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Sample records for genetically diverse marburg

  1. Marburg Virus Reverse Genetics Systems

    Directory of Open Access Journals (Sweden)

    Kristina Maria Schmidt

    2016-06-01

    Full Text Available The highly pathogenic Marburg virus (MARV is a member of the Filoviridae family and belongs to the group of nonsegmented negative-strand RNA viruses. Reverse genetics systems established for MARV have been used to study various aspects of the viral replication cycle, analyze host responses, image viral infection, and screen for antivirals. This article provides an overview of the currently established MARV reverse genetic systems based on minigenomes, infectious virus-like particles and full-length clones, and the research that has been conducted using these systems.

  2. Marburg hemorrhagic fever associated with multiple genetic lineages of virus

    DEFF Research Database (Denmark)

    Bausch, D G; Nichol, S T; Muyembe-Tamfum, J J

    2006-01-01

    Background An outbreak of Marburg hemorrhagic fever was first observed in a gold-mining village in northeastern Democratic Republic of the Congo in October 1998. Methods We investigated the outbreak of Marburg hemorrhagic fever most intensively in May and October 1999. Sporadic cases and short ch...

  3. Ebola/Marburg

    Science.gov (United States)

    ... with facebook share with twitter share with linkedin Ebola & Marburg Ebola and Marburg hemorrhagic fevers are acute ... to-person contact. Why Is the Study of Ebola & Marburg a Priority for NIAID? Marburg hemorrhagic fever ...

  4. Evaluating human genetic diversity

    National Research Council Canada - National Science Library

    This book assesses the scientific value and merit of research on human genetic differences--including a collection of DNA samples that represents the whole of human genetic diversity--and the ethical...

  5. Evaluating human genetic diversity

    National Research Council Canada - National Science Library

    ... into human evolution and origins and serving as a springboard for important medical research. It also addresses issues of confidentiality and individual privacy for participants in genetic diversity research studies.

  6. Characteristics of Filoviridae: Marburg and Ebola Viruses

    Science.gov (United States)

    Beer, Brigitte; Kurth, Reinhard; Bukreyev, Alexander

    Filoviruses are enveloped, nonsegmented negative-stranded RNA viruses. The two species, Marburg and Ebola virus, are serologically, biochemically, and genetically distinct. Marburg virus was first isolated during an outbreak in Europe in 1967, and Ebola virus emerged in 1976 as the causative agent of two simultaneous outbreaks in southern Sudan and northern Zaire. Although the main route of infection is known to be person-to-person transmission by intimate contact, the natural reservoir for filoviruses still remains a mystery.

  7. Vector choice determines immunogenicity and potency of genetic vaccines against Angola Marburg virus in nonhuman primates

    NARCIS (Netherlands)

    Geisbert, Thomas W.; Bailey, Michael; Geisbert, Joan B.; Asiedu, Clement; Roederer, Mario; Grazia-Pau, Maria; Custers, Jerome; Jahrling, Peter; Goudsmit, Jaap; Koup, Richard; Sullivan, Nancy J.

    2010-01-01

    The immunogenicity and durability of genetic vaccines are influenced by the composition of gene inserts and choice of delivery vector. DNA vectors are a promising vaccine approach showing efficacy when combined in prime-boost regimens with recombinant protein or viral vectors, but they have shown

  8. Genetic defects in DNA repair system and enhancement of intergenote transformation efficiency in Bacillus subtilis Marburg

    International Nuclear Information System (INIS)

    Matsumoto, K.; Takahashi, H.; Saito, H.; Ikeda, Y.

    1978-01-01

    Mechanisms of inefficiency in heterospecies transformation were studied with a transformation system consisting of Bacillus subtilis 168TI (trpC2thy) as recipient and of DNA prepared from partially hybrid strains of B. subtilis which had incorporated trp + DNA of B. amyloliquefaciens 203 (formerly, B. megaterium 203) in the chromosome (termed intergenote). The intergenote transformation was not so efficient as the corresponding homospecies transformation and the efficiency appeared to relate inversely with the length of heterologous portion in the intergenote. When a variety of ultraviolet light (UV) sensitive mutants, deficient in host-cell reactivation capacity, were used as recipients for the intergenote transformation, 2 out of 16 mutants exhibited significantly enhanced transformation efficiency of the trpC marker. Genetic studies by transformation showed that the trait relating to the enhancement of intergenote-transformation efficiency was always associated with the UV sensitivity, suggesting that these two traits are determined by a single gene. The efficiency of intergenote transformation was highly affected also by DNA concentration; the lower the concentration, the less the efficiency. When, however, the UV sensitive mutant was used as recipient, the effect of DNA concentration was largely diminished, suggesting the reduction of DNA-inactivating activity in the UV sensitive recipient. These results were discussed in relation to a possible excision-repair system selectively correcting the mismatched DNA in the course of intergenote transformation. (orig.) [de

  9. Marburg Virus Disease

    Science.gov (United States)

    ... twice tested undetected (negative) for Marburg, survivors should practice good hand and personal hygiene by immediately and thoroughly washing with soap and water after any physical contact with semen, including after masturbation. During this period used condoms should be handled ...

  10. Global issues of genetic diversity.

    Science.gov (United States)

    Vida, G

    1994-01-01

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

  11. Ebola Virus and Marburg Virus

    Science.gov (United States)

    Ebola virus and Marburg virus Overview Ebola virus and Marburg virus are related viruses that cause hemorrhagic fevers — illnesses marked by severe bleeding (hemorrhage), organ failure and, in many ...

  12. Genetic diversity in Trichomonas vaginalis.

    Science.gov (United States)

    Meade, John C; Carlton, Jane M

    2013-09-01

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

  13. Global change and genetic diversity

    International Nuclear Information System (INIS)

    Kremer, Antoine

    2000-01-01

    Are there grounds for concern as to the impact of global change on the future of European forests? This question is approached from the genetic angle, considering the modifications produced by climate change on the diversity and adaptive potential of forest species. In the absence of experimental data, the answers are derived from a set of arguments based on knowledge of evolutionary mechanisms involved in genetic diversity, the post-glacial history of European forests and lessons drawn from recent introductions of foreign wood species. These arguments entail less pessimistic conclusions than those generally reached for consequences attributed to global change. Even if major changes in composition could occur, past events show that genetic erosion capable of challenging the adaptive potential of species is unlikely. (author)

  14. Genetic diversity among endangered rare Dalbergia cochinchinensis

    African Journals Online (AJOL)

    hocvan

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

  15. Genetic diversity in a crop metapopulation

    NARCIS (Netherlands)

    Heerwaarden, van J.; Eeuwijk, van F.A.; Ross-Ibarra, J.

    2010-01-01

    The need to protect crop genetic resources has sparked a growing interest in the genetic diversity maintained in traditional farming systems worldwide. Although traditional seed management has been proposed as an important determinant of genetic diversity and structure in crops, no models exist that

  16. Personalized medicine and human genetic diversity.

    Science.gov (United States)

    Lu, Yi-Fan; Goldstein, David B; Angrist, Misha; Cavalleri, Gianpiero

    2014-07-24

    Human genetic diversity has long been studied both to understand how genetic variation influences risk of disease and infer aspects of human evolutionary history. In this article, we review historical and contemporary views of human genetic diversity, the rare and common mutations implicated in human disease susceptibility, and the relevance of genetic diversity to personalized medicine. First, we describe the development of thought about diversity through the 20th century and through more modern studies including genome-wide association studies (GWAS) and next-generation sequencing. We introduce several examples, such as sickle cell anemia and Tay-Sachs disease that are caused by rare mutations and are more frequent in certain geographical populations, and common treatment responses that are caused by common variants, such as hepatitis C infection. We conclude with comments about the continued relevance of human genetic diversity in medical genetics and personalized medicine more generally. Copyright © 2014 Cold Spring Harbor Laboratory Press; all rights reserved.

  17. Do species conservation assessments capture genetic diversity?

    Directory of Open Access Journals (Sweden)

    Malin C. Rivers

    2014-12-01

    Full Text Available The best known system for classifying threat status of species, the IUCN Red List, currently lacks explicit considerations of genetic diversity, and consequently may not account for potential adaptation of species to future environmental change. To address this gap, we integrate range-wide genetic analysis with IUCN Red List assessments.We calculated the loss of genetic diversity under simulated range loss for species of Delonix (Leguminosae. Simulated range loss involved random loss of populations and was intended to model ongoing habitat destruction. We found a strong relationship between loss of genetic diversity and range. Moreover, we found correspondence between levels of genetic diversity and thresholds for ‘non-threatened’ versus ‘threatened’ IUCN Red List categories.Our results support the view that current threat thresholds of the IUCN Red List criteria reflect genetic diversity, and hence evolutionary potential; although the genetic diversity distinction between threatened categories was less evident. Thus, by supplementing conventional conservation assessments with genetic data, new insights into the biological robustness of IUCN Red List assessments for targeted conservation initiatives can be achieved. Keywords: Conservation assessment, Conservation genetics, Extinction risk, Genetic diversity, IUCN Red List, Range

  18. Genetic diversity and relationships among cabbage ( Brassica ...

    African Journals Online (AJOL)

    The integration of our data with historical documents confirmed that traditional cabbage landraces cultivated in North of China were first introduced from Russia. Key words: Amplified fragment length polymorphism (AFLP), genetic diversity, cabbage (Brassica oleracea var. capitata), landraces, population structure.

  19. Genetic diversity of grasscutter (Thryonomys swinderianus ...

    African Journals Online (AJOL)

    Saharan Africa. There are very limited ecological studies on the grasscutter despite its importance as a protein resource. The objective of this study was to apply novel microsatellite markers to determine the genetic structure and diversity of ...

  20. An analysis of the genetic diversity and genetic structure of ...

    African Journals Online (AJOL)

    ajl yemi

    2011-12-26

    Dec 26, 2011 ... relief, diuresis, blood pressure and lipid metabolism. (Kawasaki et al., 2000). ... Habitat. Longitude(N),. Latitude(E). Population size. Sample size. LY. Luoyang, Henan ..... Compared with the high genetic diversity at the species.

  1. Molecular diversity and genetic relationships in Secale

    Indian Academy of Sciences (India)

    Molecular diversity and genetic relationships in Secale. E. Santos, M. Matos, P. Silva, A. M. Figueiras, C. Benito and O. Pinto-Carnide. J. Genet. 95, 273–281. Table 1. RAPD and ISSR primers used in this study. Primer. 5 –3. Primer. 5 –3. RAPDs (Operon). A1. CAGGCCCTTC. C5. CATGACCGCC. A4. AATCGGGCTG. C6.

  2. Genetic diversity in Cinnamomum zeylanicum Blume. (Lauraceae ...

    African Journals Online (AJOL)

    In this study, unweighed pair group method with arithmetic averages (UPGMA) analysis showed up to 89% genetic variation among these accessions, which is further supported by principle co-ordinate analysis (PCA). Key words: Genetic diversity, Cinnamomum zeylanicum, RAPD markers, DNA polymorphism.

  3. Implications of recurrent disturbance for genetic diversity.

    Science.gov (United States)

    Davies, Ian D; Cary, Geoffrey J; Landguth, Erin L; Lindenmayer, David B; Banks, Sam C

    2016-02-01

    Exploring interactions between ecological disturbance, species' abundances and community composition provides critical insights for ecological dynamics. While disturbance is also potentially an important driver of landscape genetic patterns, the mechanisms by which these patterns may arise by selective and neutral processes are not well-understood. We used simulation to evaluate the relative importance of disturbance regime components, and their interaction with demographic and dispersal processes, on the distribution of genetic diversity across landscapes. We investigated genetic impacts of variation in key components of disturbance regimes and spatial patterns that are likely to respond to climate change and land management, including disturbance size, frequency, and severity. The influence of disturbance was mediated by dispersal distance and, to a limited extent, by birth rate. Nevertheless, all three disturbance regime components strongly influenced spatial and temporal patterns of genetic diversity within subpopulations, and were associated with changes in genetic structure. Furthermore, disturbance-induced changes in temporal population dynamics and the spatial distribution of populations across the landscape resulted in disrupted isolation by distance patterns among populations. Our results show that forecast changes in disturbance regimes have the potential to cause major changes to the distribution of genetic diversity within and among populations. We highlight likely scenarios under which future changes to disturbance size, severity, or frequency will have the strongest impacts on population genetic patterns. In addition, our results have implications for the inference of biological processes from genetic data, because the effects of dispersal on genetic patterns were strongly mediated by disturbance regimes.

  4. An analysis of the genetic diversity and genetic structure of ...

    African Journals Online (AJOL)

    Scientific approaches to conservation of threatened species depend on a good understanding of the genetic information of wild and artificial population. The genetic diversity and structure analysis of 10 Eucommia ulmoides population was analyzed using inter-simple sequence repeat (ISSR) markers in this paper.

  5. Nephronophthisis: A Genetically Diverse Ciliopathy

    Directory of Open Access Journals (Sweden)

    Roslyn J. Simms

    2011-01-01

    Full Text Available Nephronophthisis (NPHP is an autosomal recessive cystic kidney disease and a leading genetic cause of established renal failure (ERF in children and young adults. Early presenting symptoms in children with NPHP include polyuria, nocturia, or secondary enuresis, pointing to a urinary concentrating defect. Renal ultrasound typically shows normal kidney size with increased echogenicity and corticomedullary cysts. Importantly, NPHP is associated with extra renal manifestations in 10–15% of patients. The most frequent extrarenal association is retinal degeneration, leading to blindness. Increasingly, molecular genetic testing is being utilised to diagnose NPHP and avoid the need for a renal biopsy. In this paper, we discuss the latest understanding in the molecular and cellular pathogenesis of NPHP. We suggest an appropriate clinical management plan and screening programme for individuals with NPHP and their families.

  6. Monitoring changes in genetic diversity

    CSIR Research Space (South Africa)

    Bruford, MW

    2018-01-01

    Full Text Available has thrived in many different environments over the billions of years, encoding its solutions into DNA—the heredity material. Thanks to this genetic patrimony, many species are equipped with sufficient evolutionary resi- lience to overcome rapid... for food, shelter, medicines, fuel and ecotourism income but may also include those that are ecologically important providing other key ecosystem services such as 120 M.W. Bruford et al. pollination, nutrient cycling and pest regulation (Bailey 2011...

  7. Genetic diversity, phylogeographic structure and effect of selection ...

    Indian Academy of Sciences (India)

    Abdulhakeem B. Ajibike

    2017-12-11

    Dec 11, 2017 ... RESEARCH ARTICLE. Genetic diversity, phylogeographic ... chickens as genetic resources towards ensuring food security. Keywords. genetic diversity ... PCR product as template DNA, 3.2 pmol of primer and. 8 μL of Big Dye ...

  8. Genetic diversity among endangered rare Dalbergia ...

    African Journals Online (AJOL)

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

  9. Genetic diversity of Cytospora chrysospermaisolates obtained from ...

    African Journals Online (AJOL)

    Cluster analysis of the data using Centroid method and Jaccard´s similarity coefficient, divided the isolates into six groups, showing a high genetic diversity among populations of C. chrysosperma. Although there was no correlation between geographical origins and the resulting groups of RAPD analysis, but the amount of ...

  10. Molecular diversity and genetic relationships in Secale

    Indian Academy of Sciences (India)

    The objective of this study was to quantify the molecular diversity and to determine the genetic relationships amongSecalespp. and among cultivars ofSecale ... Faculty of Sciences, Campo Grande, Lisboa, Portugal; Departamento de Genética, Facultad de Biologia, Universidad Complutense, C/ José Antonio Novais, 12, ...

  11. Neglect of genetic diversity in implementation of the Convention on Biological Diversity

    Science.gov (United States)

    Linda Laikre; Fred W. Allendorf; Laurel C. Aroner; C. Scott Baker; David P. Gregovich; Michael M. Hansen; Jennifer A. Jackson; Katherine C. Kendall; Kevin Mckelvey; Maile C. Neel; Isabelle Olivieri; Nils Ryman; Michael K. Schwartz; Ruth Short Bull; Jeffrey B. Stetz; David A. Tallmon; Barbara L. Taylor; Christina D. Vojta; Donald M. Waller; Robin S. Waples

    2009-01-01

    Genetic diversity is the foundation for all biological diversity; the persistence and evolutionary potential of species depend on it. World leaders have agreed on the conservation of genetic diversity as an explicit goal of the Convention on Biological Diversity (CBD). Nevertheless, actions to protect genetic diversity are largely lacking. With only months left to the...

  12. Does genetic diversity predict health in humans?

    Directory of Open Access Journals (Sweden)

    Hanne C Lie

    2009-07-01

    Full Text Available Genetic diversity, especially at genes important for immune functioning within the Major Histocompatibility Complex (MHC, has been associated with fitness-related traits, including disease resistance, in many species. Recently, genetic diversity has been associated with mate preferences in humans. Here we asked whether these preferences are adaptive in terms of obtaining healthier mates. We investigated whether genetic diversity (heterozygosity and standardized mean d(2 at MHC and nonMHC microsatellite loci, predicted health in 153 individuals. Individuals with greater allelic diversity (d(2 at nonMHC loci and at one MHC locus, linked to HLA-DRB1, reported fewer symptoms over a four-month period than individuals with lower d(2. In contrast, there were no associations between MHC or nonMHC heterozygosity and health. NonMHC-d(2 has previously been found to predict male preferences for female faces. Thus, the current findings suggest that nonMHC diversity may play a role in both natural and sexual selection acting on human populations.

  13. Genetic diversity of Ascaris in southwestern Uganda

    DEFF Research Database (Denmark)

    Betson, Martha; Nejsum, Peter; Llewellyn-Hughes, Julia

    2012-01-01

    . 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......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...

  14. Dr. John Marburger visits DESY

    CERN Multimedia

    2003-01-01

    Dr. John Marburger, Director of the United States Office of Science and Technology Policy, visited the research center DESY in Hamburg. The American physicist wanted to inform himself about the status of the TESLA X-ray laser and the TESLA linear collider as well as the international collaboration at DESY (1/2 page).

  15. Genetic diversity of Syrian Arabian horses.

    Science.gov (United States)

    Almarzook, S; Reissmann, M; Arends, D; Brockmann, G A

    2017-08-01

    Although Arabian horses have been bred in strains for centuries and pedigrees have been recorded in studbooks, to date, little is known about the genetic diversity within and between these strains. In this study, we tested if the three main strains of Syrian Arabian horses descend from three founders as suggested by the studbook. We examined 48 horses representing Saglawi (n = 18), Kahlawi (n = 16) and Hamdani (n = 14) strains using the Equine SNP70K BeadChip. For comparison, an additional 24 Arabian horses from the USA and three Przewalski's horses as an out group were added. Observed heterozygosis (H o ) ranged between 0.30 and 0.32, expected heterozygosity (H e ) between 0.30 and 0.31 and inbreeding coefficients (F is ) between -0.02 and -0.05, indicating high genetic diversity within Syrian strains. Likewise, the genetic differentiation between the three Syrian strains was very low (F st  horses. Among Arabian horses, we found three clusters containing either horses from the USA or horses from Syria or horses from Syria and the USA together. Individuals from the same Syrian Arabian horse strain were spread across different sub-clusters. When analyzing Syrian Arabian horses alone, the best population differentiation was found with three distinct clusters. In contrast to expectations from the studbook, these clusters did not coincide with strain affiliation. Although this finding supports the hypothesis of three founders, the genetic information is not consistent with the currently used strain designation system. The information can be used to reconsider the current breeding practice. Beyond that, Syrian Arabian horses are an important reservoir for genetic diversity. © 2017 Stichting International Foundation for Animal Genetics.

  16. Analysis of genetic diversity and construction of core collection of ...

    African Journals Online (AJOL)

    Jane

    2011-06-03

    Jun 3, 2011 ... Genetic diversity of 73 local mulberry varieties from Shanxi Province were screened using ISSR ... number effective of alleles, Nei's genetic diversity index and Shannon's ...... resources conservation program of the Agriculture.

  17. Global genetic diversity of Aedes aegypti.

    Science.gov (United States)

    Gloria-Soria, Andrea; Ayala, Diego; Bheecarry, Ambicadutt; Calderon-Arguedas, Olger; Chadee, Dave D; Chiappero, Marina; Coetzee, Maureen; Elahee, Khouaildi Bin; Fernandez-Salas, Ildefonso; Kamal, Hany A; Kamgang, Basile; Khater, Emad I M; Kramer, Laura D; Kramer, Vicki; Lopez-Solis, Alma; Lutomiah, Joel; Martins, Ademir; Micieli, Maria Victoria; Paupy, Christophe; Ponlawat, Alongkot; Rahola, Nil; Rasheed, Syed Basit; Richardson, Joshua B; Saleh, Amag A; Sanchez-Casas, Rosa Maria; Seixas, Gonçalo; Sousa, Carla A; Tabachnick, Walter J; Troyo, Adriana; Powell, Jeffrey R

    2016-11-01

    Mosquitoes, especially Aedes aegypti, are becoming important models for studying invasion biology. We characterized genetic variation at 12 microsatellite loci in 79 populations of Ae. aegypti from 30 countries in six continents, and used them to infer historical and modern patterns of invasion. Our results support the two subspecies Ae. aegypti formosus and Ae. aegypti aegypti as genetically distinct units. Ae. aegypti aegypti populations outside Africa are derived from ancestral African populations and are monophyletic. The two subspecies co-occur in both East Africa (Kenya) and West Africa (Senegal). In rural/forest settings (Rabai District of Kenya), the two subspecies remain genetically distinct, whereas in urban settings, they introgress freely. Populations outside Africa are highly genetically structured likely due to a combination of recent founder effects, discrete discontinuous habitats and low migration rates. Ancestral populations in sub-Saharan Africa are less genetically structured, as are the populations in Asia. Introduction of Ae. aegypti to the New World coinciding with trans-Atlantic shipping in the 16th to 18th centuries was followed by its introduction to Asia in the late 19th century from the New World or from now extinct populations in the Mediterranean Basin. Aedes mascarensis is a genetically distinct sister species to Ae. aegypti s.l. This study provides a reference database of genetic diversity that can be used to determine the likely origin of new introductions that occur regularly for this invasive species. The genetic uniqueness of many populations and regions has important implications for attempts to control Ae. aegypti, especially for the methods using genetic modification of populations. © 2016 John Wiley & Sons Ltd.

  18. Global Genetic Diversity of Aedes aegypti

    Science.gov (United States)

    Gloria-Soria, Andrea; Ayala, Diego; Bheecarry, Ambicadutt; Calderon-Arguedas, Olger; Chadee, Dave D.; Chiappero, Marina; Coetzee, Maureen; Elahee, Khouaildi bin; Fernandez-Salas, Ildefonso; Kamal, Hany A.; Kamgang, Basile; Khater, Emad I. M.; Kramer, Laura D.; Kramer, Vicki; Lopez-Solis, Alma; Lutomiah, Joel; Martins, Ademir; Micieli, Maria Victoria; Paupy, Christophe; Ponlawat, Alongkot; Rahola, Nil; Rasheed, Syed Basit; Richardson, Joshua B.; Saleh, Amag A.; Sanchez-Casas, Rosa Maria; Seixas, Gonçalo; Sousa, Carla A.; Tabachnick, Walter J.; Troyo, Adriana; Powell, Jeffrey R.

    2016-01-01

    Mosquitoes, especially Aedes aegypti, are becoming important models for studying invasion biology. We characterized genetic variation at 12 microsatellite loci in 79 populations of Ae. aegypti, from 30 countries in six continents and used them to infer historical and modern patterns of invasion. Our results support the two subspecies Ae. aegypti formosus and Ae. aegypti aegypti as genetically distinct units. Ae. aegypti aegypti populations outside Africa are derived from ancestral African populations and are monophyletic. The two subspecies co-occur in both East Africa (Kenya) and West Africa (Senegal). In rural/forest settings (Rabai District of Kenya) the two subspecies remain genetically distinct whereas in urban settings they introgress freely. Populations outside Africa are highly genetically structured likely due to a combination of recent founder effects, discrete discontinuous habitats, and low migration rates. Ancestral populations in sub-Saharan Africa are less genetically structured, as are the populations in Asia. Introduction of Ae. aegypti to the New World coinciding with trans-Atlantic shipping in the 16th to 18th Centuries was followed by its introduction to Asia in the late 19th Century from the New World or from now extinct populations in the Mediterranean Basin. Aedes mascarensis is a genetically distinct sister species to Ae. aegypti s.l.. This study provides a reference database of genetic diversity that can be used to determine the likely origin of new introductions that occur regularly for this invasive species. The genetic uniqueness of many populations and regions has important implications for attempts to control Ae. aegypti, especially for methods using genetic modification of populations. PMID:27671732

  19. Managing genetic diversity and society needs

    Directory of Open Access Journals (Sweden)

    Arthur da Silva Mariante

    2008-07-01

    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.

  20. Genetic diversity of Coccidioides posadasii from Brazil.

    Science.gov (United States)

    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

    2013-05-01

    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.

  1. Genetic diversity among farmer-preferred cassava landraces in ...

    African Journals Online (AJOL)

    Understanding of genetic diversity among a breeding population is an important requirement for crop improvement as it allows for the selection of diverse parental combinations and formation of heterotic pools for genetic gain. This study was carried out to determine genetic diversity within and among 51 farmer-preferred ...

  2. Assessment of the genetic diversity and pattern of relationship of ...

    African Journals Online (AJOL)

    An understanding of the extent, distribution and patterns of genetic variation is useful for estimation of any possible loss of genetic diversity and assessment of genetic variability and its potential use in breeding programs, including establishment of heterotic groups. This study assessed patterns of genetic diversity and ...

  3. Genetic diversity of four protected indigenous chicken breeds in ...

    African Journals Online (AJOL)

    joining method. Its topology reflects the general pattern of genetic differentiation among the four chicken breeds. The results also showed high genetic diversity and genetic variation among all the breeds. The information about the four local ...

  4. GENETIC DIVERSITY IN CZECH HAFLINGER HORSES

    Directory of Open Access Journals (Sweden)

    Luboš Vostrý

    2015-09-01

    Full Text Available The Haflinger as a small moutain horse breed originated from the South Tyrol district as a cross of Alpen Mountain breeds with Araber. This breed was expanding to Czech Republic during the last 25 years. The aim of this study was to analyse genetic diversity within the population using microsatellite markers. A total of 95 alleles have been detected. The highest frequency 88.18% showed allele 101 (HTG 6. The heterosigosity varied from 0.25 (HTG 6 to 0.84 (VHL 20, genetic diversity reached 0.6–0.8. The heterozygosity of the whole population studied is FIS= -0.013. The average effective number of allele per locus was 2.93 with standard deviation 1.54, with minimal and maximal level 1.30 and 7.83, respectively. Average polymorphism information content per locus was 0.608 with standard derivation 0.146, with minimal and maximal level 0.208 and 0.824, respectively. The results showed that breeding program of Czech Haflinger is optimal, including optimized mating strategies. The diversity of the population Czech Haflinger, based on a small number of microsatellites, seems to be sufficient.

  5. Genetic Diversity of Koala Retroviral Envelopes

    Directory of Open Access Journals (Sweden)

    Wenqin Xu

    2015-03-01

    Full Text Available Genetic diversity, attributable to the low fidelity of reverse transcription, recombination and mutation, is an important feature of infectious retroviruses. Under selective pressure, such as that imposed by superinfection interference, gammaretroviruses commonly adapt their envelope proteins to use alternative receptors to overcome this entry block. The first characterized koala retroviruses KoRV subgroup A (KoRV-A were remarkable in their absence of envelope genetic variability. Once it was determined that KoRV-A was present in all koalas in US zoos, regardless of their disease status, we sought to isolate a KoRV variant whose presence correlated with neoplastic malignancies. More than a decade after the identification of KoRV-A, we isolated a second subgroup of KoRV, KoRV-B from koalas with lymphomas. The envelope proteins of KoRV-A and KoRV-B are sufficiently divergent to confer the ability to bind and employ distinct receptors for infection. We have now obtained a number of additional KoRV envelope variants. In the present studies we report these variants, and show that they differ from KoRV-A and KoRV-B envelopes in their host range and superinfection interference properties. Thus, there appears to be considerable variation among KoRVs envelope genes suggesting genetic diversity is a factor following the KoRV-A infection process.

  6. Studies of Reservoir Hosts for Marburg virus

    DEFF Research Database (Denmark)

    Swanepoel, Robert; Smit, Sheilagh B; Rollin, Pierre E

    2007-01-01

    To determine reservoir hosts for Marburg virus (MARV), we examined the fauna of a mine in northeastern Democratic Republic of the Congo. The mine was associated with a protracted outbreak of Marburg hemorrhagic fever during 1998-2000. We found MARV nucleic acid in 12 bats, comprising 3.0%-3.6% of...

  7. Review: Genetic diversity and population structure of cotton ...

    African Journals Online (AJOL)

    Cotton (Gossypium spp.) is the world's leading natural fiber crop and is cultivated in diverse temperate and tropical areas. In this sense, molecular markers are important tools for polymorphism identification in genetic diversity analyses. The objective of this study was to evaluate genetic diversity and population structure in ...

  8. Assessment of genetic diversity among sugarcane cultivars using ...

    African Journals Online (AJOL)

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

  9. Genetic diversity and bottleneck studies in the Marwari horse breed

    Indian Academy of Sciences (India)

    Unknown

    [Gupta A. K., Chauhan M., Tandon S. N. and Sonia 2005 Genetic diversity and bottleneck studies in the Marwari horse breed. J. Genet. 84, 295–301] ... developed to carry out studies of genetic variation (Brad- ley et al. 1996; Canon et al. ..... 1996 Mitochondrial diversity and the origins of African and. European cattle. Proc.

  10. Loss of Genetic Diversity of Jatropha curcas L. through Domestication: Implications for Its Genetic Improvement

    DEFF Research Database (Denmark)

    Sanou, Haby; Angel Angulo-Escalante, Miguel; Martinez-Herrera, Jorge

    2015-01-01

    Jatropha curcas L. has been promoted as a “miracle” tree in many parts of the world, but recent studies have indicated very low levels of genetic diversity in various landraces. In this study, the genetic diversity of landrace collections of J. curcas was compared with the genetic diversity...

  11. Evaluation of genetic diversity of Portuguese Pinus sylvestris L ...

    Indian Academy of Sciences (India)

    Thus, with this study, we intend to evaluate the genetic diversity, structure and relationships of ... Carlo (MCMC) iterations, and different values of K (number of populations). .... such as tree form diversity and forest stand condition. According to ...

  12. Loss of genetic diversity in Maculinea populations over 10 years

    DEFF Research Database (Denmark)

    Nash, David Richard; Lomborg, Andreas Eg

    I will present the results of research on the population genetics of Maculinea alcon and M. arion in Southern scandinavia, which shows a strong decrease in genetic diversity in most populations, even if those populations are apparently otherwise healthy....

  13. Molecular analysis of genetic diversity in elite II synthetic hexaploid ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-07-20

    Jul 20, 2009 ... The presence of sufficient genetic diversity in the germplam is an important ..... Figure 1. PCR amplification profile of Elite-II SH Wheat using the primer OPG-2. .... genetic relationships among cowpea breeding lines and local.

  14. Genetic diversity of sweet potatoes collection from Northeastern Brazil

    African Journals Online (AJOL)

    Ana Veruska Cruz da Silva Muniz

    2014-02-24

    Feb 24, 2014 ... RAPD was efficient for the analysis of genetic diversity to identify groups and measure the genetic distance between ..... management program. We recommend ... The author(s) have not declared any conflict of interests.

  15. Molecular characterization and assessment of genetic diversity of ...

    African Journals Online (AJOL)

    R Madhusudhana

    genetic diversity available at molecular level among a set of phenotypically different ... allele matching and cluster analysis based on unweighted neighbor- joining (Gascuel, 1997) ..... on isozyme data-a simulation study. Theor. Appl. Genet.

  16. Molecular characterization of genetic diversity in some durum wheat ...

    African Journals Online (AJOL)

    Molecular characterization of genetic diversity in some durum wheat ... African Journal of Biotechnology ... Thus, RAPD offer a potentially simple, rapid and reliable method to evaluate genetic variation and relatedness among ten wheat ...

  17. Genetic diversity of Colletotrichum gloeosporioides in Nigeria using ...

    African Journals Online (AJOL)

    fmodupe

    2012-04-24

    Apr 24, 2012 ... gloeosporioides isolates and was effective in establishing genetic relationships ... Key words: Anthracnose disease, pathotypes, genetic diversity, amplified ..... isolates to use in an anthracnose resistance screening program.

  18. Genetic diversity of grape germplasm as revealed by microsatellite ...

    African Journals Online (AJOL)

    aghomotsegin

    In this work, cluster analysis and principal component analysis (PCA) were used to study the genetic ... Key words: Vitis vinifera L., simple sequence repeat (SSR), genetic diversity, .... The data were used for the following statistical analyses.

  19. Genetic diversity and species diversity of stream fishes covary across a land-use gradient

    Science.gov (United States)

    Blum, M.J.; Bagley, M.J.; Walters, D.M.; Jackson, S.A.; Daniel, F.B.; Chaloud, D.J.; Cade, B.S.

    2012-01-01

    Genetic diversity and species diversity are expected to covary according to area and isolation, but may not always covary with environmental heterogeneity. In this study, we examined how patterns of genetic and species diversity in stream fishes correspond to local and regional environmental conditions. To do so, we compared population size, genetic diversity and divergence in central stonerollers (Campostoma anomalum) to measures of species diversity and turnover in stream fish assemblages among similarly sized watersheds across an agriculture-forest land-use gradient in the Little Miami River basin (Ohio, USA). Significant correlations were found in many, but not all, pair-wise comparisons. Allelic richness and species richness were strongly correlated, for example, but diversity measures based on allele frequencies and assemblage structure were not. In-stream conditions related to agricultural land use were identified as significant predictors of genetic diversity and species diversity. Comparisons to population size indicate, however, that genetic diversity and species diversity are not necessarily independent and that variation also corresponds to watershed location and glaciation history in the drainage basin. Our findings demonstrate that genetic diversity and species diversity can covary in stream fish assemblages, and illustrate the potential importance of scaling observations to capture responses to hierarchical environmental variation. More comparisons according to life history variation could further improve understanding of conditions that give rise to parallel variation in genetic diversity and species diversity, which in turn could improve diagnosis of anthropogenic influences on aquatic ecosystems. ?? 2011 Springer-Verlag.

  20. Investigation of genetic diversity in flixweed ( Descurainia sophia ...

    African Journals Online (AJOL)

    Investigation of genetic diversity in flixweed ( Descurainia sophia ) germplasm from Kerman province using inter-simple sequence repeat (ISSR) and random amplified polymorphic DNA (RAPD) molecular markers.

  1. Molecular research on the genetic diversity of Tunisian date palm ...

    African Journals Online (AJOL)

    Molecular research on the genetic diversity of Tunisian date palm ( Phoenix dactylifera L.) using the random amplified microsatellite polymorphism (RAMPO) and amplified fragment length polymorphism (AFLP) methods.

  2. Restoration of coral populations in light of genetic diversity estimates

    Science.gov (United States)

    Shearer, T. L.; Porto, I.; Zubillaga, A. L.

    2009-09-01

    Due to the importance of preserving the genetic integrity of populations, strategies to restore damaged coral reefs should attempt to retain the allelic diversity of the disturbed population; however, genetic diversity estimates are not available for most coral populations. To provide a generalized estimate of genetic diversity (in terms of allelic richness) of scleractinian coral populations, the literature was surveyed for studies describing the genetic structure of coral populations using microsatellites. The mean number of alleles per locus across 72 surveyed scleractinian coral populations was 8.27 (±0.75 SE). In addition, population genetic datasets from four species ( Acropora palmata, Montastraea cavernosa, Montastraea faveolata and Pocillopora damicornis) were analyzed to assess the minimum number of donor colonies required to retain specific proportions of the genetic diversity of the population. Rarefaction analysis of the population genetic datasets indicated that using 10 donor colonies randomly sampled from the original population would retain >50% of the allelic diversity, while 35 colonies would retain >90% of the original diversity. In general, scleractinian coral populations are genetically diverse and restoration methods utilizing few clonal genotypes to re-populate a reef will diminish the genetic integrity of the population. Coral restoration strategies using 10-35 randomly selected local donor colonies will retain at least 50-90% of the genetic diversity of the original population.

  3. Genetic diversity within a dominant plant outweighs plant species diversity in structuring an arthropod community.

    Science.gov (United States)

    Crawford, Kerri M; Rudgers, Jennifer A

    2013-05-01

    Plant biodiversity is being lost at a rapid rate. This has spurred much interest in elucidating the consequences of this loss for higher trophic levels. Experimental tests have shown that both plant species diversity and genetic diversity within a plant species can influence arthropod community structure. However, the majority of these studies have been conducted in separate systems, so their relative importance is currently unresolved. Furthermore, potential interactions between the two levels of diversity, which likely occur in natural systems, have not been investigated. To clarify these issues, we conducted three experiments in a freshwater sand dune ecosystem. We (1) independently manipulated plant species diversity, (2) independently manipulated genetic diversity within the dominant plant species, Ammophila breviligulata, and (3) jointly manipulated genetic diversity within the dominant plant and species diversity. We found that genetic diversity within the dominant plant species, Ammophila breviligulata, more strongly influenced arthropod communities than plant species diversity, but this effect was dependent on the presence of other species. In species mixtures, A. breviligulata genetic diversity altered overall arthropod community composition, and arthropod richness and abundance peaked at the highest level of genetic diversity. Positive nonadditive effects of diversity were detected, suggesting that arthropods respond to emergent properties of diverse plant communities. However, in the independent manipulations where A. breviligulata was alone, effects of genetic diversity were weaker, with only arthropod richness responding. In contrast, plant species diversity only influenced arthropods when A. breviligulata was absent, and then only influenced herbivore abundance. In addition to showing that genetic diversity within a dominant plant species can have large effects on arthropod community composition, these results suggest that understanding how species

  4. Population genetic diversity and fitness in multiple environments

    Directory of Open Access Journals (Sweden)

    McGreevy Thomas J

    2010-07-01

    Full Text Available Abstract Background When a large number of alleles are lost from a population, increases in individual homozygosity may reduce individual fitness through inbreeding depression. Modest losses of allelic diversity may also negatively impact long-term population viability by reducing the capacity of populations to adapt to altered environments. However, it is not clear how much genetic diversity within populations may be lost before populations are put at significant risk. Development of tools to evaluate this relationship would be a valuable contribution to conservation biology. To address these issues, we have created an experimental system that uses laboratory populations of an estuarine crustacean, Americamysis bahia with experimentally manipulated levels of genetic diversity. We created replicate cultures with five distinct levels of genetic diversity and monitored them for 16 weeks in both permissive (ambient seawater and stressful conditions (diluted seawater. The relationship between molecular genetic diversity at presumptive neutral loci and population vulnerability was assessed by AFLP analysis. Results Populations with very low genetic diversity demonstrated reduced fitness relative to high diversity populations even under permissive conditions. Population performance decreased in the stressful environment for all levels of genetic diversity relative to performance in the permissive environment. Twenty percent of the lowest diversity populations went extinct before the end of the study in permissive conditions, whereas 73% of the low diversity lines went extinct in the stressful environment. All high genetic diversity populations persisted for the duration of the study, although population sizes and reproduction were reduced under stressful environmental conditions. Levels of fitness varied more among replicate low diversity populations than among replicate populations with high genetic diversity. There was a significant correlation

  5. Wasserversorgung und Entsorgung des Deutschordenshauses Marburg

    DEFF Research Database (Denmark)

    Atzbach, Rainer

    2009-01-01

    The residence of the German Order possessed an elaborated system of water supply and sanitation, which was using lead tubes since the 13th. c. AD. The St. Elizabeth-Church in Marburg was connected with its sanitation system.......The residence of the German Order possessed an elaborated system of water supply and sanitation, which was using lead tubes since the 13th. c. AD. The St. Elizabeth-Church in Marburg was connected with its sanitation system....

  6. Inbred or Outbred? Genetic Diversity in Laboratory Rodent Colonies

    Science.gov (United States)

    Brekke, Thomas D.; Steele, Katherine A.; Mulley, John F.

    2017-01-01

    Nonmodel rodents are widely used as subjects for both basic and applied biological research, but the genetic diversity of the study individuals is rarely quantified. University-housed colonies tend to be small and subject to founder effects and genetic drift; so they may be highly inbred or show substantial genetic divergence from other colonies, even those derived from the same source. Disregard for the levels of genetic diversity in an animal colony may result in a failure to replicate results if a different colony is used to repeat an experiment, as different colonies may have fixed alternative variants. Here we use high throughput sequencing to demonstrate genetic divergence in three isolated colonies of Mongolian gerbil (Meriones unguiculatus) even though they were all established recently from the same source. We also show that genetic diversity in allegedly “outbred” colonies of nonmodel rodents (gerbils, hamsters, house mice, deer mice, and rats) varies considerably from nearly no segregating diversity to very high levels of polymorphism. We conclude that genetic divergence in isolated colonies may play an important role in the “replication crisis.” In a more positive light, divergent rodent colonies represent an opportunity to leverage genetically distinct individuals in genetic crossing experiments. In sum, awareness of the genetic diversity of an animal colony is paramount as it allows researchers to properly replicate experiments and also to capitalize on other genetically distinct individuals to explore the genetic basis of a trait. PMID:29242387

  7. Genetic diversity and population structure of common bean ...

    African Journals Online (AJOL)

    The Ethiopian genetic center is considered to be one of the secondary centers of diversity for the common bean. This study was conducted to characterize the distribution of genetic diversity between and within ecological/geographical regions of Ethiopia. A germplasm sample of 116 landrace accessions was developed, ...

  8. Genetic diversity study of common bean ( Phaseolus vulgaris L ...

    African Journals Online (AJOL)

    In PCoA, majority individuals of Metekel (L) tended to form separate group. The result of the study confirmed the presence of genetic diversity that can be exploited to improve the productivity. This calls for a conserted efforts in the collection, conservation and sustainable use of P. vulgaris. Keywords: Genetic diversity, ISSR, ...

  9. DNA landmarks for genetic diversity assessment in tea genotypes ...

    African Journals Online (AJOL)

    Tea (Camellia sinensis) is one of the most important non-alcoholic beverages of the world. Natural genetic diversity in tea has been reduced due to continue selection in favor of desirable traits. The present study was conducted to estimate genetic diversity in tea genotypes cultivated in Pakistan using 20 randomly amplified ...

  10. Genetic diversity studies of Kherigarh cattle based on microsatellite ...

    Indian Academy of Sciences (India)

    agricultural plant species, most or all genetic diversity in live- stock exists within ..... African cattle breeds (0.506–0.697; Ibeagha-Awemu et al. 2004). However .... relationships among populations of Asian goats (Capra hircus). J. Anim. Breed. ... 120,. 73–87. Kim K. S., Yeo J. S. and Choi C. B. 2002 Genetic diversity of north-.

  11. Study on genetic diversity in Pakistani wheat varieties using simple ...

    African Journals Online (AJOL)

    Common wheat ( Triticum aestivum L.) is a grass species, cultivated world wide. Globally, it is the most important human food grain and ranks second in total production as a cereal crop behind maize. Genetic diversity evaluation of germplasm is the basis of improvement in wheat. In the present study genetic diversity of 10 ...

  12. Assessment of genetic diversity among sixty bread wheat ( Triticum ...

    African Journals Online (AJOL)

    Assessment of genetic diversity among wheat cultivars is important to ensure that a continuous pool of cultivars with varying desirable traits is maintained. In view of this, a molecular study was conducted to assess the genetic diversity of sixty wheat cultivars using sixty microsatellite markers. Amplified alleles from each ...

  13. Genetic diversity of Pakistani maize genotypes using chromosome ...

    African Journals Online (AJOL)

    For improvement of maize crop presence of genetic diversity in the germplasm is very important. This study was conducted to determine genetic diversity among 17 Pakistani maize genotypes using 10 simple sequence repeat (SSR) primer sets. All the amplification products were in the range of <250-750 bp. To estimate the ...

  14. Genetic diversity and population structure of Chinese honeybees ...

    African Journals Online (AJOL)

    Genetic diversity and population structure of Chinese honeybees (Apis cerana) under microsatellite markers. T Ji, L Yin, G Chen. Abstract. Using 21 microsatellite markers and PCR method, the polymorphisms of 20 Apis cerana honeybee populations across China was investigated and the genetic structure and diversity of ...

  15. Assessment of genetic diversity in Isabgol (Plantago ovata Forsk ...

    African Journals Online (AJOL)

    sandeep kaswan

    improvement of this crop (Dhar et al., 2005). Therefore, it is necessary to analyze or examine the genetic diversity provided by the gene pools and then harnessed for crop improvement. The concept of molecular marker is an ideal approach for this purpose. They are reliable indicator of genetic diversity because they are ...

  16. Genetic diversity and population structure of maize landraces from ...

    African Journals Online (AJOL)

    Genetic diversity and population structure of maize landraces from Côte ... However, no study on the genetic diversity of the species has been performed to date. ... The cross between two individuals from different groups might help exploit the ...

  17. Genetic diversity and bottleneck studies in the Marwari horse breed

    Indian Academy of Sciences (India)

    Genetic diversity within the Marwari breed of horses was evaluated using 26 different microsatellite pairs with 48 DNA samples from unrelated horses. This molecular characterisation was undertaken to evaluate the problem of genetic bottlenecks also, if any, in this breed. The estimated mean (± s.e.) allelic diversity was 5.9 ...

  18. Genetic diversity analysis of rice cultivars from various origins using ...

    African Journals Online (AJOL)

    Genetic diversity is of paramount importance for the success of any plant breeding program. An experiment was conducted to assess the extent of genetic diversity and similarity of 24 rice cultivars from various origins using 29 simple sequence repeat (SSR) markers. A total of 144 alleles were detected at the 29 SSR primer ...

  19. Does genetic diversity hinder parasite evolution in social insect colonies?

    DEFF Research Database (Denmark)

    Hughes, William Owen Hamar; Boomsma, Jacobus Jan

    2006-01-01

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

  20. Beauveria bassiana: quercetinase production and genetic diversity

    Directory of Open Access Journals (Sweden)

    Eula Maria de M. B Costa

    2011-03-01

    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.

  1. Beauveria bassiana: Quercetinase production and genetic diversity

    Science.gov (United States)

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

    2011-01-01

    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

  2. Genetic diversity of Echinococcus spp. in Russia.

    Science.gov (United States)

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

    2013-11-01

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

  3. Comparative riverscape genetics reveals reservoirs of genetic diversity for conservation and restoration of Great Plains fishes.

    Science.gov (United States)

    Osborne, Megan J; Perkin, Joshuah S; Gido, Keith B; Turner, Thomas F

    2014-12-01

    We used comparative landscape genetics to examine the relative roles of historical events, intrinsic traits and landscape factors in determining the distribution of genetic diversity of river fishes across the North American Great Plains. Spatial patterns of diversity were overlaid on a patch-based graphical model and then compared within and among three species that co-occurred across five Great Plains watersheds. Species differing in reproductive strategy (benthic vs. pelagic-spawning) were hypothesized to have different patterns of genetic diversity, but the overriding factor shaping contemporary patterns of diversity was the signature of past climates and geological history. Allelic diversity was significantly higher at southern latitudes for Cyprinella lutrensis and Hybognathus placitus, consistent with northward expansion from southern Pleistocene refugia. Within the historical context, all species exhibited lowered occupancy and abundance in heavily fragmented and drier upstream reaches, particularly H. placitus; a pelagic-spawning species, suggesting rates of extirpation have outpaced losses of genetic diversity in this species. Within most tributary basins, genetically diverse populations of each species persisted. Hence, reconnecting genetically diverse populations with those characterized by reduced diversity (regardless of their position within the riverine network) would provide populations with greater genetic and demographic resilience. We discuss cases where cross-basin transfer may be appropriate to enhance genetic diversity and mitigate negative effects of climate change. Overall, striking similarities in genetic patterns and in response to fragmentation and dewatering suggest a common strategy for genetic resource management in this unique riverine fish assemblage. © 2014 John Wiley & Sons Ltd.

  4. Assessment of the genetic diversity of Kenyan coconut germplasm ...

    African Journals Online (AJOL)

    Genetic diversity and relationship among 48 coconut individuals (Cocos nucifera L.) collections from the Coastal lowland of Kenya were analyzed using 15 simple sequence repeat (SSR) primer pairs. Diversity parameters were calculated using Popgene Software version 1.31. The gene diversity values ranged from 0.0408 ...

  5. Genetic diversity in Cucurbita pepo landraces from northern ...

    African Journals Online (AJOL)

    The dendrogram mainly grouped the populations according to their mature fruit colour, and then according to their geographical origin. All genetic parameters indicated that there was plentiful genetic diversity in C. pepo landraces of northern KwaZulu-Natal, South Africa. Key words: Cucurbita pepo landraces, genetic ...

  6. Contrasting genetic diversity among Oryza longistaminata (A. Chev ...

    African Journals Online (AJOL)

    Molecular markers have been used extensively in studying genetic diversity, genetic relationships and germplasm management. However, the understanding of between and within population genetic variation and how it is partitioned on the basis of geographic origin is crucial as this helps to improve sampling efficiency.

  7. Genetic diversity of canine olfactory receptors

    Directory of Open Access Journals (Sweden)

    Hitte Christophe

    2009-01-01

    Full Text Available Abstract Background Evolution has resulted in large repertoires of olfactory receptor (OR genes, forming the largest gene families in mammalian genomes. Knowledge of the genetic diversity of olfactory receptors is essential if we are to understand the differences in olfactory sensory capability between individuals. Canine breeds constitute an attractive model system for such investigations. Results We sequenced 109 OR genes considered representative of the whole OR canine repertoire, which consists of more than 800 genes, in a cohort of 48 dogs of six different breeds. SNP frequency showed the overall level of polymorphism to be high. However, the distribution of SNP was highly heterogeneous among OR genes. More than 50% of OR genes were found to harbour a large number of SNP, whereas the rest were devoid of SNP or only slightly polymorphic. Heterogeneity was also observed across breeds, with 25% of the SNP breed-specific. Linkage disequilibrium within OR genes and OR clusters suggested a gene conversion process, consistent with a mean level of polymorphism higher than that observed for introns and intergenic sequences. A large proportion (47% of SNP induced amino-acid changes and the Ka/Ks ratio calculated for all alleles with a complete ORF indicated a low selective constraint with respect to the high level of redundancy of the olfactory combinatory code and an ongoing pseudogenisation process, which affects dog breeds differently. Conclusion Our demonstration of a high overall level of polymorphism, likely to modify the ligand-binding capacity of receptors distributed differently within the six breeds tested, is the first step towards understanding why Labrador Retrievers and German Shepherd Dogs have a much greater potential for use as sniffer dogs than Pekingese dogs or Greyhounds. Furthermore, the heterogeneity in OR polymorphism observed raises questions as to why, in a context in which most OR genes are highly polymorphic, a subset of

  8. Effects of complex life cycles on genetic diversity: cyclical parthenogenesis.

    Science.gov (United States)

    Rouger, R; Reichel, K; Malrieu, F; Masson, J P; Stoeckel, S

    2016-11-01

    Neutral patterns of population genetic diversity in species with complex life cycles are difficult to anticipate. Cyclical parthenogenesis (CP), in which organisms undergo several rounds of clonal reproduction followed by a sexual event, is one such life cycle. Many species, including crop pests (aphids), human parasites (trematodes) or models used in evolutionary science (Daphnia), are cyclical parthenogens. It is therefore crucial to understand the impact of such a life cycle on neutral genetic diversity. In this paper, we describe distributions of genetic diversity under conditions of CP with various clonal phase lengths. Using a Markov chain model of CP for a single locus and individual-based simulations for two loci, our analysis first demonstrates that strong departures from full sexuality are observed after only a few generations of clonality. The convergence towards predictions made under conditions of full clonality during the clonal phase depends on the balance between mutations and genetic drift. Second, the sexual event of CP usually resets the genetic diversity at a single locus towards predictions made under full sexuality. However, this single recombination event is insufficient to reshuffle gametic phases towards full-sexuality predictions. Finally, for similar levels of clonality, CP and acyclic partial clonality (wherein a fixed proportion of individuals are clonally produced within each generation) differentially affect the distribution of genetic diversity. Overall, this work provides solid predictions of neutral genetic diversity that may serve as a null model in detecting the action of common evolutionary or demographic processes in cyclical parthenogens (for example, selection or bottlenecks).

  9. Genetic diversity as assessed by morphological and microsatellite ...

    African Journals Online (AJOL)

    lap

    2012-10-18

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

  10. Genetic diversity in Oroxylum indicum (L.) Vent. (Bignoniaceae), a ...

    African Journals Online (AJOL)

    SERVER

    2008-02-05

    Feb 5, 2008 ... Keywords: Conservation, genetic diversity, Oroxylum indicum, RAPD (Random Amplified Polymorphic DNA). ... Srilanka, Philippines and Indonesia. In India it is distri- .... indicum since pollination occurs by bats and black ...

  11. Effects of space flight factors on genetic diversity of Buchloe ...

    African Journals Online (AJOL)

    Jane

    2011-10-05

    Oct 5, 2011 ... results for wheat coleoptiles, lettuce hypocotyls, and garden-cress ... space radiation dose for plant seeds at linear energy transfer (LET) space was 4.79 ... information content (PIC), total genetic diversity of materials i and j.

  12. Genetic Diversity in Sub continental Land race cultivars

    African Journals Online (AJOL)

    M. shahbaz

    2012-05-31

    May 31, 2012 ... 1Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan. ... Narrowing genetic diversity is a limiting factor in wheat breeding. .... DNA was extracted following the modified.

  13. Analysis of genetic diversity in Arrhenatherum elatius Germplasm ...

    African Journals Online (AJOL)

    Jane

    2011-07-25

    Jul 25, 2011 ... The genetic diversity of 19 Arrhenatherum elatius accessions was analyzed ... can be used as novel DNA markers for genomic .... phylogenies and evolutionary biology. .... struction Project of the Beijing Academy of Agriculture.

  14. Genetic diversity of sweet potatoes collection from Northeastern Brazil

    African Journals Online (AJOL)

    Ana Veruska Cruz da Silva Muniz

    2014-02-24

    Feb 24, 2014 ... RAPD was efficient for the analysis of genetic diversity to identify groups and measure the .... the molecular characterization of accessions using RAPD ..... clusters of individuals using the software Structure: a simulation study.

  15. Genetic diversity in coastal and inland desert populations of ...

    African Journals Online (AJOL)

    ajl yemi

    2011-11-14

    Nov 14, 2011 ... 0.00196 showed low degree of differentiation among populations. .... number of amplification products per primer varied from 6 to 14, and these ..... strategies on genetic diversity estimates obtained with RAPD markers in ...

  16. Assessment of the genetic diversity of Kenyan coconut germplasm ...

    African Journals Online (AJOL)

    HP-PROBOOK

    2016-10-05

    Oct 5, 2016 ... Genetic diversity and relationship among 48 coconut individuals (Cocos nucifera L.) collections from ... Cluster analysis was constructed using DARwin program version 6.0. ... effective crop improvement programme.

  17. Genetic diversity study of common bean (Phaseolus vulgaris L ...

    African Journals Online (AJOL)

    SAM

    2014-09-03

    Sep 3, 2014 ... Key words: Genetic diversity, ISSR, Phaseolus vulgaris. INTRODUCTION ..... effective germplasm conservation and for setting germ- plasm collection ... conservation and research programs of the species. Furthermore, the ...

  18. Analysis of genetic diversity in chickpea ( Cicer arietinum L ...

    African Journals Online (AJOL)

    Genetic diversity of seven chickpea (Cicer arietinum L.) cultivars of Pakistani origin ... effective method to determine the variations among the chickpea cultivars. ... to broaden the germplasm base in the future for chickpea breeding programs.

  19. Assessing the genetic diversity of 48 groundnut ( Arachis hypogaea ...

    African Journals Online (AJOL)

    Assessing the genetic diversity of 48 groundnut ( Arachis hypogaea L. ) ... both at the phenotypic and molecular level is important in all plant breeding programs. ... other and could therefore serve as effective parental material for future work.

  20. Analysis of genetic diversity and estimation of inbreeding coefficient ...

    African Journals Online (AJOL)

    STORAGESEVER

    2010-01-18

    Jan 18, 2010 ... Key words: Genetic diversity, microsatellite markers, Caspian horse breed. INTRODUCTION ... heterozygosity, observed and effective number of alleles at each ... computer program version 1.31 (Yeh et al., 1999). Based on ...

  1. Genetic diversity of Bambara groundnut (Vigna subterranea (L ...

    African Journals Online (AJOL)

    FORRESTER

    2015-01-28

    Jan 28, 2015 ... The existence of genetic diversity in germplasm collections is crucial for cultivar development. ... program for Bambara groundnut, a thorough under- ..... na* = Observed number of alleles; ne* = Effective number of alleles ...

  2. Analysis of genetic diversity in mango ( Mangifera indica L.) using ...

    African Journals Online (AJOL)

    Analysis of genetic diversity in mango ( Mangifera indica L.) using isozymetic polymorphism. ... All the isozymes, used in the present study showed polymorphism for mango. A total of 25 different electrophoretic ... HOW TO USE AJOL.

  3. Appraisal of biochemical and genetic diversity of mango cultivars ...

    African Journals Online (AJOL)

    Appraisal of biochemical and genetic diversity of mango cultivars using molecular markers. ... Mango (Mangifera indica L.) is one of the oldest fruit crops and is broadly cultivated worldwide. To determine the level of ... HOW TO USE AJOL.

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

    African Journals Online (AJOL)

    STORAGESEVER

    2009-09-15

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

  5. Genetic diversity for nutritional traits in the leaves of baobab ...

    African Journals Online (AJOL)

    User

    Key words: Adansonia digitata, Genetic variability, diversity, populations, and clusters. INTRODUCTION ... competition with the crops for nutrient, water, and sunlight, more ... (11° 11'N, 07° 38'E, attitude 688 m above sea level). The experiment ...

  6. Effects of landscape fragmentation on genetic diversity of Stipa ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-08-04

    Aug 4, 2009 ... Effects of landscape fragmentation on genetic diversity of Stipa krylovii ..... nation plant tends to anemophily, this pollination mode enable it to have the .... sity on newly isolated tropical islands: a test of a null hypothesis and.

  7. Genetic diversity in three morphological types of Astragalus ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-09-15

    Sep 15, 2009 ... high genetic diversity suggested that each type had a potential to develop new strains or cultivars and .... herbs and widespread distributed species (Yao et al.,. 2008) ... 1) A. membranaceus var. mongholicus is a cross-.

  8. Human immunodeficiency virus type-1 (HIV-1) genetic diversity and ...

    African Journals Online (AJOL)

    PROGMANAGER

    2013-04-24

    Apr 24, 2013 ... objective of this study was to determine the genetic diversity of HIV-1 and the prevalence of antiretroviral (ARV) ... individuals in resource limited settings. Key words: ... management of HIV infection even as antiretroviral (ARV).

  9. Genetic diversity, classification and comparative study on the larval ...

    African Journals Online (AJOL)

    Genetic diversity, classification and comparative study on the larval phenotypic ... B. mori showed different performance based on larval phenotypic data. The analysis of variance regarding the studied traits showed that different strains have ...

  10. Assessment of the genetic diversity and pattern of relationship of ...

    African Journals Online (AJOL)

    SAM

    2014-04-02

    Apr 2, 2014 ... Cluster and principal coordinate analysis of the 30 ... The FST value (0.63) indicated a very high genetic differentiation as expected for ..... diversity) using Markov chain method showed that the ..... WL, Lee M, Porter K (2000).

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

    African Journals Online (AJOL)

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

  12. Morphological classification of genetic diversity in cultivated okra ...

    African Journals Online (AJOL)

    Morphological classification of genetic diversity in cultivated okra, Abelmoschus esculentus (L) Moench using principal component analysis (PCA) and single linkage cluster analysis (SLCA). CC Nwangburuka, OB Kehinde, DK Ojo, OA Denton, AR Popoola ...

  13. Analysis of genetic diversity inpigeonpeagermplasm using ...

    Indian Academy of Sciences (India)

    Navya

    2016-11-25

    Nov 25, 2016 ... accessions from Orissa (105) and AP (15) do not group with any Indian accessions. ... In the present work, comparison between SSAP and REMAP revealed ... (sequence-specific amplified polymorphism) for genetic analysis of sweet potato. ... Sharma,V.and Nandinemi, M.R. 2014 Assessment of genetic ...

  14. Genetic diversity, population structure, and traditional culture of Camellia reticulata.

    Science.gov (United States)

    Xin, Tong; Huang, Weijuan; De Riek, Jan; Zhang, Shuang; Ahmed, Selena; Van Huylenbroeck, Johan; Long, Chunlin

    2017-11-01

    Camellia reticulata is an arbor tree that has been cultivated in southwestern China by various sociolinguistic groups for esthetic purposes as well as to derive an edible seed oil. This study examined the influence of management, socio-economic factors, and religion on the genetic diversity patterns of Camellia reticulata utilizing a combination of ethnobotanical and molecular genetic approaches. Semi-structured interviews and key informant interviews were carried out with local communities in China's Yunnan Province. We collected plant material ( n  = 190 individuals) from five populations at study sites using single-dose AFLP markers in order to access the genetic diversity within and between populations. A total of 387 DNA fragments were produced by four AFLP primer sets. All DNA fragments were found to be polymorphic (100%). A relatively high level of genetic diversity was revealed in C. reticulata samples at both the species ( H sp  = 0.3397, I sp  = 0.5236) and population (percentage of polymorphic loci = 85.63%, H pop  = 0.2937, I pop  = 0.4421) levels. Findings further revealed a relatively high degree of genetic diversity within C. reticulata populations (Analysis of Molecular Variance = 96.31%). The higher genetic diversity within populations than among populations of C. reticulata from different geographies is likely due to the cultural and social influences associated with its long cultivation history for esthetic and culinary purposes by diverse sociolinguistic groups. This study highlights the influence of human management, socio-economic factors, and other cultural variables on the genetic and morphological diversity of C. reticulata at a regional level. Findings emphasize the important role of traditional culture on the conservation and utilization of plant genetic diversity.

  15. A call for tiger management using "reserves" of genetic diversity.

    Science.gov (United States)

    Bay, Rachael A; Ramakrishnan, Uma; Hadly, Elizabeth A

    2014-01-01

    Tigers (Panthera tigris), like many large carnivores, are threatened by anthropogenic impacts, primarily habitat loss and poaching. Current conservation plans for tigers focus on population expansion, with the goal of doubling census size in the next 10 years. Previous studies have shown that because the demographic decline was recent, tiger populations still retain a large amount of genetic diversity. Although maintaining this diversity is extremely important to avoid deleterious effects of inbreeding, management plans have yet to consider predictive genetic models. We used coalescent simulations based on previously sequenced mitochondrial fragments (n = 125) from 5 of 6 extant subspecies to predict the population growth needed to maintain current genetic diversity over the next 150 years. We found that the level of gene flow between populations has a large effect on the local population growth necessary to maintain genetic diversity, without which tigers may face decreases in fitness. In the absence of gene flow, we demonstrate that maintaining genetic diversity is impossible based on known demographic parameters for the species. Thus, managing for the genetic diversity of the species should be prioritized over the riskier preservation of distinct subspecies. These predictive simulations provide unique management insights, hitherto not possible using existing analytical methods.

  16. Classification of genetic diversity and choice of parents for ...

    African Journals Online (AJOL)

    Thirty-one accessions of cowpea of diverse eco-geographic origins were evaluated for genetic diversity using principal component analysis (PCA), single linkage cluster analysis (SLCA) and canonical techniques. The accessions were classified into six groups by PCA and SLCA while canonical technique identified five ...

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

    African Journals Online (AJOL)

    sunny t

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

  18. Assessment of genetic diversity among sixty bread wheat (Triticum ...

    African Journals Online (AJOL)

    Mwale

    2016-05-25

    May 25, 2016 ... the highest genetic diversity followed by genome B while genome D was the lowest diverse. Cluster ... and 95% of people in the developing countries eat wheat or maize in ... area for wheat production in China due to pressure from ...... hypertension in the stroke-prone spontaneously hypertensive rat. Cell.

  19. Genetic diversity of Tamarindus indica populations: Any clues on the ...

    African Journals Online (AJOL)

    Tamarindus indica is a domesticated species of high economic value for the Sahel region. Despite this importance, very few data is available on its diversity as well as its structure leading to controversial discussions on its origin. Thus it is questionable whether the knowledge of its genetic diversity and organisation may ...

  20. Genetic diversity of endangered populations of Butia capitata ...

    African Journals Online (AJOL)

    The flora and fauna of the Cerrado biome in central Brazil both show great diversity and high levels of endemism. Butia capitata is a palm native to this biome that has significant economic, social, and environmental value. We sought to identify and quantify the genetic diversity of four fragmented populations of B. capitata ...

  1. Human impacts on genetic diversity in forest ecosystems

    Energy Technology Data Exchange (ETDEWEB)

    Ledig, F T [Inst. of Forest Genetics, Southwest Forest and Range Experiment Station, USDA Forest Service, Berkeley (US)

    1992-01-01

    Humans have converted forest to agricultural and urban uses, exploited species, fragmented wildlands, changed the demographic structure of forests, altered habitat, degraded the environment with atmospheric and soil pollutants, introduced exotic pests and competitors, and domesticated favored species. None of these activities is new; perhaps with the exception of atmospheric pollution, they date back to prehistory. All have impacted genetic diversity by their influence on the evolutionary processes of extinction, selection, drift, gene flow, and mutation, sometimes increasing diversity, as int he case of domestication, but often reducing it. Even in the absence of changes in diversity, mating systems were altered, changing the genetic structure of populations. Demographic changes influenced selection by increasing the incidence of disease. Introduction of exotic diseases, insects, mammalian herbivores, and competing vegetation has had the best-documented effects on genetic diversity, reducing both species diversity and intraspecific diversity. Deforestation has operated on a vast scale to reduce diversity by direct elimination of locally-adapted populations. Atmospheric pollution and global warming will be a major threat in the near future, particularly because forests are fragmented and migration is impeded. Past impacts can be estimated with reference to expert knowledge, but hard data are often laching. Baselines are needed to quantify future impacts and provide an early warning of problems. Genetic inventories of indicator species can provide the baselines against which to measure changes in diversity. (author) (44 refs.).

  2. The characterization of goat genetic diversity : Towards a genomic approach

    NARCIS (Netherlands)

    Ajmone-Marsan, P.; Colli, L.; Han, J. L.; Achilli, A.; Lancioni, H.; Joost, S.; Crepaldi, P.; Pilla, F.; Stella, A.; Taberlet, P.; Boettcher, P.; Negrini, R.; Lenstra, J. A.

    2014-01-01

    The investigation of genetic diversity at molecular level has been proposed as a valuable complement and sometimes proxy to phenotypic diversity of local breeds and is presently considered as one of the FAO priorities for breed characterization. By recommending a set of selected molecular markers

  3. 1 Hierarchical Approaches to the Analysis of Genetic Diversity in ...

    African Journals Online (AJOL)

    2015-04-14

    Apr 14, 2015 ... Study of genetic diversity is the process by which variation ... diversity tree is available, a core collection can be selected by .... are numerous natural factors, such as hybridization and clinical .... to develop a deeper understanding of the topic .... This can be detected by southern hybridization after running ...

  4. Genetic diversity of Przewalski's gazelle using noninvasive DNA and ...

    African Journals Online (AJOL)

    According to the genetic similarity and geographical closeness, we suggested that six populations should be managed as three separate conservation units and habitat corridors should be built to link the Yuanzhe, Hudong-Ketu, Haergai and Sand Island populations. Key words: Habitat fragment, genetic diversity, ...

  5. Genetic diversity analysis and conservation of the Chinese herb ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-10-05

    Oct 5, 2009 ... Salvia miltiorrhiza is an economically important floral herb. However, little work has been conducted to further our understanding of the genetics of this herb. In this study, a representative set of germplasm of. S. miltiorrhiza populations was used to analyze genetic diversity using amplified fragment length.

  6. The loss of genetic diversity in the Chinese paddlefish (Psephurus ...

    Indian Academy of Sciences (India)

    Unknown

    The loss of genetic diversity in the Chinese paddlefish. (Psephurus gladius Martens) as revealed by DNA fingerprinting. XUE-CHANG WU*. College of Life Sciences and the Key Laboratory of Conservation Genetics and Reproductive Biology for Endangered. Wild Animals of the Ministry of Education, Zhejiang University, ...

  7. Assessing the genetic diversity of cultivars and wild soybeans using ...

    African Journals Online (AJOL)

    USER

    2010-08-02

    Aug 2, 2010 ... The average genetic diversity index of wild soybeans and landraces was 1.5421 and ... genetic identity (0.5265) and gene flow (1.8338) between wild soybeans and cultivars ..... The project was financed by the National Natural Science .... Biology and Biotechnology Centre, University of Alberta, Alberta.

  8. Estimation of genetic diversity between three Saudi sheep breeds ...

    African Journals Online (AJOL)

    Estimation of genetic diversity between three Saudi sheep breeds using DNA markers. AAG Adam, NB Hamza, MAW Salim, KS Khalil. Abstract. The genetic variation of Najdi, Harri and Awassi breeds of Saudi sheep prevailing in Raniah province of Makka district were assessed and compared to Sudanese Desert sheep ...

  9. Assessment of genetic diversity within sour cherry clones

    DEFF Research Database (Denmark)

    Clausen, Sabine Karin; Andersen, Sven Bode; Henriksen, K.

    2013-01-01

    of improved breeding material. However, no differences in allele profile were found between or within the clones, calling into question the extent of the available genetic diversity and indicating that the observed variance in yield may have to be explained by other genetic mechanisms, including epigenetic...

  10. Evaluation of genetic diversity of Portuguese Pinus sylvestris L.

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 92; Online resources. Evaluation of genetic diversity of Portuguese Pinus sylvestris L. populations based on molecular data and inferences about the future use of this germplasm. J. Cipriano A. Carvalho C. Fernandes M. J. Gaspar J. Pires J. Bento L. Roxo J. Louzada J. Lima- ...

  11. Genetic diversity analysis in the Hypericum perforatum populations ...

    African Journals Online (AJOL)

    Assessment of genetic variability among the Hypericum perforatum populations is critical to the development of effective conservation strategies in the Kashmir valley. To obtain accurate estimates of genetic diversity among and within populations of H. perforatum, inter-simple sequence repeats (ISSR) markers were used.

  12. Assessing genetic diversity of perennial ryegrass ( Lolium perenne L ...

    African Journals Online (AJOL)

    In this study, inter-simple sequence repeat (ISSR) markers were used to compare genetic diversity between commercial cultivars and natural germplasm which were obtained from Europe, Africa, Asia, and North America. There was a relatively high genetic variation in the whole collection judged by the polymorphism rate ...

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

    Indian Academy of Sciences (India)

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

  14. Genetic diversity analysis and conservation of the Chinese herb ...

    African Journals Online (AJOL)

    Salvia miltiorrhiza is an economically important floral herb. However, little work has been conducted to further our understanding of the genetics of this herb. In this study, a representative set of germplasm of. S. miltiorrhiza populations was used to analyze genetic diversity using amplified fragment length polymorphism ...

  15. Morphological and molecular genetic diversity of Syrian indigenous ...

    African Journals Online (AJOL)

    Domestic goats in Syria may provide an interesting source of genetic variability due to its proximity to the centers of domestication. This study aimed to assess the morphological variation, genetic diversity and population substructure of the Syrian goat populations. Commonly, three goat genotypes are distinguished in Syria, ...

  16. Molecular evaluation of genetic diversity and association studies in ...

    Indian Academy of Sciences (India)

    Molecular evaluation of genetic diversity and association studies in rice. (Oryza sativa L.) C. Vanniarajan, K. K. Vinod and Andy Pereira. J. Genet. 91, 9–19. Table 1. Chromosome-wise distribution of SSR alleles and their number (k), polymorphic information content (PIC) and allele discrimination index (Dm). Chromosome.

  17. Genetic diversity and population structure of sweet cassava using ...

    African Journals Online (AJOL)

    The objective of this study was to evaluate the population structure and genetic diversity among 66 sweet cassava (Manihot esculenta Crantz) traditional accessions collected in Maringa, Parana, Brazil, using microsatellite molecular markers. Population structure was analyzed by means of genetic distances and ...

  18. Genetic diversity of Bambara groundnut ( Vigna subterranea (L ...

    African Journals Online (AJOL)

    The existence of genetic diversity in germplasm collections is crucial for cultivar development. Genetic relationships among 105 Bambara groundnuts (Vigna subterranea (L) Verdc.) accessions from Kenya were evaluated using 12 microsatellite markers. The Bambara landraces were collected from farmers in the western ...

  19. Genetic diversity, population structure and marker trait associations ...

    Indian Academy of Sciences (India)

    Supplementary data: Genetic diversity, population structure and marker trait associations for seed quality traits in cotton (Gossypium hirsutum). Ashok Badigannavar and Gerald O. Myers. J. Genet. 94, 87–94. Table 1. List of cotton germplasm lines used in this study. Germplasm no. Cultivar. Region. Germplasm no. Cultivar.

  20. Genetic diversity among old Portuguese bread wheat cultivars and ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 88; Issue 3. Genetic diversity among old Portuguese bread wheat cultivars and botanical varieties evaluated by ITS rDNA PCR-RFLP markers. A. Carvalho H. Guedes-Pinto J. Lima-Brito. Research Note Volume 88 Issue 3 December 2009 pp 363-367 ...

  1. Genetic relationships and diversity of Jatropha curcas accessions in ...

    African Journals Online (AJOL)

    This study has been undertaken to assess the extent of genetic diversity in a representative set of 16 accessions of Jatropha curcas. Inter-simple sequence repeat (ISSR) analysis was used to establish the genetic relationship among the accessions. From the eight ISSR primers used, the number of amplicons per primers ...

  2. Study of genetic diversity in Sudanese sesame (Sesamum indicum L ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-12-17

    Dec 17, 2008 ... Study of genetic diversity in Sudanese sesame. (Sesamum indicum L.) germplasm using random amplified polymorphic DNA (RAPD) markers. E. Abdellatef 1*, R. Sirelkhatem 1, M. M. Mohamed Ahmed1, K. H. Radwan2 and. M. M. Khalafalla1. 1Commission for Biotechnology and Genetic Engineering, ...

  3. Molecular based assessment of genetic diversity of xoconostle ...

    African Journals Online (AJOL)

    aghomotsegin

    2014-01-08

    Jan 8, 2014 ... Xoconostle or acidic prickly pear is an important fruit in Mexico; it is produced by a ... study, we report for the first time the estimation of genetic diversity within a set ... demonstrates the high genetic variation among genotypes of .... O. leucotricha Salm-Dyck × O. joconostle F.A.C Weber Zacatecas Wild Stock.

  4. Genetic diversity of Toxoplama 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 bioa...

  5. Study on genetic diversity in Pakistani wheat varieties using simple ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-09-01

    Sep 1, 2009 ... Common wheat (Triticum aestivum L.) is a grass species, cultivated world wide. Globally, it is ... A high degree of genetic polymorphism was observed among the wheat varieties with average ... cold, heat, soil salinization and water logging and (ii) ... and to find genetically most diverse genotypes of wheat.

  6. Low genetic diversity of Phytophthora infestans population in potato ...

    African Journals Online (AJOL)

    AJL

    genetic diversity of P. infestans and geographical origin. These results provided a foundation for making integrated control measures in the future. Key words: Phytophthora infestans, population genetics, simple-sequence repeat (SSR), potato late blight. INTRODUCTION. Phytophthora infestans (Mont.) de Bary, causing the ...

  7. Microsatellite genotyping reveals high genetic diversity but low ...

    African Journals Online (AJOL)

    JMwacharos

    2016-03-16

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

  8. Molecular diversity and genetic relationships in Secale

    Indian Academy of Sciences (India)

    2001); and molecular methods such as amplified fragment length polymorphism ... to the maintenance and rational use of germplasm resources in the improvement of ... study of diversity of ScMATE1 gene in different species of. Secale genus.

  9. Genetic diversity among sorghum landraces and polymorphism ...

    African Journals Online (AJOL)

    breeding program through marker-assisted selection. ... Keywords: Sorghum, diversity, stay-green trait, marker, polymorphism. ..... Na: Number of different alleles; Na Freq: Frequency of different alleles; Ne: Number of effective alleles; ...

  10. GENETIC DIVERSITY AND ECO-GEOGRAPHICAL DISTRIBUTION ...

    African Journals Online (AJOL)

    ACSS

    Department of Microbial, Cellular & Molecular Biology, Addis Ababa University, Ethiopia ... floccifolia were analysed for genetic variation and inter-relationships using 20 microsatellite ... categorised as one of the most problematic weeds.

  11. ONLINE RESOURCES Assessment of Genetic Diversity and ...

    Indian Academy of Sciences (India)

    Sony

    Keywords: Population genetic structure, Safflower, simple sequence repeat, C. oxyacanthus,. AMOVA .... next-generation sequencing methods, the most dinucleotide repeats were AT (Lee et al. 2014; .... seeds by wind to far distances. Indeed ...

  12. Genetic diversity in two Italian almond collections

    Directory of Open Access Journals (Sweden)

    Maria Pia Rigoldi

    2015-01-01

    Conclusion: The extensive genetic variability present in the Sardinian and Apulian almond germplasm indicates that these materials represent an important source of genes for the improvement of the crop.

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

    Science.gov (United States)

    Lifjeld, Jan T; Gohli, Jostein; Johnsen, Arild

    2013-10-01

    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.2013). Spurgin (2013) 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. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

  14. Genetic and metabolite diversity of Sardinian populations of Helichrysum italicum.

    Science.gov (United States)

    Melito, Sara; Sias, Angela; Petretto, Giacomo L; Chessa, Mario; Pintore, Giorgio; Porceddu, Andrea

    2013-01-01

    Helichrysum italicum (Asteraceae) is a small shrub endemic to the Mediterranean Basin, growing in fragmented and diverse habitats. The species has attracted attention due to its secondary metabolite content, but little effort has as yet been dedicated to assessing the genetic and metabolite diversity present in these populations. Here, we describe the diversity of 50 H. italicum populations collected from a range of habitats in Sardinia. H. italicum plants were AFLP fingerprinted and the composition of their leaf essential oil characterized by GC-MS. The relationships between the genetic structure of the populations, soil, habitat and climatic variables and the essential oil chemotypes present were evaluated using Bayesian clustering, contingency analyses and AMOVA. The Sardinian germplasm could be partitioned into two AFLP-based clades. Populations collected from the southwestern region constituted a homogeneous group which remained virtually intact even at high levels of K. The second, much larger clade was more diverse. A positive correlation between genetic diversity and elevation suggested the action of natural purifying selection. Four main classes of compounds were identified among the essential oils, namely monoterpenes, oxygenated monoterpenes, sesquiterpenes and oxygenated sesquiterpenes. Oxygenated monoterpene levels were significantly correlated with the AFLP-based clade structure, suggesting a correspondence between gene pool and chemical diversity. The results suggest an association between chemotype, genetic diversity and collection location which is relevant for the planning of future collections aimed at identifying valuable sources of essential oil.

  15. Genetic and metabolite diversity of Sardinian populations of Helichrysum italicum.

    Directory of Open Access Journals (Sweden)

    Sara Melito

    Full Text Available BACKGROUND: Helichrysum italicum (Asteraceae is a small shrub endemic to the Mediterranean Basin, growing in fragmented and diverse habitats. The species has attracted attention due to its secondary metabolite content, but little effort has as yet been dedicated to assessing the genetic and metabolite diversity present in these populations. Here, we describe the diversity of 50 H. italicum populations collected from a range of habitats in Sardinia. METHODS: H. italicum plants were AFLP fingerprinted and the composition of their leaf essential oil characterized by GC-MS. The relationships between the genetic structure of the populations, soil, habitat and climatic variables and the essential oil chemotypes present were evaluated using Bayesian clustering, contingency analyses and AMOVA. KEY RESULTS: The Sardinian germplasm could be partitioned into two AFLP-based clades. Populations collected from the southwestern region constituted a homogeneous group which remained virtually intact even at high levels of K. The second, much larger clade was more diverse. A positive correlation between genetic diversity and elevation suggested the action of natural purifying selection. Four main classes of compounds were identified among the essential oils, namely monoterpenes, oxygenated monoterpenes, sesquiterpenes and oxygenated sesquiterpenes. Oxygenated monoterpene levels were significantly correlated with the AFLP-based clade structure, suggesting a correspondence between gene pool and chemical diversity. CONCLUSIONS: The results suggest an association between chemotype, genetic diversity and collection location which is relevant for the planning of future collections aimed at identifying valuable sources of essential oil.

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

    International Nuclear Information System (INIS)

    Kumar, V.; Bhagwat, S.G.

    2011-01-01

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

  17. genetic diversity among sorghum landraces of southwestern

    African Journals Online (AJOL)

    ACSS

    2016-05-14

    May 14, 2016 ... La classification numérique a généré un dendrogramme avec trois groupes. Le poids ... process of evolution, through farmer selection within crop diversity, to .... on days to 50% flowering, plant height, number of leaves, length ...

  18. Genetic fingerprinting and phylogenetic diversity of Staphylococcus ...

    African Journals Online (AJOL)

    Genetic fingerprinting of 18 different isolates of Staphylococcus aureus from Nigeria using random amplified polymorphic DNA (RAPD) was carried out. Ten out of 100 Operon primers showed polymorphism among the isolates tested generating 88 bands, 51 of which were polymorphic with sizes ranging between 200 and ...

  19. Great ape genetic diversity and population history

    DEFF Research Database (Denmark)

    Prado-Martinez, Javier; Sudmant, Peter H; Kidd, Jeffrey M

    2013-01-01

    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...

  20. Ensuring the genetic diversity of potatoes

    Science.gov (United States)

    Opportunities for advances in the potato crop through genetics are great, since potato has many needs for improvement, and many related species with the traits required are available. Genebanks provide a centralized and specialized resource for providing the services of acquisition, classification, ...

  1. The Host Genetic Diversity in Malaria Infection

    Directory of Open Access Journals (Sweden)

    Vitor R. R. de Mendonça

    2012-01-01

    Full Text Available Populations exposed to Plasmodium infection develop genetic mechanisms of protection against severe disease. The clinical manifestation of malaria results primarily from the lysis of infected erythrocytes and subsequent immune and inflammatory responses. Herein, we review the genetic alterations associated with erythrocytes or mediators of the immune system, which might influence malaria outcome. Moreover, polymorphisms in genes related to molecules involved in mechanisms of cytoadherence and their influence on malaria pathology are also discussed. The results of some studies have suggested that the combinatorial effects of a set of genetic factors in the erythrocyte-immunology pathway might be relevant to host resistance or susceptibility against Plasmodium infection. However, these results must be interpreted with caution because of the differences observed in the functionality and frequency of polymorphisms within different populations. With the recent advances in molecular biology techniques, more robust studies with reliable data have been reported, and the results of these studies have identified individual genetic factors for consideration in preventing severe disease and the individual response to treatment.

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

    Science.gov (United States)

    Huang, Yi-Min; Xia, Meng-Ying; Huang, Shi

    2013-05-01

    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.

  3. High genetic diversity of Jatropha curcas assessed by ISSR.

    Science.gov (United States)

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

    2017-05-31

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

  4. SSR Analysis of Genetic Diversity Among 192 Diploid Potato Cultivars

    Directory of Open Access Journals (Sweden)

    Xiaoyan Song

    2016-05-01

    Full Text Available In potato breeding, it is difficult to improve the traits of interest at the tetraploid level due to the tetrasomic inheritance. A promising alternative is diploid breeding. Thus it is necessary to assess the genetic diversity of diploid potato germplasm for efficient exploration and deployment of desirable traits. In this study, we used SSR markers to evaluate the genetic diversity of diploid potato cultivars. To screen polymorphic SSR markers, 55 pairs of SSR primers were employed to amplify 39 cultivars with relatively distant genetic relationships. Among them, 12 SSR markers with high polymorphism located at 12 chromosomes were chosen to evaluate the genetic diversity of 192 diploid potato cultivars. The primers produced 6 to 18 bands with an average of 8.2 bands per primer. In total, 98 bands were amplified from 192 cultivars, and 97 of them were polymorphic. Cluster analysis using UPGMA showed the genetic relationships of all accessions tested: 186 of the 192 accessions could be distinguished by only 12 pairs of SSR primers, and the 192 diploid cultivars were divided into 11 groups, and 83.3% constituted the first group. Clustering results showed relatively low genetic diversity among 192 diploid cultivars, with closer relationship at the molecular level. The results can provide molecular basis for diploid potato breeding.

  5. Genetic Diversity of Turf-Type Tall Fescue Using Diversity Arrays Technology

    Czech Academy of Sciences Publication Activity Database

    Baird, J. H.; Kopecký, David; Lukaszewski, A.J.; Green, R. J.; Bartoš, Jan; Doležel, Jaroslav

    2012-01-01

    Roč. 52, č. 1 (2012), s. 408-412 ISSN 0011-183X Institutional research plan: CEZ:AV0Z50380511 Keywords : Festuca arundinacea * Diversity Arrays Technology (DArT) * Low genetic polymorphism Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.513, year: 2012

  6. Genetic diversity analysis of common beans based on molecular markers

    Directory of Open Access Journals (Sweden)

    Homar R. Gill-Langarica

    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.

  7. Genetic diversity assessed by microsatellite markers in sweet corn cultivars

    Directory of Open Access Journals (Sweden)

    Ana Daniela Lopes

    2015-12-01

    Full Text Available Information on genetic diversity is essential to the characterization and utilization of germplasm. The genetic diversity of twenty-two sweet corn cultivars (seventeen open-pollinated varieties, OPV, and five hybrids, H was investigated by applying simple sequence repeat markers. A total of 257 primers were tested, of which 160 were found to be usable in terms of high reproducibility for all the samples tested; 45 were polymorphic loci, of which 30 were used to assess the genetic diversity of sweet corn cultivars. We detected a total of 86 alleles using 30 microsatellite primers. The mean polymorphism was 82 %. The highest heterozygosity values (Ho = 0.20 were found in the PR030-Doce Flor da Serra and BR427 III OPVs, whereas the lowest values (0.14 were recorded in the MG161-Branco Doce and Doce Cubano OPVs. The polymorphism information content ranged from 0.19 (Umc2319 to 0.71 (Umc2205. The analysis of molecular variance revealed that most of the genetic variability was concentrated within the cultivars of sweet corn (75 %, with less variability between them (25 %. The consensus tree derived from the neighbor-joining (NJ algorithm using 1,000 bootstrapping replicates revealed seven genetically different groups. Nei’s diversity values varied between 0.103 (Doce do Hawai × CNPH-1 cultivars and 0.645 (Amarelo Doce × Lili cultivars, indicating a narrow genetic basis. The Lili hybrid was the most distant cultivar, as revealed by Principal Coordinates Analysis and the NJ tree. This study on genetic diversity will be useful for planning future studies on sweet corn genetic resources and can complement the breeding programs for this crop.

  8. Genetic diversity analysis of common beans based on molecular markers

    Directory of Open Access Journals (Sweden)

    Homar R. Gill-Langarica

    2011-01-01

    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.

  9. Genetic diversity analysis of common beans based on molecular markers.

    Science.gov (United States)

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

    2011-10-01

    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.

  10. Pyrosequencing and genetic diversity of microeukaryotes

    DEFF Research Database (Denmark)

    Harder, Christoffer Bugge

    carefully selected waterworks (Article IV), where the bacterial metabolic diversity and its important for water purification was described. Building on this, the most important part of the thesis consists of two pyrosequencing analyses of protozoa with newly developed 18S primers. One specifically targets...... Cercozoa, a particularly abundant phylum of protozoa (Article III), on heath land that had been subjected to prolonged artificially induced drought in a Danish free-air climate-manipulation experiment (CLIMAITE). Article III showed that the testate cercozoan forms responded negatively to prolonged drought...

  11. Dolutegravir reshapes the genetic diversity of HIV-1 reservoirs.

    Science.gov (United States)

    Gantner, Pierre; Lee, Guinevere Q; Rey, David; Mesplede, Thibault; Partisani, Marialuisa; Cheneau, Christine; Beck-Wirth, Geneviève; Faller, Jean-Pierre; Mohseni-Zadeh, Mahsa; Martinot, Martin; Wainberg, Mark A; Fafi-Kremer, Samira

    2018-04-01

    Better understanding of the dynamics of HIV reservoirs under ART is a critical step to achieve a functional HIV cure. Our objective was to assess the genetic diversity of archived HIV-1 DNA over 48 weeks in blood cells of individuals starting treatment with a dolutegravir-based regimen. Eighty blood samples were prospectively and longitudinally collected from 20 individuals (NCT02557997) including: acutely (n = 5) and chronically (n = 5) infected treatment-naive individuals, as well as treatment-experienced individuals who switched to a dolutegravir-based regimen and were either virologically suppressed (n = 5) or had experienced treatment failure (n = 5). The integrase and V3 loop regions of HIV-1 DNA isolated from PBMCs were analysed by pyrosequencing at baseline and weeks 4, 24 and 48. HIV-1 genetic diversity was calculated using Shannon entropy. All individuals achieved or maintained viral suppression throughout the study. A low and stable genetic diversity of archived HIV quasispecies was observed in individuals starting treatment during acute infection. A dramatic reduction of the genetic diversity was observed at week 4 of treatment in the other individuals. In these patients and despite virological suppression, a recovery of the genetic diversity of the reservoirs was observed up to 48 weeks. Viral variants bearing dolutegravir resistance-associated substitutions at integrase position 50, 124, 230 or 263 were detected in five individuals (n = 5/20, 25%) from all groups except those who were ART-failing at baseline. None of these substitutions led to virological failure. These data demonstrate that the genetic diversity of the HIV-1 reservoir is reshaped following the initiation of a dolutegravir-based regimen and strongly suggest that HIV-1 can continue to replicate despite successful treatment.

  12. Genetic diversity of Plasmodium vivax and Plasmodium falciparum in Honduras.

    Science.gov (United States)

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

    2012-11-26

    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. 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. 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.

  13. Genetic diversity and relationships of Vietnamese and European pig breeds

    Energy Technology Data Exchange (ETDEWEB)

    Thuy, N T.D. [Department of Animal Breeding and Biotechnology, University of Hohenheim, Stuttgart (Germany); Institute of Biotechnology (IBT), National Center for Natural Science and Technology, Hanoi (Viet Nam); Melchinger, E; Kuss, A W; Peischl, T; Bartenschlager, H; Geldermann, H [Department of Animal Breeding and Biotechnology, University of Hohenheim, Stuttgart (Germany); Cuong, N V [Institute of Biotechnology (IBT), National Center for Natural Science and Technology, Hanoi (Viet Nam)

    2005-07-01

    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)

  14. Genetic diversity and relationships of Vietnamese and European pig breeds

    International Nuclear Information System (INIS)

    Thuy, N.T.D.; Melchinger, E.; Kuss, A.W.; Peischl, T.; Bartenschlager, H.; Geldermann, H.; Cuong, N.V.

    2005-01-01

    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)

  15. Bartonella Prevalence and Genetic Diversity in Small Mammals from Ethiopia

    DEFF Research Database (Denmark)

    Meheretu, Yonas; Leirs, Herwig E.l.; Welegerima, Kiros

    2013-01-01

    More than 500 small mammals were trapped at 3 localities in northern Ethiopia to investigate Bartonella infection prevalence and the genetic diversity of the Bartonella spp. We extracted total DNA from liver samples and performed PCR using the primers 1400F and 2300R targeting 852 bp of the Barto......More than 500 small mammals were trapped at 3 localities in northern Ethiopia to investigate Bartonella infection prevalence and the genetic diversity of the Bartonella spp. We extracted total DNA from liver samples and performed PCR using the primers 1400F and 2300R targeting 852 bp...

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

    Science.gov (United States)

    Clark, Rulon W; Brown, William S; Stechert, Randy; Zamudio, Kelly R

    2010-08-01

    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.

  17. Genetic diversity among ancient Nordic populations

    DEFF Research Database (Denmark)

    Melchior, Linea Cecilie; Lynnerup, Niels; Siegismund, Hans Redlef

    2010-01-01

    , the success rate varied substantially between sites; the highest rates were obtained with untouched, freshly excavated material, whereas heavy handling, archeological preservation and storage for many years influenced the ability to obtain authentic endogenic DNA. While the nucleotide diversity at two...... the ancient Danes (average 13%) than among extant Danes and Scandinavians ( approximately 2.5%) as well as among other ancient population samples reported. Haplogroup I could therefore have been an ancient Southern Scandinavian type "diluted" by later immigration events. Interestingly, the two Neolithic...... samples (4,200 YBP, Bell Beaker culture) that were typed were haplogroup U4 and U5a, respectively, and the single Bronze Age sample (3,300-3,500 YBP) was haplogroup U4. These two haplogroups have been associated with the Mesolithic populations of Central and Northern Europe. Therefore, at least...

  18. HIV Genetic Diversity and Drug Resistance

    Science.gov (United States)

    Santos, André F.; Soares, Marcelo A.

    2010-01-01

    Most of the current knowledge on antiretroviral (ARV) drug development and resistance is based on the study of subtype B of HIV-1, which only accounts for 10% of the worldwide HIV infections. Cumulative evidence has emerged that different HIV types, groups and subtypes harbor distinct biological properties, including the response and susceptibility to ARV. Recent laboratory and clinical data highlighting such disparities are summarized in this review. Variations in drug susceptibility, in the emergence and selection of specific drug resistance mutations, in viral replicative capacity and in the dynamics of resistance acquisition under ARV selective pressure are discussed. Clinical responses to ARV therapy and associated confounding factors are also analyzed in the context of infections by distinct HIV genetic variants. PMID:21994646

  19. Natural Selection and Genetic Diversity in the Butterfly Heliconius melpomene.

    Science.gov (United States)

    Martin, Simon H; Möst, Markus; Palmer, William J; Salazar, Camilo; McMillan, W Owen; Jiggins, Francis M; Jiggins, Chris D

    2016-05-01

    A combination of selective and neutral evolutionary forces shape patterns of genetic diversity in nature. Among the insects, most previous analyses of the roles of drift and selection in shaping variation across the genome have focused on the genus Drosophila A more complete understanding of these forces will come from analyzing other taxa that differ in population demography and other aspects of biology. We have analyzed diversity and signatures of selection in the neotropical Heliconius butterflies using resequenced genomes from 58 wild-caught individuals of Heliconius melpomene and another 21 resequenced genomes representing 11 related species. By comparing intraspecific diversity and interspecific divergence, we estimate that 31% of amino acid substitutions between Heliconius species are adaptive. Diversity at putatively neutral sites is negatively correlated with the local density of coding sites as well as nonsynonymous substitutions and positively correlated with recombination rate, indicating widespread linked selection. This process also manifests in significantly reduced diversity on longer chromosomes, consistent with lower recombination rates. Although hitchhiking around beneficial nonsynonymous mutations has significantly shaped genetic variation in H. melpomene, evidence for strong selective sweeps is limited overall. We did however identify two regions where distinct haplotypes have swept in different populations, leading to increased population differentiation. On the whole, our study suggests that positive selection is less pervasive in these butterflies as compared to fruit flies, a fact that curiously results in very similar levels of neutral diversity in these very different insects. Copyright © 2016 by the Genetics Society of America.

  20. Genetic diversity in wild populations of Paulownia fortune.

    Science.gov (United States)

    Li, H Y; Ru, G X; Zhang, J; Lu, Y Y

    2014-11-01

    The genetic diversities of 16 Paulownia fortunei populations involving 143 individuals collected from 6 provinces in China were analyzed using amplified fragment length polymorphism (AFLP). A total of 9 primer pairs with 1169 polymorphic loci were screened out, and each pair possessed 132 bands on average. The percentage of polymorphic bands (98.57%), the effective number of alleles (1.2138-1.2726), Nei's genetic diversity (0.1566-0.1887), and Shannon's information index (0.2692-0.3117) indicated a plentiful genetic diversity and different among Paulownia fortunei populations. The genetic differentiation coefficient between populations was 0.2386, while the gene flow was 1.0954, and the low gene exchange promoted genetic differentiation. Analysis of variance indicated that genetic variation mainly occurred within populations (81.62% of total variation) rather than among populations (18.38%). The 16 populations were divided by unweighted pair-group method with arithmetic means (UPGMA) into 4 groups with obvious regionalism, in which the populations with close geographical locations (latitude) were clustered together.

  1. Defining the landscape of adaptive genetic diversity.

    Science.gov (United States)

    Eckert, Andrew J; Dyer, Rodney J

    2012-06-01

    Whether they are used to describe fitness, genome architecture or the spatial distribution of environmental variables, the concept of a landscape has figured prominently in our collective reasoning. The tradition of landscapes in evolutionary biology is one of fitness mapped onto axes defined by phenotypes or molecular sequence states. The characteristics of these landscapes depend on natural selection, which is structured across both genomic and environmental landscapes, and thus, the bridge among differing uses of the landscape concept (i.e. metaphorically or literally) is that of an adaptive phenotype and its distribution across geographical landscapes in relation to selective pressures. One of the ultimate goals of evolutionary biology should thus be to construct fitness landscapes in geographical space. Natural plant populations are ideal systems with which to explore the feasibility of attaining this goal, because much is known about the quantitative genetic architecture of complex traits for many different plant species. What is less known are the molecular components of this architecture. In this issue of Molecular Ecology, Parchman et al. (2012) pioneer one of the first truly genome-wide association studies in a tree that moves us closer to this form of mechanistic understanding for an adaptive phenotype in natural populations of lodgepole pine (Pinus contorta Dougl. ex Loud.). © 2012 Blackwell Publishing Ltd.

  2. Population structure and genetic diversity of Sudanese native chickens

    African Journals Online (AJOL)

    The objectives of this study were to analyze genetic diversity and population structure of Sudanese native chicken breeds involved in a conservation program. Five Sudanese native chicken breeds were compared with populations studied previously, which included six purebred lines, six African populations and one ...

  3. Genetic structure and diversity of East African taro [ Colocasia ...

    African Journals Online (AJOL)

    Taro [Colocasia esculenta (L) Schott] is mainly produced in Africa by small holder farmers and plays an important role in the livelihood of millions of poor people in less developed countries. The genetic diversity of East African taro has not been determined. This study utilizes six microsatellite primers to analyze five ...

  4. Genetic diversity of Cryptosporidium spp. in captive reptiles

    Czech Academy of Sciences Publication Activity Database

    Xiao, L.; Ryan, U. M.; Graczyk, T. K.; Limor, J.; Li, L.; Kombert, M.; Junge, R.; Sulaiman, I. M.; Zhou, L.; Arrowood, M. J.; Koudela, Břetislav; Modrý, David; Lal, A. A.

    2004-01-01

    Roč. 70, č. 2 (2004), s. 891-899 ISSN 0099-2240 R&D Projects: GA ČR GA524/00/P015 Institutional research plan: CEZ:AV0Z6022909 Keywords : Cryptosporidium * reptiles * genetic diversity Subject RIV: EG - Zoology Impact factor: 3.810, year: 2004

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

    African Journals Online (AJOL)

    Dr.Ola

    2013-05-15

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

  6. Estimate of genetic diversity in cassutinga ( Croton heliotropiifolius ...

    African Journals Online (AJOL)

    Estimate of genetic diversity in cassutinga (Croton heliotropiifolius) based on molecular markers. Tallita de Oliveira Rocha, Janaina Silva Freitas, Elisa Susilene Lisboa dos Santos, Murilo Marques Scaldaferri, Claudine Gonçalves de Oliveira, Carlos Bernard Moreno Cerqueira-Silva ...

  7. Genetic diversity of Annona senegalensis Pers. populations as ...

    African Journals Online (AJOL)

    Annona senegalensis Pers. is one of the wild fruit tree for domestication in southern Africa. An assessment of the genetic diversity in A. senegalensis would assist in planning for future germplasm collection, conservation and fruit domestication programmes. During 2004 to 2006 nine populations were collected from different ...

  8. Estimation of genetic diversity of the Kenyan yam (Dioscorea spp ...

    African Journals Online (AJOL)

    MUTHAMIA

    2013-10-02

    Oct 2, 2013 ... The botany, ethnobotany, use and possible future of yams in West Africa. Econ. Bot. 26:301-318. Beebe S, Sckroch PW, Tohme J, Duque MC, Pedraza F, Nienhuis J. (2000). Structure of genetic diversity among common bean landraces of Middle American origin based on correspondence analysis of. RAPD ...

  9. Genetic diversity and reproductive success in mandrills (Mandrillus sphinx).

    Science.gov (United States)

    Charpentier, M; Setchell, J M; Prugnolle, F; Knapp, L A; Wickings, E J; Peignot, P; Hossaert-McKey, M

    2005-11-15

    Recent studies of wild animal populations have shown that estimators of neutral genetic diversity, such as mean heterozygosity, are often correlated with various fitness traits, such as survival, disease susceptibility, or reproductive success. We used two estimators of genetic diversity to explore the relationship between heterozygosity and reproductive success in male and female mandrills (Mandrillus sphinx) living in a semifree ranging setting in Gabon. Because social rank is known to influence reproductive success in both sexes, we also examined the correlation between genetic diversity and social rank in females, and acquisition of alpha status in males, as well as length of alpha male tenure. We found that heterozygous individuals showed greater reproductive success, with both females and males producing more offspring. However, heterozygosity influenced reproductive success only in dominant males, not in subordinates. Neither the acquisition of alpha status in males, nor social rank in females, was significantly correlated with heterozygosity, although more heterozygous alpha males showed longer tenure than homozygous ones. We also tested whether the benefits of greater genetic diversity were due mainly to a genome-wide effect of inbreeding depression or to heterosis at one or a few loci. Multilocus effects best explained the correlation between heterozygosity and reproductive success and tenure, indicating the occurrence of inbreeding depression in this mandrill colony.

  10. Genetic structure and diversity within and among six populations of ...

    African Journals Online (AJOL)

    Yomi

    2010-04-24

    Apr 24, 2010 ... Genetic structure and diversity within and among six populations of .... Lyopholized samples were ground to a fine powder. DNA extraction ..... 22(3): 287-292. Pei YL, Zou, YP, Yin Z, Wang XQ, Zhang ZX, Hong DY (1995).

  11. Genetic diversity of Mycobacterium tuberculosis in Mbarara, South ...

    African Journals Online (AJOL)

    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 ...

  12. Study of genetic diversity in finger millet (Eleusine coracana L ...

    African Journals Online (AJOL)

    STORAGESEVER

    2010-07-19

    Jul 19, 2010 ... Radioactive detection. Yes/No. No. Yes/No. No. Yes/No. Yes/No. Development costs. Medium. Low. Medium. Medium/High. High. Medium. Start-up costs. Medium/High. Low. Medium. High. High. Medium. Applications. Genetic diversity, polyploidy, hybridization, phylogeny, mating system. Fingerprinting,.

  13. Genetic diversity of bitter taste receptor gene family in Sichuan

    Indian Academy of Sciences (India)

    Genetic diversity of bitter taste receptor gene family in Sichuan domestic and Tibetan chicken populations. YUAN SU DIYAN LI UMA GAUR YAN WANG NAN WU BINLONG CHEN HONGXIAN XU HUADONG YIN YAODONG HU QING ZHU. RESEARCH ARTICLE Volume 95 Issue 3 September 2016 pp 675-681 ...

  14. DNA methylation and genetic diversity analysis of genus Cycas in ...

    African Journals Online (AJOL)

    mallory

    2012-01-12

    Jan 12, 2012 ... elucidate the role of epigenetics in the genetic diversity of these plants. MATERIALS AND METHODS. Plant materials and DNA extraction. 66 Cycas samples consisting of 10 species and one subspecies were collected from the Nong Nooch Tropical Garden, Chonburi province, Thailand. For each species ...

  15. Genetic diversity among four Eucalyptus species (myrtaceae) based ...

    African Journals Online (AJOL)

    The results indicate that 16 positive and 13 negative markers were detected. The marker fragments size ranged between 175 to 630 bp for the negative markers and 235 to 945 bp for the positive markers. Key words: Eucalyptus, random amplified polymorphic DNA (RAPD), genetic diversity, DNA fingerprinting PCR, ...

  16. Molecular analysis of genetic diversity in elite II synthetic hexaploid ...

    African Journals Online (AJOL)

    The present study was conducted to assess the genetic diversity of Elite-II synthetic hexaploid (SH) wheat by genome DNA fingerprinting as revealed by random amplified polymorphic DNA (RAPD) analysis. Ten decamer RAPD primers (OPG-1, OPG-2, OPG-3, OPG-4, OPG-5, OPA-3, OPA-4, OPA-5, OPA-8, and OPA-15) ...

  17. Genetic diversity and molecular characterization of physic nut ...

    African Journals Online (AJOL)

    ajl

    2013-02-27

    Feb 27, 2013 ... 2Department of Plant Science, Federal University of Viçosa, Viçosa, Minas Gerais, Brazil. ... primers were used to characterize toxicity alleles, and none of the accessions presented patterns ... accessions from India (Gupta et al., 2008; Gohil and. Pandya .... ISSR primers, generally low genetic diversity was.

  18. Genetic diversity of Shaanxi soybean landraces based on ...

    African Journals Online (AJOL)

    DR TONUKARI NYEROVWO

    2011-06-06

    Jun 6, 2011 ... Fax: +86. 29 87082604. Abbreviations: NEsp, Northeastern spring .... the present study, genetic diversity of this primary core .... spectroscopy DA7200 (Sweden Perten instruments Company). ... All primers were synthesized ..... 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 MS. SSR Locus. G e n e tic d.

  19. Genetic diversity of intensive cultured and wild tiger shrimp Penaeus ...

    African Journals Online (AJOL)

    The objective of this study was to assess the genetic diversity of intensive cultured and wild tiger shrimp Penaeus monodon (Fabricius) in Malaysia using six microsatellite markers (CSCUPmo1, CSCUPmo2, CSCUPmo3, CSCUPmo4, CSCUPmo6 and CSCUPmo7). The mean numbers of allele, observed heterozygosis, ...

  20. Molecular genetic diversity study of Lepidium sativum population ...

    African Journals Online (AJOL)

    Vostro 2520

    Generally, Tigray and Amhara regions showed moderate to high diversity in ISSR analysis. ... other crops. The main purpose of its cultivation in. Ethiopia is to use it as a medicinal plant. It is used for human abdominal ache and diarrhea. Moreover, L. ... of 10 primers were obtained from the Genetic Research Laboratory.

  1. Human immunodeficiency virus type-1 (HIV-1) genetic diversity and ...

    African Journals Online (AJOL)

    The presence of human immunodeficiency virus (HIV) type-1 diversity has an impact on vaccine efficacy and drug resistance. It is important to know the circulating genetic variants and associated drug-resistance mutations in the context of scale up of antiretroviral therapy (ART) in Nigeria. The objective of this study was to ...

  2. Conserving genetic diversity in Ponderosa Pine ecosystem restoration

    Science.gov (United States)

    L.E. DeWald

    2017-01-01

    Restoration treatments in the ponderosa pine (Pinus ponderosa P. & C. Lawson) ecosystems of the southwestern United States often include removing over 80 percent of post-EuroAmerican settlement-aged trees to create healthier forest structural conditions. These types of stand density reductions can have negative effects on genetic diversity. Allozyme analyses...

  3. The use of microsatellite markers for genetic diversity assessment of ...

    African Journals Online (AJOL)

    In this study, gene diversity and genetic relationships among 30 genotypes of genus Hordeum from Kerman province (Iran) were assessed using 10 simple sequence repeat (SSR) primers. Seven of these markers were highly polymorphic. A total of 96 alleles were detected. The number of alleles per microsatellite marker ...

  4. Genetic Diversity of Local and Introduced Sweet Potato [Ipomoea ...

    African Journals Online (AJOL)

    This study was therefore conducted to estimate the genetic diversity of 114 Sweet potato [Ipomoea batatas (L.) Lam] accessions obtained from Nigeria, Asia, Latin America and Local collections along with two improved varieties. Accessions were planted in 2012/13 cropping season at Haramaya University, eastern Ethiopia ...

  5. Genetic diversity of two Tunisian sheep breeds using random ...

    African Journals Online (AJOL)

    Random amplified polymorphic DNA (RAPD) markers were used to study genetic diversity and population structure in six sheep populations belonging to two native Tunisian breeds (the Barbarine and the Western thin tail). A total of 96 samples were typed using eight RAPD primers. 62 bands were scored, of which 44 ...

  6. Molecular evaluation of genetic diversity and association studies in ...

    Indian Academy of Sciences (India)

    In the present study, we tested rice genotypes that included un(der)exploited landraces of Tamil Nadu along with indica and japonica test cultivars to ascertain their genetic diversity structure. Highly polymorphic microsatellite markers were used for generating marker segregation data. A novel measure, allele discrimination ...

  7. Evaluation of genetic diversity in barley ( Hordeum vulgare L.) from ...

    African Journals Online (AJOL)

    This study aimed to determine the genetic diversity and relationships among barley varieties (Hordeum vulgare L.) growing at Wollo Highland areas by using hordein and agro-morphological traits. Twenty (20) varieties were laid down in randomized complete block design (RCBD) design with three replications; they were ...

  8. Assessment of genetic diversity among maize accessions using inter ...

    African Journals Online (AJOL)

    Assessment of genetic diversity among maize accessions using inter simple sequence repeats (ISSR) markers. AT do Amaral Júnior, EC de Oliveira, LSA Gonçalves, CA Scapim, LS Candido, TR da Conceição Silva, C Vittorazzi, KS da Cunha ...

  9. Assessment of genetic diversity for some Iraqi date palms ( Phoenix ...

    African Journals Online (AJOL)

    Amplified fragment length polymorphisms (AFLP) were used to evaluate the genetic diversity between 18 date palm (Phoenix dactylifera L.) varieties (11 females and 7 males) collected from the center of Iraq. Six primer pairs were applied to detect polymorphism between varieties. A total of 83 polymorphic AFLP fragments ...

  10. Genetic diversity in barley landraces (Hordeum vulgare L. subsp.

    Indian Academy of Sciences (India)

    Genetic diversity in barley landraces (Hordeum vulgare L. subsp. vulgare) originated from Crescent Fertile region as detected by seed storage proteins. RIM MZID FARHAT CHIBANI RAYDA BEN AYED MOHSEN HANANA JOELLE BREIDI RABIH KABALAN SAMIH EL-HAJJ HASSAN MACHLAB AHMED REBAI LAMIS ...

  11. Preliminary molecular analysis of the genetic diversity of some ...

    African Journals Online (AJOL)

    In the arid and semi arid areas, salt bush (Atriplex) represents an important forage resource. The characterization of the genetic diversity of these species is useful for their classification, their conservation and their improvement. In this context, we used the random amplified polymorphic DNA-polymerase chain reaction ...

  12. Genetic diversity of Santalum album using random amplified ...

    African Journals Online (AJOL)

    In the present study Random Amplified Polymorphic DNA (RAPD) technique was used to accesses the genetic diversity among 30 accessions of S. album collected from different parts of South India. A total of 248 polymorphic amplicons were obtained from 30 primers. The value of Jaccard coefficient ranged from 0.66 to ...

  13. Estimation of genetic diversity of the Kenyan yam ( Dioscorea spp ...

    African Journals Online (AJOL)

    Data was analyzed for genetic diversity, ordination and analysis of molecular variance with GenAIEx software. A total of 131 alleles were amplified with a minimum of two alleles and a maximum of 13 alleles per primer with a minimum allele size of 64 bp and a maximum of 368 bp. Accessions from Eastern province had the ...

  14. Assessing genetic diversity and phylogeographic structure of duck ...

    African Journals Online (AJOL)

    In this study, the maternal genetic diversity and phylogenetic relationship of Nigerian duck populations were assessed. A total of 591 base pair fragment of the mitochondrial DNA (mtDNA) D-loop region of 87 indigenous ducks from two populations in Nigeria were analyzed. Seven haplotypes and 70 polymorphic sites were ...

  15. Genetic diversity and conservation of Mexican forest trees

    Science.gov (United States)

    C. Wehenkel; S. Mariscal-Lucero; J.P. Jaramillo-Correa; C.A. López-Sánchez; J.J. Vargas Hernández; C. Sáenz-Romero

    2017-01-01

    Over the last 200 years, humans have impacted the genetic diversity of forest trees. Because of widespread deforestation and over-exploitation, about 9,000 tree species are listed worldwide as threatened with extinction, including more than half of the ~600 known conifer taxa. A comprehensive review of the floristic-taxonomic literature compiled a list of 4,331...

  16. Genetic diversity of Actinobacillus lignieresii isolates from different hosts

    DEFF Research Database (Denmark)

    Kokotovic, Branko; Angen, Øystein; Bisgaard, Magne

    2011-01-01

    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 comprisin...

  17. Genetic diversity in selected stud and commercial herds of the ...

    African Journals Online (AJOL)

    The Afrikaner is one of three indigenous cattle breeds found in South Africa. Afrikaner cattle were originally extensively used for crossbreeding purposes and breed development. The objective of this study was to determine the genetic diversity of selected stud and commercial herds from the whole South African Afrikaner ...

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

    African Journals Online (AJOL)

    STORAGESEVER

    2008-07-18

    Jul 18, 2008 ... species grows to 2-15 m tall with a flat or rounded crown. (Maundu et al., 1999). ... Our knowledge on the structure of genetic diversity of. A. senegal in Kenya ..... conclusion that spatial organization of local populations and the ...

  19. Analysis of Genetic diversity and reltionships in local Tunisian barley ...

    African Journals Online (AJOL)

    Yomi

    tools in the characterization and evaluation of genetic diversity within and between species and populations. It has been shown that different markers might reveal different classes of variation (Powell et al., 1996; Russell et al., 1997). It is correlated with the genome fraction surveyed by each kind of marker, their distribution ...

  20. Genetic diversity and in vitro antibiotic susceptibility profile of ...

    African Journals Online (AJOL)

    We assessed the genetic diversity of forty Salmonella isolates obtained from selected domestic water and waste water sources in the Eastern Cape Province of South Africa using DNA fingerprinting and antibiotic susceptibility profile as test indices. Restriction digests and SDS/PAGE as well as the DNA dendograms of the ...

  1. Genetic diversity in Ethiopian mustard ( Bbrassica carinata a. braun ...

    African Journals Online (AJOL)

    In this study, genetic diversity in 60 Ethiopian mustard genotypes, collected from 16 regions of Ethiopia, were assessed using the techniques of cluster and ... for the majority of traits of interest: seed yield/plot, seed yield/plant, biomass/plot, biomass/plant, plant height, number of pods/plant, 1000 seeds' weight and oil content ...

  2. Assessment of genetic diversity in different clones of Dalbergia ...

    African Journals Online (AJOL)

    Genetic diversity of forty (40) clones of Dalbergia sissoo Roxb was analyzed using randomly amplified polymorphic DNA (RAPD) markers by selecting 30 decamer primers, which were later reduced to 10 based on the preliminary PCR amplification. A total of 129 distinct DNA fragments (bands) were amplified, of which 104 ...

  3. Analysis of genetic diversity and construction of core collection of ...

    African Journals Online (AJOL)

    Jane

    2011-06-03

    Jun 3, 2011 ... Genetic diversity of 73 local mulberry varieties from Shanxi Province were screened using ISSR markers, with l5 primers combinations selected for their reproducibility and polymorphism. 129 bands were amplified, of which 115 bands showed polymorphism and the ratio of polymorphism bands was.

  4. Assessment of genetic diversity among accessions of two traditional ...

    African Journals Online (AJOL)

    Assessment of genetic diversity among accessions of two traditional leafy vegetables (Acmella uliginosa (L.) and Justicia tenella (Nees) T.) consumed in Benin using amplified fragment length polymorphism (AFLP) markers. K Adéoti, A Rival, A Dansi, BS Ahohuendo, S Santoni, T Beule, A Nato, Y Henry, A Ahanchédé, ...

  5. Evaluation of genetic diversity in rice using simple sequence repeats ...

    African Journals Online (AJOL)

    The genetic diversity of 64 rice genotypes using 20 SSR primers on chromosome number 7-12 was investigated. DNA was extracted by modified cetyl trimethyl ammonium bromide (CTAB) method. The banding pattern was recorded in the form of 0-1 data sheet which was analyzed using unweighted pair group method with ...

  6. Assessing the genetic diversity of cultivars and wild soybeans using ...

    African Journals Online (AJOL)

    In this study, we demonstrated the differences of genetic diversity level among 40 soybean accessions of cultivars, landraces and wild soybeans collected in the Shanxi Agricultural University using 40 simple sequence repeat (SSR) primer pairs. The structure based on model result showed that the cultivars, landraces and ...

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

    Indian Academy of Sciences (India)

    FRANCISCO MORINHA

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

  8. Genetic diversity of Pogonatherum paniceum (Lam.) Hack in ...

    African Journals Online (AJOL)

    Inter-simple sequence repeats markers were used to estimate the genetic diversity of Pogonatherum paniceum (Lam.) Hack. from Sichuan Province, Yunnan Province, Chongqing City and Guangxi Zhuang Autonomous Region in China. 100 primers were carried out on 22 wild populations, 14 could produce highly ...

  9. Genetic diversity of Pogonatherum paniceum (Lam.) Hack. in ...

    African Journals Online (AJOL)

    Amplified fragment length polymorphism (AFLP) markers were used to estimate the genetic diversity of Pogonatherum paniceum (Lam.) Hack. from Sichuan Province, Yunnan Province, Chongqing City and. Guangxi Zhuang autonomous Region in China. 10 primer combinations were carried out on 180 different individuals ...

  10. Using genomic information to conserve genetic diversity in livestock

    NARCIS (Netherlands)

    Eynard, Sonia E.

    2018-01-01

    Concern about the status of livestock breeds and their conservation has increased as selection and small population sizes caused loss of genetic diversity. Meanwhile, dense SNP chips and whole genome sequences (WGS) became available, providing opportunities to accurately quantify the impact of

  11. Molecular genetic diversity and genetic structure of Vietnamese indigenous pig populations

    DEFF Research Database (Denmark)

    Pham, L. D.; Do, Duy Ngoc; Nam, L. Q.

    2014-01-01

    The study characterized genetic diversity and genetic structure of five indigenous pig populations (Ha Lang, Muong Te, Mong Cai, Lung and Lung Pu), two wild pig populations (Vietnamese and Thai wild pigs) and an exotic pig breed (Yorkshire) using FAO/ISAG recommended 16 microsatellite markers...

  12. Genetic Diversity Of Plukenetia Volubilis L. Assessed By ISSR Markers*

    Directory of Open Access Journals (Sweden)

    Ocelák M.

    2015-12-01

    Full Text Available The diversity and genetic relationships in 173 sacha inchi samples were analyzed using ISSR markers. Thirty ISSR primers were used, only 8 showed variability in tested samples. ISSR fragments ranged from 200 to 2500 bp. The mean number of bands per primer was 12 and the average number of polymorphic bands per primer was 11. The lowest percentages of polymorphic bands (27%, gene diversity (0.103, and Shannon’s information index (0.15 were exhibited by the Santa Lucia population, which was also geographically most distant. This fact may be attributed to a very small size of this group. In contrast, the Dos de Mayo population exhibited the highest percentage of polymorphic bands (78%, and the Santa Cruz population the highest Nei’s gene diversity index (0.238 and Shannon’s information index (0.357. The obtained level of genetic variability was 36% among tested populations and 64% within populations. Although the diversity indices were low, a cluster analysis revealed 8 clusters containing mainly samples belonging to individual populations. Principal coordinate analysis clearly distinguished Chumbaquihui, Pucallpa, Dos de Mayo, and Aguas de Oro populations, the others were intermixed. The obtained results indicated the level of genetic diversity present in this location of Peru, although it is influenced by anthropological aspects and independent on the geographical distances.

  13. Genetic diversity of Entamoeba: Novel ribosomal lineages from cockroaches.

    Directory of Open Access Journals (Sweden)

    Tetsuro Kawano

    Full Text Available Our current taxonomic perspective on Entamoeba is largely based on small-subunit ribosomal RNA genes (SSU rDNA from Entamoeba species identified in vertebrate hosts with minor exceptions such as E. moshkovskii from sewage water and E. marina from marine sediment. Other Entamoeba species have also been morphologically identified and described from non-vertebrate species such as insects; however, their genetic diversity remains unknown. In order to further disclose the diversity of the genus, we investigated Entamoeba spp. in the intestines of three cockroach species: Periplaneta americana, Blaptica dubia, and Gromphadorhina oblongonota. We obtained 134 Entamoeba SSU rDNA sequences from 186 cockroaches by direct nested PCR using the DNA extracts of intestines from cockroaches, followed by scrutinized BLASTn screening and phylogenetic analyses. All the sequences identified in this study were distinct from those reported from known Entamoeba species, and considered as novel Entamoeba ribosomal lineages. Furthermore, they were positioned at the base of the clade of known Entamoeba species and displayed remarkable degree of genetic diversity comprising nine major groups in the three cockroach species. This is the first report of the diversity of SSU rDNA sequences from Entamoeba in non-vertebrate host species, and should help to understand the genetic diversity of the genus Entamoeba.

  14. Determination of genetic diversity among some almond accessions

    Directory of Open Access Journals (Sweden)

    Pinar Hasan

    2015-01-01

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

  15. Genetic Diversity and Spatial Genetic Structure of the Grassland Perennial Saxifraga granulata along Two River Systems.

    Directory of Open Access Journals (Sweden)

    Sascha van der Meer

    Full Text Available Due to changes in land use, the natural habitats of an increasing number of plant species have become more and more fragmented. In landscapes that consist of patches of suitable habitat, the frequency and extent of long-distance seed dispersal can be expected to be an important factor determining local genetic diversity and regional population structure of the remaining populations. In plant species that are restricted to riparian habitats, rivers can be expected to have a strong impact on the dynamics and spatial genetic structure of populations as they may enable long-distance seed dispersal and thus maintain gene flow between fragmented populations. In this study, we used polymorphic microsatellite markers to investigate the genetic diversity and the spatial genetic structure of 28 populations of Saxifraga granulata along two rivers in central Belgium. We hypothesized that rivers might be essential for gene flow among increasingly isolated populations of this species. Genetic diversity was high (HS = 0.68, which to a certain extent can be explained by the octoploid nature of S. granulata in the study area. Populations along the Dijle and Demer rivers were also highly differentiated (G"ST = 0.269 and 0.164 and DEST = 0.190 and 0.124, respectively and showed significant isolation-by-distance, indicating moderate levels of gene flow primarily between populations that are geographically close to each other. Along the river Demer population genetic diversity was higher upstream than downstream, suggesting that seed dispersal via the water was not the primary mode of dispersal. Overall, these results indicate that despite increasing fragmentation populations along both rivers were highly genetically diverse. The high ploidy level and longevity of S. granulata have most likely buffered negative effects of fragmentation on genetic diversity and the spatial genetic structure of populations in riparian grasslands.

  16. Transferability of Cucurbita SSR markers for genetic diversity assessment of Turkish bottle gourd (Lagenaria siceraria) genetic resources

    Science.gov (United States)

    The genetic diversity present in crop landraces represents a valuable genetic resource for breeding and genetic studies. Bottle gourd (Lagenaria siceraria) landraces in Turkey are highly genetically diverse. However, the limited genomic resources available for this crop hinder the molecular characte...

  17. Estimating intraspecific genetic diversity from community DNA metabarcoding data

    Directory of Open Access Journals (Sweden)

    Vasco Elbrecht

    2018-04-01

    Full Text Available Background DNA metabarcoding is used to generate species composition data for entire communities. However, sequencing errors in high-throughput sequencing instruments are fairly common, usually requiring reads to be clustered into operational taxonomic units (OTUs, losing information on intraspecific diversity in the process. While Cytochrome c oxidase subunit I (COI haplotype information is limited in resolving intraspecific diversity it is nevertheless often useful e.g. in a phylogeographic context, helping to formulate hypotheses on taxon distribution and dispersal. Methods This study combines sequence denoising strategies, normally applied in microbial research, with additional abundance-based filtering to extract haplotype information from freshwater macroinvertebrate metabarcoding datasets. This novel approach was added to the R package “JAMP” and can be applied to COI amplicon datasets. We tested our haplotyping method by sequencing (i a single-species mock community composed of 31 individuals with 15 different haplotypes spanning three orders of magnitude in biomass and (ii 18 monitoring samples each amplified with four different primer sets and two PCR replicates. Results We detected all 15 haplotypes of the single specimens in the mock community with relaxed filtering and denoising settings. However, up to 480 additional unexpected haplotypes remained in both replicates. Rigorous filtering removes most unexpected haplotypes, but also can discard expected haplotypes mainly from the small specimens. In the monitoring samples, the different primer sets detected 177–200 OTUs, each containing an average of 2.40–3.30 haplotypes per OTU. The derived intraspecific diversity data showed population structures that were consistent between replicates and similar between primer pairs but resolution depended on the primer length. A closer look at abundant taxa in the dataset revealed various population genetic patterns, e.g. the stonefly

  18. Genetic Diversity and Population Structure of Theileria annulata in Oman.

    Science.gov (United States)

    Al-Hamidhi, Salama; H Tageldin, Mohammed; Weir, William; Al-Fahdi, Amira; Johnson, Eugene H; Bobade, Patrick; Alqamashoui, Badar; Beja-Pereira, Albano; Thompson, Joanne; Kinnaird, Jane; Shiels, Brian; Tait, Andy; Babiker, Hamza

    2015-01-01

    Theileriosis, caused by a number of species within the genus Theileria, is a common disease of livestock in Oman. It is a major constraint to the development of the livestock industry due to a high rate of morbidity and mortality in both cattle and sheep. Since little is currently known about the genetic diversity of the parasites causing theileriosis in Oman, the present study was designed to address this issue with specific regard to T. annulata in cattle. Blood samples were collected from cattle from four geographically distinct regions in Oman for genetic analysis of the Theileria annulata population. Ten genetic markers (micro- and mini-satellites) representing all four chromosomes of T. annulata were applied to these samples using a combination of PCR amplification and fragment analysis. The resultant genetic data was analysed to provide a first insight into the structure of the T. annulata population in Oman. We applied ten micro- and mini-satellite markers to a total of 310 samples obtained from different regions (174 [56%] from Dhofar, 68 [22%] from Dhira, 44 [14.5%] from Batinah and 24 [8%] from Sharqia). A high degree of allelic diversity was observed among the four parasite populations. Expected heterozygosity for each site ranged from 0.816 to 0.854. A high multiplicity of infection was observed in individual hosts, with an average of 3.3 to 3.4 alleles per locus, in samples derived from Batinah, Dhofar and Sharqia regions. In samples from Dhira region, an average of 2.9 alleles per locus was observed. Mild but statistically significant linkage disequilibrium between pairs of markers was observed in populations from three of the four regions. In contrast, when the analysis was performed at farm level, no significant linkage disequilibrium was observed. Finally, no significant genetic differentiation was seen between the four populations, with most pair-wise FST values being less than 0.03. Slightly higher FST values (GST' = 0.075, θ = 0.07) were

  19. Genetic Diversity and Population Structure of Theileria annulata in Oman.

    Directory of Open Access Journals (Sweden)

    Salama Al-Hamidhi

    Full Text Available Theileriosis, caused by a number of species within the genus Theileria, is a common disease of livestock in Oman. It is a major constraint to the development of the livestock industry due to a high rate of morbidity and mortality in both cattle and sheep. Since little is currently known about the genetic diversity of the parasites causing theileriosis in Oman, the present study was designed to address this issue with specific regard to T. annulata in cattle.Blood samples were collected from cattle from four geographically distinct regions in Oman for genetic analysis of the Theileria annulata population. Ten genetic markers (micro- and mini-satellites representing all four chromosomes of T. annulata were applied to these samples using a combination of PCR amplification and fragment analysis. The resultant genetic data was analysed to provide a first insight into the structure of the T. annulata population in Oman.We applied ten micro- and mini-satellite markers to a total of 310 samples obtained from different regions (174 [56%] from Dhofar, 68 [22%] from Dhira, 44 [14.5%] from Batinah and 24 [8%] from Sharqia. A high degree of allelic diversity was observed among the four parasite populations. Expected heterozygosity for each site ranged from 0.816 to 0.854. A high multiplicity of infection was observed in individual hosts, with an average of 3.3 to 3.4 alleles per locus, in samples derived from Batinah, Dhofar and Sharqia regions. In samples from Dhira region, an average of 2.9 alleles per locus was observed. Mild but statistically significant linkage disequilibrium between pairs of markers was observed in populations from three of the four regions. In contrast, when the analysis was performed at farm level, no significant linkage disequilibrium was observed. Finally, no significant genetic differentiation was seen between the four populations, with most pair-wise FST values being less than 0.03. Slightly higher FST values (GST' = 0.075,

  20. Population genetic diversity and hybrid detection in captive zebras.

    Science.gov (United States)

    Ito, Hideyuki; Langenhorst, Tanya; Ogden, Rob; Inoue-Murayama, Miho

    2015-08-21

    Zebras are members of the horse family. There are three species of zebras: the plains zebra Equus quagga, the Grevy's zebra E. grevyi and the mountain zebra E. zebra. The Grevy's zebra and the mountain zebra are endangered, and hybridization between the Grevy's zebra and the plains zebra has been documented, leading to a requirement for conservation genetic management within and between the species. We characterized 28 microsatellite markers in Grevy's zebra and assessed cross-amplification in plains zebra and two of its subspecies, as well as mountain zebra. A range of standard indices were employed to examine population genetic diversity and hybrid populations between Grevy's and plains zebra were simulated to investigate subspecies and hybrid detection. Microsatellite marker polymorphism was conserved across species with sufficient variation to enable individual identification in all populations. Comparative diversity estimates indicated greater genetic variation in plains zebra and its subspecies than Grevy's zebra, despite potential ascertainment bias. Species and subspecies differentiation were clearly demonstrated and F1 and F2 hybrids were correctly identified. These findings provide insights into captive population genetic diversity in zebras and support the use of these markers for identifying hybrids, including the known hybrid issue in the endangered Grevy's zebra.

  1. The influence of recombination on human genetic diversity.

    Directory of Open Access Journals (Sweden)

    Chris C A Spencer

    2006-09-01

    Full Text Available In humans, the rate of recombination, as measured on the megabase scale, is positively associated with the level of genetic variation, as measured at the genic scale. Despite considerable debate, it is not clear whether these factors are causally linked or, if they are, whether this is driven by the repeated action of adaptive evolution or molecular processes such as double-strand break formation and mismatch repair. We introduce three innovations to the analysis of recombination and diversity: fine-scale genetic maps estimated from genotype experiments that identify recombination hotspots at the kilobase scale, analysis of an entire human chromosome, and the use of wavelet techniques to identify correlations acting at different scales. We show that recombination influences genetic diversity only at the level of recombination hotspots. Hotspots are also associated with local increases in GC content and the relative frequency of GC-increasing mutations but have no effect on substitution rates. Broad-scale association between recombination and diversity is explained through covariance of both factors with base composition. To our knowledge, these results are the first evidence of a direct and local influence of recombination hotspots on genetic variation and the fate of individual mutations. However, that hotspots have no influence on substitution rates suggests that they are too ephemeral on an evolutionary time scale to have a strong influence on broader scale patterns of base composition and long-term molecular evolution.

  2. Concordance between botanical groups and genetic diversity in peanut

    Directory of Open Access Journals (Sweden)

    Ingrid Pinheiro Machado

    Full Text Available ABSTRACT The aims of this study were to characterize peanut accessions of germplasm collection of the CCA/UFC and check consistency between the pre-existing botanical groups to estimates of genetic diversity. For this were conducted a trial with 43 accessions of peanut in a randomized block design with three replications. To characterization were used 21 morphological descriptors, where revealed large genetic variation. The mass hundred grains trait showed the main discriminating factors, with relative percentage of 22.1%. The cluster obtained with the linkage complete method, it was possible to view the dendrogram the formation of seven groups based on the Mahalanobis distance. By principal components analysis was identified phenotypic diversity among genotypes. The first three components explained 81% of the total variation. Subsequently, built a three-dimensional scatter chart for access of visualization, eight groups being formed. There was medium magnitude of agreement between the botanical groups and genetic diversity, both by the dendrogram and graphic dispersion proving the dissimilarity between genotypes of different botanic groups. Therefore, crossings between group access botanical Spanish or Valencia with those belonging to the Virginia group should generate segregating populations with high genetic potential.

  3. Genetic diversity affects colony survivorship in commercial honey bee colonies

    Science.gov (United States)

    Tarpy, David R.; vanEngelsdorp, Dennis; Pettis, Jeffrey S.

    2013-08-01

    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.

  4. Evaluation of genetic diversity in different Pakistani wheat land races

    International Nuclear Information System (INIS)

    Mahmood, T.; Siddiqua, A.; Rasheed, A.; Nazar, N.

    2011-01-01

    Wheat is one of the main sources of nutrition worldwide. Genetic improvement of the seed makes wheat a source of high quality flour for human consumption and for other industrial uses. With the help of molecular markers, the available germplasm of wheat can be assessed for future breeding programs. Therefore, the aim of the present work was to analyze the genetic diversity among 15 Pakistani wheat land races based on Random Amplified Polymorphism DNA (RAPD) markers. A total of 284 DNA fragments were amplified, ranging in size from 200bp to 1100bp by using six primers. The number of DNA fragments for each primer varied from 2 (OPC-6) to 9 (OPC-8) with an average of 6 fragments per primer. Out of 284 amplified products, 120 were monomorphic and 137 were polymorphic showing an average of 7.8% polymorphism per primer. One specific marker was detected both for OPC-1 and OPC-8, two for OPC-5, while no RAPD specific marker was detected for the remaining primers. The genetic similarity index values ranged from 0.36 to 0.93, with an average of 0.64. Maximum genetic similarity (91%) was observed between Sur bej and Khushkawa. On the contrary, minimum genetic similarity (32%) was observed in Khushkaba-1 and Khushkawa. The dendrogram resulting from the NTSYS cluster analysis showed that the studied genotypes are divided into two main clusters from the same node. The first cluster contained 13 land races, while the second cluster contained only 2 land races. The dendrogram clustered the genotypes into 5 groups and showed efficiency in identifying genetic variability. These results indicated the usefulness of RAPD technique in estimating the genetic diversity among wheat genetic resources. (author)

  5. Genetic Diversity of Aromatic Rice Germplasm Revealed By SSR Markers

    Directory of Open Access Journals (Sweden)

    Saba Jasim Aljumaili

    2018-01-01

    Full Text Available Aromatic rice cultivars constitute a small but special group of rice and are considered the best in terms of quality and aroma. Aroma is one of the most significant quality traits of rice, and variety with aroma has a higher price in the market. This research was carried out to study the genetic diversity among the 50 aromatic rice accessions from three regions (Peninsular Malaysia, Sabah, and Sarawak with 3 released varieties as a control using the 32 simple sequence repeat (SSR markers. The objectives of this research were to quantify the genetic divergence of aromatic rice accessions using SSR markers and to identify the potential accessions for introgression into the existing rice breeding program. Genetic diversity index among the three populations such as Shannon information index (I ranged from 0.25 in control to 0.98 in Sabah population. The mean numbers of effective alleles and Shannon’s information index were 0.36 and 64.90%, respectively. Similarly, the allelic diversity was very high with mean expected heterozygosity (He of 0.60 and mean Nei’s gene diversity index of 0.36. The dendrogram based on UPGMA and Nei’s genetic distance classified the 53 rice accessions into 10 clusters. Analysis of molecular variance (AMOVA revealed that 89% of the total variation observed in this germplasm came from within the populations, while 11% of the variation emanated among the populations. These results reflect the high genetic differentiation existing in this aromatic rice germplasm. Using all these criteria and indices, seven accessions (Acc9993, Acc6288, Acc6893, Acc7580, Acc6009, Acc9956, and Acc11816 from three populations have been identified and selected for further evaluation before introgression into the existing breeding program and for future aromatic rice varietal development.

  6. Genetic Diversity of Aromatic Rice Germplasm Revealed By SSR Markers.

    Science.gov (United States)

    Jasim Aljumaili, Saba; Rafii, M Y; Latif, M A; Sakimin, Siti Zaharah; Arolu, Ibrahim Wasiu; Miah, Gous

    2018-01-01

    Aromatic rice cultivars constitute a small but special group of rice and are considered the best in terms of quality and aroma. Aroma is one of the most significant quality traits of rice, and variety with aroma has a higher price in the market. This research was carried out to study the genetic diversity among the 50 aromatic rice accessions from three regions (Peninsular Malaysia, Sabah, and Sarawak) with 3 released varieties as a control using the 32 simple sequence repeat (SSR) markers. The objectives of this research were to quantify the genetic divergence of aromatic rice accessions using SSR markers and to identify the potential accessions for introgression into the existing rice breeding program. Genetic diversity index among the three populations such as Shannon information index ( I ) ranged from 0.25 in control to 0.98 in Sabah population. The mean numbers of effective alleles and Shannon's information index were 0.36 and 64.90%, respectively. Similarly, the allelic diversity was very high with mean expected heterozygosity ( H e ) of 0.60 and mean Nei's gene diversity index of 0.36. The dendrogram based on UPGMA and Nei's genetic distance classified the 53 rice accessions into 10 clusters. Analysis of molecular variance (AMOVA) revealed that 89% of the total variation observed in this germplasm came from within the populations, while 11% of the variation emanated among the populations. These results reflect the high genetic differentiation existing in this aromatic rice germplasm. Using all these criteria and indices, seven accessions (Acc9993, Acc6288, Acc6893, Acc7580, Acc6009, Acc9956, and Acc11816) from three populations have been identified and selected for further evaluation before introgression into the existing breeding program and for future aromatic rice varietal development.

  7. Genetic Diversity of Aromatic Rice Germplasm Revealed By SSR Markers

    Science.gov (United States)

    Jasim Aljumaili, Saba; Sakimin, Siti Zaharah; Arolu, Ibrahim Wasiu; Miah, Gous

    2018-01-01

    Aromatic rice cultivars constitute a small but special group of rice and are considered the best in terms of quality and aroma. Aroma is one of the most significant quality traits of rice, and variety with aroma has a higher price in the market. This research was carried out to study the genetic diversity among the 50 aromatic rice accessions from three regions (Peninsular Malaysia, Sabah, and Sarawak) with 3 released varieties as a control using the 32 simple sequence repeat (SSR) markers. The objectives of this research were to quantify the genetic divergence of aromatic rice accessions using SSR markers and to identify the potential accessions for introgression into the existing rice breeding program. Genetic diversity index among the three populations such as Shannon information index (I) ranged from 0.25 in control to 0.98 in Sabah population. The mean numbers of effective alleles and Shannon's information index were 0.36 and 64.90%, respectively. Similarly, the allelic diversity was very high with mean expected heterozygosity (He) of 0.60 and mean Nei's gene diversity index of 0.36. The dendrogram based on UPGMA and Nei's genetic distance classified the 53 rice accessions into 10 clusters. Analysis of molecular variance (AMOVA) revealed that 89% of the total variation observed in this germplasm came from within the populations, while 11% of the variation emanated among the populations. These results reflect the high genetic differentiation existing in this aromatic rice germplasm. Using all these criteria and indices, seven accessions (Acc9993, Acc6288, Acc6893, Acc7580, Acc6009, Acc9956, and Acc11816) from three populations have been identified and selected for further evaluation before introgression into the existing breeding program and for future aromatic rice varietal development. PMID:29736396

  8. Analysis of genetic diversity in Bolivian llama populations using microsatellites.

    Science.gov (United States)

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

    2013-08-01

    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. © 2012 Blackwell Verlag GmbH.

  9. Genetic diversity and environmental associations of sacsaoul ( Haloxylon ammodendron)

    Science.gov (United States)

    Zhang, Linjing; Zhao, Guifang; Yue, Ming; Pan, Xiaoling

    2003-07-01

    Random amplified polymorphic DNA (RAPD) markers were used to assess levels and patterns of genetic diversity in H. ammodendron (Chenopodiaceae). A total of 117 plants from 6 subpopulations on oasis-desert ecotone was analyzed by 16 arbitrarily chosen primers resulting in highly reproducible RAPD bands. The analysis of molecular variance (AMOVA) with distances among individuals showed that most of the variation (74%) occurred among individuals within subpopulations, which is expected for a crossing organism, and 26% of variation among subpopulations. Estimates of Shannon index and Nei"s index from allele frequencies corroborated AMOVA partitioning in H. ammodendron. UPGMA cluster analyses, based on genetic distance, do not revealed grouping of some geographically proximate populations. This is the first report of the partitioning of genetic variability within and between subpopulations of H. ammodendron and provides important baseline data for optimizing sampling strategies and for conserving the genetic resources of this species. The Percentage of polymorphic loci was as high as 96%, presumably being response to oasis-desert ecotone. There were gene flows (Nm=5.38 individuals/generation), based on gene differentiation coefficient (GST was 0.1567) between subpopulations, and strong habitat selection override the gene flow to maintain the subpopulation differentiation. Correlation analyses showed that there was significant relationship between genetic diversity and soil CL ion.

  10. Turtle carapace anomalies: the roles of genetic diversity and environment.

    Directory of Open Access Journals (Sweden)

    Guillermo Velo-Antón

    2011-04-01

    Full Text Available Phenotypic anomalies are common in wild populations and multiple genetic, biotic and abiotic factors might contribute to their formation. Turtles are excellent models for the study of developmental instability because anomalies are easily detected in the form of malformations, additions, or reductions in the number of scutes or scales.In this study, we integrated field observations, manipulative experiments, and climatic and genetic approaches to investigate the origin of carapace scute anomalies across Iberian populations of the European pond turtle, Emys orbicularis. The proportion of anomalous individuals varied from 3% to 69% in local populations, with increasing frequency of anomalies in northern regions. We found no significant effect of climatic and soil moisture, or climatic temperature on the occurrence of anomalies. However, lower genetic diversity and inbreeding were good predictors of the prevalence of scute anomalies among populations. Both decreasing genetic diversity and increasing proportion of anomalous individuals in northern parts of the Iberian distribution may be linked to recolonization events from the Southern Pleistocene refugium.Overall, our results suggest that developmental instability in turtle carapace formation might be caused, at least in part, by genetic factors, although the influence of environmental factors affecting the developmental stability of turtle carapace cannot be ruled out. Further studies of the effects of environmental factors, pollutants and heritability of anomalies would be useful to better understand the complex origin of anomalies in natural populations.

  11. Exploiting a wheat EST database to assess genetic diversity.

    Science.gov (United States)

    Karakas, Ozge; Gurel, Filiz; Uncuoglu, Ahu Altinkut

    2010-10-01

    Expressed sequence tag (EST) markers have been used to assess variety and genetic diversity in wheat (Triticum aestivum). In this study, 1549 ESTs from wheat infested with yellow rust were used to examine the genetic diversity of six susceptible and resistant wheat cultivars. The aim of using these cultivars was to improve the competitiveness of public wheat breeding programs through the intensive use of modern, particularly marker-assisted, selection technologies. The F(2) individuals derived from cultivar crosses were screened for resistance to yellow rust at the seedling stage in greenhouses and adult stage in the field to identify DNA markers genetically linked to resistance. Five hundred and sixty ESTs were assembled into 136 contigs and 989 singletons. BlastX search results showed that 39 (29%) contigs and 96 (10%) singletons were homologous to wheat genes. The database-matched contigs and singletons were assigned to eight functional groups related to protein synthesis, photosynthesis, metabolism and energy, stress proteins, transporter proteins, protein breakdown and recycling, cell growth and division and reactive oxygen scavengers. PCR analyses with primers based on the contigs and singletons showed that the most polymorphic functional categories were photosynthesis (contigs) and metabolism and energy (singletons). EST analysis revealed considerable genetic variability among the Turkish wheat cultivars resistant and susceptible to yellow rust disease and allowed calculation of the mean genetic distance between cultivars, with the greatest similarity (0.725) being between Harmankaya99 and Sönmez2001, and the lowest (0.622) between Aytin98 and Izgi01.

  12. Study on genetic diversity of some Iranian Pistachio (Pistacia vera L ...

    African Journals Online (AJOL)

    hope&shola

    2010-11-08

    Nov 8, 2010 ... Keywords: Pistacia vera, genetic diversity, clustering, population parameters. .... used to detect DNA polymorphism and genetic diversity in ..... Project on Underutilized ... 2nd. nat. symp. of cellular and molecular biology.

  13. Unexpected high genetic diversity in small populations suggests maintenance by associative overdominance

    DEFF Research Database (Denmark)

    Schou, Mads F.; Loeschcke, Volker; Bechsgaard, Jesper

    2017-01-01

    fragmented populations. More genetic diversity was retained in areas of low recombination, suggesting that associative overdominance, driven by disfavoured homozygosity of recessive deleterious alleles, is responsible for the maintenance of genetic diversity in smaller populations. Consistent...

  14. ASSOCIATIONS BETWEEN GENETIC DIVERSITY AND ANTHROPOGENIC DISTURBANCE IN MIDWESTERN STREAM-DWELLING MINNOWS

    Science.gov (United States)

    Anthropogenic disturbances may leave imprints on patterns of intraspecific genetic diversity through their effects on population size, adaptation, migration, and mutation. We examined patterns of genetic diversity for a stream-dwelling minnow (the central stoneroller, Campostoma...

  15. Assessment of genetic diversity of Xanthomonas oryzae pv. oryzae

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    @@Bacterial blight of rice, caused by Xanthomonas oryzae pv. Oryzae(Xoo. ), is one of the major rice diseases in China. Making clear the shift of genetic diversity of the pathogen will provide important information for rice breeding. Strains collected from 11 provinces located in Southern region of the Changjiang River in China were assessed by using inoculation method and IS-PCR(Insertion Sequence-Based Polymerase Chain Reaction) analysis.

  16. Genetic diversity of siderophore-producing bacteria of tobacco rhizosphere

    OpenAIRE

    Tian, Fang; Ding, Yanqin; Zhu, Hui; Yao, Liangtong; Du, Binghai

    2009-01-01

    The genetic diversity of siderophore-producing bacteria of tobacco rhizosphere was studied by amplified ribosomal DNA restriction analysis (ARDRA), 16S rRNA sequence homology and phylogenetics analysis methods. Studies demonstrated that 85% of the total 354 isolates produced siderophores in iron limited liquid medium. A total of 28 ARDRA patterns were identified among the 299 siderophore-producing bacterial isolates. The 28 ARDRA patterns represented bacteria of 14 different genera belonging ...

  17. Probing genetic diversity to characterize red rot resistance in sugarcane

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-10-15

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

  18. Genetic diversity for fermentable carbohydrates production in alfalfa

    Energy Technology Data Exchange (ETDEWEB)

    Castonguay, Y.; Bertrand, A.; Duceppe, M.O.; Dube, M.P.; Michaud, R. [Agriculture and Agri-Food Canada, Quebec City, PQ (Canada)

    2009-07-01

    Alfalfa has many attributes that renders it suitable for bioethanol production, including its adaptability to diverse environmental conditions without any need for nitrogen fertilizer. However research is needed to develop biofuel-type alfalfa with improved biomass production and standability, increased persistence, and better cell wall degradability. The ethanol conversion rates from alfalfa biomass could be increased by genetically improving the accumulation of readily fermentable non-structural carbohydrates (NSC). This presentation reported on a screening project where genotypes with superior cell wall degradability were identified. NSC accumulation within 300 genotypes was randomly selected within six genetic backgrounds from Europe and North America. Biochemical analyses of dried stems revealed a large genetic variability for NSC content, with concentrations ranging from 20 to 100 mg per g DW. NSC variability was considerably higher in a genetic background of European origin compared to the other populations, therefore emphasizing the potential for genetic improvement for that trait. A modified commercial enzymatic cocktail known as AcceleraseTM 1000 Genencor is being developed to optimize the degradation of alfalfa biomass. DNA extracted from genotypes with the highest and lowest cell wall degradability or NSC accumulation will be pooled and used for bulk segregant analysis of DNA polymorphisms using the PCR-based sequence-related amplified polymorphism technique. It was concluded that the commercial release of biofuel-type alfalfa can be accelerated if the genetic markers associated with these traits can be identified.

  19. Genetic diversity of tambaqui broodstocks in stock enhancement programs

    Directory of Open Access Journals (Sweden)

    Americo Moraes Neto

    2017-06-01

    Full Text Available Natural populations of tambaqui (Colossoma macropomum have significantly decreased in recent decades especially due to human extraction activities. So that the environmental impact may be reduced, the restocking of fish and increase in fish production are enhanced. Genetic evaluations using molecular markers are essential for this purpose. Current study evaluates the genetic variability of two tambaqui broodstocks used in restocking programs. Sixty-five samples (33 samples from broodstock A and 32 samples from broodstock B were collected. DNA was extracted from caudal fin samples, with the amplification of four microsatellite loci: Cm1A11 (EU685307 Cm1C8 (EU685308 Cm1F4 (EU685311 and Cm1H8 (EU685315. Fourteen alleles in the stock of broodstock A were produced, five alleles for Cm1A11 locus (230, 255, 260, 270 and 276 bp, three alleles Cm1C8 (239, 260, and 273 bp, two alleles Cm1F4 (211 and 245 bp, four alleles for Cm1H8 (275, 290, 320 and 331 bp and two unique alleles were found for Cm1A11 loci (alleles 270 and 276 bp and Cm1H8 (alleles 275 and 331 bp. In broodstock B, ten alleles were produced, the same alleles of the first stock except for alleles 270 and 276 bp in Cm1A11 locus and 275 and 331 bp in Cm1H8 locus. Broodstock A revealed low frequency alleles in Cm1A11 loci, Cm1C8, Cm1F4 and Cm1H8, whereas broodstock B had no locus with low allelic frequency. Loci Cm1A11, Cm1C8 and Cm1H8 exhibited significant deficit of heterozygotes in both broodstocks, revealing changes in Hardy-Weinberg equilibrium. Genetic diversity between stocks was 0.1120, whilst genetic similarity was 0.894, with FST rate = 0.05, and Nm = 3.93, indicating gene flow between the two broodstocks. Results show that broodstocks are genetically closely related, with no great genetic variability. Strategies such as a previous genetic analysis of breeding with its marking, use of a large Ne crossing between the most genetically divergent specimens, and the introduction of new

  20. Genetic diversity and relationship analysis of Gossypium arboreum accessions.

    Science.gov (United States)

    Liu, F; Zhou, Z L; Wang, C Y; Wang, Y H; Cai, X Y; Wang, X X; Zhang, Z S; Wang, K B

    2015-11-19

    Simple sequence repeat techniques were used to identify the genetic diversity of 101 Gossypium arboreum accessions collected from India, Vietnam, and the southwest of China (Guizhou, Guangxi, and Yunnan provinces). Twenty-six pairs of SSR primers produced a total of 103 polymorphic loci with an average of 3.96 polymorphic loci per primer. The average of the effective number of alleles, Nei's gene diversity, and Shannon's information index were 0.59, 0.2835, and 0.4361, respectively. The diversity varied among different geographic regions. The result of principal component analysis was consistent with that of unweighted pair group method with arithmetic mean clustering analysis. The 101 G. arboreum accessions were clustered into 2 groups.

  1. Genetic Diversity in Natural Populations of New World Leishmania

    Directory of Open Access Journals (Sweden)

    Cupolillo Elisa

    1998-01-01

    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.

  2. Assessing Date Palm Genetic Diversity Using Different Molecular Markers.

    Science.gov (United States)

    Atia, Mohamed A M; Sakr, Mahmoud M; Adawy, Sami S

    2017-01-01

    Molecular marker technologies which rely on DNA analysis provide powerful tools to assess biodiversity at different levels, i.e., among and within species. A range of different molecular marker techniques have been developed and extensively applied for detecting variability in date palm at the DNA level. Recently, the employment of gene-targeting molecular marker approaches to study biodiversity and genetic variations in many plant species has increased the attention of researchers interested in date palm to carry out phylogenetic studies using these novel marker systems. Molecular markers are good indicators of genetic distances among accessions, because DNA-based markers are neutral in the face of selection. Here we describe the employment of multidisciplinary molecular marker approaches: amplified fragment length polymorphism (AFLP), start codon targeted (SCoT) polymorphism, conserved DNA-derived polymorphism (CDDP), intron-targeted amplified polymorphism (ITAP), simple sequence repeats (SSR), and random amplified polymorphic DNA (RAPD) to assess genetic diversity in date palm.

  3. Extraordinary Genetic Diversity in a Wood Decay Mushroom.

    Science.gov (United States)

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

    2015-10-01

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

  4. Broad-Scale Genetic Diversity of Cannabis for Forensic Applications.

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    Christophe Dufresnes

    Full Text Available Cannabis (hemp and marijuana is an iconic yet controversial crop. On the one hand, it represents a growing market for pharmaceutical and agricultural sectors. On the other hand, plants synthesizing the psychoactive THC produce the most widespread illicit drug in the world. Yet, the difficulty to reliably distinguish between Cannabis varieties based on morphological or biochemical criteria impedes the development of promising industrial programs and hinders the fight against narcotrafficking. Genetics offers an appropriate alternative to characterize drug vs. non-drug Cannabis. However, forensic applications require rapid and affordable genotyping of informative and reliable molecular markers for which a broad-scale reference database, representing both intra- and inter-variety variation, is available. Here we provide such a resource for Cannabis, by genotyping 13 microsatellite loci (STRs in 1 324 samples selected specifically for fibre (24 hemp varieties and drug (15 marijuana varieties production. We showed that these loci are sufficient to capture most of the genome-wide diversity patterns recently revealed by NGS data. We recovered strong genetic structure between marijuana and hemp and demonstrated that anonymous samples can be confidently assigned to either plant types. Fibres appear genetically homogeneous whereas drugs show low (often clonal diversity within varieties, but very high genetic differentiation between them, likely resulting from breeding practices. Based on an additional test dataset including samples from 41 local police seizures, we showed that the genetic signature of marijuana cultivars could be used to trace crime scene evidence. To date, our study provides the most comprehensive genetic resource for Cannabis forensics worldwide.

  5. Broad-Scale Genetic Diversity of Cannabis for Forensic Applications.

    Science.gov (United States)

    Dufresnes, Christophe; Jan, Catherine; Bienert, Friederike; Goudet, Jérôme; Fumagalli, Luca

    2017-01-01

    Cannabis (hemp and marijuana) is an iconic yet controversial crop. On the one hand, it represents a growing market for pharmaceutical and agricultural sectors. On the other hand, plants synthesizing the psychoactive THC produce the most widespread illicit drug in the world. Yet, the difficulty to reliably distinguish between Cannabis varieties based on morphological or biochemical criteria impedes the development of promising industrial programs and hinders the fight against narcotrafficking. Genetics offers an appropriate alternative to characterize drug vs. non-drug Cannabis. However, forensic applications require rapid and affordable genotyping of informative and reliable molecular markers for which a broad-scale reference database, representing both intra- and inter-variety variation, is available. Here we provide such a resource for Cannabis, by genotyping 13 microsatellite loci (STRs) in 1 324 samples selected specifically for fibre (24 hemp varieties) and drug (15 marijuana varieties) production. We showed that these loci are sufficient to capture most of the genome-wide diversity patterns recently revealed by NGS data. We recovered strong genetic structure between marijuana and hemp and demonstrated that anonymous samples can be confidently assigned to either plant types. Fibres appear genetically homogeneous whereas drugs show low (often clonal) diversity within varieties, but very high genetic differentiation between them, likely resulting from breeding practices. Based on an additional test dataset including samples from 41 local police seizures, we showed that the genetic signature of marijuana cultivars could be used to trace crime scene evidence. To date, our study provides the most comprehensive genetic resource for Cannabis forensics worldwide.

  6. Genetic diversity and trait genomic prediction in a pea diversity panel.

    Science.gov (United States)

    Burstin, Judith; Salloignon, Pauline; Chabert-Martinello, Marianne; Magnin-Robert, Jean-Bernard; Siol, Mathieu; Jacquin, Françoise; Chauveau, Aurélie; Pont, Caroline; Aubert, Grégoire; Delaitre, Catherine; Truntzer, Caroline; Duc, Gérard

    2015-02-21

    Pea (Pisum sativum L.), a major pulse crop grown for its protein-rich seeds, is an important component of agroecological cropping systems in diverse regions of the world. New breeding challenges imposed by global climate change and new regulations urge pea breeders to undertake more efficient methods of selection and better take advantage of the large genetic diversity present in the Pisum sativum genepool. Diversity studies conducted so far in pea used Simple Sequence Repeat (SSR) and Retrotransposon Based Insertion Polymorphism (RBIP) markers. Recently, SNP marker panels have been developed that will be useful for genetic diversity assessment and marker-assisted selection. A collection of diverse pea accessions, including landraces and cultivars of garden, field or fodder peas as well as wild peas was characterised at the molecular level using newly developed SNP markers, as well as SSR markers and RBIP markers. The three types of markers were used to describe the structure of the collection and revealed different pictures of the genetic diversity among the collection. SSR showed the fastest rate of evolution and RBIP the slowest rate of evolution, pointing to their contrasted mode of evolution. SNP markers were then used to predict phenotypes -the date of flowering (BegFlo), the number of seeds per plant (Nseed) and thousand seed weight (TSW)- that were recorded for the collection. Different statistical methods were tested including the LASSO (Least Absolute Shrinkage ans Selection Operator), PLS (Partial Least Squares), SPLS (Sparse Partial Least Squares), Bayes A, Bayes B and GBLUP (Genomic Best Linear Unbiased Prediction) methods and the structure of the collection was taken into account in the prediction. Despite a limited number of 331 markers used for prediction, TSW was reliably predicted. The development of marker assisted selection has not reached its full potential in pea until now. This paper shows that the high-throughput SNP arrays that are being

  7. Characterisation of the genetic diversity of Brucella by multilocus sequencing

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    MacMillan Alastair P

    2007-04-01

    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

  8. Genetic calibration of species diversity among North America's freshwater fishes.

    Science.gov (United States)

    April, Julien; Mayden, Richard L; Hanner, Robert H; Bernatchez, Louis

    2011-06-28

    Freshwater ecosystems are being heavily exploited and degraded by human activities all over the world, including in North America, where fishes and fisheries are strongly affected. Despite centuries of taxonomic inquiry, problems inherent to species identification continue to hamper the conservation of North American freshwater fishes. Indeed, nearly 10% of species diversity is thought to remain undescribed. To provide an independent calibration of taxonomic uncertainty and to establish a more accessible molecular identification key for its application, we generated a standard reference library of mtDNA sequences (DNA barcodes) derived from expert-identified museum specimens for 752 North American freshwater fish species. This study demonstrates that 90% of known species can be delineated using barcodes. Moreover, it reveals numerous genetic discontinuities indicative of independently evolving lineages within described species, which points to the presence of morphologically cryptic diversity. From the 752 species analyzed, our survey flagged 138 named species that represent as many as 347 candidate species, which suggests a 28% increase in species diversity. In contrast, several species of parasitic and nonparasitic lampreys lack such discontinuity and may represent alternative life history strategies within single species. Therefore, it appears that the current North American freshwater fish taxonomy at the species level significantly conceals diversity in some groups, although artificially creating diversity in others. In addition to providing an easily accessible digital identification system, this study identifies 151 fish species for which taxonomic revision is required.

  9. Genetic diversity of disease-associated loci in Turkish population.

    Science.gov (United States)

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

    2015-04-01

    Many consortia and international projects have investigated the human genetic variation of a large number of ethno-geographic groups. However, populations with peculiar genetic features, such as the Turkish population, are still absent in publically available datasets. To explore the genetic predisposition to health-related traits of the Turkish population, we analyzed 34 genes associated with different health-related traits (for example, lipid metabolism, cardio-vascular diseases, hormone metabolism, cellular detoxification, aging and energy metabolism). We observed relevant differences between the Turkish population and populations with non-European ancestries (that is, Africa and East Asia) in some of the investigated genes (that is, AGT, APOE, CYP1B1, GNB3, IL10, IL6, LIPC and PON1). As most complex traits are highly polygenic, we developed polygenic scores associated with different health-related traits to explore the genetic diversity of the Turkish population with respect to other human groups. This approach showed significant differences between the Turkish population and populations with non-European ancestries, as well as between Turkish and Northern European individuals. This last finding is in agreement with the genetic structure of European and Middle East populations, and may also agree with epidemiological evidences about the health disparities of Turkish communities in Northern European countries.

  10. Characterization of genetic diversity of bird-of-paradise accessions

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    Alessandro Aparecido Brito dos Santos

    2018-04-01

    Full Text Available This study aimed to characterize genetic diversity in the bird-of-paradise (Strelitzia reginae collection at the Universidade do Estado de Mato Grosso Carlos Alberto Reyes Maldonado (UNEMAT by estimating genetic divergence among genotypes based on agronomic characteristics. Seven agronomic characters were evaluated with average Euclidean distance. The UPGMA (Unweighted Pair Group Method with Arithmetic Mean hierarchical clustering method was used between groups, as well as Tocher’s optimization clustering method and principal component analysis (PCA, in order to classify the genotypes with maximum similarity between groups. Measures of genetic dissimilarity with average Euclidean distance verified the existence of genetic variability among accessions since the amplitude of dissimilarity values ranged from 1.09 to 36.97. Tocher’s clustering method verified the formation of two distinct groups. UPGMA hierarchical clustering, based on the dissimilarity matrix, verified the formation of three groups with 30% cutoff point. Based on the main components analysis, we verified genetic divergence between the bird-of-paradise accessions in the UNEMAT Collection. The most promising combinations for future crosses in breeding programs comprise accessions 1, 11, and 23 and accession 1 as the most divergent among the accessions evaluated.

  11. Genetic and phenotypic diversity of Rhizobium isolates from Southern Ecuador

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    Roldán Torres-Gutiérrez

    Full Text Available ABSTRACT Rhizobium-legume symbioses play relevant roles in agriculture but have not been well studied in Ecuador. The aim of this study was to characterize the genetic and phenotypic diversity of Rhizobium isolates associated with Phaseolus vulgaris from southern Ecuador. Morpho-cultural characterization, biochemical tests and physiological analyses were conducted to authenticate and determine the diversity of bacteria Rhizobium-like isolates. The genetic diversity of the isolates was determined by molecular techniques, which consisted of bacteria DNA extraction and amplification and sequencing of the 16S rRNA gene. The nodulation parameters and nitrogen fixation for P. vulgaris under greenhouse conditions were also assessed to determine the phenotypic diversity among isolates. Furthermore, bacteria indole-acetic-acid production was evaluated by the colorimetric method. Morpho-cultural and biochemical characteristic assessments demonstrated that Rhizobium-like bacteria was associated with the P. vulgaris nodules. The diversity among the isolates, as determined by physiological analyses, revealed the potential of several isolates to grow at different pH values, salinity conditions and temperatures. Partial sequencing of the 16S rRNA gene identified the Rhizobium genus in every sampling site. From a total of 20 aligned sequences, nine species of Rhizobium were identified. Nodule formation and biomass, as well as nitrogen fixation, showed an increase in plant phenotypic parameters, which could be influenced by IAA production, especially for the strains R. mesoamericanum NAM1 and R. leguminosarum bv. viciae COL6. These results demonstrated the efficiency of native symbiotic diazotrophic strains inoculants for legume production. This work can serve as the basis for additional studies of native Rhizobium strains and to help spread the use of biofertilizers in Ecuadorian fields.

  12. Genetic diversity in cattle from eight regions in Costa Rica

    International Nuclear Information System (INIS)

    Cordero-Solorzano, Juan Miguel; Leon-Rodriguez, Bernal; Chacon-Gonzalez, Idania; Vargas-Leiton, Bernardo; Martinez-Pichardo, Marco

    2016-01-01

    The degree of inter-regional genetic diversity is explored in cattle of Costa Rica. 1498 DNA samples were collected of eight different regions of the country during the year 2013. Allelic frequencies and major population genetic parameters are calculated for eighteen microsatellite markers. An analysis of molecular variance is performed. The genetic distances between cattle of different regions are calculated. A high degree of diversity, with an average number of 14,6±1,01 alleles observed and 5,6+0,37 effective alleles per marker is observed at the national level. The heterozygosity observed (Ho) has been 0,76±0,01 and the expected (He) 0,81±0,01. Polymorphic information content (PIC) and inbreeding index (F_I_S) have been of 0,79±0,06 and 0,06±0,004, respectively. At the regional level, HO has varied from 0,73 ± 0,02 in the Central Sur region to 0,78 ±0,01 in the Huetar Norte region. Three clearly differentiated groups are shown by the dendrogram , with the Central Metropolitana and Central Occidental regions in a group: Huetar Caribe, Central Sur, Pacifico Central and Chorotega in a second group; and Huetar Norte and Brunca in a third intermediate group. Estimates of genetic differentiation R_S_T have been significant between regions of different groups and among regions of the same group have remained without being significant. Genetic differences between regions are related with differentiated proliferation of racial types according to their adaptability to the agroecological conditions and production systems prevailing in each region. (author) [es

  13. Exploiting a wheat EST database to assess genetic diversity

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    Ozge Karakas

    2010-01-01

    Full Text Available Expressed sequence tag (EST markers have been used to assess variety and genetic diversity in wheat (Triticum aestivum. In this study, 1549 ESTs from wheat infested with yellow rust were used to examine the genetic diversity of six susceptible and resistant wheat cultivars. The aim of using these cultivars was to improve the competitiveness of public wheat breeding programs through the intensive use of modern, particularly marker-assisted, selection technologies. The F2 individuals derived from cultivar crosses were screened for resistance to yellow rust at the seedling stage in greenhouses and adult stage in the field to identify DNA markers genetically linked to resistance. Five hundred and sixty ESTs were assembled into 136 contigs and 989 singletons. BlastX search results showed that 39 (29% contigs and 96 (10% singletons were homologous to wheat genes. The database-matched contigs and singletons were assigned to eight functional groups related to protein synthesis, photosynthesis, metabolism and energy, stress proteins, transporter proteins, protein breakdown and recycling, cell growth and division and reactive oxygen scavengers. PCR analyses with primers based on the contigs and singletons showed that the most polymorphic functional categories were photosynthesis (contigs and metabolism and energy (singletons. EST analysis revealed considerable genetic variability among the Turkish wheat cultivars resistant and susceptible to yellow rust disease and allowed calculation of the mean genetic distance between cultivars, with the greatest similarity (0.725 being between Harmankaya99 and Sönmez2001, and the lowest (0.622 between Aytin98 and Izgi01.

  14. Invasion success in Cogongrass (Imperata cylindrica): A population genetic approach exploring genetic diversity and historical introductions

    Science.gov (United States)

    Rima D. Lucardi; Lisa E. Wallace; Gary N. Ervin

    2014-01-01

    Propagule pressure significantly contributes to and limits the potential success of a biological invasion, especially during transport, introduction, and establishment. Events such as multiple introductions of foreign parent material and gene flow among them can increase genetic diversity in founding populations, often leading to greater invasion success. We applied...

  15. Assessment of Genetic Diversity and Population Genetic Structure of Corylus mandshurica in China Using SSR Markers.

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    Jian-Wei Zong

    Full Text Available Corylus mandshurica, also known as pilose hazelnut, is an economically and ecologically important species in China. In this study, ten polymorphic simple sequence repeat (SSR markers were applied to evaluate the genetic diversity and population structure of 348 C. mandshurica individuals among 12 populations in China. The SSR markers expressed a relatively high level of genetic diversity (Na = 15.3, Ne = 5.6604, I = 1.8853, Ho = 0.6668, and He = 0.7777. According to the coefficient of genetic differentiation (Fst = 0.1215, genetic variation within the populations (87.85% were remarkably higher than among populations (12.15%. The average gene flow (Nm = 1.8080 significantly impacts the genetic structure of C. mandshurica populations. The relatively high gene flow (Nm = 1.8080 among wild C. mandshurica may be caused by wind-pollinated flowers, highly nutritious seeds and self-incompatible mating system. The UPGMA (unweighted pair group method of arithmetic averages dendrogram was divided into two main clusters. Moreover, the results of STRUCTURE analysis suggested that C. mandshurica populations fell into two main clusters. Comparison of the UPGMA dendrogram and the Bayesian STRUCTURE analysis showed general agreement between the population subdivisions and the genetic relationships among populations of C. mandshurica. Group I accessions were located in Northeast China, while Group II accessions were in North China. It is worth noting that a number of genetically similar populations were located in the same geographic region. The results further showed that there was obvious genetic differentiation among populations from Northeast China to North China. Results from the Mantel test showed a weak but still significant positive correlation between Nei's genetic distance and geographic distance (km among populations (r = 0.419, P = 0.005, suggesting that genetic differentiation in the 12 C. mandshurica populations might be related to geographic

  16. Assessment of Genetic Diversity and Population Genetic Structure of Corylus mandshurica in China Using SSR Markers.

    Science.gov (United States)

    Zong, Jian-Wei; Zhao, Tian-Tian; Ma, Qing-Hua; Liang, Li-Song; Wang, Gui-Xi

    2015-01-01

    Corylus mandshurica, also known as pilose hazelnut, is an economically and ecologically important species in China. In this study, ten polymorphic simple sequence repeat (SSR) markers were applied to evaluate the genetic diversity and population structure of 348 C. mandshurica individuals among 12 populations in China. The SSR markers expressed a relatively high level of genetic diversity (Na = 15.3, Ne = 5.6604, I = 1.8853, Ho = 0.6668, and He = 0.7777). According to the coefficient of genetic differentiation (Fst = 0.1215), genetic variation within the populations (87.85%) were remarkably higher than among populations (12.15%). The average gene flow (Nm = 1.8080) significantly impacts the genetic structure of C. mandshurica populations. The relatively high gene flow (Nm = 1.8080) among wild C. mandshurica may be caused by wind-pollinated flowers, highly nutritious seeds and self-incompatible mating system. The UPGMA (unweighted pair group method of arithmetic averages) dendrogram was divided into two main clusters. Moreover, the results of STRUCTURE analysis suggested that C. mandshurica populations fell into two main clusters. Comparison of the UPGMA dendrogram and the Bayesian STRUCTURE analysis showed general agreement between the population subdivisions and the genetic relationships among populations of C. mandshurica. Group I accessions were located in Northeast China, while Group II accessions were in North China. It is worth noting that a number of genetically similar populations were located in the same geographic region. The results further showed that there was obvious genetic differentiation among populations from Northeast China to North China. Results from the Mantel test showed a weak but still significant positive correlation between Nei's genetic distance and geographic distance (km) among populations (r = 0.419, P = 0.005), suggesting that genetic differentiation in the 12 C. mandshurica populations might be related to geographic distance. These

  17. Genetic diversity of Aspergillus fumigatus in indoor hospital environments.

    Science.gov (United States)

    Araujo, Ricardo; Amorim, António; Gusmão, Leonor

    2010-09-01

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

  18. Genetic Diversity of Pectobacterium carotovorum subsp. brasiliensis Isolated in Korea

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    Dong Hwan Lee

    2014-06-01

    Full Text Available The plant pathogenic bacterial genus Pectobacteirum consists of heterogeneous strains. The P. carotovorum species is a complex strain showing divergent characteristics, and a new subspecies named P. carotovorum subsp. brasiliensis has been identified recently. In this paper, we re-identified the P. carotovorum subsp. brasiliensis isolates from those classified under the subspecies carotovorum and newly isolated P. carotovorum subsp. brasiliensis strains. All isolates were able to produce plant cell-wall degrading enzymes such as pectate lyase, polygalacturonase, cellulase and protease. We used genetic and biochemical methods to examine the diversity of P. carotovorum subsp. brasiliensis isolates, and found genetic diversity within the brasiliensis subsp. isolates in Korea. The restriction fragment length polymorphism analysis based on the recA gene revealed a unique pattern for the brasiliensis subspecies. The Korean brasiliensis subsp. isolates were divided into four clades based on pulsed-field gel electrophoresis. However, correlations between clades and isolated hosts or year could not be found, suggesting that diverse brasiliensis subsp. isolates existed.

  19. Limited Genetic Diversity Preceded Extinction of the Tasmanian Tiger

    Science.gov (United States)

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

    2012-01-01

    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

  20. Genetic diversity of Colombian sheep by microsatellite markers

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    Ricardo Ocampo

    2016-03-01

    Full Text Available In Colombia the sheep production systems are managed under extensive conditions and mainly correspond to peasant production systems so their genetic management has led to increased homozygosity and hence productivity loss. The aim of this study was to determine the genetic diversity in 549 individuals corresponding to 13 sheep breeds in Colombia, using a panel of 11 microsatellite molecular markers. One hundred and fifty seven alleles were found (average of 14.27 alleles/locus, with a range of observed and expected heterozygosity from 0.44 to 0.84 and 0.67 to 0.86, respectively. Thirty-three of 143 Hardy Weinberg tests performed showed significant deviations (p < 0.05 due to a general lack of heterozygous individuals. The Fis ranged from 0.01 in Corriedale to 0.15 for the Persian Black Head breed, suggesting that there are presenting low to moderate levels of inbreeding. Overall, Colombian sheep showed high levels of genetic diversity which is very important for future selection and animal breeding programs.

  1. Genetic diversity and paternal origin of domestic donkeys.

    Science.gov (United States)

    Han, H; Chen, N; Jordana, J; Li, C; Sun, T; Xia, X; Zhao, X; Ji, C; Shen, S; Yu, J; Ainhoa, F; Chen, H; Lei, C; Dang, R

    2017-12-01

    Numerous studies have been conducted to investigate genetic diversity, origins and domestication of donkey using autosomal microsatellites and the mitochondrial genome, whereas the male-specific region of the Y chromosome of modern donkeys is largely uncharacterized. In the current study, 14 published equine Y chromosome-specific microsatellites (Y-STR) were investigated in 395 male donkey samples from China, Egypt, Spain and Peru using fluorescent labeled microsatellite markers. The results showed that seven Y-STRs-EcaYP9, EcaYM2, EcaYE2, EcaYE3, EcaYNO1, EcaYNO2 and EcaYNO4-were male specific and polymorphic, showing two to eight alleles in the donkeys studied. A total of 21 haplotypes corresponding to three haplogroups were identified, indicating three independent patrilines in domestic donkey. These markers are useful for the study the Y-chromosome diversity and population genetics of donkeys in Africa, Europe, South America and China. © 2017 Stichting International Foundation for Animal Genetics.

  2. Molecular markers: a potential resource for ginger genetic diversity studies.

    Science.gov (United States)

    Ismail, Nor Asiah; Rafii, M Y; Mahmud, T M M; Hanafi, M M; Miah, Gous

    2016-12-01

    Ginger is an economically important and valuable plant around the world. Ginger is used as a food, spice, condiment, medicine and ornament. There is available information on biochemical aspects of ginger, but few studies have been reported on its molecular aspects. The main objective of this review is to accumulate the available molecular marker information and its application in diverse ginger studies. This review article was prepared by combing material from published articles and our own research. Molecular markers allow the identification and characterization of plant genotypes through direct access to hereditary material. In crop species, molecular markers are applied in different aspects and are useful in breeding programs. In ginger, molecular markers are commonly used to identify genetic variation and classify the relatedness among varieties, accessions, and species. Consequently, it provides important input in determining resourceful management strategies for ginger improvement programs. Alternatively, a molecular marker could function as a harmonizing tool for documenting species. This review highlights the application of molecular markers (isozyme, RAPD, AFLP, SSR, ISSR and others such as RFLP, SCAR, NBS and SNP) in genetic diversity studies of ginger species. Some insights on the advantages of the markers are discussed. The detection of genetic variation among promising cultivars of ginger has significance for ginger improvement programs. This update of recent literature will help researchers and students select the appropriate molecular markers for ginger-related research.

  3. Are Eimeria Genetically Diverse, and Does It Matter?

    Science.gov (United States)

    Clark, Emily L; Tomley, Fiona M; Blake, Damer P

    2017-03-01

    Eimeria pose a risk to all livestock species as a cause of coccidiosis, reducing productivity and compromising animal welfare. Pressure to reduce drug use in the food chain makes the development of cost-effective vaccines against Eimeria essential. For novel vaccines to be successful, understanding genetic and antigenic diversity in field populations is key. Eimeria species that infect chickens are most significant, with Eimeria tenella among the best studied and most economically important. Genome-wide single nucleotide polymorphism (SNP)-based haplotyping has been used to determine population structure, genotype distribution, and potential for cross-fertilization between E. tenella strains. Here, we discuss recent developments in our understanding of diversity for Eimeria in relation to its specialized life cycle, distribution across the globe, and the challenges posed to vaccine development. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. Diversity Controlling Genetic Algorithm for Order Acceptance and Scheduling Problem

    Directory of Open Access Journals (Sweden)

    Cheng Chen

    2014-01-01

    Full Text Available Selection and scheduling are an important topic in production systems. To tackle the order acceptance and scheduling problem on a single machine with release dates, tardiness penalty, and sequence-dependent setup times, in this paper a diversity controlling genetic algorithm (DCGA is proposed, in which a diversified population is maintained during the whole search process through survival selection considering both the fitness and the diversity of individuals. To measure the similarity between individuals, a modified Hamming distance without considering the unaccepted orders in the chromosome is adopted. The proposed DCGA was validated on 1500 benchmark instances with up to 100 orders. Compared with the state-of-the-art algorithms, the experimental results show that DCGA improves the solution quality obtained significantly, in terms of the deviation from upper bound.

  5. Genetic diversity of Bromeliaceae species from the Atlantic Forest.

    Science.gov (United States)

    Sheu, Y; Cunha-Machado, A S; Gontijo, A B P L; Favoreto, F C; Soares, T B C; Miranda, F D

    2017-04-20

    The Bromeliaceae family includes a range of species used for many purposes, including ornamental use and use as food, medicine, feed, and fiber. The state of Espírito Santo, Brazil is a center of diversity for this family in the Atlantic Forest. We evaluated the genetic diversity of five populations of the Bromeliaceae family, including specimens of the genera Aechmea, Billbergia (subfamily Bromelioideae), and Pitcairnia (subfamily Pitcairnioidea), all found in the Atlantic Forest and distributed in the state of Espírito Santo. The number of alleles per locus in populations ranged from two to six and the fixation index (F), estimated for some simple sequence repeats in bromeliad populations, was less than zero in all populations. All markers in the Pitcairnia flammea population were in Hardy-Weinberg equilibrium (P Atlantic Forest remnants in the south of Espírito Santo state.

  6. Genetics, Genomics and Evolution of Ergot Alkaloid Diversity

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    Carolyn A. Young

    2015-04-01

    Full Text Available The ergot alkaloid biosynthesis system has become an excellent model to study evolutionary diversification of specialized (secondary metabolites. This is a very diverse class of alkaloids with various neurotropic activities, produced by fungi in several orders of the phylum Ascomycota, including plant pathogens and protective plant symbionts in the family Clavicipitaceae. Results of comparative genomics and phylogenomic analyses reveal multiple examples of three evolutionary processes that have generated ergot-alkaloid diversity: gene gains, gene losses, and gene sequence changes that have led to altered substrates or product specificities of the enzymes that they encode (neofunctionalization. The chromosome ends appear to be particularly effective engines for gene gains, losses and rearrangements, but not necessarily for neofunctionalization. Changes in gene expression could lead to accumulation of various pathway intermediates and affect levels of different ergot alkaloids. Genetic alterations associated with interspecific hybrids of Epichloë species suggest that such variation is also selectively favored. The huge structural diversity of ergot alkaloids probably represents adaptations to a wide variety of ecological situations by affecting the biological spectra and mechanisms of defense against herbivores, as evidenced by the diverse pharmacological effects of ergot alkaloids used in medicine.

  7. Range-edge genetic diversity: locally poor extant southern patches maintain a regionally diverse hotspot in the seagrass Zostera marina.

    Science.gov (United States)

    Diekmann, Onno E; Serrão, Ester A

    2012-04-01

    Refugial populations at the rear edge are predicted to contain higher genetic diversity than those resulting from expansion, such as in post-glacial recolonizations. However, peripheral populations are also predicted to have decreased diversity compared to the centre of a species' distribution. We aim to test these predictions by comparing genetic diversity in populations at the limits of distribution of the seagrass Zostera marina, with populations in the species' previously described central diversity 'hotspot'. Zostera marina populations show decreased allelic richness, heterozygosity and genotypic richness in both the 'rear' edge and the 'leading' edge compared to the diversity 'hotspot' in the North Sea/Baltic region. However, when populations are pooled, genetic diversity at the southern range is as high as in the North Sea/Baltic region while the 'leading edge' remains low in genetic diversity. The decreased genetic diversity in these southern Iberian populations compared to more central populations is possibly the effect of drift because of small effective population size, as a result of reduced habitat, low sexual reproduction and low gene flow. However, when considering the whole southern edge of distribution rather than per population, diversity is as high as in the central 'hotspot' in the North Sea/Baltic region. We conclude that diversity patterns assessed per population can mask the real regional richness that is typical of rear edge populations, which have played a key role in the species biogeographical history and as marginal diversity hotspots have very high conservation value. © 2012 Blackwell Publishing Ltd.

  8. A hamster model for Marburg virus infection accurately recapitulates Marburg hemorrhagic fever.

    Science.gov (United States)

    Marzi, Andrea; Banadyga, Logan; Haddock, Elaine; Thomas, Tina; Shen, Kui; Horne, Eva J; Scott, Dana P; Feldmann, Heinz; Ebihara, Hideki

    2016-12-15

    Marburg virus (MARV), a close relative of Ebola virus, is the causative agent of a severe human disease known as Marburg hemorrhagic fever (MHF). No licensed vaccine or therapeutic exists to treat MHF, and MARV is therefore classified as a Tier 1 select agent and a category A bioterrorism agent. In order to develop countermeasures against this severe disease, animal models that accurately recapitulate human disease are required. Here we describe the development of a novel, uniformly lethal Syrian golden hamster model of MHF using a hamster-adapted MARV variant Angola. Remarkably, this model displayed almost all of the clinical features of MHF seen in humans and non-human primates, including coagulation abnormalities, hemorrhagic manifestations, petechial rash, and a severely dysregulated immune response. This MHF hamster model represents a powerful tool for further dissecting MARV pathogenesis and accelerating the development of effective medical countermeasures against human MHF.

  9. Genetic diversity of Dactylorhiza incarnata (Orchidaceae in northern Poland

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    Aleksandra M. Naczk

    2016-05-01

    Full Text Available The genetic structure of Dactylorhiza incarnata var. incarnata populations is shaped not only by historical events such as recolonization after ice sheet retreat or limited seed and pollen dispersal, but also the bottleneck effect. During the last decade, D. incarnata var. incarnata has also experienced a strong decline in population numbers and sizes, due to habitat loss and fragmentation. In the present research genetic diversity was examined in eight populations located in northern Poland, using six nuclear microsatellites loci. At the species level our results showed a moderate mean level of genetic diversity (A = 4.67; Ae = 2.73; Rs = 4.48; Ho = 0.438; FIS = 0.224, which varied among the studied populations (A: 2.17–3.67; Ae: 1.55–2.69; Rs: 1.31–1.61; Ho: 0.292–0.631; FIS: −0.283–0.340. A considerable overabundance of homozygotes was detected in four populations (FIS within the range of 0.067–0.340, and in the remaining populations an excess of heterozygotes was observed. The average apparent out-crossing rate was also calculated (ta = 0.980, and primarily indicated a tendency to out-cross within the species. Moderate genetic differentiation was found among the studied populations (FST = 0.149; RST = 0.174; p < 0.05. The differentiation of the populations corresponded to relatively low gene flow value (Nm = 0.426 among populations, which amounted to only one migrant every second generation.

  10. Genetic diversity, structure and differentiation in cultivate walnut (Juglans regia L.)

    Science.gov (United States)

    M. Aradhya; K. Woeste; D. Velasco

    2012-01-01

    An analysis of genetic structure and differentiation in cultivated walnut (Juglans regia) using 15 microsatellite loci revealed a considerable amount of genetic variation with a mild genetic structure indicating five genetic groups corresponding to the centers of diversity within the home range of walnut in Eurasia. Despite the narrow genetic...

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

    International Nuclear Information System (INIS)

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

    2016-01-01

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

  12. Genetic Competence Drives Genome Diversity in Bacillus subtilis

    Science.gov (United States)

    Chevreux, Bastien; Serra, Cláudia R; Schyns, Ghislain; Henriques, Adriano O

    2018-01-01

    Abstract Prokaryote genomes are the result of a dynamic flux of genes, with increases achieved via horizontal gene transfer and reductions occurring through gene loss. The ecological and selective forces that drive this genomic flexibility vary across species. Bacillus subtilis is a naturally competent bacterium that occupies various environments, including plant-associated, soil, and marine niches, and the gut of both invertebrates and vertebrates. Here, we quantify the genomic diversity of B. subtilis and infer the genome dynamics that explain the high genetic and phenotypic diversity observed. Phylogenomic and comparative genomic analyses of 42 B. subtilis genomes uncover a remarkable genome diversity that translates into a core genome of 1,659 genes and an asymptotic pangenome growth rate of 57 new genes per new genome added. This diversity is due to a large proportion of low-frequency genes that are acquired from closely related species. We find no gene-loss bias among wild isolates, which explains why the cloud genome, 43% of the species pangenome, represents only a small proportion of each genome. We show that B. subtilis can acquire xenologous copies of core genes that propagate laterally among strains within a niche. While not excluding the contributions of other mechanisms, our results strongly suggest a process of gene acquisition that is largely driven by competence, where the long-term maintenance of acquired genes depends on local and global fitness effects. This competence-driven genomic diversity provides B. subtilis with its generalist character, enabling it to occupy a wide range of ecological niches and cycle through them. PMID:29272410

  13. Genetic diversity of Iranian rice germplasm based on morphological traits

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    nade ali bagheri

    2009-06-01

    Full Text Available Study of genetic diversity of rice is very important for rice breeders. In this study 64 genotypes for 14 agronomic traits were evaluated. Phenotypic variation coefficients of some of traits were high which showed essential variation in this traits. Principal component analysis detected 6 components which explained 74.66 percent of the total variations. The first component was related to generative traits such as number of spiklet per panicle, number of full grain per panicle, date of 50% flowering and length of panicle. In the third component, the date of complete maturity with -0.730 has negative effects on yield. Correlation analysis of morphological traits indicated a negative and significant relationship between early maturity and plant height, which showed early maturity cultivars had higher plant type. Results of stepwise regression analysis for early maturity, indicated that three traits such as date of 50% flowering, number of full grain per panicle and plant height showed higher variation and explained 54.3 percent of total early maturity variations. All traits were classified into 2 groups, by cluster analysis and traits belonged to early maturity classified as a sub-group. Genotypes were classified into 4 groups by using method of Ward,s minimum variance and squared Euclidean distance. Native cultivars from the view point of early maturity and yield components had useful information for rice breeding. Key words: Genetic diversity, rice, morphological traits.

  14. Enhancing (crop) plant photosynthesis by introducing novel genetic diversity.

    Science.gov (United States)

    Dann, Marcel; Leister, Dario

    2017-09-26

    Although some elements of the photosynthetic light reactions might appear to be ideal, the overall efficiency of light conversion to biomass has not been optimized during evolution. Because crop plants are depleted of genetic diversity for photosynthesis, efforts to enhance its efficiency with respect to light conversion to yield must generate new variation. In principle, three sources of natural variation are available: (i) rare diversity within extant higher plant species, (ii) photosynthetic variants from algae, and (iii) reconstruction of no longer extant types of plant photosynthesis. Here, we argue for a novel approach that outsources crop photosynthesis to a cyanobacterium that is amenable to adaptive evolution. This system offers numerous advantages, including a short generation time, virtually unlimited population sizes and high mutation rates, together with a versatile toolbox for genetic manipulation. On such a synthetic bacterial platform, 10 000 years of (crop) plant evolution can be recapitulated within weeks. Limitations of this system arise from its unicellular nature, which cannot reproduce all aspects of crop photosynthesis. But successful establishment of such a bacterial host for crop photosynthesis promises not only to enhance the performance of eukaryotic photosynthesis but will also reveal novel facets of the molecular basis of photosynthetic flexibility.This article is part of the themed issue 'Enhancing photosynthesis in crop plants: targets for improvement'. © 2017 The Author(s).

  15. Insights into Penicillium roqueforti Morphological and Genetic Diversity

    Science.gov (United States)

    Gillot, Guillaume; Jany, Jean-Luc; Coton, Monika; Le Floch, Gaétan; Debaets, Stella; Ropars, Jeanne; López-Villavicencio, Manuela; Dupont, Joëlle; Branca, Antoine; Giraud, Tatiana; Coton, Emmanuel

    2015-01-01

    Fungi exhibit substantial morphological and genetic diversity, often associated with cryptic species differing in ecological niches. Penicillium roqueforti is used as a starter culture for blue-veined cheeses, being responsible for their flavor and color, but is also a common spoilage organism in various foods. Different types of blue-veined cheeses are manufactured and consumed worldwide, displaying specific organoleptic properties. These features may be due to the different manufacturing methods and/or to the specific P. roqueforti strains used. Substantial morphological diversity exists within P. roqueforti and, although not taxonomically valid, several technological names have been used for strains on different cheeses (e.g., P. gorgonzolae, P. stilton). A worldwide P. roqueforti collection from 120 individual blue-veined cheeses and 21 other substrates was analyzed here to determine (i) whether P. roqueforti is a complex of cryptic species, by applying the Genealogical Concordance Phylogenetic Species Recognition criterion (GC-PSR), (ii) whether the population structure assessed using microsatellite markers correspond to blue cheese types, and (iii) whether the genetic clusters display different morphologies. GC-PSR multi-locus sequence analyses showed no evidence of cryptic species. The population structure analysis using microsatellites revealed the existence of highly differentiated populations, corresponding to blue cheese types and with contrasted morphologies. This suggests that the population structure has been shaped by different cheese-making processes or that different populations were recruited for different cheese types. Cheese-making fungi thus constitute good models for studying fungal diversification under recent selection. PMID:26091176

  16. Neonicotinoid pesticides can reduce honeybee colony genetic diversity.

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    Nadège Forfert

    Full Text Available Neonicotinoid insecticides can cause a variety of adverse sub-lethal effects in bees. In social species such as the honeybee, Apis mellifera, queens are essential for reproduction and colony functioning. Therefore, any negative effect of these agricultural chemicals on the mating success of queens may have serious consequences for the fitness of the entire colony. Queens were exposed to the common neonicotinoid pesticides thiamethoxam and clothianidin during their developmental stage. After mating, their spermathecae were dissected to count the number of stored spermatozoa. Furthermore, their worker offspring were genotyped with DNA microsatellites to determine the number of matings and the genotypic composition of the colony. Colonies providing the male mating partners were also inferred. Both neonicotinoid and control queens mated with drones originating from the same drone source colonies, and stored similar number of spermatozoa. However, queens reared in colonies exposed to both neonicotinoids experienced fewer matings. This resulted in a reduction of the genetic diversity in their colonies (i.e. higher intracolonial relatedness. As decreased genetic diversity among worker bees is known to negatively affect colony vitality, neonicotinoids may have a cryptic effect on colony health by reducing the mating frequency of queens.

  17. Genetic diversity in Spanish donkey breeds using microsatellite DNA markers

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    Jordana Jordi

    2001-07-01

    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.

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

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

    2011-12-01

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

  19. Genetic diversity among five T4-like bacteriophages

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    Bertrand Claire

    2006-05-01

    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

  20. Genetic diversity among and within cultured cyanobionts of diverse species of Azolla.

    Science.gov (United States)

    Sood, A; Prasanna, R; Prasanna, B M; Singh, P K

    2008-01-01

    The cyanobionts isolated from 10 Azolla accessions belonging to 6 species (Azolla mexicana, A. microphylla, A. rubra, A. caroliniana, A. filiculoides, A. pinnata) were cultured under laboratory conditions and analyzed on the basis of whole cell protein profiles and molecular marker dataset generated using repeat sequence primers (STRR(mod) and HipTG). The biochemical and molecular marker profiles of the cyanobionts were compared with those of the free-living cyanobacteria and symbiotic Nostoc strains from Anthoceros sp., Cycas sp. and Gunnera monoika. Cluster analysis revealed the genetic diversity among the selected strains, and identified 3 distinct clusters. Group 1 included cyanobionts from all the 10 accessions of Azolla, group 2 comprised all the symbiotic Nostoc strains, while group 3 included the free-living cyanobacteria belonging to the genera Nostoc and Anabaena. The interrelationships among the Azolla cyanobionts were further revealed by principal component analysis. Cyanobionts from A. caroliniana-A. microphylla grouped together while cyanobionts associated with A. mexicana-A. filiculoides along with A. pinnata formed another group. A. rubra cyanobionts had intermediate relationship with both the subgroups. This is the first study analyzing the diversity existing among the cultured cyanobionts of diverse Azolla species through the use of biochemical and molecular profiles and also the genetic distinctness of these free-living cyanobionts as compared to cyanobacterial strains of the genera Anabaena and Nostoc.

  1. Genetic diversity in tef [Eragrostis tef (Zucc. Trotter

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    Kebebew eAssefa

    2015-03-01

    Full Text Available Tef [Eragrostis tef (Zucc. Trotter] is a cereal crop resilient to adverse climatic and soil conditions, and possessing desirable storage properties. Although tef provides high quality food and grows under marginal conditions unsuitable for other cereals, it is considered to be an orphan crop because it has benefited little from genetic improvement. Hence, unlike other cereals such as maize and wheat, the productivity of tef is extremely low. In spite of the low productivity, tef is widely cultivated by over six million small-scale farmers in Ethiopia where it is annually grown on more than three million hectares of land, accounting for over 30% of the total cereal acreage. Tef, a tetraploid with 40 chromosomes (2n=4x=40, belongs to the Family Poaceae and, together with finger millet (Eleusine coracana Gaertn, to the Subfamily Chloridoideae. It was believed to have originated in Ethiopia. There are about 350 Eragrostis species of which E. tef is the only species cultivated for human consumption. At the present time, the gene bank in Ethiopia holds over five thousand tef accessions collected from geographical regions diverse in terms of climate and elevation. These germplasm accessions appear to have huge variability with regard to key agronomic and nutritional traits. In order to properly utilize the variability in developing new tef cultivars, various techniques have been implemented to catalog the extent and unravel the patterns of genetic diversity. In this review, we show some recent initiatives investigating the diversity of tef using genomics, transcriptomics and proteomics and discuss the prospect of these efforts in providing molecular resources that can aid modern tef breeding.

  2. Genomic and Genetic Diversity within the Pseudomonas fluorescens Complex.

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    Daniel Garrido-Sanz

    Full Text Available The Pseudomonas fluorescens complex includes Pseudomonas strains that have been taxonomically assigned to more than fifty different species, many of which have been described as plant growth-promoting rhizobacteria (PGPR with potential applications in biocontrol and biofertilization. So far the phylogeny of this complex has been analyzed according to phenotypic traits, 16S rDNA, MLSA and inferred by whole-genome analysis. However, since most of the type strains have not been fully sequenced and new species are frequently described, correlation between taxonomy and phylogenomic analysis is missing. In recent years, the genomes of a large number of strains have been sequenced, showing important genomic heterogeneity and providing information suitable for genomic studies that are important to understand the genomic and genetic diversity shown by strains of this complex. Based on MLSA and several whole-genome sequence-based analyses of 93 sequenced strains, we have divided the P. fluorescens complex into eight phylogenomic groups that agree with previous works based on type strains. Digital DDH (dDDH identified 69 species and 75 subspecies within the 93 genomes. The eight groups corresponded to clustering with a threshold of 31.8% dDDH, in full agreement with our MLSA. The Average Nucleotide Identity (ANI approach showed inconsistencies regarding the assignment to species and to the eight groups. The small core genome of 1,334 CDSs and the large pan-genome of 30,848 CDSs, show the large diversity and genetic heterogeneity of the P. fluorescens complex. However, a low number of strains were enough to explain most of the CDSs diversity at core and strain-specific genomic fractions. Finally, the identification and analysis of group-specific genome and the screening for distinctive characters revealed a phylogenomic distribution of traits among the groups that provided insights into biocontrol and bioremediation applications as well as their role as

  3. Elevated Genetic Diversity in the Emerging Blueberry Pathogen Exobasidium maculosum

    Science.gov (United States)

    Stewart, Jane E.; Brooks, Kyle; Brannen, Phillip M.; Cline, William O.; Brewer, Marin T.

    2015-01-01

    Emerging diseases caused by fungi are increasing at an alarming rate. Exobasidium leaf and fruit spot of blueberry, caused by the fungus Exobasidium maculosum, is an emerging disease that has rapidly increased in prevalence throughout the southeastern USA, severely reducing fruit quality in some plantings. The objectives of this study were to determine the genetic diversity of E. maculosum in the southeastern USA to elucidate the basis of disease emergence and to investigate if populations of E. maculosum are structured by geography, host species, or tissue type. We sequenced three conserved loci from 82 isolates collected from leaves and fruit of rabbiteye blueberry (Vaccinium virgatum), highbush blueberry (V. corymbosum), and southern highbush blueberry (V. corymbosum hybrids) from commercial fields in Georgia and North Carolina, USA, and 6 isolates from lowbush blueberry (V. angustifolium) from Maine, USA, and Nova Scotia, Canada. Populations of E. maculosum from the southeastern USA and from lowbush blueberry in Maine and Nova Scotia are distinct, but do not represent unique species. No difference in genetic structure was detected between different host tissues or among different host species within the southeastern USA; however, differentiation was detected between populations in Georgia and North Carolina. Overall, E. maculosum showed extreme genetic diversity within the conserved loci with 286 segregating sites among the 1,775 sequenced nucleotides and each isolate representing a unique multilocus haplotype. However, 94% of the nucleotide substitutions were silent, so despite the high number of mutations, selective constraints have limited changes to the amino acid sequences of the housekeeping genes. Overall, these results suggest that the emergence of Exobasidium leaf and fruit spot is not due to a recent introduction or host shift, or the recent evolution of aggressive genotypes of E. maculosum, but more likely as a result of an increasing host population

  4. Elevated Genetic Diversity in the Emerging Blueberry Pathogen Exobasidium maculosum.

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    Jane E Stewart

    Full Text Available Emerging diseases caused by fungi are increasing at an alarming rate. Exobasidium leaf and fruit spot of blueberry, caused by the fungus Exobasidium maculosum, is an emerging disease that has rapidly increased in prevalence throughout the southeastern USA, severely reducing fruit quality in some plantings. The objectives of this study were to determine the genetic diversity of E. maculosum in the southeastern USA to elucidate the basis of disease emergence and to investigate if populations of E. maculosum are structured by geography, host species, or tissue type. We sequenced three conserved loci from 82 isolates collected from leaves and fruit of rabbiteye blueberry (Vaccinium virgatum, highbush blueberry (V. corymbosum, and southern highbush blueberry (V. corymbosum hybrids from commercial fields in Georgia and North Carolina, USA, and 6 isolates from lowbush blueberry (V. angustifolium from Maine, USA, and Nova Scotia, Canada. Populations of E. maculosum from the southeastern USA and from lowbush blueberry in Maine and Nova Scotia are distinct, but do not represent unique species. No difference in genetic structure was detected between different host tissues or among different host species within the southeastern USA; however, differentiation was detected between populations in Georgia and North Carolina. Overall, E. maculosum showed extreme genetic diversity within the conserved loci with 286 segregating sites among the 1,775 sequenced nucleotides and each isolate representing a unique multilocus haplotype. However, 94% of the nucleotide substitutions were silent, so despite the high number of mutations, selective constraints have limited changes to the amino acid sequences of the housekeeping genes. Overall, these results suggest that the emergence of Exobasidium leaf and fruit spot is not due to a recent introduction or host shift, or the recent evolution of aggressive genotypes of E. maculosum, but more likely as a result of an increasing

  5. Elevated Genetic Diversity in the Emerging Blueberry Pathogen Exobasidium maculosum.

    Science.gov (United States)

    Stewart, Jane E; Brooks, Kyle; Brannen, Phillip M; Cline, William O; Brewer, Marin T

    2015-01-01

    Emerging diseases caused by fungi are increasing at an alarming rate. Exobasidium leaf and fruit spot of blueberry, caused by the fungus Exobasidium maculosum, is an emerging disease that has rapidly increased in prevalence throughout the southeastern USA, severely reducing fruit quality in some plantings. The objectives of this study were to determine the genetic diversity of E. maculosum in the southeastern USA to elucidate the basis of disease emergence and to investigate if populations of E. maculosum are structured by geography, host species, or tissue type. We sequenced three conserved loci from 82 isolates collected from leaves and fruit of rabbiteye blueberry (Vaccinium virgatum), highbush blueberry (V. corymbosum), and southern highbush blueberry (V. corymbosum hybrids) from commercial fields in Georgia and North Carolina, USA, and 6 isolates from lowbush blueberry (V. angustifolium) from Maine, USA, and Nova Scotia, Canada. Populations of E. maculosum from the southeastern USA and from lowbush blueberry in Maine and Nova Scotia are distinct, but do not represent unique species. No difference in genetic structure was detected between different host tissues or among different host species within the southeastern USA; however, differentiation was detected between populations in Georgia and North Carolina. Overall, E. maculosum showed extreme genetic diversity within the conserved loci with 286 segregating sites among the 1,775 sequenced nucleotides and each isolate representing a unique multilocus haplotype. However, 94% of the nucleotide substitutions were silent, so despite the high number of mutations, selective constraints have limited changes to the amino acid sequences of the housekeeping genes. Overall, these results suggest that the emergence of Exobasidium leaf and fruit spot is not due to a recent introduction or host shift, or the recent evolution of aggressive genotypes of E. maculosum, but more likely as a result of an increasing host population

  6. Parallel responses of species and genetic diversity to El Nino Southern Oscillation-induced environmental destruction

    NARCIS (Netherlands)

    Cleary, D.F.R.; Fauvelot, C.Y.; Genner, J.; Menken, S.B.J.; Mooers, A.O.

    2006-01-01

    Species diversity within communities and genetic diversity within species are two fundamental levels of biodiversity. Positive relationships between species richness and within-species genetic diversity have recently been documented across natural and semi-natural habitat islands, leading Vellend to

  7. Genetic diversity assessment in brassica germplasm based on morphological attributes

    International Nuclear Information System (INIS)

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

    2015-01-01

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

  8. Genetic diversity revealed by AFLP markers in Albanian goat breeds

    Directory of Open Access Journals (Sweden)

    Hoda Anila

    2012-01-01

    Full Text Available The amplified fragment length polymorphism (AFLP technique with three EcoRI/TaqI primer combinations was used in 185 unrelated individuals, representative of 6 local goat breeds of Albania, and 107 markers were generated. The mean Nei’s expected heterozygosity value for the whole population was 0.199 and the mean Shannon index was 0.249, indicating a high level of within-breed diversity. Wright’s FST index, Nei’s unbiased genetic distance and Reynolds’ genetic distance were calculated. Pairwise Fst values among the populations ranged from 0.019 to 0.047. A highly significant average FST of 0.031 was estimated, showing a low level of breed subdivision. Most of the variation is accounted for by differences among individuals. Cluster analysis based on Reynolds’ genetic distance between breeds and PCA were performed. An individual UPGMA tree based on Jaccard’s similarity index showed clusters with individuals from all goat breeds. Analysis of population structure points to a high level of admixture among breeds.

  9. Genetic diversity of water use efficiency in Jerusalem artichoke (Helianthus tuberosus L.) germplasm

    Science.gov (United States)

    Genetic diversity in crop germplasm is an important resource for crop improvement, but information on genetic diversity is rare for Jerusalem artichoke, especially for traits related to water use efficiency. The objectives of this study were to investigate genetic variations for water use and water...

  10. Genetic diversity in the feline leukemia virus gag gene.

    Science.gov (United States)

    Kawamura, Maki; Watanabe, Shinya; Odahara, Yuka; Nakagawa, So; Endo, Yasuyuki; Tsujimoto, Hajime; Nishigaki, Kazuo

    2015-06-02

    Feline leukemia virus (FeLV) belongs to the Gammaretrovirus genus and is horizontally transmitted among cats. FeLV is known to undergo recombination with endogenous retroviruses already present in the host during FeLV-subgroup A infection. Such recombinant FeLVs, designated FeLV-subgroup B or FeLV-subgroup D, can be generated by transduced endogenous retroviral env sequences encoding the viral envelope. These recombinant viruses have biologically distinct properties and may mediate different disease outcomes. The generation of such recombinant viruses resulted in structural diversity of the FeLV particle and genetic diversity of the virus itself. FeLV env diversity through mutation and recombination has been studied, while gag diversity and its possible effects are less well understood. In this study, we investigated recombination events in the gag genes of FeLVs isolated from naturally infected cats and reference isolates. Recombination and phylogenetic analyses indicated that the gag genes often contain endogenous FeLV sequences and were occasionally replaced by entire endogenous FeLV gag genes. Phylogenetic reconstructions of FeLV gag sequences allowed for classification into three distinct clusters, similar to those previously established for the env gene. Analysis of the recombination junctions in FeLV gag indicated that these variants have similar recombination patterns within the same genotypes, indicating that the recombinant viruses were horizontally transmitted among cats. It remains to be investigated whether the recombinant sequences affect the molecular mechanism of FeLV transmission. These findings extend our understanding of gammaretrovirus evolutionary patterns in the field. Copyright © 2015 Elsevier B.V. All rights reserved.

  11. Translating conservation genetics into management: Pan-European minimum requirements for dynamic conservation units of forest tree genetic diversity

    OpenAIRE

    Koskela, Jarkko; Lefèvre, François; Schueler, Silvio; Kraigher, Hojka; Olrik, Ditte C.; Hubert, Jason; Longauer, Roman; Bozzano, Michele; Yrjänä, Leena; Alizoti, Paraskevi; Rotach, Peter; Vietto, Lorenzo; Bordács, Sándor; Myking, Tor; Eysteinsson, Thröstur

    2013-01-01

    This paper provides a review of theoretical and practical aspects related to genetic management of forest trees. The implementation of international commitments on forest genetic diversity has been slow and partly neglected. Conservation of forest genetic diversity is still riddled with problems, and complexities of national legal and administrative structures. Europe is an example of a complex region where the dis- tribution ranges of tree species extend across large geographical areas with ...

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

    Directory of Open Access Journals (Sweden)

    Flávio de Oliveira Francisco

    2013-01-01

    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.

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

    Directory of Open Access Journals (Sweden)

    Boris Briñez R.

    2011-05-01

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

  14. Fatty Acid Diversity is Not Associated with Neutral Genetic Diversity in Native Populations of the Biodiesel Plant Jatropha curcas L.

    Science.gov (United States)

    Martínez-Díaz, Yesenia; González-Rodríguez, Antonio; Rico-Ponce, Héctor Rómulo; Rocha-Ramírez, Víctor; Ovando-Medina, Isidro; Espinosa-García, Francisco J

    2017-01-01

    Jatropha curcas L. (Euphorbiaceae) is a shrub native to Mexico and Central America, which produces seeds with a high oil content that can be converted to biodiesel. The genetic diversity of this plant has been widely studied, but it is not known whether the diversity of the seed oil chemical composition correlates with neutral genetic diversity. The total seed oil content, the diversity of profiles of fatty acids and phorbol esters were quantified, also, the genetic diversity obtained from simple sequence repeats was analyzed in native populations of J. curcas in Mexico. Using the fatty acids profiles, a discriminant analysis recognized three groups of individuals according to geographical origin. Bayesian assignment analysis revealed two genetic groups, while the genetic structure of the populations could not be explained by isolation-by-distance. Genetic and fatty acid profile data were not correlated based on Mantel test. Also, phorbol ester content and genetic diversity were not associated. Multiple linear regression analysis showed that total oil content was associated with altitude and seasonality of temperature. The content of unsaturated fatty acids was associated with altitude. Therefore, the cultivation planning of J. curcas should take into account chemical variation related to environmental factors. © 2017 Wiley-VHCA AG, Zurich, Switzerland.

  15. Italian Common Bean Landraces: History, Genetic Diversity and Seed Quality

    Directory of Open Access Journals (Sweden)

    Angela R. Piergiovanni

    2010-05-01

    Full Text Available The long tradition of common bean cultivation in Italy has allowed the evolution of many landraces adapted to restricted areas. Nowadays, in response to market demands, old landraces are gradually being replaced by improved cultivars. However, landraces still survive in marginal areas of several Italian regions. Most of them appear severely endangered with risk of extinction due to the advanced age of the farmers and the socio-cultural context where they are cultivated. The present contribution is an overview of the state of the art about the knowledge of Italian common bean germplasm, describing the most important and recent progresses made in its characterization, including genetic diversity and nutritional aspects.

  16. Genetic diversity of flavonoid content in leaf of hawthorn resources

    International Nuclear Information System (INIS)

    Zhao, Y.; Wang, G.; Liu, Z.

    2014-01-01

    Hawthorn (Cratageus spp.) are important medicinal plants. Flavonoids are the main active ingredient in hawthorn. With the help of hawthorn leaf flavonoids efficient detection system, vitexin, rhamnosylvitexin, hyperin, rutin and quercetin of 122 hawthorn resources was precisely measured.The flavonoid contents of 10 hawthorn species were explicited. The comparation of flavonoids revealed the abundant genetic diversity of hawthorn flavones. Large variable coefficient has been observed among 5 flavonoid monomer traits. The coefficients of variation were 44.17%, 132.2%, 157.08%, 113.91% and 31.05 for Vitexin, Rhamnosylvitexin, Hyperoside, Rutin and Quercetin respectively. The sum of these 5 flavonoid monomer contents represented the total flavonoids in hawthorn. The total coefficients of variation was 44.01%. Some high-content-flavone and valuable leaf resources were found. This research could provide accurate date for further production, breeding and the effective use of medicinal resources. (author)

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

    OpenAIRE

    Özlem ÖZBEK; Betül Uçar GIDIK

    2013-01-01

    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 com...

  18. Genetic Diversity and Spatial Genetic Structure of an Epiphytic Bromeliad in Costa Rican Montane Secondary Forest Patches

    NARCIS (Netherlands)

    Cascante-Marín, A.; Oostermeijer, G.; Wolf, J.; Fuchs, E.J.

    2014-01-01

    Information on genetic variation and its distribution in tropical plant populations relies mainly on studies of ground-rooted species, while genetic information of epiphytic plants is still limited. Particularly, the effect of forest successional condition on genetic diversity and structure of

  19. Epidemiology and genetic diversity of Taenia asiatica: a systematic review.

    Science.gov (United States)

    Ale, Anita; Victor, Bjorn; Praet, Nicolas; Gabriël, Sarah; Speybroeck, Niko; Dorny, Pierre; Devleesschauwer, Brecht

    2014-01-22

    Taenia asiatica has made a remarkable journey through the scientific literature of the past 50 years, starting with the paradoxical observation of high prevalences of T. saginata-like tapeworms in non-beef consuming populations, to the full description of its mitochondrial genome. Experimental studies conducted in the 1980s and 1990s have made it clear that the life cycle of T. asiatica is comparable to that of T. saginata, except for pigs being the preferential intermediate host and liver the preferential location of the cysts. Whether or not T. asiatica can cause human cysticercosis, as is the case for Taenia solium, remains unclear. Given the specific conditions needed to complete its life cycle, in particular the consumption of raw or poorly cooked pig liver, the transmission of T. asiatica shows an important ethno-geographical association. So far, T. asiatica has been identified in Taiwan, South Korea, Indonesia, the Philippines, Thailand, south-central China, Vietnam, Japan and Nepal. Especially this last observation indicates that its distribution is not restricted to South-East-Asia, as was thought so far. Indeed, the molecular tools developed over the last 20 years have made it increasingly possible to differentiate T. asiatica from other taeniids. Such tools also indicated that T. asiatica is related more closely to T. saginata than to T. solium, feeding the debate on its taxonomic status as a separate species versus a subspecies of T. saginata. Furthermore, the genetic diversity within T. asiatica appears to be very minimal, indicating that this parasite may be on the verge of extinction. However, recent studies have identified potential hybrids between T. asiatica and T. saginata, reopening the debate on the genetic diversity of T. asiatica and its status as a separate species.

  20. Epidemiology and genetic diversity of Taenia asiatica: a systematic review

    Science.gov (United States)

    2014-01-01

    Taenia asiatica has made a remarkable journey through the scientific literature of the past 50 years, starting with the paradoxical observation of high prevalences of T. saginata-like tapeworms in non-beef consuming populations, to the full description of its mitochondrial genome. Experimental studies conducted in the 1980s and 1990s have made it clear that the life cycle of T. asiatica is comparable to that of T. saginata, except for pigs being the preferential intermediate host and liver the preferential location of the cysts. Whether or not T. asiatica can cause human cysticercosis, as is the case for Taenia solium, remains unclear. Given the specific conditions needed to complete its life cycle, in particular the consumption of raw or poorly cooked pig liver, the transmission of T. asiatica shows an important ethno-geographical association. So far, T. asiatica has been identified in Taiwan, South Korea, Indonesia, the Philippines, Thailand, south-central China, Vietnam, Japan and Nepal. Especially this last observation indicates that its distribution is not restricted to South-East-Asia, as was thought so far. Indeed, the molecular tools developed over the last 20 years have made it increasingly possible to differentiate T. asiatica from other taeniids. Such tools also indicated that T. asiatica is related more closely to T. saginata than to T. solium, feeding the debate on its taxonomic status as a separate species versus a subspecies of T. saginata. Furthermore, the genetic diversity within T. asiatica appears to be very minimal, indicating that this parasite may be on the verge of extinction. However, recent studies have identified potential hybrids between T. asiatica and T. saginata, reopening the debate on the genetic diversity of T. asiatica and its status as a separate species. PMID:24450957

  1. Genetic diversity of Echinococcus granulosus in center of Iran.

    Science.gov (United States)

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

    2014-08-01

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

  2. High local genetic diversity of canine parvovirus from Ecuador.

    Science.gov (United States)

    Aldaz, Jaime; García-Díaz, Juan; Calleros, Lucía; Sosa, Katia; Iraola, Gregorio; Marandino, Ana; Hernández, Martín; Panzera, Yanina; Pérez, Ruben

    2013-09-27

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

  3. GENETIC DIVERSITY IN ACCESSIONS OF Stylosanthes spp. USING MORPHOAGRONOMIC DESCRIPTORS

    Directory of Open Access Journals (Sweden)

    RONALDO SIMÃO DE OLIVEIRA

    2016-01-01

    Full Text Available The great diversity of plants in the Brazilian Semiarid environment represents a vital natural resource for the human populations of these areas. Many of these plants have been subject to extractivism and among these, the species of the genus Stylosanthes , which have occurrence in this region, show great potential, however, studies on this topic are limited, and little is known about the existing variability among these plants. Therefore, further study is necessary, to facilitate the development of cultivars. This might reduce the scarcity of fodder supply in this region, but to commence a plant breeding programme, it is essential to identify genetic variability. Therefore, this study evaluated 25 accessions of Stylosanthes spp., to identify the most suitable candidates to be parents in a plant breeding programme for the semiarid region of the state of Bahia. Two experiments were carried out in different sites in an experimental design of randomized blocks with four replicates, with a spacing of 3.0 × 8.0 m. A large amount of genetic diversity was observed among accessions and the genotypes BGF 08 - 007, BGF 08 - 016, BGF 08 - 015 and BGF 08 - 021 were the most divergent in the overall evaluation. For the structuring of segregating populations, it is recommended to combine the genotypes BGF 08 - 016, BGF 08 - 015, BGF 08 - 007 and BGF 08 - 006, and for the interspecific crosses, a hybrid from the accession BGF - 024 with the accessions BGF 08 - 016 or BGF 08 - 015. This might generate superior individuals for mass descriptors, which are the most important for animal forage breeding.

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

    Directory of Open Access Journals (Sweden)

    Malice M.

    2009-01-01

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

  5. Assessing Genetic Diversity after Mangrove Restoration in Brazil: Why Is It So Important?

    Directory of Open Access Journals (Sweden)

    Renan Granado

    2018-04-01

    Full Text Available Vital for many marine and terrestrial species, and several other environmental services, such as carbon sink areas, the mangrove ecosystem is highly threatened due to the proximity of large urban centers and climate change. The forced fragmentation of this ecosystem affects the genetic diversity distribution among natural populations. Moreover, while restoration efforts have increased, few studies have analyzed how recently-planted areas impact the original mangrove genetic diversity. We analyzed the genetic diversity of two mangroves species (Laguncularia racemosa and Avicennia schaueriana in three areas in Brazil, using inter-simple sequence repeat (ISSR markers. Using the local approach, we identified the genetic diversity pool of a restored area compared to nearby areas, including the remnant plants inside the restored area, one well-conserved population at the shore of Guanabara Bay, and one impacted population in Araçá Bay. The results for L. racemosa showed that the introduced population has lost genetic diversity by drift, but remnant plants with high genetic diversity or incoming propagules could help improve overall genetic diversity. Avicennia schaueriana showed similar genetic diversity, indicating an efficient gene flow. The principal component analysis showing different connections between both species indicate differences in gene flow and dispersal efficiencies, highlighting the needed for further studies. Our results emphasize that genetic diversity knowledge and monitoring associated with restoration actions can help avoid bottlenecks and other pitfalls, especially for the mangrove ecosystem.

  6. Genetic signatures of ecological diversity along an urbanization gradient.

    Science.gov (United States)

    Kelly, Ryan P; O'Donnell, James L; Lowell, Natalie C; Shelton, Andrew O; Samhouri, Jameal F; Hennessey, Shannon M; Feist, Blake E; Williams, Gregory D

    2016-01-01

    Despite decades of work in environmental science and ecology, estimating human influences on ecosystems remains challenging. This is partly due to complex chains of causation among ecosystem elements, exacerbated by the difficulty of collecting biological data at sufficient spatial, temporal, and taxonomic scales. Here, we demonstrate the utility of environmental DNA (eDNA) for quantifying associations between human land use and changes in an adjacent ecosystem. We analyze metazoan eDNA sequences from water sampled in nearshore marine eelgrass communities and assess the relationship between these ecological communities and the degree of urbanization in the surrounding watershed. Counter to conventional wisdom, we find strongly increasing richness and decreasing beta diversity with greater urbanization, and similar trends in the diversity of life histories with urbanization. We also find evidence that urbanization influences nearshore communities at local (hundreds of meters) rather than regional (tens of km) scales. Given that different survey methods sample different components of an ecosystem, we then discuss the advantages of eDNA-which we use here to detect hundreds of taxa simultaneously-as a complement to traditional ecological sampling, particularly in the context of broad ecological assessments where exhaustive manual sampling is impractical. Genetic data are a powerful means of uncovering human-ecosystem interactions that might otherwise remain hidden; nevertheless, no sampling method reveals the whole of a biological community.

  7. Genetic diversity of Toxoplasma gondii isolates from Ethiopian feral cats.

    Science.gov (United States)

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

    2013-09-01

    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. Published by Elsevier B.V.

  8. Genetic diversity and antifungal susceptibility of Fusarium isolates in onychomycosis.

    Science.gov (United States)

    Rosa, Priscila D; Heidrich, Daiane; Corrêa, Carolina; Scroferneker, Maria Lúcia; Vettorato, Gerson; Fuentefria, Alexandre M; Goldani, Luciano Z

    2017-09-01

    Fusarium species have emerged as an important human pathogen in skin disease, onychomycosis, keratitis and invasive disease. Onychomycosis caused by Fusarium spp. The infection has been increasingly described in the immunocompetent and immunosuppressed hosts. Considering onychomycosis is a difficult to treat infection, and little is known about the genetic variability and susceptibility pattern of Fusarium spp., further studies are necessary to understand the pathogenesis and better to define the appropriate antifungal treatment for this infection. Accordingly, the objective of this study was to describe the in vitro susceptibility to different antifungal agents and the genetic diversity of 35 Fusarium isolated from patients with onychomycosis. Fusarium spp. were isolated predominantly from female Caucasians, and the most frequent anatomical location was the nail of the hallux. Results revealed that 25 (71.4%) of isolates belonged to the Fusarium solani species complex, followed by 10 (28.5%) isolates from the Fusarium oxysporum species complex. Noteworthy, the authors report the first case of Neocosmospora rubicola isolated from a patient with onychomycosis. Amphotericin B was the most effective antifungal agent against the majority of isolates (60%, MIC ≤4 μg/mL), followed by voriconazole (34.2%, MIC ≤4 μg/mL). In general, Fusarium species presented MIC values >64 μg/mL for fluconazole, itraconazole and terbinafine. Accurate pathogen identification, characterisation and susceptibility testing provide a better understanding of pathogenesis of Fusarium in onychomycosis. © 2017 Blackwell Verlag GmbH.

  9. Genetic diversity of pestivirus isolates in cattle from Western Austria.

    Science.gov (United States)

    Hornberg, Andrea; Fernández, Sandra Revilla; Vogl, Claus; Vilcek, Stefan; Matt, Monika; Fink, Maria; Köfer, Josef; Schöpf, Karl

    2009-03-30

    The genetic diversity of bovine viral diarrhoea virus (BVDV) isolates in infected cattle from Tyrol and Vorarlberg (Austria) was investigated. Blood samples were collected within the compulsory Austrian BVDV control programme during 2005 and 2006. The 5'-untranslated region (5'-UTR) and partially the N-terminal autoprotease (N(pro)) were amplified by one-step reverse transcriptase-polymerase chain reaction (RT-PCR) and the PCR products were subsequently sequenced. Phylogenetic analysis based on 5'-UTR and N(pro) sequences demonstrated that almost all isolates (307/310) were of the BVDV-1 genotype. They were clustered into eight different subtypes, here listed by their frequency of occurrence: BVDV-1h (143), BVDV-1f (79), BVDV-1b (41), BVDV-1d (28), BVDV-1e (6), BVDV-1a (4), BVDV-1g (3) and BVDV1-k (3). Two pestivirus isolates were typed as BVDV-2 and one isolate as BDV closely related to Gifhorn strain (BDV-3). Correlation among isolates could only be observed at the farm level, i.e., within a herd. However, no correlation between the genetic and geographical distances could be observed above the farm level. Because of the wide distribution of certain BVDV-1 subtypes and the low prevalence of herd-specific strains, a determination of tracing routes of infection was not possible. Furthermore, recombination events were not detected.

  10. The Genetic Diversity of Mesodinium and Associated Cryptophytes.

    Science.gov (United States)

    Johnson, Matthew D; Beaudoin, David J; Laza-Martinez, Aitor; Dyhrman, Sonya T; Fensin, Elizabeth; Lin, Senjie; Merculief, Aaron; Nagai, Satoshi; Pompeu, Mayza; Setälä, Outi; Stoecker, Diane K

    2016-01-01

    Ciliates from the genus Mesodinium are globally distributed in marine and freshwater ecosystems and may possess either heterotrophic or mixotrophic nutritional modes. Members of the Mesodinium major/rubrum species complex photosynthesize by sequestering and maintaining organelles from cryptophyte prey, and under certain conditions form periodic or recurrent blooms (= red tides). Here, we present an analysis of the genetic diversity of Mesodinium and cryptophyte populations from 10 environmental samples (eight globally dispersed habitats including five Mesodinium blooms), using group-specific primers for Mesodinium partial 18S, ITS, and partial 28S rRNA genes as well as cryptophyte large subunit RuBisCO genes ( rbcL ). In addition, 22 new cryptophyte and four new M. rubrum cultures were used to extract DNA and sequence rbcL and 18S-ITS-28S genes, respectively, in order to provide a stronger phylogenetic context for our environmental sequences. Bloom samples were analyzed from coastal Brazil, Chile, two Northeastern locations in the United States, and the Pribilof Islands within the Bering Sea. Additionally, samples were also analyzed from the Baltic and Barents Seas and coastal California under non-bloom conditions. Most blooms were dominated by a single Mesodinium genotype, with coastal Brazil and Chile blooms composed of M. major and the Eastern USA blooms dominated by M. rubrum variant B. Sequences from all four blooms were dominated by Teleaulax amphioxeia -like cryptophytes. Non-bloom communities revealed more diverse assemblages of Mesodinium spp., including heterotrophic species and the mixotrophic Mesodinium chamaeleon . Similarly, cryptophyte diversity was also higher in non-bloom samples. Our results confirm that Mesodinium blooms may be caused by M. major , as well as multiple variants of M. rubrum , and further implicate T. amphioxeia as the key cryptophyte species linked to these phenomena in temperate and subtropical regions.

  11. The genetic diversity of Mesodinium and associated cryptophytes

    Directory of Open Access Journals (Sweden)

    Matthew David Johnson

    2016-12-01

    Full Text Available Ciliates from the genus Mesodinium are globally distributed in marine and freshwater ecosystems and may possess either heterotrophic or mixotrophic nutritional modes. Members of the M. major/rubrum species complex photosynthesize by sequestering and maintaining organelles from cryptophyte prey, and under certain conditions form periodic or recurrent blooms (= red tides. Here we present an analysis of the genetic diversity of Mesodinium and cryptophyte populations from 10 environmental samples (8 globally dispersed habitats including 5 Mesodinium blooms, using group-specific primers for Mesodinium partial 18S, ITS, and partial 28S rRNA genes as well as cryptophyte large subunit RuBisCO genes (rbcL. In addition, 22 new cryptophyte and 4 new M. rubrum cultures were used to extract DNA and sequence rbcL and 18S-ITS-28S genes, respectively, in order to provide a stronger phylogenetic context for our environmental sequences. Bloom samples were analyzed from coastal Brazil, Chile, two Northeastern locations in the United States, and the Pribilof Islands within the Bering Sea. Additionally, samples were also analyzed from the Baltic and Barents Seas and coastal California under non-bloom conditions. Most blooms were dominated by a single Mesodinium genotype, with coastal Brazil and Chile blooms composed of M. major and the Eastern USA blooms dominated by M. rubrum variant B. Sequences from all 4 blooms were dominated by T. amphioxeia-like cryptophytes. Non-bloom communities revealed more diverse assemblages of Mesodinium spp., including heterotrophic species and the mixotrophic M. chamaeleon. Similarly, cryptophyte diversity was also higher in non-bloom samples. Our results confirm that Mesodinium blooms may be caused by M. major, as well as multiple variants of M. rubrum, and further implicate T. amphioxeia as the key cryptophyte species linked to these phenomena in temperate and subtropical regions.

  12. [Marburg and Ebola hemorrhagic fevers--pathogens, epidemiology and therapy].

    Science.gov (United States)

    Stock, Ingo

    2014-09-01

    Marburg and Ebola hemorrhagic fevers are severe, systemic viral diseases affecting humans and non-human primates. They are characterized by multiple symptoms such as hemorrhages, fever, headache, muscle and abdominal pain, chills, sore throat, nausea, vomiting and diarrhea. Elevated liver-associated enzyme levels and coagulopathy are also associated with these diseases. Marburg and Ebola hemorrhagic fevers are caused by (Lake victoria) Marburg virus and different species of Ebola viruses, respectively. They are enveloped, single-stranded RNA viruses and belong to the family of filoviridae. Case fatality rates of filovirus disease outbreaks are among the highest reported for any human pathogen, ranging from 25 to 90% or more. Outbreaks of Marburg and Ebola hemorrhagic fever occur in certain regions of equatorial Africa at irregular intervals. Since 2000, the number of outbreaks has increased. In 2014, the biggest outbreak of a filovirus-induced hemorrhagic fever that has been documented so far occurred from March to July 2014 in Guinea, Sierra Leone, Liberia and Nigeria. The outbreak was caused by a new variant of Zaire Ebola-Virus, affected more than 2600 people (stated 20 August) and was associated with case-fatality rates of up to 67% (Guinea). Treatment of Marburg and Ebola hemorrhagic fevers is symptomatic and supportive, licensed antiviral agents are currently not available. Recently, BCX4430, a promising synthetic adenosine analogue with high in vitro and in vivo activity against filoviruses and other RNA viruses, has been described. BCX4430 inhibits viral RNA polymerase activity and protects cynomolgus macaques from Marburg virus infection when administered as late as 48 hours after infection. Nucleic acid-based products, recombinant vaccines and antibodies appear to be less suitable for the treatment of Marburg and Ebola hemorrhagic fevers.

  13. Genetic diversity of Echinococcus multilocularis on a local scale.

    Science.gov (United States)

    Knapp, J; Guislain, M-H; Bart, J M; Raoul, F; Gottstein, B; Giraudoux, P; Piarroux, R

    2008-05-01

    Echinococcusmultilocularis is the causative agent of human Alveolar Echinococcosis (AE), and it is one of the most lethal zoonotic infections in the Northern Hemisphere. In France, the eastern and central regions are endemic areas; Franche-Comté, Lorraine and Auvergne are particularly contaminated. Recently, several human cases were recorded in the French Ardennes area, a region adjacent to the western border of the E. multilocularis range in France. A previous study in this focus described a prevalence of over 50% of the parasite in red foxes. The present study investigated the genetic diversity of adult worms collected from foxes in a 900km(2) area in the Ardennes. Instead of a conventional mitochondrial target (ATP6), two microsatellite targets (EmsB and NAK1) were used. A total of 140 adult worms isolated from 25 red foxes were genotyped. After hierarchical clustering analyses, the EmsB target enabled us to distinguish two main assemblages, each divided into sub-groups, yielding the differentiation of six clusters or assemblage profiles. Thirteen foxes (52% of the foxes) each harbored worms from at least two different assemblage profiles, suggesting they had become infected by several sources. Using the NAK1 target, we identified 3 alleles, two found in association with the two EmsB assemblages. With the NAK1 target, we investigated the parasite breeding system and the possible causes of genetic diversification. Only one fox harbored hybrid worms, indicative of a possible (and rare) occurrence of recombination, although multiple infections have been observed in foxes. These results confirm the usefulness of microsatellite targets for assessing genetic polymorphism in a geographically restricted local range.

  14. sGD: software for estimating spatially explicit indices of genetic diversity.

    Science.gov (United States)

    Shirk, A J; Cushman, S A

    2011-09-01

    Anthropogenic landscape changes have greatly reduced the population size, range and migration rates of many terrestrial species. The small local effective population size of remnant populations favours loss of genetic diversity leading to reduced fitness and adaptive potential, and thus ultimately greater extinction risk. Accurately quantifying genetic diversity is therefore crucial to assessing the viability of small populations. Diversity indices are typically calculated from the multilocus genotypes of all individuals sampled within discretely defined habitat patches or larger regional extents. Importantly, discrete population approaches do not capture the clinal nature of populations genetically isolated by distance or landscape resistance. Here, we introduce spatial Genetic Diversity (sGD), a new spatially explicit tool to estimate genetic diversity based on grouping individuals into potentially overlapping genetic neighbourhoods that match the population structure, whether discrete or clinal. We compared the estimates and patterns of genetic diversity using patch or regional sampling and sGD on both simulated and empirical populations. When the population did not meet the assumptions of an island model, we found that patch and regional sampling generally overestimated local heterozygosity, inbreeding and allelic diversity. Moreover, sGD revealed fine-scale spatial heterogeneity in genetic diversity that was not evident with patch or regional sampling. These advantages should provide a more robust means to evaluate the potential for genetic factors to influence the viability of clinal populations and guide appropriate conservation plans. © 2011 Blackwell Publishing Ltd.

  15. Animal models for Ebola and Marburg virus infections

    Science.gov (United States)

    Nakayama, Eri; Saijo, Masayuki

    2013-01-01

    Ebola and Marburg hemorrhagic fevers (EHF and MHF) are caused by the Filoviridae family, Ebolavirus and Marburgvirus (ebolavirus and marburgvirus), respectively. These severe diseases have high mortality rates in humans. Although EHF and MHF are endemic to sub-Saharan Africa. A novel filovirus, Lloviu virus, which is genetically distinct from ebolavirus and marburgvirus, was recently discovered in Spain where filoviral hemorrhagic fever had never been reported. The virulence of this virus has not been determined. Ebolavirus and marburgvirus are classified as biosafety level-4 (BSL-4) pathogens and Category A agents, for which the US government requires preparedness in case of bioterrorism. Therefore, preventive measures against these viral hemorrhagic fevers should be prepared, not only in disease-endemic regions, but also in disease-free countries. Diagnostics, vaccines, and therapeutics need to be developed, and therefore the establishment of animal models for EHF and MHF is invaluable. Several animal models have been developed for EHF and MHF using non-human primates (NHPs) and rodents, which are crucial to understand pathophysiology and to develop diagnostics, vaccines, and therapeutics. Rhesus and cynomolgus macaques are representative models of filovirus infection as they exhibit remarkably similar symptoms to those observed in humans. However, the NHP models have practical and ethical problems that limit their experimental use. Furthermore, there are no inbred and genetically manipulated strains of NHP. Rodent models such as mouse, guinea pig, and hamster, have also been developed. However, these rodent models require adaptation of the virus to produce lethal disease and do not mirror all symptoms of human filovirus infection. This review article provides an outline of the clinical features of EHF and MHF in animals, including humans, and discusses how the animal models have been developed to study pathophysiology, vaccines, and therapeutics. PMID:24046765

  16. Animal models for Ebola and Marburg virus infections

    Directory of Open Access Journals (Sweden)

    Eri eNakayama

    2013-09-01

    Full Text Available Ebola and Marburg hemorrhagic fevers (EHF and MHF are caused by the Filoviridae family, Ebolavirus and Marburgvirus (ebolavirus and marburgvirus, respectively. These severe diseases have high mortality rates in humans. Although EHF and MHF are endemic to sub-Saharan Africa. A novel filovirus, Lloviu virus, which is genetically distinct from ebolavirus and marburgvirus, was recently discovered in Spain where filoviral hemorrhagic fever had never been reported. The virulence of this virus has not been determined. Ebolavirus and marburgvirus are classified as biosafety level-4 (BSL-4 pathogens and Category A agents, for which the US government requires preparedness in case of bioterrorism. Therefore, preventive measures against these viral hemorrhagic fevers should be prepared, not only in disease-endemic regions, but also in disease-free countries. Diagnostics, vaccines, and therapeutics need to be developed, and therefore the establishment of animal models for EHF and MHF is invaluable. Several animal models have been developed for EHF and MHF using nonhuman primates (NHPs and rodents, which are crucial to understand pathophysiology and to develop diagnostics, vaccines, and therapeutics. Rhesus and cynomolgus macaques are representative models of filovirus infection as they exhibit remarkably similar symptoms to those observed in humans. However, the NHP models have practical and ethical problems that limit their experimental use. Furthermore, there are no inbred and genetically manipulated strains of NHP. Rodent models such as mouse, guinea pig, and hamster, have also been developed. However, these rodent models require adaptation of the virus to produce lethal disease and do not mirror all symptoms of human filovirus infection. This review article provides an outline of the clinical features of EHF and MHF in animals, including humans, and discusses how the animal models have been developed to study pathophysiology, vaccines, and therapeutics.

  17. Global to local genetic diversity indicators of evolutionary potential in tree species within and outside forests

    DEFF Research Database (Denmark)

    Graudal, Lars; Aravanopoulos, Filippos; Bennadji, Zohra

    2014-01-01

    -monitoring schemes. Here, we provide a review and an assessment of the different attempts made to provide such indicators for tree genetic diversity from the global level down to the level of the management unit. So far, no generally accepted indicators have been provided as international standards, nor tested...... for their possible use in practice. We suggest that indicators for monitoring genetic diversity and dynamics should be based on ecological and demographic surrogates of adaptive diversity as well as genetic markers capable of identifying genetic erosion and gene flow. A comparison of past and present genecological...... distributions (patterns of genetic variation of key adaptive traits in the ecological space) of selected species is a realistic way of assessing the trend of intra-specific variation, and thus provides a state indicator of tree genetic diversity also able to reflect possible pressures threatening genetic...

  18. Genetic diversity of pheasants from natural habitat and farm ...

    African Journals Online (AJOL)

    The original source of the pheasants living in the natural habitat is the farm, and the present genetic variation between the two groups of birds can be interpreted as an effect of natural selection. Keywords: Common pheasant (Phasianus colchicus), genetic distance, genetic polymorphism, genetic similarities, genetic ...

  19. Comparison of the Pathogenesis of the Angola and Ravn Strains of Marburg Virus in the Outbred Guinea Pig Model.

    Science.gov (United States)

    Cross, Robert W; Fenton, Karla A; Geisbert, Joan B; Ebihara, Hideki; Mire, Chad E; Geisbert, Thomas W

    2015-10-01

    Phylogenetic comparisons of known Marburg virus (MARV) strains reveal 2 distinct genetic lineages: Ravn and the Lake Victoria Marburg complex (eg, Musoke, Popp, and Angola strains). Nucleotide variances of >20% between Ravn and other MARV genomes suggest that differing virulence between lineages may accompany this genetic divergence. To date, there exists limited systematic experimental evidence of pathogenic differences between MARV strains. Uniformly lethal outbred guinea pig models of MARV-Angola (MARV-Ang) and MARV-Ravn (MARV-Rav) were developed by serial adaptation. Changes in genomic sequence, weight, temperature, histopathologic findings, immunohistochemical findings, hematologic profiles, circulating biochemical enzyme levels, coagulation parameters, viremia levels, cytokine levels, eicanosoid levels, and nitric oxide production were compared between strains. MARV-Rav infection resulted in delayed increases in circulating inflammatory and prothrombotic elements, notably lower viremia levels, less severe histologic alterations, and a delay in mean time to death, compared with MARV-Ang infection. Both strains produced more marked coagulation abnormalities than previously seen in MARV-infected mice or inbred guinea pigs. Although both strains exhibit great similarity to pathogenic markers of human and nonhuman primate MARV infection, these data highlight several key differences in pathogenicity that may serve to guide the choice of strain and model used for development of vaccines or therapeutics for Marburg hemorrhagic fever. Published by Oxford University Press on behalf of the Infectious Diseases Society of America 2015. This work is written by (a) US Government employee(s) and is in the public domain in the US.

  20. Estimation of genetic diversity between three Saudi sheep breeds ...

    African Journals Online (AJOL)

    Aghomotsegin

    2015-10-14

    Oct 14, 2015 ... The cluster analysis shows that Najdi breed is genetically different from both Harri and Awassi and .... Genetic distance value of 0.0 reflects very high similarity between ..... The State of the Worlds Animal Genetic Resources for.

  1. Noninvasive genetics provides insights into the population size and genetic diversity of an Amur tiger population in China.

    Science.gov (United States)

    Wang, Dan; Hu, Yibo; Ma, Tianxiao; Nie, Yonggang; Xie, Yan; Wei, Fuwen

    2016-01-01

    Understanding population size and genetic diversity is critical for effective conservation of endangered species. The Amur tiger (Panthera tigris altaica) is the largest felid and a flagship species for wildlife conservation. Due to habitat loss and human activities, available habitat and population size are continuously shrinking. However, little is known about the true population size and genetic diversity of wild tiger populations in China. In this study, we collected 55 fecal samples and 1 hair sample to investigate the population size and genetic diversity of wild Amur tigers in Hunchun National Nature Reserve, Jilin Province, China. From the samples, we determined that 23 fecal samples and 1 hair sample were from 7 Amur tigers: 2 males, 4 females and 1 individual of unknown sex. Interestingly, 2 fecal samples that were presumed to be from tigers were from Amur leopards, highlighting the significant advantages of noninvasive genetics over traditional methods in studying rare and elusive animals. Analyses from this sample suggested that the genetic diversity of wild Amur tigers is much lower than that of Bengal tigers, consistent with previous findings. Furthermore, the genetic diversity of this Hunchun population in China was lower than that of the adjoining subpopulation in southwest Primorye Russia, likely due to sampling bias. Considering the small population size and relatively low genetic diversity, it is urgent to protect this endangered local subpopulation in China. © 2015 International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and John Wiley & Sons Australia, Ltd.

  2. Genetic Diversity, Population Structure and Ancestral Origin of Australian Wheat

    Directory of Open Access Journals (Sweden)

    Reem Joukhadar

    2017-12-01

    assist with maintaining genetic diversity for long-term selection gains and to plan future breeding programs.

  3. Genetic Diversity, Population Structure and Ancestral Origin of Australian Wheat.

    Science.gov (United States)

    Joukhadar, Reem; Daetwyler, Hans D; Bansal, Urmil K; Gendall, Anthony R; Hayden, Matthew J

    2017-01-01

    maintaining genetic diversity for long-term selection gains and to plan future breeding programs.

  4. Genetic Diversity Among Botulinum Neurotoxin Producing Clostridial Strains

    Energy Technology Data Exchange (ETDEWEB)

    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

    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.

  5. Genetic Diversity as Consequence of a Microaerobic and Neutrophilic Lifestyle.

    Directory of Open Access Journals (Sweden)

    Nora-Johanna Krüger

    2016-05-01

    Full Text Available As a neutrophilic bacterium, Helicobacter pylori is growth deficient under extreme acidic conditions. The gastric pathogen is equipped with an acid survival kit, regulating urease activity by a pH-gated urea channel, opening below pH 6.5. After overcoming acid stress, the bacterium's multiplication site is situated at the gastric mucosa with near neutral pH. The pathogen exhibits exceptional genetic variability, mainly due to its capability of natural transformation, termed competence. Using single cell analysis, we show here that competence is highly regulated in H. pylori. DNA uptake complex activity was reversibly shut down below pH 6.5. pH values above 6.5 opened a competence window, in which competence development was triggered by the combination of pH increase and oxidative stress. In contrast, addition of sublethal concentrations of the DNA-damaging agents ciprofloxacin or mitomycin C did not trigger competence development under our conditions. An oxygen-sensitive mutant lacking superoxide dismutase (sodB displayed a higher competent fraction of cells than the wild type under comparable conditions. In addition, the sodB mutant was dependent on adenine for growth in broth and turned into non-cultivable coccoid forms in its absence, indicating that adenine had radical quenching capacity. Quantification of periplasmically located DNA in competent wild type cells revealed outstanding median imported DNA amounts of around 350 kb per cell within 10 min of import, with maximally a chromosomal equivalent (1.6 Mb in individual cells, far exceeding previous amounts detected in other Gram-negative bacteria. We conclude that the pathogen's high genetic diversity is a consequence of its enormous DNA uptake capacity, triggered by intrinsic and extrinsic oxidative stress once a neutral pH at the site of chronic host colonization allows competence development.

  6. GENETIC DIVERSITY OF INTERSPECIFIC HYBRIDS OF THE GENUS ALLIUM L.

    Directory of Open Access Journals (Sweden)

    V. S. Romanov

    2018-01-01

    Full Text Available Selection based on interspecific hybridization of fundamentally new plant forms with a unique combination of genetic material allows expanding the scope of genotypic and phenotypic variability. In this work the comparative analysis of plants of interspecific hybrids of genus Allium L. from various inbred descendants of combinations of crossing of species A. cepa х A. vavilovii and A. cepa х A. fistulosum on selection traits is carried out.Forms were identified: by mass of the bulb more than 100 g; with contrasting coloration of dry cover scales bulbs; by the index of the shape of the bulb; on the resistance to peronosporosis of plants of the first year of vegetation and seed plants; by the number of arrows; height of the arrow; on seed production with a sufficiently high percentage of fertile plants. Plants of interspecific hybrids of onions formed bulbs weighing from 20 to 120 g, with white, golden-yellow, dark golden-yellow, brownish and dark purple color of dry covering scales of a bulb. Plants of interspecific hybrids of onions were flat and round-flat shape of the bulb with the frequency of symptoms ranging from 6.9 to 93.3% and from 11.7 to 93.3%. In a phytopathological evaluation of interspecific hybrids of onions the first year of vegetation identified plants with resistance to downy mildew is from 0 to 4.0 points. Was studied the frequency of occurrence of plants in the progenies weight, colour, bulb type, number, height of the seedstalk, seed productivity and resistance to downy mildew. The increase of genetic diversity in onion plants obtained on the basis of interspecific hybridization, backcrossing and inbreeding is shown.

  7. Genetic diversity of Phytophthora infestans in the Northern Andean region.

    Science.gov (United States)

    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

    2011-02-09

    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, β-tubulin and Avr3a) and one mitochondrial (Cox1) region were analyzed in isolates of P. infestans sampled from different hosts in Colombia and Venezuela. 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. 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.

  8. Genetic diversity of Phytophthora infestans in the Northern Andean region

    Directory of Open Access Journals (Sweden)

    Grünwald Niklaus J

    2011-02-01

    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, β-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.

  9. Genetic Resources in the “Calabaza Pipiana” Squash (Cucurbita argyrosperma) in Mexico: Genetic Diversity, Genetic Differentiation and Distribution Models

    Science.gov (United States)

    Sánchez-de la Vega, Guillermo; Castellanos-Morales, Gabriela; Gámez, Niza; Hernández-Rosales, Helena S.; Vázquez-Lobo, Alejandra; Aguirre-Planter, Erika; Jaramillo-Correa, Juan P.; Montes-Hernández, Salvador; Lira-Saade, Rafael; Eguiarte, Luis E.

    2018-01-01

    Analyses of genetic variation allow understanding the origin, diversification and genetic resources of cultivated plants. Domesticated taxa and their wild relatives are ideal systems for studying genetic processes of plant domestication and their joint is important to evaluate the distribution of their genetic resources. Such is the case of the domesticated subspecies C. argyrosperma ssp. argyrosperma, known in Mexico as calabaza pipiana, and its wild relative C. argyrosperma ssp. sororia. The main aim of this study was to use molecular data (microsatellites) to assess the levels of genetic variation and genetic differentiation within and among populations of domesticated argyrosperma across its distribution in Mexico in comparison to its wild relative, sororia, and to identify environmental suitability in previously proposed centers of domestication. We analyzed nine unlinked nuclear microsatellite loci to assess levels of diversity and distribution of genetic variation within and among populations in 440 individuals from 19 populations of cultivated landraces of argyrosperma and from six wild populations of sororia, in order to conduct a first systematic analysis of their genetic resources. We also used species distribution models (SDMs) for sororia to identify changes in this wild subspecies’ distribution from the Holocene (∼6,000 years ago) to the present, and to assess the presence of suitable environmental conditions in previously proposed domestication sites. Genetic variation was similar among subspecies (HE = 0.428 in sororia, and HE = 0.410 in argyrosperma). Nine argyrosperma populations showed significant levels of inbreeding. Both subspecies are well differentiated, and genetic differentiation (FST) among populations within each subspecies ranged from 0.152 to 0.652. Within argyrosperma we found three genetic groups (Northern Mexico, Yucatan Peninsula, including Michoacan and Veracruz, and Pacific coast plus Durango). We detected low levels of gene

  10. Genetic Resources in the “Calabaza Pipiana” Squash (Cucurbita argyrosperma in Mexico: Genetic Diversity, Genetic Differentiation and Distribution Models

    Directory of Open Access Journals (Sweden)

    Guillermo Sánchez-de la Vega

    2018-03-01

    Full Text Available Analyses of genetic variation allow understanding the origin, diversification and genetic resources of cultivated plants. Domesticated taxa and their wild relatives are ideal systems for studying genetic processes of plant domestication and their joint is important to evaluate the distribution of their genetic resources. Such is the case of the domesticated subspecies C. argyrosperma ssp. argyrosperma, known in Mexico as calabaza pipiana, and its wild relative C. argyrosperma ssp. sororia. The main aim of this study was to use molecular data (microsatellites to assess the levels of genetic variation and genetic differentiation within and among populations of domesticated argyrosperma across its distribution in Mexico in comparison to its wild relative, sororia, and to identify environmental suitability in previously proposed centers of domestication. We analyzed nine unlinked nuclear microsatellite loci to assess levels of diversity and distribution of genetic variation within and among populations in 440 individuals from 19 populations of cultivated landraces of argyrosperma and from six wild populations of sororia, in order to conduct a first systematic analysis of their genetic resources. We also used species distribution models (SDMs for sororia to identify changes in this wild subspecies’ distribution from the Holocene (∼6,000 years ago to the present, and to assess the presence of suitable environmental conditions in previously proposed domestication sites. Genetic variation was similar among subspecies (HE = 0.428 in sororia, and HE = 0.410 in argyrosperma. Nine argyrosperma populations showed significant levels of inbreeding. Both subspecies are well differentiated, and genetic differentiation (FST among populations within each subspecies ranged from 0.152 to 0.652. Within argyrosperma we found three genetic groups (Northern Mexico, Yucatan Peninsula, including Michoacan and Veracruz, and Pacific coast plus Durango. We detected low

  11. Highways block gene flow and cause a rapid decline in genetic diversity of desert bighorn sheep

    NARCIS (Netherlands)

    Epps, CW; Palsboll, PJ; Wehausen, JD; Roderick, GK; Ramey, RR; McCullough, DR

    2005-01-01

    The rapid expansion of road networks has reduced connectivity among populations of flora and fauna. The resulting isolation is assumed to increase population extinction rates, in part because of the loss of genetic diversity. However, there are few cases where loss of genetic diversity has been

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

    DEFF Research Database (Denmark)

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

    2016-01-01

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

  13. Elm genetic diversity and hybridization in the presence of Dutch elm disease

    Science.gov (United States)

    Johanne Brunet; Raymond P. Guries

    2017-01-01

    The impact of Dutch elm disease (DED) on the genetic diversity of slippery elm (Ulmus rubra) is summarized and its potential impact on the genetic diversity of other North American native elms, American elm (U. americana), rock elm (U. thomasii), winged elm (U. alata), cedar elm (

  14. Conservation of biodiversity in sugar pine: effects of the blister rust epidemic on genetic diversity

    Science.gov (United States)

    Constance I. Millar; Bohun B. Kinloch; Robert D. Westfall

    1992-01-01

    Genetic diversity in sugar plne will be severely reduced by the blister rust pandemic predicted within the next 50 to 75 years. We model effects of the epidemic on genetic diversity at the stand and landscape levels for both natural and artificial regeneration. In natural stands, because natural frequencies of the dominant gene (R) for resistance are low, the most...

  15. Use of SNP markers to conserve genome-wide genetic diversity in livestock

    NARCIS (Netherlands)

    Engelsma, K.A.

    2012-01-01

    Conservation of genetic diversity in livestock breeds is important since it is, both within and between breeds, under threat. The availability of large numbers of SNP markers has resulted in new opportunities to estimate genetic diversity in more detail, and to improve prioritization of animals

  16. Do Farmers reduce genetic diversity when they domesticate tropical trees? a case study from Amazonia.

    NARCIS (Netherlands)

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

    2005-01-01

    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

  17. Elm genetic diversity and hybridization in the presence of Dutch elm disease

    Science.gov (United States)

    Dutch elm disease (DED) has devastated native North American elm species for more than 75 years. The impact of DED on the genetic diversity of one native elm species, U. rubra or slippery elm, is summarized and its potential impact on the genetic diversity of the other four North American native elm...

  18. Study of human genetic diversity : inferences on population origin and history

    OpenAIRE

    Haber, Marc, 1980-

    2013-01-01

    Patterns of human genetic diversity suggest that all modern humans originated from a small population in Africa that expanded rapidly 50,000 years ago to occupy the whole world. While moving into new environments, genetic drift and natural selection affected populations differently, creating genetic structure. By understanding the genetic structure of human populations, we can reconstruct human history and understand the genetic basis of diseases. The work presented here contributes to the on...

  19. Genetic diversity of populations of the dioecious Myrsine coriacea (Primulaceae in the Atlantic Forest

    Directory of Open Access Journals (Sweden)

    Roberta Pena da Paschoa

    2018-04-01

    Full Text Available ABSTRACT Although a species’ sexual system may influence the genetic diversity of its populations in their natural environment, there have been few such studies involving indigenous species of the Atlantic Forest. Here we study Myrsine coriacea, a dioecious tree widely used in reforestation programs despite a lack of information about its natural interpopulation genetic variation. To address this knowledge gap, intra- and interpopulation genetic diversity were measured for male and female individuals of ten natural populations using ISSR markers. Greater intrapopulation genetic diversity indicated interpopulation gene flow, regardless of isolation and distance between populations. Multivariate analyses detected significant differences in genetic diversity between populations, but not between males and females, which indicates that genetic diversity did not differ between the two sex morphs. Distance between populations was unrelated to genetic diversity. Myrsine coriacea has not experienced a loss of genetic variability despite the characteristic segregated spatial distribution of its populations. These results suggest that obligatory cross-pollination and dispersal by birds may be important mechanisms for the maintenance of genetic diversity in natural populations of M. coriacea.

  20. Genetic Diversity of Acacia mangium Seed Orchard in Wonogiri Indonesia Using Microsatellite Markers

    Directory of Open Access Journals (Sweden)

    VIVI YUSKIANTI

    2012-09-01

    Full Text Available Genetic diversity is important in tree improvement programs. To evaluate levels of genetic diversity of first generation Acacia mangium seedling seed orchard in Wonogiri, Central Java, Indonesia, three populations from each region of Papua New Guinea (PNG and Queensland, Australia (QLD were selected and analyzed using 25 microsatellite markers. Statistical analysis showed that PNG populations have higher number of detected alleles and level of genetic diversity than QLD populations. This study provides a basic information about the genetic background of the populations used in the development of an A. mangium seed orchard in Indonesia.

  1. Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil)

    DEFF Research Database (Denmark)

    Miller, Webb; Hayes, Vanessa M.; Ratan, Aakrosh

    2011-01-01

    The Tasmanian devil (Sarcophilus harrisii) is threatened with extinction because of a contagious cancer known as Devil Facial Tumor Disease. The inability to mount an immune response and to reject these tumors might be caused by a lack of genetic diversity within a dwindling population. Here we...... that the observed low genetic diversity in today's population preceded the Devil Facial Tumor Disease disease outbreak by at least 100 y. Using a genetically characterized breeding stock based on the genome sequence will enable preservation of the extant genetic diversity in future Tasmanian devil populations....

  2. Genetic diversity of dog breeds: within-breed diversity comparing genealogical and molecular data.

    Science.gov (United States)

    Leroy, G; Verrier, E; Meriaux, J C; Rognon, X

    2009-06-01

    The genetic diversity of 61 dog breeds raised in France was investigated. Genealogical analyses were performed on the pedigree file of the French kennel club. A total of 1514 dogs were also genotyped using 21 microsatellite markers. For animals born from 2001 to 2005, the average coefficient of inbreeding ranged from 0.2% to 8.8% and the effective number of ancestors ranged from 9 to 209, according to the breed. The mean value of heterozygosity was 0.62 over all breeds (range 0.37-0.77). At the breed level, few correlations were found between genealogical and molecular parameters. Kinship coefficients and individual similarity estimators were, however, significantly correlated, with the best mean correlation being found for the Lynch & Ritland estimator (r = 0.43). According to both approaches, it was concluded that special efforts should be made to maintain diversity for three breeds, namely the Berger des Pyrénées, Braque Saint-Germain and Bull Terrier.

  3. A preliminary examination of genetic diversity in the Indian false vampire bat Megaderma lyra

    Directory of Open Access Journals (Sweden)

    Emmanuvel Rajan, K.

    2006-12-01

    Full Text Available Habitat loss and fragmentation have serious consequences for species extinction as well as genetic diversity within a species. Random Amplified Polymorphic DNA (RAPD analysis was employed to assess the genetic diversity within and between four natural populations of M. lyra. Our results suggest that the genetic diversity varied from 0.21 to 0.26 with a mean of 0.11 to 0.13 (± SD. The mean Gst value of 0.15 was obtained from all four populations and estimated average Nm (1.41 showing gene flow between the populations. AMOVA analysis showed 88.96% within and 11.04% among the studied populations. Cluster analyses of RAPD phenotypes showed that specimens were not grouped by geographical origin. The genetic diversity found in the M. lyra population may be explained by its breeding behaviors. Though preliminary, the results indicate that all four populations should be considered to maintain the genetic diversity.

  4. Genetic Diversity of Some Capparis L. Species Growing in Syria

    Directory of Open Access Journals (Sweden)

    Bassam Al- Safadi

    2014-12-01

    Full Text Available This work investigated the genetic diversity and relationships among Capparis species growing in Syria using IRAP and ISSR techniques. Forty-seven samples of three Capparis species genotypes were collected from 21 different locations in Syria. The genotypes were morphologically identified based on the descriptions available in the literature. When IRAP technique was used, an average of 71.5% of the amplified fragments were polymorphic compared to 82.04% in ISSR. Morphological characterization along with the cluster and PCoA analyses of the data divided the studied genotypes into three groups. The groups included genotypes identified as Capparis spinosa L, C. sicula Duh., and C. aegyptia Lam. Based on the morphological description, molecular studies and statistical analyses of this study, C. aegyptia could be suggested as a separate species and not a varietal rank of C. spinosa(C. spinosa var. aegyptia (Lam.. Two samples (Alep1 and Idl were not placed in any of the three distinctive groups, despite their closeness morphologically to C. spinosa. In PCoA analysis, sample Alep1 came between C. sicula and C. spinosa and Idl was placed between C. sicula and C. aegyptia. Although hybridization between Capparis species could occur, it was not clear from the present study if these two genotypes were hybrids.

  5. Genotyping of ancient Mycobacterium tuberculosis strains reveals historic genetic diversity.

    Science.gov (United States)

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

    2014-04-22

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

  6. Genetic diversity of hepatitis B virus (HBV) in Madagascar.

    Science.gov (United States)

    Andriamandimby, Soa Fy; Lo Presti, Alessandra; Lai, Alessia; Olive, Marie-Marie; Angeletti, Silvia; De Florio, Lucia; Cella, Eleonora; Razafindramparany, Minoharimbola; Ravalohery, Jean-Piere; Andriamamonjy, Seta; Gioffrè, Sonia; Zehender, Gianguglielmo; Mottini, Giovanni; Ciccozzi, Massimo; Heraud, Jean-Michel

    2016-12-01

    Hepatitis B virus (HBV) is a DNA virus belonging to Hepadnaviridae family. Chronic infection with HBV is one major risk factor of hepatic disease. In Madagascar, former studies classified the country as part of high endemic area, as HBV prevalence can reach 23% in general population. However, this prevalence differs largely between urban and rural areas and is estimated to be, respectively, 5% and 26%. The aims of the present study were to describe the genetic diversity of HBV strains from different regions of Madagascar, and to describe the viral gene flow throughout the country by using phylogenetic analysis. This is the first large-scale molecular and phylogenetic study analyzing HBV sequences from 28 different Malagasy areas, never sampled in the past. In this study, the most prevalent genotype/sub-genotypes was E. Migration analysis showed a gene flow from zone 3 (rural) to zone 2 (suburban), and a greater gene flow from the middle part of Madagascar to the north than to the south. It is important to study the HBV infections in Madagascar and to monitor the potential spread of this viral strain inside this country. J. Med. Virol. 88:2138-2144, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  7. Genetic diversity of some chili (Capsicum annuum L. genotypes

    Directory of Open Access Journals (Sweden)

    M.J. Hasan

    2014-06-01

    Full Text Available A study on genetic diversity was conducted with 54 Chili (Capsicum annuum L. genotypes through Mohalanobis’s D2 and principal component analysis for twelve quantitative characters viz. plant height, number of secondary branch/plant, canopy breadth , days to first flowering, days to 50% flowering, fruits/plant, 5 fruits weight, fruit length, fruit diameter, seeds/fruit, 1000 seed weight and yield/plant were taken into consideration. Cluster analysis was used for grouping of 54 chili genotypes and the genotypes were fallen into seven clusters. Cluster II had maximum (13 and cluster III had the minimum number (1 of genotypes. The highest inter-cluster distance was observed between cluster I and III and the lowest between cluster II and VII. The characters yield/plant, canopy breadth, secondary branches/plant, plant height and seeds/fruit contributed most for divergence in the studied genotypes. Considering group distance, mean performance and variability the inter genotypic crosses between cluster I and cluster III, cluster III and cluster VI, cluster II and cluster III and cluster III and cluster VII may be suggested to use for future hybridization program.

  8. Assessment of Genetic Diversity among Pleurotus spp. Isolates from Jordan

    Directory of Open Access Journals (Sweden)

    Hanan Aref Hasan

    2018-04-01

    Full Text Available Pleurotus is considered an important genus that belongs to the family Pleurotaceae and includes the edible King Oyster mushroom (Pleurotus eryngii. In the present study, 19 Pleurotus isolates were collected from two locations in the north of Jordan (Tell ar-Rumman and Um-Qais. The morphological characteristics among collected isolates revealed that there was a morphological similarity among the collected isolates. Nucleotide sequence analysis of the internal transcribed spacer (ITS1–5.8S rDNA–ITS4 region and 28S nuclear large subunit (nLSU in the ribosomal DNA gene of the isolated stains showed that all of them share over 98% sequence similarity with P. eryngii. Genetic diversity among the collected strains was assessed using inter simple sequence repeat (ISSR analysis using 18 different primer pairs. Using this approach, 141 out of 196 bands obtained were considered polymorphic and the highest percentage of polymorphism was observed using primer UBC827 (92.3% with an overall Polymorphism Information Content (PIC value of 70.56%. Cluster analysis showed that the Jordanian Pleurotus isolates fall into two main clades with a coefficient of similarity values ranging from 0.59 to 0.74 with a clear clustering based on collection sites. The results of the present study reveal that molecular techniques of ISSR and rDNA sequencing can greatly aid in classification and identification of Pleurotus spp. in Jordan.

  9. Genetic diversity of a Daugava basin brown trout (Salmo trutta brood stock

    Directory of Open Access Journals (Sweden)

    Schmidt Thomas

    2017-01-01

    Full Text Available Genetics play an increasingly important role in the conservation of threatened fish populations. We have examined twelve microsatellite markers to determine the genetic diversity of a brood stock of brown trout from the Latvian Daugava river basin, used in a local supportive breeding program and compared diversity values to other Baltic populations. Allelic data was further inspected for indications of increased inbreeding. Additionally, we have analyzed the mitochondrial control region to classify the population within a broader phylogenetic framework. We found that the genetic diversity was comparatively low, but there was no strong evidence of high inbreeding. A newly detected mitochondrial haplotype indicates unnoticed genetic diversity of “Atlantic lineage” brown trout in the Daugava basin region. Our study provides first genetic details on resident brown trout from the Baltic Daugava river basin to improve the regional conservation management of this valuable genetic resource and contributes phylogeographically useful information.

  10. Is there a positive relationship between naturalness and genetic diversity in forest tree communities?

    OpenAIRE

    Wehenkel, C.; Corral-Rivas, J. J.; Castellanos-Bocaz, H. A.; Pinedo-Alvarez, A.

    2009-01-01

    The concepts of genetic diversity and naturalness are well known as measures of conservation values and as descriptors of state or condition. A lack of research evaluating the relationship between genetic diversity and naturalness in biological communities, along with the possible implications in terms of evolutionary aspects and conservation management, make this subject particularly important as regards forest tree communities.We therefore examined the following hypothesis: the genetic dive...

  11. Genetic diversity and structure in a collection of tulip cultivars assessed by SNP markers

    NARCIS (Netherlands)

    Tang, N.; Shahin, A.; Bijman, P.J.J.; Liu, J.; Tuyl, van J.M.; Arens, P.

    2013-01-01

    Although tulip is one of the most important bulbous crops worldwide, the genetic background of most cultivars is unclear at present. The purposes of this study are to investigate genetic diversity and to identify the genetic structure and relationships among tulip cultivars. A total of 236

  12. Genetic structure and diversity of the black and rufous sengiin Tanzanian coastal forests

    Czech Academy of Sciences Publication Activity Database

    Sabuni, C. A.; Van Houtte, N.; Gryseels, S.; Maganga, S. L. S.; Makundi, R. H.; Leirs, H.; Goüy de Bellocq, Joëlle

    2016-01-01

    Roč. 300, č. 4 (2016), s. 305-313 ISSN 0952-8369 Institutional support: RVO:68081766 Keywords : Rhynchocyon petersi * vulnerable * conservation genetics * coastal forests * Beamys hindei * genetic structure * genetic diversity * habitat fragmentation Subject RIV: EH - Ecology, Behaviour Impact factor: 2.186, year: 2016

  13. Genetic diversity and phylogeny of the Christmas Island flying fox (Pteropus melanotus natalis)

    Czech Academy of Sciences Publication Activity Database

    Phalen, D. N.; Hall, J.; Ganesh, G.; Hartigan, Ashlie; Smith, C.; De Jong, C.; Field, H.; Rose, K.

    2017-01-01

    Roč. 98, č. 2 (2017), s. 428-437 ISSN 0022-2372 Institutional support: RVO:60077344 Keywords : diversity * flying fox * mitochondrial DNA * phylogeny * Pteropus melanotus natalis Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Genetics and heredity (medical genetics to be 3) Impact factor: 1.630, year: 2016

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

    Science.gov (United States)

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

    2009-08-01

    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.

  15. Genetic diversity is related to climatic variation and vulnerability in threatened bull trout

    Science.gov (United States)

    Kovach, Ryan; Muhlfeld, Clint C.; Wade, Alisa A.; Hand, Brian K.; Whited, Diane C.; DeHaan, Patrick W.; Al-Chokhachy, Robert K.; Luikart, Gordon

    2015-01-01

    Understanding how climatic variation influences ecological and evolutionary processes is crucial for informed conservation decision-making. Nevertheless, few studies have measured how climatic variation influences genetic diversity within populations or how genetic diversity is distributed across space relative to future climatic stress. Here, we tested whether patterns of genetic diversity (allelic richness) were related to climatic variation and habitat features in 130 bull trout (Salvelinus confluentus) populations from 24 watersheds (i.e., ~4–7th order river subbasins) across the Columbia River Basin, USA. We then determined whether bull trout genetic diversity was related to climate vulnerability at the watershed scale, which we quantified on the basis of exposure to future climatic conditions (projected scenarios for the 2040s) and existing habitat complexity. We found a strong gradient in genetic diversity in bull trout populations across the Columbia River Basin, where populations located in the most upstream headwater areas had the greatest genetic diversity. After accounting for spatial patterns with linear mixed models, allelic richness in bull trout populations was positively related to habitat patch size and complexity, and negatively related to maximum summer temperature and the frequency of winter flooding. These relationships strongly suggest that climatic variation influences evolutionary processes in this threatened species and that genetic diversity will likely decrease due to future climate change. Vulnerability at a watershed scale was negatively correlated with average genetic diversity (r = −0.77;P bull trout and other imperiled species. Genetic diversity is already depressed where climatic vulnerability is highest; it will likely erode further in the very places where diversity may be most needed for future persistence.

  16. Genetic structure and genetic diversity of Swietenia macrophylla in areas subjected to selective logging in Quintana Roo, Mexico

    OpenAIRE

    Alcalá, Raúl Ernesto; Cruz, Silvia De la; Gutiérrez-Granados, Gabriel

    2015-01-01

    The hypothesis that selective logging has a negative effect by altering the genetic parameters of tropical tree species was evaluated. The genetic diversity and genetic structure between adult trees (N = 47) and saplings (N = 50) of Swietenia macrophylla were contrasted within an area subjected to selective logging in the Mayan zone. Although differences in the number of alleles and in their frequencies were detected between both groups, the observed and expected heterozygosity and the coeffi...

  17. Comparative analysis of genetic diversity among Chinese watermelon germplasmsusing SSR and SRAP markers, and implications for future genetic improvement

    OpenAIRE

    WANG, PANGQIAO; LI, QIONG; Hu, Jianbin; SU, YAN

    2015-01-01

    The genetic diversity of watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai] in China, the world's largest producer of watermelon fruits, has not been examined. Two molecular markers, sequence-related amplified polymorphism (SRAP) and simple sequence repeat (SSR), were used to investigate the genetic variation and genetic relationship among 54 Chinese watermelon accessions, as well as 7 accessions from Africa, the United States, and Japan. SRAP assay generated 312 bands, ...

  18. Genetic diversity and relationship of Indian cattle inferred from microsatellite and mitochondrial DNA markers.

    Science.gov (United States)

    Sharma, Rekha; Kishore, Amit; Mukesh, Manishi; Ahlawat, Sonika; Maitra, Avishek; Pandey, Ashwni Kumar; Tantia, Madhu Sudan

    2015-06-30

    Indian agriculture is an economic symbiosis of crop and livestock production with cattle as the foundation. Sadly, the population of indigenous cattle (Bos indicus) is declining (8.94% in last decade) and needs immediate scientific management. Genetic characterization is the first step in the development of proper management strategies for preserving genetic diversity and preventing undesirable loss of alleles. Thus, in this study we investigated genetic diversity and relationship among eleven Indian cattle breeds using 21 microsatellite markers and mitochondrial D loop sequence. The analysis of autosomal DNA was performed on 508 cattle which exhibited sufficient genetic diversity across all the breeds. Estimates of mean allele number and observed heterozygosity across all loci and population were 8.784 ± 0.25 and 0.653 ± 0.014, respectively. Differences among breeds accounted for 13.3% of total genetic variability. Despite high genetic diversity, significant inbreeding was also observed within eight populations. Genetic distances and cluster analysis showed a close relationship between breeds according to proximity in geographic distribution. The genetic distance, STRUCTURE and Principal Coordinate Analysis concluded that the Southern Indian Ongole cattle are the most distinct among the investigated cattle populations. Sequencing of hypervariable mitochondrial DNA region on a subset of 170 cattle revealed sixty haplotypes with haplotypic diversity of 0.90240, nucleotide diversity of 0.02688 and average number of nucleotide differences as 6.07407. Two major star clusters for haplotypes indicated population expansion for Indian cattle. Nuclear and mitochondrial genomes show a similar pattern of genetic variability and genetic differentiation. Various analyses concluded that the Southern breed 'Ongole' was distinct from breeds of Northern/ Central India. Overall these results provide basic information about genetic diversity and structure of Indian cattle which

  19. Genetic diversity of Halla horses using microsatellite markers

    Directory of Open Access Journals (Sweden)

    Joo-Hee Seo

    2016-11-01

    Full Text Available Abstract Background Currently about 26,000 horses are breeding in Korea and 57.2% (14,776 horses of them are breeding in Jeju island. According to the statistics published in 2010, the horses breeding in Jeju island are subdivided into Jeju horse (6.1%, Thoroughbred (18.8% and Halla horse (75.1%. Halla horses are defined as a crossbreed between Jeju and Thoroughbred horses and are used for horse racing, horse riding and horse meat production. However, little research has been conducted on Halla horses because of the perception of crossbreed and people’s weighted interest toward Jeju horses. Method Using 17 Microsatellite (MS Markers recommended by International Society for Animal Genetics (ISAG, genomic DNAs were extracted from the hair roots of 3,880 Halla horses breeding in Korea and genetic diversity was identified by genotyping after PCR was performed. Results and conclusion In average, 10.41 alleles (from 6 alleles in HTG7 to 17 alleles in ASB17 were identified after the analysis using 17 MS Markers. The mean value of Hobs was 0.749 with a range from 0.612(HMS1 to 0.857(ASB2. Also, it was found that Hexp and PIC values were lowest in HMS1 (0.607 and 0.548, respectively, and highest in LEX3(0.859 and 0.843, respectively, and the mean value of Hexp was 0.760 and that of PIC was 0.728. 17 MS markers used in this studies were considered as appropriate markers for the polymorphism analysis of Halla horses. The frequency for the appearance of identical individuals was 5.90 × 10−20 when assumed as random mating population and when assumed as half-sib and full-sib population, frequencies were 4.08 × 10−15 and 3.56 × 10−8, respectively. Based on these results, the 17 MS markers can be used adequately for the Individual Identification and Parentage Verification of Halla horses. Remarkably, allele M and Q of ASB23 marker, G of HMS2 marker, H and L of HTG6 marker, L of HTG7 marker, E of LEX3 marker were the specific alleles

  20. DNA markers reveal genetic structure and localized diversity of ...

    African Journals Online (AJOL)

    uqhdesma

    2016-10-12

    Oct 12, 2016 ... STRUCTURE analysis revealed 4 clusters of genetically ..... 10000 cycles and 50000 Markov Chain Monte Carlo (MCMC) iterations and 10 replicate runs performed for each K value to ..... WL, Lee M, Porter K (2000). Genetic ...

  1. Development of Pineapple Microsatellite Markers and Germplasm Genetic Diversity Analysis

    Directory of Open Access Journals (Sweden)

    Suping Feng

    2013-01-01

    Full Text Available 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.

  2. Development of Pineapple Microsatellite Markers and Germplasm Genetic Diversity Analysis

    Science.gov (United States)

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

    2013-01-01

    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

  3. Genetic diversity and structure found in samples of Eritrean bread wheat

    DEFF Research Database (Denmark)

    Desta, Zeratsion Abera; Orabi, Jihad; Jahoor, Ahmed

    2014-01-01

    Genetic diversity and structure plays a key role in the selection of parents for crosses in plant breeding programmes. The aim of the present study was to analyse the genetic diversity and structure of Eritrean bread wheat accessions. We analysed 284 wheat accessions from Eritrea using 30 simple...... sequence repeat markers. A total of 539 alleles were detected. The allele number per locus ranged from 2 to 21, with a mean allele number of 9.2. The average genetic diversity index was 0.66, with values ranging from 0.01 to 0.89. Comparing the three genomes of wheat, the B genome had the highest genetic...... diversity (0.66) and the D genome the lowest diversity (0.61). A STRUCTURE analysis based on the Bayesian model-based cluster analysis followed by a graphical representation of the distances by non-parametric multidimensional scaling revealed a distinct partition of the Eritrean wheat accessions into two...

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

    Directory of Open Access Journals (Sweden)

    Juliana Morini Küpper Cardoso Perseguini

    2011-01-01

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

  5. Assessment of the genetic diversity in five generations of a ...

    African Journals Online (AJOL)

    Genetic variation among and within five generations of an inbred commercial captive line of Litopenaeus vannamei and genetic distance among them were evaluated by random amplified polymorphic DNA (RAPD), using descriptive and genetic similarity analyses for dominant markers at single- and multi-populational level ...

  6. Rice diversity panels available through the genetic stocks oryza collection

    Science.gov (United States)

    The Genetic Stocks Oryza (GSOR) Collection was established in 2004 at the USDA-ARS, Dale Bumpers National Rice Research Center (DBNRRC) located in Stuttgart, AR. The mission of GSOR is to provide unique genetic resources to the rice research community for genetic and genomics related research. GSOR ...

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

    Science.gov (United States)

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

    2013-01-01

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

  8. Genetic diversity and differentiation of Mongolian indigenous cattle populations

    Energy Technology Data Exchange (ETDEWEB)

    Lkhagva, B [International Livestock Research Institute - ILRI, P.O. Box 30709, Nairobi (Kenya) and Mongolian State Agricultural University, Zaisan, Ulaanbaatar 210153 (Mongolia); Ochieng, J W; Hanotte, O; Jianlin, H [International Livestock Research Institute - ILRI, P.O. Box 30709, Nairobi (Kenya); Yoon, D H [National Livestock Research Institute, RDA, 441-350, Suwon (Korea)

    2003-07-01

    Livestock production plays an important role in Mongolian economy. Over the last decade it has contributed to around 80-90% of the gross domestic agricultural products and to 30% of the revenues generated from exportations. Cattle is one of the five traditional and most important livestock species of Mongolia together with horse, sheep, goat and camel. Out of a total of 1.57 millions Mongolian cattle, 1.55 millions supposedly belong to three indigenous Bos taurus cattle breeds, namely Mongol, Selenge and Khalkhun Golun, all herded under extensive pastoral systems. Indigenous Mongolian cattle are generally small but look sturdy and strong. They have a well-off coat of hair, solid forward looking shoulders and short stubby snouts, and they are used for meat, milk and transport. Beef production contributes to 30% of the total meat supply in Mongolia. The Mongol breed is by the far the commonest with 1.53 million animals and it is found almost throughout the country. The Selenge breed, found in Selenge province and numbering 9000 heads, was developed in middle of the 20th century by crossing the Kazakh Whiteheaded with the local Mongol cattle. The Khalkhun Golun breed was developed from local Mongol cattle and it is distributed in Eastern and Suhbaatar provinces with about 10,000 heads. Until now, to the best of our knowledge, only a single population of Mongolian cattle has been studied with microsatellite DNA markers and no information is available on the genetic relationship between the Mongolian indigenous cattle breeds. In this study, we collected samples from two populations of the Mongol cattle (sampled at Ikhtamir soum in North Hangay province and Tsogt soum in Govi Altay province) and one population of the Khalkhun Golun cattle (sampled at Tumentsogt soum in Suhbaatar province). Samples were characterised with nine microsatellite markers MGTG4B, ILSTS005, ILSTS006, ILSTS008, ILSTS023, ILSTS028, ILSTS036, ILSTS050 and ILSTS103. To assess the genetic diversity

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

    Science.gov (United States)

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

    2017-08-01

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

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

    Science.gov (United States)

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

    2017-08-01

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

  11. Genetic diversity and distribution of Senegalia senegal (L.) Britton under climate change scenarios in West Africa

    Science.gov (United States)

    Duque-Lazo, Joaquín; Durka, Walter; Hauenschild, Frank; Schnitzler, Jan; Michalak, Ingo; Ogundipe, Oluwatoyin Temitayo; Muellner-Riehl, Alexandra Nora

    2018-01-01

    Climate change is predicted to impact species’ genetic diversity and distribution. We used Senegalia senegal (L.) Britton, an economically important species distributed in the Sudano-Sahelian savannah belt of West Africa, to investigate the impact of climate change on intraspecific genetic diversity and distribution. We used ten nuclear and two plastid microsatellite markers to assess genetic variation, population structure and differentiation across thirteen sites in West Africa. We projected suitable range, and potential impact of climate change on genetic diversity using a maximum entropy approach, under four different climate change scenarios. We found higher genetic and haplotype diversity at both nuclear and plastid markers than previously reported. Genetic differentiation was strong for chloroplast and moderate for the nuclear genome. Both genomes indicated three spatially structured genetic groups. The distribution of Senegalia senegal is strongly correlated with extractable nitrogen, coarse fragments, soil organic carbon stock, precipitation of warmest and coldest quarter and mean temperature of driest quarter. We predicted 40.96 to 6.34 per cent of the current distribution to favourably support the species’ ecological requirements under future climate scenarios. Our results suggest that climate change is going to affect the population genetic structure of Senegalia senegal, and that patterns of genetic diversity are going to influence the species’ adaptive response to climate change. Our study contributes to the growing evidence predicting the loss of economically relevant plants in West Africa in the next decades due to climate change. PMID:29659603

  12. Assessment of Genetic Diversity, Relationships and Structure among Korean Native Cattle Breeds Using Microsatellite Markers

    Directory of Open Access Journals (Sweden)

    Sangwon Suh

    2014-11-01

    Full Text Available Four Korean native cattle (KNC breeds—Hanwoo, Chikso, Heugu, and Jeju black—are entered in the Domestic Animal Diversity Information System of the United Nations Food and Agriculture Organization (FAO. The objective of this study was to assess the genetic diversity, phylogenetic relationships and population structure of these KNC breeds (n = 120 and exotic breeds (Holstein and Charolais, n = 56. Thirty microsatellite loci recommended by the International Society for Animal Genetics/FAO were genotyped. These genotypes were used to determine the allele frequencies, allelic richness, heterozygosity and polymorphism information content per locus and breed. Genetic diversity was lower in Heugu and Jeju black breeds. Phylogenetic analysis, Factorial Correspondence Analysis and genetic clustering grouped each breed in its own cluster, which supported the genetic uniqueness of the KNC breeds. These results will be useful for conservation and management of KNC breeds as animal genetic resources.

  13. Genetic Diversity of the Black Mangrove Avicennia germinans (L. Stearn in Northwestern Mexico

    Directory of Open Access Journals (Sweden)

    Olivia Millán-Aguilar

    2016-09-01

    Full Text Available Mangrove forests of Mexico have been threatened by the effects of anthropogenic activities during the last decades, mostly related to aquaculture, agriculture, livestock and urban development. Genetic diversity and fine-scale genetic structure of two generations of the black mangrove Avicennia germinans (L. Stearn were investigated in perturbed and preserved sites from three lagoon systems in Sinaloa, Mexico. Genetic diversity and overall genetic structure were similar between perturbed and preserved sites. However, lower levels of fine-scale spatial genetic structure were observed in two of the younger (sapling generations. We attribute this to differences in local dynamics of each lagoon system, their status of conservation and levels of fragmentation. Also, low connectivity and the effects of disturbance could restrict the movement of pollinators and seed dispersal capabilities, resulting in low levels of genetic diversity and signs of inbreeding. Perturbed populations of A. germinans may play an important role in in situ conservation of this complex ecosystem.

  14. Marburg haemorrhagic fever: recent advances | AdegborO | African ...

    African Journals Online (AJOL)

    With the exception of a vaccine for yellow fever and ribavirin, which is used for treatment of some arenaviral infections, no specific chemotherapy for viral hemorrhagic fever exists. Only supportive treatment is possible The filoviruses, Marburg virus (MARV) and Ebola virus (EBOV), have been associated with hemorrhagic ...

  15. Relationships among walleye population characteristics and genetic diversity in northern Wisconsin Lakes

    Science.gov (United States)

    Waterhouse, Matthew D.; Sloss, Brian L.; Isermann, Daniel A.

    2014-01-01

    The maintenance of genetic integrity is an important goal of fisheries management, yet little is known regarding the effects of management actions (e.g., stocking, harvest regulations) on the genetic diversity of many important fish species. Furthermore, relationships between population characteristics and genetic diversity remain poorly understood. We examined relationships among population demographics (abundance, recruitment, sex ratio, and mean age of the breeding population), stocking intensity, and genetic characteristics (heterozygosity, effective number of alleles, allelic richness, Wright's inbreeding coefficient, effective population size [Ne], mean d2 [a measure of inbreeding], mean relatedness, and pairwise population ΦST estimates) for 15 populations of Walleye Sander vitreus in northern Wisconsin. We also tested for potential demographic and genetic influences on Walleye body condition and early growth. Combinations of demographic variables explained 47.1–79.8% of the variation in genetic diversity. Skewed sex ratios contributed to a reduction in Ne and subsequent increases in genetic drift and relatedness among individuals within populations; these factors were correlated to reductions in allelic richness and early growth rate. Levels of inbreeding were negatively related to both age-0 abundance and mean age, suggesting Ne was influenced by recruitment and generational overlap. A negative relationship between the effective number of alleles and body condition suggests stocking affected underlying genetic diversity of recipient populations and the overall productivity of the population. These relationships may result from poor performance of stocked fish, outbreeding depression, or density-dependent factors. An isolation-by-distance pattern of genetic diversity was apparent in nonstocked populations, but was disrupted in stocked populations, suggesting that stocking affected genetic structure. Overall, demographic factors were related to genetic

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

    Directory of Open Access Journals (Sweden)

    Pereira Albano

    2001-05-01

    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

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

    Science.gov (United States)

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

    2010-06-01

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

  18. Distribution of Marburg virus in Africa: An evolutionary approach.

    Science.gov (United States)

    Zehender, Gianguglielmo; Sorrentino, Chiara; Veo, Carla; Fiaschi, Lisa; Gioffrè, Sonia; Ebranati, Erika; Tanzi, Elisabetta; Ciccozzi, Massimo; Lai, Alessia; Galli, Massimo

    2016-10-01

    The aim of this study was to investigate the origin and geographical dispersion of Marburg virus, the first member of the Filoviridae family to be discovered. Seventy-three complete genome sequences of Marburg virus isolated from animals and humans were retrieved from public databases and analysed using a Bayesian phylogeographical framework. The phylogenetic tree of the Marburg virus data set showed two significant evolutionary lineages: Ravn virus (RAVV) and Marburg virus (MARV). MARV divided into two main clades; clade A included isolates from Uganda (five from the European epidemic in 1967), Kenya (1980) and Angola (from the epidemic of 2004-2005); clade B included most of the isolates obtained during the 1999-2000 epidemic in the Democratic Republic of the Congo (DRC) and a group of Ugandan isolates obtained in 2007-2009. The estimated mean evolutionary rate of the whole genome was 3.3×10(-4) substitutions/site/year (credibility interval 2.0-4.8). The MARV strain had a mean root time of the most recent common ancestor of 177.9years ago (YA) (95% highest posterior density 87-284), thus indicating that it probably originated in the mid-XIX century, whereas the RAVV strain had a later origin dating back to a mean 33.8 YA. The most probable location of the MARV ancestor was Uganda (state posterior probability, spp=0.41), whereas that of the RAVV ancestor was Kenya (spp=0.71). There were significant migration rates from Uganda to the DRC (Bayes Factor, BF=42.0) and in the opposite direction (BF=5.7). Our data suggest that Uganda may have been the cradle of Marburg virus in Africa. Copyright © 2016 Elsevier B.V. All rights reserved.

  19. Genetic diversity and domestication origin of tea plant Camellia taliensis (Theaceae) as revealed by microsatellite markers.

    Science.gov (United States)

    Zhao, Dong-Wei; Yang, Jun-Bo; Yang, Shi-Xiong; Kato, Kenji; Luo, Jian-Ping

    2014-01-09

    Tea is one of the most popular beverages in the world. Many species in the Thea section of the Camellia genus can be processed for drinking and have been domesticated. However, few investigations have focused on the genetic consequence of domestication and geographic origin of landraces on tea plants using credible wild and planted populations of a single species. Here, C. taliensis provides us with a unique opportunity to explore these issues. Fourteen nuclear microsatellite loci were employed to determine the genetic diversity and domestication origin of C. taliensis, which were represented by 587 individuals from 25 wild, planted and recently domesticated populations. C. taliensis showed a moderate high level of overall genetic diversity. The greater reduction of genetic diversity and stronger genetic drift were detected in the wild group than in the recently domesticated group, indicating the loss of genetic diversity of wild populations due to overexploitation and habitat fragmentation. Instead of the endangered wild trees, recently domesticated individuals were used to compare with the planted trees for detecting the genetic consequence of domestication. A little and non-significant reduction in genetic diversity was found during domestication. The long life cycle, selection for leaf traits and gene flow between populations will delay the emergence of bottleneck in planted trees. Both phylogenetic and assignment analyses suggested that planted trees may have been domesticated from the adjacent central forest of western Yunnan and dispersed artificially to distant places. This study contributes to the knowledge about levels and distribution of genetic diversity of C. taliensis and provides new insights into genetic consequence of domestication and geographic origin of planted trees of this species. As an endemic tea source plant, wild, planted and recently domesticated C. taliensis trees should all be protected for their unique genetic characteristics, which

  20. DEVELOPMENT OF AQUATIC MODELS FOR TESTING THE RELATIONSHIP BETWEEN GENETIC DIVERSITY AND POPULATION EXTINCTION RISK

    Science.gov (United States)

    The relationship between population adaptive potential and extinction risk in a changing environment is not well understood. Although the expectation is that genetic diversity is directly related to the capacity of populations to adapt, the statistical and predictive aspects of ...

  1. Analysis of the genetic diversity of selected East African sweet potato

    African Journals Online (AJOL)

    Aghomotsegin

    Taiwan. Orange. 65. Mugande x New kawogo 2. Uganda. Cream. 66. Bungoma. Uganda .... African countries is still very slow due to financial and technical .... IPGRI, Rome,. Italy and Institute for Genetic Diversity, Ithaca, New York, USA. ISBN:.

  2. Genetic diversity for sustainable rice blast management in China: adoption and impact

    NARCIS (Netherlands)

    Revilla-Molina, I.M.

    2009-01-01

    Keywords: Disease management, genetic diversity, rice interplanting, competition, resource complementarity, technical efficiency, production function, Magnaporthe grisea

    The experience on rice blast in Yunnan Province, China, is one of the most successful and widely publicized examples

  3. On indigenous production, genetic diversity and crop ecology of enset (Ensete ventricosum (Welw.) Cheesman)

    NARCIS (Netherlands)

    Tsegaye, A.

    2002-01-01

    Keywords : Enset, staple, indigenous knowledge, genetic diversity, AFLP, characterisation, conservation, Leaf Appearance Rate, Radiation Use Efficiency, yield potential, transplanting, leaf pruning, fermentation, 'kocho', food

  4. Present status of genetic diversity of Potamogeton praelongus populations in the Czech Republic

    Czech Academy of Sciences Publication Activity Database

    Kitner, M.; Prausová, R.; Adamec, Lubomír

    2013-01-01

    Roč. 53, č. 1 (2013), s. 73-86 ISSN 0079-2047 Institutional support: RVO:67985939 Keywords : genetic diversity * micropopulation * conservation Subject RIV: EF - Botanics Impact factor: 0.388, year: 2013

  5. Genetic Diversity and Population Structure of Two Tomato Species from the Galapagos Islands

    KAUST Repository

    Pailles, Yveline; Ho, Shwen; Pires, Inê s S.; Tester, Mark A.; Negrã o, Só nia; Schmö cke, Sandra M.

    2017-01-01

    with cultivated tomato. However, information about genetic diversity and relationships within and between populations is necessary to use these resources efficiently in plant breeding. In this study, we analyzed 3,974 polymorphic SNP markers, obtained through

  6. Molecular Genetic Diversity of Date (Phoenix dactylifera) Germplasm in Qatar based on Microsatellite Markers

    KAUST Repository

    Ahmed, Talaat

    2016-01-01

    Depending on morphological traits alone, studying the genetic diversity of date palm is a very difficult task since morphological characteristics are highly affected by the environment. DNA markers are excellent option that can help and enhance

  7. Genetic diversity of a large set of horse breeds raised in France assessed by microsatellite polymorphism

    Science.gov (United States)

    2009-01-01

    The genetic diversity and structure of horses raised in France were investigated using 11 microsatellite markers and 1679 animals belonging to 34 breeds. Between-breed differences explained about ten per cent of the total genetic diversity (Fst = 0.099). Values of expected heterozygosity ranged from 0.43 to 0.79 depending on the breed. According to genetic relationships, multivariate and structure analyses, breeds could be classified into four genetic differentiated groups: warm-blooded, draught, Nordic and pony breeds. Using complementary maximisation of diversity and aggregate diversity approaches, we conclude that particular efforts should be made to conserve five local breeds, namely the Boulonnais, Landais, Merens, Poitevin and Pottok breeds. PMID:19284689

  8. Genetic diversity of a large set of horse breeds raised in France assessed by microsatellite polymorphism

    Directory of Open Access Journals (Sweden)

    Mériaux Jean-Claude

    2009-01-01

    Full Text Available Abstract The genetic diversity and structure of horses raised in France were investigated using 11 microsatellite markers and 1679 animals belonging to 34 breeds. Between-breed differences explained about ten per cent of the total genetic diversity (Fst = 0.099. Values of expected heterozygosity ranged from 0.43 to 0.79 depending on the breed. According to genetic relationships, multivariate and structure analyses, breeds could be classified into four genetic differentiated groups: warm-blooded, draught, Nordic and pony breeds. Using complementary maximisation of diversity and aggregate diversity approaches, we conclude that particular efforts should be made to conserve five local breeds, namely the Boulonnais, Landais, Merens, Poitevin and Pottok breeds.

  9. Patterns of ancestry and genetic diversity in reintroduced populations of the slimy sculpin: Implications for conservation

    Science.gov (United States)

    Huff, David D.; Miller, Loren M.; Vondracek, Bruce C.

    2010-01-01

    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.

  10. Genetic structure and diversity of the Neem Germplasm Bank from ...

    African Journals Online (AJOL)

    Particular

    2013-05-15

    May 15, 2013 ... ... fragment length polymorphism; AMOVA, molecular variance analysis. ... are technically simple, suitable for large-scale germplasm ... Brazil, our study aims to evaluate the genetic structure and genetic ... voltage of 100 V for 90 min. Gel was .... which does not justify an extra effort in labor (Bekessy et.

  11. Genetic diversity of Najdi sheep based on microsatellite analysis ...

    African Journals Online (AJOL)

    The prime objective of this research was to measure the genetic polymorphism of main sheep breed of Saudi Arabia, Najdi. Randomly selected 49 blood samples were used to extract the DNA followed by polymerase chain reaction (PCR), using 19 microsatellite markers, which were used to investigate the genetic ...

  12. Genetic diversity and population structure analysis to construct a core collection from a large Capsicum germplasm.

    Science.gov (United States)

    Lee, Hea-Young; Ro, Na-Young; Jeong, Hee-Jin; Kwon, Jin-Kyung; Jo, Jinkwan; Ha, Yeaseong; Jung, Ayoung; Han, Ji-Woong; Venkatesh, Jelli; Kang, Byoung-Cheorl

    2016-11-14

    Conservation of genetic diversity is an essential prerequisite for developing new cultivars with desirable agronomic traits. Although a large number of germplasm collections have been established worldwide, many of them face major difficulties due to large size and a lack of adequate information about population structure and genetic diversity. Core collection with a minimum number of accessions and maximum genetic diversity of pepper species and its wild relatives will facilitate easy access to genetic material as well as the use of hidden genetic diversity in Capsicum. To explore genetic diversity and population structure, we investigated patterns of molecular diversity using a transcriptome-based 48 single nucleotide polymorphisms (SNPs) in a large germplasm collection comprising 3,821 accessions. Among the 11 species examined, Capsicum annuum showed the highest genetic diversity (H E  = 0.44, I = 0.69), whereas the wild species C. galapagoense showed the lowest genetic diversity (H E  = 0.06, I = 0.07). The Capsicum germplasm collection was divided into 10 clusters (cluster 1 to 10) based on population structure analysis, and five groups (group A to E) based on phylogenetic analysis. Capsicum accessions from the five distinct groups in an unrooted phylogenetic tree showed taxonomic distinctness and reflected their geographic origins. Most of the accessions from European countries are distributed in the A and B groups, whereas the accessions from Asian countries are mainly distributed in C and D groups. Five different sampling strategies with diverse genetic clustering methods were used to select the optimal method for constructing the core collection. Using a number of allelic variations based on 48 SNP markers and 32 different phenotypic/morphological traits, a core collection 'CC240' with a total of 240 accessions (5.2 %) was selected from within the entire Capsicum germplasm. Compared to the other core collections, CC240 displayed higher

  13. Genetic diversity characterization of cassava cultivars (Manihot esculenta Crantz.: I RAPD markers

    Directory of Open Access Journals (Sweden)

    Colombo Carlos

    1998-01-01

    Full Text Available RAPD markers were used to investigate the genetic diversity of 31 Brazilian cassava clones. The results were compared with the genetic diversity revealed by botanical descriptors. Both sets of variates revealed identical relationships among the cultivars. Multivariate analysis of genetic similarities placed genotypes destinated for consumption "in nature" in one group, and cultivars useful for flour production in another. Brazil?s abundance of landraces presents a broad dispersion and is consequently an important resource of genetic variability. The botanical descriptors were not able to differentiate thirteen pairs of cultivars compared two-by-two, while only one was not differentiated by RAPD markers. These results showed the power of RAPD markers over botanical descriptors in studying genetic diversity, identifying duplicates, as well as validating, or improving a core collection. The latter is particularly important in this vegetatively propagated crop.

  14. Characterization of genetic diversity of native 'Ancho' chili populations of Mexico using microsatellite markers

    OpenAIRE

    Rocío Toledo-Aguilar; Higinio López-Sánchez; Amalio Santacruz-Varela; Ernestina Valadez-Moctezuma; Pedro A López; Víctor H Aguilar-Rincón; Víctor A González-Hernández; Humberto Vaquera-Huerta

    2016-01-01

    'Ancho' type chilis (Capsicum annuum L. var. annuum) are an important ingredient in the traditional cuisine of Mexico and so are in high demand. It includes six native sub-types with morphological and fruit color differences. However, the genetic diversity of the set of these sub­types has not been determined. The objective of this study was to characterize the genetic diversity of native Mexican ancho chili populations using microsatellites and to determine the relationship among these popul...

  15. Genetic diversity of Pinus halepensis Mill. populations detected by RAPD loci

    OpenAIRE

    Gómez , Aránzazu; Alía , Ricardo; Bueno , María

    2001-01-01

    International audience; Genetic diversity of Pinus halepensis Mill. was analysed in nine populations (six Spanish populations and one each from Tunisia, France and Greece). Twenty four RAPD loci were amplified with 60 megagametophyte DNA samples from each population. Populations' contribution to Nei gene diversity and to allelic richness were calculated. Results showed higher within population genetic variation but also a $G_{{\\rm ST}} = 13.6\\%$ higher than those detected in previous studies ...

  16. Genetic diversity of bats coronaviruses in the Atlantic Forest hotspot biome, Brazil.

    Science.gov (United States)

    Góes, Luiz Gustavo Bentim; Campos, Angélica Cristine de Almeida; Carvalho, Cristiano de; Ambar, Guilherme; Queiroz, Luzia Helena; Cruz-Neto, Ariovaldo Pereira; Munir, Muhammad; Durigon, Edison Luiz

    2016-10-01

    Bats are notorious reservoirs of genetically-diverse and high-profile pathogens, and are playing crucial roles in the emergence and re-emergence of viruses, both in human and in animals. In this report, we identified and characterized previously unknown and diverse genetic clusters of bat coronaviruses in the Atlantic Forest Biome, Brazil. These results highlight the virus richness of bats and their possible roles in the public health. Copyright © 2016 Elsevier B.V. All rights reserved.

  17. Paradox of Genetic Diversity in the Case of Prionic Diseases in Sheep Breeds from Romania

    Directory of Open Access Journals (Sweden)

    Gheorghe Hrinca

    2016-05-01

    Full Text Available The main target of this debate is the revaluation of the biodiversity concept and especially of its significance in the animal husbandry field. The paper analyzes the genetic diversity at the determinant locus of scrapie (PrP in the sheep breeds from Romania: Palas Merino, Tsigai, Tsurcana, Botosani Karakul, Palas Meat Breed and Palas Milk Breed. The prionic genetic diversity (d has been quantified by means of informational energy (e. This study highlights the impact of increasing the genetic diversity from the PrP locus level on the health status of ovine species and especially on human food safety. The informational statistics processing shows that the resistance / susceptibility to scrapie is in relation to the degree of prionic genetic diversity. The limitation of genetic diversity by selecting the individuals possessing the ARR allele in both homozygous status and in combination with alleles ARQ, ARH AHQ confers to sheep herds certain levels of resistance to contamination with scrapie disease. Instead, promoting to reproduction also individuals possessing the VRQ allele in all possible genotypic combinations (including ARR allele increases genetic diversity but also has as effect increasing the susceptibility of sheep to prion disease onset. From the point of view of morbid phenomenon, the Botosani Karakul breed is clearly advantaged compared to all other indigenous sheep breeds from Romania. For methodological coherency in the interpretative context of this issue, the genetic diversity was analyzed in association with the heterozygosity degree of breeds and their Hardy-Weinberg genetic equilibrium at the PrP locus level. Finally, the paper refers to decisions that the improvers must take to achieve the genetic prophylaxis in the scrapie case taking into account the polymorphism degree of prion protein.

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

    Science.gov (United States)

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

    2016-12-01

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

  19. Climatic changes can drive the loss of genetic diversity in a Neotropical savanna tree species.

    Science.gov (United States)

    Lima, Jacqueline S; Ballesteros-Mejia, Liliana; Lima-Ribeiro, Matheus S; Collevatti, Rosane G

    2017-11-01

    The high rates of future climatic changes, compared with the rates reported for past changes, may hamper species adaptation to new climates or the tracking of suitable conditions, resulting in significant loss of genetic diversity. Trees are dominant species in many biomes and because they are long-lived, they may not be able to cope with ongoing climatic changes. Here, we coupled ecological niche modelling (ENM) and genetic simulations to forecast the effects of climatic changes on the genetic diversity and the structure of genetic clusters. Genetic simulations were conditioned to climatic variables and restricted to plant dispersal and establishment. We used a Neotropical savanna tree as species model that shows a preference for hot and drier climates, but with low temperature seasonality. The ENM predicts a decreasing range size along the more severe future climatic scenario. Additionally, genetic diversity and allelic richness also decrease with range retraction and climatic genetic clusters are lost for both future scenarios, which will lead genetic variability to homogenize throughout the landscape. Besides, climatic genetic clusters will spatially reconfigure on the landscape following displacements of climatic conditions. Our findings indicate that climate change effects will challenge population adaptation to new environmental conditions because of the displacement of genetic ancestry clusters from their optimal conditions. © 2017 John Wiley & Sons Ltd.

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

    Directory of Open Access Journals (Sweden)

    Özlem ÖZBEK

    2013-02-01

    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.

  1. The DNA of coral reef biodiversity: predicting and protecting genetic diversity of reef assemblages.

    Science.gov (United States)

    Selkoe, Kimberly A; Gaggiotti, Oscar E; Treml, Eric A; Wren, Johanna L K; Donovan, Mary K; Toonen, Robert J

    2016-04-27

    Conservation of ecological communities requires deepening our understanding of genetic diversity patterns and drivers at community-wide scales. Here, we use seascape genetic analysis of a diversity metric, allelic richness (AR), for 47 reef species sampled across 13 Hawaiian Islands to empirically demonstrate that large reefs high in coral cover harbour the greatest genetic diversity on average. We found that a species's life history (e.g. depth range and herbivory) mediates response of genetic diversity to seascape drivers in logical ways. Furthermore, a metric of combined multi-species AR showed strong coupling to species richness and habitat area, quality and stability that few species showed individually. We hypothesize that macro-ecological forces and species interactions, by mediating species turnover and occupancy (and thus a site's mean effective population size), influence the aggregate genetic diversity of a site, potentially allowing it to behave as an apparent emergent trait that is shaped by the dominant seascape drivers. The results highlight inherent feedbacks between ecology and genetics, raise concern that genetic resilience of entire reef communities is compromised by factors that reduce coral cover or available habitat, including thermal stress, and provide a foundation for new strategies for monitoring and preserving biodiversity of entire reef ecosystems. © 2016 The Authors.

  2. Genetic diversity and structure analysis based on hordein protein polymorphism in barley landrace populations from jordan

    International Nuclear Information System (INIS)

    Baloch, A.W.; Ali, M.; Baloch, A.M.; Mangan, B.U.N.; Song, W

    2014-01-01

    Jordan is unanimously considered to be one of the centers of genetic diversity for barley, where wild and landraces of barley has been grown under different climatic conditions. The genetic diversity and genetic structure based on hordein polymorphism was assessed in 90 different accessions collected from four different sites of Jordan. A-PAGE was used to reveal hordein polymorphism among the genotypes. A total of 29 distinct bands were identified, out of them 9 bands were distinguished for D, 11 for C, and 9 for the B hordein regions. The observed genetic similarity was an exceptionally high between the populations than expected, which is probably due to high gene flow estimated between them. The genetic diversity parameters were not differ largely among the populations, indicating that local selection of a particular site did not play a key role in shaping genetic diversity. Analysis of molecular variance (AMOVA) revealed significant population structure when accessions were structured according to population site. There was 94% of hordein variation resided within the populations and only 8% present among the populations. Both Bayesian and Principale Coordinate Analysis (PCoA) concordantly demonstrated admixture genotypes of the landraces barley populations. Consequently, none of the population found to be clustered separately according to its population site. It is concluded that this approach can be useful to explore the germplasm for genetic diversity but perhaps is not suitable for determining phylogenic relations in barley. (author)

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

    Science.gov (United States)

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

    2012-01-01

    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

  4. Genetic diversity of five goat breeds in China based on microsatellite ...

    African Journals Online (AJOL)

    The mean heterozygosity (H) of the populations ranged from 0.7936 to 0.8202. The mean number of effective allele (Ne) of the populations ranged from 5.3373 to 5.8812 and the coefficient of genetic differentiation between breeds was 0.0620. It was suggested that the five goat populations have abundant genetic diversity ...

  5. Evaluation of genetic diversity of Panicum turgidum Forssk from Saudi Arabia.

    Science.gov (United States)

    Assaeed, Abdulaziz M; Al-Faifi, Sulieman A; Migdadi, Hussein M; El-Bana, Magdy I; Al Qarawi, Abdulaziz A; Khan, Mohammad Altaf

    2018-01-01

    The genetic diversity of 177 accessions of Panicum turgidum Forssk, representing ten populations collected from four geographical regions in Saudi Arabia, was analyzed using amplified fragment length polymorphism (AFLP) markers. A set of four primer-pairs with two/three selective nucleotides scored 836 AFLP amplified fragments (putative loci/genome landmarks), all of which were polymorphic. Populations collected from the southern region of the country showed the highest genetic diversity parameters, whereas those collected from the central regions showed the lowest values. Analysis of molecular variance (AMOVA) revealed that 78% of the genetic variability was attributable to differences within populations. Pairwise values for population differentiation and genetic structure were statistically significant for all variances. The UPGMA dendrogram, validated by principal coordinate analysis-grouped accessions, corresponded to the geographical origin of the accessions. Mantel's test showed that there was a significant correlation between the genetic and geographical distances ( r  = 0.35, P  < 0.04). In summary, the AFLP assay demonstrated the existence of substantial genetic variation in P. turgidum . The relationship between the genetic diversity and geographical source of P. turgidum populations of Saudi Arabia, as revealed through this comprehensive study, will enable effective resource management and restoration of new areas without compromising adaptation and genetic diversity.

  6. Analysis of genetic diversity of Piper spp. in Hainan Island (China ...

    African Journals Online (AJOL)

    Inter-simple sequence repeat (ISSR) analysis was used to evaluate the genetic variation of Piper spp. from Hainan, China. 247 polymorphic bands out of a total of 248 (99.60%) were generated from 74 individual plants of Piper spp. The overall level of genetic diversity among Piper spp. in Hainan was high, with the mean ...

  7. Genetic diversity based on SSR markers in maize (Zea mays L.)

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 87; Issue 3. Genetic diversity based on SSR markers in maize (Zea mays L.) landraces from Wuling mountain region in China. Yao Qi-Lun Fang Ping Kang Ke-Cheng Pan Guang-Tang. Research Note Volume 87 Issue 3 December 2008 pp 287-291 ...

  8. Genetic diversity of Dyera polyphylla (Miq.) Steenis populations used in tropical peatland restoration in Indonesia

    NARCIS (Netherlands)

    Tata, Hesti Lestari; Muchugi, A.; Kariba, R.; Noordwijk, van M.

    2018-01-01

    Dyera polyphylla is a native tree species of peat swamp forests in Southeast Asia. Where it has been used in peatland restoration, the trees are of uncertain genetic origin. We analysed the genetic diversity of seven populations of D. polyphylla (9–20 individual trees per population) from both

  9. [Genetic diversity analysis of Andrographis paniculata in China based on SRAP and SNP].

    Science.gov (United States)

    Chen, Rong; Wang, Xiao-Yun; Song, Yu-Ning; Zhu, Yun-feng; Wang, Peng-liang; Li, Min; Zhong, Guo-Yue

    2014-12-01

    In order to reveal genetic diversity of domestic Andrographis paniculata and its impact on quality, genetic backgrounds of 103 samples from 7 provinces in China were analyzed using SRAP marker and SNP marker. Genetic structures of the A. paniculata populations were estimated with Powermarker V 3.25 and Mega 6.0 software, and polymorphic SNPs were identified with CodonCode Aligner software. The results showed that the genetic distances of domestic A. paniculata germplasm ranged from 0. 01 to 0.09, and no polymorphic SNPs were discovered in coding sequence fragments of ent-copalyl diphosphate synthase. A. paniculata germplasm from various regions in China had poor genetic diversity. This phenomenon was closely related to strict self-fertilization and earlier introduction from the same origin. Therefore, genetic background had little impact on variable qualities of A. paniculata in domestic market. Mutation breeding, polyploid breeding and molecular breeding were proposed as promising strategies in germplasm innovation.

  10. Genetic diversity in pigeonpea [Cajanus cajan (L.) Millsp ...

    African Journals Online (AJOL)

    USER

    2010-05-31

    May 31, 2010 ... India and a presumed secondary centre of diversity in East Africa were evaluated using six microsatellite ... Other growing regions include Southeast Asia, Central ...... adaptation to environmental or cultural practices. The.

  11. Analysis of genetic diversity and population structure in upland ...

    Indian Academy of Sciences (India)

    Mulugeta Seyoum

    2018-06-09

    Jun 9, 2018 ... diversity and population structure at DNA level, 302 elite upland cotton germplasm accessions ...... conservation of cotton germplasm in China (English abstract). ... and Alishah O. 2011 Inter simple sequence repeats (ISSR).

  12. Genetic diversity among natural populations of Ottelia acuminata ...

    African Journals Online (AJOL)

    PRECIOUS

    2009-11-16

    Nov 16, 2009 ... is essential for establishing effective and efficient conser- vation and breeding ... overlaid with 40 µl mineral oil. Amplifications were .... Diversity for Nineteen Populations of Pinus sibirica Du Tour with. Technique of ISSR.

  13. The genetic diversity and population structure of common bean ...

    African Journals Online (AJOL)

    SAM

    2014-07-16

    Jul 16, 2014 ... polymorphic molecular markers for use in hybridization and variety development. Genomic ... The model-based cluster analysis of SSR diversity in the ...... clusters of individuals using the software STRUCTURE: A simulation.

  14. RAPD analysis for genetic diversity of two populations of Mystus ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-09-01

    Sep 1, 2009 ... and other aquatic ecosystem and the ecological complexes. ... is a property at the population level while the functional diversity concept ... warm water fish species, which are distributed all over the world. ..... Phylogenetic.

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

    NARCIS (Netherlands)

    van de Wouw, M.J.; Van Dijk, P.J.; Huiskes, A.H.L.

    2008-01-01

    Aim To determine patterns in diversity of a major Antarctic plant species, including relationships of Antarctic populations with those outside the Antarctic zone. Location Antarctic Peninsula, Maritime Antarctica, sub-Antarctic islands, Falkland Islands and South America. Methods Amplified fragment

  16. Genetic diversity in rhizobial isolates determined by RAPDs

    African Journals Online (AJOL)

    STORAGESEVER

    2009-06-17

    Jun 17, 2009 ... diversity. It was found that Rhizobium isolates from Agricultural Research Station - Aliyar Nagar ... establish effective nitrogen fixing symbiosis system with .... package (Numerical taxonomy analysis program package, Exeter.

  17. Genetic diversity of Chrysichthys nigrodigitatus in the Lagos lagoon ...

    African Journals Online (AJOL)

    s

    2012-11-13

    Nov 13, 2012 ... polymerase chain reaction (PCR); CHOBA, Chrysichthys nigrodigitatus .... PRE had the highest value for nucleotide diversity followed by LAG. .... Amazon Basin offers preliminary evidence for the first case of. “homing” for an ...

  18. Comparative results of RAPD and ISSR markers for genetic diversity ...

    African Journals Online (AJOL)

    PRECIOUS

    the mean level of genetic similarity with populations of M. baccifera by using RAPD .... The statistical data for 9 RAPD and 17 ISSR primers used for analyzing 12 accessions of M. .... (Numerical Taxonomy and Multivariate Analysis System, Bio-.

  19. Assessing the genetic diversity of 48 groundnut (Arachis hypogaea L.)

    African Journals Online (AJOL)

    Richard

    2015-08-12

    Aug 12, 2015 ... genetic variations in cultivated crops, especially groundnut. Key words: Phenotypic traits, DNA extraction, PCR amplification, simple sequence repeats ..... of N2 fixation in groundnut (Arachis hypogaea L.) and cowpea (Vigna.

  20. Genetic diversity analysis of Labeo gonius (Hamilton, 1822) in three ...

    African Journals Online (AJOL)

    a

    2013-05-08

    May 8, 2013 ... tool to characterize population-level genetic variation in various fish species ... rise to protein variants called allozymes that differ slightly in electric charges. ..... Black Sea Coast. Acta zool. Bulg. ... Inc., Florida, USA. 350 pp.

  1. Species and genetic diversity in the genus Drosophila inhabiting the ...

    Indian Academy of Sciences (India)

    BASHISTH N. SINGH∗. Genetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi 221 005, India .... resource of food which they get from urban refuse. Similarly, ... Drosophila Information Service (USA). On the basis of.

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

    African Journals Online (AJOL)

    Dr.Ola

    2013-05-15

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

  3. Phenotypic and molecular evaluation of genetic diversity of rapeseed

    African Journals Online (AJOL)

    STORAGESEVER

    2009-10-05

    Oct 5, 2009 ... basis of elite oilseed rape breeding material has been narrowed by an intensive .... breeding programs was the basic reason for detailed genetic analysis. ...... A periodical of Scientific Research on Field and. Vegetable Crops ...

  4. Genetic diversity of Pogonatherum paniceum (Lam.) Hack in ...

    African Journals Online (AJOL)

    STORAGESEVER

    2010-03-08

    # ... Significant correlation between genetic and geographic altitude distances among populations was found by Mantel test. The high score ..... extreme growth conditions such as arid surface of bare rock. These biological and ...

  5. Assessment of genetic diversity among maize accessions using inter ...

    African Journals Online (AJOL)

    NRCC

    2011-11-07

    Nov 7, 2011 ... Key words: Zea mays, Tripsacum sp., genetic narrowing, gene pool, DNA markers. INTRODUCTION ... coding, genomic mapping and evolutionary biology (Reddy et al., 2002). ... (http://www.r-project.org). RESULTS AND ...

  6. Comparative evaluation of genetic diversity using RAPD, SSR and ...

    Indian Academy of Sciences (India)

    1Department of Molecular Biology and Genetic Engineering, 2Ranichauri Hill Campus, G. B. Pant University of Agriculture ... Comparison of RAPD, SSR and cytochrome P450 gene based markers, in terms of the ...... project programme.

  7. Evaluation of genetic diversity between toxic and non toxic Jatropha ...

    African Journals Online (AJOL)

    Massimo

    Indian varieties and a non-toxic variety of Mexican origin by means of about 400 RAPD ... evaluate the level of polymorphism and the capacity to discriminate between the ..... Population genetic software for teaching and research. Mol. Ecol.

  8. Genetic diversity assessment of farmers' and improved potato ...

    African Journals Online (AJOL)

    Biniam M

    2016-08-31

    Aug 31, 2016 ... 2010) but with the new molecular technologies in breeding programs ... genetic characterization with each having its own pros and cons (Nováková et al., 2010). Simple ..... Education Commission for funding the field work and.

  9. Genetic diversity in Nigerian brinjal eggplant (Solanum melongena L.)

    African Journals Online (AJOL)

    SAM

    2014-05-21

    May 21, 2014 ... because previous studies to establish genetic relationships among taxa are mainly based on ... bility, morphological data can lead to ambiguous interpre- .... Big. Base bigger than top. 004. Dark Purple. Big. Flat with wide base.

  10. Genetic diversity analysis in the Hypericum perforatum populations ...

    African Journals Online (AJOL)

    user

    2014-01-01

    Jan 1, 2014 ... 2Cancer Genetics Lab, Department of Biochemistry, Maulana Azad Medical College and Associated ... sciatica and depression (Ghasemi et al., 2013; Barnes et .... environmental factors for each sampling site were also.

  11. Molecular evaluation of genetic diversity and association studies in ...

    Indian Academy of Sciences (India)

    2012-04-05

    Apr 5, 2012 ... Phenotypic data were collected for yield and component traits. Pattern of ...... ical isolation, evolutionary time gaps, mutation, selection and genetic drift ..... along chromosome 1 of maize (Zea mays ssp. mays L.). Proc. Natl.

  12. Phylogeography, genetic diversity and demographic history of the ...

    Indian Academy of Sciences (India)

    FATAH ZAREI

    loop region of individuals representing four Kurdish groups from Iran .... research studies were performed on the origin and genetic landscape of the Kurds, ... haplogroups were determined on the basis of diagnostic sites using the PhyloTree 16 ...

  13. Genetic diversity and population structure of maize landraces from ...

    African Journals Online (AJOL)

    pc

    2016-11-02

    Nov 2, 2016 ... useful in selection. The cross between two individuals from different groups might help exploit the ... primers used are labeled with different colored .... with a view to detect a structuring of accessions in genetically different ...

  14. Genetic diversity of indigenous chicken ecotypes in Jordan

    African Journals Online (AJOL)

    Jane

    2010-10-11

    Oct 11, 2010 ... DNA polymorphism of 4 indigenous chicken ecotypes was assessed in Jordan using random amplified ... Such technology is random amplified polymorphic DNA. (RAPD) ..... ping from genetics lab for animal and plant at MU.

  15. Genetic diversity in Egyptian and Saudi goat breeds using ...

    African Journals Online (AJOL)

    SARAH

    2013-12-30

    Dec 30, 2013 ... rational breeding strategy for genetic improvement of goats in Egypt and Saudi Arabia. The studied. Mediterranean breeds sampled from African and Asian populations seem to have ..... West Asia and North Africa, Vol. 2.

  16. Genetic diversity analysis of various red spider mite- resistant ...

    African Journals Online (AJOL)

    User

    2011-05-02

    May 2, 2011 ... 3Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Ya'an, 625014, P. R. ... Random amplified polymorphic DNA (RAPD) is a DNA ..... spider mite-resistant, bumper, high-quality and disease-.

  17. An understanding of the underlying genetic diversity within and ...

    African Journals Online (AJOL)

    AMuchugi

    2016-08-03

    AFLP). Four primer ... outcrossing and pollinated by small bees (e.g. Trigona) and other insects ... for assessing plants' genetic resources by improving our ..... populations of tropical trees and cultivated trees Meru oak (Vitex ...

  18. Molecular genetic diversity in cocoa clones with potential for ...

    African Journals Online (AJOL)

    Adeilson

    2016-11-02

    Nov 2, 2016 ... This study aimed to assess the genetic variability in groups of 11 ... INTRODUCTION .... Iquitos Maraño (or Mixed) Calabacilo ... method (Doyle and Doyle, 1990; Bertolde et al., 2010). ..... Further studies on a concise list of.

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

    Directory of Open Access Journals (Sweden)

    Jorge Assis

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

  20. Inbreeding and Genetic Diversity in Three Imported Swine Breeds in China Using Pedigree Data

    Directory of Open Access Journals (Sweden)

    G. Q. Tang

    2013-06-01

    Full Text Available The accumulation of inbreeding and the loss of genetic diversity is a potential problem in the modern swine breeds in China. Therefore, the purpose of this study was to analyze the pedigrees of Chinese Duroc (CD, Landrace (CL and Yorkshire (CY swine to estimate the past and current rates of inbreeding, and to identify the main causes of genetic diversity loss. Pedigree files from CD, CL and CY containing, 4529, 16,776 and 22,600 records, respectively, were analyzed. Pedigree completeness indexes of the three breeds, accounting for one generation back, were 83.72, 93.93 and 93.59%, respectively. The estimated average annual inbreeding rates for CD, CL and CY in recent three years were 0.21, 0.19 and 0.13%, respectively. The estimated average percentage of genetic diversity loss within each breed in recent three years was about 8.92, 2.19, and 3.36%, respectively. The average relative proportion of genetic diversity loss due to unequal contributions of founders in CD, CL and CY was 69.09, 57.95 and 60.57%, and due to random genetic drift was 30.91, 42.05 and 39.43%, respectively. The estimated current effective population size for CD, CL and CY was 76, 117 and 202, respectively. Therefore, CD has been found to have lost considerable genetic diversity, demanding priority for optimizing the selection and mating to control future coancestry and inbreeding. Unequal contribution of founders was a major cause of genetic diversity loss in Chinese swine breeds and random genetic drift also showed substantial impact on the loss of diversity.

  1. Genetic Diversity of Selected Mangifera Species Revealed by Inter Simple Sequence Repeats Markers

    OpenAIRE

    Ariffin, Zulhairil; Md Sah, Muhammad Shafie; Idris, Salma; Hashim, Nuradni

    2015-01-01

    ISSR markers were employed to reveal genetic diversity and genetic relatedness among 28 Mangifera accessions collected from Yan (Kedah), Bukit Gantang (Perak), Sibuti (Sarawak), and Papar (Sabah). A total of 198 markers were generated using nine anchored primers and one nonanchored primer. Genetic variation among the 28 accessions of Mangifera species including wild relatives, landraces, and clonal varieties is high, with an average degree of polymorphism of 98% and mean Shannon index, H0=7.5...

  2. Genetic Diversity and Population Structure of Mesoamerican Jaguars (Panthera onca): Implications for Conservation and Management.

    Science.gov (United States)

    Wultsch, Claudia; Caragiulo, Anthony; Dias-Freedman, Isabela; Quigley, Howard; Rabinowitz, Salisa; Amato, George

    2016-01-01

    Mesoamerican jaguars (Panthera onca) have been extirpated from over 77% of their historic range, inhabiting fragmented landscapes at potentially reduced population sizes. Maintaining and restoring genetic diversity and connectivity across human-altered landscapes has become a major conservation priority; nonetheless large-scale genetic monitoring of natural populations is rare. This is the first regional conservation genetic study of jaguars to primarily use fecal samples collected in the wild across five Mesoamerican countries: Belize, Costa Rica, Guatemala, Honduras, and Mexico. We genotyped 445 jaguar fecal samples and examined patterns of genetic diversity and connectivity among 115 individual jaguars using data from 12 microsatellite loci. Overall, moderate levels of genetic variation were detected (NA = 4.50 ± 1.05, AR = 3.43 ± 0.22, HE = 0.59 ± 0.04), with Mexico having the lowest genetic diversity, followed by Honduras, Guatemala, Belize, and Costa Rica. Population-based gene flow measures (FST = 0.09 to 0.15, Dest = 0.09 to 0.21), principal component analysis, and Bayesian clustering applied in a hierarchical framework revealed significant genetic structure in Mesoamerican jaguars, roughly grouping individuals into four genetic clusters with varying levels of admixture. Gene flow was highest among Selva Maya jaguars (northern Guatemala and central Belize), whereas genetic differentiation among all other sampling sites was moderate. Genetic subdivision was most pronounced between Selva Maya and Honduran jaguars, suggesting limited jaguar movement between these close geographic regions and ultimately refuting the hypothesis of contemporary panmixia. To maintain a critical linkage for jaguars dispersing through the Mesoamerican landscape and ensure long-term viability of this near threatened species, we recommend continued management and maintenance of jaguar corridors. The baseline genetic data provided by this study underscores the importance of

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

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    Alexandra Erfmeier

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

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

    Science.gov (United States)

    Erfmeier, Alexandra; Hantsch, Lydia; Bruelheide, Helge

    2013-01-01

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

  5. Increased Mitochondrial Genetic Diversity in Persons Infected With Hepatitis C VirusSummary

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    David S. Campo

    2016-09-01

    Full Text Available Background & Aims: The host genetic environment contributes significantly to the outcomes of hepatitis C virus (HCV infection and therapy response, but little is known about any effects of HCV infection on the host beyond any changes related to adaptive immune responses. HCV persistence is associated strongly with mitochondrial dysfunction, with liver mitochondrial DNA (mtDNA genetic diversity linked to disease progression. Methods: We evaluated the genetic diversity of 2 mtDNA genomic regions (hypervariable segments 1 and 2 obtained from sera of 116 persons using next-generation sequencing. Results: Results were as follows: (1 the average diversity among cases with seronegative acute HCV infection was 4.2 times higher than among uninfected controls; (2 the diversity level among cases with chronic HCV infection was 96.1 times higher than among uninfected controls; and (3 the diversity was 23.1 times higher among chronic than acute cases. In 2 patients who were followed up during combined interferon and ribavirin therapy, mtDNA nucleotide diversity decreased dramatically after the completion of therapy in both patients: by 100% in patient A after 54 days and by 70.51% in patient B after 76 days. Conclusions: HCV infection strongly affects mtDNA genetic diversity. A rapid decrease in mtDNA genetic diversity observed after therapy-induced HCV clearance suggests that the effect is reversible, emphasizing dynamic genetic relationships between HCV and mitochondria. The level of mtDNA nucleotide diversity can be used to discriminate recent from past infections, which should facilitate the detection of recent transmission events and thus help identify modes of transmission. Keywords: Disease Biomarkers, mtDNA, Noninvasive

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

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    Melissa D Conrad

    Full Text Available 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 appropriate tools. The development of a panel of microsatellite makers and SNPs from mining the parasite's genome sequence has paved the way to a global analysis of the genetic structure of the pathogen and association with clinical phenotypes.Here we utilize a panel of T. vaginalis-specific genetic markers to genotype 235 isolates from Mexico, Chile, India, Australia, Papua New Guinea, Italy, Africa and the United States, including 19 clinical isolates recently collected from 270 women attending New York City sexually transmitted disease clinics. Using population genetic analysis, we show that T. vaginalis is a genetically diverse parasite with a unique population structure consisting of two types present in equal proportions world-wide. Parasites belonging to the two types (type 1 and type 2 differ significantly in the rate at which they harbor the T. vaginalis virus, a dsRNA virus implicated in parasite pathogenesis, and in their sensitivity to the widely-used drug, metronidazole. We also uncover evidence of genetic exchange, indicating a sexual life-cycle of the parasite despite an absence of morphologically-distinct sexual stages.Our study represents the first robust and comprehensive evaluation of global T. vaginalis genetic diversity and population structure. Our identification of a unique two-type structure, and the clinically relevant phenotypes associated with them, provides a new dimension for understanding T. vaginalis pathogenesis. In addition, our demonstration of the possibility of genetic exchange in the parasite has important implications for genetic research and control of the disease.

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

    Science.gov (United States)

    Conrad, Melissa D; Gorman, Andrew W; Schillinger, Julia A; Fiori, Pier Luigi; Arroyo, Rossana; Malla, Nancy; Dubey, Mohan Lal; Gonzalez, Jorge; Blank, Susan; Secor, William E; Carlton, Jane M

    2012-01-01

    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 appropriate tools. The development of a panel of microsatellite makers and SNPs from mining the parasite's genome sequence has paved the way to a global analysis of the genetic structure of the pathogen and association with clinical phenotypes. Here we utilize a panel of T. vaginalis-specific genetic markers to genotype 235 isolates from Mexico, Chile, India, Australia, Papua New Guinea, Italy, Africa and the United States, including 19 clinical isolates recently collected from 270 women attending New York City sexually transmitted disease clinics. Using population genetic analysis, we show that T. vaginalis is a genetically diverse parasite with a unique population structure consisting of two types present in equal proportions world-wide. Parasites belonging to the two types (type 1 and type 2) differ significantly in the rate at which they harbor the T. vaginalis virus, a dsRNA virus implicated in parasite pathogenesis, and in their sensitivity to the widely-used drug, metronidazole. We also uncover evidence of genetic exchange, indicating a sexual life-cycle of the parasite despite an absence of morphologically-distinct sexual stages. Our study represents the first robust and comprehensive evaluation of global T. vaginalis genetic diversity and population structure. Our identification of a unique two-type structure, and the clinically relevant phenotypes associated with them, provides a new dimension for understanding T. vaginalis pathogenesis. In addition, our demonstration of the possibility of genetic exchange in the parasite has important implications for genetic research and control of the disease.

  8. Analysis of Genetic Diversity of Two Mangrove Species with Morphological Alterations in a Natural Environment

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    Catarina Fonseca Lira-Medeiros

    2015-04-01

    Full Text Available Mangrove is an ecosystem subjected to tide, salinity and nutrient variations. These conditions are stressful to most plants, except to mangrove plants that are well-adapted. However, many mangrove areas have extremely stressful conditions, such as salt marshes, and the plants nearby usually present morphological alterations. In Sepetiba Bay, two species of mangrove plants, Avicennia schaueriana and Laguncularia racemosa, have poor development near a salt marsh (SM compared to plants at the riverside (RS, which is considered a favorable habitat in mangroves. The level of genetic diversity and its possible correlation with the morphological divergence of SM and RS plants of both species were assessed by AFLP molecular markers. We found moderate genetic differentiation between A. schaueriana plants from SM and RS areas and depleted genetic diversity on SM plants. On the other hand, Laguncularia racemosa plants had no genetic differentiation between areas. It is possible that a limited gene flow among the studied areas might be acting more intensely on A. schaueriana plants, resulting in the observed genetic differentiation. The populations of Laguncularia racemosa appear to be well connected, as genetic differentiation was not significant between the SM and RS populations. Gene flow and genetic drift are acting on neutral genetic diversity of these two mangrove species in the studied areas, and the observed genetic differentiation of A. schaueriana plants might be correlated with its morphological variation. For L. racemosa, morphological alterations could be related to epigenetic phenomena or adaptive loci polymorphism that should be further investigated.

  9. Curcumin profiing and genetic diversity of different accessions of Curcuma longa L.

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    Neelam Arya

    2016-01-01

    Full Text Available Objective: To investigate the genetic diversity and variation in active compound of turmeric rhizomes collected from different niches of Uttarakhand. Methods: Genetic diversity and relationship of Curcuma longa accessions was evaluated by random amplification polymorphism DNA analysis and curcumin profiling was evaluated by high performance liquid chromatography method. Results: The curcumin contents in 20 accessions of turmeric rhizomes were found to be in the range of 0.90% to 3.26%. All accessions were separated into six groups (92% genetic similarity by using 10 decamer oligonucleotide primers for the amplification of genomic DNA. Conclusions: The results indicated the possibility of selecting high quality clones for large scale production.

  10. Analysis of genetic diversity of certain species of Piper using RAPD-based molecular markers.

    Science.gov (United States)

    Chowdhury, Utpal; Tanti, Bhaben; Rethy, Parakkal; Gajurel, Padma Raj

    2014-09-01

    The utility of RAPD markers in assessing genetic diversity and phenetic relationships of six different species of Piper from Northeast India was investigated. Polymerase chain reaction (PCR) with four arbitrary 10-mer oligonucleotide primers applied to the six species produced a total of 195 marker bands, of which, 159 were polymorphic. On average, six RAPD fragments were amplified per reaction. In the UPGMA phenetic dendrogram based on Jaccard's coefficient, the different accessions of Piper showed a high level of genetic variation. This study may be useful in identifying diverse genetic stocks of Piper, which may then be conserved on a priority basis.

  11. Genetic diversity of popcorn genotypes using molecular analysis.

    Science.gov (United States)

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

    2015-08-19

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

  12. Genotyping-By-Sequencing for Plant Genetic Diversity Analysis: A Lab Guide for SNP Genotyping

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    Gregory W. Peterson

    2014-10-01

    Full Text Available Genotyping-by-sequencing (GBS has recently emerged as a promising genomic approach for exploring plant genetic diversity on a genome-wide scale. However, many uncertainties and challenges remain in the application of GBS, particularly in non-model species. Here, we present a GBS protocol we developed and use for plant genetic diversity analysis. It uses two restriction enzymes to reduce genome complexity, applies Illumina multiplexing indexes for barcoding and has a custom bioinformatics pipeline for genotyping. This genetic diversity-focused GBS (gd-GBS protocol can serve as an easy-to-follow lab guide to assist a researcher through every step of a GBS application with five main components: sample preparation, library assembly, sequencing, SNP calling and diversity analysis. Specifically, in this presentation, we provide a brief overview of the GBS approach, describe the gd-GBS procedures, illustrate it with an application to analyze genetic diversity in 20 flax (Linum usitatissimum L. accessions and discuss related issues in GBS application. Following these lab bench procedures and using the custom bioinformatics pipeline, one could generate genome-wide SNP genotype data for a conventional genetic diversity analysis of a non-model plant species.

  13. Stable genetic diversity despite parasite and pathogen spread in honey bee colonies

    Science.gov (United States)

    Jara, Laura; Muñoz, Irene; Cepero, Almudena; Martín-Hernández, Raquel; Serrano, José; Higes, Mariano; De la Rúa, Pilar

    2015-10-01

    In the last decades, the rapid spread of diseases, such as varroosis and nosemosis, associated with massive honey bee colonies mortality around the world has significantly decreased the number and size of honey bee populations and possibly their genetic diversity. Here, we compare the genetic diversity of Iberian honey bee colonies in two samplings performed in 2006 and 2010 in relation to the presence of the pathogenic agents Nosema apis, Nosema ceranae, and Varroa destructor in order to determine whether parasite and pathogen spread in honey bee colonies reflects changes in genetic diversity. We found that the genetic diversity remained similar, while the incidence of N. ceranae increased and the incidence of N. apis and V. destructor decreased slightly. These results indicate that the genetic diversity was not affected by the presence of these pathogenic agents in the analyzed period. However, the two groups of colonies with and without Nosema/Varroa detected showed significant genetic differentiation (G test). A detailed analysis of the allelic segregation of microsatellite loci in Nosema/Varroa-negative colonies and parasitized ones revealed two outlier loci related to genes involved in immune response.

  14. Stable genetic diversity despite parasite and pathogen spread in honey bee colonies.

    Science.gov (United States)

    Jara, Laura; Muñoz, Irene; Cepero, Almudena; Martín-Hernández, Raquel; Serrano, José; Higes, Mariano; De la Rúa, Pilar

    2015-10-01

    In the last decades, the rapid spread of diseases, such as varroosis and nosemosis, associated with massive honey bee colonies mortality around the world has significantly decreased the number and size of honey bee populations and possibly their genetic diversity. Here, we compare the genetic diversity of Iberian honey bee colonies in two samplings performed in 2006 and 2010 in relation to the presence of the pathogenic agents Nosema apis, Nosema ceranae, and Varroa destructor in order to determine whether parasite and pathogen spread in honey bee colonies reflects changes in genetic diversity. We found that the genetic diversity remained similar, while the incidence of N. ceranae increased and the incidence of N. apis and V. destructor decreased slightly. These results indicate that the genetic diversity was not affected by the presence of these pathogenic agents in the analyzed period. However, the two groups of colonies with and without Nosema/Varroa detected showed significant genetic differentiation (G test). A detailed analysis of the allelic segregation of microsatellite loci in Nosema/Varroa-negative colonies and parasitized ones revealed two outlier loci related to genes involved in immune response.

  15. Genetic Diversity Analysis in 27 Tomato Accessions Using Morphological and Molecular Markers

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    Catur Herison

    2018-02-01

    Full Text Available Genetic diversity is the most important aspect in tomato breeding activities. Better assessment on the diversity of the collected accessions will come up with better result of the cultivar development. This study aimed at analyzing the genetic diversity of 27 tomato accessions by morphological and molecular markers. Twenty seven accessions collected from various regions of Indonesia were planted in the field and evaluated for their morphological traits, and RAPD analyzed for their molecular markers. The UPGMA clustering analyzes, elaborating the combination of morphological and molecular data, indicated that the tomato accessions could be grouped into 5 major groups with 70 % genetic similarity levels. Current study indicated that although many accessions came from different locations, they congregated into the same group. Cherry, Kudamati 1 and Lombok 3 were the farthest genetic distant accessions to the others. Those three genotypes will be the most valuable accessions, when they were crossed with other accessions, for designing a prospective breeding program in the future.

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

    Science.gov (United States)

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

    2017-09-21

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

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

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    Toraj KHABIRI

    2013-02-01

    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 ω type of geliadins. Conversely, the lowest number of bands were pertained to the β 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 β type while, the lowest one was belonged to ω type. Cluster analysis using complete linkage method divided populations into two separated groups in which genetic diversity does not follow from geographical distribution.

  18. Genetic diversity and population structure of Sitodiplosis mosellana in Northern China.

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    Yun Duan

    Full Text Available The wheat midge, Sitodiplosis mosellana, is an important pest in Northern China. We tested the hypothesis that the population structure of this species arises during a range expansion over the past 30 years. This study used microsatellite and mitochondrial loci to conduct population genetic analysis of S. mosellana across its distribution range in China. We found strong genetic structure among the 16 studied populations, including two genetically distinct groups (the eastern and western groups, broadly consistent with the geography and habitat fragmentation. These results underline the importance of natural barriers in impeding dispersal and gene flow of S. mosellana populations. Low to moderate genetic diversity among the populations and moderate genetic differentiation (F ST = 0.117 between the two groups were also found. The populations in the western group had lower genetic diversity, higher genetic differentiation and lower gene flow (F ST = 0.116, Nm = 1.89 than those in the eastern group (F ST = 0.049, Nm = 4.91. Genetic distance between populations was positively and significantly correlated with geographic distance (r = 0.56, P<0.001. The population history of this species provided no evidence for population expansion or bottlenecks in any of these populations. Our data suggest that the distribution of genetic diversity, genetic differentiation and population structure of S. mosellana have resulted from a historical event, reflecting its adaptation to diverse habitats and forming two different gene pools. These results may be the outcome of a combination of restricted gene flow due to geographical and environmental factors, population history, random processes of genetic drift and individual dispersal patterns. Given the current risk status of this species in China, this study can offer useful information for forecasting outbreaks and designing effective pest management programs.

  19. Low genetic diversity and minimal population substructure in the endangered Florida manatee: implications for conservation

    Science.gov (United States)

    Tucker, Kimberly Pause; Hunter, Margaret E.; Bonde, Robert K.; Austin, James D.; Clark, Ann Marie; Beck, Cathy A.; McGuire, Peter M.; Oli, Madan K.

    2012-01-01

    Species of management concern that have been affected by human activities typically are characterized by low genetic diversity, which can adversely affect their ability to adapt to environmental changes. We used 18 microsatellite markers to genotype 362 Florida manatees (Trichechus manatus latirostris), and investigated genetic diversity, population structure, and estimated genetically effective population size (Ne). The observed and expected heterozygosity and average number of alleles were 0.455 ± 0.04, 0.479 ± 0.04, and 4.77 ± 0.51, respectively. All measures of Florida manatee genetic diversity were less than averages reported for placental mammals, including fragmented or nonideal populations. Overall estimates of differentiation were low, though significantly greater than zero, and analysis of molecular variance revealed that over 95% of the total variance was among individuals within predefined management units or among individuals along the coastal subpopulations, with only minor portions of variance explained by between group variance. Although genetic issues, as inferred by neutral genetic markers, appear not to be critical at present, the Florida manatee continues to face demographic challenges due to anthropogenic activities and stochastic factors such as red tides, oil spills, and disease outbreaks; these can further reduce genetic diversity of the manatee population.

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

    International Nuclear Information System (INIS)

    Chen, Shao-Bo; Ding, When-Young; Qiu, Jia-Biao; Wang, Guang-Yin; Zhou, Zhi-Min; Chen- Jiao-Fei; Ai, Wewi-ming; Wang, Cheng-Yi; Xie, Qi-Lang

    2010-01-01

    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)

  1. Local genetic diversity of sorghum in a village in northern Cameroon: structure and dynamics of landraces.

    Science.gov (United States)

    Barnaud, Adeline; Deu, Monique; Garine, Eric; McKey, Doyle; Joly, Hélène I

    2007-01-01

    We present the first study of patterns of genetic diversity of sorghum landraces at the local scale. Understanding landrace diversity aids in deciphering evolutionary forces under domestication, and has applications in the conservation of genetic resources and their use in breeding programs. Duupa farmers in a village in Northern Cameroon distinguished 59 named sorghum taxa, representing 46 landraces. In each field, seeds are sown as a mixture of landraces (mean of 12 landraces per field), giving the potential for extensive gene flow. What level of genetic diversity underlies the great morphological diversity observed among landraces? Given the potential for gene flow, how well defined genetically is each landrace? To answer these questions, we recorded spatial patterns of planting and farmers' perceptions of landraces, and characterized 21 landraces using SSR markers. Analysis using distance and clustering methods grouped the 21 landraces studied into four clusters. These clusters correspond to functionally and ecologically distinct groups of landraces. Within-landrace genetic variation accounted for 30% of total variation. The average F(is) over landraces was 0.68, suggesting high inbreeding within landraces. Differentiation among landraces was substantial and significant (F(st) = 0.36). Historical factors, variation in breeding systems, and farmers' practices all affected patterns of genetic variation. Farmers' practices are key to the maintenance, despite gene flow, of landraces with different combinations of agronomically and ecologically pertinent traits. They must be taken into account in strategies of conservation and use of genetic resources.

  2. Evaluation of genetic diversity in Piper spp using RAPD and SRAP markers.

    Science.gov (United States)

    Jiang, Y; Liu, J-P

    2011-11-29

    Random amplified polymorphic DNA (RAPD) and sequence-related amplified polymorphism (SRAP) analysis were applied to 74 individual plants of Piper spp in Hainan Island. The results showed that the SRAP technique may be more informative and more efficient and effective for studying genetic diversity of Piper spp than the RAPD technique. The overall level of genetic diversity among Piper spp in Hainan was relatively high, with the mean Shannon diversity index being 0.2822 and 0.2909, and the mean Nei's genetic diversity being 0.1880 and 0.1947, calculated with RAPD and SRAP data, respectively. The ranges of the genetic similarity coefficient were 0.486-0.991 and 0.520-1.000 for 74 individual plants of Piper spp (the mean genetic distance was 0.505 and 0.480) and the within-species genetic distance ranged from 0.063 to 0.291 and from 0.096 to 0.234, estimated with RAPD and SRAP data, respectively. These genetic indices indicated that these species are closely related genetically. The dendrogram generated with the RAPD markers was topologically different from the dendrogram based on SRAP markers, but the SRAP technique clearly distinguished all Piper spp from each other. Evaluation of genetic variation levels of six populations showed that the effective number of alleles, Nei's gene diversity and the Shannon information index within Jianfengling and Diaoluoshan populations are higher than those elsewhere; consequently conservation of wild resources of Piper in these two regions should have priority.

  3. Genetic diversity detection of the domestic horse (Equus caballus by genes associated with coat color

    Directory of Open Access Journals (Sweden)

    Luz Correa A

    2015-09-01

    Full Text Available Objective. To assess the population structure and genetic diversity in populations of domestic horse (Equus caballus in the municipality Cienaga de Oro-Córdoba (Colombia. Materials and methods. Random sampling were conducted between August and October 2013, in adult animals on farms seven districts, which was carried out phenotypic characterization of each animal, based on autosomal markers encoding morphological Extension (E , Agouti (A, Cream (C, White (W, Gray (G, Tobiano (TO, Overo (O and Roan (RN. Population genetic parameters: allele frequency, genetic diversity, gene flow, Hardy-Weinberg equilibrium and genetic distance were calculated through the program POPGENE 1.31; the genetic structure was assessed using the program FSTAT v. 2.9.3.2. Results. 341 individuals were analyzed in the seven populations studied, where the Extension gene Was the MOST faq frequently as the Overo and Tobiano genes showed the lowest values. Insignificant values of genetic variability and population recorded a global level, likewise, low genetic differentiation among populations, accompanied by a high gene flow was obtained; an excess of heterozygotes at population and global level was observed; to this is added the presence of Hardy-Weinberg equilibrium in all populations relative to the markers studied and low genetic distance values were reported. Conclusions. The populations are highly genetically related, a situation that may result from the existing geographical proximity between them, favoring genetic exchange and the establishment of a metapopulation.

  4. Entropy and Information Approaches to Genetic Diversity and its Expression: Genomic Geography

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    William B. Sherwin

    2010-07-01

    Full Text Available This article highlights advantages of entropy-based genetic diversity measures, at levels from gene expression to landscapes. Shannon’s entropy-based diversity is the standard for ecological communities. The exponentials of Shannon’s and the related “mutual information” excel in their ability to express diversity intuitively, and provide a generalised method of considering microscopic behaviour to make macroscopic predictions, under given conditions. The hierarchical nature of entropy and information allows integrated modeling of diversity along one DNA sequence, and between different sequences within and among populations, species, etc. The aim is to identify the formal connections between genetic diversity and the flow of information to and from the environment.

  5. Phenotypic and genetic diversity of the species Lactobacillus rhamnosus

    NARCIS (Netherlands)

    Ceapa, C.D.

    2016-01-01

    The thesis explores the diversity of Lactobacillus rhamnosus, a species from which strains are studied for their anti-inflammatory, anti-allergic, and diarrhea preventing effects. The work combines observations on the behavior of the bacteria in a simplified laboratory setting (use of

  6. Genetic diversity in green gram accessions as revealed by STMS ...

    African Journals Online (AJOL)

    Molecular characterization of green gram (Vigna radiata (L.) Wilczek) germplasm is essential for scientific assessment of variability and diversity for its better utilization in breeding programs. In this study, 120 accessions of green gram were analysed for 27 Sequence Tagged Microsatellites (STMS) loci. For data analysis ...

  7. DNA markers reveal genetic structure and localized diversity of ...

    African Journals Online (AJOL)

    uqhdesma

    2016-10-12

    Oct 12, 2016 ... cluster, and landraces from this area also exhibited the greatest allelic diversity and the highest number of private alleles. ..... number of clusters (K) was varied from one to ten with a burn-in of ..... Review Front. Plant Sci. 5:484 ...

  8. Phylogeography, genetic diversity and demographic history of the ...

    Indian Academy of Sciences (India)

    Our data indicated that most of the Kurds mtDNA lineages belong to branches of the haplogroups with the Western Eurasian origin; with small fractions of the Eastern Eurasian and sub-Saharan African lineages. The low level of mtDNA diversity observed in the Havrami group presented a bias towards isolation or increased ...

  9. Analysis of genetic diversity in pigeon pea germplasm using ...

    Indian Academy of Sciences (India)

    MANEESHA

    2017-08-16

    Aug 16, 2017 ... fied polymorphic DNA (RAPD), simple sequence repeats. (SSR), amplified fragment length polymorphism (AFLP), single-nucleotide polymorphisms (SNPs), diversity array technology (DArT), genic-simple sequence repeats (genic-. SSR) etc. (see review by Varshney et al. 2013). Since retrotransposons are ...

  10. (SSR) markers for analysis of genetic diversity in African rice ...

    African Journals Online (AJOL)

    Bonny Oloka

    2015-05-06

    May 6, 2015 ... and conservation. To address this knowledge gap, 10 highly polymorphic rice simple sequence repeat. (SSR) markers were used to characterize 99 rice genotypes to determine their diversity and place them in their different population groups. The SSR markers were multiplexed in 3 panels to increase their.

  11. Genetic diversity of gliadin pattern, morphological traits and baking ...

    African Journals Online (AJOL)

    USER

    2010-02-15

    Feb 15, 2010 ... diversity of 102 double haploids of wheat (sent from. CIMMYT) through studying gliadin protein ... biomass, yield per plant, harvest index, number of grains per spike, spike density, spike length, plant ... per spike, also 6 baking quality traits, protein content, gluten index,. SDS sedimentation, sedimentation ...

  12. Genetic diversity and population structure of leaf-nosed bat ...

    African Journals Online (AJOL)

    Genetic variation and population structure of the leaf-nosed bat Hipposideros speoris were estimated using 16S rRNA sequence and microsatellite analysis. Twenty seven distinct mitochondrial haplotypes were identified from 186 individuals, sampled from eleven populations. FST test revealed significant variations ...

  13. Genetic diversity assessment of farmers' and improved potato ...

    African Journals Online (AJOL)

    The principal coordinate analysis (PCoA) revealed that the local farmers' Eritrean samples are different from the Kenyan, Rwandese and even the imported varieties. Genetic distance analysis generated three clusters correlating with the PCoA findings. Cluster I consisted of 45 samples with 6 sub-clusters; Cluster II ...

  14. Genetic diversity of Sorghum bicolor (L.) Moench landraces from ...

    African Journals Online (AJOL)

    An unweighted pair group method arithmetic average (UPGMA) clustering and principal coordinate analysis (PCoA) based on DICE coefficient revealed three major genetic groups supported by two main components: the botanical race and the morpho-physiological characteristics of the grains (colour and degree of ...

  15. Assessing genetic diversity of Hamdani sheep breed in Kurdistan ...

    African Journals Online (AJOL)

    The genetic variation in Hamdani sheep in the Kurdistan region of Iraq was studied using 35 microsatellite markers. All 35 markers were found to be highly polymorphic. The mean number of observed alleles ranged from four at BMS1494 to twenty five at BM6444 and INRABERN185 loci. The polymorphic information ...

  16. Understanding the genetic diversity of South Africa's peoples

    African Journals Online (AJOL)

    genetic conditions, such as fragile X mental retardation syndrome, myotonic dystrophy ... similar mutations – an area within or close to the gene where there ... risk of having children and grandchildren with severe intellectual disability. Further, the ... cognitive decline and psychiatric symptoms, shows some unique features in ...

  17. Genetic diversity in Jatropha species from different regions of Brazil ...

    African Journals Online (AJOL)

    Phenotypic and genetic studies of a population are important for plant ... Qualitative and quantitative characters showed variability between accesses and may serve ... Average percentage of polymorphism found for inter-simple sequence repeat ... By Country · List All Titles · Free To Read Titles This Journal is Open Access.

  18. Effects of landscape fragmentation on genetic diversity of Stipa ...

    African Journals Online (AJOL)

    To determine if and how these disturbances have impacted on genetic structure of S. krylovii populations, an inter-simple sequence repeat (ISSR) markers was used to characterize them for the first time in China. S. krylovii populations from 10 isolated patches were compared with population from unbroken natural ...

  19. Genetic Diversity of Rose germplasm based on RAPD analysis

    African Journals Online (AJOL)

    AHSAN IQBAL

    2012-06-12

    Jun 12, 2012 ... identification and analysis of genetic variation within a collection of 4 species and 30 accessions of rose using RAPD analysis technique. The results showed the molecular distinctions among the ... that range in colour from white and yellow to many shades of pink and red have been developed. Since.

  20. Genetic diversity of Colletotrichum gloeosporioides in Nigeria using ...

    African Journals Online (AJOL)

    fmodupe

    2012-04-24

    Apr 24, 2012 ... The genetic variation in C. gloeosporioides is important in choosing strategies to ... conidia size and shape, and presence or absence of setae (Sutton ... E-mail: aduramigbaa@run.edu.ng. ... 8190 Afr. J. Biotechnol. ... different Colletotrichum species (Guthrice et al., 1992). ... 11 blade fitted onto a holder was.