 autosomal single-nucleotide polymorphisms from over 200 Sorbs individuals. We compare the Sorbs with other European individuals, including samples from population isolates. Despite their geographical proximity to German speakers, the Sorbs showed greatest genetic similarity to Polish and Czech individuals, consistent with the linguistic proximity of Sorbian to other West Slavic languages. The Sorbs also showed evidence of subtle levels of genetic isolation in comparison with samples from non-isolated European populations. The level of genetic isolation was less than that observed for the Sardinians and French Basque, who were clear outliers on multiple measures of isolation. The finding of the Sorbs as only a minor genetic isolate demonstrates the need to genetically characterize putative population isolates, as they possess a wide range of levels of isolation because of their different demographic histories.

Veeramah KR; Tönjes A; Kovacs P; Gross A; Wegmann D; Geary P; Gasperikova D; Klimes I; Scholz M; Novembre J; Stumvoll M

2011-09-01

184

Genetic diversity and admixture patterns in Indian populations.  

Science.gov (United States)

India is a diverse land whose population holds the history of waves of human dispersal. Recent studies suggest two major ancestral contributions to most of the Indian sub-populations. However, present day Indians are thought to contain huge genetic diversity derived consequent to multiple cultural, linguistic and geographical variations. Genome-wide survey of individuals from current North (N-In) and South (S-In) India along with populations from HapMap Phase III and Indian sub-populations from HUGO Pan-Asian SNP Consortium is performed. Multivariate analysis (MDS and PCA) was carried out after merging data from the current study and other consortia. Indian sub-populations clustered separately from populations of major global geographical regions in MDS and PCA in a loose agglomeration except for two Indian subpopulations clustering near far eastern populations. F(st) values indicated diversity among Indian sub-populations which was substantiated by STRUCTURE analysis suggesting the possibility of additional admixture events. PMID:22892377

Chakrabarti, Biswaroop; Kumar, Sunil; Singh, Randeep; Dimitrova, Nevenka

2012-08-08

185

Genetic diversity of Mycobacterium tuberculosis in Mbarara, South Western Uganda.  

UK PubMed Central (United Kingdom)

BACKGROUND: We determined the genetic diversity of mycobacteria isolated from tuberculosis patients in Mbarara Uganda, using region of difference (RD) analysis and spacer oligonucleotide typing (spoligotyping). METHODS: Sputum samples were cultured on Lowenstein Jensen media. The isolates were characterized using RD analysis and spoligotyping. RESULTS: The majority (92.8%) of the patients were new cases, 60% were males and 44% were HIV positive with a mean age of 33.7 years. All the 125 isolates were identified as M.tuberculosis sensu stricto. Most (92.8%) of the isolates were modern strains. Spoligotyping revealed 79 spoligotype patterns, with an overall diversity of 63.2%. Sixty (48%) isolates formed 16 clusters each consisting of 2-15 isolates. Mst (59.2 %) of the isolates were Uganda genotype strains. The major shared spoligotypes in our sample were SIT 135 (T2-Uganda) with 12 isolates and SIT 128 (T2) with 5 isolates. Sixty nine (87%) patterns had not yet been defined in the SpolDB4.0.database. CONCLUSION: The TB epidemic in Mbarara is caused mainly by modern M.tuberculosis strains of the Uganda genotype. The wide diversity of strains may indicate that the majority of the TB cases are reactivation rather than re-infection. However this needs to be ascertained with more discriminative finger printing techniques.

Bazira J; Matte M; Asiimwe BB; Joloba LM

2010-12-01

186

Role of telomere dysfunction in genetic intratumor diversity.  

UK PubMed Central (United Kingdom)

Most solid tumors are unable to maintain the stability of their genomes at the chromosome level. Indeed, cancer cells display highly rearranged karyotypes containing translocations, amplifications, deletions, and gains and losses of whole chromosomes, which reshuffle steadily. This chromosomal instability most likely occurs early in the development of cancer, and may represent an important step in promoting the multiple genetic changes required for the initiation and/or progression of the disease. Different mechanisms may underlie chromosome instability in cancer cells, but a prominent role for telomeres, the tip of linear chromosomes, has been determined. Telomeres are ribonucleoprotein structures that prevent natural chromosome ends being recognized as DNA double-strand breaks, by adopting a loop structure. Loss of telomere function appears from either alteration on telomere-binding proteins or from the progressive telomere shortening that normally occurs under physiological conditions in the majority of cells in tissues. Importantly, unmasked telomeres may either trigger the senescent phenotype that has been linked to the aging process or may initiate the chromosome instability needed for cancer development, depending on the integrity of the DNA damage checkpoint responses. Telomere dysfunction contributes to chromosome instability through end-to-end chromosome fusions entering breakage-fusion-bridge (BFB) cycles. Resolution of chromatin bridge intermediates is likely to contribute greatly to the generation of segmental chromosome amplification events, unbalanced chromosome rearrangements, and whole chromosome aneuploidy. Noteworthy is the fact that telomere length heterogeneity among individuals may directly influence the scrambling of the genome at tumor initiation. However, reiterated BFB cycles would randomly reorganize the cell karyotype, thus increasing the genetic diversity that characterizes tumor cells. Even though a direct link is still lacking, multiple evidence lead one to believe that telomere dysfunction directly contributes to cancer development in humans. The expansion of highly unstable cells due to telomere dysfunction enhances the genetic diversity needed to fuel specific mutations that may promote cell immortalization and the acquisition of a tumor phenotype.

Genescà A; Pampalona J; Frías C; Domínguez D; Tusell L

2011-01-01

187

Role of telomere dysfunction in genetic intratumor diversity.  

Science.gov (United States)

Most solid tumors are unable to maintain the stability of their genomes at the chromosome level. Indeed, cancer cells display highly rearranged karyotypes containing translocations, amplifications, deletions, and gains and losses of whole chromosomes, which reshuffle steadily. This chromosomal instability most likely occurs early in the development of cancer, and may represent an important step in promoting the multiple genetic changes required for the initiation and/or progression of the disease. Different mechanisms may underlie chromosome instability in cancer cells, but a prominent role for telomeres, the tip of linear chromosomes, has been determined. Telomeres are ribonucleoprotein structures that prevent natural chromosome ends being recognized as DNA double-strand breaks, by adopting a loop structure. Loss of telomere function appears from either alteration on telomere-binding proteins or from the progressive telomere shortening that normally occurs under physiological conditions in the majority of cells in tissues. Importantly, unmasked telomeres may either trigger the senescent phenotype that has been linked to the aging process or may initiate the chromosome instability needed for cancer development, depending on the integrity of the DNA damage checkpoint responses. Telomere dysfunction contributes to chromosome instability through end-to-end chromosome fusions entering breakage-fusion-bridge (BFB) cycles. Resolution of chromatin bridge intermediates is likely to contribute greatly to the generation of segmental chromosome amplification events, unbalanced chromosome rearrangements, and whole chromosome aneuploidy. Noteworthy is the fact that telomere length heterogeneity among individuals may directly influence the scrambling of the genome at tumor initiation. However, reiterated BFB cycles would randomly reorganize the cell karyotype, thus increasing the genetic diversity that characterizes tumor cells. Even though a direct link is still lacking, multiple evidence lead one to believe that telomere dysfunction directly contributes to cancer development in humans. The expansion of highly unstable cells due to telomere dysfunction enhances the genetic diversity needed to fuel specific mutations that may promote cell immortalization and the acquisition of a tumor phenotype. PMID:21925300

Genescà, Anna; Pampalona, Judit; Frías, Cristina; Domínguez, Daniel; Tusell, Laura

2011-01-01

188

Late Quaternary loss of genetic diversity in muskox (Ovibos)  

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Full Text Available Abstract Background The modern wildherd of the tundra muskox (Ovibos moschatus) is native only to the New World (northern North America and Greenland), and its genetic diversity is notably low. However, like several other megafaunal mammals, muskoxen enjoyed a holarctic distribution during the late Pleistocene. To investigate whether collapse in range and loss of diversity might be correlated, we collected mitochondrial sequence data (hypervariable region and cytochrome b) from muskox fossil material recovered from localities in northeastern Asia and the Arctic Archipelago of northern North America, dating from late Pleistocene to late Holocene, and compared our results to existing databases for modern muskoxen. Results Two classes of haplotypes were detected in the fossil material. "Surviving haplotypes" (SHs), closely similar or identical to haplotypes found in modern muskoxen and ranging in age from ~22,000 to ~160 yrbp, were found in all New World samples as well as some samples from northeastern Asia. "Extinct haplotypes" (EHs), dating between ~44,000 and ~18,000 yrbp, were found only in material from the Taimyr Peninsula and New Siberian Islands in northeastern Asia. EHs were not found in the Holocene muskoxen specimens available for this study, nor have they been found in other studies of extant muskox populations. Conclusion We provisionally interpret this evidence as showing that genetic variability was reduced in muskoxen after the Last Glacial Maximum but before the mid-Holocene, or roughly within the interval 18,000-4,000 yrbp. Narrowing this gap further will require the recovery of more fossils and additional genetic information from this interval.

MacPhee Ross DE; Tikhonov Alexei N; Mol Dick; Greenwood Alex D

2005-01-01

189

Molecular genetic diversity in populations of the stingless bee Plebeia remota: A case study  

Scientific Electronic Library Online (English)

Full Text Available Abstract in english Genetic diversity is a major component of the biological diversity of an ecosystem. The survival of a population may be seriously threatened if its genetic diversity values are low. In this work, we measured the genetic diversity of the stingless bee Plebeia remota based on molecular data obtained by analyzing 15 microsatellite loci and sequencing two mitochondrial genes. Population structure and genetic diversity differed depending on the molecular marker analyzed: micro (more) satellites showed low population structure and moderate to high genetic diversity, while mitochondrial DNA (mtDNA) showed high population structure and low diversity in three populations. Queen philopatry and male dispersal behavior are discussed as the main reasons for these findings.

Francisco, Flávio de Oliveira; Santiago, Leandro Rodrigues; Arias, Maria Cristina

2013-01-01

190

Molecular genetic diversity in populations of the stingless bee Plebeia remota: A case study  

Directory of Open Access Journals (Sweden)

Full Text Available Genetic diversity is a major component of the biological diversity of an ecosystem. The survival of a population may be seriously threatened if its genetic diversity values are low. In this work, we measured the genetic diversity of the stingless bee Plebeia remota based on molecular data obtained by analyzing 15 microsatellite loci and sequencing two mitochondrial genes. Population structure and genetic diversity differed depending on the molecular marker analyzed: microsatellites showed low population structure and moderate to high genetic diversity, while mitochondrial DNA (mtDNA) showed high population structure and low diversity in three populations. Queen philopatry and male dispersal behavior are discussed as the main reasons for these findings.

Flávio de Oliveira Francisco; Leandro Rodrigues Santiago; Maria Cristina Arias

2013-01-01

191

Indigenous cattle in Sri Lanka: Production systems and genetic diversity  

International Nuclear Information System (INIS)

[en] Full text: The production status, farming systems and genetic diversity of indigenous cattle in Sri Lanka were evaluated using six geographically distinct populations in Sri Lanka, which is a small island located below the southern tip of Indian subcontinent. The indigenous cattle population of the country is considered as a non-descript type mixture of genotypes, and represent more than the half of total cattle population of 1.2 million heads. Six distinct indigenous populations (NE, NC, So, No, TK and Th) were investigated for morphological and genetic differences. The respective farming systems were also evaluated to complete the requirement in developing conservation and utilization strategies. The sampling was carried out based on the non-existence of artificial insemination facilities to assure the target populations are indigenous. The six populations were assumed genetically isolated from each other in the absence of nomadic pattern of rearing and regular cattle migration. The farming systems were analyzed using a pre-tested structured questionnaire by single visits to each location. Single visits were practiced, as there is no variation in farming system according to the period of the year. Morphometric measurements were taken during the visit and the genetic variation was assessed within and between five populations using 15 autosomal and two Y-specific microsatellite markers. The farming system analysis revealed that indigenous cattle are reared as a traditional practice in all the regions of the country under limited or no input situations. Since the low productivity masks its real contribution to the rural livelihood, the level of utilization was confounded within the attributes of respective farming systems. The contribution of indigenous cattle to total tangible income ranged from 0% to 90% in different regions reflecting the high variation in the purpose of keeping indigenous cattle. Integration with crop, especially with paddy was the common feature in systems across the regions. Morphometric measurements identified the specific phenotypic characteristics resulted by geographical isolation and selective breeding. Though vary according to the regional preferences, the compact body, narrow face, small horns and humps with shades of brown and black coat colour described the indigenous cattle phenotype in general. The diversity analysis based on microsatellite genotyping indicated that indigenous cattle in Sri Lanka has a high genetic diversity with average number of alleles per locus ranging from 7.9 to 8.5. Average heterozygosity of different regions varied within a narrow range (0.72 ± 0.04 to 0.76 ± 0.03). The genetic distances (DA) between regions were low (ranged between 0.085 and 0.066) suggesting a similar mixture of genotypes across regions despite the geographical isolation. However, two genetic clusters were visible though no relationship of those clusters with the geographical distribution of different regions could be observed. Introgression of taurine cattle was evidenced in one of the cattle populations (NC) as suggested by the Y-specific microsatellite analysis (author)

2009-01-01

192

Genetic diversity of Plasmodium vivax isolates from Azerbaijan  

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Full Text Available Abstract Background Plasmodium vivax, although causing a less serious disease than Plasmodium falciparum, is the most widespread of the four human malarial species. Further to the recent recrudescence of P. vivax cases in the Newly Independent States (NIS) of central Asia, a survey on the genetic diversity and dissemination in Azerbaijan was undertaken. Azerbaijan is at the crossroads of Asia and, as such, could see a rise in the number of cases, although an effective malaria control programme has been established in the country. Methods Thirty-six P. vivax isolates from Central Azerbaijan were characterized by analysing the genetic polymorphism of the circumsporozoite protein (CSP) and the merozoite surface protein 1 (MSP-1) genes, using PCR amplifications and amplicons sequencing. Results Analysis of CSP sequences showed that all the processed isolates belong to the VK 210 type, with variations in the alternation of alanine residue (A) or aspartic acid residue (D) in the repeat motif GDRA(A/D)GQPA along the sequence. As far as MSP-1 genotyping is concerned, it was found that the majority of isolates analysed belong to Belem and Sal I types. Five recombinant isolates were also identified. Combined analysis with the two genetic markers allowed the identification of 19 plasmodial sub-types. Conclusion The results obtained in the present study indicate that there are several P. vivax clones circulating in Azerbaijan and, consequently, a careful malaria surveillance could be of paramount importance to identify, at early stage, the occurrence of possible P. vivax malaria outbreaks.

Leclerc Marie; Menegon Michela; Cligny Alexandra; Noyer Jean; Mammadov Suleyman; Aliyev Namig; Gasimov Elkhan; Majori Giancarlo; Severini Carlo

2004-01-01

193

Genetic diversity of 'Uba' mango tree using ISSR markers.  

UK PubMed Central (United Kingdom)

In this study, the genetic diversity of 'Ubá' mango trees cultivated at the Zona da Mata of Minas Gerais State, Brazil, was assessed, to identify whether there is variability in the plants grown in the region, justifying the mass selection as a breeding method. We used 102 accessions. Leaves were collected for extraction of genomic DNA, which was amplified with nine ISSR primers. The data obtained by the analysis of electrophoretic patterns were arranged in a binary matrix, considering 0 for the absence and 1 for the presence of bands. Based on these data, we performed the analysis of genetic dissimilarity and carried out the cluster analysis by the methods of Tocher and graphical dispersion. The most similar accessions are 144 and 150, both coming from Ubá, while the most divergent ones are 29 and 97, from Visconde do Rio Branco. The grouping by the Tocher method separated the accessions into six groups, 94.1% of which were allocated in the first group and showed that there is no separation of accessions depending on the sampling sites. The 3D scatter plot reinforces this conclusion. There is genetic variability among the accessions of 'Ubá' mango tree evaluated. Therefore, it is possible to make mass selection in open-pollinated populations.

Rocha A; Salomão LC; Salomão TM; Cruz CD; de Siqueira DL

2012-02-01

194

Genetic diversity of 'Ubá' mango tree using ISSR markers.  

Science.gov (United States)

In this study, the genetic diversity of 'Ubá' mango trees cultivated at the Zona da Mata of Minas Gerais State, Brazil, was assessed, to identify whether there is variability in the plants grown in the region, justifying the mass selection as a breeding method. We used 102 accessions. Leaves were collected for extraction of genomic DNA, which was amplified with nine ISSR primers. The data obtained by the analysis of electrophoretic patterns were arranged in a binary matrix, considering 0 for the absence and 1 for the presence of bands. Based on these data, we performed the analysis of genetic dissimilarity and carried out the cluster analysis by the methods of Tocher and graphical dispersion. The most similar accessions are 144 and 150, both coming from Ubá, while the most divergent ones are 29 and 97, from Visconde do Rio Branco. The grouping by the Tocher method separated the accessions into six groups, 94.1% of which were allocated in the first group and showed that there is no separation of accessions depending on the sampling sites. The 3D scatter plot reinforces this conclusion. There is genetic variability among the accessions of 'Ubá' mango tree evaluated. Therefore, it is possible to make mass selection in open-pollinated populations. PMID:21644009

Rocha, Aline; Salomão, Luiz Carlos Chamhum; Salomão, Tânia Maria Fernandes; Cruz, Cosme Damião; de Siqueira, Dalmo Lopes

2012-02-01

195

Managing Genetic Variation to Conserve Genetic Diversity in Goats and Sheep  

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Full Text Available Domestic goat and sheep populations maintained for many generations with small numbers of male and female parents, or declining in total numbers, not only endure accumulated genetic drift but also a steady rise in inbreeding, which can be directly attributed to dispersive forces of evolutionary significance that influence gene frequency. Increasing effective population size shows theoretical promise in lessening the impact on erosion of biodiversity from genetic drift. For example, doubling the effective numbers of parents which increases effective population size reduces rate of inbreeding by nearly one-half in many of the scenarios in the present study. Similarly, equalizing the number of male and female parents can decrease the variance among progeny of each parent, which in turn increases effective population size. The recurring erosion of domestic goat and sheep diversity has contributed to decreased fecundity, reduced fitness and poor adaptability, all known to influence efficiency of production. The potential loss in performance of livestock and poultry following many generations of accumulated genetic drift, which often goes unnoticed, can be predicted for specific populations from precise estimates of their mean value, additive genetic variance and heritability along with their effective number of male and female parents. For example, when the effective population size decreases from 200 to 40, the potential reduction in mean performance for economically important traits of goat and sheep populations following 20 generations of accumulated genetic drift will nearly double. In contrast, increasing effective population size from 200 to 600 will have the potential reduction in mean performance. The accumulation of favourable mutations could imply an effective population size of 100 or more, which is equal to a rise in rate of inbreeding of 0.5% or less, may be acceptable in sustaining genetic response to artificial selection in commercial breeding populations. The application of quantitative genetic principles related to inbreeding and genetic drift make it possible to safeguard against erosion of genetic diversity in endangered breeds, populations and landraces while lessening the impact from potential loss in their performance. Conservation of domestic animal diversity can be achieved by managing the erosion of genetic variation based on breeding strategies which promote the mating of sires to all dams, in either ‘random bred’ or ‘balanced pedigreed’ breeding structure for populations of endangered domestic goats and sheep. Obviously, the in-situ and ex-situ conservation of live animals, along with cryogenic preservation of their gametes, stem cells, somatic cells, blood and gonads will be complementary to conservation breeding.

J. N. B. Shrestha; G. H. Crow; M.I. Soysal

2010-01-01

196

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

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

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

2011-01-01

197

Genetic characterization of northeastern Italian population isolates in the context of broader European genetic diversity.  

UK PubMed Central (United Kingdom)

Population genetic studies on European populations have highlighted Italy as one of genetically most diverse regions. This is possibly due to the country's complex demographic history and large variability in terrain throughout the territory. This is the reason why Italy is enriched for population isolates, Sardinia being the best-known example. As the population isolates have a great potential in disease-causing genetic variants identification, we aimed to genetically characterize a region from northeastern Italy, which is known for isolated communities. Total of 1310 samples, collected from six geographically isolated villages, were genotyped at >145000 single-nucleotide polymorphism positions. Newly genotyped data were analyzed jointly with the available genome-wide data sets of individuals of European descent, including several population isolates. Despite the linguistic differences and geographical isolation the village populations still show the greatest genetic similarity to other Italian samples. The genetic isolation and small effective population size of the village populations is manifested by higher levels of genomic homozygosity and elevated linkage disequilibrium. These estimates become even more striking when the detected substructure is taken into account. The observed level of genetic isolation in Friuli-Venezia Giulia region is more extreme according to several measures of isolation compared with Sardinians, French Basques and northern Finns, thus proving the status of an isolate.

Esko T; Mezzavilla M; Nelis M; Borel C; Debniak T; Jakkula E; Julia A; Karachanak S; Khrunin A; Kisfali P; Krulisova V; Aušrelé Ku?inskiené Z; Rehnström K; Traglia M; Nikitina-Zake L; Zimprich F; Antonarakis SE; Estivill X; Glava? D; Gut I; Klovins J; Krawczak M; Ku?inskas V; Lathrop M; Macek M; Marsal S; Meitinger T; Melegh B; Limborska S; Lubinski J; Paolotie A; Schreiber S; Toncheva D; Toniolo D; Wichmann HE; Zimprich A; Metspalu M; Gasparini P; Metspalu A; D'Adamo P

2013-06-01

198

Genetic characterization of northeastern Italian population isolates in the context of broader European genetic diversity  

Science.gov (United States)

Population genetic studies on European populations have highlighted Italy as one of genetically most diverse regions. This is possibly due to the country's complex demographic history and large variability in terrain throughout the territory. This is the reason why Italy is enriched for population isolates, Sardinia being the best-known example. As the population isolates have a great potential in disease-causing genetic variants identification, we aimed to genetically characterize a region from northeastern Italy, which is known for isolated communities. Total of 1310 samples, collected from six geographically isolated villages, were genotyped at >145?000 single-nucleotide polymorphism positions. Newly genotyped data were analyzed jointly with the available genome-wide data sets of individuals of European descent, including several population isolates. Despite the linguistic differences and geographical isolation the village populations still show the greatest genetic similarity to other Italian samples. The genetic isolation and small effective population size of the village populations is manifested by higher levels of genomic homozygosity and elevated linkage disequilibrium. These estimates become even more striking when the detected substructure is taken into account. The observed level of genetic isolation in Friuli-Venezia Giulia region is more extreme according to several measures of isolation compared with Sardinians, French Basques and northern Finns, thus proving the status of an isolate.

Esko, Tonu; Mezzavilla, Massimo; Nelis, Mari; Borel, Christelle; Debniak, Tadeusz; Jakkula, Eveliina; Julia, Antonio; Karachanak, Sena; Khrunin, Andrey; Kisfali, Peter; Krulisova, Veronika; Ausrele Kucinskiene, Zita; Rehnstrom, Karola; Traglia, Michela; Nikitina-Zake, Liene; Zimprich, Fritz; Antonarakis, Stylianos E; Estivill, Xavier; Glavac, Damjan; Gut, Ivo; Klovins, Janis; Krawczak, Michael; Kucinskas, Vaidutis; Lathrop, Mark; Macek, Milan; Marsal, Sara; Meitinger, Thomas; Melegh, Bela; Limborska, Svetlana; Lubinski, Jan; Paolotie, Aarno; Schreiber, Stefan; Toncheva, Draga; Toniolo, Daniela; Wichmann, H-Erich; Zimprich, Alexander; Metspalu, Mait; Gasparini, Paolo; Metspalu, Andres; D'Adamo, Pio

2013-01-01

199

Genetic Variability and Diversity in Okra (Abelmoschus esculentus L. Moench)  

Directory of Open Access Journals (Sweden)

Full Text Available In the present investigation an attempt has been made to evaluate the genetic variability of some yield contributingcharacters, and the genetic diversity in fifty genotypes of okra collected from the NBPGR New Delhi, India. Analysis ofvariance indicated significant difference among the genotypes for different morphological characters. High values of GCV,PCV, heritability and genetic advance (% of mean) observed for number of fruiting nodes, number of ridges per fruit, plantheight and number of fruiting nodes indicated these characters might be controlled by additive genes. On the basis of D2analysis, the 50 genotypes could be grouped into 5 clusters. Cluster I had the highest number of genotypes (45) followed bycluster II (2). Remaining clusters were monogenotypic. Plant height had the highest contribution towards the total geneticdivergence. The highest intra-cluster distances were recorded in cluster I followed by cluster II. The maximum inter-clusterdistance was recorded between cluster IV and cluster II, followed by cluster V and cluster II. Among the 50 genotypes, IC-332454 showed the highest cluster mean for fruit yield per plant and number of fruits per plant. The genotypes which were inthe cluster V, III and II also exhibited significant performance for fruit yield per plant, number of fruits per plant and plantheight sequentially. On the basis of groupings of individual genotypes into different clusters, contribution of individualcharacter towards total genetic divergence, inter-cluster distance and cluster mean, the genotypes such as IC-9856B, IC-331157, IC-342075, IC-332453 and IC-43736 were found promising for using in the hybridization programme.

Pradip K. Akotkar, D.K. De and A.K. Pal

2010-01-01

200

Inhibition of BET bromodomain targets genetically diverse glioblastoma.  

UK PubMed Central (United Kingdom)

PURPOSE: Glioblastoma is refractory to conventional therapies. The bromodomain and extraterminal domain (BET) proteins are epigenetic readers that selectively bind to acetylated lysine residues on histone tails. These proteins recently emerged as important therapeutic targets in NUT midline carcinoma and several types of hematopoietic cancers. In this study, the therapeutic potential of a novel BET bromodomain inhibitor, JQ1, was assessed in a panel of genetically heterogeneous glioblastoma samples. EXPERIMENTAL DESIGN: The antineoplastic effects of JQ1 were shown using ex vivo cultures derived from primary glioblastoma xenograft lines and surgical specimens of different genetic background. The in vivo efficacy was assessed in orthotopic glioblastoma tumors. RESULTS: We showed that JQ1 induced marked G1 cell-cycle arrest and apoptosis, which was phenocopied by knockdown of individual BET family members. JQ1 treatment resulted in significant changes in expression of genes that play important roles in glioblastoma such as c-Myc, p21(CIP1/WAF1), hTERT, Bcl-2, and Bcl-xL. Unlike the observations in some hematopoietic cancer cell lines, exogenous c-Myc did not significantly protect glioblastoma cells against JQ1. In contrast, ectopically expressed Bcl-xL partially rescued cells from JQ1-induced apoptosis, and knockdown of p21(CIP1/WAF1) attenuated JQ1-induced cell-cycle arrest. Cells genetically engineered for Akt hyperactivation or p53/Rb inactivation did not compromise JQ1 efficacy, suggesting that these frequently mutated signaling pathways may not confer resistance to JQ1. Furthermore, JQ1 significantly repressed growth of orthotopic glioblastoma tumors. CONCLUSION: Our results suggest potentially broad therapeutic use of BET bromodomain inhibitors for treating genetically diverse glioblastoma tumors.

Cheng Z; Gong Y; Ma Y; Lu K; Lu X; Pierce LA; Thompson RC; Muller S; Knapp S; Wang J

2013-04-01

 
 
 
 
201

EFFECTS OF CHEMICAL CONTAMINANTS ON GENETIC DIVERSITY IN NATURAL POPULATIONS: IMPLICATIONS FOR BIOMONITORING AND ECOTOXICOLOGY  

Science.gov (United States)

The conservation of genetic diversity has emerged as one of the central issues in conservation biology. Although researchers in the areas of evolutionary biology, population management, and conservation biology routinely investigate genetic variability in natural populations, onl...

202

Genetic diversity of Dekkera bruxellensis yeasts isolated from Australian wineries.  

UK PubMed Central (United Kingdom)

Yeasts of the genus Dekkera and its anamorph Brettanomyces represent a significant spoilage issue for the global wine industry. Despite this, there is limited knowledge of genetic diversity and strain distribution within wine and winery-related environments. In this study, amplified fragment length polymorphism (AFLP) analysis was conducted on 244 Dekkera bruxellensis isolates from red wine made in 31 winemaking regions of Australia. The results indicated there were eight genotypes among the isolates, and three of these were commonly found across multiple winemaking regions. Analysis of 26S rRNA gene sequences provided further evidence of three common, conserved groups, whereas a phylogeny based upon the AFLP data demonstrated that the most common D. bruxellensis genotype (I) in Australian red wine was highly divergent from the D. bruxellensis type strain (CBS 74).

Curtin CD; Bellon JR; Henschke PA; Godden PW; de Barros Lopes MA

2007-05-01

203

Genetic diversity of Dekkera bruxellensis yeasts isolated from Australian wineries.  

Science.gov (United States)

Yeasts of the genus Dekkera and its anamorph Brettanomyces represent a significant spoilage issue for the global wine industry. Despite this, there is limited knowledge of genetic diversity and strain distribution within wine and winery-related environments. In this study, amplified fragment length polymorphism (AFLP) analysis was conducted on 244 Dekkera bruxellensis isolates from red wine made in 31 winemaking regions of Australia. The results indicated there were eight genotypes among the isolates, and three of these were commonly found across multiple winemaking regions. Analysis of 26S rRNA gene sequences provided further evidence of three common, conserved groups, whereas a phylogeny based upon the AFLP data demonstrated that the most common D. bruxellensis genotype (I) in Australian red wine was highly divergent from the D. bruxellensis type strain (CBS 74). PMID:17233769

Curtin, Chris D; Bellon, Jennifer R; Henschke, Paul A; Godden, Peter W; de Barros Lopes, Miguel A

2007-01-15

204

Genetic diversity and population structure of Sugarcane mosaic virus.  

UK PubMed Central (United Kingdom)

Sugarcane mosaic virus (SCMV) is one of the causal pathogens of mosaic diseases on sugarcane, maize, sorghum and some other graminaceous species with worldwide distribution. The global genetic diversity and molecular evolution of SCMV capsid protein (CP) gene were investigated with the nucleotide sequences available in the GenBank database. Phylogenetic analyses revealed that SCMV isolates clustered in relation to their original hosts, and geographically distinct isolates from maize or sugarcane clustered differently. The populations between maize and sugarcane showed frequent gene flows; but within maize or sugarcane geography distinct isolates had infrequent gene flow. Recombination existed in the region of CP cistron and 3'-untranslated region (UTR). Most of the codons in the CP gene were under negative selection or neutral evolution except for codons 27 and 48, which were under positive selection. This study provided systematic analyses of the evolutionary processes contributing to the observed diversification of SCMV populations.

Li Y; Liu R; Zhou T; Fan Z

2013-01-01

205

Genetic diversity of Gallibacterium anatis isolates from different chicken flocks  

DEFF Research Database (Denmark)

Amplified fragment length polymorphisms (AFLPs) were used to characterize the genotypic diversity of a total of 114 Gallibacterium anatis isolates originating from a reference collection representing 15 biovars from four countries and isolates obtained from tracheal and cloacal swab samples of chickens from an organic, egg-producing flock and a layer parent flock. A subset of strains was also characterized by pulsed-field gel electrophoresis and biotyping. The organic flock isolates were characterized by more than 94% genetic similarity, indicating that only a single clone was apparent in the flock. The layer parent flock isolates were grouped into two subclusters, each with similarity above 90%. One subcluster contained only tracheal isolates, while the other primarily included cloacal isolates. In conclusion, we show that AFLP analysis enables fingerprinting of G. anatis, which seems to have a clonal. population structure within natural populations. There was further evidence of clonal lineages, which may have adapted to different sites within the same animal.

Bojesen, A.M.; Torpdahl, Mia

2003-01-01

206

High local genetic diversity of canine parvovirus from Ecuador.  

UK PubMed Central (United Kingdom)

Canine parvovirus (CPV) comprises three antigenic variants (2a, 2b, and 2c) that are distributed globally with different frequencies and levels of genetic variability. CPVs from central Ecuador were herein analyzed to characterize the strains and to provide new insights into local viral diversity, evolution, and pathogenicity. Variant prevalence was analyzed by PCR and partial sequencing for 53 CPV-positive samples collected during 2011 and 2012. The full-length VP2 gene was sequenced in 24 selected strains and a maximum-likelihood phylogenetic tree was constructed using both Ecuadorian and worldwide strains. Ecuadorian CPVs have a remarkable genetic diversity that includes the circulation of all three variants and the existence of different evolutionary groups or lineages. CPV-2c was the most prevalent variant (54.7%), confirming the spread of this variant in America. Ecuadorian CPV-2c strains clustered in two lineages, which represent the first evidence of polyphyletic CPV-2c circulating in South America. CPV-2a strains constituted 41.5% of the samples and clustered in a single lineage. The two detected CPV-2b strains (3.8%) were clearly polyphyletic and appeared related to Ecuadorian CPV-2a or foreign CPV-2b strains. Besides the substitution at residue 426 that is used to identify the variants, two amino acid changes occurred in Ecuadorian strains: Val139Iso and Thr440Ser. Ser(440) occurred in a biologically relevant domain of VP2 and is here described for the first time in CPV. The associations of Ecuadorian CPV-2c and CPV-2a with clinical symptoms indicate that dull mentation, hemorrhagic gastroenteritis and hypothermia occurred more frequently in infection with CPV-2c than with CPV-2a.

Aldaz J; García-Díaz J; Calleros L; Sosa K; Iraola G; Marandino A; Hernández M; Panzera Y; Pérez R

2013-09-01

207

Molecular epidemiology and genetic diversity of Campylobacter jejuni in ruminants.  

UK PubMed Central (United Kingdom)

Multi-locus sequence typing was performed on 1003 Campylobacter jejuni isolates collected in a 2-year longitudinal study of 15 dairy farms and four sheep farms in Lancashire, UK. There was considerable farm-level variation in occurrence and prevalence of clonal complexes (CC). Clonal complexes ST61, ST21, ST403 and ST45 were most prevalent in cattle while in sheep CC ST42, ST21, ST48 and ST52 were most prevalent. CC ST45, a complex previously shown to be more common in summer months in human cases, was more prevalent in summer in our ruminant samples. Gene flow analysis demonstrated a high level of genetic heterogeneity at the within-farm level. Sequence-type diversity was greater in cattle compared to sheep, in cattle at pasture vs. housed, and in isolates from farms on the Pennines compared to the Southern Fylde. Sequence-type diversity was greatest in isolates belonging to CC ST21, ST45 and ST206.

Grove-White DH; Leatherbarrow AJ; Cripps PJ; Diggle PJ; French NP

2011-11-01

208

Molecular epidemiology and genetic diversity of Campylobacter jejuni in ruminants.  

Science.gov (United States)

Multi-locus sequence typing was performed on 1003 Campylobacter jejuni isolates collected in a 2-year longitudinal study of 15 dairy farms and four sheep farms in Lancashire, UK. There was considerable farm-level variation in occurrence and prevalence of clonal complexes (CC). Clonal complexes ST61, ST21, ST403 and ST45 were most prevalent in cattle while in sheep CC ST42, ST21, ST48 and ST52 were most prevalent. CC ST45, a complex previously shown to be more common in summer months in human cases, was more prevalent in summer in our ruminant samples. Gene flow analysis demonstrated a high level of genetic heterogeneity at the within-farm level. Sequence-type diversity was greater in cattle compared to sheep, in cattle at pasture vs. housed, and in isolates from farms on the Pennines compared to the Southern Fylde. Sequence-type diversity was greatest in isolates belonging to CC ST21, ST45 and ST206. PMID:21134320

Grove-White, D H; Leatherbarrow, A J H; Cripps, P J; Diggle, P J; French, N P

2010-12-07

209

Genetic diversity of symbiotic cyanobacteria in Cycas revoluta (Cycadaceae).  

Science.gov (United States)

The diversity of cyanobacterial species within the coralloid roots of an individual and populations of Cycas revoluta was investigated based on 16S rRNA gene sequences. Sixty-six coralloid roots were collected from nine natural populations of cycads on Kyushu and the Ryukyu Islands, covering the entire distribution range of the species. Approximately 400 bp of the 5'-end of 16S rRNA genes was amplified, and each was identified by denaturing gradient gel electrophoresis. Most coralloid roots harbored only one cyanobiont, Nostoc, whereas some contained two or three, representing cyanobiont diversity within a single coralloid root isolated from a natural habitat. Genotypes of Nostoc within a natural population were occasionally highly diverged and lacked DNA sequence similarity, implying genetic divergence of Nostoc. On the other hand, Nostoc genotypes showed no phylogeographic structure across the distribution range, while host cycads exhibited distinct north-south differentiation. Cycads may exist in symbiosis with either single or multiple Nostoc strains in natural soil habitats. PMID:22537413

Yamada, Shuntaro; Ohkubo, Satoshi; Miyashita, Hideaki; Setoguchi, Hiroaki

2012-05-23

210

Genetic diversity of symbiotic cyanobacteria in Cycas revoluta (Cycadaceae).  

UK PubMed Central (United Kingdom)

The diversity of cyanobacterial species within the coralloid roots of an individual and populations of Cycas revoluta was investigated based on 16S rRNA gene sequences. Sixty-six coralloid roots were collected from nine natural populations of cycads on Kyushu and the Ryukyu Islands, covering the entire distribution range of the species. Approximately 400 bp of the 5'-end of 16S rRNA genes was amplified, and each was identified by denaturing gradient gel electrophoresis. Most coralloid roots harbored only one cyanobiont, Nostoc, whereas some contained two or three, representing cyanobiont diversity within a single coralloid root isolated from a natural habitat. Genotypes of Nostoc within a natural population were occasionally highly diverged and lacked DNA sequence similarity, implying genetic divergence of Nostoc. On the other hand, Nostoc genotypes showed no phylogeographic structure across the distribution range, while host cycads exhibited distinct north-south differentiation. Cycads may exist in symbiosis with either single or multiple Nostoc strains in natural soil habitats.

Yamada S; Ohkubo S; Miyashita H; Setoguchi H

2012-09-01

211

Genetic diversity of ITS sequences of Bursaphelenchus xylophilus.  

Science.gov (United States)

The sequence variation of internal transcribed spacer (ITS) regions of ribosomal DNA has been routinely used for species identification and species-level phylogeny of the pinewood nematode, Bursaphelenchus xylophilus. In this study, the intraspecies ITS genetic diversity of B. xylophilus was evaluated. Three pinewood nematode isolates from the United States, Japan, and Portugal were used for polymerase chain reaction (PCR) ITS region amplification and sequencing. Multiple peaks were observed in sequencing chromatograms from ITS regions of American and Japanese isolates, suggesting the presence of more than one ribosomal sequence for each isolate. PCR products were further cloned and 10 clones of each isolate were subsequently sequenced. Additionally, the ITS regions of individual nematodes from each isolate were amplified, cloned and sequenced. Among the 3 B. xylophilus isolates analyzed, an intraspecific and intra-isolate molecular variability was found. The intra-isolate ITS molecular diversity in the American isolate was higher than that in the Japanese and Portuguese isolates. However, the level of sequence variation observed within isolates was about the same as that described among ITS repeats within individuals. PMID:23096915

Cardoso, J M S; Fonseca, L; Abrantes, I

2012-12-19

212

Genetic diversity of ITS sequences of Bursaphelenchus xylophilus.  

UK PubMed Central (United Kingdom)

The sequence variation of internal transcribed spacer (ITS) regions of ribosomal DNA has been routinely used for species identification and species-level phylogeny of the pinewood nematode, Bursaphelenchus xylophilus. In this study, the intraspecies ITS genetic diversity of B. xylophilus was evaluated. Three pinewood nematode isolates from the United States, Japan, and Portugal were used for polymerase chain reaction (PCR) ITS region amplification and sequencing. Multiple peaks were observed in sequencing chromatograms from ITS regions of American and Japanese isolates, suggesting the presence of more than one ribosomal sequence for each isolate. PCR products were further cloned and 10 clones of each isolate were subsequently sequenced. Additionally, the ITS regions of individual nematodes from each isolate were amplified, cloned and sequenced. Among the 3 B. xylophilus isolates analyzed, an intraspecific and intra-isolate molecular variability was found. The intra-isolate ITS molecular diversity in the American isolate was higher than that in the Japanese and Portuguese isolates. However, the level of sequence variation observed within isolates was about the same as that described among ITS repeats within individuals.

Cardoso JM; Fonseca L; Abrantes I

2012-01-01

213

Genetic and Functional Diversity of Pseudomonas aeruginosa Lipopolysaccharide.  

UK PubMed Central (United Kingdom)

Lipopolysccharide (LPS) is an integral component of the Pseudomonas aeruginosa cell envelope, occupying the outer leaflet of the outer membrane in this Gram-negative opportunistic pathogen. It is important for bacterium-host interactions and has been shown to be a major virulence factor for this organism. Structurally, P. aeruginosa LPS is composed of three domains, namely, lipid A, core oligosaccharide, and the distal O antigen (O-Ag). Most P. aeruginosa strains produce two distinct forms of O-Ag, one a homopolymer of D-rhamnose that is a common polysaccharide antigen (CPA, formerly termed A band), and the other a heteropolymer of three to five distinct (and often unique dideoxy) sugars in its repeat units, known as O-specific antigen (OSA, formerly termed B band). Compositional differences in the O units among the OSA from different strains form the basis of the International Antigenic Typing Scheme for classification via serotyping of different strains of P. aeruginosa. The focus of this review is to provide state-of-the-art knowledge on the genetic and resultant functional diversity of LPS produced by P. aeruginosa. The underlying factors contributing to this diversity will be thoroughly discussed and presented in the context of its contributions to host-pathogen interactions and the control/prevention of infection.

Lam JS; Taylor VL; Islam ST; Hao Y; Kocíncová D

2011-01-01

214

Concordance between genetic and species diversity in coral reef fishes across the Pacific Ocean biodiversity gradient.  

UK PubMed Central (United Kingdom)

The relationship between genetic diversity and species diversity provides insights into biogeography and historic patterns of evolution and is critical for developing contemporary strategies for biodiversity conservation. Although concordant large-scale clines in genetic and species diversity have been described for terrestrial organisms, whether these parameters co-vary in marine species remains largely unknown. We examined patterns of genetic diversity for 11 coral reef fish species sampled at three locations across the Pacific Ocean species diversity gradient (Australia: ?1600 species; New Caledonia: ?1400 species; French Polynesia: ?800 species). Combined genetic diversity for all 11 species paralleled the decline in species diversity from West to East, with French Polynesia exhibiting lowest total haplotype and nucleotide diversities. Haplotype diversity consistently declined toward French Polynesia in all and nucleotide diversity in the majority of species. The French Polynesian population of most species also exhibited significant genetic differentiation from populations in the West Pacific. A number of factors may have contributed to the general positive correlation between genetic and species diversity, including location and time of species origin, vicariance events, reduced gene flow with increasing isolation, and decreasing habitat area from West to East. However, isolation and habitat area, resulting in reduced population size, are likely to be the most influential.

Messmer V; Jones GP; Munday PL; Planes S

2012-12-01

215

Genetic diversity of Toxoplasma gondii isolates from Ethiopian feral cats.  

UK PubMed Central (United Kingdom)

Recent studies indicate greater genetic variability among isolates of Toxoplasma gondii worldwide than previously thought. However, there is no information on genetic diversity of T. gondii from any host in Ethiopia. In the present study, genotyping was performed on viable T. gondii isolates by bioassays in mice from tissues and feces of 27 cats from Ethiopia. Viable T. gondii was isolated from hearts of 26 cats, feces alone of 1 cat, and feces and tissues of 6 cats; in total there were 33 isolates. Genotyping was performed on DNA from cell-cultured derived T. gondii tachyzoites and by using 10 PCR-restriction fragment length polymorphism markers (SAG1, SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1, and Apico). Four genotypes were recognized, including ToxoDB #1 (Type II clonal, nine isolates), ToxoDB #2 (Type III, five isolates), Toxo DB #3 (Type II variant, ten isolates), and ToxoDB #20 (nine isolates). Of interest is the isolation of different genotypes from tissues and feces of two cats, suggesting re-infection or mixed strain T. gondii infection. These findings are of epidemiological significance with respect to shedding of oocysts by cats. This is the first report of genotyping of T. gondii from any host in Ethiopia.

Dubey JP; Choudhary S; Tilahun G; Tiao N; Gebreyes WA; Zou X; Su C

2013-09-01

216

Genetic diversity of Leishmania infantum field populations from Brazil  

Directory of Open Access Journals (Sweden)

Full Text Available Leishmania infantum (syn. Leishmania chagasi) is the etiological agent of visceral leishmaniasis (VL) in Brazil. The epidemiology of VL is poorly understood. Therefore, a more detailed molecular characterization at an intraspecific level is certainly needed. Herein, three independent molecular methods, multilocus microsatellite typing (MLMT), random amplification of polymorphic DNA (RAPD) and simple sequence repeats-polymerase chain reaction (SSR-PCR), were used to evaluate the genetic diversity of 53 L. infantum isolates from five different endemic areas in Brazil. Population structures were inferred by distance-based and Bayesian-based approaches. Eighteen very similar genotypes were detected by MLMT, most of them differed in only one locus and no correlation was found between MLMT profiles, geographical origin or the estimated population structure. However, complex profiles composed of 182 bands obtained by both RAPD and SSR-PCR assays gave different results. Unweighted pair group method with arithmetic mean trees built from these data revealed a high degree of homogeneity within isolates of L. infantum. Interestingly, despite this genetic homogeneity, most of the isolates clustered according to their geographical origin.

Marcela Segatto; Lucas Secchim Ribeiro; Dorcas Lamounier Costa; Carlos Henrique Nery Costa; Márcia Rosa de Oliveira; Sílvio Fernando Guimarães Carvalho; Andréa Mara Macedo; Helder Magno Silva Valadares; Reynaldo Dietze; Cristiana Ferreira Alves de Brito; Elenice Moreira Lemos

2012-01-01

217

Genetic diversity of Toxoplasma gondii isolates from Ethiopian feral cats.  

Science.gov (United States)

Recent studies indicate greater genetic variability among isolates of Toxoplasma gondii worldwide than previously thought. However, there is no information on genetic diversity of T. gondii from any host in Ethiopia. In the present study, genotyping was performed on viable T. gondii isolates by bioassays in mice from tissues and feces of 27 cats from Ethiopia. Viable T. gondii was isolated from hearts of 26 cats, feces alone of 1 cat, and feces and tissues of 6 cats; in total there were 33 isolates. Genotyping was performed on DNA from cell-cultured derived T. gondii tachyzoites and by using 10 PCR-restriction fragment length polymorphism markers (SAG1, SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1, and Apico). Four genotypes were recognized, including ToxoDB #1 (Type II clonal, nine isolates), ToxoDB #2 (Type III, five isolates), Toxo DB #3 (Type II variant, ten isolates), and ToxoDB #20 (nine isolates). Of interest is the isolation of different genotypes from tissues and feces of two cats, suggesting re-infection or mixed strain T. gondii infection. These findings are of epidemiological significance with respect to shedding of oocysts by cats. This is the first report of genotyping of T. gondii from any host in Ethiopia. PMID:23411374

Dubey, J P; Choudhary, S; Tilahun, G; Tiao, N; Gebreyes, W A; Zou, X; Su, C

2013-01-24

218

Genetic diversity of Leishmania infantum field populations from Brazil  

Scientific Electronic Library Online (English)

Full Text Available Abstract in english Leishmania infantum (syn. Leishmania chagasi) is the etiological agent of visceral leishmaniasis (VL) in Brazil. The epidemiology of VL is poorly understood. Therefore, a more detailed molecular characterization at an intraspecific level is certainly needed. Herein, three independent molecular methods, multilocus microsatellite typing (MLMT), random amplification of polymorphic DNA (RAPD) and simple sequence repeats-polymerase chain reaction (SSR-PCR), were used to evalua (more) te the genetic diversity of 53 L. infantum isolates from five different endemic areas in Brazil. Population structures were inferred by distance-based and Bayesian-based approaches. Eighteen very similar genotypes were detected by MLMT, most of them differed in only one locus and no correlation was found between MLMT profiles, geographical origin or the estimated population structure. However, complex profiles composed of 182 bands obtained by both RAPD and SSR-PCR assays gave different results. Unweighted pair group method with arithmetic mean trees built from these data revealed a high degree of homogeneity within isolates of L. infantum. Interestingly, despite this genetic homogeneity, most of the isolates clustered according to their geographical origin.

Segatto, Marcela; Ribeiro, Lucas Secchim; Costa, Dorcas Lamounier; Costa, Carlos Henrique Nery; Oliveira, Márcia Rosa de; Carvalho, Sílvio Fernando Guimarães; Macedo, Andréa Mara; Valadares, Helder Magno Silva; Dietze, Reynaldo; Brito, Cristiana Ferreira Alves de; Lemos, Elenice Moreira

2012-02-01

219

Assessment of Genetic Diversity across differentially adopted rice ecotypes  

Directory of Open Access Journals (Sweden)

Full Text Available Rice is an important staple food and a rich source of carbohydrates for 90% of South and Southeast Asians. Geneticdiversity of naturally adopted upland lines along with few germplasm collections in Karnataka were studied basedon 13 SSR loci on chromosome 1. A total of 24 individuals belonging to 3 differentially adopted groups [Upland(8), landraces (8) and cultivated varieties (8)] had a moderate to high level of genetic variability at groups level withnumber of alleles ranging from 5 to 23 (average 11.5) and PIC from 0.51 to 0.94 (average 0.79). The heterozygosityvaried from 0.39 to as high as 0.70. Over all genetic diversity of 0.81 was revealed indicating a high level of geneticvariation among these individuals. At the similarity coefficient of 7, all the lines were clearly grouped in 3 clusters.All cultivated types grouped in one cluster (cluster 1) except Rasi and CTH 1 which were included in cluster 2 andcluster 3 respectively. Cluster 1 contained 9 cultivated genotypes, where as cluster 2 contained 11 land races andcluster 3 had 4 upland lines. Out of 4 upland lines one line (AC-35341) intermixed, with C1 and three lines (PS-229,JBT-37/4 and AC-35310) with C3. The study of SSR markers on chromosome 1 facilitated the classification of theselines according to their adaptability. The information about the genetics of these populations will be for specificchromosomes and will be very useful for rice breeding programs, especially for gene mapping and ultimately formarker assisted selection programs.

Sridevi, G1., Raju, B.R2., Mohankumar, M.V2* and Sheshshayee, M, S.

2012-01-01

220

Multi-objective Genetic Algorithm for Association Rule Mining Using a Homogeneous Dedicated Cluster of Workstations  

Directory of Open Access Journals (Sweden)

Full Text Available This study presents a fast and scalable multi-objective association rule mining technique using genetic algorithm from large database. The objective functions such as confidence factor, comprehensibility and interestingness can be thought of as different objectives of our association rule-mining problem and is treated as the basic input to the genetic algorithm. The outcomes of our algorithm are the set of non-dominated solutions. However, in data mining the quantity of data is growing rapidly both in size and dimensions. Furthermore, the multi-objective genetic algorithm (MOGA) tends to be slow in comparison with most classical rule mining methods. Hence, to overcome these difficulties we propose a fast and scalability technique using the inherent parallel processing nature of genetic algorithm and a homogeneous dedicated network of workstations (NOWs). Our algorithm exploit both data and control parallelism by distributing the data being mined and the population of individuals across all available processors. The experimental result shows that the algorithm has been found suitable for large database with an encouraging speed up.

S. Dehuri; A. K. Jagadev; A. Ghosh; R. Mall

2006-01-01

 
 
 
 
221

The effect of inoculum dose on the genetic diversity detected within Helicoverpa armigera nucleopolyhedrovirus populations.  

Science.gov (United States)

Environmental and infection variables may affect the genetic diversity of baculovirus populations. In this study, Helicoverpa armigera nucleopolyhedrovirus (HearNPV) was used as a model system for studying the effects of a key infection variable, inoculum dose, on the genetic diversity within nucleopolyhedrovirus populations. Diversity and equitability indices were calculated from DNA polymerase-specific denaturing gradient gel electrophoresis profiles obtained from individual H. armigera neonate larvae inoculated with either an LD5 or LD95 of HearNPV. Although the genetic diversity detected in larvae treated with an LD95 was not statistically different from the diversity detected in the HearNPV inoculum samples, there was a statistically significant difference in the genetic diversity detected in the LD5-inoculated larvae compared with the genetic diversity detected in the HearNPV samples used for the inoculations. The study suggests that inoculum dose needs to be considered carefully in experiments that evaluate HearNPV genetic diversity or in studies where differences in genetic diversity may have phenotypic consequences. PMID:23929831

Baillie, Vicky Lynne; Bouwer, Gustav

2013-08-08

222

The effect of inoculum dose on the genetic diversity detected within Helicoverpa armigera nucleopolyhedrovirus populations.  

UK PubMed Central (United Kingdom)

Environmental and infection variables may affect the genetic diversity of baculovirus populations. In this study, Helicoverpa armigera nucleopolyhedrovirus (HearNPV) was used as a model system for studying the effects of a key infection variable, inoculum dose, on the genetic diversity within nucleopolyhedrovirus populations. Diversity and equitability indices were calculated from DNA polymerase-specific denaturing gradient gel electrophoresis profiles obtained from individual H. armigera neonate larvae inoculated with either an LD5 or LD95 of HearNPV. Although the genetic diversity detected in larvae treated with an LD95 was not statistically different from the diversity detected in the HearNPV inoculum samples, there was a statistically significant difference in the genetic diversity detected in the LD5-inoculated larvae compared with the genetic diversity detected in the HearNPV samples used for the inoculations. The study suggests that inoculum dose needs to be considered carefully in experiments that evaluate HearNPV genetic diversity or in studies where differences in genetic diversity may have phenotypic consequences.

Baillie VL; Bouwer G

2013-11-01

223

AFLP analysis on genetic diversity and genetic structure of Eupatorium adenophorum populations in China  

UK PubMed Central (United Kingdom)

Eupatorium adenophorum Crofton weed is one of the most widespread invasive species in China. Its genetic diversity and population structure in China were analyzed by amplified fragment length polymorphism AFLP. Three primer pairs were selected for the analysis and 490 bands were produced from 62 E. adenophorum populations of 5 major geographic areas in China, of which 328 bands showed polymorphic P was 59.4%. Diversity levels of populations were relatively high, mean expected heterozygosity H was 0.154, mean Shannon index I was 0.241. At the regional level, the AMOVA indicated that about 70.25% variations in the data set were from genotypic variations within populations, 8.04% variations due to regional differences, and the remaining 21.71% due to differences among populations within the provincial regions. Cluster analysis based on the UPGMA method grouped the majority of the 62 E. adenophorum populations into four main clusters, which correspond with their geographic regions. It is concluded that E. adenophorum spread mainly by wind or water and its genetic diversity level in newly invaded area is lower than that in former invaded areas.

Huang Wenkun; Guo Jianying; Wan Fanghao; Gao Bida; Xie Bingyan

224

Inbreeding, outbreeding and environmental effects on genetic diversity in 46 walleye (Sander vitreus) populations.  

Science.gov (United States)

Genetic diversity is recognized as an important population attribute for both conservation and evolutionary purposes; however, the functional relationships between the environment, genetic diversity, and fitness-related traits are poorly understood. We examined relationships between selected lake parameters and population genetic diversity measures in 46 walleye (Sander vitreus) populations across the province of Ontario, Canada, and then tested for relationships between six life history traits (in three categories: growth, reproductive investment, and mortality) that are closely related to fitness, and genetic diversity measures (heterozygosity, d2, and Wright's inbreeding coefficient). Positive relationships were observed between lake surface area, growing degree days, number of species, and hatchery supplementation versus genetic diversity. Walleye early growth rate was the only life history trait significantly correlated with population heterozygosity in both males and females. The relationship between FIS and male early growth rate was negative and significant (P outbreeding depression are not yet seriously impacting Ontario walleye populations. PMID:16448402

Cena, Christopher J; Morgan, George E; Malette, Michael D; Heath, Daniel D

2006-02-01

225

Allozyme diversity and genetic structure of the leafy cactus (Pereskia guamacho [Cactaceae]).  

UK PubMed Central (United Kingdom)

We examined levels of genetic variation and genetic structure in the leafy cactus (Pereskia guamacho) in arid and semiarid zones in Venezuela. We surveyed genetic diversity within 17 populations using 19 allozyme loci. Genetic diversity was relatively high at both the species (P(s) = 89%, A(s) = 3.26, AP(s) = 3.53, H(es) = 0.24) and population (P(p) = 63%, A(p) = 1.90, AP(p) = 2.42, H(ep) = 0.20) levels. A significant deficit of heterozygote individuals was detected within populations in the Paraguana Peninsula region (F(IS) = 0.301). Relatively low levels of population differentiation were detected at macrogeographic (G(ST) = 0.112) and regional levels (G(ST) = 0.044 for peninsula region and G(ST) = 0.074 for mainland region), suggesting substantial genetic exchange among populations; however, gene flow in this species seems to be regulated by the distance among populations. Overall, estimates of genetic diversity found in P. guamacho are concordant with the pattern observed for other cacti surveyed, namely high levels of polymorphism and genetic diversity with one common allele and several rare alleles per locus. Differences in gene dispersal systems between this species and other cacti studied were not reflected in the patterns of genetic diversity observed. The concentration of the highest estimates of genetic variation in northwestern Venezuela suggests a potential reservoir of plant genetic diversity within xerophilous ecosystems in northern South America.

Nassar JM; Hamrick JL; Fleming TH

2002-05-01

226

Topographic diversity and islands of natural vegetation: aids in re-establishing bird and mammal communities on reclaimed mines  

Energy Technology Data Exchange (ETDEWEB)

This study examines the effects of diverse topography and 'islands' of undisturbed vegetation on bird and mammal populations of reclaimed mine spoils. In New Mexico, species on adjacent man-made cliffs and islands of undisturbed vegetation contributed 22% of the bird species diversity and 35% of bird species richness measured on reclaimed areas. In Colorado, an unreclaimed area with diverse topography was compared to a reclaimed area with relatively uniform topography. Fifteen bird species were observed on reclaimed spoils compared to 46 on unreclaimed spoils. Bird abundance, species richness and species diversity on reclaimed spoils were 25, 28, and 45% of that on unreclaimed spoils, respectively. Rodent species richness (one species) and diversity (H' equals O) were lower on reclaimed spoils than in any other habitat. Abundance and species richness of larger mammals were also highest on unreclaimed spoils. The diverse topography of unreclaimed spoils has resulted in diverse vegetation which affected bird populations, whereas mammals were affected more directly by the terrain. The topographic features which caused the observed effects are artifacts of strip mining and thus cost less than the smooth terrain which is often created on reclaimed mined spoils. 21 references.

Steele, B.B.; Grant, C.V.

1982-12-01

227

An assessment of the Central-China pig genetic diversity using Weitzman approach  

Directory of Open Access Journals (Sweden)

Full Text Available The genetic diversity of livestock breeds plays an important role in livestock production, but the significant loss of breeds is threatening genetic diversity of farm animal genetic resources (AnGR). The Weitzman approach which was accepted as a framework for assessment of genetic diversity on AnGR was exploited. In this study, several measurement indexes of genetic diversity, involving total genetic diversity, contributions of each breed to the total diversity, marginal diversities, conservation potential, were calculated based on microsatellite marker data of 20 Central-China type pig populations. Total genetic diversity of twenty Central-China pig breeds was 11,707 and expected diversity was 66.96% of the total genetic diversity. Jinhua pig had the greatest contribution to overall genetic diversity (8.90%), followed by Wannan Spotted pig (7.46%), Shengxian Spotted pig (7.40%), and Leping pig (7.04%). Jinhua pig also had the highest conservation potential (783.53), followed by Shengxian Spotted pig (454.53), Hang pig (366.68), and Large Black-White pig (343.17). Shown as the derived maximum-likelihood tree, the 20 Central-China type pig breeds were clustered into three groups. The pig breeds from Hunan or Hubei Province, such as Daweizi pig, Shaziling pig and Ningxiang pig, formed a group; Nancheng pig clustered with Shengxian Spotted pig and Hang pig; The third cluster was Jinhua pig and Wannan Spotted pig. Furthermore, the advantages and drawbacks of Weitzman approach were discussed. We hope to provide objective and rational criteria and strategy for decision-making in conservation of Central-China type pig breeds.

Zhenzhen Liu; Xiuying Guo; Baoyu Li; Ming Wang; Xi Wang; Keliang Wu

2010-01-01

228

Genetic Diversity Among Botulinum Neurotoxin Producing Clostridial Strains  

Energy Technology Data Exchange (ETDEWEB)

Clostridium botulinum is a taxonomic designation for many diverse anaerobic spore forming rod-shaped bacteria which have the common property of producing botulinum neurotoxins (BoNTs). The BoNTs are exoneurotoxins that can cause severe paralysis and even death in humans and various other animal species. A collection of 174 C. botulinum strains were examined by amplified fragment length polymorphism (AFLP) analysis and by sequencing of the 16S rRNA gene and BoNT genes to examine genetic diversity within this species. This collection contained representatives of each of the seven different serotypes of botulinum neurotoxins (BoNT A-G). Analysis of the16S rRNA sequences confirmed earlier reports of at least four distinct genomic backgrounds (Groups I-IV) each of which has independently acquired one or more BoNT serotypes through horizontal gene transfer. AFLP analysis provided higher resolution, and can be used to further subdivide the four groups into sub-groups. Sequencing of the BoNT genes from serotypes A, B and E in multiple strains confirmed significant sequence variation within each serotype. Four distinct lineages within each of the BoNT A and B serotypes, and five distinct lineages of serotype E strains were identified. The nucleotide sequences of the seven serotypes of BoNT were compared and show varying degrees of interrelatedness and recombination as has been previously noted for the NTNH gene which is linked to BoNT. These analyses contribute to the understanding of the evolution and phylogeny within this species and assist in the development of improved diagnostics and therapeutics for treatment of botulism.

Hill, K K; Smith, T J; Helma, C H; Ticknor, L O; Foley, B T; Svennson, R T; Brown, J L; Johnson, E A; Smith, L A; Okinaka, R T; Jackson, P J; Marks, J D

2006-07-06

229

A genetic programming based business process mining approach  

Digital Repository Infrastructure Vision for European Research (DRIVER)

As business processes become ever more complex there is a need for companies to understand the processes they already have in place. To undertake this manually would be time consuming. The practice of process mining attempts to automatically construct the correct representation of a process based on...

Turner, Christopher James

230

Pulsed Field Gel Electrophoresis and Genetic Diversity in Mycobacterium tuberculosis  

Directory of Open Access Journals (Sweden)

Full Text Available AbstractBackground and objective: Tuberculosis is a considerable public health problem due to its high risk of person-to-person transmission, morbidity, and mortality especially in developing countries. According to the World Health Organization there is the emergence of multi-drug resistant M. tuberculosis and the association of TB with HIV has led to TB being declared. Molecular genotyping methods are important in detecting the dominance of transmission or reinfection in a population. During one year study genotyping of 100 of M. tuberculosis (M.t.) isolates from patients referred to Pasteur Institute of Iran were accomplished with PFGE method. Material and methods: After identification of M.t. isolates and performing of antibiotic susceptibility test using standard methods, Melted Incert agarose and lysozyme were mixed with bacterial suspension to prepare PFGE plaques. After lyses and washing process the plaques digested with XbaI restriction enzyme. Finally the digested DNA fragments on 1% agarose with PFGE method were stained with ethidium bromide and analyzed with GelcomparII software.Results: Dendrogram of genetic diversity among 100 M.t. isolates were obtained in comparison of molecular weight marker and revealed two common types. Pulsotype A with 71 isolates and just one MDR and pulsotype B included 29 isolates and 3 MDR cases. No correlation between antibiotypes and pulsotypes were observed.Conclusion: It is very important to know about the existence of any clonal expansion of special M.t. genotypes with resistant strains. Our research shows 3 MDR isolates into the low incidence pulsotype B which could be an alarm for more accurate MDR-TB surveillance program. Probably such observed limited polymorphism may be due to conservation of restriction sites of XbaI enzyme. In order to investigate the genetic relatedness of isolates using other restriction enzymes and different molecular typing methods simultaneously were recommended.

Mohammad Poyeede; Esmaeil Jabarzade; Morteza Masoumi; Reza Ranjbar; Zeynab Ahmadi; Mahnaz Saifi

2013-01-01

231

Genetic diversity based on morphological data in Panicum maximum hybrids  

Directory of Open Access Journals (Sweden)

Full Text Available The objective of this experiment was to evaluate the genetic divergence between hybrids obtained from 10 sexual genitors of the Panicum maximum breeding program at Embrapa Beef Cattle. For this, the following morphological descriptors were used: plant height, growth habit, leaf aspect, leaf waxiness, hair density on the sheath (DePB) and blade (DePL), degree of hardiness of the hairs on the leaf sheath (DuPB) and blade (DuPL) and length of hairs on the sheath and blade. The characteristics growth habit and waxiness were not included in the analysis for being invariant. The phenotypic correlations were low and, therefore, not used to eliminate variables. By the principal component analysis, an 84.3% accumulation of the variation was observed until the fourth component. The last four principal components presented an estimate lower than 0.7 and allowed the identification of the variables DePB, DuPB and DuPL as the least important for diversity studies. The morphological characters used were not efficient to distinguish the progenies, but allowed the formation of morphological groups that converged with the graphic analysis of the principal components. An apparent error rate of 17.04% was observed in the classification of the individuals in the groups and 55.5% in the classification of the individuals in the progenies. The individuals in the P. maximum half-sib progenies are genetically divergent, but may not be grouped with only the descriptors used in this experiment. The pubescence characteristics were the least important in the discrimination of the genotypes.

Janaina Azevedo Martuscello; Thiago Gomes dos Santos Braz; Liana Jank; Daniel de Noronha Figueiredo Vieira da Cunha; Dilermando Miranda da Fonseca

2012-01-01

232

Genetic diversity among isolates of stemphylium solani from cotton  

Directory of Open Access Journals (Sweden)

Full Text Available The fungus Stemphylium solani causes leaf blight of tomato (Lycopersicon esculentum) in Brazil. In recent years, severe epidemics of a new leaf blight of cotton (Gossipium hyrsutum) caused by S. solani occurred in three major cotton-growing Brazilian states (PR, MT and GO). Molecular analysis was performed to assess the genetic diversity among the S. solani isolates from cotton, and to verify their relationship with representative S. solani isolates from tomato. Random amplified polymorphic DNA (RAPD) markers and internal transcribed spacers of ribosomal DNA (rDNA) were used to compare 33 monosporic isolates of S. solani (28 from cotton and five from tomato). An isolate of Alternaria macrospora from cotton was also used for comparison. RAPD analysis showed the presence of polymorphism between the genera and the species. The A. macrospora and the S. solani isolates from cotton and tomato were distinct from each other, and fell into separate groups. Variation by geographic region was observed for the tomato isolates but not for the cotton isolates. Amplifications of the ITS region using the primer pair ITS4/ITS5 resulted in a single PCR product of approximately 600 bp for all the isolates. Similarly, when amplified fragments were digested with eight restriction enzymes, identical banding patterns were observed for all the isolates. Hence, rDNA analysis revealed no inter-generic or intra-specific variation. The genetic difference observed between the cotton and the tomato isolates provides evidence that S. solani attacking cotton in Brazil belongs to a distinct genotype.

MEHTA Y.R.

2001-01-01

233

Genetic diversity based on morphological data in Panicum maximum hybrids  

Scientific Electronic Library Online (English)

Full Text Available Abstract in english The objective of this experiment was to evaluate the genetic divergence between hybrids obtained from 10 sexual genitors of the Panicum maximum breeding program at Embrapa Beef Cattle. For this, the following morphological descriptors were used: plant height, growth habit, leaf aspect, leaf waxiness, hair density on the sheath (DePB) and blade (DePL), degree of hardiness of the hairs on the leaf sheath (DuPB) and blade (DuPL) and length of hairs on the sheath and blade. T (more) he characteristics growth habit and waxiness were not included in the analysis for being invariant. The phenotypic correlations were low and, therefore, not used to eliminate variables. By the principal component analysis, an 84.3% accumulation of the variation was observed until the fourth component. The last four principal components presented an estimate lower than 0.7 and allowed the identification of the variables DePB, DuPB and DuPL as the least important for diversity studies. The morphological characters used were not efficient to distinguish the progenies, but allowed the formation of morphological groups that converged with the graphic analysis of the principal components. An apparent error rate of 17.04% was observed in the classification of the individuals in the groups and 55.5% in the classification of the individuals in the progenies. The individuals in the P. maximum half-sib progenies are genetically divergent, but may not be grouped with only the descriptors used in this experiment. The pubescence characteristics were the least important in the discrimination of the genotypes.

Martuscello, Janaina Azevedo; Braz, Thiago Gomes dos Santos; Jank, Liana; Cunha, Daniel de Noronha Figueiredo Vieira da; Fonseca, Dilermando Miranda da

2012-09-01

234

Gut microbiology - broad genetic diversity, yet specific metabolic niches.  

Science.gov (United States)

Analysis of 16S ribosomal RNA (rRNA)-encoding gene sequences from gut microbial ecosystems reveals bewildering genetic diversity. Some metabolic functions, such as glucose utilisation, are fairly widespread throughout the genetic spectrum. Others, however, are not. Despite so many phylotypes being present, single species or perhaps only two or three species often carry out key functions. Among ruminal bacteria, only three species can break down highly structured cellulose, despite the prevalence and importance of cellulose in ruminant diets, and one of those species, Fibrobacter succinogenes, is distantly related to the most abundant ruminal species. Fatty acid biohydrogenation in the rumen, particularly the final step of biohydrogenation of C18 fatty acids, stearate formation, is achieved only by a small sub-group of bacteria related to Butyrivibrio fibrisolvens. Individuals who lack Oxalobacter formigenes fail to metabolise oxalate and suffer kidney stones composed of calcium oxalate. Perhaps the most celebrated example of the difference a single species can make is the 'mimosine story' in ruminants. Mimosine is a toxic amino acid found in the leguminous plant, Leucaena leucocephala. Mimosine can cause thyroid problems by being converted to the goitrogen, 3-hydroxy-4(1H)-pyridone, in the rumen. Observations that mimosine-containing plants were toxic to ruminants in some countries but not others led to the discovery of Synergistes jonesii, which metabolises 3-hydroxy-4(1H)-pyridone and protects animals from toxicity. Thus, despite the complexities indicated by molecular microbial ecology and genomics, it should never be forgotten that gut communities contain important metabolic niches inhabited by species with highly specific metabolic capability. PMID:22443591

John Wallace, R

2008-05-01

235

Genetic diversity of Phytophthora infestans in the Northern Andean region  

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Full Text Available Abstract Background Phytophthora infestans (Mont.) de Bary, the causal agent of potato late blight, is responsible for tremendous crop losses worldwide. Countries in the northern part of the Andes dedicate a large proportion of the highlands to the production of potato, and more recently, solanaceous fruits such as cape gooseberry (Physalis peruviana) and tree tomato (Solanum betaceum), all of which are hosts of this oomycete. In the Andean region, P. infestans populations have been well characterized in Ecuador and Peru, but are poorly understood in Colombia and Venezuela. To understand the P. infestans population structure in the Northern part of the Andes, four nuclear regions (ITS, Ras, ?-tubulin and Avr3a) and one mitochondrial (Cox1) region were analyzed in isolates of P. infestans sampled from different hosts in Colombia and Venezuela. Results Low genetic diversity was found within this sample of P. infestans isolates from crops within several regions of Colombia and Venezuela, revealing the presence of clonal populations of the pathogen in this region. We detected low frequency heterozygotes, and their distribution patterns might be a consequence of a high migration rate among populations with poor effective gene flow. Consistent genetic differentiation exists among isolates from different regions. Conclusions The results here suggest that in the Northern Andean region P. infestans is a clonal population with some within-clone variation. P. infestans populations in Venezuela reflect historic isolation that is being reinforced by a recent self-sufficiency of potato seeds. In summary, the P. infestans population is mainly shaped by migration and probably by the appearance of variants of key effectors such as Avr3a.

Cárdenas Martha; Grajales Alejandro; Sierra Roberto; Rojas Alejandro; González-Almario Adriana; Vargas Angela; Marín Mauricio; Fermín Gustavo; Lagos Luz E; Grünwald Niklaus J; Bernal Adriana; Salazar Camilo; Restrepo Silvia

2011-01-01

236

Genetic diversity of Phytophthora infestans in the Northern Andean region.  

UK PubMed Central (United Kingdom)

BACKGROUND: Phytophthora infestans (Mont.) de Bary, the causal agent of potato late blight, is responsible for tremendous crop losses worldwide. Countries in the northern part of the Andes dedicate a large proportion of the highlands to the production of potato, and more recently, solanaceous fruits such as cape gooseberry (Physalis peruviana) and tree tomato (Solanum betaceum), all of which are hosts of this oomycete. In the Andean region, P. infestans populations have been well characterized in Ecuador and Peru, but are poorly understood in Colombia and Venezuela. To understand the P. infestans population structure in the Northern part of the Andes, four nuclear regions (ITS, Ras, ?-tubulin and Avr3a) and one mitochondrial (Cox1) region were analyzed in isolates of P. infestans sampled from different hosts in Colombia and Venezuela. RESULTS: Low genetic diversity was found within this sample of P. infestans isolates from crops within several regions of Colombia and Venezuela, revealing the presence of clonal populations of the pathogen in this region. We detected low frequency heterozygotes, and their distribution patterns might be a consequence of a high migration rate among populations with poor effective gene flow. Consistent genetic differentiation exists among isolates from different regions. CONCLUSIONS: The results here suggest that in the Northern Andean region P. infestans is a clonal population with some within-clone variation. P. infestans populations in Venezuela reflect historic isolation that is being reinforced by a recent self-sufficiency of potato seeds. In summary, the P. infestans population is mainly shaped by migration and probably by the appearance of variants of key effectors such as Avr3a.

Cárdenas M; Grajales A; Sierra R; Rojas A; González-Almario A; Vargas A; Marín M; Fermín G; Lagos LE; Grünwald NJ; Bernal A; Salazar C; Restrepo S

2011-01-01

237

Assessing the contribution of breeds to genetic diversity in conservation schemes  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract The quantitative assessment of genetic diversity within and between populations is important for decision making in genetic conservation plans. In this paper we define the genetic diversity of a set of populations, S, as the maximum genetic variance that can be obtained in a random mating population that is bred from the set of populations S. First we calculated the relative contribution of populations to a core set of populations in which the overlap of genetic diversity was minimised. This implies that the mean kinship in the core set should be minimal. The above definition of diversity differs from Weitzman diversity in that it attempts to conserve the founder population (and thus minimises the loss of alleles), whereas Weitzman diversity favours the conservation of many inbred lines. The former is preferred in species where inbred lines suffer from inbreeding depression. The application of the method is illustrated by an example involving 45 Dutch poultry breeds. The calculations used were easy to implement and not computer intensive. The method gave a ranking of breeds according to their contributions to genetic diversity. Losses in genetic diversity ranged from 2.1% to 4.5% for different subsets relative to the entire set of breeds, while the loss of founder genome equivalents ranged from 22.9% to 39.3%.

Eding Herwin; Crooijmans Richard PMA; Groenen Martien AM; Meuwissen Theo HE

2002-01-01

238

Reconsideration for conservation units of wild Primula sieboldii in Japan based on adaptive diversity and molecular genetic diversity.  

UK PubMed Central (United Kingdom)

Primula sieboldii E. Morren is a perennial clonal herb that is widely distributed in Japan, but in danger of extinction in the wild. In a previous study, we revealed the genetic diversity of the species using chloroplast and nuclear DNA and used this information to define conservation units. However, we lacked information on adaptive genetic diversity, which is important for long-term survival and, thus, for the definition of conservation units. In order to identify adaptive traits that showed adaptive differentiation among populations, we studied the genetic variation in six quantitative traits within and among populations for 3 years in a common garden using 110 genets from five natural populations from three regions of Japan. The number of days to bud initiation was adaptive quantitative trait for which the degree of genetic differentiation among populations (QST) was considerably larger than that in eight microsatellite markers (FST). The relationship between this trait and environmental factors revealed that the number of days to bud initiation was negatively correlated, with the mean temperature during the growing period at each habitat. This suggests that adaptive differentiation in the delay before bud initiation was caused by selective pressure resulting from temperature differences among habitats. Our results suggest that based on adaptive diversity and neutral genetic diversity, the Saitama population represents a new conservation unit.

Yoshida Y; Honjo M; Kitamoto N; Ohsawa R

2009-08-01

239

Reconsideration for conservation units of wild Primula sieboldii in Japan based on adaptive diversity and molecular genetic diversity.  

Science.gov (United States)

Primula sieboldii E. Morren is a perennial clonal herb that is widely distributed in Japan, but in danger of extinction in the wild. In a previous study, we revealed the genetic diversity of the species using chloroplast and nuclear DNA and used this information to define conservation units. However, we lacked information on adaptive genetic diversity, which is important for long-term survival and, thus, for the definition of conservation units. In order to identify adaptive traits that showed adaptive differentiation among populations, we studied the genetic variation in six quantitative traits within and among populations for 3 years in a common garden using 110 genets from five natural populations from three regions of Japan. The number of days to bud initiation was adaptive quantitative trait for which the degree of genetic differentiation among populations (QST) was considerably larger than that in eight microsatellite markers (FST). The relationship between this trait and environmental factors revealed that the number of days to bud initiation was negatively correlated, with the mean temperature during the growing period at each habitat. This suggests that adaptive differentiation in the delay before bud initiation was caused by selective pressure resulting from temperature differences among habitats. Our results suggest that based on adaptive diversity and neutral genetic diversity, the Saitama population represents a new conservation unit. PMID:19640318

Yoshida, Yasuko; Honjo, Masanori; Kitamoto, Naoko; Ohsawa, Ryo

2009-08-01

240

Genetic structure, diversity, and allelic richness in composite collection and reference set in chickpea (Cicer arietinum L.)  

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Full Text Available Abstract Background Plant genetic resources (PGR) are the basic raw materials for future genetic progress and an insurance against unforeseen threats to agricultural production. An extensive characterization of PGR provides an opportunity to dissect structure, mine allelic variations, and identify diverse accessions for crop improvement. The Generation Challenge Program http://www.generationcp.org conceptualized the development of "composite collections" and extraction of "reference sets" from these for more efficient tapping of global crop-related genetic resources. In this study, we report the genetic structure, diversity and allelic richness in a composite collection of chickpea using SSR markers, and formation of a reference set of 300 accessions. Results The 48 SSR markers detected 1683 alleles in 2915 accessions, of which, 935 were considered rare, 720 common and 28 most frequent. The alleles per locus ranged from 14 to 67, averaged 35, and the polymorphic information content was from 0.467 to 0.974, averaged 0.854. Marker polymorphism varied between groups of accessions in the composite collection and reference set. A number of group-specific alleles were detected: 104 in Kabuli, 297 in desi, and 69 in wild Cicer; 114 each in Mediterranean and West Asia (WA), 117 in South and South East Asia (SSEA), and 10 in African region accessions. Desi and kabuli shared 436 alleles, while wild Cicer shared 17 and 16 alleles with desi and kabuli, respectively. The accessions from SSEA and WA shared 74 alleles, while those from Mediterranean 38 and 33 alleles with WA and SSEA, respectively. Desi chickpea contained a higher proportion of rare alleles (53%) than kabuli (46%), while wild Cicer accessions were devoid of rare alleles. A genotype-based reference set captured 1315 (78%) of the 1683 composite collection alleles of which 463 were rare, 826 common, and 26 the most frequent alleles. The neighbour-joining tree diagram of this reference set represents diversity from all directions of the tree diagram of the composite collection. Conclusion The genotype-based reference set, reported here, is an ideal set of germplasm for allele mining, association genetics, mapping and cloning gene(s), and in applied breeding for the development of broad-based elite breeding lines/cultivars with superior yield and enhanced adaptation to diverse environments.

Upadhyaya Hari D; Dwivedi Sangam L; Baum Michael; Varshney Rajeev K; Udupa Sripada M; Gowda Cholenahalli LL; Hoisington David; Singh Sube

2008-01-01

 
 
 
 
241

Genetic diversity and genetic structure in the population mithun Bos frontalis) analyzed by allozyme  

UK PubMed Central (United Kingdom)

In the present study, analysis of 44 gene loci in the population Mithun (Bosfrontalis) of 30 indiyiduals were carried out by means of horisontal starch gel electrophoresis. Genotype and gene frequency were generally simillar, the polymorphism was found only in Est. Amy--I and Tf. The avarage heterozygosity (H) is 0.0262, the proportion of polymorphic loci (P) is 0.0682 and the mean number of alleles (A) is 1.0909. The results revealed that the Mithun was depauperate in genetic diversity from the point of view of enzyme gene. Thus the Mithun may have encountered a severe bottleneck in population size, possibly associated with the initial founding event in history. As far as the current status under natural conditions of the Mithun is concerned, we discussed the breeding and conservation of the Mithun preliminarily in the view of genetic management.

Nie Long; Shi Liming; He Xiangdong; Zhao Yulong; Mu Wengang; Zhang Jianliang

1995-01-01

242

Bacteria diversity and arsenic mobilization in rock biofilm from an ancient gold and arsenic mine.  

UK PubMed Central (United Kingdom)

In this paper we characterize the biofilm community from an ancient Z?oty Stok gold and arsenic mine. Bacterial diversity was examined using a culture-independent technique based on 16S rRNA gene amplification, cloning and sequencing. We show that unexpectedly the microbial diversity of this community was extremely high (more than 190 OTUs detected), with the most numerous members from Rhizobiales (?-Proteobacteria). Although the level of rock biofilm diversity was similar to the microbial mat community we have previously characterized in the same adit, its taxonomic composition was completely different. Detailed analysis of functional arrA and aioA genes, chemical properties of siderophores found in pore water as well as the biofilm chemical composition suggest that the biofilm community contributes to arsenic pollution of surrounding water in a biogeochemical cycle similar to the one observed in bacterial mats. To interpret our results concerning the biological arsenic cycle, we applied the theory of ecological pyramids of Charles Elton.

Tomczyk-?ak K; Kaczanowski S; Drewniak L; Dmoch L; Sklodowska A; Zielenkiewicz U

2013-09-01

243

Algal diversity in flowing waters at an acidic mine drainage "barrens" in central Pennsylvania, USA.  

UK PubMed Central (United Kingdom)

Microscopic investigations were undertaken to decipher the diversity in the lotic algal communities from acidic waters (pH 2.4-3.2) flowing overland in sheets and channels at an acid mine drainage (AMD) barrens near Kylertown, PA, USA. Microscopic observations, supplemented with taxonomic keys, aided in identification of the dominant algae, and measurement of carbon from adjacent soils was undertaken. The unicellular protist Euglena sp. was most abundant in slower flowing waters (i.e., pool near point of emergence and surficial flow sheets), while Ulothrix sp. was most abundant in faster flowing water from the central stream channel. A diverse range of unicellular microalgae such as Chlorella, Cylindrocystis, Botryococcus, and Navicula and several filamentous forms identified as Microspora, Cladophora, and Binuclearia were also recorded. The observed high algal diversity may be related to the long duration of AMD flow at this site which has led to the development of adapted algal communities. The comparatively higher carbon content in soil materials adjacent to slower flowing water sampling locations provides evidence for the important role of algae as primary producers in this extreme environment.

Prasanna R; Ratha SK; Rojas C; Bruns MA

2011-11-01

244

Dilated cardiomyopathy: the complexity of a diverse genetic architecture.  

UK PubMed Central (United Kingdom)

Remarkable progress has been made in understanding the genetic basis of dilated cardiomyopathy (DCM). Rare variants in >30 genes, some also involved in other cardiomyopathies, muscular dystrophy, or syndromic disease, perturb a diverse set of important myocardial proteins to produce a final DCM phenotype. Large, publicly available datasets have provided the opportunity to evaluate previously identified DCM-causing mutations, and to examine the population frequency of sequence variants similar to those that have been observed to cause DCM. The frequency of these variants, whether associated with dilated or hypertrophic cardiomyopathy, is greater than estimates of disease prevalence. This mismatch might be explained by one or more of the following possibilities: that the penetrance of DCM-causing mutations is lower than previously thought, that some variants are noncausal, that DCM prevalence is higher than previously estimated, or that other more-complex genomics underlie DCM. Reassessment of our assumptions about the complexity of the genomic and phenomic architecture of DCM is warranted. Much about the genomic basis of DCM remains to be investigated, which will require comprehensive genomic studies in much larger cohorts of rigorously phenotyped probands and family members than previously examined.

Hershberger RE; Hedges DJ; Morales A

2013-09-01

245

Virulence and competitive ability in genetically diverse malaria infections.  

Science.gov (United States)

Explaining parasite virulence is a great challenge for evolutionary biology. Intuitively, parasites that depend on their hosts for their survival should be benign to their hosts, yet many parasites cause harm. One explanation for this is that within-host competition favors virulence, with more virulent strains having a competitive advantage in genetically diverse infections. This idea, which is well supported in theory, remains untested empirically. Here we provide evidence that within-host competition does indeed select for high parasite virulence. We examine the rodent malaria Plasmodium chabaudi in laboratory mice, a parasite-host system in which virulence can be easily monitored and competing strains quantified by using strain-specific real-time PCR. As predicted, we found a strong relationship between parasite virulence and competitive ability, so that more virulent strains have a competitive advantage in mixed-strain infections. In transmission experiments, we found that the strain composition of the parasite populations in mosquitoes was directly correlated with the composition of the blood-stage parasite population. Thus, the outcome of within-host competition determined relative transmission success. Our results imply that within-host competition is a major factor driving the evolution of virulence and can explain why many parasites harm their hosts. PMID:15894623

de Roode, Jacobus C; Pansini, Riccardo; Cheesman, Sandra J; Helinski, Michelle E H; Huijben, Silvie; Wargo, Andrew R; Bell, Andrew S; Chan, Brian H K; Walliker, David; Read, Andrew F

2005-05-13

246

Genetic diversity of marine animals in China: a summary and prospectiveness  

Directory of Open Access Journals (Sweden)

Full Text Available Genetic diversity can reflect the origin and evolution of species. It can also inform the practices of genetic conservation, breeding and genetic improvement, even stabilization of marine ecosystem. In the past two decades, accumulating studies have focused on the genetic diversity of major marine fish and shellfish in China. Here we summarize the achievements of this area and its application to taxonomy, germplasm identification, phylogenetic evolutionary biology, analysis of population genetic structure, genetic breeding and so on. We hope to provide new insights into research on genetic diversity of marine animals, and promote the healthy development of the aquaculture industry in order to achieve the management and sustainable use of marine animals.

Zhaoxia Cui; Huan Zhang; Linsheng Song; Feng You

2011-01-01

247

Y-chromosome diversity in native mexicans reveals continental transition of genetic structure in the Americas  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The genetic characterization of Native Mexicans is important to understand multiethnic based features influencing the medical genetics of present Mexican populations, as well as to the reconstruct the peopling of the Americas. We describe the Y-chromosome genetic diversity of 197 Native Mexicans fro...

Sandoval Mendoza, Karla; Moreno Estrada, Andrés; Mendizábal, Isabel; Underhill, Peter; López Valenzuela, María

248

Bacterial diversity and composition of an alkaline uranium mine tailings-water interface.  

UK PubMed Central (United Kingdom)

The microbial diversity and biogeochemical potential associated with a northern Saskatchewan uranium mine watertailings interface was examined using culture-dependent and -independent techniques. Morphologically-distinct colonies from uranium mine water-tailings and a reference lake (MC) obtained using selective and non-selective media were selected for 16S rRNA gene sequencing and identification, revealing that culturable organisms from the uranium tailings interface were dominated by Firmicutes and Betaproteobacteria; whereas, MC organisms mainly consisted of Bacteroidetes and Gammaproteobacteria. Ion Torrent (IT) 16S rRNA metagenomic analysis carried out on extracted DNA from tailings and MC interfaces demonstrated the dominance of Firmicutes in both of the systems. Overall, the tailings-water interface environment harbored a distinct bacterial community relative to the MC, reflective of the ambient conditions (i.e., total dissolved solids, pH, salinity, conductivity, heavy metals) dominating the uranium tailings system. Significant correlations among the physicochemical data and the major bacterial groups present in the tailings and MC were also observed. Presence of sulfate reducing bacteria demonstrated by culture-dependent analyses and the dominance of Desulfosporosinus spp. indicated by Ion Torrent analyses within the tailings-water interface suggests the existence of anaerobic microenvironments along with the potential for reductive metabolic processes.

Khan NH; Bondici VF; Medihala PG; Lawrence JR; Wolfaardt GM; Warner J; Korber DR

2013-09-01

249

Genetic diversity is positively associated with fine-scale momentary abundance of an invasive ant.  

Science.gov (United States)

Many introduced species become invasive despite genetic bottlenecks that should, in theory, decrease the chances of invasion success. By contrast, population genetic bottlenecks have been hypothesized to increase the invasion success of unicolonial ants by increasing the genetic similarity between descendent populations, thus promoting co-operation. We investigated these alternate hypotheses in the unicolonial yellow crazy ant, Anoplolepis gracilipes, which has invaded Arnhem Land in Australia's Northern Territory. We used momentary abundance as a surrogate measure of invasion success, and investigated the relationship between A. gracilipes genetic diversity and its abundance, and the effect of its abundance on species diversity and community structure. We also investigated whether selected habitat characteristics contributed to differences in A. gracilipes abundance, for which we found no evidence. Our results revealed a significant positive association between A. gracilipes genetic diversity and abundance. Invaded communities were less diverse and differed in structure from uninvaded communities, and these effects were stronger as A. gracilipes abundance increased. These results contradict the hypothesis that genetic bottlenecks may promote unicoloniality. However, our A. gracilipes study population has diverged since its introduction, which may have obscured evidence of the bottleneck that would likely have occurred on arrival. The relative importance of genetic diversity to invasion success may be context dependent, and the role of genetic diversity may be more obvious in the absence of highly favorable novel ecological conditions. PMID:23139870

Gruber, Monica A M; Hoffmann, Benjamin D; Ritchie, Peter A; Lester, Philip J

2012-07-24

250

Genetic diversity is positively associated with fine-scale momentary abundance of an invasive ant.  

UK PubMed Central (United Kingdom)

Many introduced species become invasive despite genetic bottlenecks that should, in theory, decrease the chances of invasion success. By contrast, population genetic bottlenecks have been hypothesized to increase the invasion success of unicolonial ants by increasing the genetic similarity between descendent populations, thus promoting co-operation. We investigated these alternate hypotheses in the unicolonial yellow crazy ant, Anoplolepis gracilipes, which has invaded Arnhem Land in Australia's Northern Territory. We used momentary abundance as a surrogate measure of invasion success, and investigated the relationship between A. gracilipes genetic diversity and its abundance, and the effect of its abundance on species diversity and community structure. We also investigated whether selected habitat characteristics contributed to differences in A. gracilipes abundance, for which we found no evidence. Our results revealed a significant positive association between A. gracilipes genetic diversity and abundance. Invaded communities were less diverse and differed in structure from uninvaded communities, and these effects were stronger as A. gracilipes abundance increased. These results contradict the hypothesis that genetic bottlenecks may promote unicoloniality. However, our A. gracilipes study population has diverged since its introduction, which may have obscured evidence of the bottleneck that would likely have occurred on arrival. The relative importance of genetic diversity to invasion success may be context dependent, and the role of genetic diversity may be more obvious in the absence of highly favorable novel ecological conditions.

Gruber MA; Hoffmann BD; Ritchie PA; Lester PJ

2012-09-01

251

Spatio-temporal dynamics of genetic diversity in Sorghum bicolor in Niger.  

UK PubMed Central (United Kingdom)

The dynamics of crop genetic diversity need to be assessed to draw up monitoring and conservation priorities. However, few surveys have been conducted in centres of diversity. Sub-Saharan Africa is the centre of origin of sorghum. Most Sahel countries have been faced with major human, environmental and social changes in recent decades, which are suspected to cause genetic erosion. Sorghum is the second staple cereal in Niger, a centre of diversity for this crop. Niger was submitted to recurrent drought period and to major social changes during these last decades. We report here on a spatio-temporal analysis of sorghum genetic diversity, conducted in 71 villages covering the rainfall gradient and range of agro-ecological conditions in Niger's agricultural areas. We used 28 microsatellite markers and applied spatial and genetic clustering methods to investigate change in genetic diversity over a 26-year period (1976-2003). Global genetic differentiation between the two collections was very low (F (st) = 0.0025). Most of the spatial clusters presented no major differentiation, as measured by F (st), and showed stability or an increase in allelic richness, except for two of them located in eastern Niger. The genetic clusters identified by Bayesian analysis did not show a major change between the two collections in the distribution of accessions between them or in their spatial location. These results suggest that farmers' management has globally preserved sorghum genetic diversity in Niger.

Deu M; Sagnard F; Chantereau J; Calatayud C; Vigouroux Y; Pham JL; Mariac C; Kapran I; Mamadou A; Gérard B; Ndjeunga J; Bezançon G

2010-05-01

252

Spatio-temporal dynamics of genetic diversity in Sorghum bicolor in Niger.  

Science.gov (United States)

The dynamics of crop genetic diversity need to be assessed to draw up monitoring and conservation priorities. However, few surveys have been conducted in centres of diversity. Sub-Saharan Africa is the centre of origin of sorghum. Most Sahel countries have been faced with major human, environmental and social changes in recent decades, which are suspected to cause genetic erosion. Sorghum is the second staple cereal in Niger, a centre of diversity for this crop. Niger was submitted to recurrent drought period and to major social changes during these last decades. We report here on a spatio-temporal analysis of sorghum genetic diversity, conducted in 71 villages covering the rainfall gradient and range of agro-ecological conditions in Niger's agricultural areas. We used 28 microsatellite markers and applied spatial and genetic clustering methods to investigate change in genetic diversity over a 26-year period (1976-2003). Global genetic differentiation between the two collections was very low (F (st) = 0.0025). Most of the spatial clusters presented no major differentiation, as measured by F (st), and showed stability or an increase in allelic richness, except for two of them located in eastern Niger. The genetic clusters identified by Bayesian analysis did not show a major change between the two collections in the distribution of accessions between them or in their spatial location. These results suggest that farmers' management has globally preserved sorghum genetic diversity in Niger. PMID:20062963

Deu, Monique; Sagnard, F; Chantereau, J; Calatayud, C; Vigouroux, Y; Pham, J L; Mariac, C; Kapran, I; Mamadou, A; Gérard, B; Ndjeunga, J; Bezançon, G

2010-01-09

253

Genetic diversity of Guernsey population using pedigree data and gene-dropping simulations.  

UK PubMed Central (United Kingdom)

The objectives of this study were to analyze the trend of within-breed genetic diversity and identify major causes leading to loss of genetic diversity in Guernsey breed in three countries. Pedigree files of Canadian (GCN), South African (GSA) and American (GUS) Guernsey populations containing 130 927, 18 593 and 1 851 624 records, respectively, were analyzed. Several parameters derived from the in-depth pedigree analyses were used to measure trends and current levels of genetic diversity. Pedigree completeness index of GCN, GSA and GUS populations, in the most recent year (2007), was 97%, 74% and 79%, respectively, considering four generations back in the analysis. The rate of inbreeding in each population was 0.19%, 0.16% and 0.17% between 2002 and 2007, respectively. For the same period, the estimated effective population size for GCN, GSA and GUS was 46, 57 and 46, respectively. The estimated percentage of genetic diversity lost within each population over the last four decades was 8%, 3% and 5%, respectively. The relative proportion of genetic diversity lost due to random genetic drift in the three populations was 93%, 91% and 86%, respectively. In conclusion, the results suggested that GCN and GUS have lost more genetic diversity than GSA over the past four decades, and this loss is gaining momentum due to increasing rates of inbreeding. Therefore, strategies such as optimum contribution selection and migration of genetic material are advised to increase effective population size, particularly in GCN and GUS.

Melka MG; Sargolzaei M; Miglior F; Schenkel F

2013-02-01

254

Efficient Spatial Data mining using Integrated Genetic Algorithm and ACO  

Directory of Open Access Journals (Sweden)

Full Text Available Spatial data plays a key role in numerous applications such as network traffic, distributed security applications such as banking, retailing, etc., The spatial data is essential mine, useful for decision making and the knowledge discovery of interesting facts from large amounts of data. Many private institutions, organizations collect the number of congestion on the network while packets of data are sent, the flow of data and the mobility of the same. In addition other databases provide the additional information about the client who has sent the data, the server who has to receive the data, total number of clients on the network, etc. These data contain a mine of useful information for the network traffic risk analysis. Initially study was conducted to identify and predict the number of nodes in the system; the nodes can either be a client or a server. It used a decision tree that studies from the traffic risk in a network. However, this method is only based on tabular data and does not exploit geo routing location. Using the data, combined to trend data relating to the network, the traffic flow, demand, load, etc., this work aims at deducing relevant risk models to help in network traffic safety task. The existing work provided a pragmatic approach to multi-layer geo-data mining. The process behind was to prepare input data by joining each layer table using a given spatial criterion, then applying a standard method to build a decision tree. The existing work did not consider multi-relational data mining domain. The quality of a decision tree depends, on the quality of the initial data which are incomplete, incorrect or non relevant data inevitably leads to erroneous results. The proposed model develops an ant colony algorithm integrated with GA for the discovery of spatial trend patterns found in a network traffic risk analysis database. The proposed ant colony based spatial data mining algorithm applies the emergent intelligent behavior of ant colonies. The experimental results on a network traffic (trend layer) spatial database show that our method has higher efficiency in performance of the discovery process compared to other existing approaches using non-intelligent decision tree heuristics.

K Sankar; V Venkatachalam

2011-01-01

255

Development of pineapple microsatellite markers and germplasm genetic diversity analysis.  

UK PubMed Central (United Kingdom)

Two methods were used to develop pineapple microsatellite markers. Genomic library-based SSR development: using selectively amplified microsatellite assay, 86 sequences were generated from pineapple genomic library. 91 (96.8%) of the 94 Simple Sequence Repeat (SSR) loci were dinucleotide repeats (39 AC/GT repeats and 52 GA/TC repeats, accounting for 42.9% and 57.1%, resp.), and the other three were mononucleotide repeats. Thirty-six pairs of SSR primers were designed; 24 of them generated clear bands of expected sizes, and 13 of them showed polymorphism. EST-based SSR development: 5659 pineapple EST sequences obtained from NCBI were analyzed; among 1397 nonredundant EST sequences, 843 were found containing 1110 SSR loci (217 of them contained more than one SSR locus). Frequency of SSRs in pineapple EST sequences is 1SSR/3.73?kb, and 44 types were found. Mononucleotide, dinucleotide, and trinucleotide repeats dominate, accounting for 95.6% in total. AG/CT and AGC/GCT were the dominant type of dinucleotide and trinucleotide repeats, accounting for 83.5% and 24.1%, respectively. Thirty pairs of primers were designed for each of randomly selected 30 sequences; 26 of them generated clear and reproducible bands, and 22 of them showed polymorphism. Eighteen pairs of primers obtained by the one or the other of the two methods above that showed polymorphism were selected to carry out germplasm genetic diversity analysis for 48 breeds of pineapple; similarity coefficients of these breeds were between 0.59 and 1.00, and they can be divided into four groups accordingly. Amplification products of five SSR markers were extracted and sequenced, corresponding repeat loci were found and locus mutations are mainly in copy number of repeats and base mutations in the flanking region.

Feng S; Tong H; Chen Y; Wang J; Chen Y; Sun G; He J; Wu Y

2013-01-01

256

Development of pineapple microsatellite markers and germplasm genetic diversity analysis.  

Science.gov (United States)

Two methods were used to develop pineapple microsatellite markers. Genomic library-based SSR development: using selectively amplified microsatellite assay, 86 sequences were generated from pineapple genomic library. 91 (96.8%) of the 94 Simple Sequence Repeat (SSR) loci were dinucleotide repeats (39 AC/GT repeats and 52 GA/TC repeats, accounting for 42.9% and 57.1%, resp.), and the other three were mononucleotide repeats. Thirty-six pairs of SSR primers were designed; 24 of them generated clear bands of expected sizes, and 13 of them showed polymorphism. EST-based SSR development: 5659 pineapple EST sequences obtained from NCBI were analyzed; among 1397 nonredundant EST sequences, 843 were found containing 1110 SSR loci (217 of them contained more than one SSR locus). Frequency of SSRs in pineapple EST sequences is 1SSR/3.73?kb, and 44 types were found. Mononucleotide, dinucleotide, and trinucleotide repeats dominate, accounting for 95.6% in total. AG/CT and AGC/GCT were the dominant type of dinucleotide and trinucleotide repeats, accounting for 83.5% and 24.1%, respectively. Thirty pairs of primers were designed for each of randomly selected 30 sequences; 26 of them generated clear and reproducible bands, and 22 of them showed polymorphism. Eighteen pairs of primers obtained by the one or the other of the two methods above that showed polymorphism were selected to carry out germplasm genetic diversity analysis for 48 breeds of pineapple; similarity coefficients of these breeds were between 0.59 and 1.00, and they can be divided into four groups accordingly. Amplification products of five SSR markers were extracted and sequenced, corresponding repeat loci were found and locus mutations are mainly in copy number of repeats and base mutations in the flanking region. PMID:24024187

Feng, Suping; Tong, Helin; Chen, You; Wang, Jingyi; Chen, Yeyuan; Sun, Guangming; He, Junhu; Wu, Yaoting

2013-08-19

257

Concordance between vocal and genetic diversity in crested gibbons  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Gibbons or small apes are, next to great apes, our closest living relatives, and form the most diverse group of contemporary hominoids. A characteristic trait of gibbons is their species-specific song structure, which, however, exhibits a certain amount of inter- and intra-individual variation. Although differences in gibbon song structure are routinely applied as taxonomic tool to identify subspecies and species, it remains unclear to which degree acoustic and phylogenetic differences are correlated. To trace this issue, we comparatively analyse song recordings and mitochondrial cytochrome b gene sequence data from 22 gibbon populations representing six of the seven crested gibbon species (genus Nomascus). In addition, we address whether song similarity and geographic distribution can support a recent hypothesis about the biogeographic history of crested gibbons. Results The acoustic analysis of 92 gibbon duets confirms the hypothesised concordance between song structure and phylogeny. Based on features of male and female songs, we can not only distinguish between N. nasutus, N. concolor and the four southern species (N. leucogenys, N. siki, N. annamensis, N. gabriellae), but also between the latter by applying more detailed analysis. In addition to the significant correlation between song structure and genetic similarity, we find a similar high correlation between song similarity and geographic distance. Conclusions The results show that the structure of crested gibbon songs is not only a reliable tool to verify phylogenetic relatedness, but also to unravel geographic origins. As vocal production in other nonhuman primate species appears to be evolutionarily based, it is likely that loud calls produced by other species can serve as characters to elucidate phylogenetic relationships.

Thinh Van; Hallam Chris; Roos Christian; Hammerschmidt Kurt

2011-01-01

258

Genetic diversity of Cryptosporidium isolates from patients in North India.  

UK PubMed Central (United Kingdom)

BACKGROUND: Cryptosporidiosis is a significant cause of diarrheal illness in both immunocompetent and immunocompromised populations. Cryptosporidium species infect a wide range of hosts including humans. Different species are morphologically indistinguishable, and molecular techniques have become the key to detection and source tracking. The present study was designed to study the genetic diversity of human Cryptosporidium isolates in North India. METHODS: Cryptosporidium oocysts were detected in stool samples by special staining of fecal smears. DNA was extracted with a Qiagen kit and all samples were genotyped by small subunit ribosomal ribonucleic acid (SSU rRNA)-based nested PCR-restriction fragment length polymorphism (RFLP) tool using enzymes SspI and VspI. Cryptosporidium hominis and Cryptosporidium parvum isolates were subtyped by sequence analysis of the nested PCR amplified gp60 gene. RESULTS: Fifty-three fecal samples were found to be positive for Cryptosporidium oocysts. RFLP analysis revealed 39 isolates as C. hominis and 13 isolates of C. parvum; one sample failed amplification. gp60-based sequencing of C. hominis and C. parvum divided them into eight subgenotype families and 17 subtypes. gp60-based sequencing identified seven cases of mixed infection with C. hominis and C. parvum/Cryptosporidium meleagridis and showed the presence of C. meleagridis in six HIV-positive patients that were indistinguishable in RFLP. CONCLUSIONS: Cryptosporidium isolates obtained in the present study from patients in North India belonged to three species, eight subgenotype families, and 17 subtypes. The existence of many Cryptosporidium species, subgenotypes, and subtypes along with mixed infections reveals the complexity of Cryptosporidium transmission; this heterogeneity indicates stable cryptosporidiosis transmission in North India. The results may have further implications in understanding the epidemiology and control of this infection.

Sharma P; Sharma A; Sehgal R; Malla N; Khurana S

2013-08-01

259

Genetic diversity in Brazilian populations of Aedes albopictus  

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Full Text Available Random amplified polymorphic DNA (RAPD) analysis technique was undertaken in Aedes albopictus populations from three states in Brazil, Rio de Janeiro (RJ), Minas Gerais (MG) and Pernambuco (PE), to estimate the level of genetic variability and levels of genetic exchange between populations. Allele and genotype frequencies were measured on 47 RAPD loci. Average observed heterozigosity (Ho) ranged from 0.282 in MG to 0.355 in Casa Forte (PE) population. Genetic distances estimates indicated that RJ and MG were more genetically similar than populations from PE. Genetic variation observed in local Brazilian populations was attributed to genetic drift associated with restricted gene flow in recently established populations.

CFJ Ayres; TPA Romão; MAV Melo-Santos; AF Furtado

2002-01-01

260

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

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Full Text Available Background & objectives: 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-3alpha (msp-3?) and assessed its suitability as high-resolution genetic marker for population genetic studies. Methods: 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?. Results: We observed three distinct PCR alleles at msp-3?, and among them allele A showed significantly high frequency (53%, ?2 = 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? 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? in the field isolates. Interpretation & conclusion: 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? could be a high-resolution marker for genetic diversity studies among P. vivax field isolates.

Surendra Kumar Prajapati; Hema Joshi; Neena Valecha

2010-01-01

 
 
 
 
261

Genetic diversity measures of local European beef cattle breeds for conservation purposes  

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Full Text Available Abstract This study was undertaken to determine the genetic structure, evolutionary relationships, and the genetic diversity among 18 local cattle breeds from Spain, Portugal, and France using 16 microsatellites. Heterozygosities, estimates of Fst, genetic distances, multivariate and diversity analyses, and assignment tests were performed. Heterozygosities ranged from 0.54 in the Pirenaica breed to 0.72 in the Barrosã breed. Seven percent of the total genetic variability can be attributed to differences among breeds (mean Fst = 0.07; P

Cañón Javier; Alexandrino Paolo; Bessa Isabel; Carleos Carlos; Carretero Yolanda; Dunner Susana; Ferran Nuno; Garcia David; Jordana Jordi; Laloë Denis; Pereira Albano; Sanchez Armand; Moazami-Goudarzi Katayoun

2001-01-01

262

Effects of Habitat Fragmentation on Population Genetic Diversity of Endangered Plant Euonymus chloranthoides Yang  

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Full Text Available Habitat fragmentation is the main threat to the survival of many species, species response to habitat fragmentation differently; the information of genetic diversity has great significance to protect species. Euonymus chloranthoides Yang is an endangered plant endemic to Chongqing. The population of this plant in Jinyun Mountain has been fragmented seriously because of the highway construction, tour development and so on. Some populations are small and isolated. Four populations in Jinyun maintain were selected to study the effects of habitat fragmentation on population genetic diversity of E. chloranthoides. The results of ISSR experiment show that the GST is 0.406 2 which means 59.38% of the genetic diversity exists within the population, and 40.62% of the genetic diversity exists among populations, the level of population differentiation is high due to long isolation, low dispersal distance of pollen and seed. The PPB of the population with highest genetic diversity is 64.58%, The genetic diversity of Banzigou population, the smallest one, is the lowest, and the PPB of this population is 29.17%, which means small population do harm to the maintenance of genetic diversity. The gene flow (Nm) is 0.730 9, which is difficult to counteract the differentiation caused by genetic drift. Cluster analysis show he nearest populations cluster first, which mean that the genetic differentiation is affected by spatial distance. In-situ conservation should be strengthened to protect the small populations, and gene flow among populations should be improved to prevent the further genetic loss of small populations.

HU Shi-jun; YAN Xiao-hui; HE Ping; ZHANG Chun-ping

2013-01-01

263

SNP-revealed genetic diversity in wild emmer wheat correlates with ecological factors.  

UK PubMed Central (United Kingdom)

BACKGROUND: Patterns of genetic diversity between and within natural plant populations and their driving forces are of great interest in evolutionary biology. However, few studies have been performed on the genetic structure and population divergence in wild emmer wheat using a large number of EST-related single nucleotide polymorphism (SNP) markers. RESULTS: In the present study, twenty-five natural wild emmer wheat populations representing a wide range of ecological conditions in Israel and Turkey were used. Genetic diversity and genetic structure were investigated using over 1,000 SNP markers. A moderate level of genetic diversity was detected due to the biallelic property of SNP markers. Clustering based on Bayesian model showed that grouping pattern is related to the geographical distribution of the wild emmer wheat. However, genetic differentiation between populations was not necessarily dependent on the geographical distances. A total of 33 outlier loci under positive selection were identified using a FST-outlier method. Significant correlations between loci and ecogeographical factors were observed. CONCLUSIONS: Natural selection appears to play a major role in generating adaptive structures in wild emmer wheat. SNP markers are appropriate for detecting selectively-channeled adaptive genetic diversity in natural populations of wild emmer wheat. This adaptive genetic diversity is significantly associated with ecological factors.

Ren J; Chen L; Sun D; You FM; Wang J; Peng Y; Nevo E; Beiles A; Sun D; Luo MC; Peng J

2013-01-01

264

Peak and persistent excess of genetic diversity following an abrupt migration increase.  

UK PubMed Central (United Kingdom)

Genetic diversity is essential for population survival and adaptation to changing environments. Demographic processes (e.g., bottleneck and expansion) and spatial structure (e.g., migration, number, and size of populations) are known to shape the patterns of the genetic diversity of populations. However, the impact of temporal changes in migration on genetic diversity has seldom been considered, although such events might be the norm. Indeed, during the millions of years of a species' lifetime, repeated isolation and reconnection of populations occur. Geological and climatic events alternately isolate and reconnect habitats. We analytically document the dynamics of genetic diversity after an abrupt change in migration given the mutation rate and the number and sizes of the populations. We demonstrate that during transient dynamics, genetic diversity can reach unexpectedly high values that can be maintained over thousands of generations. We discuss the consequences of such processes for the evolution of species based on standing genetic variation and how they can affect the reconstruction of a population's demographic and evolutionary history from genetic data. Our results also provide guidelines for the use of genetic data for the conservation of natural populations.

Alcala N; Streit D; Goudet J; Vuilleumier S

2013-03-01

265

Genetic diversity in populations of Acrocomia aculeata (Arecaceae) in the northern region of Minas Gerais, Brazil.  

UK PubMed Central (United Kingdom)

Macaúba (Acrocomia aculeata) is a palm of economic importance, widely distributed in natural forests from Mexico to Uruguay. We analyzed the genetic diversity of populations of macaúba (A. aculeata) in the northern region of the State of Minas Gerais, Brazil. Young leaves from 10 macaúba individuals encompassing 49 genotypes of macaúba were collected from Montes Claros, Itacambira, Brasília de Minas, Mirabela, and Grão Mogol. After extraction and amplification of samples, the amplified fragments were separated by electrophoresis. We found high levels of genetic diversity within the populations. Genetic diversity indices were high, except in the Itacambira and Mirabela populations. Results show that Mirabela and Itacambira populations can require conservation strategies because they present lower values of genetic diversity.

Oliveira DA; Melo Júnior AF; Brandão MM; Rodrigues LA; Menezes EV; Ferreira PR

2012-01-01

266

Genetic diversity in populations of Acrocomia aculeata (Arecaceae) in the northern region of Minas Gerais, Brazil.  

Science.gov (United States)

Macaúba (Acrocomia aculeata) is a palm of economic importance, widely distributed in natural forests from Mexico to Uruguay. We analyzed the genetic diversity of populations of macaúba (A. aculeata) in the northern region of the State of Minas Gerais, Brazil. Young leaves from 10 macaúba individuals encompassing 49 genotypes of macaúba were collected from Montes Claros, Itacambira, Brasília de Minas, Mirabela, and Grão Mogol. After extraction and amplification of samples, the amplified fragments were separated by electrophoresis. We found high levels of genetic diversity within the populations. Genetic diversity indices were high, except in the Itacambira and Mirabela populations. Results show that Mirabela and Itacambira populations can require conservation strategies because they present lower values of genetic diversity. PMID:22535388

Oliveira, D A; Melo Júnior, A F; Brandão, M M; Rodrigues, L A; Menezes, E V; Ferreira, P R B

2012-03-08

267

Recent increase of genetic diversity in Plasmodium vivax population in the Republic of Korea  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Abstract Background The reemergence of Plasmodium vivax in South Korea since 1993 represents a serious public health concern. Despite the importance in understanding genetic diversity for control strategies, however, studies remain inconclusive with the general premise that...

Honma Hajime; Kim Jung-Yeon; Palacpac Nirianne MQ; Mita Toshihiro; Lee Wonja; Horii Toshihiro; Tanabe Kazuyuki

268

High genetic diversity of Plasmodium vivax on the north coast of Papua New Guinea.  

UK PubMed Central (United Kingdom)

Despite having the highest Plasmodium vivax burden in the world, molecular epidemiological data from Papua New Guinea (PNG) for this parasite remain limited. To investigate the molecular epidemiology of P. vivax in PNG, 574 isolates collected from four catchment sites in East Sepik (N = 1) and Madang (N = 3) Provinces were genotyped using the markers MS16 and msp1F3. Genetic diversity and prevalence of P. vivax was determined for all sites. Despite a P. vivax infection prevalence in the East Sepik (15%) catchments less than one-half the prevalence of the Madang catchments (27-35%), genetic diversity was similarly high in all populations (He = 0.77-0.98). High genetic diversity, despite a marked difference in infection prevalence, suggests a large reservoir of diversity in P. vivax populations of PNG. Significant reductions in transmission intensity may, therefore, be required to reduce the diversity of parasite populations in highly endemic countries such as PNG.

Arnott A; Barnadas C; Senn N; Siba P; Mueller I; Reeder JC; Barry AE

2013-07-01

269

High genetic diversity of Plasmodium vivax on the north coast of Papua New Guinea.  

Science.gov (United States)

Despite having the highest Plasmodium vivax burden in the world, molecular epidemiological data from Papua New Guinea (PNG) for this parasite remain limited. To investigate the molecular epidemiology of P. vivax in PNG, 574 isolates collected from four catchment sites in East Sepik (N = 1) and Madang (N = 3) Provinces were genotyped using the markers MS16 and msp1F3. Genetic diversity and prevalence of P. vivax was determined for all sites. Despite a P. vivax infection prevalence in the East Sepik (15%) catchments less than one-half the prevalence of the Madang catchments (27-35%), genetic diversity was similarly high in all populations (He = 0.77-0.98). High genetic diversity, despite a marked difference in infection prevalence, suggests a large reservoir of diversity in P. vivax populations of PNG. Significant reductions in transmission intensity may, therefore, be required to reduce the diversity of parasite populations in highly endemic countries such as PNG. PMID:23690553

Arnott, Alicia; Barnadas, Celine; Senn, Nicolas; Siba, Peter; Mueller, Ivo; Reeder, John C; Barry, Alyssa E

2013-05-20

270

Population genetic diversity of Rhodiola dumulosa in Northern China inferred from AFLP makers  

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Full Text Available Aims Rhodiola dumulosa (Crassulaceae) is a perennial herbaceous plant. It grows among rocks on mountains at 1 600–3 900 m, and its populations are spatially scattered in their areas of distribution. Our objectives were to study the population genetic diversity and genetic structure of R. dumulosa in northern China and determinerelationships between genetic diversity and environmental factors.Methods We analyzed 776 individuals from 25 natural populations using amplified fragment length polymorphism (AFLP) markers.Important findings We obtained 398 unambiguous bands from the four pairs of selective primers, 312 bands (78.46%) of which were polymorphic across all individuals. The Nei’s gene diversity was 0.364 9, and the Shannon’s information index was 0.542 2 at the species level. Therefore, there was a high level of genetic diversitywithin R. dumulosa populations in northern China. The population genetic differentiation index Gst was 0.150 7, and the indirect estimate of gene flow Nm was 2.82, which indicated that genetic differentiation among northern populations was low and gene exchange was frequent. Analysis of molecular variance (AMOVA) revealed that the majority of AFLP variations resided within populations (67.9%). The STRUCTURE and UPGMA cluster analyses showed that the closely related populations are geographically restricted and occur in proximity to each other. This result was confirmed by the Mantel test, which revealed a significant positive correlation (r = 0.512 9, p < 0.001) between geographical distance and genetic distance. In addition, the correlation analysis of population genetic diversity and altitude showed a significant negative relationship (p < 0.05), i.e., population genetic diversity decreased with increasing altitude. However, there was no significant correlation between genetic diversity and slope direction. The software Dfdist was used to detect outliers caused by altitude, but the results were non-significant. All research results showed that geographical distance affected genetic distance significantly.

ZHANG Yun-Hong; HOU Yan; LOU An-Ru

2010-01-01

271

[Genetic diversity and genetic relationship of Jatropha curcas L. in Sichuan and Yunnan evaluated by cpSSR markers].  

UK PubMed Central (United Kingdom)

OBJECTIVE: The genetic diversity and genetic relationship of Jatropha curcas resources in Sichuan and Yunnan were studied in order to provide a theoretical basis for breeding fine varieties and protecting germplasm resources. METHOD: Ten J. curcas populations were studied by 12 cpSSR primers in this paper. On the base of amplified bands, genetic diversity parameters were analyzed by POPGENE version 1.32. Furthermore, UPGMA tree of 10 J. curcas populations established from pairwise population distance by NTSYSpc version 2.10. RESULT: Twenty-two polymorphic bands were detected, and the percentage of polymorphic loci (P) was 76.28%. Among of the 10 J. curcas populations, the average percentage of polymorphic loci of YNSB was higher than that of the other populations, and it reached 95.45%; On the other hand, that of YNLS was the lowest in all populations, and it was 45.45%. Nei's gene diversity index(H(e)), Shannon information index(I), Effective Num of alleles(A(e)) were respectively 0.4020, 0.576 7, 1.713 6. The total gene diversity (H(T)), the gene differentiation coefficient (G(st)), the gene flow (N(m)) and the gene diversity within populations (H(s)) were 0.443 3, 0.080 2, 3.058 5, 0.405 1, 0.035 7, respectively. The highest gene diversity ratio was showed within populations and the lowest among populations. The results by AMOVA analysis showed that 91.02% of genetic variation existed within populations while 8.98% of genetic variation existed among populations. On the base of the results, the conclusion was extracted that variation existed mainly within populations, and the variation within populations was bigger than that among populations. The result was consistent with that of the gene differentiation coefficient. The order of the genetic diversity was YNLS population < XSBN population < SCHPZ population < SCHD population < SCJH population < YNPR population < SCLB population < YNSB population < YNFY population < SCHL population. The range of Nei's genetic identity and genetic distance of 10 respectively populations were respectively 0.812 7-0.979 8, 0.020 4-0.207 3. All these showed the similarity was higher and there was a close relationship among the 10 respectively populations; Results based on the cluster analysis showed that 10 respectively populations were divided into 2 groups: one was SCJH population and CHPZ population, the other was SCHL population, SCHD population, SCLB population, YNSB population, YNFY population, YNPR population, XSBN population and YNLS population. CONCLUSION: Significant genetic diversity was observed among respectively resources in Sichuan and Yunnan. On the other hand, genetic relationship was close between populations.

Pu G; Zhou L; Xiang Q; ma Y

2012-01-01

272

Comparative genetic diversity and genetic structure of three chinese silkworm species Bombyx mori L. (Lepidoptera: Bombycidae), Antheraea pernyi Guérin-Meneville and Samia cynthia ricini donovan (Lepidoptera: Saturniidae)  

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Full Text Available The genetic diversity and genetic structure of three Chinese silkworm species Bombyx mori L., Antheraea pernyi Guérin-Meneville and Samia cynthia ricini Donovan were comparatively assessed based on RAPD markers. At the species level, A. pernyi and B. mori showed high levels of genetic diversity, whereas S. cynthia ricini showed low level of genetic diversity. However, at the strain level, A. pernyi had relatively highest genetic diversity and B. mori had lowest genetic diversity. Analysis of molecular variance (AMOVA) suggested that 60% and 72% of genetic variation resided within strains in A. pernyi and S. cynthia ricini, respectively, whereas only 16% of genetic variation occurred within strains in B. mori. In UPGMA dendrogram, individuals of A. pernyi and B. mori formed the strain-specific genetic clades, whereas those of S. cynthia ricini were distributed in a mixed way. The implications of these results for the conservation and utilization in breeding programs of three silkworm species are discussed.

Yan-Qun Liu; Li Qin; Yu-Ping li; Huan Wang; Run-Xi Xia; Yong-Hong Qi; Xi-Sheng li; Cheng Lu; Zhong-Huai Xiang

2010-01-01

273

Genetic diversity of Annona crassiflora (Annonaceae) in northern Minas Gerais State.  

Science.gov (United States)

Genetic diversity analyses of tropical tree species are relevant to landscape management, plant genetic resource inventory, and biological conservation of threatened species. Annona crassiflora is an endangered fruit tree native to the Cerrado biome that is threatened by reduction of natural populations and fruit extraction. We examined the intra- and interpopulational genetic diversity of this species in the northern region of Minas Gerais State. Seventy-two individuals from four natural populations were genotyped using RAPD markers. We found moderate genetic diversity among populations, with Shannon's I index varying between 0.31 and 0.44, and Nei's genetic diversity (H(E)) for the population set equal to 0.31. AMOVA indicated a greater genetic variation within (77.38%) rather than among populations (22.62%), tending towards isolation by distance (Mantel's r = 0.914; P = 0.089). Nei's genetic identity estimates among populations revealed a hierarchical pattern of genetic similarity of form [(CA1, CA2), MC], [(GM)], corroborating the high genetic differentiation between spatially isolated populations. PMID:21968724

Cota, L G; Vieira, F A; Melo Júnior, A F; Brandão, M M; Santana, K N O; Guedes, M L; Oliveira, D A

2011-09-23

274

Genetic diversity of Annona crassiflora (Annonaceae) in northern Minas Gerais State.  

UK PubMed Central (United Kingdom)

Genetic diversity analyses of tropical tree species are relevant to landscape management, plant genetic resource inventory, and biological conservation of threatened species. Annona crassiflora is an endangered fruit tree native to the Cerrado biome that is threatened by reduction of natural populations and fruit extraction. We examined the intra- and interpopulational genetic diversity of this species in the northern region of Minas Gerais State. Seventy-two individuals from four natural populations were genotyped using RAPD markers. We found moderate genetic diversity among populations, with Shannon's I index varying between 0.31 and 0.44, and Nei's genetic diversity (H(E)) for the population set equal to 0.31. AMOVA indicated a greater genetic variation within (77.38%) rather than among populations (22.62%), tending towards isolation by distance (Mantel's r = 0.914; P = 0.089). Nei's genetic identity estimates among populations revealed a hierarchical pattern of genetic similarity of form [(CA1, CA2), MC], [(GM)], corroborating the high genetic differentiation between spatially isolated populations.

Cota LG; Vieira FA; Melo Júnior AF; Brandão MM; Santana KN; Guedes ML; Oliveira DA

2011-01-01

275

Patterns of ancestry and genetic diversity in reintroduced populations of the slimy sculpin: implications for conservation  

UK PubMed Central (United Kingdom)

Reintroductions are a common approach for preserving intraspecific biodiversity in fragmented landscapes. However, they may exacerbate the reduction in genetic diversity initially caused by population fragmentation because the effective population size of reintroduced populations is often smaller and reintroduced populations also tend to be more geographically isolated than native populations. Mixing genetically divergent sources for reintroduction purposes is a practice intended to increase genetic diversity. We documented the outcome of reintroductions from three mixed sources on the ancestral composition and genetic variation of a North American fish, the slimy sculpin (Cottus cognatus). We used microsatellite markers to evaluate allelic richness and heterozygosity in the reintroduced populations relative to computer simulated expectations. Sculpins in reintroduced populations exhibited higher levels of heterozygosity and allelic richness than any single source, but only slightly higher than the single most genetically diverse source population. Simulations intended to mimic an ideal scenario for maximizing genetic variation in the reintroduced populations also predicted increases, but they were only moderately greater than the most variable source population. We found that a single source contributed more than the other two sources at most reintroduction sites. We urge caution when choosing whether to mix source populations in reintroduction programs. Genetic characteristics of candidate source populations should be evaluated prior to reintroduction if feasible. When combined with knowledge of the degree of genetic distinction among sources, simulations may allow the genetic diversity benefits of mixing populations to be weighed against the risks of outbreeding depression in reintroduced and nearby populations.

Huff DavidD; Miller LorenM; Vondracek Bruce

2010-12-01

276

Estimation of Genetic Diversity in Sheep (Ovis aries) using Randomly Amplified Polymorphic DNA  

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Full Text Available Domestic sheep (Ovis aries) belongs to order Artiod actyla. Despite its great economic importance, not much work has been done in Pakistan on breeding and genetics of sheep. Present research was initiated to analyze DNA based genetic diversity in Pakistani breeds of sheep. Total genomic DNA was isolated from blood of Rambouillet, Kaghani and Ramghani breeds. Polymerase Chain Reactions (PCR) were carried out using six Randomly Amplified Polymorphic DNA (RAPD) primers. Amplified fragments ranged in size from 500 bp to 2000 bp. On average, 3 alleles per genotype were amplified. Average genetic distance estimate ranged from 30-100%. Eleven comparisons showed maximum genetic diversity (GD = 100%) while 6 comparisons sowed minimum genetic diversity (GD = 30%) for the loci detected using 6 RAPD primers. Phylogenetic elaboration among the 14 sheep accessions were carried out using dendrogram analysis. The 14 accessions of sheep were grouped into 5 clusters comprising 3 , 3, 3, 3 and 2 accessions, respectively.

M. Qasim,

2011-01-01

277

Genetic diversity in three endangered pitcher plant species (Sarracenia; Sarraceniaceae) is lower than widespread congeners.  

UK PubMed Central (United Kingdom)

• Premise of the study: Narrow-ranging, rare species often exhibit levels of genetic diversity lower than more common or widespread congeners. These taxa are at increased risk of extinction due to threats associated with natural as well as anthropogenic events. We assessed genetic variation in three federally endangered Sarracenia species. We discuss maintenance of genetic diversity and evolutionary implications of rarity. • Methods: We analyzed three noncoding chloroplast regions and nine microsatellite loci in populations spanning the geographic ranges of S. oreophila, S. alabamensis, and S. jonesii. The same microsatellite loci were used to examine a single field site of three more widespread species (S. alata, S. leucophylla, and S. rubra subsp. wherryi). • Key results: All three endangered species have experienced reductions in population size and numbers. All show considerably less variation than more widespread members of the genus. Sarracenia alabamensis maintains the greatest microsatellite variation but has the fewest remaining populations and may be under the greatest threat. More widespread S. oreophila maintains surprising chloroplast diversity, yet exhibits little microsatellite diversity. Sarracenia jonesii lacks chloroplast diversity, yet maintains greater microsatellite diversity than S. oreophila. • Conclusions: The three endangered species differ in levels and structure of diversity, yet not in predictable ways, emphasizing that unique demographic and ecological histories, rather than current distribution and population size, best explain present patterns of genetic variation. Maintenance of remaining genetic variation is important, but preventing further habitat loss and degradation is critical.

Furches MS; Small RL; Furches A

2013-10-01

278

Genetic diversity in three endangered pitcher plant species (Sarracenia; Sarraceniaceae) is lower than widespread congeners.  

UK PubMed Central (United Kingdom)

• Premise of the study: Narrow-ranging, rare species often exhibit levels of genetic diversity lower than more common or widespread congeners. These taxa are at increased risk of extinction due to threats associated with natural as well as anthropogenic events. We assessed genetic variation in three federally endangered Sarracenia species. We discuss maintenance of genetic diversity and evolutionary implications of rarity.• Methods: We analyzed three noncoding chloroplast regions and nine microsatellite loci in populations spanning the geographic ranges of S. oreophila, S. alabamensis, and S. jonesii. The same microsatellite loci were used to examine a single field site of three more widespread species (S. alata, S. leucophylla, and S. rubra subsp. wherryi).• Key results: All three endangered species have experienced reductions in population size and numbers. All show considerably less variation than more widespread members of the genus. Sarracenia alabamensis maintains the greatest microsatellite variation but has the fewest remaining populations and may be under the greatest threat. More widespread S. oreophila maintains surprising chloroplast diversity, yet exhibits little microsatellite diversity. Sarracenia jonesii lacks chloroplast diversity, yet maintains greater microsatellite diversity than S. oreophila.• Conclusions: The three endangered species differ in levels and structure of diversity, yet not in predictable ways, emphasizing that unique demographic and ecological histories, rather than current distribution and population size, best explain present patterns of genetic variation. Maintenance of remaining genetic variation is important, but preventing further habitat loss and degradation is critical.

Furches MS; Small RL; Furches A

2013-10-01

279

Phylogenetic Comparative Methods Strengthen Evidence for Reduced Genetic Diversity among Endangered Tetrapods  

UK PubMed Central (United Kingdom)

The fitness of species with little genetic diversity is expected to be affected by inbreeding and an inability to respond to environmental change. Conservation theory suggests that endangered species will generally demonstrate lower genetic diversity than taxa that are not threatened. This hypothesis has been challenged because the time frame of anthropogenic extinction may be too fast to expect genetic factors to significantly contribute. I conducted a meta-analysis to examine how genetic diversity in 894 tetrapods correlates with extinction threat level. Because species are not evolutionarily independent, I used a phylogenetic regression framework to address this issue. Mean genetic diversity of tetrapods, as assessed by protein heterozygosity, was 29.7-31.5% lower on average in threatened species than in their nonthreatened relatives, a highly significant reduction. Within amphibians as diversity decreased extinction risk increased in phylogenetic models, but not in nonphylogenetic regressions. The effects of threatened status on diversity also remained significant after accounting for body size in mammals. These results support the hypothesis that genetic effects on population fitness are important in the extinction process.

FLIGHT PATRICKA

2010-10-01

280

Phylogenetic comparative methods strengthen evidence for reduced genetic diversity among endangered tetrapods.  

UK PubMed Central (United Kingdom)

The fitness of species with little genetic diversity is expected to be affected by inbreeding and an inability to respond to environmental change. Conservation theory suggests that endangered species will generally demonstrate lower genetic diversity than taxa that are not threatened. This hypothesis has been challenged because the time frame of anthropogenic extinction may be too fast to expect genetic factors to significantly contribute. I conducted a meta-analysis to examine how genetic diversity in 894 tetrapods correlates with extinction threat level. Because species are not evolutionarily independent, I used a phylogenetic regression framework to address this issue. Mean genetic diversity of tetrapods, as assessed by protein heterozygosity, was 29.7-31.5% lower on average in threatened species than in their nonthreatened relatives, a highly significant reduction. Within amphibians as diversity decreased extinction risk increased in phylogenetic models, but not in nonphylogenetic regressions. The effects of threatened status on diversity also remained significant after accounting for body size in mammals. These results support the hypothesis that genetic effects on population fitness are important in the extinction process.

Flight PA

2010-10-01

 
 
 
 
281

Genetic diversity and genetic exchange in Trypanosoma cruzi: dual drug-resistant "progeny" from episomal transformants  

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Full Text Available Extensive characterisation of Trypanosoma cruzi by isoenzyme phenotypes has separated the species into three principal zymodeme groups, Z1, Z2 and Z3, and into many individual zymodemes. There is marked diversity within Z2. A strong correlation has been demonstrated between the strain clusters determined by isoenzymes and those obtained using random amplified polymorphic DNA (RAPD) profiles. Polymorphisms in ribosomal RNA genes, in mini-exon genes, and microsatellite fingerprinting indicate the presence of at least two principal T. cruzi genetic lineages. Lineage 1 appears to correspond with Z2 and lineage 2 with Z1. Z1 (lineage 2) is associated with Didelphis. Z2 (lineage 1) may be associated with a primate host. Departures from Hardy-Weinberg equilibrium and linkage disequilibrium indicate that propagation of T. cruzi is predominantly clonal. Nevertheless, two studies show putative homozygotes and heterozygotes circulating sympatrically: the allozyme frequencies for phosphoglucomutase, and hybrid RAPD profiles suggest that genetic exchange may be a current phenomenon in some T. cruzi transmission cycles. We were able to isolate dual drug-resistant T. cruzi biological clones following copassage of putative parents carrying single episomal drug-resistant markers. A multiplex PCR confirmed that dual drug-resistant clones carried both episomal plasmids. Preliminary karyotype analysis suggests that recombination may not be confined to the extranuclear genome.

JR Stothard; IA Frame; MA Miles

1999-01-01

282

Allozyme diversity and genetic structure of the leafy cactus (Pereskia guamacho [Cactaceae]).  

Science.gov (United States)

We examined levels of genetic variation and genetic structure in the leafy cactus (Pereskia guamacho) in arid and semiarid zones in Venezuela. We surveyed genetic diversity within 17 populations using 19 allozyme loci. Genetic diversity was relatively high at both the species (P(s) = 89%, A(s) = 3.26, AP(s) = 3.53, H(es) = 0.24) and population (P(p) = 63%, A(p) = 1.90, AP(p) = 2.42, H(ep) = 0.20) levels. A significant deficit of heterozygote individuals was detected within populations in the Paraguana Peninsula region (F(IS) = 0.301). Relatively low levels of population differentiation were detected at macrogeographic (G(ST) = 0.112) and regional levels (G(ST) = 0.044 for peninsula region and G(ST) = 0.074 for mainland region), suggesting substantial genetic exchange among populations; however, gene flow in this species seems to be regulated by the distance among populations. Overall, estimates of genetic diversity found in P. guamacho are concordant with the pattern observed for other cacti surveyed, namely high levels of polymorphism and genetic diversity with one common allele and several rare alleles per locus. Differences in gene dispersal systems between this species and other cacti studied were not reflected in the patterns of genetic diversity observed. The concentration of the highest estimates of genetic variation in northwestern Venezuela suggests a potential reservoir of plant genetic diversity within xerophilous ecosystems in northern South America. PMID:12195035

Nassar, J M; Hamrick, J L; Fleming, T H

283

Genetic diversity of Mexican brook lamprey Lampetra (Tetrapleurodon) geminis (Alvarez del Villar, 1966).  

UK PubMed Central (United Kingdom)

Lampreys are the only surviving representatives of the oldest known vertebrates. The Mexican lamprey L. geminis (nonparasitic), is particularly interesting, because it is an endemic, biogeographical relict, and a threatened species. RAPD markers were used to describe genetic diversity in L. geminis. A total of 77 specimens were collected from five populations, three in the Río Grande de Morelia-Cuitzeo basin and two in the Río Duero-Lerma-Chapala basin, México. Eighty-eight RAPD markers were obtained from eight primers. Genetic diversity within each population was estimated using Shannon's index (S), heterozygosity (H) and gene diversity (h). These estimates revealed significant variation within populations, although a variance homogeneity test (HOMOVA) showed no significant differences among populations or between basins. Nei genetic distance values indicate a low genetic differentiation among populations. Analysis of molecular variance (AMOVA) indicates that most of the genetic diversity occurs within populations (91.4%), but that a statistically significant amount is found among populations (P < 0.001). Principal coordinates and cluster analyses of RAPD phenotypes show that specimens are not grouped by geographical origin. The genetic diversity found within L. geminis populations may be explained by its breeding system and an overlapping of generations. The scarce genetic differentiation among populations is likely to the low rate of DNA change that characterizes the lamprey group.

Mejía O; Polaco OJ; Zúñiga G

2004-11-01

284

Genetic diversity of Mexican brook lamprey Lampetra (Tetrapleurodon) geminis (Alvarez del Villar, 1966).  

Science.gov (United States)

Lampreys are the only surviving representatives of the oldest known vertebrates. The Mexican lamprey L. geminis (nonparasitic), is particularly interesting, because it is an endemic, biogeographical relict, and a threatened species. RAPD markers were used to describe genetic diversity in L. geminis. A total of 77 specimens were collected from five populations, three in the Río Grande de Morelia-Cuitzeo basin and two in the Río Duero-Lerma-Chapala basin, México. Eighty-eight RAPD markers were obtained from eight primers. Genetic diversity within each population was estimated using Shannon's index (S), heterozygosity (H) and gene diversity (h). These estimates revealed significant variation within populations, although a variance homogeneity test (HOMOVA) showed no significant differences among populations or between basins. Nei genetic distance values indicate a low genetic differentiation among populations. Analysis of molecular variance (AMOVA) indicates that most of the genetic diversity occurs within populations (91.4%), but that a statistically significant amount is found among populations (P < 0.001). Principal coordinates and cluster analyses of RAPD phenotypes show that specimens are not grouped by geographical origin. The genetic diversity found within L. geminis populations may be explained by its breeding system and an overlapping of generations. The scarce genetic differentiation among populations is likely to the low rate of DNA change that characterizes the lamprey group. PMID:15609555

Mejía, Omar; Polaco, Oscar J; Zúñiga, Gerardo

2004-11-01

285

Genetic diversity and evolution of Chinese traditional medicinal fungus Polyporus umbellatus (Polyporales, Basidiomycota).  

UK PubMed Central (United Kingdom)

BACKGROUND: Polyporus umbellatus is an important medicinal fungus distributed throughout most area of China. Its wide distribution may have resulted in substantial intraspecific genetic diversity for the fungus, potentially creating variation in its medical value. To date, we know little about the intraspecific genetic diversity of P. umbellatus. METHODOLOGY/PRINCIPAL FINDINGS: The objective of this research was to assess genetic differences of P. umbellatus from geographically diverse regions of China based on nrDNA ITS and 28S rRNA (LSU, large subunit) sequences. Significant sequence variations in the ITS and LSU sequences were detected. All sclerotial samples were clustered into four clades based on phylogenetic analysis of ITS, LSU and a combined data set of both regions. Heterogeneity of ITS and LSU sequences was detected in 5 and 7 samples respectively. All clone sequences clustered into the same clade except for one LSU clone sequences (from Henan province) which clustered into two clades (Clade I and Clade II). Significant genetic divergence in P. umbellatus was observed and the genetic diversification was greater among sclerotial samples from Shaanxi, Henan and Gansu provinces than among other provinces. Polymorphism of ITS and LSU sequences indicated that in China, P. umbellatus may spread from a center (Shaanxi, Henan and Gansu province) to other regions. CONCLUSIONS/SIGNIFICANCE: We found sclerotial samples of P. umbellatus contained levels of intraspecific genetic diversity. These findings suggested that P. umbellatus populations in Shaanxi, Henan and Gansu are important resources of genetic diversity and should be conserved accordingly.

Xing X; Ma X; Hart MM; Wang A; Guo S

2013-01-01

286

Genetic Diversity and Evolution of Chinese Traditional Medicinal Fungus Polyporus umbellatus (Polyporales, Basidiomycota)  

Science.gov (United States)

Background Polyporus umbellatus is an important medicinal fungus distributed throughout most area of China. Its wide distribution may have resulted in substantial intraspecific genetic diversity for the fungus, potentially creating variation in its medical value. To date, we know little about the intraspecific genetic diversity of P. umbellatus. Methodology/Principal Findings The objective of this research was to assess genetic differences of P. umbellatus from geographically diverse regions of China based on nrDNA ITS and 28S rRNA (LSU, large subunit) sequences. Significant sequence variations in the ITS and LSU sequences were detected. All sclerotial samples were clustered into four clades based on phylogenetic analysis of ITS, LSU and a combined data set of both regions. Heterogeneity of ITS and LSU sequences was detected in 5 and 7 samples respectively. All clone sequences clustered into the same clade except for one LSU clone sequences (from Henan province) which clustered into two clades (Clade I and Clade II). Significant genetic divergence in P. umbellatus was observed and the genetic diversification was greater among sclerotial samples from Shaanxi, Henan and Gansu provinces than among other provinces. Polymorphism of ITS and LSU sequences indicated that in China, P. umbellatus may spread from a center (Shaanxi, Henan and Gansu province) to other regions. Conclusions/Significance We found sclerotial samples of P. umbellatus contained levels of intraspecific genetic diversity. These findings suggested that P. umbellatus populations in Shaanxi, Henan and Gansu are important resources of genetic diversity and should be conserved accordingly.

Xing, Xiaoke; Ma, Xueting; Hart, Miranda M.; Wang, Airong; Guo, Shunxing

2013-01-01

287

Genetic Diversity in Commercial Rapeseed (Brassica napus L.) Varieties from Turkey as Revealed by RAPD  

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Full Text Available In cultivated commercial crop species, genetic diversity tends to decrease because of the extensive breeding processes. Therefore, germplasm of commercial crop species, such as Brassica napus L. should be evaluated and the genotypes, which have higher genetic diversity index, should be addressed as potential parental cross materials in breeding programs. In this study, the genetic diversity was analysed by using randomly amplified polymorphic DNA analysis (RAPD) technique in nine Turkish commercial rapeseed varieties. The RAPD primers (10-mer oligonucleotides) produced 51 scorable loci, 31 loci of which were polymorphic (60.78%) and 20 loci (39.22%) were monomorphic The RAPD bands were scored as binary matrix data and were analysed using POPGENE version 1.32. At locus level, the values of genetic diversity within population (Hs) and total (HT) were 0.15 and 0.19 respectively. The genetic differentiation (GST) and the gene flow (Nm) values between the populations were 0.20 and 2.05 respectively. The mean number of alleles (na), the mean number of effective alleles (nae), and the mean value of genetic diversity (He) were 2.00, 1.26, and 0.19 respectively. According to Pearson’s correlation, multiple regression and principal component analyses, eco-geographical conditions in combination had significant effect on genetic indices of commercial B. napus L. varieties were discussed.

Özlem ÖZBEK; Betül Uçar GIDIK

2013-01-01

288

Genetic diversity in Brazilian populations of Aedes albopictus  

Scientific Electronic Library Online (English)

Full Text Available Abstract in english Random amplified polymorphic DNA (RAPD) analysis technique was undertaken in Aedes albopictus populations from three states in Brazil, Rio de Janeiro (RJ), Minas Gerais (MG) and Pernambuco (PE), to estimate the level of genetic variability and levels of genetic exchange between populations. Allele and genotype frequencies were measured on 47 RAPD loci. Average observed heterozigosity (Ho) ranged from 0.282 in MG to 0.355 in Casa Forte (PE) population. Genetic distances es (more) timates indicated that RJ and MG were more genetically similar than populations from PE. Genetic variation observed in local Brazilian populations was attributed to genetic drift associated with restricted gene flow in recently established populations.

Ayres, CFJ; Romão, TPA; Melo-Santos, MAV; Furtado, AF

2002-09-01

289

Low level of genetic diversity in cultivated Pigeonpea compared to its wild relatives is revealed by diversity arrays technology.  

Science.gov (United States)

Understanding the distribution of genetic diversity among individuals, populations and gene pools is crucial for the efficient management of germplasm collections and breeding programs. Diversity analysis is routinely carried out using sequencing of selected gene(s) or molecular marker technologies. Here we report on the development of Diversity Arrays Technology (DArT) for pigeonpea (Cajanus cajan) and its wild relatives. DArT tests thousands of genomic loci for polymorphism and provides the binary scores for hundreds of markers in a single hybridization-based assay. We tested eight complexity reduction methods using various combinations of restriction enzymes and selected PstI/HaeIII genomic representation with the largest frequency of polymorphic clones (19.8%) to produce genotyping arrays. The performance of the PstI/HaeIII array was evaluated by typing 96 accessions representing nearly 20 species of Cajanus. A total of nearly 700 markers were identified with the average call rate of 96.0% and the scoring reproducibility of 99.7%. DArT markers revealed genetic relationships among the accessions consistent with the available information and systematic classification. Most of the diversity was among the wild relatives of pigeonpea or between the wild species and the cultivated C. cajan. Only 64 markers were polymorphic among the cultivated accessions. Such narrow genetic base is likely to represent a serious impediment to breeding progress in pigeonpea. Our study shows that DArT can be effectively applied in molecular systematics and biodiversity studies. PMID:16845522

Yang, Shiying; Pang, Wen; Ash, Gavin; Harper, John; Carling, Jason; Wenzl, Peter; Huttner, Eric; Zong, Xuxiao; Kilian, Andrzej

2006-07-15

290

High and Distinct Range-Edge Genetic Diversity despite Local Bottlenecks.  

Science.gov (United States)

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 Saccorhizapolyschides, 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. PMID:23967038

Assis, Jorge; Castilho Coelho, Nelson; Alberto, Filipe; Valero, Myriam; Raimondi, Pete; Reed, Dan; Alvares Serrão, Ester

2013-07-10

291

High and Distinct Range-Edge Genetic Diversity despite Local Bottlenecks.  

UK PubMed Central (United Kingdom)

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 Saccorhizapolyschides, 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.

Assis J; Castilho Coelho N; Alberto F; Valero M; Raimondi P; Reed D; Alvares Serrão E

2013-01-01

292

High and Distinct Range-Edge Genetic Diversity despite Local Bottlenecks  

Science.gov (United States)

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 Saccorhizapolyschides, 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.

Assis, Jorge; Castilho Coelho, Nelson; Alberto, Filipe; Valero, Myriam; Raimondi, Pete; Reed, Dan; Alvares Serrao, Ester

2013-01-01

293

Genetic diversity in Tunisia: a study based on the GM polymorphism of human immunoglobulins.  

Science.gov (United States)

The GM polymorphism of human immunoglobulins is analyzed in three Berber populations of southern Tunisia and compared to other GM data. Genetic diversity among Tunisian populations is higher than that among Europeans but does not exhibit any significant geographic or linguistic structure. This result suggests a complex pattern of genetic differentiation. PMID:15754972

Fadhlaoui-Zid, Karima; Dugoujon, Jean-Michel; Elgaaied, Amel; Amor, Mohamed Ben; Yacoubi, Besma; Elkhil, Houssien Kodjet; Sanchez-Mazas, Alicia

2004-08-01

294

Mitochondrial DNA-based genetic diversity of genus Lygus (Hemiptera: Miridae) in North America  

Science.gov (United States)

The genus Lygus is widely distributed in North American and Eurasian continents. It is the most-studied genus in the family Miridae. However, very less information on the genetic diversity of this genus is available. Studying genetic variation among Lygus pest species and thereby constructing a ...

295

Genetic diversity and invasion success of alien species: where are we and where should we go?  

Directory of Open Access Journals (Sweden)

Full Text Available Genetic diversity is hypothesized to affect the invasiveness of alien species. Although many alien species have experienced genetic bottlenecks during invasion, multiple introductions and intra- or inter- specific hybridization may result in high levels of genetic variation that are comparable to native conspecifics. This genetic variation could enable plants to adapt to novel habitats through rapid evolution. However, research has shown that genetic uniformity sometimes has little effect on invasiveness, and instead, may even aid successful invasion by some alien species. These results suggest that high levels of genetic diversity are not always necessary in biological invasions. In this review, we explore relationships between genetic diversity and successful invasions. We examine the possible mechanisms through which genetic diversity can influence the short-term success and long-term evolution of alien species. Additionally, we raise and discuss issues that deserve attention in future studies. Future research should unite invasion ecology and other ecological disciplines in order to deepen our understanding of the ecological and evolutionary processes involved with biological invasions.

Wen Shi; Yu-peng Geng; Xiaokun Ou

2010-01-01

296

Genetic diversity of carrot (Daucus carota L.) cultivars revealed by analysis of SSR loci  

Science.gov (United States)

In this work we evaluate a collection of 88 carrot cultivars and landraces for polymorphisms at SSR loci and use the obtained markers to assess the genetic diversity, and we show molecular evidence for divergence between Asiatic and Western carrot genetic pools. The use of primer pairs flanking repe...

297

Genetic Diversity of Some Populations of Iranian Melon Using SSR Markers  

Digital Repository Infrastructure Vision for European Research (DRIVER)

To study the genetic diversity of the melon collection at the National Plant Genetic of Iran, 35 genotypes were planted at Bu Ali Sina University Hamedan in 2004 and were evaluated with 15 micro satellite SSR markers. Micro satellite markers in the upper levels showed polymorphisms and 87% of th...

J.A. Kohpayegani; M. Behbahani

298

Mapping genetic diversity of cherimoya (Annona cherimola Mill.): application of spatial analysis for conservation and use of plant genetic resources.  

UK PubMed Central (United Kingdom)

There is a growing call for inventories that evaluate geographic patterns in diversity of plant genetic resources maintained on farm and in species' natural populations in order to enhance their use and conservation. Such evaluations are relevant for useful tropical and subtropical tree species, as many of these species are still undomesticated, or in incipient stages of domestication and local populations can offer yet-unknown traits of high value to further domestication. For many outcrossing species, such as most trees, inbreeding depression can be an issue, and genetic diversity is important to sustain local production. Diversity is also crucial for species to adapt to environmental changes. This paper explores the possibilities of incorporating molecular marker data into Geographic Information Systems (GIS) to allow visualization and better understanding of spatial patterns of genetic diversity as a key input to optimize conservation and use of plant genetic resources, based on a case study of cherimoya (Annona cherimola Mill.), a Neotropical fruit tree species. We present spatial analyses to (1) improve the understanding of spatial distribution of genetic diversity of cherimoya natural stands and cultivated trees in Ecuador, Bolivia and Peru based on microsatellite molecular markers (SSRs); and (2) formulate optimal conservation strategies by revealing priority areas for in situ conservation, and identifying existing diversity gaps in ex situ collections. We found high levels of allelic richness, locally common alleles and expected heterozygosity in cherimoya's putative centre of origin, southern Ecuador and northern Peru, whereas levels of diversity in southern Peru and especially in Bolivia were significantly lower. The application of GIS on a large microsatellite dataset allows a more detailed prioritization of areas for in situ conservation and targeted collection across the Andean distribution range of cherimoya than previous studies could do, i.e. at province and department level in Ecuador and Peru, respectively.

Zonneveld Mv; Scheldeman X; Escribano P; Viruel MA; Van Damme P; Garcia W; Tapia C; Romero J; Sigueñas M; Hormaza JI

2012-01-01

299

Mapping genetic diversity of cherimoya (Annona cherimola Mill.): application of spatial analysis for conservation and use of plant genetic resources.  

Science.gov (United States)

There is a growing call for inventories that evaluate geographic patterns in diversity of plant genetic resources maintained on farm and in species' natural populations in order to enhance their use and conservation. Such evaluations are relevant for useful tropical and subtropical tree species, as many of these species are still undomesticated, or in incipient stages of domestication and local populations can offer yet-unknown traits of high value to further domestication. For many outcrossing species, such as most trees, inbreeding depression can be an issue, and genetic diversity is important to sustain local production. Diversity is also crucial for species to adapt to environmental changes. This paper explores the possibilities of incorporating molecular marker data into Geographic Information Systems (GIS) to allow visualization and better understanding of spatial patterns of genetic diversity as a key input to optimize conservation and use of plant genetic resources, based on a case study of cherimoya (Annona cherimola Mill.), a Neotropical fruit tree species. We present spatial analyses to (1) improve the understanding of spatial distribution of genetic diversity of cherimoya natural stands and cultivated trees in Ecuador, Bolivia and Peru based on microsatellite molecular markers (SSRs); and (2) formulate optimal conservation strategies by revealing priority areas for in situ conservation, and identifying existing diversity gaps in ex situ collections. We found high levels of allelic richness, locally common alleles and expected heterozygosity in cherimoya's putative centre of origin, southern Ecuador and northern Peru, whereas levels of diversity in southern Peru and especially in Bolivia were significantly lower. The application of GIS on a large microsatellite dataset allows a more detailed prioritization of areas for in situ conservation and targeted collection across the Andean distribution range of cherimoya than previous studies could do, i.e. at province and department level in Ecuador and Peru, respectively. PMID:22253801

Zonneveld, Maarten van; Scheldeman, Xavier; Escribano, Pilar; Viruel, María A; Van Damme, Patrick; Garcia, Willman; Tapia, César; Romero, José; Sigueñas, Manuel; Hormaza, José I

2012-01-09

300

Parental selection of wheat lines based on phenotypic characterization and genetic diversity  

Directory of Open Access Journals (Sweden)

Full Text Available Parental selection is an important step in breeding programs, and genetic variability increases the chances of obtaining variance in progenies. The objectives of this study were to phenotype 29 wheat genotypes and determine the genetic variability among them, in order to identify potential parental lines for breeding programs at Embrapa Wheat. For phenotyping, traits such as plant height, cycle and grains characteristics were assessed and the data were analyzed by the Euclidean distance. The genetic distance was estimated using 97 microsatellite molecular markers and the data were analyzed by Nei72 coefficient. The average distance observed for phenotyping was 10.1, and the genetic distance was 31 %. SSR markers were efficient for selecting genetically diverse genotypes despite their phenotypic similarity, and lines PF 9027, PF 950351, PF 030132, PF 979002, PF 040488 and IWT 04019 can be used as parental for future crosses, since they have genetic diversity and suitable agronomic traits.

Alice Casassola; Sandra Patussi Brammer; Márcia Soares Chaves; Paula Wiethölter; Eduardo Caierão

2013-01-01

 
 
 
 
301

Genetic Diversity and Population Structure of Rice Pathogen Ustilaginoidea virens in China  

Science.gov (United States)

Rice false smut caused by the fungal pathogen Ustilaginoideavirens is becoming a destructive disease throughout major rice-growing countries. Information about its genetic diversity and population structure is essential for rice breeding and efficient control of the disease. This study compared the genome sequences of two U. virens isolates. Three SNP-rich genomic regions were identified as molecular markers that could be used to analyze the genetic diversity and population structure of U. virens in China. A total of 56 multilocus sequence types (haplotypes) were identified out of 162 representative isolates from 15 provinces covering five major rice-growing areas in China. However, the phylogeny, based on sequences at individual SNP-rich regions, strongly conflicted with each other and there were significant genetic differences between different geographical populations. Gene flow between the different geographical populations and genetic differentiation within each geographical population were also detected. In addition, genetic recombination and genetic isolation resulting from geographic separation was also found.

Tan, Xinqiu; Yu, Yufei; He, Haiyong; Zhang, Xinyu; Liu, Yongfeng; Wang, Shu; Sun, Wenxian; Cai, Lei; Li, Shaojie

2013-01-01

302

Mining for Optimised Data Using Clustering Along with Fuzzy Association Rules and Genetic Algorithms  

Directory of Open Access Journals (Sweden)

Full Text Available Data mining also known as knowledge discovery in databases has been recognized as a promising newarea for database research. The proposed work in this paper is about optimizing the data with clusteringand fuzzy association rules using multi-objective genetic algorithms. This algorithm is implemented in twophases. In the first phase it optimizes the data to reduce the number of comparisons using clustering. Inthe second phase it is implemented with multi-objective genetic algorithms to find the optimum number offuzzy association rules using threshold value and fitness function.

G.V.S.N.R.V.Prasad; Y. Dhanalakshmi; V.Vijaya Kumar; I. Ramesh Babu

2010-01-01

303

Opportunities for text mining in the FlyBase genetic literature curation workflow.  

UK PubMed Central (United Kingdom)

FlyBase is the model organism database for Drosophila genetic and genomic information. Over the last 20 years, FlyBase has had to adapt and change to keep abreast of advances in biology and database design. We are continually looking for ways to improve curation efficiency and efficacy. Genetic literature curation focuses on the extraction of genetic entities (e.g. genes, mutant alleles, transgenic constructs) and their associated phenotypes and Gene Ontology terms from the published literature. Over 2000 Drosophila research articles are now published every year. These articles are becoming ever more data-rich and there is a growing need for text mining to shoulder some of the burden of paper triage and data extraction. In this article, we describe our curation workflow, along with some of the problems and bottlenecks therein, and highlight the opportunities for text mining. We do so in the hope of encouraging the BioCreative community to help us to develop effective methods to mine this torrent of information. DATABASE URL: http://flybase.org

McQuilton P

2012-01-01

304

Genetic Diversity in Mazandaranian Native Cattle: A Comparison with Holstein Cattle, using ISSR Marker  

Directory of Open Access Journals (Sweden)

Full Text Available This study was carried out to investigate genetic diversity in Mazandaranian native cattle population comparised to the Holstein breed, using Inter Simple Sequence Repeats (ISSR) marker. A total of 175 animals, including 71 native and 104 cattle of Holstein breed were screened. The extraction of DNA samples were carried out, using modified salting out method. A 19-mer oligonucleotide, (GA)9C, was used as primer in PCR reactions. The PCR products showed 15 different fragments with length ranged from 120 to1600 bp in the two breeds.. Genetic variation indexes, including effective number of alleles, Shannon index, Nei’s gene diversity and standard genetic distance were estimated, using POPGene software. Generally, the estimated genetic variation indexes showed low levels of diversity in the two breeds. However, Nei's gene diversity and Shannon index estimation was observed almost two folds in native cattle compared to Holstein breed. Less levels of diversity in Holstein cattle may be because of applying intensive selection programs. Conversely, native cattle have been less affected by selection. Therefore, it seems that Mazandaranian native cattle probably are better for breeding programs than Holstein cattle. Results showed that ISSR Markers are reliable and can be used in genetic diversity investigations.

S. Pashaei; M.A. Azari; S. Hasani; A. Khanahmadi; J. Rostamzadeh

2009-01-01

305

Do farmers reduce genetic diversity when they domesticate tropical trees? A case study from Amazonia.  

UK PubMed Central (United Kingdom)

Agroforestry ecosystems may be an important resource for conservation and sustainable use of tropical trees, but little is known of the genetic diversity they contain. Inga edulis, a widespread indigenous fruit tree in South America, is used as a model to assess the maintenance of genetic diversity in five planted vs. five natural stands in the Peruvian Amazon. Analysis of five SSR (simple sequence repeat) loci indicated lower allelic variation in planted stands [mean corrected allelic richness 31.3 (planted) and 39.3 (natural), P = 0.009]. Concerns regarding genetic erosion in planted Amazonian tree stands appear valid, although allelic variation on-farm is still relatively high.

Hollingsworth PM; Dawson IK; Goodall-Copestake WP; Richardson JE; Weber JC; Sotelo Montes C; Pennington RT

2005-02-01

306

Do farmers reduce genetic diversity when they domesticate tropical trees? A case study from Amazonia.  

Science.gov (United States)

Agroforestry ecosystems may be an important resource for conservation and sustainable use of tropical trees, but little is known of the genetic diversity they contain. Inga edulis, a widespread indigenous fruit tree in South America, is used as a model to assess the maintenance of genetic diversity in five planted vs. five natural stands in the Peruvian Amazon. Analysis of five SSR (simple sequence repeat) loci indicated lower allelic variation in planted stands [mean corrected allelic richness 31.3 (planted) and 39.3 (natural), P = 0.009]. Concerns regarding genetic erosion in planted Amazonian tree stands appear valid, although allelic variation on-farm is still relatively high. PMID:15660940

Hollingsworth, P M; Dawson, I K; Goodall-Copestake, W P; Richardson, J E; Weber, J C; Sotelo Montes, C; Pennington, R T

2005-02-01

307

Genetic Diversity among Flue-cured Tobacco Cultivars Based on RAPD and AFLP Markers  

Directory of Open Access Journals (Sweden)

Full Text Available The aim of this work was to study the genetic diversity among flue-cured tobacco cultivars. RAPD and AFLP analyses were used to assess the genetic similarity among selected accessions of flue-cured tobacco. Seventy eight RAPD and 154 AFLP polymorphic bands were obtained and used to assess the genetic diversity among 28 tobacco accessions. The cultivar relationships were estimated through the cluster analysis (UPGMA) based on RAPD data and AFLP data. The accessions were grouped into three major clusters and these shared common ancestry clustered together.

Han Yao Zhang; Xiao Zhen Liu; Chuan Sheng He; Yu Ming Yang

2008-01-01

308

Genetic Diversity among Flue-cured Tobacco Cultivars Based on RAPD and AFLP Markers  

Scientific Electronic Library Online (English)

Full Text Available Abstract in english The aim of this work was to study the genetic diversity among flue-cured tobacco cultivars. RAPD and AFLP analyses were used to assess the genetic similarity among selected accessions of flue-cured tobacco. Seventy eight RAPD and 154 AFLP polymorphic bands were obtained and used to assess the genetic diversity among 28 tobacco accessions. The cultivar relationships were estimated through the cluster analysis (UPGMA) based on RAPD data and AFLP data. The accessions were grouped into three major clusters and these shared common ancestry clustered together.

Zhang, Han Yao; Liu, Xiao Zhen; He, Chuan Sheng; Yang, Yu Ming

2008-12-01

309

Genetic Diversity of Some Mediterranean Populations of the Cultivated Alfalfa (Medicago sativa L.) Using ISSR Markers  

Directory of Open Access Journals (Sweden)

Full Text Available The genetic diversity within 29 populations, when 15 populations are local originating in the Tunisian south and 12 introduced of Italy, Austerely, France and Morocco, was analysed by ISSR markers (Inter Simple Repeat sequence). The genetic similarity between these various populations is estimated by the index of Rogers and Tanimoto. Genetic diversity is analyzed by one statistical procedure: hierarchical classification. The total number of bands varied between the various populations from 9-16. The percentage of total polymorphism is about 60%. Four large groups were obtained.

L. Touil; F. Guesmi; K. Fares; A. Ferchichi

2008-01-01

310

Mining  

Energy Technology Data Exchange (ETDEWEB)

Mechanisation in US coal mining has advanced so far that 80% of the minerals required by the US industries are produced by less than 1% of the working population. The development of mechanisation is described using the example of the coal mining sector.

Marovelli, R.L.; Karhnak, J.M.

1982-11-01

311

Effect of fluoride pollution on genetic diversity of a medicinal tree, Syzygium cumini.  

UK PubMed Central (United Kingdom)

Syzygium cumini Linn. (Myrtaceae) is a medicinal tree (Jamun) used worldwide in treatment of diabetes. However, no molecular data is available on genetic polymorphism and its relationship, if any with fluoride pollution. In the present study, the genetic variability of two populations of S. cumini growing in fluoride rich soils and normal soils located in Rajasthan and Haryana regions of India, respectively was determined using random amplified polymorphic DNA (RAPD) markers. Different measures of diversity in Rajasthan populations: Shannon's index of phenotypic diversity (I) = 0.440; Nei's genetic diversity (h) = 0.292; effective number of alleles per locus (Ne) = 1.497; total species diversity (Hsp) = 0.307 and within population diversity (Hpop) = 0.158 showed high diversity in comparison to Haryana populations. Thus, it seems that Rajasthan population responds with increased genetic variation resulting possibly from new mutation that affect allele frequencies as a consequence of adaptation to contaminated environment. This may imply that the increased diversity levels may act as a buffer to combat fluoride stress. Cluster analysis and principal component analysis (PCA) results showed mixing between the populations.

Khan S; Baunthiyal M; Kumari A; Sharma V

2012-07-01

312

Effect of fluoride pollution on genetic diversity of a medicinal tree, Syzygium cumini.  

Science.gov (United States)

Syzygium cumini Linn. (Myrtaceae) is a medicinal tree (Jamun) used worldwide in treatment of diabetes. However, no molecular data is available on genetic polymorphism and its relationship, if any with fluoride pollution. In the present study, the genetic variability of two populations of S. cumini growing in fluoride rich soils and normal soils located in Rajasthan and Haryana regions of India, respectively was determined using random amplified polymorphic DNA (RAPD) markers. Different measures of diversity in Rajasthan populations: Shannon's index of phenotypic diversity (I) = 0.440; Nei's genetic diversity (h) = 0.292; effective number of alleles per locus (Ne) = 1.497; total species diversity (Hsp) = 0.307 and within population diversity (Hpop) = 0.158 showed high diversity in comparison to Haryana populations. Thus, it seems that Rajasthan population responds with increased genetic variation resulting possibly from new mutation that affect allele frequencies as a consequence of adaptation to contaminated environment. This may imply that the increased diversity levels may act as a buffer to combat fluoride stress. Cluster analysis and principal component analysis (PCA) results showed mixing between the populations. PMID:23360002

Khan, Suphiya; Baunthiyal, Mamta; Kumari, Alka; Sharma, Vinay

2012-07-01

313

Plasmodium falciparum populations from northeastern Myanmar display high levels of genetic diversity at multiple antigenic loci.  

Science.gov (United States)

Levels of genetic diversity of the malaria parasites and multiclonal infections are correlated with transmission intensity. In order to monitor the effect of strengthened malaria control efforts in recent years at the China-Myanmar border area, we followed the temporal dynamics of genetic diversity of three polymorphic antigenic markers msp1, msp2, and glurp in the Plasmodium falciparum populations. Despite reduced malaria prevalence in the region, parasite populations exhibited high levels of genetic diversity. Genotyping 258 clinical samples collected in four years detected a total of 22 PCR size alleles. Multiclonal infections were detected in 45.7% of the patient samples, giving a minimum multiplicity of infection of 1.41. The majority of alleles experienced significant temporal fluctuations through the years. Haplotype diversity based on the three-locus genotypes ranged from the lowest in 2009 at 0.33 to the highest in 2010 at 0.80. Sequencing of msp1 fragments from 36 random samples of five allele size groups detected 13 different sequences, revealing an additional layer of genetic complexity. This study suggests that despite reduced prevalence of malaria infections in this region, the parasite population size and transmission intensity remained high enough to allow effective genetic recombination of the parasites and continued maintenance of genetic diversity. PMID:23000544

Yuan, Lili; Zhao, Hui; Wu, Lanou; Li, Xiaomei; Parker, Daniel; Xu, Shuhui; Zhao, Yousheng; Feng, Guohua; Wang, Ying; Yan, Guiyun; Fan, Qi; Yang, Zhaoqing; Cui, Liwang

2012-09-20

314

Plasmodium falciparum populations from northeastern Myanmar display high levels of genetic diversity at multiple antigenic loci.  

UK PubMed Central (United Kingdom)

Levels of genetic diversity of the malaria parasites and multiclonal infections are correlated with transmission intensity. In order to monitor the effect of strengthened malaria control efforts in recent years at the China-Myanmar border area, we followed the temporal dynamics of genetic diversity of three polymorphic antigenic markers msp1, msp2, and glurp in the Plasmodium falciparum populations. Despite reduced malaria prevalence in the region, parasite populations exhibited high levels of genetic diversity. Genotyping 258 clinical samples collected in four years detected a total of 22 PCR size alleles. Multiclonal infections were detected in 45.7% of the patient samples, giving a minimum multiplicity of infection of 1.41. The majority of alleles experienced significant temporal fluctuations through the years. Haplotype diversity based on the three-locus genotypes ranged from the lowest in 2009 at 0.33 to the highest in 2010 at 0.80. Sequencing of msp1 fragments from 36 random samples of five allele size groups detected 13 different sequences, revealing an additional layer of genetic complexity. This study suggests that despite reduced prevalence of malaria infections in this region, the parasite population size and transmission intensity remained high enough to allow effective genetic recombination of the parasites and continued maintenance of genetic diversity.

Yuan L; Zhao H; Wu L; Li X; Parker D; Xu S; Zhao Y; Feng G; Wang Y; Yan G; Fan Q; Yang Z; Cui L

2013-01-01

315

Genetic diversity and variation among botanical varieties of old Portuguese wheat cultivars revealed by ISSR assays.  

Science.gov (United States)

Inter-simple sequence repeats (ISSRs) were used for genetic diversity analyses of an Old Portuguese wheat collection. Eighteen primers produced 96.3 and 98.5% of ISSR polymorphism in bread and durum wheat cultivars, respectively. The unweighted pair group method with arithmetical averages (UPGMA) phenogram clearly split all cultivars based on their species/ploidy, reflecting a defined genetic structure. ISSRs revealed high genetic diversity at interspecific, intraspecific, and intercultivar levels. Thirty-three exclusive ISSR markers were found. Cultivars were clustered according to their botanical varieties and, in a few cases, with their homonym(s). No statistically significant differences were found between genetic diversity parameters of durum and bread wheat, probably due to high intraspecific diversity. Similar analyses were performed among botanical varieties, and their relationships were defined. Cladograms resembled UPGMA clustering. This highly genetically diverse Old wheat collection will be conserved and maintained, and it could be further used in breeding programs to widen the narrow genetic basis of modern wheat varieties and to avoid the loss of rare and unique alleles. PMID:19184405

Carvalho, Ana; Lima-Brito, José; Maçãs, Benvindo; Guedes-Pinto, Henrique

2009-01-31

316

Genetic diversity and variation among botanical varieties of old Portuguese wheat cultivars revealed by ISSR assays.  

UK PubMed Central (United Kingdom)

Inter-simple sequence repeats (ISSRs) were used for genetic diversity analyses of an Old Portuguese wheat collection. Eighteen primers produced 96.3 and 98.5% of ISSR polymorphism in bread and durum wheat cultivars, respectively. The unweighted pair group method with arithmetical averages (UPGMA) phenogram clearly split all cultivars based on their species/ploidy, reflecting a defined genetic structure. ISSRs revealed high genetic diversity at interspecific, intraspecific, and intercultivar levels. Thirty-three exclusive ISSR markers were found. Cultivars were clustered according to their botanical varieties and, in a few cases, with their homonym(s). No statistically significant differences were found between genetic diversity parameters of durum and bread wheat, probably due to high intraspecific diversity. Similar analyses were performed among botanical varieties, and their relationships were defined. Cladograms resembled UPGMA clustering. This highly genetically diverse Old wheat collection will be conserved and maintained, and it could be further used in breeding programs to widen the narrow genetic basis of modern wheat varieties and to avoid the loss of rare and unique alleles.

Carvalho A; Lima-Brito J; Maçãs B; Guedes-Pinto H

2009-04-01

317

Hitchhiker’s guide to genetic diversity in socially structured populations  

Directory of Open Access Journals (Sweden)

Full Text Available When selection increases the frequency of a beneficial gene substitution it can also increase the frequencies of linked neutral alleles through a process called genetic hitchhiking. A model built to investigate reduced genetic diversity in Pleistocene hominins shows that genetic hitchhiking can have a strong effect on neutral diversity in the presence of culturally mediated migration. Under conditions in which genetic and cultural variants are transmitted symmetrically, neutral genes may also hitchhike to higher frequencies on the coattails of adaptive cultural traits through a process called cultural hitchhiking. Cultural hitchhiking has been proposed to explain why some species of matrilineal whales display relatively low levels of mitochondrial DNA diversity, and it may be applicable to humans as well. This paper provides a critical review of recent models of both types of hitch­­hi­king in socially structured populations. The models’ assumptions and predictions are compared and discussed in the hope that studies of reduced genetic diversity in humans might improve our understanding of reduced genetic diversity in other species, and vice versa [Current Zoology 58 (1): 287-297, 2012].

L. S. PREMO

2012-01-01

318

Assessment of genetic diversity and population structure of Vietnamese indigenous cattle populations by microsatellites  

DEFF Research Database (Denmark)

Cattle play a very important role in agriculture and food security in Vietnam. A high level of cattle diversity exists and serves different needs of Vietnamese cattle keepers but has not yet been molecularly characterized. This study evaluates the genetic diversity and structure of Vietnamese indigenous cattle populations, using microsatellite markers. A total of 410 individuals from six indigenous cattle populations and an exotic breed was characterized using 27 microsatellite markers A total of 362 alleles was detected and the number of alleles per locus ranged from 8 (INRA005 and ILSTS005) to 17 (ETH185). The level of gene diversity was high indicated by a mean expected heterozygosity (He) across populations and loci of 0.73. Level of inbreeding (mean FIS=0.05) and genetic differentiation (mean FST=0.04) was moderate. The phylogenetic tree based on Reynolds genetic distance reflected geographic distances. Structure analysis indicated five homogeneous clusters. The Brahman, Lang Son, Ha Giang and U Dau Riu cattle were assigned to independent clusters while Nghe An, Thanh Hoa and Phu Yen cattle were grouped in a single cluster. We conclude that Vietnamese indigenous cattle have high levels of genetic diversity and distinct genetic structures. Based on these results, we recommend that for conservation homogenous populations (Nghe An, Thanh Hoa and Phu Yen) can be grouped to reduce costs and U Dau Riu, Lang Son and Ha Giang populations should be conserved separately to avoid loss of genetic diversity.

Pham, Lan Doan; Do, Duy Ngoc

2013-01-01

319

Extensive intra-host genetic diversity uncovered in Cryptosporidium parvum using Next Generation Sequencing.  

UK PubMed Central (United Kingdom)

The theory about the Cryptosporidium life cycle predicts genetic diversity of sporozoites within the host. Nevertheless, the Cryptosporidium intra-host genetic diversity is difficult to study using conventional Sanger sequencing or electrophoretic resolution of amplicons, due to the methods' inability to resolve mixtures of templates. We analysed the within-isolate genetic diversity of two Cryptosporidium parvum isolates sharing common descent, by combining the use of Next Generation Sequencing and cloning of PCR amplicons with database searches. The analysis focused on the single-copy 70 kDa heat shock protein (HSP70) and the 60kDa surface glycoprotein (gp60) genes, which allowed any diversity to be ascribed to the presence of a heterogeneous population of sporozoites. The results indicated an unprecedented intra-host genetic diversity, with two HSP70 and 10 gp60 alleles in these isolates, in spite of the initial resolution of one allele per locus using Sanger sequencing. At both loci, the predominant alleles were those initially identified by Sanger sequencing. A significant (p<0.01) overrepresentation of gp60 alleles previously reported in New Zealand was observed. These results further our understanding of the genetic structure of C. parvum populations, and expose the limitations of the use of non-axenic isolates as operational taxonomic units of genetic studies of cryptosporidiosis.

Grinberg A; Biggs PJ; Dukkipati VS; George TT

2013-04-01

320

Stress-related hormones and genetic diversity in sea otters (Enhydra lutris)  

Science.gov (United States)

Sea otters (Enhydra lutris) once ranged throughout the coastal regions of the north Pacific, but were extirpated throughout their range during the fur trade of the 18th and 19th centuries, leaving only small, widely scattered, remnant populations. All extant sea otter populations are believed to have experienced a population bottleneck and thus have lost genetic variation. Populations that undergo severe population reduction and associated inbreeding may suffer from a general reduction in fitness termed inbreeding depression. Inbreeding depression may result in decreased testosterone levels in males, and reduced ability to respond to stressful stimuli associated with an increase in the stress-related adrenal glucocorticoid hormones, cortisol and corticosterone. We investigated correlations of testosterone, cortisol, and corticosterone with genetic diversity in sea otters from five populations. We found a significant negative correlation between genetic diversity and both mean population-level (r2 = 0.27, P < 0.001) and individual-level (r2 = 0.54, P < 0.001) corticosterone values, as well as a negative correlation between genetic diversity and cortisol at the individual level (r2 = 0.17, P = 0.04). No relationship was found between genetic diversity and testosterone (P = 0.57). The strength of the correlations, especially with corticosterone, suggests potential negative consequences for overall population health, particularly for populations with the lowest genetic diversity. ?? 2009 by the Society for Marine Mammalogy.

Larson, S.; Monson, D.; Ballachey, B.; Jameson, R.; Wasser, S. K.

2009-01-01

 
 
 
 
321

Description and analysis of genetic diversity among squash accessions  

Scientific Electronic Library Online (English)

Full Text Available Abstract in portuguese A abobrinha de inverno compõe um cultivo agrícola com valor econômico determinado exercendo, no entanto, um papel importante em zonas caracterizadas por um cultivo menos intensivo. Na Grécia, o cultivo da abobrinha se baseia, principalmente, em variedades locais conservadas a muitos anos por agricultores locais. Uma parte do cultivo nuclear da abobrinha, que é conservada pelo Banco Grego de Genes, foi melhorada utilizando-se dados morfológicos e moleculares, especia (more) lmente dezesseis cultivos de abobrinha classificados incompletamente, que foram diferenciados apenas com base em características morfológicas, em relação a uma avaliação à resistência contra o Fusarium Oxysporum, em dois isolamentos. Foi realizada uma análise molecular utilizando DNA Polimórficos Casual Amplificados índices (RAPDs), revelando um alto nível de polimorfismo. Para estudar a diversidade genética entre a coleção de abobrinhas, um procedimento de agrupamento foi realizado usando-se o algoritmo U.P.G.M.A. Dois dendrogramas independentes, um morfofisiológico e outro para dados moleculares, foram coletados, classificando as coleções em dois e três grupos básicos, respectivamente. Apesar do número diferente dos grupos, foram introduzidas muitas semelhanças entre os dois dendrogramas e um terceiro dendrograma foi produzido como resultado da combinação dos dois primeiros, baseado na distância de Gower e no algoritmo de agrupamento U.P.G.M.A. Para determinar o número ótimo dos grupos, a aproximação "upper tail" foi aplicada. O grupo mais aceitável das coleções foi conseguido usando-se índices RAPD, assim como a combinação dos dois grupos de dados diferentes, classificando as coleções em três grupos consideravelmente diferentes. Os grupos que correspondem às três espécies cultivadas diferentemente, que correspondem às três espécies cultivadas diferentemente por C.máxima Duch., C.moschata Duch. e C. pepo L. além disso, os mesmos resultados foram conseguidos usando-se a "Principal Component Analysis". Abstract in english In this work, the part of the squash core collection, maintained in the Greek Gene Bank, was assessed using the morphological and molecular data. Sixteen incompletely classified accessions of the squash were characterized along with an evaluation of their resistance against two isolates of Fusarium oxysporum. A molecular analysis using Random Amplified Polymorphic DNA (RAPD) markers was also performed, revealing high level of polymorphism. To study the genetic diversity a (more) mong the squash accessions, a clustering procedure using Unweighed Pair Group Method and Arithmetic Average (UPGMA) algorithm was also adopted. Two independent dendrograms, one for the morphophysiological and one for molecular data were obtained, classifying the accessions into two and three main clusters, respectively. Despite the different number of the clusters there were many similarities between these two dendrograms, and a third dendrogram resulting from their combination was also produced, based on Gower's distance and UPGMA clustering algorithm. In order to determine the optimal number of clusters, the upper tail approach was applied. The more reliable clustering of the accessions was accomplished using RAPD markers as well as the combination of the two different data sets, classifying the accessions into three significantly different groups. These groups corresponded to the three different cultivated species of C. maxima Duch., C. moschata Duch., and C. pepo L. The same results were also obtained using Principal Component Analysis.

Tsivelikas, Athanasios L.; Koutita, Olga; Anastasiadou, Anastasia; Skaracis, George N.; Traka-Mavrona, Ekaterini; Koutsika-Sotiriou, Metaxia

2009-04-01

322

Genetic diversity and population structure of Teucrium polium (Lamiaceae) in Tunisia.  

UK PubMed Central (United Kingdom)

Random amplified polymorphic DNA markers were used to assess the genetic diversity within and among seven Tunisian diploid and polyploid populations of Teucrium polium L. from five bioclimatic areas. Out of the 141 bands generated from eight selected primers, 124 were polymorphic. The genetic diversity within a population (Shannon's index) was high and varied according both the ploidal levels and bioclimatic zones. The genetic differentiation among populations assessed by G (ST) and Phi(ST) statistics was high, suggesting a low level of gene flow among them. The major proportion of the variation was attributable to individual differences within populations. The UPGMA analysis based on Nei and Li's coefficient showed that individuals from each population clustered together. In a dendrogram using the Phi(ST) distance matrix, population grouping is concordant with bioclimates and cytotypes. Conservation strategies should take into account the level of the genetic diversity of the populations according to their bioclimate and ploidal levels.

Boulila A; Béjaoui A; Messaoud C; Boussaid M

2010-02-01

323

Genetic diversity and population structure of Teucrium polium (Lamiaceae) in Tunisia.  

Science.gov (United States)

Random amplified polymorphic DNA markers were used to assess the genetic diversity within and among seven Tunisian diploid and polyploid populations of Teucrium polium L. from five bioclimatic areas. Out of the 141 bands generated from eight selected primers, 124 were polymorphic. The genetic diversity within a population (Shannon's index) was high and varied according both the ploidal levels and bioclimatic zones. The genetic differentiation among populations assessed by G (ST) and Phi(ST) statistics was high, suggesting a low level of gene flow among them. The major proportion of the variation was attributable to individual differences within populations. The UPGMA analysis based on Nei and Li's coefficient showed that individuals from each population clustered together. In a dendrogram using the Phi(ST) distance matrix, population grouping is concordant with bioclimates and cytotypes. Conservation strategies should take into account the level of the genetic diversity of the populations according to their bioclimate and ploidal levels. PMID:20094842

Boulila, Abdennacer; Béjaoui, Afef; Messaoud, Chokri; Boussaid, Mohamed

2009-11-22

324

Genetic diversity among the land races of sorghum collected in Tamil Nadu  

Directory of Open Access Journals (Sweden)

Full Text Available Sixty three local land races of sorghum (Sorghum bicolor L.) collected from different parts of Tamil Nadu were evaluated fortheir genetic diversity based on nine characters. The genotypes were grouped into 14 clusters indicating high genetic divergenceamong them. The study indicated no definite relationship between geographic and genetic diversity and geographic diversitycannot be used as an index of genetic diversity. Based on the inter cluster distance and cluster mean for various characters itcould be seen that the clusters VI, X, XII were the most divergent from the other clusters. The genotypes from these parentspossibly be utilized for hybridization programme. Days to flowering, plant height, ear head length and grain weight contributed

K. Ganesamurthy D. Punitha and M. Elangovan

2010-01-01

325

Assessing Genetic Diversity Based on Gliadin Proteins in Aegilops cylindrica Populations from Northwest of Iran  

Directory of Open Access Journals (Sweden)

Full Text Available Wild wheat progenitors served as a valuable gene pool in breeding perspectives. In this respect, gliadins could be an important tool in assessing genetic variability as protein markers. Thus, genetic diversity of gliadin protein patterns in seventeen populations of Aegilops cylindrica collected from northwest of Iran were investigated using acid polyacrylamide gel electrophoresis. Results showed that the highest number of bands in the electrophoregrams were related to the ? type of geliadins. Conversely, the lowest number of bands were pertained to the ? type of gliadins. Genetic diversity between populations was greater than within population variation. Assessment of total variation for the three gliadin types indicated that the highest total variation was related to ? type while, the lowest one was belonged to ? type. Cluster analysis using complete linkage method divided populations into two separated groups in which genetic diversity does not follow from geographical distribution.

Toraj KHABIRI; Rasool ASGHARI-ZAKARIA; Nasser ZARE; Omid SOFALIAN

2013-01-01

326

Exploration of intra- and inter-population genetic diversity in Hedysarum coronarium L. by AFLP markers.  

UK PubMed Central (United Kingdom)

Amplified fragment length polymorphism (AFLP) markers were used to characterize the genetic diversity within and among natural populations and cultivars of Hedysarum coronarium. Twelve populations within Tunisia were evaluated with three AFLP primer combinations. A total of 207 reproducible bands was detected of which 178 (86%) were polymorphic. The great discriminative power of AFLP markers and their ability to represent genetic relationships among Hedysarum plants was demonstrated. Genetic diversity within and among populations was assessed through Principal Component Analysis (PCA) and cluster analysis by using the Neighbor-joining clustering algorithm. AFLP technology has provided evidence of a high degree of intra- and inter-population genetic diversity in H. coronarium. AFLP banding patterns provided molecular markers correlated with the plants' geotropism. In addition, AFLP markers can differentiate wild accessions from cultivars. Moreover, geographical origins did not correspond to population clustering.

Marghali S; Panaud O; Lamy F; Ghariani S; Sarr A; Marrakchi M; Trifi-Farah N

2005-05-01

327

Assessment of genetic diversity in maize inbred lines using RAPD markers  

Directory of Open Access Journals (Sweden)

Full Text Available RAPD molecular markers were used to analyze genetic diversity between 16 corn lines. Twenty-two primerswere used resulting in the amplification of 265 fragments, of which 237 (84.44%) were polymorphic. Using the UPGMAmethod the genetic associations obtained showed 5 distinct heterotic groups. A principal coordinates analysis also showed anassociation of lines in 5 groups, in agreement with the results observed in the dendrogram. A bootstrap procedure wasapplied to verify whether the amount of markers used was sufficient to ensure reliability of the results, the procedure showeda coefficient of variation of 8.3%, suggesting that the markers were sufficient to assess genetic diversity between the analyzedlines. The high rate of polymorphism between lines revealed by RAPD markers indicated that the method is efficient to analyzegenetic diversity in corn lines and that the genetic divergence can be used to establish consistent heterotic groups between cornlines.

Daniela Cristina Bruel; Valeria Carpentieri-Pípolo; Claudete de Fátima Ruas; Antonio Carlos Gerage; Silvia Graciele Hülse de Souza

2007-01-01

328

Measurement of genetic diversity of virulence in populations of Xanthomonas oryzae pv. oryzae in India  

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Full Text Available This work was designed to ascertain the extent of genetic diversity in the pathogen population of Xanthomonas oryzae pv. oryzae (Xoo), the causal organism of bacterial blight of rice. The virulence of 52 strains of Xoo, collected from 12 rice growing states of India, were clip-inoculated on 16 rice genotypes possessing known genes for resistance. Based on the genetic distance, estimated by multivariate analysis isolates of Xoo could be classified into 13 clusters and five broad groups. The genetic variability of virulence in populations of Xoo was also measured by estimation of diversity indices viz. Shannon’s information function (H’), Levin’s diversity index (B), Hill’s generalized entropy (H2), trophic diversity index (D), dominance of virulence factors (?), the index of evenness or equitability (JH,), genetic richness index (d) and normalized pathotypic diversity index (Hn). Wide genetic diversity in the pathogen populations from the country as well as from the eastern and southern regions was indicated by high estimates of H', B, H2, D, ?, d and low JH,. High estimates of Hn were attained for almost all populations of Xoo. With regard to the states, genotypic and pathotypic diversities were high in Andhra Pradesh and Orissa, while pathotypic diversity was high in the pathogen population from Gujarat, Punjab, Madhya Pradesh, Uttar Pradesh and Tamil Nadu. The existence of high diversities and the grouping of the pathogen isolates into clusters of similar in virulence facilitated a better understanding of the population structure of Xoo, to guide regional rice breeding programs and the deployment of resistance genes in disease control strategy.

Debabrata Nayak; Lotan K. Bose; Udaya D. Singh; Sanjay Singh; Parsuram Nayak

2008-01-01

329

Genetic diversity of indigenous Rhizobium leguminosarum bv. viciae isolates nodulating two different host plants during soil restoration with alfalfa  

Energy Technology Data Exchange (ETDEWEB)

A total of 360 Rhizobium leguminosarum bv. viciae strains was isolated from three brown-coal mining restoration fields of different age and plant cover (without and in the first and second year of alfalfa, Medicago sativa, cultivation) using two host species (Vicia hirsuta and Pisum sativum) as capture plants. The strains were genetically typed by restriction fragment length polymorphism analysis of polymerase chain reaction (PCR)-generated 16S-23S ribosomal DNA intergenic spacer regions (IGS-RFLP) and characterized by plasmid profiles and RFLP analysis of amplified nodABC genes. The R. leguminosarum bv. viciae population was dominated by the same group of strains (irrespective of the trap plant used). According to type richness, the genetic diversity of indigenous R. leguminosarum in the second year of restoration was lower than in the first year and it resembled that of the fallow field, except for plasmid types, in which it was higher than that of the fallow field. Some of the less frequent nodABC genotypes were associated with distinct chromosomal IGS genotypes and symbiotic plasmids (pSyms) of different sizes, indicating that horizontal transfer and rearrangements of pSym can occur in natural environments. However, the dominant pSym and chromosomal genotypes were strictly correlated suggesting a genetically stable persistence of the prevailing R. leguminosarum bv, viciae genotypes in the absence of its host plant.

Zhang, X.X.; Kosier, B.; Priefer, U.B. [Rheinisch-Westfaelische TH Aachen, Aachen (Germany)

2001-09-01

330

Genetic diversity of indigenous Rhizobium leguminosarum bv. viciae isolates nodulating two different host plants during soil restoration with alfalfa.  

UK PubMed Central (United Kingdom)

A total of 360 Rhizobium leguminosarum bv. viciae strains was isolated from three brown-coal mining restoration fields of different age and plant cover (without and in the first and second year of alfalfa, Medicago sativa, cultivation) using two host species (Vicia hirsuta and Pisum sativum) as capture plants. The strains were genetically typed by restriction fragment length polymorphism analysis of polymerase chain reaction (PCR)-generated 16S-23S ribosomal DNA intergenic spacer regions (IGS-RFLP) and characterized by plasmid profiles and RFLP analysis of amplified nodABC genes. The R. leguminosarum bv. viciae population was dominated by the same group of strains (irrespective of the trap plant used). According to type richness, the genetic diversity of indigenous R. leguminosarum in the second year of restoration was lower than in the first year and it resembled that of the fallow field, except for plasmid types, in which it was higher than that of the fallow field. Some of the less frequent nodABC genotypes were associated with distinct chromosomal IGS genotypes and symbiotic plasmids (pSyms) of different sizes, indicating that horizontal transfer and rearrangements of pSym can occur in natural environments. However, the dominant pSym and chromosomal genotypes were strictly correlated suggesting a genetically stable persistence of the prevailing R. leguminosarum bv. viciae genotypes in the absence of its host plant.

Zhang XX; Kosier B; Priefer UB

2001-09-01

331

The genetic diversity of the mangrove kandelia obovata in China revealed by ISSR analysis  

International Nuclear Information System (INIS)

The genetic diversity of 7 populations of Kandelia obovata in China was characterized using inter simple sequence repeats (ISSR) technique. A total of 50 primers were screened, of which 9 polymorphic and informative patterns were selected to determine genetic relationships. ISSR amplification was conducted on 140 individuals from 7 populations, and 88 polymorphic loci were detected from 106 total loci. The total percentage of polymorphic loci (PPL) was 83.02%. The percentage of PPL at the population level ranged from 32.08% to 47.17%, with an average of 39.89%. Nei's gene diversity (H) and Shannon's information index (I) of K. obovata at the species level were 0.3631 and 0.5203, respectively. The genetic differentiation coefficient (Gst) among populations was 0.5548. Among populations component accounted for 55.48% of the total variation, whereas the within populations component accounted for 44.52%, suggesting that genetic differentiation among K. obovata populations was relatively high. The gene flow among populations was 0.4012, indicating that gene flow was low among geographically diverse populations of K. obovata. The results of the genetic diversity and cluster analysis suggest that geographical isolation of K. obovata populations mainly results in low gene flow and random genetic drift, leading to genetic differentiation. (author)

2010-01-01

332

Greater Genetic Diversity in Spatially Restricted Coral Reef Fishes Suggests Secondary Contact among Differentiated Lineages  

Directory of Open Access Journals (Sweden)

Full Text Available The maintenance of genetic diversity is a central goal of conservation. It is the raw material for evolutionary change and if lost, can accelerate extinction of species. According to theory, total genetic diversity should be less in species with restricted ranges and in populations on the margins of distributional ranges, making such species or populations more vulnerable to environmental perturbations. Using mtDNA and nuclear Inter Simple Sequence Repeat (ISSR) data we investigated how the genetic diversity and structure of three con-generic species pairs of coral reef fishes (Pomacentridae) was related to species’ range size and position of populations within these ranges. Estimates of genetic structure did not differ significantly among species, but mtDNA and nucDNA genetic diversities were up to 10 times greater in spatially restricted species compared to their widespread congeners. In two of the three species pairs, the distribution of genetic variation indicated secondary contact among differentiated lineages in the spatially restricted species. In contrast, the widespread species displayed a typical signature of population expansion suggesting recent genetic bottlenecks, possibly associated with the (re) colonization of the Great Barrier Reef. These results indicate that historical processes, involving hybridization and founder effects, possibly associated with Pleistocene sea level fluctuations, have differentially influenced the widespread and spatially restricted coral reef damselfish species studied here.

Line K. Bay; M. Julian Caley

2011-01-01

333

Loss of genetic diversity as a signature of apricot domestication and diffusion into the Mediterranean Basin.  

UK PubMed Central (United Kingdom)

BACKGROUND: Domestication generally implies a loss of diversity in crop species relative to their wild ancestors because of genetic drift through bottleneck effects. Compared to native Mediterranean fruit species like olive and grape, the loss of genetic diversity is expected to be more substantial for fruit species introduced into Mediterranean areas such as apricot (Prunus armeniaca L.), which was probably primarily domesticated in China. By comparing genetic diversity among regional apricot gene pools in several Mediterranean areas, we investigated the loss of genetic diversity associated with apricot selection and diffusion into the Mediterranean Basin. RESULTS: According to the geographic origin of apricots and using Bayesian clustering of genotypes, Mediterranean apricot (207 genotypes) was structured into three main gene pools: 'Irano-Caucasian', 'North Mediterranean Basin' and 'South Mediterranean Basin'. Among the 25 microsatellite markers used, only one displayed deviations from the frequencies expected under neutrality. Similar genetic diversity parameters were obtained within each of the three main clusters using both all SSR loci and only 24 SSR loci based on the assumption of neutrality. A significant loss of genetic diversity, as assessed by the allelic richness and private allelic richness, was revealed from the 'Irano-Caucasian' gene pool, considered as a secondary centre of diversification, to the northern and southwestern Mediterranean Basin. A substantial proportion of shared alleles was specifically detected when comparing gene pools from the 'North Mediterranean Basin' and 'South Mediterranean Basin' to the secondary centre of diversification. CONCLUSIONS: A marked domestication bottleneck was detected with microsatellite markers in the Mediterranean apricot material, depicting a global image of two diffusion routes from the 'Irano-Caucasian' gene pool: North Mediterranean and Southwest Mediterranean. This study generated genetic insight that will be useful for management of Mediterranean apricot germplasm as well as genetic selection programs related to adaptive traits.

Bourguiba H; Audergon JM; Krichen L; Trifi-Farah N; Mamouni A; Trabelsi S; D'Onofrio C; Asma BM; Santoni S; Khadari B

2012-01-01

334

Genetic diversity of Callosobruchus maculatus (Fab.) (Coleoptera: Bruchidae) populations  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Variations in esterase pattern and genetic similarity of six populations (Madurai, Nagapattinam, Coimbatore, Thiruvannamalai, Chennai and Vellore) of Callosobruchus maculatus were assessed. Among the populations studied, esterase pattern of the Coimbatore population is distinctly different then the...

M Raja; S John William; K Jahir Hussain

335

Genetic diversity of Sardinian goat population based on microsatellites  

Directory of Open Access Journals (Sweden)

Full Text Available During the last century, the selection for production traits of the main livestock species has led to a reduction in number of local populations with consequent loss of genetic variability. In Sardinia, the genetic improvement strategy has been based on selection for the local pure breed in sheep, whereas in the other species (cattle, swine and goat), an often unplanned crossbreeding with improved breeds has been applied.

T. Sechi; M.G. Usai; S. Casu; A. Carta

2010-01-01

336

Analysis of genetic diversity of Guizotia abyssinica from Ethiopia using inter simple sequence repeat markers.  

Science.gov (United States)

Within and among population genetic diversity of 37 Guizotia abyssinica populations from Ethiopia were analyzed using inter simple sequence repeats (ISSRs). Five primers amplified a total of 118 genomic DNA fragments across a total of 370 individuals of which 106 were polymorphic (89.83%). The average number of polymorphic bands per primer was 21.2. More bands were generated by primer UBC 888 (BDB(CA)(7.) The total genetic diversity (Ht) and the coefficient of genetic differentiation (Gst) were 0.4115 and 0.0918 respectively, while the within population genetic diversity (Hs) and the among population genetic diversity(Dst) were 0.3738 and 0.03776 respectively suggesting more variability within the populations than among them. The standard genetic distances between the G. abyssinica populations of the eight regions ranged from 0.0281 (between Wollo and Gojam) to 0.1148 (between Jimma and Hararghe). Generally, the standard genetic distances are smaller between populations of neighboring regions and highest between those of Jimma and the other regions, ranging from 0.0696 (between Jimma and Shewa) to 0.1148 (between Jimma and Hararghe). The ISSR based UPGMA clustering using the standardized genetic distances matrix also placed populations from neighboring regions closer than those from farther apart areas, while the UPGMA clustering by regions based on the standard genetic distances produced three clusters following the proximity and the contiguity of the regions. The mean Shannon Weaver diversity indices for the populations of the eight regions ranged from 0.8197 (Jimma) to 0.9176 (Hararghe), with a mean of 0.8841 for the whole material. PMID:17567436

Petros, Yohannes; Merker, Arnulf; Zeleke, Habtamu

2007-03-01

337

Analysis of genetic diversity of Guizotia abyssinica from Ethiopia using inter simple sequence repeat markers.  

UK PubMed Central (United Kingdom)

Within and among population genetic diversity of 37 Guizotia abyssinica populations from Ethiopia were analyzed using inter simple sequence repeats (ISSRs). Five primers amplified a total of 118 genomic DNA fragments across a total of 370 individuals of which 106 were polymorphic (89.83%). The average number of polymorphic bands per primer was 21.2. More bands were generated by primer UBC 888 (BDB(CA)(7.) The total genetic diversity (Ht) and the coefficient of genetic differentiation (Gst) were 0.4115 and 0.0918 respectively, while the within population genetic diversity (Hs) and the among population genetic diversity(Dst) were 0.3738 and 0.03776 respectively suggesting more variability within the populations than among them. The standard genetic distances between the G. abyssinica populations of the eight regions ranged from 0.0281 (between Wollo and Gojam) to 0.1148 (between Jimma and Hararghe). Generally, the standard genetic distances are smaller between populations of neighboring regions and highest between those of Jimma and the other regions, ranging from 0.0696 (between Jimma and Shewa) to 0.1148 (between Jimma and Hararghe). The ISSR based UPGMA clustering using the standardized genetic distances matrix also placed populations from neighboring regions closer than those from farther apart areas, while the UPGMA clustering by regions based on the standard genetic distances produced three clusters following the proximity and the contiguity of the regions. The mean Shannon Weaver diversity indices for the populations of the eight regions ranged from 0.8197 (Jimma) to 0.9176 (Hararghe), with a mean of 0.8841 for the whole material.

Petros Y; Merker A; Zeleke H

2007-03-01

338

Genetic diversity analysis of Bt cotton genotypes in Pakistan using simple sequence repeat markers.  

Science.gov (United States)

The popularity of genetically modified insect resistant (Bt) cotton has promoted large scale monocultures, which is thought to worsen the problem of crop genetic homogeneity. Information on genetic diversity among Bt cotton varieties is lacking. We evaluated genetic divergence among 19 Bt cotton genotypes using simple sequence repeat (SSR) markers. Thirty-seven of 104 surveyed primers were found informative. Fifty-two primers selected on the basis of reported intra-hirsutum polymorphism in a cotton marker database showed a high degree of polymorphism, 56% compared to 13% for randomly selected primers. A total of 177 loci were amplified, with an average of 1.57 loci per primer, generating 38 markers. The amplicons ranged in size from 98 to 256 bp. The genetic similarities among the 19 genotypes ranged from 0.902 to 0.982, with an average of 0.947, revealing a lack of diversity. Similarities among genotypes from public sector organizations were higher than genotypes developed by private companies. Hybrids were found to be more distant compared to commercial cultivars and advanced breeding lines. Cluster analysis grouped the 19 Bt cotton genotypes into three major clusters and two independent entries. Cultivars IR-3701, Ali Akbar-802 and advanced breeding line VH-259 grouped in subcluster B2, with very narrow genetic distances despite dissimilar parentage. We found a very high level of similarity among Pakistani-bred Bt cotton varieties, which means that genetically diverse recurrent parents should be included to enhance genetic diversity. The intra-hirsutum polymorphic SSRs were found to be highly informative for molecular genetic diversity studies in these cotton varieties. PMID:22535395

Ullah, I; Iram, A; Iqbal, M Z; Nawaz, M; Hasni, S M; Jamil, S

2012-03-14

339

Genetic diversity analysis of Bt cotton genotypes in Pakistan using simple sequence repeat markers.  

UK PubMed Central (United Kingdom)

The popularity of genetically modified insect resistant (Bt) cotton has promoted large scale monocultures, which is thought to worsen the problem of crop genetic homogeneity. Information on genetic diversity among Bt cotton varieties is lacking. We evaluated genetic divergence among 19 Bt cotton genotypes using simple sequence repeat (SSR) markers. Thirty-seven of 104 surveyed primers were found informative. Fifty-two primers selected on the basis of reported intra-hirsutum polymorphism in a cotton marker database showed a high degree of polymorphism, 56% compared to 13% for randomly selected primers. A total of 177 loci were amplified, with an average of 1.57 loci per primer, generating 38 markers. The amplicons ranged in size from 98 to 256 bp. The genetic similarities among the 19 genotypes ranged from 0.902 to 0.982, with an average of 0.947, revealing a lack of diversity. Similarities among genotypes from public sector organizations were higher than genotypes developed by private companies. Hybrids were found to be more distant compared to commercial cultivars and advanced breeding lines. Cluster analysis grouped the 19 Bt cotton genotypes into three major clusters and two independent entries. Cultivars IR-3701, Ali Akbar-802 and advanced breeding line VH-259 grouped in subcluster B2, with very narrow genetic distances despite dissimilar parentage. We found a very high level of similarity among Pakistani-bred Bt cotton varieties, which means that genetically diverse recurrent parents should be included to enhance genetic diversity. The intra-hirsutum polymorphic SSRs were found to be highly informative for molecular genetic diversity studies in these cotton varieties.

Ullah I; Iram A; Iqbal MZ; Nawaz M; Hasni SM; Jamil S

2012-01-01

340

Studies on Genetic Diversity in Pakistani Wheat Varieties using Randomly Amplified Polymorphic DNA  

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Full Text Available To improve yield and quality of wheat, presence of genetic diversity is an important prerequisite. To estimate the extent of genetic variability, DNA markers including Randomly Amplified Polymorphic DNA (RAPD) have been widely used in various crops of agronomic importance. During present study, RAPDs were used to estimate genetic relationship among 10 Pakistani wheat varieties and to identify genetically diverse genotypes which can be used in future breeding programs. RAPD primers used during present study produced an average of 1.9 alleles per primer. Size of scorable fragments ranged from 250-1000 bp. A high level of genetic dissimilarity (GD = up to 63%) was estimated among the wheat varieties. Ten wheat varieties were grouped in 3 clusters using dendrogram analysis. Clusters A, B and C comprised land races, derivatives of Mexi-Pak and elite lines having alien gene, respectively.

Aisha Naz; Zahoor Ahmed Swati; Imtiaz A. khan

2006-01-01

 
 
 
 
341

Genetic diversity and population structure of Celosia argentea and related species revealed by SRAP.  

UK PubMed Central (United Kingdom)

Genetic diversity of 16 populations of Celosia argentea L. and 6 populations of Celosia cristata L. in China was investigated using sequence-related amplified polymorphism (SRAP). Ten SRAP primer combinations generated 507 scorable amplification bands ranging from 50 to 2000 bp, among which 274 were polymorphic, with an average of 54 polymorphic bands per primer combination. The unweighted pair group method of arithmetic averages (UPGMA) cluster analysis enabled construction of a phylogenetic tree for estimating genetic distance among populations, which agreed well with the geographic origin information. Twenty-two populations were distinctly separated into two major genetic groups. One typical representative fragment, M1E6 in C. argentea, provided an alternative approach to distinguish C. argentea from C. cristata. Also, great genetic diversity found in C. argentea populations by significant geographic difference was confirmed by a high level of population genetics parameters. The information may be beneficial to future breeding selection and conservation management for populations of C. argentea.

Feng N; Xue Q; Guo Q; Zhao R; Guo M

2009-08-01

342

Genetic Diversity among Mentha Populations in Egypt as Reflected by Isozyme Polymorphism  

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Full Text Available Isozyme polymorphism has been used to measure genetic diversity, genetic population structure and for the estimation of the amount of genetic divergence within and between populations and species of Mentha in Egypt. Ten isozyme systems revealed 31 isozyme loci and a total of 79 alleles in 32 populations of M. longifolia, five populations of M. spicata and one population of M. piperita. The examined populations of M. longifolia and M. spicata showed high levels of genetic variation that might be due to out-breeding and wide dispersal of seeds and pollen grains. Three alleles were scored in all populations; however, no diagnostic alleles at the species level were detected in the 31 isozyme loci. This suggests that the three species may be of hybrid origin or have recently been derived from an ancestor harboring high levels of genetic diversity. The tree illustrating genetic distance among the examined accessions of Mentha indicated obvious discrimination of the three species and the isolation of their populations from each other. At the infra-specific level, the geographically proximal populations exhibited higher genetic similarity than those that geographically distant, indicating environmental impact on the genetic diversity in the genus Mentha in Egypt.

Abd El-Zaher M.A. Mustafa; Abdelfattah Badr; Mohammed A. El-Galaly; Ahmed A. Mobarak; Mervat G. Hassan

2005-01-01

343

Genetic diversity and demographic instability in Riftia pachyptila tubeworms from eastern Pacific hydrothermal vents  

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Full Text Available Abstract Background Deep-sea hydrothermal vent animals occupy patchy and ephemeral habitats supported by chemosynthetic primary production. Volcanic and tectonic activities controlling the turnover of these habitats contribute to demographic instability that erodes genetic variation within and among colonies of these animals. We examined DNA sequences from one mitochondrial and three nuclear gene loci to assess genetic diversity in the siboglinid tubeworm, Riftia pachyptila, a widely distributed constituent of vents along the East Pacific Rise and Galápagos Rift. Results Genetic differentiation (FST) among populations increased with geographical distances, as expected under a linear stepping-stone model of dispersal. Low levels of DNA sequence diversity occurred at all four loci, allowing us to exclude the hypothesis that an idiosyncratic selective sweep eliminated mitochondrial diversity alone. Total gene diversity declined with tectonic spreading rates. The southernmost populations, which are subjected to superfast spreading rates and high probabilities of extinction, are relatively homogenous genetically. Conclusions Compared to other vent species, DNA sequence diversity is extremely low in R. pachyptila. Though its dispersal abilities appear to be effective, the low diversity, particularly in southern hemisphere populations, is consistent with frequent local extinction and (re)colonization events.

Coykendall D Katharine; Johnson Shannon B; Karl Stephen A; Lutz Richard A; Vrijenhoek Robert C

2011-01-01

344

Genetic diversity in cultivars and landraces of Oryza sativa subsp. indica as revealed by AFLP markers.  

Science.gov (United States)

Genetic diversity among 49 Indian accessions of rice (Oryza sativa subsp. indica), including 29 landraces from Jeypore, 12 modern cultivars, and 8 traditional cultivars from Tamil Nadu, was investigated using AFLP markers. In total, nine primer combinations revealed 664 AFLPs, 408 of which were found to be polymorphic. The percentage of polymorphic AFLPs was approximately the same within the cultivars and landraces. Similar results were obtained when genetic diversity values were estimated using the Shannon-Weiner index of diversity. Genetic diversity was slightly higher in the modern cultivars than in the traditional cultivars from Tamil Nadu. Among the landraces from Jeypore, the lowland landraces showed the highest diversity. The present study showed that the process of breeding modern cultivars did not appear to cause significant genetic erosion in rice. Cluster analysis and the first component of principle component analysis (PCA) both showed a clear demarcation between the cultivars and landraces as separate groups, although the genetic distance between them was narrow. The modern cultivars were positioned between the landraces from Jeypore and the traditional cultivars from Tamil Nadu. The second component of PCA further separated medium and upland landraces from lowland landraces, with the lowland landraces found closest to the traditional and modern cultivars. PMID:12033612

Prashanth, S R; Parani, M; Mohanty, B P; Talame, V; Tuberosa, R; Parida, A

2002-06-01

345

Genetic diversity in cultivars and landraces of Oryza sativa subsp. indica as revealed by AFLP markers.  

UK PubMed Central (United Kingdom)

Genetic diversity among 49 Indian accessions of rice (Oryza sativa subsp. indica), including 29 landraces from Jeypore, 12 modern cultivars, and 8 traditional cultivars from Tamil Nadu, was investigated using AFLP markers. In total, nine primer combinations revealed 664 AFLPs, 408 of which were found to be polymorphic. The percentage of polymorphic AFLPs was approximately the same within the cultivars and landraces. Similar results were obtained when genetic diversity values were estimated using the Shannon-Weiner index of diversity. Genetic diversity was slightly higher in the modern cultivars than in the traditional cultivars from Tamil Nadu. Among the landraces from Jeypore, the lowland landraces showed the highest diversity. The present study showed that the process of breeding modern cultivars did not appear to cause significant genetic erosion in rice. Cluster analysis and the first component of principle component analysis (PCA) both showed a clear demarcation between the cultivars and landraces as separate groups, although the genetic distance between them was narrow. The modern cultivars were positioned between the landraces from Jeypore and the traditional cultivars from Tamil Nadu. The second component of PCA further separated medium and upland landraces from lowland landraces, with the lowland landraces found closest to the traditional and modern cultivars.

Prashanth SR; Parani M; Mohanty BP; Talame V; Tuberosa R; Parida A

2002-06-01

346

Genetic Diversity Analysis of CIMMYT Bread Wheat (Triticum aestivum L.) Lines by SRAP Markers  

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Full Text Available Genetic diversity is one of the key factors for the improvement of many crop plants including wheat. Many wheat scientistshave studied genetic diversity in wheat germplasm using different molecular markers which have provided a powerfulapproach to analyze genetic relationships among wheat germplasms. In this study, genetic diversity of CIMMYT(International maize and wheat improvement center) bread wheat lines collected from Russia was evaluated using 30sequence-related amplified polymorphism (SRAP) primer combinations. 686 DNA band was obtained from the 23 primercombinations and approximately 90% of them were found to be polymorphic. Ratio of polymorphic loci, Shannon'sdiversity index and gene diversity were found 82.61%, 0.39 and 0.26 respectively. The three main clusters were found byusing UPGMA (Unweighted Pair Group Method with Arithmetic Mean) cluster analysis method and the average rate ofgenetic similarity with 0.462. Two main clusters were shown in principal component analysis (PCA) which is consistentwith the result of UPGMA. It can be concluded that SRAP markers can be used for wheat genetic diversity studies and havepotential linkage mapping, molecular characterizations and marker assisted selection (MAS) breeding.

Ertugrul FILIZ

2012-01-01

347

Resequencing microarray probe design for typing genetically diverse viruses: human rhinoviruses and enteroviruses  

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Full Text Available Abstract Background Febrile respiratory illness (FRI) has a high impact on public health and global economics and poses a difficult challenge for differential diagnosis. A particular issue is the detection of genetically diverse pathogens, i.e. human rhinoviruses (HRV) and enteroviruses (HEV) which are frequent causes of FRI. Resequencing Pathogen Microarray technology has demonstrated potential for differential diagnosis of several respiratory pathogens simultaneously, but a high confidence design method to select probes for genetically diverse viruses is lacking. Results Using HRV and HEV as test cases, we assess a general design strategy for detecting and serotyping genetically diverse viruses. A minimal number of probe sequences (26 for HRV and 13 for HEV), which were potentially capable of detecting all serotypes of HRV and HEV, were determined and implemented on the Resequencing Pathogen Microarray RPM-Flu v.30/31 (Tessarae RPM-Flu). The specificities of designed probes were validated using 34 HRV and 28 HEV strains. All strains were successfully detected and identified at least to species level. 33 HRV strains and 16 HEV strains could be further differentiated to serotype level. Conclusion This study provides a fundamental evaluation of simultaneous detection and differential identification of genetically diverse RNA viruses with a minimal number of prototype sequences. The results demonstrated that the newly designed RPM-Flu v.30/31 can provide comprehensive and specific analysis of HRV and HEV samples which implicates that this design strategy will be applicable for other genetically diverse viruses.

Wang Zheng; Malanoski Anthony P; Lin Baochuan; Kidd Carolyn; Long Nina C; Blaney Kate M; Thach Dzung C; Tibbetts Clark; Stenger David A

2008-01-01

348

Extensive genetic diversity, unique population structure and evidence of genetic exchange in the sexually transmitted parasite Trichomonas vaginalis  

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Trichomonas vaginalis is the causative agent of human trichomoniasis, the most common non-viral sexually transmitted infection world-wide. Despite its prevalence, little is known about the genetic diversity and population structure of this haploid parasite due to the lack of...

Conrad, Melissa D.; Gorman, Andrew W.; Schillinger, Julia A.; Fiori, Pier Luigi; Arroyo Verastegui, Rossana; Malla, Nancy

349

Mapping Genetic Diversity of Cherimoya (Annona cherimola Mill.): Application of Spatial Analysis for Conservation and Use of Plant Genetic Resources  

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There is a growing call for inventories that evaluate geographic patterns in diversity of plant genetic resources maintained on farm and in species' natural populations in order to enhance their use and conservation. Such evaluations are relevant for useful tropical and subtropical tree species, as ...

van Zonneveld, Maarten; Scheldeman, Xavier; Escribano, Pilar; Viruel, María A.; Van Damme, Patrick; Garcia, Willman

350

Genetic diversity in populations of asexual and sexual bag worm moths (Lepidoptera: Psychidae).  

UK PubMed Central (United Kingdom)

BACKGROUND: Despite the two-fold cost of sex, most of the higher animals reproduce sexually. The advantage of sex has been suggested to be its ability, through recombination, to generate greater genetic diversity than asexuality, thus enhancing adaptation in a changing environment. We studied the genetic diversity and the population structure of three closely related species of bag worm moths: two strictly sexual (Dahlica charlottae and Siederia rupicolella) and one strictly asexual (D. fennicella). These species compete for the same resources and share the same parasitoids. RESULTS: Allelic richness was comparable between the sexual species but it was higher than in the asexual species. All species showed high heterozygote deficiency and a large variation was observed among FIS values across loci and populations. Large genetic differentiation was observed between populations confirming the poor dispersal ability of these species. The asexual species showed lower genotype diversity than the sexual species. Nevertheless, genotype diversity was high in all asexual populations. CONCLUSION: The three different species show a similar population structure characterised by high genetic differentiation among populations and low dispersal. Most of the populations showed high heterozygote deficiency likely due to the presence of null alleles at most of the loci and/or to the Wahlund effect. Although the parthenogenetic D. fennicella shows reduced genetic diversity compared to the sexual species, it still shows surprisingly high genotype diversity. While we can not totally rule out the presence of cryptic sex, would explain this high genotype diversity, we never observed sex in the parthenogenetic D. fennicella, nor was there any other evidence of this. Alternatively, a non-clonal parthenogenetic reproduction, such as automictic thelytoky, could explain the high genotypic diversity observed in D. fennicella.

Grapputo A; Kumpulainen T; Mappes J; Parri S

2005-01-01

351

Genetic diversity in Napier grass (Pennisetum purpureum) cultivars: implications for breeding and conservation.  

Science.gov (United States)

Napier grass is an important forage crop for dairy production in the tropics; as such, its existing genetic diversity needs to be assessed for conservation. The current study assessed the genetic variation of Napier grass collections from selected regions in Eastern Africa and the International Livestock Research Institute Forage Germplasm-Ethiopia. The diversity of 281 cultivars was investigated using five selective amplified fragment length polymorphism (AFLP) markers and classical population genetic parameters analysed using various software. The number of bands generated was 216 with fragments per primer set ranging from 50 to 115. Mean percentage polymorphic loci was 63.40. Genetic diversity coefficients based on Nei's genetic diversity ranged from 0.0783 to 0.2142 and Shannon's information index ranged from 0.1293 to 0.3445. The Fst value obtained was moderately significant (Fst = 0.1688). Neighbour-joining analysis gave two distinct clusters which did not reflect geographical locations. Analysis of molecular variance showed all variance components to be highly significant (P < 0.001), indicating more variation within (91 %) than between populations (9 %). Results suggested moderate genetic differentiation among Napier grass populations sampled, which could imply a high germplasm exchange within the region. The AFLP markers used in this study efficiently discriminate among cultivars and could be useful in identification and germplasm conservation. PMID:23671788

Wanjala, Bramwel W; Obonyo, Meshack; Wachira, Francis N; Muchugi, Alice; Mulaa, Margaret; Harvey, Jagger; Skilton, Robert A; Proud, Janice; Hanson, Jean

2013-05-11

352

Genetic diversity in Napier grass (Pennisetum purpureum) cultivars: implications for breeding and conservation.  

UK PubMed Central (United Kingdom)

Napier grass is an important forage crop for dairy production in the tropics; as such, its existing genetic diversity needs to be assessed for conservation. The current study assessed the genetic variation of Napier grass collections from selected regions in Eastern Africa and the International Livestock Research Institute Forage Germplasm-Ethiopia. The diversity of 281 cultivars was investigated using five selective amplified fragment length polymorphism (AFLP) markers and classical population genetic parameters analysed using various software. The number of bands generated was 216 with fragments per primer set ranging from 50 to 115. Mean percentage polymorphic loci was 63.40. Genetic diversity coefficients based on Nei's genetic diversity ranged from 0.0783 to 0.2142 and Shannon's information index ranged from 0.1293 to 0.3445. The Fst value obtained was moderately significant (Fst = 0.1688). Neighbour-joining analysis gave two distinct clusters which did not reflect geographical locations. Analysis of molecular variance showed all variance components to