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Sample records for distinct genetic markers

  1. Analysis of genetic distance between Peruvian Alpaca (Vicugna Pacos showing two distinct fleece phenotypes, Suri and Huacaya, by means of microsatellite markers

    Directory of Open Access Journals (Sweden)

    Carlo Renieri

    2011-10-01

    Full Text Available Two coat phenotypes exist in Alpaca, Huacaya and Suri. The two coats show different fleece structure, textile characteristics and prices on the market. Although present scientific knowledge suggests a simple genetic model of inheritance, there is a tendency to manage and consider the two phenotypes as two different breeds. A 13 microsatellite panel was used in this study to assess genetic distance between Suri and Huacaya alpacas in a sample of non-related animals from two phenotypically pure flocks at the Illpa-Puno experimental station in Quimsachata, Peru. The animals are part of a germplasm established approximately 20 years ago and have been bred separately according to their coat type since then. Genetic variability parameters were also calculated. The data were statistically analyzed using the software Genalex 6.3, Phylip 3.69 and Fstat 2.9.3.2. The sample was tested for Hardy-Weinberg equilibrium (HWE and after strict Bonferroni correction only one locus (LCA37 showed deviation from equilibrium (Ploci associations showed significant disequilibrium. Observed heterozygosis (Ho= 0.766; SE=0.044, expected heterozygosis (He=0.769; SE=0.033, number of alleles (Na=9.667, SE=0.772 and Fixation index (F=0.004; SE=0.036 are comparable to data from previous studies. Measures of genetic distance were 0.06 for Nei’s and 0.03 for Cavalli-Sforza’s. The analysis of molecular variance reported no existing variance between populations. Considering the origin of the animals, their post domestication evolution and the reproductive practices in place, the results do not show genetic differentiation between the two populations for the studied loci.

  2. Puerto Rico and Florida manatees represent genetically distinct groups

    Science.gov (United States)

    Hunter, Margaret E.; Mignucci-Giannoni, Antonio A.; Tucker, Kimberly Pause; King, Timothy L.; Bonde, Robert K.; Gray, Brian A.; McGuire, Peter M.

    2012-01-01

    The West Indian manatee (Trichechus manatus) populations in Florida (T. m. latirostris) and Puerto Rico (T. m. manatus) are considered distinct subspecies and are listed together as endangered under the United States Endangered Species Act. Sustained management and conservation efforts for the Florida subspecies have led to the suggested reclassification of the species to a threatened or delisted status. However, the two populations are geographically distant, morphologically distinct, and habitat degradation and boat strikes continue to threaten the Puerto Rico population. Here, 15 microsatellite markers and mitochondrial control region sequences were used to determine the relatedness of the two populations and investigate the genetic diversity and phylogeographic organization of the Puerto Rico population. Highly divergent allele frequencies were identified between Florida and Puerto Rico using microsatellite (F ST = 0.16; R ST = 0.12 (P ST = 0.66; Φ ST = 0.50 (P E = 0.45; NA = 3.9), were similar, but lower than those previously identified in Florida (HE = 0.48, NA = 4.8). Within Puerto Rico, the mitochondrial genetic diversity values (π = 0.001; h = 0.49) were slightly lower than those previously reported (π = 0.002; h = 0.54) and strong phylogeographic structure was identified (F ST global = 0.82; Φ ST global = 0.78 (P population size (N = 250), and distinct threats and habitat emphasize the need for separate protections in Puerto Rico. Conservation efforts including threat mitigation, migration corridors, and protection of subpopulations could lead to improved genetic variation in the endangered Puerto Rico manatee population.

  3. Molecular markers unravel intraspecific and interspecific genetic ...

    Indian Academy of Sciences (India)

    [Kotwal S., Dhar M. K., Kour B., Raj K. and Kaul S. 2013 Molecular markers unravel intraspecific and interspecific genetic variability in ... of bowel problems including chronic constipation, amoebic ..... while to select parents from accessions, Pov80 and Pov79 ... nology (DBT), Govt. of India, for financial assistance in the form.

  4. Rice genetic marker database: An identification of single nucleotide ...

    African Journals Online (AJOL)

    based genetic marker system to provide information about SNP and QTL markers in rice. The SNP marker database provides 7,227 SNP markers including location information on chromosomes by using genetic map. It allows users to access a ...

  5. Inflammatory Genetic Markers of Prostate Cancer Risk

    Energy Technology Data Exchange (ETDEWEB)

    Tindall, Elizabeth A.; Hayes, Vanessa M. [Cancer Genetics Group, Children’s Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, University of New South Wales, PO Box 81, Randwick, NSW 2031 (Australia); University of New South Wales, Kensington Campus, Sydney, NSW 2052 (Australia); Petersen, Desiree C., E-mail: dpetersen@ccia.unsw.edu.au [Cancer Genetics Group, Children’s Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, University of New South Wales, PO Box 81, Randwick, NSW 2031 (Australia)

    2010-06-08

    Prostate cancer is the most common cancer in Western society males, with incidence rates predicted to rise with global aging. Etiology of prostate cancer is however poorly understood, while current diagnostic tools can be invasive (digital rectal exam or biopsy) and/or lack specificity for the disease (prostate-specific antigen (PSA) testing). Substantial histological, epidemiological and molecular genetic evidence indicates that inflammation is important in prostate cancer pathogenesis. In this review, we summarize the current status of inflammatory genetic markers influencing susceptibility to prostate cancer. The focus will be on inflammatory cytokines regulating T-helper cell and chemokine homeostasis, together with the Toll-like receptors as key players in the host innate immune system. Although association studies indicating a genetic basis for prostate cancer are presently limited mainly due to lack of replication, larger and more ethnically and clinically defined study populations may help elucidate the true contribution of inflammatory gene variants to prostate cancer risk.

  6. Inflammatory Genetic Markers of Prostate Cancer Risk

    International Nuclear Information System (INIS)

    Tindall, Elizabeth A.; Hayes, Vanessa M.; Petersen, Desiree C.

    2010-01-01

    Prostate cancer is the most common cancer in Western society males, with incidence rates predicted to rise with global aging. Etiology of prostate cancer is however poorly understood, while current diagnostic tools can be invasive (digital rectal exam or biopsy) and/or lack specificity for the disease (prostate-specific antigen (PSA) testing). Substantial histological, epidemiological and molecular genetic evidence indicates that inflammation is important in prostate cancer pathogenesis. In this review, we summarize the current status of inflammatory genetic markers influencing susceptibility to prostate cancer. The focus will be on inflammatory cytokines regulating T-helper cell and chemokine homeostasis, together with the Toll-like receptors as key players in the host innate immune system. Although association studies indicating a genetic basis for prostate cancer are presently limited mainly due to lack of replication, larger and more ethnically and clinically defined study populations may help elucidate the true contribution of inflammatory gene variants to prostate cancer risk

  7. Autosomal and mtDNA Markers Affirm the Distinctiveness of Lions in West and Central Africa

    Science.gov (United States)

    Bertola, Laura D.; Tensen, Laura; van Hooft, Pim; White, Paula A.; Driscoll, Carlos A.; Henschel, Philipp; Caragiulo, Anthony; Dias-Freedman, Isabela; Sogbohossou, Etotépé A.; Tumenta, Pricelia N.; Jirmo, Tuqa H.; de Snoo, Geert R.

    2015-01-01

    The evolutionary history of a species is key for understanding the taxonomy and for the design of effective management strategies for species conservation. The knowledge about the phylogenetic position of the lion (Panthera leo) in West/Central Africa is largely based on mitochondrial markers. Previous studies using mtDNA only have shown this region to hold a distinct evolutionary lineage. In addition, anthropogenic factors have led to a strong decline in West/Central African lion numbers, thus, the conservation value of these populations is particularly high. Here, we investigate whether autosomal markers are concordant with previously described phylogeographic patterns, and confirm the unique position of the West/Central African lion. Analysis of 20 microsatellites and 1,454 bp of the mitochondrial DNA in 16 lion populations representing the entire geographic range of the species found congruence in both types of markers, identifying four clusters: 1) West/Central Africa, 2) East Africa, 3) Southern Africa and 4) India. This is not in line with the current taxonomy, as defined by the IUCN, which only recognizes an African and an Asiatic subspecies. There are no indications that genetic diversity in West/Central Africa lions is lower than in either East or Southern Africa, however, given this genetic distinction and the recent declines of lion numbers in this region, we strongly recommend prioritization of conservation projects in West/Central Africa. As the current taxonomic nomenclature does not reflect the evolutionary history of the lion, we suggest that a taxonomic revision of the lion is warranted. PMID:26466139

  8. Autosomal and mtDNA Markers Affirm the Distinctiveness of Lions in West and Central Africa.

    Science.gov (United States)

    Bertola, Laura D; Tensen, Laura; van Hooft, Pim; White, Paula A; Driscoll, Carlos A; Henschel, Philipp; Caragiulo, Anthony; Dias-Freedman, Isabela; Sogbohossou, Etotépé A; Tumenta, Pricelia N; Jirmo, Tuqa H; de Snoo, Geert R; de Iongh, Hans H; Vrieling, Klaas

    2015-01-01

    The evolutionary history of a species is key for understanding the taxonomy and for the design of effective management strategies for species conservation. The knowledge about the phylogenetic position of the lion (Panthera leo) in West/Central Africa is largely based on mitochondrial markers. Previous studies using mtDNA only have shown this region to hold a distinct evolutionary lineage. In addition, anthropogenic factors have led to a strong decline in West/Central African lion numbers, thus, the conservation value of these populations is particularly high. Here, we investigate whether autosomal markers are concordant with previously described phylogeographic patterns, and confirm the unique position of the West/Central African lion. Analysis of 20 microsatellites and 1,454 bp of the mitochondrial DNA in 16 lion populations representing the entire geographic range of the species found congruence in both types of markers, identifying four clusters: 1) West/Central Africa, 2) East Africa, 3) Southern Africa and 4) India. This is not in line with the current taxonomy, as defined by the IUCN, which only recognizes an African and an Asiatic subspecies. There are no indications that genetic diversity in West/Central Africa lions is lower than in either East or Southern Africa, however, given this genetic distinction and the recent declines of lion numbers in this region, we strongly recommend prioritization of conservation projects in West/Central Africa. As the current taxonomic nomenclature does not reflect the evolutionary history of the lion, we suggest that a taxonomic revision of the lion is warranted.

  9. Autosomal and mtDNA Markers Affirm the Distinctiveness of Lions in West and Central Africa.

    Directory of Open Access Journals (Sweden)

    Laura D Bertola

    Full Text Available The evolutionary history of a species is key for understanding the taxonomy and for the design of effective management strategies for species conservation. The knowledge about the phylogenetic position of the lion (Panthera leo in West/Central Africa is largely based on mitochondrial markers. Previous studies using mtDNA only have shown this region to hold a distinct evolutionary lineage. In addition, anthropogenic factors have led to a strong decline in West/Central African lion numbers, thus, the conservation value of these populations is particularly high. Here, we investigate whether autosomal markers are concordant with previously described phylogeographic patterns, and confirm the unique position of the West/Central African lion. Analysis of 20 microsatellites and 1,454 bp of the mitochondrial DNA in 16 lion populations representing the entire geographic range of the species found congruence in both types of markers, identifying four clusters: 1 West/Central Africa, 2 East Africa, 3 Southern Africa and 4 India. This is not in line with the current taxonomy, as defined by the IUCN, which only recognizes an African and an Asiatic subspecies. There are no indications that genetic diversity in West/Central Africa lions is lower than in either East or Southern Africa, however, given this genetic distinction and the recent declines of lion numbers in this region, we strongly recommend prioritization of conservation projects in West/Central Africa. As the current taxonomic nomenclature does not reflect the evolutionary history of the lion, we suggest that a taxonomic revision of the lion is warranted.

  10. Short Communication: Genetic linkage map of Cucurbita maxima with molecular and morphological markers.

    Science.gov (United States)

    Ge, Y; Li, X; Yang, X X; Cui, C S; Qu, S P

    2015-05-22

    Cucurbita maxima is one of the most widely cultivated vegetables in China and exhibits distinct morphological characteristics. In this study, genetic linkage analysis with 57 simple-sequence repeats, 21 amplified fragment length polymorphisms, 3 random-amplified polymorphic DNA, and one morphological marker revealed 20 genetic linkage groups of C. maxima covering a genetic distance of 991.5 cM with an average of 12.1 cM between adjacent markers. Genetic linkage analysis identified the simple-sequence repeat marker 'PU078072' 5.9 cM away from the locus 'Rc', which controls rind color. The genetic map in the present study will be useful for better mapping, tagging, and cloning of quantitative trait loci/gene(s) affecting economically important traits and for breeding new varieties of C. maxima through marker-assisted selection.

  11. Distinct genetic alterations in colorectal cancer.

    Directory of Open Access Journals (Sweden)

    Hassan Ashktorab

    Full Text Available BACKGROUND: Colon cancer (CRC development often includes chromosomal instability (CIN leading to amplifications and deletions of large DNA segments. Epidemiological, clinical, and cytogenetic studies showed that there are considerable differences between CRC tumors from African Americans (AAs and Caucasian patients. In this study, we determined genomic copy number aberrations in sporadic CRC tumors from AAs, in order to investigate possible explanations for the observed disparities. METHODOLOGY/PRINCIPAL FINDINGS: We applied genome-wide array comparative genome hybridization (aCGH using a 105k chip to identify copy number aberrations in samples from 15 AAs. In addition, we did a population comparative analysis with aCGH data in Caucasians as well as with a widely publicized list of colon cancer genes (CAN genes. There was an average of 20 aberrations per patient with more amplifications than deletions. Analysis of DNA copy number of frequently altered chromosomes revealed that deletions occurred primarily in chromosomes 4, 8 and 18. Chromosomal duplications occurred in more than 50% of cases on chromosomes 7, 8, 13, 20 and X. The CIN profile showed some differences when compared to Caucasian alterations. CONCLUSIONS/SIGNIFICANCE: Chromosome X amplification in male patients and chromosomes 4, 8 and 18 deletions were prominent aberrations in AAs. Some CAN genes were altered at high frequencies in AAs with EXOC4, EPHB6, GNAS, MLL3 and TBX22 as the most frequently deleted genes and HAPLN1, ADAM29, SMAD2 and SMAD4 as the most frequently amplified genes. The observed CIN may play a distinctive role in CRC in AAs.

  12. Molecular marker systems for Oenothera genetics.

    Science.gov (United States)

    Rauwolf, Uwe; Golczyk, Hieronim; Meurer, Jörg; Herrmann, Reinhold G; Greiner, Stephan

    2008-11-01

    The genus Oenothera has an outstanding scientific tradition. It has been a model for studying aspects of chromosome evolution and speciation, including the impact of plastid nuclear co-evolution. A large collection of strains analyzed during a century of experimental work and unique genetic possibilities allow the exchange of genetically definable plastids, individual or multiple chromosomes, and/or entire haploid genomes (Renner complexes) between species. However, molecular genetic approaches for the genus are largely lacking. In this study, we describe the development of efficient PCR-based marker systems for both the nuclear genome and the plastome. They allow distinguishing individual chromosomes, Renner complexes, plastomes, and subplastomes. We demonstrate their application by monitoring interspecific exchanges of genomes, chromosome pairs, and/or plastids during crossing programs, e.g., to produce plastome-genome incompatible hybrids. Using an appropriate partial permanent translocation heterozygous hybrid, linkage group 7 of the molecular map could be assigned to chromosome 9.8 of the classical Oenothera map. Finally, we provide the first direct molecular evidence that homologous recombination and free segregation of chromosomes in permanent translocation heterozygous strains is suppressed.

  13. Polymorphic microsatellite markers for genetic studies of African ...

    African Journals Online (AJOL)

    Administrator

    2011-09-26

    Sep 26, 2011 ... Many wild animal species lack informative genetic markers for analysing genetic variation and ... which act as important buffer zones between human and wildlife. ..... amplification tests of ungulate primers in the endangered.

  14. The efficiency of mitochondrial DNA markers in constructing genetic ...

    African Journals Online (AJOL)

    The efficiency of mitochondrial DNA markers in constructing genetic relationship among Oryx species. ... These data were used to provide the genetic kinship among different Oryx species. The complete cytochrome b gene ... Key words: Conservation, endangered species, Oryx, mitochondrial DNA (mtDNA) markers.

  15. Comparison of genetic detection efficiency of different markers ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-06-03

    Jun 3, 2009 ... Chinese native sheep populations, Hu sheep, Tong sheep, Small-tailed Han sheep and Tan sheep were used to study the efficiency of genetic markers. The genetic markers used in this study include morphological and ecological indices, blood protein enzyme, microsatellite DNA and the combination of.

  16. 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.

  17. Single Nucleotide Polymorphism Markers for Genetic Mapping in Drosophila melanogaster

    OpenAIRE

    Hoskins, Roger A.; Phan, Alexander C.; Naeemuddin, Mohammed; Mapa, Felipa A.; Ruddy, David A.; Ryan, Jessica J.; Young, Lynn M.; Wells, Trent; Kopczynski, Casey; Ellis, Michael C.

    2001-01-01

    For nearly a century, genetic analysis in Drosophila melanogaster has been a powerful tool for analyzing gene function, yet Drosophila lacks the molecular genetic mapping tools that recently have revolutionized human, mouse, and plant genetics. Here, we describe the systematic characterization of a dense set of molecular markers in Drosophila by using a sequence tagged site-based physical map of the genome. We identify 474 biallelic markers in standard laboratory strains of Drosophila that sp...

  18. Enzyme markers in inbred rat strains: genetics of new markers and strain profiles.

    Science.gov (United States)

    Adams, M; Baverstock, P R; Watts, C H; Gutman, G A

    1984-08-01

    Twenty-six inbred strains of the laboratory rat (Rattus norvegicus) were examined for electrophoretic variation at an estimated 97 genetic loci. In addition to previously documented markers, variation was observed for the enzymes aconitase, aldehyde dehydrogenase, and alkaline phosphatase. The genetic basis of these markers (Acon-1, Ahd-2, and Akp-1) was confirmed. Linkage analysis between 35 pairwise comparisons revealed that the markers Fh-1 and Pep-3 are linked. The strain profiles of the 25 inbred strains at 11 electrophoretic markers are given.

  19. Genetically Distinct Subsets within ANCA-Associated Vasculitis

    Science.gov (United States)

    Lyons, Paul A.; Rayner, Tim F.; Trivedi, Sapna; Holle, Julia U.; Watts, Richard A.; Jayne, David R.W.; Baslund, Bo; Brenchley, Paul; Bruchfeld, Annette; Chaudhry, Afzal N.; Tervaert, Jan Willem Cohen; Deloukas, Panos; Feighery, Conleth; Gross, Wolfgang L.; Guillevin, Loic; Gunnarsson, Iva; P, Lorraine Harper M.R.C; Hrušková, Zdenka; Little, Mark A.; Martorana, Davide; Neumann, Thomas; Ohlsson, Sophie; Padmanabhan, Sandosh; Pusey, Charles D.; Salama, Alan D.; Sanders, Jan-Stephan F.; Savage, Caroline O.; Segelmark, Mårten; Stegeman, Coen A.; Tesař, Vladimir; Vaglio, Augusto; Wieczorek, Stefan; Wilde, Benjamin; Zwerina, Jochen; Rees, Andrew J.; Clayton, David G.; Smith, Kenneth G.C.

    2013-01-01

    BACKGROUND Antineutrophil cytoplasmic antibody (ANCA)–associated vasculitis is a severe condition encompassing two major syndromes: granulomatosis with polyangiitis (formerly known as Wegener’s granulomatosis) and microscopic polyangiitis. Its cause is unknown, and there is debate about whether it is a single disease entity and what role ANCA plays in its pathogenesis. We investigated its genetic basis. METHODS A genomewide association study was performed in a discovery cohort of 1233 U.K. patients with ANCA-associated vasculitis and 5884 controls and was replicated in 1454 Northern European case patients and 1666 controls. Quality control, population stratification, and statistical analyses were performed according to standard criteria. RESULTS We found both major-histocompatibility-complex (MHC) and non-MHC associations with ANCA-associated vasculitis and also that granulomatosis with polyangiitis and microscopic polyangiitis were genetically distinct. The strongest genetic associations were with the antigenic specificity of ANCA, not with the clinical syndrome. Anti–proteinase 3 ANCA was associated with HLA-DP and the genes encoding α1-antitrypsin (SERPINA1) and proteinase 3 (PRTN3) (P = 6.2×10−89, P = 5.6×10−12, and P = 2.6×10−7, respectively). Anti–myeloperoxidase ANCA was associated with HLA-DQ (P = 2.1×10−8). CONCLUSIONS This study confirms that the pathogenesis of ANCA-associated vasculitis has a genetic component, shows genetic distinctions between granulomatosis with polyangiitis and microscopic polyangiitis that are associated with ANCA specificity, and suggests that the response against the autoantigen proteinase 3 is a central pathogenic feature of proteinase 3 ANCA–associated vasculitis. These data provide preliminary support for the concept that proteinase 3 ANCA–associated vasculitis and myeloperoxidase ANCA–associated vasculitis are distinct autoimmune syndromes. (Funded by the British Heart Foundation and others.) PMID

  20. Genetic Determinism and the Innate-Acquired Distinction in Medicine

    Science.gov (United States)

    2009-01-01

    This article illustrates in which sense genetic determinism is still part of the contemporary interactionist consensus in medicine. Three dimensions of this consensus are discussed: kinds of causes, a continuum of traits ranging from monogenetic diseases to car accidents, and different kinds of determination due to different norms of reaction. On this basis, this article explicates in which sense the interactionist consensus presupposes the innate–acquired distinction. After a descriptive Part 1, Part 2 reviews why the innate–acquired distinction is under attack in contemporary philosophy of biology. Three arguments are then presented to provide a limited and pragmatic defense of the distinction: an epistemic, a conceptual, and a historical argument. If interpreted in a certain manner, and if the pragmatic goals of prevention and treatment (ideally specifying what medicine and health care is all about) are taken into account, then the innate–acquired distinction can be a useful epistemic tool. It can help, first, to understand that genetic determination does not mean fatalism, and, second, to maintain a system of checks and balances in the continuing nature–nurture debates. PMID:20234831

  1. Molecular markers for genetic diversity and phylogeny research of ...

    African Journals Online (AJOL)

    Brazilian sheep descended from several breeds brought to the New World by Portuguese and Spanish colonists, and they have evolved and adapted to local climatic variations and acquired tolerance or resistance to many diseases. Molecular markers are widely used in analyzing genetic variability, and markers such as ...

  2. 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 ...

  3. Application of genetic markers in seed testing and plant breeding

    Directory of Open Access Journals (Sweden)

    Nikolić Zorica

    2010-01-01

    Full Text Available Genetic markers have been used at Institute of Field and Vegetable Crops in Novi Sad for a number of years, both for seed quality control and for research purposes. The Laboratory for Seed Testing was the first in the former Yugoslavia to use the method of control of hybrid seed genetic purity based on enzymatic polymorphism. This paper presents the application of protein markers, isozymes, seed storage proteins and DNA markers for evaluation of seed and breeding materials of various agricultural crops in Serbia.

  4. 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.

  5. Identification of novel genetic markers of breast cancer survival

    NARCIS (Netherlands)

    Q. Guo (Qi); M.K. Schmidt (Marjanka); P. Kraft (Peter); S. Canisius (Sander); C. Chen (Constance); S. Khan (Sofia); J.P. Tyrer (Jonathan); M.K. Bolla (Manjeet); Q. Wang (Qing); J. Dennis (Joe); K. Michailidou (Kyriaki); M. Lush (Michael); S. Kar (Siddhartha); J. Beesley (Jonathan); A.M. Dunning (Alison); M. Shah (Mitul); K. Czene (Kamila); H. Darabi (Hatef); M. Eriksson (Mikael); D. Lambrechts (Diether); C. Weltens (Caroline); K. Leunen; S.E. Bojesen (Stig); B.G. Nordestgaard (Børge); S.F. Nielsen (Sune); H. Flyger (Henrik); J. Chang-Claude (Jenny); A. Rudolph (Anja); P. Seibold (Petra); D. Flesch-Janys (Dieter); C. Blomqvist (Carl); K. Aittomäki (Kristiina); R. Fagerholm (Rainer); T.A. Muranen (Taru); F.J. Couch (Fergus); J.E. Olson (Janet); C. Vachon (Celine); I.L. Andrulis (Irene); J.A. Knight (Julia); G. Glendon (Gord); A.-M. Mulligan (Anna-Marie); A. Broeks (Annegien); F.B.L. Hogervorst (Frans); C.A. Haiman (Christopher); B.E. Henderson (Brian); F.R. Schumacher (Fredrick); L. Le Marchand (Loic); J. Hopper (John); H. Tsimiklis (Helen); C. Apicella (Carmel); M.C. Southey (Melissa); A. Cox (Angela); S.S. Cross (Simon); M.W.R. Reed (Malcolm); G.G. Giles (Graham G.); R.L. Milne (Roger L.); C.A. McLean (Catriona Ann); R. Winqvist (Robert); K. Pykäs (Katri); A. Jukkola-Vuorinen (Arja); M. Grip (Mervi); M.J. Hooning (Maartje); A. Hollestelle (Antoinette); J.W.M. Martens (John W. M.); A.M.W. van den Ouweland (Ans); F. Marme (Federick); A. Schneeweiss (Andreas); R. Yang (Rongxi); B. Burwinkel (Barbara); J.D. Figueroa (Jonine); S.J. Chanock (Stephen); J. Lissowska (Jolanta); E.J. Sawyer (Elinor); I.P. Tomlinson (Ian); M. Kerin (Michael); N. Miller (Nicola); H. Brenner (Hermann); A.K. Dieffenbach (Aida Karina); V. Arndt (Volker); B. Holleczek (B.); A. Mannermaa (Arto); V. Kataja (Vesa); V-M. Kosma (Veli-Matti); J.M. Hartikainen (J.); J. Li (Jingmei); J.S. Brand (Judith S.); M.K. Humphreys (Manjeet); P. Devilee (Peter); R.A.E.M. Tollenaar (Rob); C.M. Seynaeve (Caroline); P. Radice (Paolo); P. Peterlongo (Paolo); B. Bonnani (Bernardo); P. Mariani (Paolo); P.A. Fasching (Peter); M.W. Beckmann (Matthias); R. Hein (Rebecca); A.B. Ekici (Arif); G. Chenevix-Trench (Georgia); R. Balleine (Rosemary); K.-A. Phillips (Kelly-Anne); J. Benítez (Javier); M.P. Zamora (Pilar); J.I. Arias Pérez (José Ignacio); P. Menéndez (Primitiva); A. Jakubowska (Anna); J. Lubinski (Jan); K. Jaworska-Bieniek (Katarzyna); K. Durda (Katarzyna); U. Hamann (Ute); M. Kabisch (Maria); H.U. Ulmer (Hans); T. Rud̈iger (Thomas); S. Margolin (Sara); V. Kristensen (Vessela); S. Nord (Silje); D.G. Evans (Gareth); J. Abraham (Jean); H. Earl (Helena); L. Hiller (Louise); J.A. Dunn (J.); S. Bowden (Sarah); C.D. Berg (Christine); D. Campa (Daniele); W.R. Diver (Ryan); S.M. Gapstur (Susan M.); M.M. Gaudet (Mia); S.E. Hankinson (Susan); R.N. Hoover (Robert); A. Hüsing (Anika); R. Kaaks (Rudolf); M.J. Machiela (Mitchell J.); W.C. Willett (Walter C.); M. Barrdahl (Myrto); F. Canzian (Federico); S.-F. Chin (Suet-Feung); C. Caldas (Carlos); D. Hunter (David); S. Lindstrom (Stephen); M. García-Closas (Montserrat); P. Hall (Per); D.F. Easton (Douglas); D. Eccles (Diana); N. Rahman (Nazneen); H. Nevanlinna (Heli); P.D.P. Pharoah (Paul)

    2015-01-01

    textabstractBackground: Survival after a diagnosis of breast cancer varies considerably between patients, and some of this variation may be because of germline genetic variation. We aimed to identify genetic markers associated with breast cancer-specific survival. Methods: We conducted a large

  6. 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.

  7. 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.

  8. Microsatellite markers reveal low genetic differentiation among ...

    African Journals Online (AJOL)

    Ben

    Assignment. 1* Khai Apple Game Reserve, Kathu, Northern Cape ... Previous genetic studies on Camelidae in Dubai, Germany, Australia, Kenya and Ethiopia mainly reporting the ... All the biological samples were deposited in the Bio-Bank at.

  9. Genetic prognostic markers in colorectal cancer.

    OpenAIRE

    Houlston, R S; Tomlinson, I P

    1997-01-01

    The contribution of molecular genetics to colorectal cancer has been restricted largely to relatively rare inherited tumours and to the detection of germline mutations predisposing to these cancers. However, much is now also known about somatic events leading to colorectal cancer. A number of studies has been undertaken examining possible relations between genetic features and prognostic indices. While many of these studies are small and inconclusive, it is clear that a number of different pa...

  10. Indel Group in Genomes (IGG) Molecular Genetic Markers1[OPEN

    Science.gov (United States)

    Burkart-Waco, Diana; Kuppu, Sundaram; Britt, Anne; Chetelat, Roger

    2016-01-01

    Genetic markers are essential when developing or working with genetically variable populations. Indel Group in Genomes (IGG) markers are primer pairs that amplify single-locus sequences that differ in size for two or more alleles. They are attractive for their ease of use for rapid genotyping and their codominant nature. Here, we describe a heuristic algorithm that uses a k-mer-based approach to search two or more genome sequences to locate polymorphic regions suitable for designing candidate IGG marker primers. As input to the IGG pipeline software, the user provides genome sequences and the desired amplicon sizes and size differences. Primer sequences flanking polymorphic insertions/deletions are produced as output. IGG marker files for three sets of genomes, Solanum lycopersicum/Solanum pennellii, Arabidopsis (Arabidopsis thaliana) Columbia-0/Landsberg erecta-0 accessions, and S. lycopersicum/S. pennellii/Solanum tuberosum (three-way polymorphic) are included. PMID:27436831

  11. Genetic markers for flowering in perennial ryegrass

    DEFF Research Database (Denmark)

    Paina, Cristiana; Byrne, Stephen; Andersen, Jeppe Reitan

    2011-01-01

    Perennial ryegrass (Lolium perenne L.) is the principal forage grass utilized in Danish agriculture and underpins the beef and dairy sectors. It is characterized as having high digestibility, high nutritional value, and high productivity during vegetative growth. However, at the reproductive growth...... genes will be converted to molecular markers and mapped in an existing mapping population previously characterized for flowering time and vernalization response. References: Amasino, R.M., Michaels S.D. (2010). The Timing of Flowering. Plant Physiology 154: 516–520 Greenup, A., W. Peacock, W.J., Dennis...

  12. Uniparental genetic markers in South Amerindians

    Directory of Open Access Journals (Sweden)

    Rafael Bisso-Machado

    2012-01-01

    Full Text Available A comprehensive review of uniparental systems in South Amerindians was undertaken. Variability in the Y-chromosome haplogroups were assessed in 68 populations and 1,814 individuals whereas that of Y-STR markers was assessed in 29 populations and 590 subjects. Variability in the mitochondrial DNA (mtDNA haplogroup was examined in 108 populations and 6,697 persons, and sequencing studies used either the complete mtDNA genome or the highly variable segments 1 and 2. The diversity of the markers made it difficult to establish a general picture of Y-chromosome variability in the populations studied. However, haplogroup Q1a3a* was almost always the most prevalent whereas Q1a3* occurred equally in all regions, which suggested its prevalence among the early colonizers. The STR allele frequencies were used to derive a possible ancient Native American Q-clade chromosome haplotype and five of six STR loci showed significant geographic variation. Geographic and linguistic factors moderately influenced the mtDNA distributions (6% and 7%, respectively and mtDNA haplogroups A and D correlated positively and negatively, respectively, with latitude. The data analyzed here provide rich material for understanding the biological history of South Amerindians and can serve as a basis for comparative studies involving other types of data, such as cultural data.

  13. Assessment of Cultivar Distinctness in Alfalfa: A Comparison of Genotyping-by-Sequencing, Simple-Sequence Repeat Marker, and Morphophysiological Observations

    Directory of Open Access Journals (Sweden)

    Paolo Annicchiarico

    2016-07-01

    Full Text Available Cultivar registration agencies typically require morphophysiological trait-based distinctness of candidate cultivars. This requirement is difficult to achieve for cultivars of major perennial forages because of their genetic structure and ever-increasing number of registered material, leading to possible rejection of agronomically valuable cultivars. This study aimed to explore the value of molecular markers applied to replicated bulked plants (three bulks of 100 independent plants each per cultivar to assess alfalfa ( L. subsp. cultivar distinctness. We compared genotyping-by-sequencing information based on 2902 polymorphic single-nucleotide polymorphism (SNP markers (>30 reads per DNA sample with morphophysiological information based on 11 traits and with simple-sequence repeat (SSR marker information from 41 polymorphic markers for their ability to distinguish 11 alfalfa landraces representative of the germplasm from northern Italy. Three molecular criteria, one based on cultivar differences for individual SSR bands and two based on overall SNP marker variation assessed either by statistically significant cultivar differences on principal component axes or discriminant analysis, distinctly outperformed the morphophysiological criterion. Combining the morphophysiological criterion with either molecular marker method increased discrimination among cultivars, since morphophysiological diversity was unrelated to SSR marker-based diversity ( = 0.04 and poorly related to SNP marker-based diversity ( = 0.23, < 0.15. The criterion based on statistically significant SNP allele frequency differences was less discriminating than morphophysiological variation. Marker-based distinctness, which can be assessed at low cost and without interactions with testing conditions, could validly substitute for (or complement morphophysiological distinctness in alfalfa cultivar registration schemes. It also has interest in sui generis registration systems aimed at

  14. Radiation application on development of marker genes for genetic manipulation

    International Nuclear Information System (INIS)

    Lee, Young Il

    1997-04-01

    This state of art report was dealt with the recent progress of genetic engineering techniques and prospect of gene manipulation. Especially the selection of new genetic marker genes such as variants to environmental stress, pest or insect resistance, herbicide resistance and nutritional requirement was reviewed by using plant cell and tissue culture combined with radiation mutation induction. Biotechnology has taken us from the era hybrid plants to the era of transgenic plants. Although there are still many problems to solve in transformation method and the regeneration of transformed cell and tissue. Genetic marker genes are very important material to improve the technique of genetic manipulation. Most of the genes have been developed by radiation. (author). 180 refs., 6 tabs

  15. Psoriasis and cardiometabolic traits: modest association but distinct genetic architectures

    Science.gov (United States)

    Koch, Manja; Baurecht, Hansjörg; Ried, Janina S.; Rodriguez, Elke; Schlesinger, Sabrina; Volks, Natalie; Gieger, Christian; Rückert, Ina-Maria; Heinrich, Luise; Willenborg, Christina; Smith, Catherine; Peters, Annette; Thorand, Barbara; Koenig, Wolfgang; Lamina, Claudia; Jansen, Henning; Kronenberg, Florian; Seissler, Jochen; Thiery, Joachim; Rathmann, Wolfgang; Schunkert, Heribert; Erdmann, Jeanette; Barker, Jonathan; Nair, Rajan P; Tsoi, Lam C; Elder, James T; Mrowietz, Ulrich; Weichenthal, Michael; Mucha, Sören; Schreiber, Stefan; Franke, Andre; Schmitt, Jochen; Lieb, Wolfgang; Weidinger, Stephan

    2015-01-01

    Psoriasis has been linked to cardiometabolic diseases, but epidemiological findings are inconsistent. We investigated the association between psoriasis and cardiometabolic outcomes in a German cross-sectional study (n=4.185) and a prospective cohort of German Health Insurance beneficiaries (n=1.811.098). A potential genetic overlap was explored using genome-wide data from >22.000 coronary artery disease (CAD) and >4.000 psoriasis cases, and with a dense genotyping study of cardiometabolic risk loci on 927 psoriasis cases and 3.717 controls. Controlling for major confounders, in the cross-sectional analysis psoriasis was significantly associated with type 2 diabetes (T2D, adjusted odd’s ratio OR=2.36; 95% confidence interval CI=1.26–4.41) and myocardial infarction (MI, OR=2.26, 95% CI=1.03–4.96). In the longitudinal study, psoriasis slightly increased the risk for incident T2D (adjusted relative risk RR=1.11; 95%CI=1.08–1.14) and MI (RR=1.14; 95%CI=1.06–1.22), with highest risk increments in systemically treated psoriasis, which accounted for 11 and 17 excess cases of T2D and MI per 10,000 person-years. Except for weak signals from within the MHC, there was no evidence for genetic risk loci shared between psoriasis and cardiometabolic traits. Our findings suggest that psoriasis, in particular severe psoriasis, increases risk for T2D and MI, and that the genetic architecture of psoriasis and cardiometabolic traits is largely distinct. PMID:25599394

  16. Use of multiple genetic markers in prediction of breeding values.

    NARCIS (Netherlands)

    Arendonk, van J.A.M.; Tier, B.; Kinghorn, B.P.

    1994-01-01

    Genotypes at a marker locus give information on transmission of genes from parents to offspring and that information can be used in predicting the individuals' additive genetic value at a linked quantitative trait locus (MQTL). In this paper a recursive method is presented to build the gametic

  17. Genetic diversity and identification of variety-specific AFLP markers ...

    African Journals Online (AJOL)

    In all the fenugreek varieties, a total of 25 variety-specific AFLP markers were found. Phylogenetic trees among 5 plant varieties were constructed based on Nei's coefficient standard genetic distances using unweighted pair group method with arithmetic mean (UPGMA) method. For RAPD and AFLP analysis, Gujarat Methi-1 ...

  18. Random amplified polymorphic DNA (RAPD) markers reveal genetic ...

    African Journals Online (AJOL)

    The present study evaluated genetic variability of superior bael genotypes collected from different parts of Andaman Islands, India using fruit characters and random amplified polymorphic DNA (RAPD) markers. Genomic DNA extracted from leaf material using cetyl trimethyl ammonium bromide (CTAB) method was ...

  19. Simple sequence repeat marker development and genetic mapping ...

    Indian Academy of Sciences (India)

    polymorphic SSR (simple sequence repeats) markers from libraries enriched for GA, CAA and AAT repeats, as well as 6 ... ers for quinoa was the development of a genetic linkage map ...... Weber J. L. 1990 Informativeness of human (dC-dA)n.

  20. Oxidative Stress Markers and Genetic Polymorphisms of Glutathione ...

    African Journals Online (AJOL)

    Hence, we evaluated the serum levels of oxidative stress markers and investigated genetic polymorphisms of glutathione S-transferase associated with autism. Materials and Methods: Forty-two children clinically diagnosed with ASD using the Diagnostic and Statistical Manual for Mental Disorders (DSM-5) criteria and a ...

  1. Evaluation of algorithms used to order markers on genetic maps.

    Science.gov (United States)

    Mollinari, M; Margarido, G R A; Vencovsky, R; Garcia, A A F

    2009-12-01

    When building genetic maps, it is necessary to choose from several marker ordering algorithms and criteria, and the choice is not always simple. In this study, we evaluate the efficiency of algorithms try (TRY), seriation (SER), rapid chain delineation (RCD), recombination counting and ordering (RECORD) and unidirectional growth (UG), as well as the criteria PARF (product of adjacent recombination fractions), SARF (sum of adjacent recombination fractions), SALOD (sum of adjacent LOD scores) and LHMC (likelihood through hidden Markov chains), used with the RIPPLE algorithm for error verification, in the construction of genetic linkage maps. A linkage map of a hypothetical diploid and monoecious plant species was simulated containing one linkage group and 21 markers with fixed distance of 3 cM between them. In all, 700 F(2) populations were randomly simulated with 100 and 400 individuals with different combinations of dominant and co-dominant markers, as well as 10 and 20% of missing data. The simulations showed that, in the presence of co-dominant markers only, any combination of algorithm and criteria may be used, even for a reduced population size. In the case of a smaller proportion of dominant markers, any of the algorithms and criteria (except SALOD) investigated may be used. In the presence of high proportions of dominant markers and smaller samples (around 100), the probability of repulsion linkage increases between them and, in this case, use of the algorithms TRY and SER associated to RIPPLE with criterion LHMC would provide better results.

  2. Genetic variability in local Brazilian horse lines using microsatellite markers.

    Science.gov (United States)

    Silva, A C M; Paiva, S R; Albuquerque, M S M; Egito, A A; Santos, S A; Lima, F C; Castro, S T; Mariante, A S; Correa, P S; McManus, C M

    2012-04-10

    Genetic variability at 11 microsatellite markers was analyzed in five naturalized/local Brazilian horse breeds or genetic groups. Blood samples were collected from 328 animals of the breeds Campeira (Santa Catarina State), Lavradeira (Roraima State), Pantaneira (Pantanal Mato-Grossense), Mangalarga Marchador (Minas Gerais State), as well as the genetic group Baixadeiro (Maranhão State), and the exotic breeds English Thoroughbred and Arab. We found significant genetic variability within evaluated microsatellite loci, with observed heterozygosis varying between 0.426 and 0.768 and polymorphism information content values of 0.751 to 0.914. All breeds showed high inbreeding coefficients and were not in Hardy-Weinberg equilibrium. The smallest genetic distance was seen between the Pantaneira and Arab breeds. The principal component analyzes and Bayesian approach demonstrated that the exotic breeds have had a significant influence on the genetic formation of the local breeds, with introgression of English Throroughbred in Pantaneira and Lavradeira, as well as genetic proximity between the Arab, Pantaneira and Mangalarga Marchador populations. This study shows the need to conserve traits acquired by naturalized horse breeds over centuries of natural selection in Brazil due to the genetic uniqueness of each group, suggesting a reduced gene flow between them. These results reinforce the need to include these herds in animal genetic resource conservation programs to maximize the genetic variability and conserve useful allele combinations.

  3. Incorporation of conventional genetic markers and RAPD markers into an RFLP based map in maize

    International Nuclear Information System (INIS)

    Coe, E.H. Jr.; McMullen, M.D.; Polacco, M.; Davis, G.L.; Chao, S.

    1998-01-01

    Integration of classical genetic markers, in particular mutants, onto the maize Restriction Fragment Length Polymorphism (RFLP) map will provide the tools necessary to further our understanding of plant development and of complex traits. Initially integration was accomplished by visual alignment of common markers and sometimes involved the use of information from several different molecular maps to determine the relative placement of a single mutant. The maize core marker set was designed to provide a common set of markers which could be used for integration of map data. We have completed the mapping, of 56 mutants on chromosome one relative to the core marker set. Phenotypes included whole plant, seedling, and kernel effects and represented a variety of biological processes. Since these mutants were previously located to chromosome arm, mapping required the use of only seven markers per mutant to define the correct bin location. Two mistakes in marker order relative to the classical map were identified, as well as, six groups of mutants which require allelism testing. Placement of mutants and cDNAs into bins using, the core markers provides a necessary resource for identification of gene function in maize. (author)

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

    Directory of Open Access Journals (Sweden)

    Claudia Lougon Paiva

    2014-09-01

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

  5. Use of toxicogenomics for identifying genetic markers of pulmonary oedema

    International Nuclear Information System (INIS)

    Balharry, Dominique; Oreffo, Victor; Richards, Roy

    2005-01-01

    This study was undertaken primarily to identify genetic markers of oedema and inflammation. Mild pulmonary injury was induced following the instillation of the oedema-producing agent, bleomycin (0.5 units). Oedema was then confirmed by conventional toxicology (lavage protein levels, free cell counts and lung/body weight ratios) and histology 3 days post-bleomycin instillation.The expression profile of 1176 mRNA species was determined for bleomycin-exposed lung (Clontech Atlas macroarray, n = 9). To obtain pertinent results from these data, it was necessary to develop a simple, effective method for bioinformatic analysis of altered gene expression. Data were log 10 transformed followed by global normalisation. Differential gene expression was accepted if: (a) genes were statistically significant (P ≤ 0.05) from a two-tailed t test; (b) genes were consistently outside a two standard deviation (SD) range from control levels. A combination of these techniques identified 31 mRNA transcripts (approximately 3%) which were significantly altered in bleomycin treated tissue. Of these genes, 26 were down-regulated whilst only five were up-regulated. Two distinct clusters were identified, with 17 genes classified as encoding hormone receptors, and nine as encoding ion channels. Both these clusters were consistently down-regulated.The magnitude of the changes in gene expression were quantified and confirmed by Q-PCR (n = 6), validating the macroarray data and the bioinformatic analysis employed.In conclusion, this study has developed a suitable macroarray analysis procedure and provides the basis for a better understanding of the gene expression changes occurring during the early phase of drug-induced pulmonary oedema

  6. Survey of genetic structure of geese using novel microsatellite markers

    Directory of Open Access Journals (Sweden)

    Fang-Yu Lai

    2018-02-01

    Full Text Available Objective The aim of this study was to create a set of microsatellite markers with high polymorphism for the genetic monitoring and genetic structure analysis of local goose populations. Methods Novel microsatellite markers were isolated from the genomic DNA of white Roman geese using short tandem repeated probes. The DNA segments, including short tandem repeats, were tested for their variability among four populations of geese from the Changhua Animal Propagation Station (CAPS. The selected microsatellite markers could then be used to monitor genetic variability and study the genetic structures of geese from local geese farms. Results 14 novel microsatellite loci were isolated. In addition to seven known loci, two multiplex sets were constructed for the detection of genetic variations in geese populations. The average of allele number, the effective number of alleles, the observed heterozygosity, the expected heterozygosity, and the polymorphism information content were 11.09, 5.145, 0.499, 0.745, and 0.705, respectively. The results of analysis of molecular variance and principal component analysis indicated a contracting white Roman cluster and a spreading Chinese cluster. In white Roman populations, the CAPS populations were depleted to roughly two clusters when K was set equal to 6 in the Bayesian cluster analysis. The founders of private farm populations had a similar genetic structure. Among the Chinese geese populations, the CAPS populations and private populations represented different clads of the phylogenetic tree and individuals from the private populations had uneven genetic characteristics according to various analyses. Conclusion Based on this study’s analyses, we suggest that the CAPS should institute a proper breeding strategy for white Roman geese to avoid further clustering. In addition, for preservation and stable quality, the Chinese geese in the CAPS and the aforementioned proper breeding scheme should be introduced to

  7. Genetic analysis of 430 Chinese Cynodon dactylon accessions using sequence-related amplified polymorphism markers.

    Science.gov (United States)

    Huang, Chunqiong; Liu, Guodao; Bai, Changjun; Wang, Wenqiang

    2014-10-21

    Although Cynodon dactylon (C. dactylon) is widely distributed in China, information on its genetic diversity within the germplasm pool is limited. The objective of this study was to reveal the genetic variation and relationships of 430 C. dactylon accessions collected from 22 Chinese provinces using sequence-related amplified polymorphism (SRAP) markers. Fifteen primer pairs were used to amplify specific C. dactylon genomic sequences. A total of 481 SRAP fragments were generated, with fragment sizes ranging from 260-1800 base pairs (bp). Genetic similarity coefficients (GSC) among the 430 accessions averaged 0.72 and ranged from 0.53-0.96. Cluster analysis conducted by two methods, namely the unweighted pair-group method with arithmetic averages (UPGMA) and principle coordinate analysis (PCoA), separated the accessions into eight distinct groups. Our findings verify that Chinese C. dactylon germplasms have rich genetic diversity, which is an excellent basis for C. dactylon breeding for new cultivars.

  8. 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

  9. Adaptive genetic markers discriminate migratory runs of Chinook salmon (Oncorhynchus tshawytscha) amid continued gene flow.

    Science.gov (United States)

    O'Malley, Kathleen G; Jacobson, Dave P; Kurth, Ryon; Dill, Allen J; Banks, Michael A

    2013-12-01

    Neutral genetic markers are routinely used to define distinct units within species that warrant discrete management. Human-induced changes to gene flow however may reduce the power of such an approach. We tested the efficiency of adaptive versus neutral genetic markers in differentiating temporally divergent migratory runs of Chinook salmon (Oncorhynchus tshawytscha) amid high gene flow owing to artificial propagation and habitat alteration. We compared seven putative migration timing genes to ten microsatellite loci in delineating three migratory groups of Chinook in the Feather River, CA: offspring of fall-run hatchery broodstock that returned as adults to freshwater in fall (fall run), spring-run offspring that returned in spring (spring run), and fall-run offspring that returned in spring (FRS). We found evidence for significant differentiation between the fall and federally listed threatened spring groups based on divergence at three circadian clock genes (OtsClock1b, OmyFbxw11, and Omy1009UW), but not neutral markers. We thus demonstrate the importance of genetic marker choice in resolving complex life history types. These findings directly impact conservation management strategies and add to previous evidence from Pacific and Atlantic salmon indicating that circadian clock genes influence migration timing.

  10. 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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1999-07-01

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

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

    International Nuclear Information System (INIS)

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

    1999-01-01

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

  13. Genetic distinctions between autoimmune hepatitis in Italy and North America.

    Science.gov (United States)

    Muratori, Paolo; Czaja, Albert-J; Muratori, Luigi; Pappas, Georgios; Maccariello, Silvana; Cassani, Fabio; Granito, Alessandro; Ferrari, Rodolfo; Mantovani, Vilma; Lenzi, Marco; Bianchi, Francesco-B

    2005-03-28

    Our goals were to analyze the known genetic predispositions for autoimmune hepatitis (AIH) in AIH Italian population and to compare them with North American counterparts. Human leukocyte antigens (HLA) B8, C7, DR3, DR4, DR7, DR11, DR13, DQ2 and the B8-DR3-DQ2 phenotype were determined by microlymphocytotoxicity and polymerase chain reaction in 74 Italian patients (57 with type 1 and 17 with type 2 AIH) and 149 North American patients with type 1 AIH, and in adequate controls. B8-DR3-DQ2 occurred more frequently in Italian patients with type 1 AIH than in Italian controls (30% vs 7%, P<0.0001), but less frequently than in North American counterparts (30% vs 48%, P = 0.02). DR4 occurred less frequently in Italian patients with type 1 AIH (23% vs 43%, P = 0.01) and in controls (16% vs 34%, P = 0.0003) than in North American counterparts. No differences were found in alleles' frequency between type 1 and type 2 Italian AIH patients. DR11 had a frequency lower in type 1 Italian AIH patients than controls (17% vs 35%, P = 0.01). HLA DR4 is not associated with AIH in Italy. The known HLA risk factors for AIH occur similarly in Italian patients with type 1 and type 2 AIH, and they are less frequent than in North American patients. B8-DR3-DQ2 is the predominant phenotype of type 1 AIH also in Italy, and HLA DR11 may be a regionally distinctive protective factor against type 1 AIH.

  14. Genetic variability of Pantaneiro horse using RAPD-PCR markers

    OpenAIRE

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

    2007-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Roghayeh Najafzadeh

    2014-01-01

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

  16. Genetic variability in Brazilian wheat cultivars assessed by microsatellite markers

    Directory of Open Access Journals (Sweden)

    Ivan Schuster

    2009-01-01

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

  17. On coding genotypes for genetic markers with multiple alleles in genetic association study of quantitative traits

    Directory of Open Access Journals (Sweden)

    Wang Tao

    2011-09-01

    Full Text Available Abstract Background In genetic association study of quantitative traits using F∞ models, how to code the marker genotypes and interpret the model parameters appropriately is important for constructing hypothesis tests and making statistical inferences. Currently, the coding of marker genotypes in building F∞ models has mainly focused on the biallelic case. A thorough work on the coding of marker genotypes and interpretation of model parameters for F∞ models is needed especially for genetic markers with multiple alleles. Results In this study, we will formulate F∞ genetic models under various regression model frameworks and introduce three genotype coding schemes for genetic markers with multiple alleles. Starting from an allele-based modeling strategy, we first describe a regression framework to model the expected genotypic values at given markers. Then, as extension from the biallelic case, we introduce three coding schemes for constructing fully parameterized one-locus F∞ models and discuss the relationships between the model parameters and the expected genotypic values. Next, under a simplified modeling framework for the expected genotypic values, we consider several reduced one-locus F∞ models from the three coding schemes on the estimability and interpretation of their model parameters. Finally, we explore some extensions of the one-locus F∞ models to two loci. Several fully parameterized as well as reduced two-locus F∞ models are addressed. Conclusions The genotype coding schemes provide different ways to construct F∞ models for association testing of multi-allele genetic markers with quantitative traits. Which coding scheme should be applied depends on how convenient it can provide the statistical inferences on the parameters of our research interests. Based on these F∞ models, the standard regression model fitting tools can be used to estimate and test for various genetic effects through statistical contrasts with the

  18. Identification of novel genetic markers of breast cancer survival

    DEFF Research Database (Denmark)

    Guo, Qi; Schmidt, Marjanka K; Kraft, Peter

    2015-01-01

    BACKGROUND: Survival after a diagnosis of breast cancer varies considerably between patients, and some of this variation may be because of germline genetic variation. We aimed to identify genetic markers associated with breast cancer-specific survival. METHODS: We conducted a large meta-analysis ......BACKGROUND: Survival after a diagnosis of breast cancer varies considerably between patients, and some of this variation may be because of germline genetic variation. We aimed to identify genetic markers associated with breast cancer-specific survival. METHODS: We conducted a large meta......-analysis of studies in populations of European ancestry, including 37954 patients with 2900 deaths from breast cancer. Each study had been genotyped for between 200000 and 900000 single nucleotide polymorphisms (SNPs) across the genome; genotypes for nine million common variants were imputed using a common reference...... panel from the 1000 Genomes Project. We also carried out subtype-specific analyses based on 6881 estrogen receptor (ER)-negative patients (920 events) and 23059 ER-positive patients (1333 events). All statistical tests were two-sided. RESULTS: We identified one new locus (rs2059614 at 11q24...

  19. Koalas (Phascolarctos cinereus) From Queensland Are Genetically Distinct From 2 Populations in Victoria.

    Science.gov (United States)

    Ruiz-Rodriguez, Christina T; Ishida, Yasuko; Murray, Neil D; O'Brien, Stephen J; Graves, Jennifer A M; Greenwood, Alex D; Roca, Alfred L

    2016-01-01

    The koala (Phascolarctos cinereus) suffered population declines and local extirpation due to hunting in the early 20th century, especially in southern Australia. Koalas were subsequently reintroduced to the Brisbane Ranges (BR) and Stony Rises (SR) by translocating individuals from a population on French Island descended from a small number of founders. To examine genetic diversity and north-south differentiation, we genotyped 13 microsatellite markers in 46 wild koalas from the BR and SR, and 27 Queensland koalas kept at the US zoos. The Queensland koalas displayed much higher heterozygosity (H O = 0.73) than the 2 southern Australian koala populations examined: H O = 0.49 in the BR, whereas H O = 0.41 in the SR. This is consistent with the historical accounts of bottlenecks and founder events affecting the southern populations and contrasts with reports of high genetic diversity in some southern populations. The 2 southern Australian koala populations were genetically similar (F ST = 0.018, P = 0.052). By contrast, northern and southern Australian koalas were highly differentiated (F ST = 0.27, P < 0.001), thereby suggesting that geographic structuring should be considered in the conservation management of koalas. Sequencing of 648bp of the mtDNA control region in Queensland koalas found 8 distinct haplotypes, one of which had not been previously detected among koalas. Queensland koalas displayed high mitochondrial haplotype diversity (H = 0.753) and nucleotide diversity (π = 0.0072), indicating along with the microsatellite data that North American zoos have maintained high levels of genetic diversity among their Queensland koalas. © The American Genetic Association 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  20. Genetic markers for western corn rootworm resistance to Bt toxin.

    Science.gov (United States)

    Flagel, Lex E; Swarup, Shilpa; Chen, Mao; Bauer, Christopher; Wanjugi, Humphrey; Carroll, Matthew; Hill, Patrick; Tuscan, Meghan; Bansal, Raman; Flannagan, Ronald; Clark, Thomas L; Michel, Andrew P; Head, Graham P; Goldman, Barry S

    2015-01-07

    Western corn rootworm (WCR) is a major maize (Zea mays L.) pest leading to annual economic losses of more than 1 billion dollars in the United States. Transgenic maize expressing insecticidal toxins derived from the bacterium Bacillus thuringiensis (Bt) are widely used for the management of WCR. However, cultivation of Bt-expressing maize places intense selection pressure on pest populations to evolve resistance. Instances of resistance to Bt toxins have been reported in WCR. Developing genetic markers for resistance will help in characterizing the extent of existing issues, predicting where future field failures may occur, improving insect resistance management strategies, and in designing and sustainably implementing forthcoming WCR control products. Here, we discover and validate genetic markers in WCR that are associated with resistance to the Cry3Bb1 Bt toxin. A field-derived WCR population known to be resistant to the Cry3Bb1 Bt toxin was used to generate a genetic map and to identify a genomic region associated with Cry3Bb1 resistance. Our results indicate that resistance is inherited in a nearly recessive manner and associated with a single autosomal linkage group. Markers tightly linked with resistance were validated using WCR populations collected from Cry3Bb1 maize fields showing significant WCR damage from across the US Corn Belt. Two markers were found to be correlated with both diet (R2 = 0.14) and plant (R2 = 0.23) bioassays for resistance. These results will assist in assessing resistance risk for different WCR populations, and can be used to improve insect resistance management strategies. Copyright © 2015 Flagel et al.

  1. Genetic diversity analysis among collected purslane (Portulaca oleracea L.) accessions using ISSR markers.

    Science.gov (United States)

    Alam, M Amirul; Juraimi, Abdul Shukor; Rafii, Mohd Yusop; Hamid, Azizah Abdul; Arolu, Ibrahim Wasiu; Abdul Latif, M

    2015-01-01

    Genetic diversity and relationships among 45 collected purslane accessions were evaluated using ISSR markers. The 28 primers gave a total of 167 bands, among which 163 were polymorphic (97.6%). The genetic diversity as estimated by Shannon's information index was 0.513, revealing a quite high level of genetic diversity in the germplasm. The average number of observed allele, effective allele, expected heterozygosity, polymorphic information content (PIC) and Nei's index were 5.96, 1.59, 0.43, 0.35 and 0.35, respectively. The UPGMA dendrogram based on Nei's genetic distance grouped the whole germplasm into 7 distinct clusters. The analysis of molecular variance (AMOVA) revealed that 89% of total variation occurred within population, while 11% were found among populations. Based on the constructed dendrogram using ISSR markers those accessions that are far from each other by virtue of genetic origin and diversity index (like Ac1 and Ac42; Ac19 and Ac45; Ac9 and Ac23; Ac18 and A25; Ac24 and Ac18) are strongly recommended to select as parent for future breeding program to develop high yielding and stress tolerant purslane variety in contribution to global food security. Copyright © 2014 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  2. Genetic diversity of worldwide Jerusalem artichoke (Helianthus tuberosus) germplasm as revealed by RAPD markers.

    Science.gov (United States)

    Wangsomnuk, P P; Khampa, S; Wangsomnuk, P; Jogloy, S; Mornkham, T; Ruttawat, B; Patanothai, A; Fu, Y B

    2011-12-12

    Jerusalem artichoke (Helianthus tuberosus) is a wild relative of the cultivated sunflower (H. annuus); it is an old tuber crop that has recently received renewed interest. We used RAPD markers to characterize 147 Jerusalem artichoke accessions from nine countries. Thirty RAPD primers were screened; 13 of them detected 357 reproducible RAPD bands, of which 337 were polymorphic. Various diversity analyses revealed several different patterns of RAPD variation. More than 93% of the RAPD variation was found within accessions of a country. Weak genetic differentiation was observed between wild and cultivated accessions. Six groups were detected in this germplasm set. Four ancestral groups were found for the Canadian germplasm. The most genetically distinct accessions were identified. These findings provide useful diversity information for understanding the Jerusalem artichoke gene pool, for conserving Jerusalem artichoke germplasm, and for choosing germplasm for genetic improvement.

  3. Genetic markers of insulin resistance in gestational diabetes

    Directory of Open Access Journals (Sweden)

    Tatiana Vasil'evna Sebko

    2009-12-01

    Full Text Available Aim. To search for genetic markers of insulin resistance and impaired insulin secretion in pregnant women with gestational diabetes mellitus (GDM. Materials and methods. A total of 100 healthy pregnant women and 185 patients with GDM were available for examination. 80 patients developedGDM during current pregnancy, in 105 it was diagnosed 4-19 years ago. 25 of the 105 GDM patients had a history of type 2 DM. The following parameterswere measured: beta-cell secretory activity (proinsulin, ITI, C-peptide, total cholesterol (CH, HDL and LDL CH, triglycerides, HbA1c,fasting glycemia. Molecular-genetic DNA testing using PCR included studies of KCNJ 11, TCF7L2, PPARG2, ADIPOQ, ADIPOR1, ADIPOR2gene polymorphism. These genes were chosen based on the published data associating them with disturbed insulin secretion and sensitivity in DM2patient. Results. Pregnant women with GDM and obesity showed elevated IRI and leptin levels compared with controls. This rise was accompanied bymarked insulin resistance in 75% of these patients. In 50% of the healthy women proinsulin and insulin secretion decreased. Obesity in pregnantpatients was associated with significant elevation of proinsulin, IRI, and C-peptyide levels and GDM with Lys/Lys genotype of polymorphous markerGlu23k of KCNJ11 gene, pro and ala allele of polymorphous marker A219T of ADIPOR2 gene. These associations suggest specific genetic featuresof GDM related to impaired insulin secretion and sensitivity. Conclusion. Studies of common genetic nature of GDM and DM2 permit to identify risk groups at the preclinical stage, plan prevention and treatmentof these disorders.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. Stable MSAP markers for the distinction of Vitis vinifera cv Pinot noir clones.

    Science.gov (United States)

    Ocaña, Juan; Walter, Bernard; Schellenbaum, Paul

    2013-11-01

    Grapevine is one of the most economically important fruit crops. Molecular markers have been used to study grapevine diversity. For instance, simple sequence repeats are a powerful tool for identification of grapevine cultivars, while amplified fragment length polymorphisms have shown their usefulness in intra-varietal diversity studies. Other techniques such as sequence-specific amplified polymorphism are based on the presence of mobile elements in the genome, but their detection lies upon their activity. Relevant attention has been drawn toward epigenetic sources of variation. In this study, a set of Vitis vinifera cv Pinot noir clones were analyzed using the methylation-sensitive amplified polymorphism technique with isoschizomers MspI and HpaII. Nine out of fourteen selective primer combinations were informative and generated two types of polymorphic fragments which were categorized as "stable" and "unstable." In total, 23 stable fragments were detected and they discriminated 92.5 % of the studied clones. Detected stable polymorphisms were either common to several clones, restricted to a few clones or unique to a single clone. The identification of these stable epigenetic markers will be useful in clonal diversity studies. We highlight the relevance of stable epigenetic variation in V. vinifera clones and analyze at which level these markers could be applicable for the development of forthright techniques for clonal distinction.

  9. 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.

  10. 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.

  11. 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

  12. Application of PCR – RFLP markers for identification of genetically delimited groups of the Calypogeia fissa complex (Jungermanniopsida, Calypogeiaceae

    Directory of Open Access Journals (Sweden)

    Buczkowska Katarzyna

    2015-06-01

    Full Text Available Currently, two subspecies are formally recognized within Calypogeia fissa: C. fissa subsp. fissa occurring in Europe and C. fissa subsp. neogea known from North America. Genetic studies have revealed a complex structure of this species. Within the European part of distribution, three genetically distinct groups PS, PB and G are distinguished. The combination of the SCAR marker Cal04 and PCR-RFLP markers with three restriction enzymes (SmaI, TaqI and TspGWI allowed the recognition of all groups within the C. fissa complex. The TaqI enzyme recognizing the restriction sites in the PCR product of SCAR marker Ca104 turned out to be the best marker

  13. Novel molecular markers of Chlamydia pecorum genetic diversity in the koala (Phascolarctos cinereus)

    Science.gov (United States)

    2011-01-01

    Background Chlamydia pecorum is an obligate intracellular bacterium and the causative agent of reproductive and ocular disease in several animal hosts including koalas, sheep, cattle and goats. C. pecorum strains detected in koalas are genetically diverse, raising interesting questions about the origin and transmission of this species within koala hosts. While the ompA gene remains the most widely-used target in C. pecorum typing studies, it is generally recognised that surface protein encoding genes are not suited for phylogenetic analysis and it is becoming increasingly apparent that the ompA gene locus is not congruent with the phylogeny of the C. pecorum genome. Using the recently sequenced C. pecorum genome sequence (E58), we analysed 10 genes, including ompA, to evaluate the use of ompA as a molecular marker in the study of koala C. pecorum genetic diversity. Results Three genes (incA, ORF663, tarP) were found to contain sufficient nucleotide diversity and discriminatory power for detailed analysis and were used, with ompA, to genotype 24 C. pecorum PCR-positive koala samples from four populations. The most robust representation of the phylogeny of these samples was achieved through concatenation of all four gene sequences, enabling the recreation of a "true" phylogenetic signal. OmpA and incA were of limited value as fine-detailed genetic markers as they were unable to confer accurate phylogenetic distinctions between samples. On the other hand, the tarP and ORF663 genes were identified as useful "neutral" and "contingency" markers respectively, to represent the broad evolutionary history and intra-species genetic diversity of koala C. pecorum. Furthermore, the concatenation of ompA, incA and ORF663 sequences highlighted the monophyletic nature of koala C. pecorum infections by demonstrating a single evolutionary trajectory for koala hosts that is distinct from that seen in non-koala hosts. Conclusions While the continued use of ompA as a fine

  14. Novel molecular markers of Chlamydia pecorum genetic diversity in the koala (Phascolarctos cinereus

    Directory of Open Access Journals (Sweden)

    Timms Peter

    2011-04-01

    Full Text Available Abstract Background Chlamydia pecorum is an obligate intracellular bacterium and the causative agent of reproductive and ocular disease in several animal hosts including koalas, sheep, cattle and goats. C. pecorum strains detected in koalas are genetically diverse, raising interesting questions about the origin and transmission of this species within koala hosts. While the ompA gene remains the most widely-used target in C. pecorum typing studies, it is generally recognised that surface protein encoding genes are not suited for phylogenetic analysis and it is becoming increasingly apparent that the ompA gene locus is not congruent with the phylogeny of the C. pecorum genome. Using the recently sequenced C. pecorum genome sequence (E58, we analysed 10 genes, including ompA, to evaluate the use of ompA as a molecular marker in the study of koala C. pecorum genetic diversity. Results Three genes (incA, ORF663, tarP were found to contain sufficient nucleotide diversity and discriminatory power for detailed analysis and were used, with ompA, to genotype 24 C. pecorum PCR-positive koala samples from four populations. The most robust representation of the phylogeny of these samples was achieved through concatenation of all four gene sequences, enabling the recreation of a "true" phylogenetic signal. OmpA and incA were of limited value as fine-detailed genetic markers as they were unable to confer accurate phylogenetic distinctions between samples. On the other hand, the tarP and ORF663 genes were identified as useful "neutral" and "contingency" markers respectively, to represent the broad evolutionary history and intra-species genetic diversity of koala C. pecorum. Furthermore, the concatenation of ompA, incA and ORF663 sequences highlighted the monophyletic nature of koala C. pecorum infections by demonstrating a single evolutionary trajectory for koala hosts that is distinct from that seen in non-koala hosts. Conclusions While the continued use of

  15. Birth Characteristics and Childhood Leukemia Risk: Correlations With Genetic Markers.

    Science.gov (United States)

    Kennedy, Amy E; Kamdar, Kala Y; Lupo, Philip J; Okcu, Mehmet F; Scheurer, Michael E; Dorak, Mehmet T

    2015-07-01

    Birth characteristics such as birth order, birth weight, birth defects, and Down syndrome showed some of the first risk associations with childhood leukemia. Examinations of correlations between birth characteristics and leukemia risk markers have been limited to birth weight-related genetic polymorphisms. We integrated information on nongenetic and genetic markers by evaluating the relationship of birth characteristics, genetic markers for childhood acute lymphoblastic leukemia (ALL) susceptibility, and ALL risk together. The multiethnic study consisted of cases with childhood ALL (n=161) and healthy controls (n=261). Birth characteristic data were collected through questionnaires, and genotyping was achieved by TaqMan SNP Genotyping Assays. We observed risk associations for birth weight over 4000 g (odds ratios [OR]=1.93; 95% confidence interval [CI], 1.16-3.19), birth length (OR=1.18 per inch; 95% CI, 1.01-1.38), and with gestational age (OR=1.10 per week; 95% CI, 1.00-1.21). Only the HFE tag single-nucleotide polymorphism (SNP) rs9366637 showed an inverse correlation with a birth characteristic, gestational age, with a gene-dosage effect (P=0.005), and in interaction with a transferrin receptor rs3817672 genotype (Pinteraction=0.05). This correlation translated into a strong association for rs9366637 with preterm birth (OR=5.0; 95% CI, 1.19-20.9). Our study provides evidence for the involvement of prenatal events in the development of childhood ALL. The inverse correlation of rs9366637 with gestational age has implications on the design of HFE association studies in birth weight and childhood conditions using full-term newborns as controls.

  16. Review: domestic animal forensic genetics - biological evidence, genetic markers, analytical approaches and challenges.

    Science.gov (United States)

    Kanthaswamy, S

    2015-10-01

    This review highlights the importance of domestic animal genetic evidence sources, genetic testing, markers and analytical approaches as well as the challenges this field is facing in view of the de facto 'gold standard' human DNA identification. Because of the genetic similarity between humans and domestic animals, genetic analysis of domestic animal hair, saliva, urine, blood and other biological material has generated vital investigative leads that have been admitted into a variety of court proceedings, including criminal and civil litigation. Information on validated short tandem repeat, single nucleotide polymorphism and mitochondrial DNA markers and public access to genetic databases for forensic DNA analysis is becoming readily available. Although the fundamental aspects of animal forensic genetic testing may be reliable and acceptable, animal forensic testing still lacks the standardized testing protocols that human genetic profiling requires, probably because of the absence of monetary support from government agencies and the difficulty in promoting cooperation among competing laboratories. Moreover, there is a lack in consensus about how to best present the results and expert opinion to comply with court standards and bear judicial scrutiny. This has been the single most persistent challenge ever since the earliest use of domestic animal forensic genetic testing in a criminal case in the mid-1990s. Crime laboratory accreditation ensures that genetic test results have the courts' confidence. Because accreditation requires significant commitments of effort, time and resources, the vast majority of animal forensic genetic laboratories are not accredited nor are their analysts certified forensic examiners. The relevance of domestic animal forensic genetics in the criminal justice system is undeniable. However, further improvements are needed in a wide range of supporting resources, including standardized quality assurance and control protocols for sample

  17. The use of genetic markers to estimate relationships between dogs in the course of criminal investigations.

    Science.gov (United States)

    Ciampolini, Roberta; Cecchi, Francesca; Spinetti, Isabella; Rocchi, Anna; Biscarini, Filippo

    2017-08-17

    Attacks on humans by dogs in a pack, though uncommon, do happen, and result in severe, sometimes fatal, injuries. We describe the role that canine genetic markers played during the investigation of a fatal dog-pack attack involving a 50-year-old male truck driver in a parking lot in Tuscany (Italy). Using canine specific STR genetic markers, the local authorities, in the course of their investigations, reconstructed the genetic relationships between the dogs that caused the deadly aggression and other dogs belonging to the owner of the parking who, at the moment of the aggression, was located in another region of Italy. From a Bayesian clustering algorithm, the most likely number of clusters was two. The average relatedness among the dogs responsible for the aggression was higher than the average relatedness among the other dogs or between the two groups. Taken together, all these results indicate that the two groups of dogs are clearly distinct. Genetic relationships showed that the two groups of dogs were not related. It was therefore unlikely that the murderous dogs belonged to the owner of the parking lot who, on grounds of this and additional evidence, was eventually acquitted.

  18. Genetic variability of watermelon accessions based on microsatellite markers.

    Science.gov (United States)

    de S Gama, R N C; Santos, C A F; de C S Dias, R

    2013-03-13

    We analyzed the genetic variability of 40 watermelon accessions collected from 8 regions of Northeastern Brazil using microsatellite markers, in order to suggest strategies of conservation and utilization of genetic variability in this species. These accessions are not commercial cultivars. They were sampled in areas of traditional farmers that usually keep their own seeds for future plantings year after year. An UPGMA dendrogram was generated from a distance matrix of the Jaccard coefficient, based on 41 alleles of 13 microsatellite loci. Analysis of molecular variance was made by partitioning between and within geographical regions. The similarity coefficient between accessions ranged from 37 to 96%; the dendrogram gave a co-phenetic value of 0.80. The among population genetic variability was high ( (^)ϕST = 0.319). Specific clusters of accessions sampled in 3 regions of Maranhão were observed while the other 5 regions did not presented specific clusters by regions. We conclude that watermelon genetic variability is not uniformly dispersed in the regions analyzed, indicating that geographical barriers or edaphoclimatic conditions have limited open mating. We suggest sampling a greater number of populations, so regional species diversity will be better represented and preserved in the germplasm bank.

  19. Genetic characterization of the Bardigiano horse using microsatellite markers

    Directory of Open Access Journals (Sweden)

    Claudio Lisa

    2010-01-01

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

  20. Pauci- and Multibacillary Leprosy: Two Distinct, Genetically Neglected Diseases

    Science.gov (United States)

    Gaschignard, Jean; Grant, Audrey Virginia; Thuc, Nguyen Van; Orlova, Marianna; Cobat, Aurélie; Huong, Nguyen Thu; Ba, Nguyen Ngoc; Thai, Vu Hong; Abel, Laurent; Schurr, Erwin; Alcaïs, Alexandre

    2016-01-01

    After sustained exposure to Mycobacterium leprae, only a subset of exposed individuals develops clinical leprosy. Moreover, leprosy patients show a wide spectrum of clinical manifestations that extend from the paucibacillary (PB) to the multibacillary (MB) form of the disease. This “polarization” of leprosy has long been a major focus of investigation for immunologists because of the different immune response in these two forms. But while leprosy per se has been shown to be under tight human genetic control, few epidemiological or genetic studies have focused on leprosy subtypes. Using PubMed, we collected available data in English on the epidemiology of leprosy polarization and the possible role of human genetics in its pathophysiology until September 2015. At the genetic level, we assembled a list of 28 genes from the literature that are associated with leprosy subtypes or implicated in the polarization process. Our bibliographical search revealed that improved study designs are needed to identify genes associated with leprosy polarization. Future investigations should not be restricted to a subanalysis of leprosy per se studies but should instead contrast MB to PB individuals. We show the latter approach to be the most powerful design for the identification of genetic polarization determinants. Finally, we bring to light the important resource represented by the nine-banded armadillo model, a unique animal model for leprosy. PMID:27219008

  1. Implication of Gastric Cancer Molecular Genetic Markers in Surgical Practice.

    Science.gov (United States)

    Nemtsova, Marina V; Strelnikov, Vladimir V; Tanas, Alexander S; Bykov, Igor I; Zaletaev, Dmitry V; Rudenko, Viktoria V; Glukhov, Alexander I; Kchorobrich, Tatiana V; Li, Yi; Tarasov, Vadim V; Barreto, George E; Aliev, Gjumrakch

    2017-10-01

    We have investigated aberrant methylation of genes CDH1, RASSF1A, MLH1, N33, DAPK, expression of genes hTERT, MMP7, MMP9, BIRC5 (survivin), PTGS2, and activity of telomerase of 106 gastric tumor samples obtained intra-operatively and 53 gastric tumor samples from the same group of patients obtained endoscopically before surgery. Biopsy specimens obtained from 50 patients with chronic calculous cholecystitis were used as a control group. Together with tissue samples obtained from different sites remote to tumors, a total of 727 samples have been studied. The selected parameters comprise a system of molecular markers that can be used in both diagnostics of gastric cancer and in dynamic monitoring of patients after surgery. Special attention was paid to the use of molecular markers for the diagnostics of malignant process in the material obtained endoscopically since the efficacy of morphological diagnostics in biopsies is compromised by intratumoral heterogeneity, which may prevent reliable identification of tumor cells in the sampling. Our data indicated that certain molecular genetic events provided more sensitive yet specific markers of the tumor. We demonstrated that molecular profiles detected in preoperative biopsies were confirmed by the material obtained intra-operatively. The use of endoscopic material facilitates gastric tumors pre-operative diagnostics, improving early detection of gastric cancer and potential effective treatment strategies.

  2. Genetic and epigenetic markers in colorectal cancer screening: recent advances.

    Science.gov (United States)

    Singh, Manish Pratap; Rai, Sandhya; Suyal, Shradha; Singh, Sunil Kumar; Singh, Nand Kumar; Agarwal, Akash; Srivastava, Sameer

    2017-07-01

    Colorectal cancer (CRC) is a heterogenous disease which develops from benign intraepithelial lesions known as adenomas to malignant carcinomas. Acquired alterations in Wnt signaling, TGFβ, MAPK pathway genes and clonal propagation of altered cells are responsible for this transformation. Detection of adenomas or early stage cancer in asymptomatic patients and better prognostic and predictive markers is important for improving the clinical management of CRC. Area covered: In this review, the authors have evaluated the potential of genetic and epigenetic alterations as markers for early detection, prognosis and therapeutic predictive potential in the context of CRC. We have discussed molecular heterogeneity present in CRC and its correlation to prognosis and response to therapy. Expert commentary: Molecular marker based CRC screening methods still fail to gain trust of clinicians. Invasive screening methods, molecular heterogeneity, chemoresistance and low quality test samples are some key challenges which need to be addressed in the present context. New sequencing technologies and integrated omics data analysis of individual or population cohort results in GWAS. MPE studies following a GWAS could be future line of research to establish accurate correlations between CRC and its risk factors. This strategy would identify most reliable biomarkers for CRC screening and management.

  3. Genetic diversity analysis of Capparis spinosa L. populations by using ISSR markers.

    Science.gov (United States)

    Liu, C; Xue, G P; Cheng, B; Wang, X; He, J; Liu, G H; Yang, W J

    2015-12-09

    Capparis spinosa L. is an important medicinal species in the Xinjiang Province of China. Ten natural populations of C. spinosa from 3 locations in North, Central, and South Xinjiang were studied using morphological trait inter simple sequence repeat (ISSR) molecular markers to assess the genetic diversity and population structure. In this study, the 10 ISSR primers produced 313 amplified DNA fragments, with 52% of fragments being polymorphic. Unweighted pair-group method with arithmetic average (UPGMA) cluster analysis indicated that 10 C. spinosa populations were clustered into 3 geographically distinct groups. The Nei gene of C. spinosa populations in different regions had Diversity and Shannon's information index ranges of 0.1312-0.2001 and 0.1004-0.1875, respectively. The 362 markers were used to construct the dendrogram based on the UPGMA cluster analysis. The dendrogram indicated that 10 populations of C. spinosa were clustered into 3 geographically distinct groups. The results showed these genotypes have high genetic diversity, and can be used for an alternative breeding program.

  4. A genetically diverse but distinct North American population of Sarcocystis neurona includes an overrepresented clone described by 12 microsatellite alleles.

    Science.gov (United States)

    Asmundsson, Ingrid M; Dubey, J P; Rosenthal, Benjamin M

    2006-09-01

    The population genetics and systematics of most coccidians remain poorly defined despite their impact on human and veterinary health. Non-recombinant parasite clones characterized by distinct transmission and pathogenesis traits persist in the coccidian Toxoplasma gondii despite opportunities for sexual recombination. In order to determine whether this may be generally true for tissue-cyst forming coccidia, and to address evolutionary and taxonomic problems within the genus Sarcocystis, we characterized polymorphic microsatellite markers in Sarcocystis neurona, the major causative agent of equine protozoal myeloencephalitis (EPM). Bayesian statistical modeling, phylogenetic reconstruction based on genotypic chord distances, and analyses of linkage disequilibrium were employed to examine the population structure within S. neurona and closely related Sarcocystis falcatula isolates from North and South America. North American S. neurona were clearly differentiated from those of South America and also from isolates of S. falcatula. Although S. neurona is characterized by substantial allelic and genotypic diversity typical of interbreeding populations, one genotype occurs with significantly excessive frequency; thus, some degree of asexual propagation of S. neurona clones may naturally occur. Finally, S. neurona isolated from disparate North American localities and diverse hosts (opossums, a Southern sea otter, and horses) comprise a single genetic population. Isolates associated with clinical neurological disease bear no obvious distinction as measured by these presumably neutral genetic markers.

  5. Genetically distinct subsets within ANCA-associated vasculitis.

    LENUS (Irish Health Repository)

    Lyons, Paul A

    2012-07-19

    Antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis is a severe condition encompassing two major syndromes: granulomatosis with polyangiitis (formerly known as Wegener\\'s granulomatosis) and microscopic polyangiitis. Its cause is unknown, and there is debate about whether it is a single disease entity and what role ANCA plays in its pathogenesis. We investigated its genetic basis.

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

    Directory of Open Access Journals (Sweden)

    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

  7. 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

  8. Assessment of genetic diversity in ragi [Eleusine coracana (L.) Gaertn] using morphological, RAPD and SSR markers.

    Science.gov (United States)

    Prabhu, Kalapad Santosh; Das, Anath Bandhu; Dikshit, Nilamani

    2018-04-25

    Finger millet (Eleusine coracana L. Gaertn., 2n=36) is one of the most important minor crops, commonly known as 'ragi' and used as a staple food grain in more than 25 countries including Africa and south Asia. Twenty-seven accessions of ragi were collected from different parts of India and were evaluated for morpho-genetic diversity studies. Simple sequence repeat (SSR) and random amplified polymorphic DNA (RAPD) markers were used for assessment of genetic diversity among 27 genotypes of E. coracana. High degree of similarity (90%) was obtained between 'IC49979A' and 'IC49974B' genotypes, whereas low level of similarity (9.09%) was found between 'IC204141' and 'IC49985' as evident in morphological and DNA markers. A total of 64 SSR and 301 RAPD amplicons were produced, out of which 87.50% and 77.20% DNA fragments showed polymorphism, respectively. The clustering pattern obtained among the genotypes corresponded well with their morphological and cytological data with a monophyletic origin of this species which was further supported by high bootstrap values and principal component analysis. Cluster analysis showed that ragi accessions were categorised into three distinct groups. Genotypes IC344761, IC340116, IC340127, IC49965 and IC49985 found accession specific in RAPD and SSR markers. The variation among ragi accessions might be used as potential source of germplasm for crop improvement.

  9. Intelligent DNA-based molecular diagnostics using linked genetic markers

    Energy Technology Data Exchange (ETDEWEB)

    Pathak, D.K.; Perlin, M.W.; Hoffman, E.P.

    1994-12-31

    This paper describes a knowledge-based system for molecular diagnostics, and its application to fully automated diagnosis of X-linked genetic disorders. Molecular diagnostic information is used in clinical practice for determining genetic risks, such as carrier determination and prenatal diagnosis. Initially, blood samples are obtained from related individuals, and PCR amplification is performed. Linkage-based molecular diagnosis then entails three data analysis steps. First, for every individual, the alleles (i.e., DNA composition) are determined at specified chromosomal locations. Second, the flow of genetic material among the individuals is established. Third, the probability that a given individual is either a carrier of the disease or affected by the disease is determined. The current practice is to perform each of these three steps manually, which is costly, time consuming, labor-intensive, and error-prone. As such, the knowledge-intensive data analysis and interpretation supersede the actual experimentation effort as the major bottleneck in molecular diagnostics. By examining the human problem solving for the task, we have designed and implemented a prototype knowledge-based system capable of fully automating linkage-based molecular diagnostics in X-linked genetic disorders, including Duchenne Muscular Dystrophy (DMD). Our system uses knowledge-based interpretation of gel electrophoresis images to determine individual DNA marker labels, a constraint satisfaction search for consistent genetic flow among individuals, and a blackboard-style problem solver for risk assessment. We describe the system`s successful diagnosis of DMD carrier and affected individuals from raw clinical data.

  10. Genetic studies and a search for molecular markers that are linked ...

    African Journals Online (AJOL)

    SERVER

    Instead, linkage analysis resulted in the construction of a molecular marker linkage map consisting of 45 ..... This limits the application of this marker type, particularly in ... primer design when one uses RAPDs. .... Concepts of Genetics. Fourth.

  11. Genetic diversity of Colombian sheep by microsatellite markers

    Directory of Open Access Journals (Sweden)

    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.

  12. Detection genetic variability of secale cereale L. by scot markers

    Directory of Open Access Journals (Sweden)

    Lenka Petrovičová

    2017-01-01

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

  13. 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.

  14. 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.

  15. Novel genetic markers associate with atrial fibrillation risk in Europeans and Japanese.

    Science.gov (United States)

    Lubitz, Steven A; Lunetta, Kathryn L; Lin, Honghuang; Arking, Dan E; Trompet, Stella; Li, Guo; Krijthe, Bouwe P; Chasman, Daniel I; Barnard, John; Kleber, Marcus E; Dörr, Marcus; Ozaki, Kouichi; Smith, Albert V; Müller-Nurasyid, Martina; Walter, Stefan; Agarwal, Sunil K; Bis, Joshua C; Brody, Jennifer A; Chen, Lin Y; Everett, Brendan M; Ford, Ian; Franco, Oscar H; Harris, Tamara B; Hofman, Albert; Kääb, Stefan; Mahida, Saagar; Kathiresan, Sekar; Kubo, Michiaki; Launer, Lenore J; MacFarlane, Peter W; Magnani, Jared W; McKnight, Barbara; McManus, David D; Peters, Annette; Psaty, Bruce M; Rose, Lynda M; Rotter, Jerome I; Silbernagel, Guenther; Smith, Jonathan D; Sotoodehnia, Nona; Stott, David J; Taylor, Kent D; Tomaschitz, Andreas; Tsunoda, Tatsuhiko; Uitterlinden, Andre G; Van Wagoner, David R; Völker, Uwe; Völzke, Henry; Murabito, Joanne M; Sinner, Moritz F; Gudnason, Vilmundur; Felix, Stephan B; März, Winfried; Chung, Mina; Albert, Christine M; Stricker, Bruno H; Tanaka, Toshihiro; Heckbert, Susan R; Jukema, J Wouter; Alonso, Alvaro; Benjamin, Emelia J; Ellinor, Patrick T

    2014-04-01

    This study sought to identify nonredundant atrial fibrillation (AF) genetic susceptibility signals and examine their cumulative relations with AF risk. AF-associated loci span broad genomic regions that may contain multiple susceptibility signals. Whether multiple signals exist at AF loci has not been systematically explored. We performed association testing conditioned on the most significant, independently associated genetic markers at 9 established AF loci using 2 complementary techniques in 64,683 individuals of European ancestry (3,869 incident and 3,302 prevalent AF cases). Genetic risk scores were created and tested for association with AF in Europeans and an independent sample of 11,309 individuals of Japanese ancestry (7,916 prevalent AF cases). We observed at least 4 distinct AF susceptibility signals on chromosome 4q25 upstream of PITX2, but not at the remaining 8 AF loci. A multilocus score comprised 12 genetic markers demonstrated an estimated 5-fold gradient in AF risk. We observed a similar spectrum of risk associated with these markers in Japanese. Regions containing AF signals on chromosome 4q25 displayed a greater degree of evolutionary conservation than the remainder of the locus, suggesting that they may tag regulatory elements. The chromosome 4q25 AF locus is architecturally complex and harbors at least 4 AF susceptibility signals in individuals of European ancestry. Similar polygenic AF susceptibility exists between Europeans and Japanese. Future work is necessary to identify causal variants, determine mechanisms by which associated loci predispose to AF, and explore whether AF susceptibility signals classify individuals at risk for AF and related morbidity. Copyright © 2014 American College of Cardiology Foundation. Published by Elsevier Inc. All rights reserved.

  16. Genetic Diversity Assessment of Portuguese Cultivated Vicia faba L. through IRAP Markers

    Directory of Open Access Journals (Sweden)

    Diana Tomás

    2016-03-01

    Full Text Available Faba bean have been grown in Portugal for a long time and locally adapted populations are still maintained on farm. The genetic diversity of four Portuguese faba bean populations that are still cultivated in some regions of the country was evaluated using the Inter Retrotransposons Amplified Polymorphism (IRAP technique. It was shown that molecular markers based on retrotransposons previously identified in other species can be efficiently used in the genetic variability assessment of Vicia faba. The IRAP experiment targeting Athila yielded the most informative banding patterns. Cluster analysis using the neighbor-joining algorithm generated a dendrogram that clearly shows the distribution pattern of V. faba samples. The four equina accessions are separated from each other and form two distinct clades while the two major faba bean accessions are not unequivocally separated by the IRAP. Fluorescent In Situ Hybridization (FISH analysis of sequences amplified by IRAP Athila revealed a wide distribution throughout V. faba chromosomes, confirming the whole-genome coverage of this molecular marker. Morphological characteristics were also assessed through cluster analysis of seed characters using the unweighted pair group method arithmetic average (UPGMA and principal component analysis (PCA, showing a clear discrimination between faba bean major and equina groups. It was also found that the seed character most relevant to distinguish accessions was 100 seed weight. Seed morphological traits and IRAP evaluation give similar results supporting the potential of IRAP analysis for genetic diversity studies.

  17. Genetic structure and inter-generic relationship of closed colony of laboratory rodents based on RAPD markers.

    Science.gov (United States)

    Kumar, Mahadeo; Kumar, Sharad

    2014-11-01

    Molecular genetic analysis was performed using random amplified polymorphic DNA (RAPD) on three commonly used laboratory bred rodent genera viz. mouse (Mus musculus), rat (Rattus norvegicus) and guinea pig (Cavia porcellus) as sampled from the breeding colony maintained at the Animal Facility, CSIR-Indian Institute of Toxicology Research, Lucknow. In this study, 60 samples, 20 from each genus, were analyzed for evaluation of genetic structure of rodent stocks based on polymorphic bands using RAPD markers. Thirty five random primers were assessed for RAPD analysis. Out of 35, only 20 primers generated a total of 56.88% polymorphic bands among mice, rats and guinea pigs. The results revealed significantly variant and distinct fingerprint patterns specific to each of the genus. Within-genera analysis, the highest (89.0%) amount of genetic homogeneity was observed in mice samples and the least (79.3%) were observed in guinea pig samples. The amount of genetic homogeneity was observed very high within all genera. The average genetic diversity index observed was low (0.045) for mice and high (0.094) for guinea pigs. The inter-generic distances were maximum (0.8775) between mice and guinea pigs; and the minimum (0.5143) between rats and mice. The study proved that the RAPD markers are useful as genetic markers for assessment of genetic structure as well as inter-generic variability assessments.

  18. THE USE OF MICROSATELLITE MARKERS TO STUDY GENETIC DIVERSITY IN INDONESIAN SHEEP

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    Jakaria

    2012-03-01

    Full Text Available The purpose of this research was to study genetic diversity in Indonesian sheep population using microsatellite markers. A total of 18 microsatellite loci have been used for genotyping Indonesian sheep. Total sheep blood 200 samples were extracted from garut sheep of fighting and meat types, purbalingga sheep, batur sheep and jember sheep populations by using a salting out method. Microsatellite loci data were analyzed using POPGENE 3.2 software. Based on this study obtained 180 alleles from 17 microsatellite loci, while average number of alleles was 6.10 alleles (6 to 18 alleles from five Indonesian sheep populations (garut sheep of fighting type, garut sheep of meat type, purbalingga sheep, batur sheep and jember sheep population. The average of observed heterozygosity (Ho and expected heterozygosity (He values were 0.5749 and 0.6896, respectively, while the genetic differentiation for inbreeding among population (FIS, within population (FIT and average genetic differentiation (FST were 0.1006, 0.1647 and 0.0712, respectively. Genetic distance and genetic tree showed that Indonesian sheep population was distinct from garut sheep of fighting and meat types, purbalingga sheep, batur sheep and jember sheep population. Based on this results were needed a strategy for conservation and breeding programs in each Indonesian sheep population.

  19. Population genetic structure of rare and endangered plants using molecular markers

    Science.gov (United States)

    Raji, Jennifer; Atkinson, Carter T.

    2013-01-01

    This study was initiated to assess the levels of genetic diversity and differentiation in the remaining populations of Phyllostegia stachyoides and Melicope zahlbruckneri in Hawai`i Volcanoes National Park and determine the extent of gene flow to identify genetically distinct individuals or groups for conservation purposes. Thirty-six Amplified Fragment Length Polymorphic (AFLP) primer combinations generated a total of 3,242 polymorphic deoxyribonucleic acid (DNA) fragments in the P. stachyoides population with a percentage of polymorphic bands (PPB) ranging from 39.3 to 65.7% and 2,780 for the M. zahlbruckneri population with a PPB of 18.8 to 64.6%. Population differentiation (Fst) of AFLP loci between subpopulations of P. stachyoides was low (0.043) across populations. Analysis of molecular variance of P. stachyoides showed that 4% of the observed genetic differentiation occurred between populations in different kīpuka and 96% when individuals were pooled from all kīpuka. Moderate genetic diversity was detected within the M. zahlbruckneri population. Bayesian and multivariate analyses both classified the P. stachyoides and M. zahlbruckneri populations into genetic groups with considerable sub-structuring detected in the P. stachyoides population. The proportion of genetic differentiation among populations explained by geographical distance was estimated by Mantel tests. No spatial correlation was found between genetic and geographic distances in both populations. Finally, a moderate but significant gene flow that could be attributed to insect or bird-mediated dispersal of pollen across the different kīpuka was observed. The results of this study highlight the utility of a multi-allelic DNA-based marker in screening a large number of polymorphic loci in small and closely related endangered populations and revealed the presence of genetically unique groups of individuals in both M. zahlbruckneri and P. stachyoides populations. Based on these findings

  20. Genetic markers of comorbid depression and alcoholism in women.

    Science.gov (United States)

    Procopio, Daniela O; Saba, Laura M; Walter, Henriette; Lesch, Otto; Skala, Katrin; Schlaff, Golda; Vanderlinden, Lauren; Clapp, Peter; Hoffman, Paula L; Tabakoff, Boris

    2013-06-01

    Alcohol dependence (AD) is often accompanied by comorbid depression. Recent clinical evidence supports the benefit of subtype-specific pharmacotherapy in treating the population of alcohol-dependent subjects with comorbid major depressive disorder (MDD). However, in many alcohol-dependent subjects, depression is a reactive response to chronic alcohol use and withdrawal and abates with a period of abstinence. Genetic markers may distinguish alcohol-dependent subjects with MDD not tied chronologically and etiologically to their alcohol consumption. In this work, we investigated the association of adenylyl cyclase genes (ADCY1-9), which are implicated in both AD and mood disorders, with alcoholism and comorbid depression. Subjects from Vienna, Austria (n = 323) were genotyped, and single nucleotide polymorphisms (1,152) encompassing the genetic locations of the 9 ADCY genes were examined. The Vienna cohort contained alcohol-dependent subjects differentiated using the Lesch Alcoholism Typology. In this typology, subjects are segregated into 4 types. Type III alcoholism is distinguished by co-occurrence of symptoms of depression and by affecting predominantly females. We identified 4 haplotypes associated with the phenotype of Type III alcoholism in females. One haplotype was in a genomic area in proximity to ADCY2, but actually within a lincRNA gene, 2 haplotypes were within ADCY5, and 1 haplotype was within the coding region of ADCY8. Three of the 4 haplotypes contributed independently to Type III alcoholism and together generated a positive predictive value of 72% and a negative predictive value of 78% for distinguishing women with a Lesch Type III diagnosis versus women designated as Type I or II alcoholics. Polymorphisms in ADCY8 and ADCY5 and within a lincRNA are associated with an alcohol-dependent phenotype in females, which is distinguished by comorbid signs of depression. Each of these genetic locations can rationally contribute to the polygenic etiology of

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

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    Jana Ondroušková

    2013-04-01

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

  2. Analysis of the genetic diversity of super sweet corn inbred lines using SSR and SSAP markers.

    Science.gov (United States)

    Ko, W R; Sa, K J; Roy, N S; Choi, H-J; Lee, J K

    2016-01-22

    In this study, we compared the efficiency of simple sequence repeat (SSR) and sequence specific amplified polymorphism (SSAP) markers for analyzing genetic diversity, genetic relationships, and population structure of 87 super sweet corn inbred lines from different origins. SSR markers showed higher average gene diversity and Shannon's information index than SSAP markers. To assess genetic relationships and characterize inbred lines using SSR and SSAP markers, genetic similarity (GS) matrices were constructed. The dendrogram using SSR marker data showed a complex pattern with nine clusters and a GS of 53.0%. For SSAP markers, three clusters were observed with a GS of 50.8%. Results of combined marker data showed six clusters with 53.5% GS. To analyze the genetic population structure of SSR and SSAP marker data, the 87 inbred lines were divided into groups I, II, and admixed based on the membership probability threshold of 0.8. Using combined marker data, the population structure was K = 3 and was divided into groups I, II, III, and admixed. This study represents a comparative analysis of SSR and SSAP marker data for the study of genetic diversity and genetic relationships in super sweet corn inbred lines. Our results would be useful for maize-breeding programs in Korea.

  3. Insights into population ecology and sexual selection in snakes through the application of DNA-based genetic markers.

    Science.gov (United States)

    Gibbs, H L; Weatherhead, P J

    2001-01-01

    Hypervariable genetic markers have revolutionized studies of kinship, behavioral ecology, and population biology in vertebrate groups such as birds, but their use in snakes remains limited. To illustrate the value of such markers in snakes, we review studies that have used microsatellite DNA loci to analyze local population differentiation and parentage in snakes. Four ecologically distinct species of snakes all show evidence for differentiation at small spatial scales (2-15 km), but with substantial differences among species. This result highlights how genetic analysis can reveal hidden aspects of the natural history of difficult-to-observe taxa, and it raises important questions about the ecological factors that may contribute to restricted gene flow. A 3-year study of genetic parentage in marked populations of the northern water snake showed that (1) participation in mating aggregations was a poor predictor of genetic-based measures of reproductive success; (2) multiple paternity was high, yet there was no detectable fitness advantage to multiple mating by females; and (3) the opportunity for selection was far higher in males than in females due to a larger variance in male reproductive success, and yet this resulted in no detectable selection on morphological variation in males. Thus genetic markers have provided accurate measures of individual reproductive success in this species, an important step toward resolving the adaptive significance of key features including multiple paternity and reversed sexual size dimorphism. Overall these studies illustrate how genetic analyses of snakes provide previously unobtainable information of long-standing interest to behavioral ecologists.

  4. Duct- and Acinar-Derived Pancreatic Ductal Adenocarcinomas Show Distinct Tumor Progression and Marker Expression

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    Rute M.M. Ferreira

    2017-10-01

    Full Text Available The cell of origin of pancreatic ductal adenocarcinoma (PDAC has been controversial. Here, we show that identical oncogenic drivers trigger PDAC originating from both ductal and acinar cells with similar histology but with distinct pathophysiology and marker expression dependent on cell of origin. Whereas acinar-derived tumors exhibited low AGR2 expression and were preceded by pancreatic intraepithelial neoplasias (PanINs, duct-derived tumors displayed high AGR2 and developed independently of a PanIN stage via non-mucinous lesions. Using orthotopic transplantation and chimera experiments, we demonstrate that PanIN-like lesions can be induced by PDAC as bystanders in adjacent healthy tissues, explaining the co-existence of mucinous and non-mucinous lesions and highlighting the need to distinguish between true precursor PanINs and PanIN-like bystander lesions. Our results suggest AGR2 as a tool to stratify PDAC according to cell of origin, highlight that not all PanIN-like lesions are precursors of PDAC, and add an alternative progression route to the current model of PDAC development.

  5. [Application of Multiple Genetic Markers in a Case of Determination of Half Sibling].

    Science.gov (United States)

    Yang, Xue; Shi, Mei-sen; Yuan, Li; Lu, Di

    2016-02-01

    A case of half sibling was determined with multiple genetic markers, which could be potentially applied for determination of half sibling relationship from same father. Half sibling relationship was detected by 39 autosomal STR genetic markers, 23 Y-chromosomal STR genetic markers and 12 X -chromosomal STR genetic markers among ZHAO -1, ZHAO -2, ZHAO -3, ZHAO -4, and ZHAO-5. According to autosomal STR, Y-STR and X-STR genotyping results, it was determined that ZHAO-4 (alleged half sibling) was unrelated with ZHAO-1 and ZHAO-2; however, ZHAO-3 (alleged half sibling), ZHAO-5 (alleged half sibling) shared same genetic profile with ZHAO-1, and ZHAO-2 from same father. It is reliable to use multiple genetic markers and family gene reconstruction to determine half sibling relationship from same father, but it is difficult to determination by calculating half sibling index with ITO and discriminant functions.

  6. Genetic characterization of Gaddi goat breed of Western Himalayas using microsatellite markers

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    Gurdeep Singh

    2015-04-01

    Full Text Available Aim: In the present study, genetic characterization of Gaddi goat breed, a native to north temperate western Himalayan region of India, was carried out for the purpose of breed characterization and assessing existing intra-population genetic diversity. Materials and Methods: Totally, 75 blood samples procured at random from genetically unrelated animals of two sexes and different age groups and true to breed type were collected from different locations in the breeding tract of these goats in Himachal Pradesh, of which only 51 samples with desired quantity and quality were subjected to further processing for DNA isolation. The multi-locus genotype data were generated on 51 Gaddi goats sampled across different regions of the breeding tract in Himachal Pradesh using 15 FAO recommended goat specific microsatellite markers, which gave amplification and observed and effective number of alleles, gene frequency, observed and expected heterozygosity were estimated through PopGene software (1.3.1. Results: A total of 135 distinct alleles were observed with mean observed and effective number of alleles as 9.0000±0.82 and 6.5874±0.56 respectively across all 15 studied loci. The maximum (15 alleles were contributed by loci DRBP1 and P19/DYA and the least (5 by SRCRSP5. The mean heterozygosity was observed to be 0.8347±0.01 ranging from 0.7584 (SRCRSP5 to 0.9156 (P19-DYA across all loci. The mean observed (HO and expected (HE heterozygosities across all loci were 0.7484±0.02 and 0.8431±0.01 respectively. The polymorphism information content (PIC value ranged from 0.7148 (SRCPS5 to 0.909 (P19-DYA with mean PIC of 0.8105±0.01 in the present study. The average heterozygosity was observed to be 0.8347±0.01 ranging from 0.7584 (SRCRSP5 to 0.9156 P19 (DYA across all loci. Conclusion: Microsatellite analysis revealed high level of polymorphism across studied microsatellite markers and informativeness of the markers for genetic diversity analysis studies in

  7. Assessment of genetic diversity among moderately drought tolerant landraces of rice using RAPD markers

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    Md. Shariful Islam

    2013-01-01

    Full Text Available Genetic diversity and relationships among six rice genotypes were investigated using five random amplified polymorphic DNA (RAPD markers. A total of 69 alleles were amplified, of which 66 were polymorphic. The size of the amplified alleles was between 0.25 and 2.35 kbp. The number of polymorphic alleles detected with each primer ranged from 7 to 24 with an average of 13.2 per primer and the polymorphism information content (PIC values varied from 0.8672 to 0.9471. Pair-wise similarity estimated the range of 0.308 to 0.718 among all the genotypes and the highest genetic similarity was found between Maloti and BRRI dhan53. Cluster analysis using UPGMA (unweighted pair group method with arithmetic averages revealed three clusters at genetic similarity of 46%. A moderately drought tolerant landrace, Boalia, formed a single cluster and the remaining genotypes grouped into distinct clusters based on their relatedness. The results showed a high level of genetic diversity among studied genotypes and this information will assist in conservation as well as selection of parents during breeding programs for the development of drought tolerant rice varieties in near future.

  8. Study Of Genetic Diversity Between Grasspea Landraces Using Morphological And Molecular Marker

    Science.gov (United States)

    Sedehi, Abbasali Vahabi; Lotfi, Asefeh; Solooki, Mahmood

    2008-01-01

    Grass pea is a beneficial crop to Iran since it has some major advantageous such as high grain and forage quality, high drought tolerance and medium level of salinity tolerance and a good native germplasm variation which accessible for breeding programs. This study was carried out to evaluate morphological traits of the grass pea landraces using a randomized complete block design with 3 replications at Research Farm of Isfahan University of Technology. To evaluate genetic diversity of 14 grass pea landraces from various locations in Iran were investigated using 32 RAPD & ISJ primers at Biocenter of University of Zabol. Analysis of variance indicated a highly significant differences among 14 grass pea landrace for the morphological traits. Average of polymorphism percentage of RAPD primer was 73.9%. Among used primer, 12 random primers showed polymorphism and a total of 56 different bands were observed in the genotypes. Jafar-abad and Sar-chahan genotypes with similarity coefficient of 66% and Khoram-abad 2 and Khoram-abad 7 genotypes with similarity coefficient of 3% were the most related and the most distinct genotypes, respectively. Fourteen primers out of 17 semi random primers produced 70 polymorphic bands which included 56% of the total 126 produced bands. Genetic relatedness among population was investigated using Jacard coefficient and unweighted pair group mean analysis (UPGMA) algorithm. The result of this research verified possibility of use of RAPD & ISJ markers for estimation of genetic diversity, management of genetic resources and determination of repetitive accessions in grass pea.

  9. Genetic diversity and relationship of global faba bean (Vicia faba L.) germplasm revealed by ISSR markers.

    Science.gov (United States)

    Wang, Hai-Fei; Zong, Xu-Xiao; Guan, Jian-Ping; Yang, Tao; Sun, Xue-Lian; Ma, Yu; Redden, Robert

    2012-03-01

    Genetic diversity and relationships of 802 faba bean (Vicia faba L.) landraces and varieties from different geographical locations of China and abroad were examined using ISSR markers. A total of 212 repeatable amplified bands were generated with 11 ISSR primers, of which 209 were polymorphic. Accessions from North China showed highest genetic diversity, while accessions from central China showed low level of diversity. Chinese spring faba bean germplasm was clearly separated from Chinese winter faba bean, based on principal component analysis and UPGMA clustering analysis. Winter accessions from Zhejiang (East China), Jiangxi (East China), Sichuan (Southwest China) and Guizhou (Southwest China) were quite distinct to that from other provinces in China. Great differentiation between Chinese accessions and those from rest of the world was shown with a UPGMA dendrogram. AMOVA analyses demonstrated large variation and differentiation within and among groups of accessions from China. As a continental geographic group, accessions from Europe were genetically closer to those from North Africa. Based on ISSR data, grouping results of accessions from Asia, Europe and Africa were obviously associated with their geographical origin. The overall results indicated that the genetic relationship of faba bean germplasm was closely associated with their geographical origin and their ecological habit.

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

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    Ali Raza

    2018-02-01

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

  11. Abraham's children in the genome era: major Jewish diaspora populations comprise distinct genetic clusters with shared Middle Eastern Ancestry.

    Science.gov (United States)

    Atzmon, Gil; Hao, Li; Pe'er, Itsik; Velez, Christopher; Pearlman, Alexander; Palamara, Pier Francesco; Morrow, Bernice; Friedman, Eitan; Oddoux, Carole; Burns, Edward; Ostrer, Harry

    2010-06-11

    For more than a century, Jews and non-Jews alike have tried to define the relatedness of contemporary Jewish people. Previous genetic studies of blood group and serum markers suggested that Jewish groups had Middle Eastern origin with greater genetic similarity between paired Jewish populations. However, these and successor studies of monoallelic Y chromosomal and mitochondrial genetic markers did not resolve the issues of within and between-group Jewish genetic identity. Here, genome-wide analysis of seven Jewish groups (Iranian, Iraqi, Syrian, Italian, Turkish, Greek, and Ashkenazi) and comparison with non-Jewish groups demonstrated distinctive Jewish population clusters, each with shared Middle Eastern ancestry, proximity to contemporary Middle Eastern populations, and variable degrees of European and North African admixture. Two major groups were identified by principal component, phylogenetic, and identity by descent (IBD) analysis: Middle Eastern Jews and European/Syrian Jews. The IBD segment sharing and the proximity of European Jews to each other and to southern European populations suggested similar origins for European Jewry and refuted large-scale genetic contributions of Central and Eastern European and Slavic populations to the formation of Ashkenazi Jewry. Rapid decay of IBD in Ashkenazi Jewish genomes was consistent with a severe bottleneck followed by large expansion, such as occurred with the so-called demographic miracle of population expansion from 50,000 people at the beginning of the 15th century to 5,000,000 people at the beginning of the 19th century. Thus, this study demonstrates that European/Syrian and Middle Eastern Jews represent a series of geographical isolates or clusters woven together by shared IBD genetic threads.

  12. Rim 2/Hipa CACTA transposon display ; A new genetic marker technique in Oryza species

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    Lee Ju

    2005-03-01

    Full Text Available Abstract Background Transposons constitute the major fractions of repetitive sequences in eukaryotes, and have been crucial in the shaping of current genomes. Transposons are generally divided into two classes according to the mechanism underlying their transposition: RNA intermediate class 1 and DNA intermediate class 2. CACTA is a class 2 transposon superfamily, which is found exclusively in plants. As some transposons, including the CACTA superfamily, are highly abundant in plant species, and their nucleotide sequences are highly conserved within a family, they can be utilized as genetic markers, using a slightly modified version of the conventional AFLP protocol. Rim2 /Hipa is a CACTA transposon family having 16 bp consensus TIR sequences to be present in high copy numbers in rice genome. This research was carried out in order to develop a Rim2/Hipa CACTA-AFLP or Rim2/Hipa CACTA-TD (transposon display, hereafter Rim2/Hipa-TD protocol for the study of genetic markers in map construction and the study of genetic diversity in rice. Results Rim2/Hipa-TD generated ample polymorphic profiles among the different rice accessions, and the amplification profiles were highly reproducible between different thermocyclers and Taq polymerases. These amplification profiles allowed for clear distinction between two different ecotypes, Japonica and Indica, of Oryza sativa. In the analysis of RIL populations, the Rim2/Hipa-TD markers were found to be segregated largely in a dominant manner, although in a few cases, non-parental bands were observed in the segregating populations. Upon linkage analysis, the Rim2/Hipa-TD markers were found to be distributed in the regions proximal to the centromeres of the chromosomes. The distribution of the Rim2/Hipa CACTA elements was surveyed in 15 different Oryza species via Rim2/Hipa-TD. While Rim2/Hipa-TD yielded ample amplification profiles between 100 to 700 bp in the AA diploid Oryza species, other species having BB, CC

  13. Assessment of genetic diversity among Indian potato (Solanum tuberosum L.) collection using microsatellite and retrotransposon based marker systems.

    Science.gov (United States)

    Sharma, Vishakha; Nandineni, Madhusudan R

    2014-04-01

    .905 were observed for REMAP, IRAP and SSR, respectively. The widespread presence and distinct DNA profiles for copia-like and gypsy-like RTNs in the examined genotypes indicate that these elements are active in the genome and may have even contributed to the potato genome organization. Although the three marker systems were capable of distinguishing all the 47 varieties; high reproducibility, low cost and ease of DNA profiling data collection make IRAP and REMAP markers highly efficient whole-genome scanning molecular probes for population genetic studies. Information obtained from the present study regarding the genetic association and distinctiveness provides an useful guide for selection of germplasm for plant breeding and conservation efforts. Copyright © 2014. Published by Elsevier Inc.

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

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    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.

  15. 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

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

    Science.gov (United States)

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

    2015-07-01

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

  17. Drought Tolerance in Pinus halepensis Seed Sources As Identified by Distinctive Physiological and Molecular Markers.

    Science.gov (United States)

    Taïbi, Khaled; Del Campo, Antonio D; Vilagrosa, Alberto; Bellés, José M; López-Gresa, María Pilar; Pla, Davinia; Calvete, Juan J; López-Nicolás, José M; Mulet, José M

    2017-01-01

    Drought is one of the main constraints determining forest species growth, survival and productivity, and therefore one of the main limitations for reforestation or afforestation. The aim of this study is to characterize the drought response at the physiological and molecular level of different Pinus halepensis (common name Aleppo pine) seed sources, previously characterized in field trials as drought-sensitive or drought-tolerant. This approach aims to identify different traits capable of predicting the ability of formerly uncharacterized seedlings to cope with drought stress. Gas-exchange, water potential, photosynthetic pigments, soluble sugars, free amino acids, glutathione and proteomic analyses were carried out on control and drought-stressed seedlings in greenhouse conditions. Gas-exchange determinations were also assessed in field-planted seedlings in order to validate the greenhouse experimental conditions. Drought-tolerant seed sources presented higher values of photosynthetic rates, water use efficiency, photosynthetic pigments and soluble carbohydrates concentrations. We observed the same pattern of variation of photosynthesis rate and maximal efficiency of PSII in field. Interestingly drought-tolerant seed sources exhibited increased levels of glutathione, methionine and cysteine. The proteomic profile of drought tolerant seedlings identified two heat shock proteins and an enzyme related to methionine biosynthesis that were not present in drought sensitive seedlings, pointing to the synthesis of sulfur amino acids as a limiting factor for drought tolerance in Pinus halepensis . Our results established physiological and molecular traits useful as distinctive markers to predict drought tolerance in Pinus halepensis provenances that could be reliably used in reforestation programs in drought prone areas.

  18. Drought Tolerance in Pinus halepensis Seed Sources As Identified by Distinctive Physiological and Molecular Markers

    Directory of Open Access Journals (Sweden)

    Khaled Taïbi

    2017-07-01

    Full Text Available Drought is one of the main constraints determining forest species growth, survival and productivity, and therefore one of the main limitations for reforestation or afforestation. The aim of this study is to characterize the drought response at the physiological and molecular level of different Pinus halepensis (common name Aleppo pine seed sources, previously characterized in field trials as drought-sensitive or drought-tolerant. This approach aims to identify different traits capable of predicting the ability of formerly uncharacterized seedlings to cope with drought stress. Gas-exchange, water potential, photosynthetic pigments, soluble sugars, free amino acids, glutathione and proteomic analyses were carried out on control and drought-stressed seedlings in greenhouse conditions. Gas-exchange determinations were also assessed in field-planted seedlings in order to validate the greenhouse experimental conditions. Drought-tolerant seed sources presented higher values of photosynthetic rates, water use efficiency, photosynthetic pigments and soluble carbohydrates concentrations. We observed the same pattern of variation of photosynthesis rate and maximal efficiency of PSII in field. Interestingly drought-tolerant seed sources exhibited increased levels of glutathione, methionine and cysteine. The proteomic profile of drought tolerant seedlings identified two heat shock proteins and an enzyme related to methionine biosynthesis that were not present in drought sensitive seedlings, pointing to the synthesis of sulfur amino acids as a limiting factor for drought tolerance in Pinus halepensis. Our results established physiological and molecular traits useful as distinctive markers to predict drought tolerance in Pinus halepensis provenances that could be reliably used in reforestation programs in drought prone areas.

  19. Genetic African Ancestry and Markers of Mineral Metabolism in CKD.

    Science.gov (United States)

    Gutiérrez, Orlando M; Parsa, Afshin; Isakova, Tamara; Scialla, Julia J; Chen, Jing; Flack, John M; Nessel, Lisa C; Gupta, Jayanta; Bellovich, Keith A; Steigerwalt, Susan; Sondheimer, James H; Wright, Jackson T; Feldman, Harold I; Kusek, John W; Lash, James P; Wolf, Myles

    2016-04-07

    Disorders of mineral metabolism are more common in African Americans with CKD than in European Americans with CKD. Previous studies have focused on the differences in mineral metabolism by self-reported race, making it difficult to delineate the importance of environmental compared with biologic factors. In a cross-sectional analysis of 3013 participants of the Chronic Renal Insufficiency Cohort study with complete data, we compared markers of mineral metabolism (phosphorus, calcium, alkaline phosphatase, parathyroid hormone, fibroblast growth factor 23, and urine calcium and phosphorus excretion) in European Americans versus African Americans and separately, across quartiles of genetic African ancestry in African Americans (n=1490). Compared with European Americans, African Americans had higher blood concentrations of phosphorus, alkaline phosphatase, fibroblast growth factor 23, and parathyroid hormone, lower 24-hour urinary excretion of calcium and phosphorus, and lower urinary fractional excretion of calcium and phosphorus at baseline (PAfrican Americans, a higher percentage of African ancestry was associated with lower 24-hour urinary excretion of phosphorus (PtrendAfrican ancestry was significantly associated with lower 24-hour urinary phosphorus excretion (each 10% higher African ancestry was associated with 39.6 mg lower 24-hour urinary phosphorus, PAfrican ancestry was associated with an absolute 1.1% lower fractional excretion of phosphorus, P=0.01). A higher percentage of African ancestry was independently associated with lower 24-hour urinary phosphorus excretion and lower fractional excretion of phosphorus among African Americans with CKD. These findings suggest that genetic variability might contribute to racial differences in urinary phosphorus excretion in CKD. Copyright © 2016 by the American Society of Nephrology.

  20. Distinctive mitochondrial genome of Calanoid copepod Calanus sinicus with multiple large non-coding regions and reshuffled gene order: Useful molecular markers for phylogenetic and population studies

    Science.gov (United States)

    2011-01-01

    Background Copepods are highly diverse and abundant, resulting in extensive ecological radiation in marine ecosystems. Calanus sinicus dominates continental shelf waters in the northwest Pacific Ocean and plays an important role in the local ecosystem by linking primary production to higher trophic levels. A lack of effective molecular markers has hindered phylogenetic and population genetic studies concerning copepods. As they are genome-level informative, mitochondrial DNA sequences can be used as markers for population genetic studies and phylogenetic studies. Results The mitochondrial genome of C. sinicus is distinct from other arthropods owing to the concurrence of multiple non-coding regions and a reshuffled gene arrangement. Further particularities in the mitogenome of C. sinicus include low A + T-content, symmetrical nucleotide composition between strands, abbreviated stop codons for several PCGs and extended lengths of the genes atp6 and atp8 relative to other copepods. The monophyletic Copepoda should be placed within the Vericrustacea. The close affinity between Cyclopoida and Poecilostomatoida suggests reassigning the latter as subordinate to the former. Monophyly of Maxillopoda is rejected. Within the alignment of 11 C. sinicus mitogenomes, there are 397 variable sites harbouring three 'hotspot' variable sites and three microsatellite loci. Conclusion The occurrence of the circular subgenomic fragment during laboratory assays suggests that special caution should be taken when sequencing mitogenomes using long PCR. Such a phenomenon may provide additional evidence of mitochondrial DNA recombination, which appears to have been a prerequisite for shaping the present mitochondrial profile of C. sinicus during its evolution. The lack of synapomorphic gene arrangements among copepods has cast doubt on the utility of gene order as a useful molecular marker for deep phylogenetic analysis. However, mitochondrial genomic sequences have been valuable markers for

  1. MOLECULAR GENETIC MARKERS AND METHODS OF THEIR IDENTIFICATION IN MODERN FISH-FARMING

    Directory of Open Access Journals (Sweden)

    I. Hrytsyniak

    2014-03-01

    Full Text Available Purpose. The application of molecular genetic markers has been widely used in modern experimental fish-farming in recent years. This methodology is currently presented by a differentiated approach with individual mechanisms and clearly defined possibilities. Numerous publications in the scientific literature that are dedicated to molecular genetic markers for the most part offer purely practical data. Thus, the synthesis and analysis of existing information on the general principles of action and the limits of the main methods of using molecular genetic markers is an actual problem. In particular, such a description will make it possible to plan more effectively the experiment and to obtain the desired results with high reliability. Findings. The main types of variable parts of DNA that can be used as molecular genetic markers in determining the level of stock hybridization, conducting genetic inventory of population and solving other problems in modern fish-farming are described in this paper. Also, the article provides an overview of principal modern methods that can be used to identify molecular genetic markers. Originality. This work is a generalization of modern ideas about the mechanisms of experiments with molecular genetic markers in fish-farming. Information is provided in the form of consistent presentation of the principles and purpose of each method, as well as significant advances during their practical application. Practical value. The proposed review of classic and modern literature data on molecular genetic markers can be used for planning, modernization and correction of research activity in modern fish-farming.

  2. 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...

  3. Genetically distinct isolates of Spirocerca sp. from a naturally infected red fox (Vulpes vulpes) from Denmark

    DEFF Research Database (Denmark)

    Al-Sabi, Mohammad Nafi Solaiman; Hansen, Mette Sif; Chriél, Mariann

    2014-01-01

    sugar-salt solu-tion, and sieving failed to detect eggs of Spirocerca sp. in feces collected from the colon.This is the first report of spirocercosis in Denmark, and may have been caused by a recentintroduction by migrating paratenic or definitive host. Analysis of two overlapping par-tial sequences...... of the cox1 gene, from individual worms, revealed distinct genetic variation(7–9%) between the Danish worms and isolates of S. lupi from Europe, Asia and Africa.This was confirmed by phylogenetic analysis that clearly separated the Danish worms fromother isolates of S. lupi. The distinct genetic differences...

  4. Genetic markers and their application in livestock breeding in South ...

    African Journals Online (AJOL)

    The ultimate use of DNA markers would be to identify quantitative trait loci (QTL) in order to practice genotypic selection. This paper reviews DNA markers (RAPD, DFP, RFLP AFLP, minisatellites, microsatellites, SNP) and provides a brief overview of the current application of these markers in animal breeding.

  5. Genetic diversity of cultivated flax (Linum usitatissimum L.) germplasm assessed by retrotransposon-based markers.

    Science.gov (United States)

    Smýkal, P; Bačová-Kerteszová, N; Kalendar, R; Corander, J; Schulman, A H; Pavelek, M

    2011-05-01

    Retrotransposon segments were characterized and inter-retrotransposon amplified polymorphism (IRAP) markers developed for cultivated flax (Linum usitatissimum L.) and the Linum genus. Over 75 distinct long terminal repeat retrotransposon segments were cloned, the first set for Linum, and specific primers designed for them. IRAP was then used to evaluate genetic diversity among 708 accessions of cultivated flax comprising 143 landraces, 387 varieties, and 178 breeding lines. These included both traditional and modern, oil (86), fiber (351), and combined-use (271) accessions, originating from 36 countries, and 10 wild Linum species. The set of 10 most polymorphic primers yielded 141 reproducible informative data points per accession, with 52% polymorphism and a 0.34 Shannon diversity index. The maximal genetic diversity was detected among wild Linum species (100% IRAP polymorphism and 0.57 Jaccard similarity), while diversity within cultivated germplasm decreased from landraces (58%, 0.63) to breeding lines (48%, 0.85) and cultivars (50%, 0.81). Application of Bayesian methods for clustering resulted in the robust identification of 20 clusters of accessions, which were unstratified according to origin or user type. This indicates an overlap in genetic diversity despite disruptive selection for fiber versus oil types. Nevertheless, eight clusters contained high proportions (70-100%) of commercial cultivars, whereas two clusters were rich (60%) in landraces. These findings provide a basis for better flax germplasm management, core collection establishment, and exploration of diversity in breeding, as well as for exploration of the role of retrotransposons in flax genome dynamics.

  6. Genetic diversity of the Northern Morocco goat population assessed with microsatellite markers

    Directory of Open Access Journals (Sweden)

    Najat El Moutchou

    2017-12-01

    Full Text Available The main goal of this work was to study the genetic diversity of the Northern Morocco goat population through the analysis of 19 microsatellites in 144 animals from 61 herds. To detect a possible population structure, three distinct geographic subpopulations were characterized as a function of climate and environmental influences. Most of the markers were highly polymorphic, and the results revealed considerable genetic variation across the studied loci. A total of 204 alleles were detected, with an average number of 10.7 per locus. The PIC average was 0.728, and four microsatellites showed a significant deviation (p< 0.05 from Hardy-Weinberg Equilibrium. Analysis of molecular variance (AMOVA indicated that only 0.5% of the variation corresponded to differences among subpopulations, and 99.5% corresponded to differences among individuals. Factorial correspondence analysis showed intense admixtures across the putative subpopulations, and the subdivision related to geographical or environmental adaptation was undetectable. The Northern Morocco goat population presented high genetic diversity and a lack of population structure. The main reason for these findings is the absence of the breed concept (reproductively closed population, resulting in uncontrolled crossbreeding with exotic breeds and other local goats.

  7. Genetic diversity of the Northern Morocco goat population assessed with microsatellite markers

    Energy Technology Data Exchange (ETDEWEB)

    El Moutchou, N.; González-Martínez, A.M.; Chentouf, M.; Lairini, K.; Rodero, E.

    2017-07-01

    The main goal of this work was to study the genetic diversity of the Northern Morocco goat population through the analysis of 19 microsatellites in 144 animals from 61 herds. To detect a possible population structure, three distinct geographic subpopulations were characterized as a function of climate and environmental influences. Most of the markers were highly polymorphic, and the results revealed considerable genetic variation across the studied loci. A total of 204 alleles were detected, with an average number of 10.7 per locus. The PIC average was 0.728, and four microsatellites showed a significant deviation (p< 0.05) from Hardy-Weinberg Equilibrium. Analysis of molecular variance (AMOVA) indicated that only 0.5% of the variation corresponded to differences among subpopulations, and 99.5% corresponded to differences among individuals. Factorial correspondence analysis showed intense admixtures across the putative subpopulations, and the subdivision related to geographical or environmental adaptation was undetectable. The Northern Morocco goat population presented high genetic diversity and a lack of population structure. The main reason for these findings is the absence of the breed concept (reproductively closed population), resulting in uncontrolled crossbreeding with exotic breeds and other local goats.

  8. Genetic diversity of the Northern Morocco goat population assessed with microsatellite markers

    International Nuclear Information System (INIS)

    El Moutchou, N.; González-Martínez, A.M.; Chentouf, M.; Lairini, K.; Rodero, E.

    2017-01-01

    The main goal of this work was to study the genetic diversity of the Northern Morocco goat population through the analysis of 19 microsatellites in 144 animals from 61 herds. To detect a possible population structure, three distinct geographic subpopulations were characterized as a function of climate and environmental influences. Most of the markers were highly polymorphic, and the results revealed considerable genetic variation across the studied loci. A total of 204 alleles were detected, with an average number of 10.7 per locus. The PIC average was 0.728, and four microsatellites showed a significant deviation (p< 0.05) from Hardy-Weinberg Equilibrium. Analysis of molecular variance (AMOVA) indicated that only 0.5% of the variation corresponded to differences among subpopulations, and 99.5% corresponded to differences among individuals. Factorial correspondence analysis showed intense admixtures across the putative subpopulations, and the subdivision related to geographical or environmental adaptation was undetectable. The Northern Morocco goat population presented high genetic diversity and a lack of population structure. The main reason for these findings is the absence of the breed concept (reproductively closed population), resulting in uncontrolled crossbreeding with exotic breeds and other local goats.

  9. [Population genetic study of Russian cosmonauts and test subjects: genetic demographic parameters and immunogenetic markers].

    Science.gov (United States)

    Kurbatova, O L; Pobedonostseva, E Iu; Prokhorovskaia, V D; Kholod, O N; Evsiukov, A N; Bogomolov, V V; Voronkov, Iu I; Filatova, L M; Larina, O N; Sidorenko, L A; Morgun, V V; Kasparanskiĭ, R R; Altukhov, Iu P

    2006-10-01

    Genetic demographic characteristics and immunogenetic markers (blood groups ABO, Rhesus, MNSs, P, Duffy, Kidd, and Kell) have been studied in a group of 132 Russian cosmonauts and test subjects (CTSG). Analysis of pedigrees has shown a high exogamy in the preceding generations: almost half of the subjects have mixed ethnic background. According to the results of genetic demographic analysis, a sample from the Moscow population was used as control group (CG). Comparison between the CTSG and CG has demonstrated significant differences in genotype frequencies for several blood group systems. The CTSG is characterized by a decreased proportion of rare interlocus genotypic combinations and an increased man heterozygosity. Analysis of the distributions of individual heterozygosity for loci with codominant expression of alleles has shown that highly heterozygous loci are more frequent in the CTSG. Taking into account that the CTSG has been thoroughly selected from the general population, it is concluded that heterozygosity is related to successful adaptation to a space flight.

  10. 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.

  11. Kazusa Marker DataBase: a database for genomics, genetics, and molecular breeding in plants

    Science.gov (United States)

    Shirasawa, Kenta; Isobe, Sachiko; Tabata, Satoshi; Hirakawa, Hideki

    2014-01-01

    In order to provide useful genomic information for agronomical plants, we have established a database, the Kazusa Marker DataBase (http://marker.kazusa.or.jp). This database includes information on DNA markers, e.g., SSR and SNP markers, genetic linkage maps, and physical maps, that were developed at the Kazusa DNA Research Institute. Keyword searches for the markers, sequence data used for marker development, and experimental conditions are also available through this database. Currently, 10 plant species have been targeted: tomato (Solanum lycopersicum), pepper (Capsicum annuum), strawberry (Fragaria × ananassa), radish (Raphanus sativus), Lotus japonicus, soybean (Glycine max), peanut (Arachis hypogaea), red clover (Trifolium pratense), white clover (Trifolium repens), and eucalyptus (Eucalyptus camaldulensis). In addition, the number of plant species registered in this database will be increased as our research progresses. The Kazusa Marker DataBase will be a useful tool for both basic and applied sciences, such as genomics, genetics, and molecular breeding in crops. PMID:25320561

  12. Autism and genetics: Clinical approach and association study with two markers of HRAS gene

    Energy Technology Data Exchange (ETDEWEB)

    Herault, J.; Petit, E.; Cherpi, C. [Laboratoire de Biochimie Medicale, Tours (France)] [and others

    1995-08-14

    Twin studies and familial aggregation studies indicate that genetic factors could play a role in infantile autism. In an earlier study, we identified a possible positive association between autism and a c-Harvey-ras (HRAS) oncogene marker at the 3{prime} end of the coding region. In an attempt to confirm this finding, we studied a larger population, well-characterized clinically and genetically. We report a positive association between autism and two HRAS markers, the 3{prime} marker used in the initial study and an additional marker in exon 1. 46 refs., 1 fig., 2 tabs.

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

    Directory of Open Access Journals (Sweden)

    Nicolas Heslot

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

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

    Science.gov (United States)

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

    2013-01-01

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

  15. Possible people, complaints, and the distinction between genetic planning and genetic engineering.

    Science.gov (United States)

    Delaney, James J

    2011-07-01

    Advances in the understanding of genetics have led to the belief that it may become possible to use genetic engineering to manipulate the DNA of humans at the embryonic stage to produce certain desirable traits. Although this currently cannot be done on a large scale, many people nevertheless object in principle to such practices. Most often, they argue that genetic enhancements would harm the children who were engineered, cause societal harms, or that the risks of perfecting the procedures are too high to proceed. However, many of these same people do not have serious objections to what is called 'genetic planning' procedures (such as the selection of sperm donors with desirable traits) that essentially have the same ends. The author calls the view that genetic engineering enhancements are impermissible while genetic planning enhancements are permissible the 'popular view', and argues that the typical reasons people give for the popular view fail to distinguish the two practices. This paper provides a principle that can salvage the popular view, which stresses that offspring from genetic engineering practices have grounds for complaint because they are identical to the pre-enhanced embryo, whereas offspring who are the result of genetic planning have no such grounds.

  16. Genomic single-nucleotide polymorphisms confirm that Gunnison and Greater sage-grouse are genetically well differentiated and that the Bi-State population is distinct

    Science.gov (United States)

    Oyler-McCance, Sara J.; Cornman, Robert S.; Jones, Kenneth L.; Fike, Jennifer

    2015-01-01

    Sage-grouse are iconic, declining inhabitants of sagebrush habitats in western North America, and their management depends on an understanding of genetic variation across the landscape. Two distinct species of sage-grouse have been recognized, Greater (Centrocercus urophasianus) and Gunnison sage-grouse (C. minimus), based on morphology, behavior, and variation at neutral genetic markers. A parapatric group of Greater Sage-Grouse along the border of California and Nevada ("Bi-State") is also genetically distinct at the same neutral genetic markers, yet not different in behavior or morphology. Because delineating taxonomic boundaries and defining conservation units is often difficult in recently diverged taxa and can be further complicated by highly skewed mating systems, we took advantage of new genomic methods that improve our ability to characterize genetic variation at a much finer resolution. We identified thousands of single-nucleotide polymorphisms (SNPs) among Gunnison, Greater, and Bi-State sage-grouse and used them to comprehensively examine levels of genetic diversity and differentiation among these groups. The pairwise multilocus fixation index (FST) was high (0.49) between Gunnison and Greater sage-grouse, and both principal coordinates analysis and model-based clustering grouped samples unequivocally by species. Standing genetic variation was lower within the Gunnison Sage-Grouse. The Bi-State population was also significantly differentiated from Greater Sage-Grouse, albeit more weakly (FST = 0.09), and genetic clustering results were consistent with reduced gene flow with Greater Sage-Grouse. No comparable genetic divisions were found within the Greater Sage-Grouse sample, which spanned the southern half of the range. Thus, we provide much stronger genetic evidence supporting the recognition of Gunnison Sage-Grouse as a distinct species with low genetic diversity. Further, our work confirms that the Bi-State population is differentiated from other

  17. (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.

  18. Genetic, Ecological and Morphological Distinctness of the Blue Mussels Mytilus trossulus Gould and M. edulis L. in the White Sea.

    Directory of Open Access Journals (Sweden)

    Marina Katolikova

    Full Text Available Two blue mussel lineages of Pliocene origin, Mytilus edulis (ME and M. trossulus (MT, co-occur and hybridize in several regions on the shores of the North Atlantic. The two species were distinguished from each other by molecular methods in the 1980s, and a large amount of comparative data on them has been accumulated since that time. However, while ME and MT are now routinely distinguished by various genetic markers, they tend to be overlooked in ecological studies since morphological characters for taxonomic identification have been lacking, and no consistent habitat differences between lineages have been reported. Surveying a recently discovered area of ME and MT co-occurrence in the White Sea and employing a set of allozyme markers for identification, we address the issue whether ME and MT are true biological species with distinct ecological characteristics or just virtual genetic entities with no matching morphological and ecological identities. We find that: (1 in the White Sea, the occurrence of MT is largely concentrated in harbors, in line with observations from other subarctic regions of Europe; (2 mixed populations of ME and MT are always dominated by purebred individuals, animals classified as hybrids constituting only ca. 18%; (3 in terms of shell morphology, 80% of MT bear a distinct uninterrupted dark prismatic strip under the ligament while 97% of ME lack this character; (4 at sites of sympatry MT is more common on algal substrates while ME mostly lives directly on the bottom. This segregation by the substrate may contribute to maintaining reproductive isolation and decreasing competition between taxa. We conclude that while ME and MT are not fully reproductively isolated, they do represent clearly distinguishable biological, ecological and morphological entities in the White Sea. It remains to be documented whether the observed morphological and ecological differences are of a local character, or whether they have simply been

  19. 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 ...

  20. 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, ...

  1. Genetic characterization of early maturing maize hybrids (Zea mays L. obtained by protein and RAPD markers

    Directory of Open Access Journals (Sweden)

    Bauer Iva

    2005-01-01

    Full Text Available Knowledge of maize germplasm genetic diversity is important for planning breeding programmes, germplasm conservation per se etc. Genetic variability of maize hybrids grown in the fields is also very important because genetic uniformity implies risks of genetic vulnerability to stress factors and can cause great losts in yield. Early maturing maize hybrids are characterized by shorter vegetation period and they are grown in areas with shorter vegetation season. Because of different climatic conditions in these areas lines and hybrids are developed with different features in respect to drought resistance and disease resistance. The objective of our study was to characterize set of early maturing maize hybrids with protein and RAPD markers and to compare this clasification with their pedigree information. RAPD markers gave significantly higher rate of polymorphism than protein markers. Better corelation was found among pedigree information and protein markers.

  2. Identifying genetic marker sets associated with phenotypes via an efficient adaptive score test

    KAUST Repository

    Cai, T.; Lin, X.; Carroll, R. J.

    2012-01-01

    the overall effect of a marker-set have been actively studied in recent years. For example, score tests derived under an Empirical Bayes (EB) framework (Liu and others, 2007. Semiparametric regression of multidimensional genetic pathway data: least

  3. 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

  4. Genetic diversity studies in pea (Pisum sativum L.) using simple sequence repeat markers.

    Science.gov (United States)

    Kumari, P; Basal, N; Singh, A K; Rai, V P; Srivastava, C P; Singh, P K

    2013-03-13

    The genetic diversity among 28 pea (Pisum sativum L.) genotypes was analyzed using 32 simple sequence repeat markers. A total of 44 polymorphic bands, with an average of 2.1 bands per primer, were obtained. The polymorphism information content ranged from 0.657 to 0.309 with an average of 0.493. The variation in genetic diversity among these cultivars ranged from 0.11 to 0.73. Cluster analysis based on Jaccard's similarity coefficient using the unweighted pair-group method with arithmetic mean (UPGMA) revealed 2 distinct clusters, I and II, comprising 6 and 22 genotypes, respectively. Cluster II was further differentiated into 2 subclusters, IIA and IIB, with 12 and 10 genotypes, respectively. Principal component (PC) analysis revealed results similar to those of UPGMA. The first, second, and third PCs contributed 21.6, 16.1, and 14.0% of the variation, respectively; cumulative variation of the first 3 PCs was 51.7%.

  5. Application of next-generation sequencing technology to study genetic diversity and identify unique SNP markers in bread wheat from Kazakhstan.

    Science.gov (United States)

    Shavrukov, Yuri; Suchecki, Radoslaw; Eliby, Serik; Abugalieva, Aigul; Kenebayev, Serik; Langridge, Peter

    2014-09-28

    New SNP marker platforms offer the opportunity to investigate the relationships between wheat cultivars from different regions and assess the mechanism and processes that have led to adaptation to particular production environments. Wheat breeding has a long history in Kazakhstan and the aim of this study was to explore the relationship between key varieties from Kazakhstan and germplasm from breeding programs for other regions. The study revealed 5,898 polymorphic markers amongst ten cultivars, of which 2,730 were mapped in the consensus genetic map. Mapped SNP markers were distributed almost equally across the A and B genomes, with between 279 and 484 markers assigned to each chromosome. Marker coverage was approximately 10-fold lower in the D genome. There were 863 SNP markers identified as unique to specific cultivars, and clusters of these markers (regions containing more than three closely mapped unique SNPs) showed specific patterns on the consensus genetic map for each cultivar. Significant intra-varietal genetic polymorphism was identified in three cultivars (Tzelinnaya 3C, Kazakhstanskaya rannespelaya and Kazakhstanskaya 15). Phylogenetic analysis based on inter-varietal polymorphism showed that the very old cultivar Erythrospermum 841 was the most genetically distinct from the other nine cultivars from Kazakhstan, falling in a clade together with the American cultivar Sonora and genotypes from Central and South Asia. The modern cultivar Kazakhstanskaya 19 also fell into a separate clade, together with the American cultivar Thatcher. The remaining eight cultivars shared a single sub-clade but were categorised into four clusters. The accumulated data for SNP marker polymorphisms amongst bread wheat genotypes from Kazakhstan may be used for studying genetic diversity in bread wheat, with potential application for marker-assisted selection and the preparation of a set of genotype-specific markers.

  6. Genetic Confirmation of Mungbean (Vigna radiata) and Mashbean (Vigna mungo) Interspecific Recombinants using Molecular Markers.

    Science.gov (United States)

    Abbas, Ghulam; Hameed, Amjad; Rizwan, Muhammad; Ahsan, Muhammad; Asghar, Muhammad J; Iqbal, Nayyer

    2015-01-01

    Molecular confirmation of interspecific recombinants is essential to overcome the issues like self-pollination, environmental influence, and inadequacy of morphological characteristics during interspecific hybridization. The present study was conducted for genetic confirmation of mungbean (female) and mashbean (male) interspecific crosses using molecular markers. Initially, polymorphic random amplified polymorphic DNA (RAPD), universal rice primers (URP), and simple sequence repeats (SSR) markers differentiating parent genotypes were identified. Recombination in hybrids was confirmed using these polymorphic DNA markers. The NM 2006 × Mash 88 was most successful interspecific cross. Most of true recombinants confirmed by molecular markers were from this cross combination. SSR markers were efficient in detecting genetic variability and recombination with reference to specific chromosomes and particular loci. SSR (RIS) and RAPD identified variability dispersed throughout the genome. In conclusion, DNA based marker assisted selection (MAS) efficiently confirmed the interspecific recombinants. The results provided evidence that MAS can enhance the authenticity of selection in mungbean improvement program.

  7. GENETIC DIVERSITY OF SOME IRANIAN SWEET CHERRY (PRUNUS AVIUM) CULTIVARS USING MICROSATELLITE MARKERS AND MORPHOLOGICAL TRAITS.

    Science.gov (United States)

    Farsad, A; Esna-Ashari, M

    2016-01-01

    The aim of this study was to characterize 23 important Iranian sweet cherry (Prunus avium) cultivars collected from different provinces of Iran and 1 foreign cultivar, which was used as control, considered for breeding programs by using 21 microsatellite markers and 27 morphological traits. In sweet cherry (Prunus avium) accessions, leaf, fruit, and stone morphological characters were evaluated during two consecutive years. The study revealed a high variability in the set of evaluated sweet cherry accessions. The majority of important correlations were determined among variables representing fruit and leaf size and variables related to color. Cluster analysis distinguished sweet cherry accessions into two distinct groups. Principal component analysis (PCA) of qualitative and quantitative morphological parameters explained over 86.59% of total variability in the first seven axes. In PCA, leaf traits such as leaf length and width, and fruit traits such as length, width, and weight, and fruit flesh and juice color were predominant in the first two components, indicating that they were useful for the assessment of sweet cherry germplasm characterization. Out of 21 SSR markers, 16 were polymorphic, producing 177 alleles that varied from 4 to 16 alleles (9.35 on average) with a mean heterozygosity value of 0.82 that produced successful amplifications and revealed DNA polymorphisms. Allele size varied from 95 to 290 bp. Cluster analyses showed that the studied sweet cherry genotypes were classified intofive main groups based mainly on their species characteristics and SSR data. In general, our results did not show a clear structuring of genetic variability within the Iranian diffusion area of sweet cherry, so it was not possible to draw any indications on regions of provenance delimitation. The results of this study contribute to a better understanding of sweet cherry genetic variations in Iran, thus making for more efficient programs aimed at preserving biodiversity and

  8. Global Distribution of Human-Associated Fecal Genetic Markers in Reference Samples from Six Continents.

    Science.gov (United States)

    Mayer, René E; Reischer, Georg H; Ixenmaier, Simone K; Derx, Julia; Blaschke, Alfred Paul; Ebdon, James E; Linke, Rita; Egle, Lukas; Ahmed, Warish; Blanch, Anicet R; Byamukama, Denis; Savill, Marion; Mushi, Douglas; Cristóbal, Héctor A; Edge, Thomas A; Schade, Margit A; Aslan, Asli; Brooks, Yolanda M; Sommer, Regina; Masago, Yoshifumi; Sato, Maria I; Taylor, Huw D; Rose, Joan B; Wuertz, Stefan; Shanks, Orin C; Piringer, Harald; Mach, Robert L; Savio, Domenico; Zessner, Matthias; Farnleitner, Andreas H

    2018-05-01

    Numerous bacterial genetic markers are available for the molecular detection of human sources of fecal pollution in environmental waters. However, widespread application is hindered by a lack of knowledge regarding geographical stability, limiting implementation to a small number of well-characterized regions. This study investigates the geographic distribution of five human-associated genetic markers (HF183/BFDrev, HF183/BacR287, BacHum-UCD, BacH, and Lachno2) in municipal wastewaters (raw and treated) from 29 urban and rural wastewater treatment plants (750-4 400 000 population equivalents) from 13 countries spanning six continents. In addition, genetic markers were tested against 280 human and nonhuman fecal samples from domesticated, agricultural and wild animal sources. Findings revealed that all genetic markers are present in consistently high concentrations in raw (median log 10 7.2-8.0 marker equivalents (ME) 100 mL -1 ) and biologically treated wastewater samples (median log 10 4.6-6.0 ME 100 mL -1 ) regardless of location and population. The false positive rates of the various markers in nonhuman fecal samples ranged from 5% to 47%. Results suggest that several genetic markers have considerable potential for measuring human-associated contamination in polluted environmental waters. This will be helpful in water quality monitoring, pollution modeling and health risk assessment (as demonstrated by QMRAcatch) to guide target-oriented water safety management across the globe.

  9. Weight of the evidence of genetic investigations of ancestry informative markers

    DEFF Research Database (Denmark)

    Tvedebrink, Torben; Eriksen, Poul Svante; Mogensen, Helle Smidt

    2018-01-01

    Ancestry-informative markers (AIMs) are markers that give information about the ancestry of individuals. They are used in forensic genetics for predicting the geographic origin of the investigated individual in crime and identification cases. In the exploration of the genogeographic origin...

  10. Genetic diversity of sweet sorghum germplasm in Mexico using AFLP and SSR markers

    Science.gov (United States)

    The objective of this work was to evaluate the diversity and genetic relationships between lines and varieties of the sweet sorghum (Sorghum bicolor) germplasm bank of the National Institute for Forestry, Agriculture and Livestock Research, Mexico, using AFLP and SSR markers. The molecular markers ...

  11. Chemotaxonomic markers of organic, natural, and genetically modified soybeans detected by direct infusion electrospray ionization mass spectrometry

    International Nuclear Information System (INIS)

    Santos, L.S.; Catharino, R.R.; Eberlin, M.N.; Tsai, S.M.

    2006-01-01

    The crude methanolic extracts of a single bean from samples of organic, natural or genetically modified (GM) soybeans [Glycine max. (Merrill) L.] were analyzed by direct infusion electrospray ionization mass spectrometry (ESI-MS). These extracts, containing the most polar natural products of soybeans (free aglycones, monoglucosides, diglucosides and esters including isoflavones and flavones) provide characteristic fingerprinting mass spectra owing to different proportions or sets of components. Spectra distinctiveness is confirmed by chemometric multivariate analysis of the ESIMS data, which place the three-types of beans into well-defined groups. When ESI-MS is applied, these polar components constitute therefore unique chemotaxonomic markers able to provide fast soybean typification. (author)

  12. Genetic Investigations Using Immuno-biochemical Markers in a Maramureş Brown Cattle Population

    Directory of Open Access Journals (Sweden)

    Nicoleta Isfan

    2011-05-01

    Full Text Available The study of the genetic markers and identifying new markers involves an increasing number of research projects in the fields of genetics of immunology, biochemical genetics, molecular genetics, quantity genetics and the genetic improvement of animals. Some studies on genes frequency determining the red cells specificity and for whey hemoglobin are approached in the present report. In this way, some blood factors, most of them belonging to B system (the most complex system in cattle have been evidenced. The lowest gene frequency was present in K factor (7%, and highest one in, O1, G’ , W and F1 (100%. In addition to basic importance on knowledge and determination of cattle population genetic structure for studied protein loci, another theme proposed to correlate hemoglobin type with some traits of economical importance: milk yield, fat and protein content, fat and protein yield. Higher performance was recorded by HbA/HbA individuals.

  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. Evaluation of genetic diversity in rice using SSR markers

    African Journals Online (AJOL)

    hemant

    2012-10-18

    Oct 18, 2012 ... advantages and disadvantages, the choice of the marker system to be used ... absence (0) of unique and shared polymorphic products was used to generate ..... and any two of them can be used to differentiate rice genotypes.

  15. Autosomal and mtDNA markers affirm the distinctiveness of lions in West and Central Africa

    NARCIS (Netherlands)

    Bertola, L.D.; Tensen, Laura; Hooft, Van Pim; White, P.A.; Driscoll, C.A.; Henschel, Philipp; Caragiulo, Anthony; Dias-Freedman, Isabela; Sogbohossou, E.A.; Tumenta, Pricelia N.; Jirmo, T.H.; Snoo, De G.R.; Iongh, De H.H.; Vrieling, Klaas

    2015-01-01

    The evolutionary history of a species is key for understanding the taxonomy and for the design of effective management strategies for species conservation. The knowledge about the phylogenetic position of the lion (Panthera leo) in West/Central Africa is largely based on mitochondrial markers.

  16. Autosomal and mtDNA Markers Affirm the Distinctiveness of Lions in West and Central Africa

    NARCIS (Netherlands)

    Bertola L.D., Tensen, L., Hooft P. van, White P.A., Driscoll C.A., Henschel P., Caragiulo A., Dias-Freedman I., Sogbohossou E.A., Tumenta P.M., Jirmo T.H., Snoo G.R. de, Iongh H.H. de, Vrieling K.

    2015-01-01

    The evolutionary history of a species is key for understanding the taxonomy and for the design of effective management strategies for species conservation. The knowledge about the phylogenetic position of the lion ( Panthera leo ) in West/Central Africa is largely based on mitochondrial markers.

  17. Behavioral and TMS Markers of Action Observation Might Reflect Distinct Neuronal Processes.

    Science.gov (United States)

    Hétu, Sébastien; Taschereau-Dumouchel, Vincent; Meziane, Hadj Boumediene; Jackson, Philip L; Mercier, Catherine

    2016-01-01

    Transcranial magnetic stimulation (TMS) studies have shown that observing an action induces muscle-specific changes in corticospinal excitability. From a signal detection theory standpoint, this pattern can be related to sensitivity, which here would measure the capacity to distinguish between two action observation conditions. In parallel to these TMS studies, action observation has also been linked to behavioral effects such as motor priming and interference. It has been hypothesized that behavioral markers of action observation could be related to TMS markers and thus represent a potentially cost-effective mean of assessing the functioning of the action-perception system. However, very few studies have looked at possible relationships between these two measures. The aim of this study was to investigate if individual differences in sensitivity to action observation could be related to the behavioral motor priming and interference effects produced by action observation. To this end, 14 healthy participants observed index and little finger movements during a TMS task and a stimulus-response compatibility task. Index muscle displayed sensitivity to action observation, and action observation resulted in significant motor priming+interference, while no significant effect was observed for the little finger in both task. Nevertheless, our results indicate that the sensitivity measured in TMS was not related to the behavioral changes measured in the stimulus-response compatibility task. Contrary to a widespread assumption, the current results indicate that individual differences in physiological and behavioral markers of action observation may be unrelated. This could have important impacts on the potential use of behavioral markers in place of more costly physiological markers of action observation in clinical settings.

  18. Behavioral and TMS markers of action observation might reflect distinct neuronal processes

    Directory of Open Access Journals (Sweden)

    Sébastien Hétu

    2016-09-01

    Full Text Available Transcranial magnetic stimulation (TMS studies have shown that observing an action induces muscle-specific changes in corticospinal excitability. From a signal detection theory standpoint, this pattern can be related to sensitivity, which here would measure the capacity to distinguish between two action observation conditions. In parallel to these TMS studies, action observation has also been linked to behavioral effects such as motor priming and interference. It has been hypothesized that behavioral markers of action observation could be related to TMS markers and thus represent a potentially cost-effective mean of assessing the functioning of the action-perception system. However, very few studies have looked at possible relationships between these two measures. The aim of this study was to investigate if individual differences in sensitivity to action observation could be related to the behavioral motor priming and interference effects produced by action observation. To this end, fourteen healthy participants observed index and little finger movements during a TMS task and a stimulus-response compatibility task. Index muscle displayed sensitivity to action observation, and action observation resulted in significant motor priming+interference, while no significant effect was observed for the little finger in both task. Nevertheless, our results indicate that the sensitivity measured in TMS was not related to the behavioral changes measured in the stimulus-response compatibility task. Contrary to a predominant assumption, the current results indicate that individual differences in physiological and behavioral markers of action observation may be unrelated. This could have important impacts on the potential use of behavioral markers in place of more costly physiological markers of action observation in clinical settings.

  19. Covariance Association Test (CVAT) Identifies Genetic Markers Associated with Schizophrenia in Functionally Associated Biological Processes.

    Science.gov (United States)

    Rohde, Palle Duun; Demontis, Ditte; Cuyabano, Beatriz Castro Dias; Børglum, Anders D; Sørensen, Peter

    2016-08-01

    Schizophrenia is a psychiatric disorder with large personal and social costs, and understanding the genetic etiology is important. Such knowledge can be obtained by testing the association between a disease phenotype and individual genetic markers; however, such single-marker methods have limited power to detect genetic markers with small effects. Instead, aggregating genetic markers based on biological information might increase the power to identify sets of genetic markers of etiological significance. Several set test methods have been proposed: Here we propose a new set test derived from genomic best linear unbiased prediction (GBLUP), the covariance association test (CVAT). We compared the performance of CVAT to other commonly used set tests. The comparison was conducted using a simulated study population having the same genetic parameters as for schizophrenia. We found that CVAT was among the top performers. When extending CVAT to utilize a mixture of SNP effects, we found an increase in power to detect the causal sets. Applying the methods to a Danish schizophrenia case-control data set, we found genomic evidence for association of schizophrenia with vitamin A metabolism and immunological responses, which previously have been implicated with schizophrenia based on experimental and observational studies. Copyright © 2016 by the Genetics Society of America.

  20. Development and characterization of highly polymorphic long TC repeat microsatellite markers for genetic analysis of peanut

    Directory of Open Access Journals (Sweden)

    Macedo Selma E

    2012-02-01

    Full Text Available Abstract Background Peanut (Arachis hypogaea L. is a crop of economic and social importance, mainly in tropical areas, and developing countries. Its molecular breeding has been hindered by a shortage of polymorphic genetic markers due to a very narrow genetic base. Microsatellites (SSRs are markers of choice in peanut because they are co-dominant, highly transferrable between species and easily applicable in the allotetraploid genome. In spite of substantial effort over the last few years by a number of research groups, the number of SSRs that are polymorphic for A. hypogaea is still limiting for routine application, creating the demand for the discovery of more markers polymorphic within cultivated germplasm. Findings A plasmid genomic library enriched for TC/AG repeats was constructed and 1401 clones sequenced. From the sequences obtained 146 primer pairs flanking mostly TC microsatellites were developed. The average number of repeat motifs amplified was 23. These 146 markers were characterized on 22 genotypes of cultivated peanut. In total 78 of the markers were polymorphic within cultivated germplasm. Most of those 78 markers were highly informative with an average of 5.4 alleles per locus being amplified. Average gene diversity index (GD was 0.6, and 66 markers showed a GD of more than 0.5. Genetic relationship analysis was performed and corroborated the current taxonomical classification of A. hypogaea subspecies and varieties. Conclusions The microsatellite markers described here are a useful resource for genetics and genomics in Arachis. In particular, the 66 markers that are highly polymorphic in cultivated peanut are a significant step towards routine genetic mapping and marker-assisted selection for the crop.

  1. Genetic similarity among strawberry cultivars assessed by RAPD and ISSR markers

    Directory of Open Access Journals (Sweden)

    Rafael Gustavo Ferreira Morales

    2011-12-01

    Full Text Available Most strawberry (Fragaria × ananassa Duchesne cultivars used in Brazil are developed in other countries, it became clear the need to start the strawberry breeding program in the country. To start a breeding program is necessary the genetic characterization of the germplasm available. Molecular markers are important tools that can be used for this purpose. The objectives of the present study were to assess the genetic similarity among 11 strawberry cultivars using RAPD and ISSR molecular markers and to indicate the possible promising crosses. The DNA of the eleven strawberry cultivars was extracted and amplified by PCR with RAPD and ISSR primers. The DNA fragments were separated in agarose gel for the RAPD markers and in polyacrylamide gel for the ISSR markers. The genetic similarity matrix was estimated by the Jaccard coefficient. Based on this matrix, the cultivars were grouped using the UPGMA method. The dendogram generated by the RAPD markers distributed the cultivars in three groups while the ISSR markers generated two groups. There was no direct relationship between the marker groups when the two types of markers were compared. The grouping proposed by the ISSR markers was more coherent with the origin and the genealogy of the cultivars than that proposed by the RAPD markers, and it can be considered the most efficient method for the study of genetic divergence in strawberry. The most promising crosses, based on the genetic divergence estimated from the RAPD and ISSR molecular data were between the Tudla and Ventana and the Oso Grande and Ventana cultivars, respectively.

  2. Congruence between morphological and molecular markers inferred from the analysis of the intra-morphotype genetic diversity and the spatial structure of Oxalis tuberosa Mol.

    Science.gov (United States)

    Pissard, Audrey; Arbizu, Carlos; Ghislain, Marc; Faux, Anne-Michèle; Paulet, Sébastien; Bertin, Pierre

    2008-01-01

    Oxalis tuberosa is an important crop cultivated in the highest Andean zones. A germplasm collection is maintained ex situ by CIP, which has developed a morphological markers system to classify the accessions into morphotypes, i.e. groups of morphologically identical accessions. However, their genetic uniformity is currently unknown. The ISSR technique was used in two experiments to determine the relationships between both morphological and molecular markers systems. The intra-morphotype genetic diversity, the spatial structures of the diversity and the congruence between both markers systems were determined. In the first experience, 44 accessions representing five morphotypes, clearly distinct from each other, were analyzed. At the molecular level, the accessions exactly clustered according to their morphotypes. However, a genetic variability was observed inside each morphotype. In the second experiment, 34 accessions gradually differing from each other on morphological base were analyzed. The morphological clustering showed no geographical structure. On the opposite, the molecular analysis showed that the genetic structure was slightly related to the collection site. The correlation between both markers systems was weak but significant. The lack of perfect congruence between morphological and molecular data suggests that the morphological system may be useful for the morphotypes management but is not appropriate to study the genetic structure of the oca. The spatial structure of the genetic diversity can be related to the evolution of the species and the discordance between the morphological and molecular structures may result from similar selection pressures at different places leading to similar forms with a different genetic background.

  3. Distinctive pattern of expression of spermatogenic molecular markers in testes of azoospermic men with non-mosaic Klinefelter syndrome.

    Science.gov (United States)

    Kleiman, Sandra E; Yogev, Leah; Lehavi, Ofer; Yavetz, Haim; Hauser, Ron

    2016-06-01

    Mature sperm cells can be found in testicular specimens extracted from azoospermic men with non-mosaic Klinefelter syndrome (KS). The present study evaluates the expression of various known molecular markers of spermatogenesis in a population of men with KS and assesses the ability of those markers to predict spermatogenesis. Two groups of men with non-obstructive azoospermia who underwent testicular sperm-retrieval procedures were included in the study: 31 had non-mosaic KS (KS group) and 91 had normal karyotype (NK group). Each group was subdivided into mixed atrophy (containing some mature sperm cells) or Sertoli cell only syndrome according to testicular histology and cytology observations. Semi-quantitative histological morphometric analysis (interstitial hyperplasia and hyalinization, tubules with cells and abnormal thickness of the basement membrane) and expression of spermatogenetic markers (DAZ, RBM, BOLL, and CDY1) were evaluated and compared among those subgroups. Clear differences in the histological morphometry and spermatogenetic marker expression were noted between the KS and NK groups. There was a significant difference in the expression of spermatogenetic markers between the subgroups of the NK group (as expected), while no difference could be discerned between the two subgroups in the KS group. We conclude that molecular spermatogenetic markers have a pattern of expression in men with KS that is distinctively different from that of men with NK, and that it precludes and limits their use for predicting spermatogenesis in the former. It is suggested that this difference might be due to the specific highly abnormal histological morphometric parameters in KS specimens.

  4. An annotated genetic map of loblolly pine based on microsatellite and cDNA markers

    Directory of Open Access Journals (Sweden)

    Wimalanathan Kokulapalan

    2011-01-01

    Full Text Available Abstract Background Previous loblolly pine (Pinus taeda L. genetic linkage maps have been based on a variety of DNA polymorphisms, such as AFLPs, RAPDs, RFLPs, and ESTPs, but only a few SSRs (simple sequence repeats, also known as simple tandem repeats or microsatellites, have been mapped in P. taeda. The objective of this study was to integrate a large set of SSR markers from a variety of sources and published cDNA markers into a composite P. taeda genetic map constructed from two reference mapping pedigrees. A dense genetic map that incorporates SSR loci will benefit complete pine genome sequencing, pine population genetics studies, and pine breeding programs. Careful marker annotation using a variety of references further enhances the utility of the integrated SSR map. Results The updated P. taeda genetic map, with an estimated genome coverage of 1,515 cM(Kosambi across 12 linkage groups, incorporated 170 new SSR markers and 290 previously reported SSR, RFLP, and ESTP markers. The average marker interval was 3.1 cM. Of 233 mapped SSR loci, 84 were from cDNA-derived sequences (EST-SSRs and 149 were from non-transcribed genomic sequences (genomic-SSRs. Of all 311 mapped cDNA-derived markers, 77% were associated with NCBI Pta UniGene clusters, 67% with RefSeq proteins, and 62% with functional Gene Ontology (GO terms. Duplicate (i.e., redundant accessory and paralogous markers were tentatively identified by evaluating marker sequences by their UniGene cluster IDs, clone IDs, and relative map positions. The average gene diversity, He, among polymorphic SSR loci, including those that were not mapped, was 0.43 for 94 EST-SSRs and 0.72 for 83 genomic-SSRs. The genetic map can be viewed and queried at http://www.conifergdb.org/pinemap. Conclusions Many polymorphic and genetically mapped SSR markers are now available for use in P. taeda population genetics, studies of adaptive traits, and various germplasm management applications. Annotating mapped

  5. Theory of mind impairment: a distinct trait-marker for schizophrenia spectrum disorders and bipolar disorder?

    Science.gov (United States)

    Bora, E; Yücel, M; Pantelis, C

    2009-10-01

    The aim of this study was to critically review the literature in order to determine if Theory of Mind (ToM) impairment can be considered a trait-marker for schizophrenia spectrum disorders and bipolar disorder (BD). After a thorough literature search, we reviewed the empirical studies investigating ToM impairments in remitted schizophrenia patients, first episode patients, subjects at high-risk (HR) for psychosis and first-degree relatives of schizophrenia patients. Studies investigating ToM impairment in other schizophrenia spectrum conditions, affective psychosis and BD were also reviewed. ToM abnormalities exist at onset and continue throughout the course of schizophrenia, persist into remission, and while less severe, are apparent in HR populations. Mentalizing impairments are also observed in other forms of psychotic illness and BD. Mentalizing impairment in schizophrenia spectrum disorders and BD might reflect underlying general cognitive deficits and residual symptom expression, rather than representing a specific trait-marker.

  6. Development and genetic mapping of SSR markers in foxtail millet [Setaria italica (L.) P. Beauv.].

    Science.gov (United States)

    Jia, Xiaoping; Zhang, Zhongbao; Liu, Yinghui; Zhang, Chengwei; Shi, Yunsu; Song, Yanchun; Wang, Tianyu; Li, Yu

    2009-02-01

    SSR markers are desirable markers in analysis of genetic diversity, quantitative trait loci mapping and gene locating. In this study, SSR markers were developed from two genomic libraries enriched for (GA)n and (CA)n of foxtail millet [Setaria italica (L.) P. Beauv.], a crop of historical importance in China. A total of 100 SSR markers among the 193 primer pairs detected polymorphism between two mapping parents of an F(2) population, i.e. "B100" of cultivated S. italica and "A10" of wild S. viridis. Excluding 14 markers with unclear amplifications, and five markers unlinked with any linkage group, a foxtail millet SSR linkage map was constructed by integrating 81 new developed SSR markers with 20 RFLP anchored markers. The 81 SSRs covered nine chromosomes of foxtail millet. The length of the map was 1,654 cM, with an average interval distance between markers of 16.4 cM. The 81 SSR markers were not evenly distributed throughout the nine chromosomes, with Ch.8 harbouring the least (3 markers) and Ch.9 harbouring the most (18 markers). To verify the usefulness of the SSR markers developed, 37 SSR markers were randomly chosen to analyze genetic diversity of 40 foxtail millet accessions. Totally 228 alleles were detected, with an average 6.16 alleles per locus. Polymorphism information content (PIC) value for each locus ranged from 0.413 to 0.847, with an average of 0.697. A positive correlation between PIC and number of alleles and between PIC and number of repeat unit were found [0.802 and 0.429, respectively (P < 0.01)]. UPGMA analysis revealed that the 40 foxtail millet cultivars could be grouped into five clusters in which the landraces' grouping was largely consistent with ecotypes while the breeding varieties from different provinces in China tended to be grouped together.

  7. 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

  8. 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 ...

  9. Genetic and Epigenetic Tumor Suppressor Gene Silencing are Distinct Molecular Phenotypes Driven by Growth Promoting Mutations in Non small Cell Lung Cancer

    International Nuclear Information System (INIS)

    Marsit, C. J.; Kelsey, K. T.; Houseman, E. A.; Kelsey, K. T.; Houseman, E. A.; Nelson, H. H.

    2008-01-01

    Both genetic and epigenetic alterations characterize human non small cell lung cancer (NSCLC), but the biological processes that create or select these alterations remain incompletely investigated. Our hypothesis posits that a roughly reciprocal relationship between the propensity for promoter hyper methylation and a propensity for genetic deletion leads to distinct molecular phenotypes of lung cancer. To test this hypothesis, we examined promoter hyper methylation of 17 tumor suppressor genes, as a marker of epigenetic alteration propensity, and deletion events at the 3p21 region, as a marker of genetic alteration. To model the complex biology between these somatic alterations, we utilized an item response theory model. We demonstrated that tumors exhibiting LOH at greater than 30% of informative alleles in the 3p21 region have a significantly reduced propensity for hyper methylation. At the same time, tumors with activating KRAS mutations showed a significantly increased propensity for hyper methylation of the loci examined, a result similar to what has been observed in colon cancer. These data suggest that NSCLCs have distinct epigenetic or genetic alteration phenotypes acting upon tumor suppressor genes and that mutation of oncogenic growth promoting genes, such as KRAS, is associated with the epigenetic phenotype.

  10. Genetic and Epigenetic Tumor Suppressor Gene Silencing Are Distinct Molecular Phenotypes Driven by Growth Promoting Mutations in Nonsmall Cell Lung Cancer

    Directory of Open Access Journals (Sweden)

    Carmen J. Marsit

    2008-01-01

    Full Text Available Both genetic and epigenetic alterations characterize human nonsmall cell lung cancer (NSCLC, but the biological processes that create or select these alterations remain incompletely investigated. Our hypothesis posits that a roughly reciprocal relationship between the propensity for promoter hypermethylation and a propensity for genetic deletion leads to distinct molecular phenotypes of lung cancer. To test this hypothesis, we examined promoter hypermethylation of 17 tumor suppressor genes, as a marker of epigenetic alteration propensity, and deletion events at the 3p21 region, as a marker of genetic alteration. To model the complex biology between these somatic alterations, we utilized an item response theory model. We demonstrated that tumors exhibiting LOH at greater than 30% of informative alleles in the 3p21 region have a significantly reduced propensity for hypermethylation. At the same time, tumors with activating KRAS mutations showed a significantly increased propensity for hypermethylation of the loci examined, a result similar to what has been observed in colon cancer. These data suggest that NSCLCs have distinct epigenetic or genetic alteration phenotypes acting upon tumor suppressor genes and that mutation of oncogenic growth promoting genes, such as KRAS, is associated with the epigenetic phenotype.

  11. A genetic linkage map of hexaploid naked oat constructed with SSR markers

    Directory of Open Access Journals (Sweden)

    Gaoyuan Song

    2015-08-01

    Full Text Available Naked oat is a unique health food crop in China. Using 202 F2 individuals derived from a hybrid between the variety 578 and the landrace Sanfensan, we constructed a genetic linkage map consisting of 22 linkage groups covering 2070.50 cM and including 208 simple sequence repeat (SSR markers. The minimum distance between adjacent markers was 0.01 cM and the average was 9.95 cM. Each linkage group contained 2–22 markers. The largest linkage group covered 174.40 cM and the shortest one covered 36.80 cM, with an average of 94.11 cM. Thirty-six markers (17.3% showing distorted segregation were distributed across linkage groups LG5 to LG22. This map complements published oat genetic maps and is applicable for quantitative trait locus analysis, gene cloning and molecular marker-assisted selection.

  12. 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.

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

    Science.gov (United States)

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

    2017-12-01

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

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

    Directory of Open Access Journals (Sweden)

    Mónica J Pajuelo

    2017-12-01

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

  15. Genetic variations and relationships of cultivated and weedy types of perilla species in Korea and Japan using multi DNA markers

    International Nuclear Information System (INIS)

    Sun, Y.; Zheng, S.; Lee, J.; Hong, S.

    2017-01-01

    The genus Perilla, known as an oil crop or a Chinese medicine, vegetable crop, is widely cultivated in East Asia. It occurs in two distinct varieties, var. frutescens and var. crispa, and their genetic relationship is still obscure. To understand the genetic diversity and relationships of the cultivated and weedy types of Perilla crops in Korea, Japan and China, we evaluated the genetic variation of 20 accessions by 3 rDNA markers. Among these three markers, the nuclear ribosomal DNA (nrDNA) internal transcribed spacers (ITS) region of Perilla crops showed less sequence variations than the 5S and 18S genes. There were abundant variable nucleotide sites appearing in the 5S and 18S genes. Especially in the 18S gene, the variable nucleotide sites showed specificity between some Perilla type and other varieties. JPN1 showed 6 special variable nucleotide sites differing from other varieties, resulting in the farthest phylogenetic relationship in the 18S tree. CHI15 shared 8 special variable sites, also showing far phylogenetic relationship with other varieties. According to the sequence analysis result, the cultivated types of Korean var. frutescens showed relatively more genetic diversity than those of Japanese var. frutescens, while Korean var. crispa showed lower genetic diversity than those of Japanese var. crispa. However, the intra- or inter-variety genetic distance did not have significant difference. This work provided more sequence resources of Perilla crops and evidences to evaluate the genetic variation and relationships. Our result would help molecular type identification, functional plant breeding and trait improvement of Perilla crops. (author)

  16. Canine Cutaneous Leishmaniasis: Dissemination and Tissue Tropism of Genetically Distinct Leishmania (Viannia braziliensis Populations

    Directory of Open Access Journals (Sweden)

    Guilherme Marx de Oliveira

    2013-01-01

    Full Text Available Little is known regarding the internal dissemination of initial cutaneous lesions and tissue tropism of Leishmania (Viannia braziliensis populations in naturally infected dogs. The aim of this study was to investigate genetic polymorphisms of L. (V. braziliensis populations in different anatomic sites of naturally infected dogs by using polymerase chain reaction (PCR and low-stringency single specific primer-PCR (LSSP-PCR techniques. The amplified products were analyzed by LSSP-PCR to investigate the genetic variability of the parasite populations present in different anatomical sites. Twenty-three out of the 52 samples gave PCR-positive results. The existence of L. (V. braziliensis strains that remained restricted to cutaneous lesions and others showing characteristics of dissemination to internal organs and healthy skin was observed. LSSP-PCR and numerical analyses revealed that parasite populations that do not disseminate were genetically similar and belonged to a separate phenetic cluster. In contrast, populations that showed spreading to internal organs displayed a more polymorphic genetic profile. Despite the heterogeneity, L. (V. braziliensis populations with identical genetic profiles were observed in popliteal and cervical lymph nodes of the same animal. Our results indicate that infection in dogs can be manifested by dissemination and tissue tropism of genetically distinct populations of L. (V. braziliensis.

  17. Microsatellite DNA as shared genetic markers among conifer species

    Science.gov (United States)

    Craig S. Echt; G.G. Vendramin; C.D. Nelson; P. Marquardt

    1999-01-01

    Polymerase chain reaction (PCR) primer pairs for 21 simple sequence repeat (SSR) loci in Pinus strobus L. and 6 in Pinus radiata D. Don. were evaluated to determine whether SSR marker amplification could be achieved in 10 other conifer species. Eighty percent of SSR primer pairs for (AC)n loci that were polymorphic in P. ...

  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. Genetic variant as a marker for bladder cancer therapy

    Science.gov (United States)

    Patients who have inherited a specific common genetic variant develop bladder cancer tumors that strongly express a protein known as prostate stem cell antigen (PSCA), which is also expressed in many pancreatic and prostate tumors, according to research a

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

    Directory of Open Access Journals (Sweden)

    Márcia de Nazaré Oliveira Ribeiro

    2011-01-01

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

  1. Using inter simple sequence repeat (ISSR) markers to study genetic ...

    African Journals Online (AJOL)

    enoh

    2012-04-10

    Apr 10, 2012 ... Genetic relationships among the cultivars was assessed by using six inter simple sequence ... polymorphism breeders of this species in order to find the ..... well as the high level of heterozygosity due to the cross- pollinating ...

  2. 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.

  3. Genetic diversity of five local Swedish chicken breeds detected by microsatellite markers.

    Directory of Open Access Journals (Sweden)

    Abiye Shenkut Abebe

    Full Text Available This study aimed at investigating the genetic diversity, relationship and population structure of 110 local Swedish chickens derived from five breeds (Gotlandshöna, Hedemorahöna, Öländsk dvärghöna, Skånsk blommehöna, and Bohuslän- Dals svarthöna, in the rest of the paper the shorter name Svarthöna is used using 24 microsatellite markers. In total, one hundred thirteen alleles were detected in all populations, with a mean of 4.7 alleles per locus. For the five chicken breeds, the observed and expected heterozygosity ranged from 0.225 to 0.408 and from 0.231 to 0.515, with the lowest scores for the Svarthöna and the highest scores for the Skånsk blommehöna breeds, respectively. Similarly, the average within breed molecular kinship varied from 0.496 to 0.745, showing high coancestry, with Skånsk blommehöna having the lowest and Svarthöna the highest coancestry. Furthermore, all breeds showed significant deviations from Hardy-Weinberg expectations. Across the five breeds, the global heterozygosity deficit (FIT was 0.545, population differentiation index (FST was 0.440, and the global inbreeding of individuals within breed (FIS was 0.187. The phylogenetic relationships of chickens were examined using neighbor-joining trees constructed at the level of breeds and individual samples. The neighbor-joining tree constructed at breed level revealed two main clusters, with Hedemorahöna and Öländsk dvärghöna breeds in one cluster, and Gotlandshöna and Svarthöna breeds in the second cluster leaving the Skånsk blommehöna in the middle. Based on the results of the STRUCTURE analysis, the most likely number of clustering of the five breeds was at K = 4, with Hedemorahöna, Gotlandshöna and Svarthöna breeds forming their own distinct clusters, while Öländsk dvärghöna and Skånsk blommehöna breeds clustered together. Losses in the overall genetic diversity of local Swedish chickens due to breeds extinction varied from -1.46% to -6

  4. Genetic diversity and geographic distribution of genetically distinct rabies viruses in the Philippines.

    Directory of Open Access Journals (Sweden)

    Mariko Saito

    Full Text Available BACKGROUND: Rabies continues to be a major public health problem in the Philippines, where 200-300 human cases were reported annually between 2001 and 2011. Understanding the phylogeography of rabies viruses is important for establishing a more effective and feasible control strategy. METHODS: We performed a molecular analysis of rabies viruses in the Philippines using rabied animal brain samples. The samples were collected from 11 of 17 regions, which covered three island groups (Luzon, Visayas, and Mindanao. Partial nucleoprotein (N gene sequencing was performed on 57 samples and complete glycoprotein (G gene sequencing was performed on 235 samples collected between 2004 and 2010. RESULTS: The Philippine strains of rabies viruses were included in a distinct phylogenetic cluster, previously named Asian 2b, which appeared to have diverged from the Chinese strain named Asian 2a. The Philippine strains were further divided into three major clades, which were found exclusively in different island groups: clades L, V, and M in Luzon, Visayas, and Mindanao, respectively. Clade L was subdivided into nine subclades (L1-L9 and clade V was subdivided into two subclades (V1 and V2. With a few exceptions, most strains in each subclade were distributed in specific geographic areas. There were also four strains that were divided into two genogroups but were not classified into any of the three major clades, and all four strains were found in the island group of Luzon. CONCLUSION: We detected three major clades and two distinct genogroups of rabies viruses in the Philippines. Our data suggest that viruses of each clade and subclade evolved independently in each area without frequent introduction into other areas. An important implication of these data is that geographically targeted dog vaccination using the island group approach may effectively control rabies in the Philippines.

  5. Using genetic markers to orient the edges in quantitative trait networks: the NEO software.

    Science.gov (United States)

    Aten, Jason E; Fuller, Tova F; Lusis, Aldons J; Horvath, Steve

    2008-04-15

    Systems genetic studies have been used to identify genetic loci that affect transcript abundances and clinical traits such as body weight. The pairwise correlations between gene expression traits and/or clinical traits can be used to define undirected trait networks. Several authors have argued that genetic markers (e.g expression quantitative trait loci, eQTLs) can serve as causal anchors for orienting the edges of a trait network. The availability of hundreds of thousands of genetic markers poses new challenges: how to relate (anchor) traits to multiple genetic markers, how to score the genetic evidence in favor of an edge orientation, and how to weigh the information from multiple markers. We develop and implement Network Edge Orienting (NEO) methods and software that address the challenges of inferring unconfounded and directed gene networks from microarray-derived gene expression data by integrating mRNA levels with genetic marker data and Structural Equation Model (SEM) comparisons. The NEO software implements several manual and automatic methods for incorporating genetic information to anchor traits. The networks are oriented by considering each edge separately, thus reducing error propagation. To summarize the genetic evidence in favor of a given edge orientation, we propose Local SEM-based Edge Orienting (LEO) scores that compare the fit of several competing causal graphs. SEM fitting indices allow the user to assess local and overall model fit. The NEO software allows the user to carry out a robustness analysis with regard to genetic marker selection. We demonstrate the utility of NEO by recovering known causal relationships in the sterol homeostasis pathway using liver gene expression data from an F2 mouse cross. Further, we use NEO to study the relationship between a disease gene and a biologically important gene co-expression module in liver tissue. The NEO software can be used to orient the edges of gene co-expression networks or quantitative trait

  6. Molecular Markers and Cotton Genetic Improvement: Current Status and Future Prospects

    Directory of Open Access Journals (Sweden)

    Waqas Malik

    2014-01-01

    Full Text Available Narrow genetic base and complex allotetraploid genome of cotton (Gossypium hirsutum L. is stimulating efforts to avail required polymorphism for marker based breeding. The availability of draft genome sequence of G. raimondii and G. arboreum and next generation sequencing (NGS technologies facilitated the development of high-throughput marker technologies in cotton. The concepts of genetic diversity, QTL mapping, and marker assisted selection (MAS are evolving into more efficient concepts of linkage disequilibrium, association mapping, and genomic selection, respectively. The objective of the current review is to analyze the pace of evolution in the molecular marker technologies in cotton during the last ten years into the following four areas: (i comparative analysis of low- and high-throughput marker technologies available in cotton, (ii genetic diversity in the available wild and improved gene pools of cotton, (iii identification of the genomic regions within cotton genome underlying economic traits, and (iv marker based selection methodologies. Moreover, the applications of marker technologies to enhance the breeding efficiency in cotton are also summarized. Aforementioned genomic technologies and the integration of several other omics resources are expected to enhance the cotton productivity and meet the global fiber quantity and quality demands.

  7. SCoT marker for the assessment of genetic diversity in saudi arabian date palm cultivars

    International Nuclear Information System (INIS)

    Qurainy, F.A.; Tarroum, M.

    2015-01-01

    Different types of molecular markers based on DNA have been used for the assessment of genetic diversity in the plant species. Start Codon Targeted Polymorphism (SCoT) marker has recently become the marker of choice in genetic diversity studies. SCoT marker was used for the assessment of genetic diversity in Saudi Arabian date palm cultivars. The percentage of polymorphic loci (PPL) at population level ranged from 3.28 to 13.11 with an average of 7.10. The Neis gene diversity (h) and Shannons Information index (I) were 0.033 and 0.046, respectively. However, at cultivar level, PPL, Neis gene diversity (h) and Shannons Information index (I) were 42.62, 0.090 and 0.155, respectively. Analysis of molecular variance (AMOVA) showed 48% of variation within the populations, whereas 52% was found among the populations. A hierarchical analysis of molecular variance revealed level of genetic differentiation among populations (52% of total variance, P = 0.001), consistent with the gene differentiation coefficient (Gst = 0.631). Unweighted pair group method of arithmetic averages (UPGMA) cluster analysis of the SCoT marker data divided the six cultivars and their populations into five main clusters at 0.95 genetic similarity coefficient level. (author)

  8. The Ventasso Horse: genetic characterization by microsatellites markers

    Directory of Open Access Journals (Sweden)

    M. Blasi

    2010-04-01

    Full Text Available The genetic structure of Ventasso Horse (VH was investigated using 12 microsatellites. The analyses were carried out on 117 VH individuals and the results were compared with those obtained analysing 11 other breeds reared in Italy. All microsatellites were polymorphic in VH and in the other breeds. A total of 124 alleles (from 6 to 19 alleles per microsatellite were detected. Average heterozygosity was 0.743 in VH and ranged from 0.613 to 0.759 in the other breeds. The mean FST value had an average value of 0.0932. Genetic distances were calculated using Nei’s standard genetic distance (Ds. The smallest Ds values were found between VH and Anglo-Arab, Thoroughbred, Maremmano and Lipizzan horse breeds. Phylogenetic trees constructed using neighbour-joining method showed two clear separate clusters: the first includes Bardigiano, Haflinger and Italian Heavy Draught Horse, the second contains the other 9 breeds.

  9. Microsatellite marker analysis of the genetic variability in Hanoverian Hounds.

    Science.gov (United States)

    Lüpke, L; Distl, O

    2005-04-01

    Genetic variability of the dog breed Hanoverian Hound was analysed using a set of 16 microsatellites. The sample of 92 dogs was representative for the total current population [n=334, inbreeding coefficient 9.2%, relationship coefficient 11.2%] with respect to the level and distribution of the inbreeding and relationship coefficients. All microsatellites used were in Hardy-Weinberg equilibrium. The average number of alleles was 6.4. The average observed heterozygosity (H(O)) was slightly higher than the expected heterozygosity (H(E)). Dinucleotide microsatellites exhibited lower polymorphism information content (PIC) than tetranucleotide microsatellites (0.52 versus 0.66). The average PIC was 0.61. The individual inbreeding coefficient was negatively related to the average H(O) of all microsatellites, whereas the proportion of genes from introducing of Hanoverian Hounds from abroad showed no relationships to H(O). We found that the genetic variability in the Hanoverian Hounds analysed here was unexpectedly higher than that previously published for dog breeds of similar population size. Even in dog breeds of larger population size heterogyzosity was seldom higher than that observed here. The rather high genetic variability as quantified by polymorphic microsatellites in Hanoverian Hounds may be due to a large genetic variation in the founder animals of this breed and to the fact that this genetic diversity could be maintained despite genetic bottlenecks experienced by this breed in the 1920s and 1950s and despite the presence of high inbreeding and relationship coefficients for more than 50 years.

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

    Science.gov (United States)

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

    2015-07-14

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

  11. Genetic markers for prediction of normal tissue toxicity after radiotherapy

    DEFF Research Database (Denmark)

    Alsner, Jan; Andreassen, Christian Nicolaj; Overgaard, Jens

    2008-01-01

    During the last decade, a number of studies have supported the hypothesis that there is an important genetic component to the observed interpatient variability in normal tissue toxicity after radiotherapy. This review summarizes the candidate gene association studies published so far on the risk...

  12. Simple sequence repeat (SSR) markers analysis of genetic diversity ...

    African Journals Online (AJOL)

    hope&shola

    2012-04-24

    Apr 24, 2012 ... erucic acid in the oil and low glucosinolate content in the meal has made rapeseed a valuable source of high quality oil for people and nutritional protein for live-stock. (Qiu et al., 2006). Previous studies have demonstrated that yellow seeds have a thinner seed coat than black seeds in the same genetic ...

  13. Genetic and molecular markers of proteinuria and glomerulosclerosis

    NARCIS (Netherlands)

    IJpelaar, Daphne Hubertina Thea

    2009-01-01

    The clinical course of renal diseases depends on the type of renal disorder, genetic factors, environmental influences, and the severity of renal fibrosis. Proteinuria is the abnormal amount of proteins present in the urine. Proteinuria is an independent risk factor for development of renal

  14. Preliminary genetic linkage map of Miscanthus sinensis with RAPD markers

    NARCIS (Netherlands)

    Atienza, S.G.; Satovic, Z.; Petersen, K.K.; Dolstra, O.; Martin, A.

    2002-01-01

    We have used an "offspring cross" mapping strategy in combination with the random amplified polymorphic DNA (RAPD) assay to construct the first genetic map of the species Miscanthus sinensis (2n = 2x = 38). This map is based on an outbred population of 89 individuals resulting from the cross between

  15. Association of susceptible genetic markers and autoantibodies in ...

    Indian Academy of Sciences (India)

    antigen (HLA) locus accounting for at least 30% of overall genetic risk. Non-HLA genes, i.e. ..... to specific regions of DNA and helps control the activity of certain genes. Encodes a transcription factor ..... The cost of such an extensive panel may ...

  16. The efficiency of mitochondrial DNA markers in constructing genetic ...

    African Journals Online (AJOL)

    Administrator

    2011-05-30

    May 30, 2011 ... To date, only parts of mitochondrial DNA from cytochrome b, 12S rRNA, 16S rRNA and non-coding D- loop had been sequenced for different species of Oryx. Discrepancy in the genetic relationship among. Oryx species was previously revealed when combinations of these sequences were analyzed. In the.

  17. 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 ...

  18. Genetic structure of earthworm populations at a regional scale: inferences from mitochondrial and microsatellite molecular markers in Aporrectodea icterica (Savigny 1826.

    Directory of Open Access Journals (Sweden)

    Magally Torres-Leguizamon

    Full Text Available Despite the fundamental role that soil invertebrates (e.g. earthworms play in soil ecosystems, the magnitude of their spatial genetic variation is still largely unknown and only a few studies have investigated the population genetic structure of these organisms. Here, we investigated the genetic structure of seven populations of a common endogeic earthworm (Aporrectodea icterica sampled in northern France to explore how historical species range changes, microevolutionary processes and human activities interact in shaping genetic variation at a regional scale. Because combining markers with distinct modes of inheritance can provide extra, complementary information on gene flow, we compared the patterns of genetic structure revealed using nuclear (7 microsatellite loci and mitochondrial markers (COI. Both types of markers indicated low genetic polymorphism compared to other earthworm species, a result that can be attributed to ancient bottlenecks, for instance due to species isolation in southern refugia during the ice ages with subsequent expansion toward northern Europe. Historical events can also be responsible for the existence of two divergent, but randomly interbreeding mitochondrial lineages within all study populations. In addition, the comparison of observed heterozygosity among microsatellite loci and heterozygosity expected under mutation-drift equilibrium suggested a recent decrease in effective size in some populations that could be due to contemporary events such as habitat fragmentation. The absence of relationship between geographic and genetic distances estimated from microsatellite allele frequency data also suggested that dispersal is haphazard and that human activities favour passive dispersal among geographically distant populations.

  19. 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.

  20. Genetic diversity of Mycosphaerella fijiensis in Brazil analyzed using an ERIC-PCR marker.

    Science.gov (United States)

    Silva, G F; Paixão, R D V; Queiroz, C B; Santana, M F; Souza, A; Sousa, N R; Hanada, R E; Gasparotto, L

    2014-09-26

    The Enterobacterial repetitive intergenic consensus (ERIC) marker was used to analyze the genetic variability of Mycosphaerella fijiensis, the causative agent of Black Sigatoka disease in banana plants. A total of 123 isolates were used, which were divided into populations based on their original hosts and collection sites in Brazil. A total of 9 loci were amplified, 77.8% of which were found to be polymorphic. The genetic diversity found in the population was 0.20. Analysis of molecular variance (AMOVA) demonstrated that the highest level of genetic variation is within populations. Cluster analysis revealed three main groups in Brazil, with no correlation between geographic and genetic distance.

  1. Genetic Diversity Analysis of Medicinally Important Horticultural Crop Aegle marmelos by ISSR Markers.

    Science.gov (United States)

    Mujeeb, Farina; Bajpai, Preeti; Pathak, Neelam; Verma, Smita Rastogi

    2017-01-01

    Inter simple sequence repeat (ISSR) markers help in identifying and determining the extent of genetic diversity in cultivars. Here, we describe their application in determining the genetic diversity of bael (Aegle marmelos Corr.). Universal ISSR primers are selected and their marker characteristics such as polymorphism information content, effective multiplex ratio and marker index have been evaluated. ISSR-PCR is then performed using universal ISSR primers to generate polymorphic bands. This information is used to determine the degree of genetic similarity among the bael varieties/accessions by cluster analysis using unweighted pair-group method with arithmetic averages (UPGMA). This technology is valuable for biodiversity conservation and for making an efficient choice of parents in breeding programs.

  2. Selfish genetic elements favor the evolution of a distinction between soma and germline.

    Science.gov (United States)

    Johnson, Louise J

    2008-08-01

    Many multicellular organisms have evolved a dedicated germline. This can benefit the whole organism, but its advantages to genetic parasites have not been explored. Here I model the evolutionary success of a selfish element, such as a transposable element or endosymbiont, which is capable of creating or strengthening a germline-soma distinction in a primitively multicellular host, and find that it will always benefit the element to do so. Genes causing germline sequestration can therefore spread in a population even if germline sequestration is maladaptive for the host organism. Costly selfish elements are expected to survive only in sexual populations, so sexual species may experience an additional push toward germline-soma distinction, and hence toward cell differentiation and multicellularity.

  3. Phylogeographic Evidence for 2 Genetically Distinct Zoonotic Plasmodium knowlesi Parasites, Malaysia.

    Science.gov (United States)

    Yusof, Ruhani; Ahmed, Md Atique; Jelip, Jenarun; Ngian, Hie Ung; Mustakim, Sahlawati; Hussin, Hani Mat; Fong, Mun Yik; Mahmud, Rohela; Sitam, Frankie Anak Thomas; Japning, J Rovie-Ryan; Snounou, Georges; Escalante, Ananias A; Lau, Yee Ling

    2016-08-01

    Infections of humans with the zoonotic simian malaria parasite Plasmodium knowlesi occur throughout Southeast Asia, although most cases have occurred in Malaysia, where P. knowlesi is now the dominant malaria species. This apparently skewed distribution prompted an investigation of the phylogeography of this parasite in 2 geographically separated regions of Malaysia, Peninsular Malaysia and Malaysian Borneo. We investigated samples collected from humans and macaques in these regions. Haplotype network analyses of sequences from 2 P. knowlesi genes, type A small subunit ribosomal 18S RNA and cytochrome c oxidase subunit I, showed 2 genetically distinct divergent clusters, 1 from each of the 2 regions of Malaysia. We propose that these parasites represent 2 distinct P. knowlesi types that independently became zoonotic. These types would have evolved after the sea-level rise at the end of the last ice age, which separated Malaysian Borneo from Peninsular Malaysia.

  4. Results for five sets of forensic genetic markers studied in a Greek population sample.

    Science.gov (United States)

    Tomas, C; Skitsa, I; Steinmeier, E; Poulsen, L; Ampati, A; Børsting, C; Morling, N

    2015-05-01

    A population sample of 223 Greek individuals was typed for five sets of forensic genetic markers with the kits NGM SElect™, SNPforID 49plex, DIPplex®, Argus X-12 and PowerPlex® Y23. No significant deviation from Hardy-Weinberg expectations was observed for any of the studied markers after Holm-Šidák correction. Statistically significant (P21) individuals for 16 autosomal STRs. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  5. Chapter 10: Mining genome-wide genetic markers.

    Directory of Open Access Journals (Sweden)

    Xiang Zhang

    Full Text Available Genome-wide association study (GWAS aims to discover genetic factors underlying phenotypic traits. The large number of genetic factors poses both computational and statistical challenges. Various computational approaches have been developed for large scale GWAS. In this chapter, we will discuss several widely used computational approaches in GWAS. The following topics will be covered: (1 An introduction to the background of GWAS. (2 The existing computational approaches that are widely used in GWAS. This will cover single-locus, epistasis detection, and machine learning methods that have been recently developed in biology, statistic, and computer science communities. This part will be the main focus of this chapter. (3 The limitations of current approaches and future directions.

  6. Distinct genetic architectures for phenotype means and plasticities in Zea mays.

    Science.gov (United States)

    Kusmec, Aaron; Srinivasan, Srikant; Nettleton, Dan; Schnable, Patrick S

    2017-09-01

    Phenotypic plasticity describes the phenotypic variation of a trait when a genotype is exposed to different environments. Understanding the genetic control of phenotypic plasticity in crops such as maize is of paramount importance for maintaining and increasing yields in a world experiencing climate change. Here, we report the results of genome-wide association analyses of multiple phenotypes and two measures of phenotypic plasticity in a maize nested association mapping (US-NAM) population grown in multiple environments and genotyped with ~2.5 million single-nucleotide polymorphisms. We show that across all traits the candidate genes for mean phenotype values and plasticity measures form structurally and functionally distinct groups. Such independent genetic control suggests that breeders will be able to select semi-independently for mean phenotype values and plasticity, thereby generating varieties with both high mean phenotype values and levels of plasticity that are appropriate for the target performance environments.

  7. Markers of Psychological Differences and Social and Health Inequalities: Possible Genetic and Phenotypic Overlaps.

    Science.gov (United States)

    Mõttus, René; Marioni, Riccardo; Deary, Ian J

    2017-02-01

    Associations between markers of ostensible psychological characteristics and social and health inequalities are pervasive but difficult to explain. In some cases, there may be causal influence flowing from social and health inequalities to psychological differences, whereas sometimes it may be the other way around. Here, we focus on the possibility that some markers that we often consider as indexing different domains of individual differences may in fact reflect at least partially overlapping genetic and/or phenotypic bases. For example, individual differences in cognitive abilities and educational attainment appear to reflect largely overlapping genetic influences, whereas cognitive abilities and health literacy may be almost identical phenomena at the phenotypic, never mind genetic, level. We make the case for employing molecular genetic data and quantitative genetic techniques to better understand the associations of psychological individual differences with social and health inequalities. We illustrate these arguments by using published findings from the Lothian Birth Cohort and the Generation Scotland studies. We also present novel findings pertaining to longitudinal stability and change in older age personality traits and some correlates of the change, molecular genetic data-based heritability estimates of Neuroticism and Extraversion, and the genetic correlations of these personality traits with markers of social and health inequalities. © 2015 The Authors. Journal of Personality published by Wiley Periodicals, Inc.

  8. Genetic Markers for Western Corn Rootworm Resistance to Bt Toxin

    OpenAIRE

    Flagel, Lex E.; Swarup, Shilpa; Chen, Mao; Bauer, Christopher; Wanjugi, Humphrey; Carroll, Matthew; Hill, Patrick; Tuscan, Meghan; Bansal, Raman; Flannagan, Ronald; Clark, Thomas L.; Michel, Andrew P.; Head, Graham P.; Goldman, Barry S.

    2015-01-01

    Western corn rootworm (WCR) is a major maize (Zea mays L.) pest leading to annual economic losses of more than 1 billion dollars in the United States. Transgenic maize expressing insecticidal toxins derived from the bacterium Bacillus thuringiensis (Bt) are widely used for the management of WCR. However, cultivation of Bt-expressing maize places intense selection pressure on pest populations to evolve resistance. Instances of resistance to Bt toxins have been reported in WCR. Developing genet...

  9. Genetic diversity and population structure assessed by SSR and SNP markers in a large germplasm collection of grape

    Science.gov (United States)

    2013-01-01

    Background The economic importance of grapevine has driven significant efforts in genomics to accelerate the exploitation of Vitis resources for development of new cultivars. However, although a large number of clonally propagated accessions are maintained in grape germplasm collections worldwide, their use for crop improvement is limited by the scarcity of information on genetic diversity, population structure and proper phenotypic assessment. The identification of representative and manageable subset of accessions would facilitate access to the diversity available in large collections. A genome-wide germplasm characterization using molecular markers can offer reliable tools for adjusting the quality and representativeness of such core samples. Results We investigated patterns of molecular diversity at 22 common microsatellite loci and 384 single nucleotide polymorphisms (SNPs) in 2273 accessions of domesticated grapevine V. vinifera ssp. sativa, its wild relative V. vinifera ssp. sylvestris, interspecific hybrid cultivars and rootstocks. Despite the large number of putative duplicates and extensive clonal relationships among the accessions, we observed high level of genetic variation. In the total germplasm collection the average genetic diversity, as quantified by the expected heterozygosity, was higher for SSR loci (0.81) than for SNPs (0.34). The analysis of the genetic structure in the grape germplasm collection revealed several levels of stratification. The primary division was between accessions of V. vinifera and non-vinifera, followed by the distinction between wild and domesticated grapevine. Intra-specific subgroups were detected within cultivated grapevine representing different eco-geographic groups. The comparison of a phenological core collection and genetic core collections showed that the latter retained more genetic diversity, while maintaining a similar phenotypic variability. Conclusions The comprehensive molecular characterization of our grape

  10. APPLICATION OF RYE SSR MARKERS FOR DETECTION OF GENETIC DIVERSITY IN TRITICALE

    Directory of Open Access Journals (Sweden)

    Želmíra Balážová

    2016-06-01

    Full Text Available Present study aims to testify usefulness of particular rye SSR markers for the detection of genetic diversity degree in the set of 20 triticale cultivars coming from different European countries. For this purpose, a set of six rye SSR markers were used. The set of six polymorphic markers provided 22 alleles with an average frequency of 3.67 alleles per locus. The number of alleles ranged between 2 (SCM43 and 5 (SCM28, SCM86. Resulting from the number and frequency of alleles diversity index (DI, polymorphic information content (PIC and probability of identity (PI were calculated. An average value of PIC for 6 SSR markers was 0.505, the highest value was calculated for rye SSR marker SCM86 (0.706. Based on UPGMA algorithm, a dendrogram was constructed. In dendrogram cultivars were divided into two main clusters. The first cluster contained two cultivars, Russian cultivar Greneder and Slovak cultivar Largus, and second included 18 cultivars. Genetically the closest were two Greek cultivars (Niobi and Thisbi and were close to other Greek cultivar Vrodi. It was possible to separate triticale cultivars of spring and winter form in dendrogram. Results showed the utility of rye microsatellite markers for estimation of genetic diversity of European triticale genotypes leading to genotype identification.

  11. Inherited Genetic Markers for Thrombophilia in Northeastern Iran (a Clinical-Based Report

    Directory of Open Access Journals (Sweden)

    Fatemeh Keify

    2014-05-01

    Full Text Available Background: Thrombophilia is a main predisposition to thrombosis due to a procoagulant state. Several point mutations play key roles in blood-clotting disorders, which are grouped under the term thrombophilia. These thrombophilic mutations are methylenetetrahydrofolate reductase (MTHFR, C677T, and A1298C, factor V Leiden (G1691A, prothrombin gene mutation (factor II, G20210A, and plasminogen activator inhibitor (PAI. In the present study, we assessed the prevalence of the above thrombophilia markers in patients with recurrent pregnancy loss or first and second trimester abortions, infertility, and failed in vitro fertilization (IVF. Methods: This study was conducted among 457 cases those were referred to detect the inherited genetic markers for thrombophilia. Markers for MTHFR, Factor II, and Factor V were assessed by polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP, and PAI was assessed by Amplification Refractory Mutation System (ARMS-PCR. Results: Two hundred sixty cases (56.89% were diagnosed as having at least one thrombophilia marker, whereas 197 cases (43.11% had no thrombophilia markers and were normal. Conclusion: According to the current study, the pattern of abnormal genetic markers for thrombophilia in northeastern Iran demonstrates the importance of genetic evaluations in patients who show clinical abnormalities with recurrent spontaneous abortion (RSA or other serious obstetric complications.

  12. Genetic linkage mapping in an F2 perennial ryegrass population using DArT markers

    DEFF Research Database (Denmark)

    Tomaszewski, Céline; Byrne, Stephen; Foito, Alexandra

    2012-01-01

    Perennial ryegrass is the principal forage grass species used in temperate agriculture. In recent years, significant efforts have been made to develop molecular marker strategies to allow cost-effective characterization of a large number of loci simultaneously. One such strategy involves using DAr......T markers, and a DArT array has recently been developed for the Lolium-Festuca complex. In this study, we report the first use of the DArTFest array to generate a genetic linkage map based on 326 markers in a Lolium perenne F2 population, consisting of 325 genotypes. For proof of concept, the map was used...

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

    Directory of Open Access Journals (Sweden)

    Dongwon Seo

    2016-04-01

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

  14. ASSOCIATION OF SOME BIOCHEMICAL-GENETIC MARKERS WITH THE REPRODUCTION PARAMETERS OF THE BOTOSANI KARAKUL EWES

    Directory of Open Access Journals (Sweden)

    GH. HRINCĂ

    2008-10-01

    Full Text Available The paper describes some associative aspects of various biochemical-genetic markers with the reproduction activity in ewes of the Botosani Karakul breed. The two most important reproduction parameters (fecundity and prolificacy were analyzed according to the genotypes or phenotypes of polymorph systems (haemoglobin, transferrin, albumin and blood potassium of females. The relationship between reproduction data and genetic markers in ewes was quantified both for each genotype (phenotype and for each mating couple type made up depending on the genotype (phenotype of the couple partners (homozygous x homozygous, homozygous x heterozygous or heterozygous x heterozygous. All these associative aspects and their results are discussed for each polymorph genetic system. The ewes which are heterozygous at different genetic marker loci are more fertile and more prolific than the ewes which are homozygous at the levels of these loci. The highest conception and lambing rates resulted from the mating couples in which both partners were heterozygous and the least lambs were obtained from the mating couples in which both partners were homozygous; the fertility and prolificacy had intermediate values in heterogeneous mating couples (heterozygotes x homozygotes but they were nearer to the case in which both mating couple partners were heterozygous. The sheep breeding field can benefit by the contribution of biochemical-genetic markers to optimize the selection criteria with a view to increasing the reproduction capacity of this species.

  15. Genetic diversity and relationships in mulberry (genus Morus as revealed by RAPD and ISSR marker assays

    Directory of Open Access Journals (Sweden)

    Thangavelu K

    2004-01-01

    Full Text Available Abstract Background The genus Morus, known as mulberry, is a dioecious and cross-pollinating plant that is the sole food for the domesticated silkworm, Bombyx mori. Traditional methods using morphological traits for classification are largely unsuccessful in establishing the diversity and relationships among different mulberry species because of environmental influence on traits of interest. As a more robust alternative, PCR based marker assays including RAPD and ISSR were employed to study the genetic diversity and interrelationships among twelve domesticated and three wild mulberry species. Results RAPD analysis using 19 random primers generated 128 discrete markers ranging from 500–3000 bp in size. One-hundred-nineteen of these were polymorphic (92%, with an average of 6.26 markers per primer. Among these were a few putative species-specific amplification products which could be useful for germplasm classification and introgression studies. The ISSR analysis employed six anchored primers, 4 of which generated 93 polymorphic markers with an average of 23.25 markers per primer. Cluster analysis of RAPD and ISSR data using the WINBOOT package to calculate the Dice coefficient resulted into two clusters, one comprising polyploid wild species and the other with domesticated (mostly diploid species. Conclusion These results suggest that RAPD and ISSR markers are useful for mulberry genetic diversity analysis and germplasm characterization, and that putative species-specific markers may be obtained which can be converted to SCARs after further studies.

  16. Genetic Diversity Analysis in 27 Tomato Accessions Using Morphological and Molecular Markers

    Directory of Open Access Journals (Sweden)

    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.

  17. Analysis of the genetic relationships and diversity among 11 populations of Xanthoceras sorbifolia using phenotypic and microsatellite marker data

    Directory of Open Access Journals (Sweden)

    Zhan Shen

    2017-03-01

    Conclusions: Microsatellite markers can be used to efficiently distinguish X. sorbifolia populations and assess their genetic diversity. The information we have provided will contribute to the conservation and management of this important plant genetic resource.

  18. Tracing the evolution of male lineages in bears using genetic markers on the Y chromosome

    OpenAIRE

    Bidon, Tobias

    2015-01-01

    The mammalian family of bears (Ursidae) comprises eight extant species, occurring on four different continents. Among them are the iconic and well-known brown and polar bears, both widely distributed across the Northern hemisphere. Their intraspecific genetic structuring has been extensively investigated, albeit with a focus on genetic markers from maternally inherited parts of their genomes (mitochondrial DNA). The evolutionary relationship and divergence time between brown and polar bears h...

  19. Monitoring Genetic Stability in Quercus serrata Thunb. Somatic Embryogenesis Using RAPD Markers

    OpenAIRE

    Ramesh C., Thakur; Susumu, Goto; Katsuaki, Ishii; S. Mohan, Jain; Forestry and Forest Products Research Institute; Fukuoka Prefecture Forest Research and Extension Center; Forestry and Forest Products Research Institute; University of Helsinki

    1999-01-01

    Genetic stability of propagules regenerated via somatic embryogenesis is of paramount importance for its application to clonal forestry. Random amplified polymorphic DNA (RAPD) markers were used to determine the genetic stability in somatic embryogenesis of Quercus serrata Thunb. (Japanese white oak). Forty samples from an embryogenic line, consisting of regenerated plantlets, somatic embryos, and embryogenic calli, were examined using 54 decanucleotide primers. A total of 6520 clear reproduc...

  20. Development of SSR Markers and Assessment of Genetic Diversity in Medicinal Chrysanthemum morifolium Cultivars.

    Science.gov (United States)

    Feng, Shangguo; He, Renfeng; Lu, Jiangjie; Jiang, Mengying; Shen, Xiaoxia; Jiang, Yan; Wang, Zhi'an; Wang, Huizhong

    2016-01-01

    Chrysanthemum morifolium, is a well-known flowering plant worldwide, and has a high commercial, floricultural, and medicinal value. In this study, simple-sequence repeat (SSR) markers were generated from EST datasets and were applied to assess the genetic diversity among 32 cultivars. A total of 218 in silico SSR loci were identified from 7300 C. morifolium ESTs retrieved from GenBank. Of all SSR loci, 61.47% of them (134) were hexa-nucleotide repeats, followed by tri-nucleotide repeats (17.89%), di-nucleotide repeats (12.39%), tetra-nucleotide repeats (4.13%), and penta-nucleotide repeats (4.13%). In this study, 17 novel EST-SSR markers were verified. Along with 38 SSR markers reported previously, 55 C. morifolium SSR markers were selected for further genetic diversity analysis. PCR amplification of these EST-SSRs produced 1319 fragments, 1306 of which showed polymorphism. The average polymorphism information content of the SSR primer pairs was 0.972 (0.938-0.993), which showed high genetic diversity among C. morifolium cultivars. Based on SSR markers, 32 C. morifolium cultivars were separated into two main groups by partitioning of the clusters using the unweighted pair group method with arithmetic mean dendrogram, which was further supported by a principal coordinate analysis plot. Phylogenetic relationship among C. morifolium cultivars as revealed by SSR markers was highly consistent with the classification of medicinal C. morifolium populations according to their origin and ecological distribution. Our results demonstrated that SSR markers were highly reproducible and informative, and could be used to evaluate genetic diversity and relationships among medicinal C. morifolium cultivars.

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

    Directory of Open Access Journals (Sweden)

    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.

  2. Genetically distinct isolates of Spirocerca sp. from a naturally infected red fox (Vulpes vulpes) from Denmark.

    Science.gov (United States)

    Al-Sabi, Mohammad Nafi Solaiman; Hansen, Mette Sif; Chriél, Mariann; Holm, Elisabeth; Larsen, Gitte; Enemark, Heidi Larsen

    2014-09-15

    Spirocerca lupi causes formation of nodules that may transform into sarcoma in the walls of aorta, esophagus and stomach of infected canids. In February 2013, post mortem examination of a red fox (Vulpes vulpes) hunted in Denmark revealed the presence of several nodules containing adult worms of Spirocerca sp. in the stomach and the omentum. The nodules largely consisted of fibrous tissue with infiltration of mononuclear cells, neutrophilic granulocytes and macrophages with hemosiderin deposition. Parasitological examination by three copromicroscopic methods, sedimentation, flotation with saturated sugar-salt solution, and sieving failed to detect eggs of Spirocerca sp. in feces collected from the colon. This is the first report of spirocercosis in Denmark, and may have been caused by a recent introduction by migrating paratenic or definitive host. Analysis of two overlapping partial sequences of the cox1 gene, from individual worms, revealed distinct genetic variation (7-9%) between the Danish worms and isolates of S. lupi from Europe, Asia and Africa. This was confirmed by phylogenetic analysis that clearly separated the Danish worms from other isolates of S. lupi. The distinct genetic differences of the current worms compared to other isolates of S. lupi may suggest the presence of a cryptic species within Spirocerca. Copyright © 2014 Elsevier B.V. All rights reserved.

  3. Clinical characteristics in genetically distinct forms of the congenital long QT syndrome

    International Nuclear Information System (INIS)

    Kawahara, Yosuke; Sawayama, Toshitami; Samukawa, Masanobu; Nezuo, Shoso; Tanaka, Junji; Suetsuna, Ryoji; Kamiyama, Norio

    1998-01-01

    The clinical characteristics in genetically distinct forms of the congenital long QT syndrome (LQTs) were examined on the balance of bilateral sympathetic nerves, and ECG findings. The subjects (mean: 19.4 years old) were three genetically distinct forms of LQTs, including 3 patients in A-family (the high risk family with sudden death), 2 patients in B-family and 3 patients in C-family. All patients met the standard diagnostic criteria according to Schwartz. As the index of the balance of bilateral sympathetic nerves, the dissociation of Tl and MIBG uptake (D) was examined and the radioactivity ratio (the A/L ratio) of anteroseptal wall to posterolateral wall was calculated. The T-wave patterns of ECG and the situation at syncope were examined. In A-family, all 3 patients showed the lowered A/L ratio, D(+), and similar T-wave patterns in ECG. The syndrome developed at exercise, and their QTc extended at exercise. In B-family, all 2 patients showed normal A/L ratio and long T-wave at QT onset, and their QTc shortened at exercise. All patients had developed syncope at rest. In C-family, all 3 patients showed a little decrease of A/L ratio and similar T-wave patterns. Their QTc extended at exercise. These results suggest that the characteristics of the sympathetic nerve balance, ECG wave patterns and the syndrome may depend on each family. (K.H.)

  4. Hierarchical spatial genetic structure in a distinct population segment of greater sage-grouse

    Science.gov (United States)

    Oyler-McCance, Sara J.; Casazza, Michael L.; Fike, Jennifer A.; Coates, Peter S.

    2014-01-01

    Greater sage-grouse (Centrocercus urophasianus) within the Bi-State Management Zone (area along the border between Nevada and California) are geographically isolated on the southwestern edge of the species’ range. Previous research demonstrated that this population is genetically unique, with a high proportion of unique mitochondrial DNA (mtDNA) haplotypes and with significant differences in microsatellite allele frequencies compared to populations across the species’ range. As a result, this population was considered a distinct population segment (DPS) and was recently proposed for listing as threatened under the U.S. Endangered Species Act. A more comprehensive understanding of the boundaries of this genetically unique population (where the Bi-State population begins) and an examination of genetic structure within the Bi-State is needed to help guide effective management decisions. We collected DNA from eight sampling locales within the Bi-State (N = 181) and compared those samples to previously collected DNA from the two most proximal populations outside of the Bi-State DPS, generating mtDNA sequence data and amplifying 15 nuclear microsatellites. Both mtDNA and microsatellite analyses support the idea that the Bi-State DPS represents a genetically unique population, which has likely been separated for thousands of years. Seven mtDNA haplotypes were found exclusively in the Bi-State population and represented 73 % of individuals, while three haplotypes were shared with neighboring populations. In the microsatellite analyses both STRUCTURE and FCA separate the Bi-State from the neighboring populations. We also found genetic structure within the Bi-State as both types of data revealed differences between the northern and southern part of the Bi-State and there was evidence of isolation-by-distance. STRUCTURE revealed three subpopulations within the Bi-State consisting of the northern Pine Nut Mountains (PNa), mid Bi-State, and White Mountains (WM) following a

  5. Genetic and stratigraphic significance of the Upper Devonian Frasnian Z Marker, west-central Alberta

    Energy Technology Data Exchange (ETDEWEB)

    Wendte, J. [Geological Survey of Canada, Calgary, AB (Canada); Stoakes, F. [Stoakes Consulting Group Ltd., Calgary, AB (Canada); Bosman, M. [Canadian Hunter Exploration Ltd., Calgary, AB (Canada); Bernstein, L. [Talisman Energy Inc., Calgary, AB (Canada)

    1995-12-01

    The stratigraphic model from the west-central Alberta basin was provided. It defined the Z Marker as a distinctive and widespread wireline log marker within the thick Frasnian Ireton shale basin succession. The marker represents an interval of condensed sedimentation and corresponds to an abrupt change from a calcareous signature below to an argillaceous character above. Toward the shelf, in the West Pembina area, the Z Marker correlates to a level within a conformable succession of nodular lime wackestones and corresponds to the base of a depositional cycle near the middle of the Lobstick member of the Nisku Formation. Further shelfward, the Z Marker continues as a well-defined log marker until the Nisku shelf margin. The stratigraphic significance of the Z Marker in delineating various oil bearing formations in Alberta were explained in great detail. The correct recognition and correlation of this marker was claimed to permit an understanding of basin evolution beyond that discernable from the existing lithostratigraphic nomenclature alone. 17 refs., 13 figs.

  6. RAPD-SCAR marker and genetic relationship analysis of three Demodex species (Acari: Demodicidae).

    Science.gov (United States)

    Zhao, Ya-E; Wu, Li-Ping

    2012-06-01

    For a long time, classification of Demodex mites has been mainly based on their hosts and phenotype characteristics. The study was the first to conduct molecular identification and genetic relationship analysis for six isolates of three Demodex species by random amplified polymorphic DNA (RAPD) and sequence-characterized amplified region (SCAR) marker. Totally, 239 DNA fragments were amplified from six Demodex isolates with 10 random primers in RAPD, of which 165 were polymorphic. Using a single primer, at least five fragments and at most 40 in the six isolates were amplified, whereas within a single isolate, a range of 35-49 fragments were amplified. DNA fingerprints of primers CZ 1-9 revealed intra- and interspecies difference in six Demodex isolates, whereas primer CZ 10 only revealed interspecies difference. The genetic distance and dendrogram showed the intraspecific genetic distances were closer than the interspecific genetic distances. The interspecific genetic distances of Demodex folliculorum and Demodex canis (0.7931-0.8140) were shorter than that of Demodex brevis and D. canis (0.8182-0.8987). The RAPD-SCAR marker displayed primer CZ 10 could be applied to identify the three Demodex species. The 479-bp fragment was specific for D. brevis, and the 261-bp fragment was specific for D. canis. The conclusion was that the RAPD-SCAR multi-marker was effective in molecular identification of three Demodex species. The genetic relationship between D. folliculorum and D. canis was nearer than that between D. folliculorum and D. brevis.

  7. Expanding Possibilities for Intervention against Small Ruminant Lentiviruses through Genetic Marker-Assisted Selective Breeding

    Science.gov (United States)

    White, Stephen N.; Knowles, Donald P.

    2013-01-01

    Small ruminant lentiviruses include members that infect sheep (ovine lentivirus [OvLV]; also known as ovine progressive pneumonia virus/maedi-visna virus) and goats (caprine arthritis encephalitis virus [CAEV]). Breed differences in seroprevalence and proviral concentration of OvLV had suggested a strong genetic component in susceptibility to infection by OvLV in sheep. A genetic marker test for susceptibility to OvLV has been developed recently based on the TMEM154 gene with validation data from over 2,800 sheep representing nine cohorts. While no single genotype has been shown to have complete resistance to OvLV, consistent association in thousands of sheep from multiple breeds and management conditions highlight a new strategy for intervention by selective breeding. This genetic marker-assisted selection (MAS) has the potential to be a useful addition to existing viral control measures. Further, the discovery of multiple additional genomic regions associated with susceptibility to or control of OvLV suggests that additional genetic marker tests may be developed to extend the reach of MAS in the future. This review will cover the strengths and limitations of existing data from host genetics as an intervention and outline additional questions for future genetic research in sheep, goats, small ruminant lentiviruses, and their host-pathogen interactions. PMID:23771240

  8. The Y chromosome as the most popular marker in genetic genealogy benefits interdisciplinary research.

    Science.gov (United States)

    Calafell, Francesc; Larmuseau, Maarten H D

    2017-05-01

    The Y chromosome is currently by far the most popular marker in genetic genealogy that combines genetic data and family history. This popularity is based on its haploid character and its close association with the patrilineage and paternal inherited surname. Other markers have not been found (yet) to overrule this status due to the low sensitivity and precision of autosomal DNA for genetic genealogical applications, given the vagaries of recombination, and the lower capacities of mitochondrial DNA combined with an in general much lower interest in maternal lineages. The current knowledge about the Y chromosome and the availability of markers with divergent mutation rates make it possible to answer questions on relatedness levels which differ in time depth; from the individual and familial level to the surnames, clan and population level. The use of the Y chromosome in genetic genealogy has led to applications in several well-established research disciplines; namely in, e.g., family history, demography, anthropology, forensic sciences, population genetics and sex chromosome evolution. The information obtained from analysing this chromosome is not only interesting for academic scientists but also for the huge and lively community of amateur genealogists and citizen-scientists, fascinated in analysing their own genealogy or surname. This popularity, however, has also some drawbacks, mainly for privacy reasons related to the DNA donor, his close family and far-related namesakes. In this review paper we argue why Y-chromosomal analysis and its genetic genealogical applications will still perform an important role in future interdisciplinary research.

  9. Expanding Possibilities for Intervention against Small Ruminant Lentiviruses through Genetic Marker-Assisted Selective Breeding

    Directory of Open Access Journals (Sweden)

    Donald P. Knowles

    2013-06-01

    Full Text Available Small ruminant lentiviruses include members that infect sheep (ovine lentivirus [OvLV]; also known as ovine progressive pneumonia virus/maedi-visna virus and goats (caprine arthritis encephalitis virus [CAEV]. Breed differences in seroprevalence and proviral concentration of OvLV had suggested a strong genetic component in susceptibility to infection by OvLV in sheep. A genetic marker test for susceptibility to OvLV has been developed recently based on the TMEM154 gene with validation data from over 2,800 sheep representing nine cohorts. While no single genotype has been shown to have complete resistance to OvLV, consistent association in thousands of sheep from multiple breeds and management conditions highlight a new strategy for intervention by selective breeding. This genetic marker-assisted selection (MAS has the potential to be a useful addition to existing viral control measures. Further, the discovery of multiple additional genomic regions associated with susceptibility to or control of OvLV suggests that additional genetic marker tests may be developed to extend the reach of MAS in the future. This review will cover the strengths and limitations of existing data from host genetics as an intervention and outline additional questions for future genetic research in sheep, goats, small ruminant lentiviruses, and their host-pathogen interactions.

  10. Distinct virulence of Rift Valley fever phlebovirus strains from different genetic lineages in a mouse model.

    Directory of Open Access Journals (Sweden)

    Tetsuro Ikegami

    Full Text Available Rift Valley fever phlebovirus (RVFV causes high rates of abortions and fetal malformations in ruminants, and hemorrhagic fever, encephalitis, or blindness in humans. Viral transmission occurs via mosquito vectors in endemic areas, which necessitates regular vaccination of susceptible livestock animals to prevent the RVF outbreaks. Although ZH501 strain has been used as a challenge strain for past vaccine efficacy studies, further characterization of other RVFV strains is important to optimize ruminant and nonhuman primate RVFV challenge models. This study aimed to characterize the virulence of wild-type RVFV strains belonging to different genetic lineages in outbred CD1 mice. Mice were intraperitoneally infected with 1x103 PFU of wild-type ZH501, Kenya 9800523, Kenya 90058, Saudi Arabia 200010911, OS1, OS7, SA75, Entebbe, or SA51 strains. Among them, mice infected with SA51, Entebbe, or OS7 strain showed rapid dissemination of virus in livers and peracute necrotic hepatitis at 2-3 dpi. Recombinant SA51 (rSA51 and Zinga (rZinga strains were recovered by reverse genetics, and their virulence was also tested in CD1 mice. The rSA51 strain reproduced peracute RVF disease in mice, whereas the rZinga strain showed a similar virulence with that of rZH501 strain. This study showed that RVFV strains in different genetic lineages display distinct virulence in outbred mice. Importantly, since wild-type RVFV strains contain defective-interfering RNA or various genetic subpopulations during passage from original viral isolations, recombinant RVFV strains generated by reverse genetics will be better suitable for reproducible challenge studies for vaccine development as well as pathological studies.

  11. Genetic approach identifies distinct asthma pathways in overweight vs normal weight children.

    Science.gov (United States)

    Butsch Kovacic, M; Martin, L J; Biagini Myers, J M; He, H; Lindsey, M; Mersha, T B; Khurana Hershey, G K

    2015-08-01

    The pathogenesis of asthma in the context of excess body weight may be distinct from asthma that develops in normal weight children. The study's objective was to explore the biology of asthma in the context of obesity and normal weight status using genetic methodologies. Associations between asthma and SNPs in 49 genes were assessed, as well as, interactions between SNPs and overweight status in child participants of the Greater Cincinnati Pediatric Clinic Repository. Asthma was significantly associated with weight (OR = 1.38; P = 0.037). The number of genes and the magnitude of their associations with asthma were notably greater when considering overweight children alone vs normal weight and overweight children together. When considering weight, distinct sets of asthma-associated genes were observed, many times with opposing effects. We demonstrated that the underlying heterogeneity of asthma is likely due in part to distinct pathogenetic pathways that depend on preceding/comorbid overweight and/or allergy. It is therefore important to consider both obesity and asthma when conducting studies of asthma. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  12. Blood group ascription as a genetic marker of hepatic hemangioma

    International Nuclear Information System (INIS)

    Polysalov, V.N.; Tarazov, P.G.

    1992-01-01

    There is no single point of view on pathogenesis of hemangiomas. The authors investigated the ABO blood types in 52 patients with hepatic hemangiomas (Group 1) and 1000 control patients (Group 2). The character of changes in the liver was established by means of reontgenoradionuclide investigation methods. The study demonstrated 61.5 % of the A blood type among the patients of Group 1. This was significantly higher than in the Group 2 and representative groups from literature (P < 0.001). Taking into account that the cells of both blood and blood vessels are formed in embryos through the mesenchyma and the heritability of blood group antigens, it is supposed that the results obtained support the genetic determination theory of pathogenesis of hepatic hemangioamas

  13. Pollen genetic markers for detection of mutagens in the environment

    International Nuclear Information System (INIS)

    Nilan, R.A.; Rosichan, J.L.; Arenaz, P.; Hodgdon, A.L.; Kleinhofs, A.

    1980-01-01

    To utilize and exploit pollen for in situ mutagen monitoring, screening and toxicology, the range of genetic traits in pollen must be identified and analyzed. To be useful for the development of mutagen detection systems proteins should be: (1) activity stainable or immunologically identifiable in the pollen, (2) the products of one to three loci; and (3) gametophytic and nuclear in origin. Several proteins, including alcohol dehydrogenase in maize, which meet these criteria are discussed. The waxy locus in barley and maize which controls starch deposition for pollen screening and mutant detection. Thirty waxy mutant lines, induced by sodium azide and gamma-rays are characterized for spontaneous and induced reversion frequencies, allelism, karyotype, amylose content, and UDPglucose glucosyltransferase (waxy gene product) activity. Twelve mutant alleles are being mapped by recombinant frequencies

  14. Genetic Markers of Human Evolution Are Enriched in Schizophrenia

    DEFF Research Database (Denmark)

    Srinivasan, Saurabh; Bettella, Francesco; Mattingsdal, Morten

    2016-01-01

    BACKGROUND: Why schizophrenia has accompanied humans throughout our history despite its negative effect on fitness remains an evolutionary enigma. It is proposed that schizophrenia is a by-product of the complex evolution of the human brain and a compromise for humans' language, creative thinking...... and ancillary information on genetic variants. We used information from the evolutionary proxy measure called the Neanderthal selective sweep (NSS) score. RESULTS: Gene loci associated with schizophrenia are significantly (p = 7.30 × 10(-9)) more prevalent in genomic regions that are likely to have undergone...... phenotypes. The false discovery rate conditional on the evolutionary proxy points to 27 candidate schizophrenia susceptibility loci, 12 of which are associated with schizophrenia and other psychiatric disorders or linked to brain development. CONCLUSIONS: Our results suggest that there is a polygenic overlap...

  15. Common and distinct genetic properties of ESCRT-II components in Drosophila.

    Directory of Open Access Journals (Sweden)

    Hans-Martin Herz

    Full Text Available BACKGROUND: Genetic studies in yeast have identified class E vps genes that form the ESCRT complexes required for protein sorting at the early endosome. In Drosophila, mutations of the ESCRT-II component vps25 cause endosomal defects leading to accumulation of Notch protein and increased Notch pathway activity. These endosomal and signaling defects are thought to account for several phenotypes. Depending on the developmental context, two different types of overgrowth can be detected. Tissue predominantly mutant for vps25 displays neoplastic tumor characteristics. In contrast, vps25 mutant clones in a wild-type background trigger hyperplastic overgrowth in a non-autonomous manner. In addition, vps25 mutant clones also promote apoptotic resistance in a non-autonomous manner. PRINCIPAL FINDINGS: Here, we genetically characterize the remaining ESCRT-II components vps22 and vps36. Like vps25, mutants of vps22 and vps36 display endosomal defects, accumulate Notch protein and--when the tissue is predominantly mutant--show neoplastic tumor characteristics. However, despite these common phenotypes, they have distinct non-autonomous phenotypes. While vps22 mutations cause strong non-autonomous overgrowth, they do not affect apoptotic resistance. In contrast, vps36 mutations increase apoptotic resistance, but have little effect on non-autonomous proliferation. Further characterization reveals that although all ESCRT-II mutants accumulate Notch protein, only vps22 and vps25 mutations trigger Notch activity. CONCLUSIONS/SIGNIFICANCE: The ESCRT-II components vps22, vps25 and vps36 display common and distinct genetic properties. Our data redefine the role of Notch for hyperplastic and neoplastic overgrowth in these mutants. While Notch is required for hyperplastic growth, it appears to be dispensable for neoplastic transformation.

  16. Molecular markers to assess genetic diversity and mutant identifications in Jatropha curcas

    International Nuclear Information System (INIS)

    Azhar Mohamad; Yie Min Kwan; Fatin Mastura Derani; Abdul Rahim Harun

    2010-01-01

    Jatropha curcas (Linnaeus) belongs to the Euphorbiaceae family, is a multipurpose use, drought resistant and perennial plant. It is an economic important crop, which generates wide interest in understanding the genetic diversity of the species towards selection and breeding of superior genotypes. Jatropha accessions are closely related family species. Thus, better understanding of the effectiveness of the different DNA-based markers is an important step towards plant germplasm characterization and evaluation. It is becoming a prerequisite for more effective application of marker techniques in breeding programs. Inter-simple sequence repeats (ISSRs) has shown rapid, simple, reproducible and inexpensive means in molecular taxonomy, conservation breeding and genetic diversity analysis. These markers were used to understand diversity and differentiate amongst accessions of Jatropha population and mutant lines generated by acute gamma radiation. The ISSR for marker applications are essential to facilitate management, conservation and genetic improvement programs towards improvement of bio-diesel production and medication substances. A total of 62 ISSR primers were optimized for polymorphism evaluations on five foreign accessions (Africa, India, Myanmar, Indonesia, Thailand), nine local accessions and two mutants of Jatropha. Optimization was resulted 54 ISSR primers affirmative for the polymorphism evaluation study, which encountered 12 ISSR primers, showed significance polymorphism amongst the accessions and mutants. Marker derived from ISSR profiling is a powerful method for identification and molecular classification of Jatropha from accession to generated mutant varieties. (author)

  17. NUTM2A-CIC fusion small round cell sarcoma: a genetically distinct variant of CIC-rearranged sarcoma.

    Science.gov (United States)

    Sugita, Shintaro; Arai, Yasuhito; Aoyama, Tomoyuki; Asanuma, Hiroko; Mukai, Wakako; Hama, Natsuko; Emori, Makoto; Shibata, Tatsuhiro; Hasegawa, Tadashi

    2017-07-01

    CIC-rearranged sarcoma is a new entity of undifferentiated small round cell sarcoma characterized by chimeric fusions with CIC rearrangement. We report a NUTM2A-CIC fusion sarcoma in a 43-year-old woman who died of rapidly progressive disease. Histologic analysis revealed multinodular proliferation of small round tumor cells with mild nuclear pleomorphism. The sclerotic fibrous septa separated the tumor into multiple nodules. Immunohistochemistry showed that the tumor cells were diffusely positive for vimentin, focally positive for cytokeratin, and negative for CD99 and NKX2.2. Tumor cells were also negative for ETV4, which was recently identified as a specific marker for CIC-rearranged sarcoma. High-throughput RNA sequencing of a formalin-fixed, paraffin-embedded clinical sample unveiled a novel NUTM2A-CIC fusion between NUTM2A exon 7 and CIC exon 12, and fluorescence in situ hybridization identified CIC and NUTM2A split signals. This case shared several clinicopathological findings with previously reported CIC-rearranged cases. We recognized the tumor as a genetically distinct variant of CIC-rearranged sarcomas with a novel NUTM2A-CIC fusion. Copyright © 2017. Published by Elsevier Inc.

  18. Shared versus distinct genetic contributions of mental wellbeing with depression and anxiety symptoms in healthy twins.

    Science.gov (United States)

    Routledge, Kylie M; Burton, Karen L O; Williams, Leanne M; Harris, Anthony; Schofield, Peter R; Clark, C Richard; Gatt, Justine M

    2016-10-30

    Mental wellbeing and mental illness symptoms are typically conceptualized as opposite ends of a continuum, despite only sharing about a quarter in common variance. We investigated the normative variation in measures of wellbeing and of depression and anxiety in 1486 twins who did not meet clinical criteria for an overt diagnosis. We quantified the shared versus distinct genetic and environmental variance between wellbeing and depression and anxiety symptoms. The majority of participants (93%) reported levels of depression and anxiety symptoms within the healthy range, yet only 23% reported a wellbeing score within the "flourishing" range: the remainder were within the ranges of "moderate" (67%) or "languishing" (10%). In twin models, measures of wellbeing and of depression and anxiety shared 50.09% of variance due to genetic factors and 18.27% due to environmental factors; the rest of the variance was due to unique variation impacting wellbeing or depression and anxiety symptoms. These findings suggest that an absence of clinically-significant symptoms of depression and anxiety does not necessarily indicate that an individual is flourishing. Both unique and shared genetic and environmental factors may determine why some individuals flourish in the absence of symptoms while others do not. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  19. Identification of novel microsatellite markers preimplantation genetic diagnosis of beta-thalassemia.

    Science.gov (United States)

    Chen, Min; Tan, Arnold S C; Cheah, Felicia S H; Saw, Eugene E L; Chong, Samuel S

    2015-12-01

    Beta (β)-thalassemia is one of the most common monogenic diseases worldwide. Affected pregnancies can be avoided through preimplantation genetic diagnosis (PGD), which commonly involves customized assays to detect the different combinations of β-globin (HBB) gene mutations present in couples, in conjunction with linkage analysis of flanking microsatellite markers. Currently, the limited number of reported closely linked markers hampers their utility in indirect linkage-based PGD for this disorder. To increase the available markers closely flanking the HBB gene, an in silico search was performed to identify all markers within 1 Mb flanking the HBB gene. Fifteen markers with potentially high polymorphism information content (PIC) and heterozygosity values were selected and optimized into a single-tube pentadecaplex PCR panel. Allele frequencies and polymorphism and heterozygosity indices of each marker were assessed in five populations. A total of 238 alleles were observed from the 15 markers. PIC was >0.7 for all markers, with expected heterozygosity and observed heterozygosity values ranging from 0.74 to 0.90 and 0.72 to 0.88, respectively. Greater than 99% of individuals were heterozygous for at least seven markers, with at least two heterozygous markers on either side of the HBB gene. The pentadecaplex marker assay also performed reliably on single cells either directly or after whole genome amplification, thus validating its use in standalone linkage-based β-thalassemia PGD or in conjunction with HBB mutation detection. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Genetic diversity of indigenous chickens from selected areas in Kenya using microsatellite markers

    Directory of Open Access Journals (Sweden)

    Okoth Noah Okumu

    2017-12-01

    Full Text Available In this study, indigenous chickens were collected from eight different regions in Kenya and kept at InCIP-Egerton University. These were studied using eighteen microsatellite markers to determine genetic variation. Statistics related to genetic variation were estimated using GenALEx6. Mean percentage polymorphic loci (PPL was 96.71% and 4% genetic variance (p ≥ 0.003 was seen between the eight populations. MCW0123 marker had the highest genetic variance of 13% among populations (p ≥ 0.003 at 95% CI. Mean He ranged from 0.351 ± 0.031 (SIB to 0.434 ± 0.022 (BM with a grand mean He of 0.399 ± 0.011 across the populations using the microsatellite markers. Nei’s genetic distance ranged from 0.016 (SIB and WP to 0.126 (NR and SIB. DARwin6.501 analysis software was used to draw the population dendrogram and two major population clusters were observed, also seen with PCoA. This study found a lot of genetic variation and relatedness within and among populations. Based on the phylogenetic tree result, it is concluded that the clustering of the chicken populations in the present study is not based on geographical proximity. The microsatellite markers used in this study were suitable for the measurement of the genetic biodiversity and relationship of Kenyan chicken populations. These results can therefore serve as an initial step to plan the conservation of indigenous chickens in Kenya.

  1. An annotated genetic map of loblolly pine based on microsatellite and cDNA markers

    Science.gov (United States)

    Craig S. Echt; Surya Saha; Konstantin V. Krutovsky; Kokulapalan Wimalanathan; John E. Erpelding; Chun Liang; C Dana Nelson

    2011-01-01

    Previous loblolly pine (Pinus taeda L.) genetic linkage maps have been based on a variety of DNA polymorphisms, such as AFLPs, RAPDs, RFLPs, and ESTPs, but only a few SSRs (simple sequence repeats), also known as simple tandem repeats or microsatellites, have been mapped in P. taeda. The objective of this study was to integrate a large set of SSR markers from a variety...

  2. Refining the genetic portrait of Portuguese Roma through X-chromosomal markers

    DEFF Research Database (Denmark)

    Pereira, Vania; Gusmão, Leonor; Valente, Cristina

    2012-01-01

    Due to differences in transmission between X-chromosomal and autosomal DNA, the comparison of data derived from both markers allows deeper insight into the forces that shape the patterns of genetic diversity in populations. In this study, we applied this comparative approach to a sample of Portug...

  3. Assessment of Genetic Diversity of Some Finger Millet (Eleusine coracana (L. Gaertn. Accessions Using Morphological Markers

    Directory of Open Access Journals (Sweden)

    D.V.S. Kaluthanthri

    2017-03-01

    Full Text Available AbstractGermplasm characterization is an important link between conservation and utilizationof plant genetic resources. The study was conducted to characterize randomly selected 20finger millet germplasm accessions obtained from Plant Genetic Resource Center,Gannoruwa, Sri Lanka using morphological markers. Morphological study was carried outusing Randomized Complete Block Design (RCBD and 15 morphological markers wererecorded. Analysis of variance (ANOVA results for quantitative morphological charactersrevealed that all quantitative morphological characters measured differed significantly(p˂0.05 among the accessions used for the study, indicating higher levels of morphologicaldiversity. According to the ANOVA results, days to flowering and days to maturity showhigh level of predictive capability while flag leaf length and number of productive tillersshow comparatively low level of predictive capability. Principal component analysisindicated that morphological characters such as days to flowering, finger number and yieldper plant were the important traits contributing for the overall variability implying thatbreeding effort on those traits can meet the targeted objective. The clustering pattern ofstudied finger millet accessions based on morphological markers comprised of two majorclusters. Both clusters comprised of Indian accessions those conserved at PGRC, Gannoruwaand as well as Sri Lankan accessions.Results of the study suggest a considerable morphological variability, which couldexist among the studied traits. Furthermore, this study revealed that the genetic diversityexisted irrespective to the geographical origin. This finding justifies the importance ofgermplasm characterization.Keywords: Finger Millet, Morphological Markers, Germplasm Accessions, GeneticDiversity, Crop Improvement

  4. On the Informativeness of Dominant and Co-Dominant Genetic Markers for Bayesian Supervised Clustering

    DEFF Research Database (Denmark)

    Guillot, Gilles; Carpentier-Skandalis, Alexandra

    2011-01-01

    We study the accuracy of a Bayesian supervised method used to cluster individuals into genetically homogeneous groups on the basis of dominant or codominant molecular markers. We provide a formula relating an error criterion to the number of loci used and the number of clusters. This formula...

  5. Genetic characterization of guava (psidium guajava l.) Germplasm in the United States using microsatellite markers

    Science.gov (United States)

    Genetic diversity of thirty five Psidium guajava accessions maintained at the USDA, National Plants Germplasm System, Hilo, HI, was characterized using 20 simple sequence repeat (SSR) markers. Diversity analysis detected a total of 178 alleles ranging from four to 16. The observed mean heterozygosit...

  6. Genetic markers, translocations and sexing genes on chromosome 2 of Ceratitis capitata

    International Nuclear Information System (INIS)

    Cladera, J.L.

    1997-01-01

    A review is presented of results obtained in a search for genetic markers, translocations and selectable genes obtained at the Instituto de Genetica, Castelar, Argentina, with special reference to chromosome 2 linked mutations and genes useful for developing self-sexing strains in Ceratitis capitata. (author)

  7. Application of marker selection to enhance estimation of genetic effects and gene interaction in cattle

    Science.gov (United States)

    Selection on important genetic markers can improve estimates of additive and dominance association effects. A composite population of beef cattle was selected for intermediate frequencies of myostatin (GDF8) F94L and µ-calpain (CAPN1) polymorphisms. Important additive associations of the GDF8 locu...

  8. A genetic linkage map of willow (Salix viminalis) based on AFLP and microsatelite markers

    NARCIS (Netherlands)

    Hanley, S.; Barker, J.H.A.; Ooijen, van J.W.; Aldam, C.; Harris, S.L.; Ahman, I.; Larsson, S.; Karp, A.

    2002-01-01

    The genus Salix (willow) contains a number of species of great value as biomass crops. Efforts to breed varieties with improved biomass yields and resistances to pests and diseases are limited by the lack of knowledge on the genetic basis of the traits. We have used AFLP and microsatellite markers

  9. Molecular genetic diversity of Punica granatum L. (pomegranate) as revealed by microsatellite DNA markers

    Science.gov (United States)

    Pomegranate (Punica granatum L.) is one of the oldest known edible fruits and more and more it arouse interest of scientific community given its numerous biological activities. However, information about its genetic resources and characterization using reliable molecular markers are still scarce. In...

  10. Assessment of genetic diversity in Chinese eared pheasant using fluorescent-AFLP markers

    DEFF Research Database (Denmark)

    Li, Xiujuan; Zhu, Yaohong; Liu, Panqi

    2010-01-01

    on the list of the world’s threatened species. In this paper, 74 individuals from the four eared pheasant species were assessed for population genetic diversity by means of fluorescent-AFLP markers. A total of 429 AFLP peaks were amplified by 11 pairs of fluorescent EcoRI/TaqI primer combinations. Out of all...... using Jaccard’s similarity coefficients (SC) and the corresponding dendrogram. It was found that there was a moderate genetic distance between the four species (SC = 0.674–0.832). Brown eared pheasant was genetically closely related to blue eared pheasant (SC = 0.832), while white eared pheasant...

  11. Microsatellite markers for population genetic studies of the blowfly Chrysomya putoria (Diptera: Calliphoridae

    Directory of Open Access Journals (Sweden)

    Rosangela Aparecida Rodrigues

    2009-11-01

    Full Text Available The investigation of the genetic variation and population structure of Chrysomya species is of great interest for both basic and applied research. However, very limited genetic information is available for this genus across its geographical distribution. Here, we describe 12 polymorphic microsatellite loci isolated from Chrysomya putoria with expected heterozygosities ranging from 0.1402-0.8312. These markers are of potential applied interest for forensic entomologists and for the characterisation of the genetic structure of C. putoria from recently colonised regions, with great promise for understanding the colonisation dynamics and spread of the genus Chrysomya in the New World.

  12. Marker-based estimation of genetic parameters in genomics.

    Directory of Open Access Journals (Sweden)

    Zhiqiu Hu

    Full Text Available Linear mixed model (LMM analysis has been recently used extensively for estimating additive genetic variances and narrow-sense heritability in many genomic studies. While the LMM analysis is computationally less intensive than the Bayesian algorithms, it remains infeasible for large-scale genomic data sets. In this paper, we advocate the use of a statistical procedure known as symmetric differences squared (SDS as it may serve as a viable alternative when the LMM methods have difficulty or fail to work with large datasets. The SDS procedure is a general and computationally simple method based only on the least squares regression analysis. We carry out computer simulations and empirical analyses to compare the SDS procedure with two commonly used LMM-based procedures. Our results show that the SDS method is not as good as the LMM methods for small data sets, but it becomes progressively better and can match well with the precision of estimation by the LMM methods for data sets with large sample sizes. Its major advantage is that with larger and larger samples, it continues to work with the increasing precision of estimation while the commonly used LMM methods are no longer able to work under our current typical computing capacity. Thus, these results suggest that the SDS method can serve as a viable alternative particularly when analyzing 'big' genomic data sets.

  13. Dog obesity--the need for identifying predisposing genetic markers.

    Science.gov (United States)

    Switonski, M; Mankowska, M

    2013-12-01

    Incidence of overweight and obesity in dogs exceeds 30%, and several breeds are predisposed to this heritable phenotype. Rapid progress of canine genomics and advanced knowledge on the genetic background of human obesity bring a unique opportunity to perform such studies in dogs. Natural candidate genes for obesity are these encoding adipokines. Extended studies in humans indicated that polymorphisms of three of them, i.e. ADIPOQ, IL1 and TNF, are associated with predisposition to obesity. On the other hand, the use of genome-wide association studies revealed an association between human obesity and polymorphism of more than 50 other genes. Until now only few preliminary reports on polymorphism of canine FTO, MC4R, MC3R and PPARG genes have been published. Since the dog is a valuable model organism for human diseases one can foresee that such studies may also contribute to an in-depth understanding of human obesity pathogenesis. Copyright © 2013 Elsevier Ltd. All rights reserved.

  14. Genetic variation and DNA fingerprinting of durian types in Malaysia using simple sequence repeat (SSR) markers.

    Science.gov (United States)

    Siew, Ging Yang; Ng, Wei Lun; Tan, Sheau Wei; Alitheen, Noorjahan Banu; Tan, Soon Guan; Yeap, Swee Keong

    2018-01-01

    Durian ( Durio zibethinus ) is one of the most popular tropical fruits in Asia. To date, 126 durian types have been registered with the Department of Agriculture in Malaysia based on phenotypic characteristics. Classification based on morphology is convenient, easy, and fast but it suffers from phenotypic plasticity as a direct result of environmental factors and age. To overcome the limitation of morphological classification, there is a need to carry out genetic characterization of the various durian types. Such data is important for the evaluation and management of durian genetic resources in producing countries. In this study, simple sequence repeat (SSR) markers were used to study the genetic variation in 27 durian types from the germplasm collection of Universiti Putra Malaysia. Based on DNA sequences deposited in Genbank, seven pairs of primers were successfully designed to amplify SSR regions in the durian DNA samples. High levels of variation among the 27 durian types were observed (expected heterozygosity, H E  = 0.35). The DNA fingerprinting power of SSR markers revealed by the combined probability of identity (PI) of all loci was 2.3×10 -3 . Unique DNA fingerprints were generated for 21 out of 27 durian types using five polymorphic SSR markers (the other two SSR markers were monomorphic). We further tested the utility of these markers by evaluating the clonal status of shared durian types from different germplasm collection sites, and found that some were not clones. The findings in this preliminary study not only shows the feasibility of using SSR markers for DNA fingerprinting of durian types, but also challenges the current classification of durian types, e.g., on whether the different types should be called "clones", "varieties", or "cultivars". Such matters have a direct impact on the regulation and management of durian genetic resources in the region.

  15. AFLP markers for the assessment of genetic diversity in european and North American potato varieties cultivated in Iran

    Directory of Open Access Journals (Sweden)

    Saeed Tarkesh Esfahani

    2009-01-01

    Full Text Available Information about the genetic diversity of potato germplasm in Iran is important for variety identification andto enhance the classification of germplasm collections and exploit them in breeding programs and for the development andintroduction of new varieties. AFLP fingerprinting was applied to a group of cultivated potato varieties to find if there is anygeographical differentiation in potato diversity from Europe and North America. The high level of polymorphism within potatovarieties and the high number of variety-specific bands suggest that AFLPs are powerful markers for diversity analysis inpotato varieties. No region-specific AFLP markers were found (present in varieties from the same origin and absent inothers. The UPGMA dendrogram revealed four distinct clusters corresponding almost to the geographical origin of thevarieties. However, the bootstrap support for branches was rather weak. No clusters clearly distinguished varieties fromEurope and North America. Varieties from the same geographical origins however tended to group together within eachcluster. The mean similarity and the UPGMA dendrogram both suggest that North American varieties have nearly identicalgenetic diversity to European varieties. The results of AMOVA revealed large within-region variations which accounted for94.5% of the total molecular variance. The between-region variation, although accounting for only 5.5% of the total variation,was statistically significant. AFLP technology was successfully used to evaluate diversity between different geographicalgroups of potatoes and is recommended for potato genetic studies.

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

    Science.gov (United States)

    Schouten, Henk J; van de Weg, W Eric; Carling, Jason; Khan, Sabaz Ali; McKay, Steven J; van Kaauwen, Martijn P W; Wittenberg, Alexander H J; Koehorst-van Putten, Herma J J; Noordijk, Yolanda; Gao, Zhongshan; Rees, D Jasper G; Van Dyk, Maria M; Jaccoud, Damian; Considine, Michael J; Kilian, Andrzej

    2012-03-01

    Diversity Arrays Technology (DArT) provides a high-throughput whole-genome genotyping platform for the detection and scoring of hundreds of polymorphic loci without any need for prior sequence information. The work presented here details the development and performance of a DArT genotyping array for apple. This is the first paper on DArT in horticultural trees. Genetic mapping of DArT markers in two mapping populations and their integration with other marker types showed that DArT is a powerful high-throughput method for obtaining accurate and reproducible marker data, despite the low cost per data point. This method appears to be suitable for aligning the genetic maps of different segregating populations. The standard complexity reduction method, based on the methylation-sensitive PstI restriction enzyme, resulted in a high frequency of markers, although there was 52-54% redundancy due to the repeated sampling of highly similar sequences. Sequencing of the marker clones showed that they are significantly enriched for low-copy, genic regions. The genome coverage using the standard method was 55-76%. For improved genome coverage, an alternative complexity reduction method was examined, which resulted in less redundancy and additional segregating markers. The DArT markers proved to be of high quality and were very suitable for genetic mapping at low cost for the apple, providing moderate genome coverage. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-011-9579-5) contains supplementary material, which is available to authorized users.

  17. Genetic diversity and population structure of Brassica oleracea germplasm in Ireland using SSR markers.

    Science.gov (United States)

    El-Esawi, Mohamed A; Germaine, Kieran; Bourke, Paula; Malone, Renee

    2016-01-01

    The most economically important Brassica oleracea species is endangered in Ireland, with no prior reported genetic characterization studies. This study assesses the genetic diversity, population structure and relationships of B. oleracea germplasm in Ireland using microsatellite (SSRs) markers. A total of 118 individuals from 25 accessions of Irish B. oleracea were genotyped. The SSR loci used revealed a total of 47 alleles. The observed heterozygosity (0.699) was higher than the expected one (0.417). Moreover, the average values of fixation indices (F) were negative, indicating excess of heterozygotes in all accessions. Polymorphic information content (PIC) values of SSR loci ranged from 0.27 to 0.66, with an average of 0.571, and classified 10 loci as informative markers (PIC>0.5) to differentiate among the accessions studied. The genetic differentiation among accessions showed that 27.1% of the total genetic variation was found among accessions, and 72.9% of the variation resided within accessions. The averages of total heterozygosity (H(T)) and intra-accession genetic diversity (H(S)) were 0.577 and 0.442, respectively. Cluster analysis of SSR data distinguished among kale and Brussels sprouts cultivars. This study provided a new insight into the exploitation of the genetically diverse spring cabbages accessions, revealing a high genetic variation, as potential resources for future breeding programs. SSR loci were effective for differentiation among the accessions studied. Copyright © 2016 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  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. Genetic Analysis of Pinus sylvestris L. and Pinus sylvestris forma turfosa L. Using RAPD Markers

    Directory of Open Access Journals (Sweden)

    Beáta ÁBRAHÁM

    2010-03-01

    Full Text Available The purpose of the present study was to determine the level of genetic diversity within and among Ciuc basin, Romania (populations from Mohos and Luci raised bogs in Harghita Mountain and Sumuleu in Ciuc Mountain Pinus sylvestris populations using molecular markers. Two of populations (Mohos and Luci seems to be the descendants that survived the continental glaciation. Genetic diversity was analyzed by RAPD (Random Amplified Polymorphic DNA. Nine primers were selected for analysis, which generated reproducible bands. On base of presence or absence of homologues bands Nei’s gene diversity, the percentage of polymorphic loci and Nei’s unbiased genetic distance were calculated. The level of genetic variation among populations was found to be low. For both populations the variation values among populations were higher than within populations. The fossil records and geological historical data explain the extremely low genetic diversity of this species. Pinus sylvestris experienced strong bottlenecks during its evolutionary history, which caused the loss of genetic variation. Genetic drift and breeding in post-bottlenecked small populations may be the major forces that contribute to low genetic diversity and genetic differentiation of populations. Human activities may have accelerated the loss of genetic diversity in Pinus sylvestris.

  20. Molecular identification and genetic variation of varieties of Styphnolobium japonicum (Fabaceae) using SRAP markers.

    Science.gov (United States)

    Sun, R X; Zhang, C H; Zheng, Y Q; Zong, Y C; Yu, X D; Huang, P

    2016-05-06

    Thirty-four Styphnolobium japonicum varieties were analyzed using sequence-related amplified polymorphism (SRAP) markers, to investigate genetic variation and test the effectiveness of SRAP markers in DNA fingerprint establishment. Twelve primer pairs were selected from 120 primer combinations for their reproducibility and high polymorphism. We found a total of 430 amplified fragments, of which 415 fragments were considered polymorphic with an average of 34.58 polymorphic fragments for each primer combination. The percentage of polymorphic fragments was 96.60%, and four primer pairs showed 100% polymorphism. Moreover, simple matched coefficients ranged between 0.68 and 0.89, with an average of 0.785, indicating that the genetic variation among varieties was relatively low. This could be because of the narrow genetic basis of the selected breeding material. Based on the similarity coefficient value of 0.76, the varieties were divided into four major groups. In addition, abundant and clear SRAP fingerprints were obtained and could be used to establish DNA fingerprints. In the DNA fingerprints, each variety had its unique pattern that could be easily distinguished from others. The results demonstrated that 34 varieties of S. japonicum had a relatively narrow genetic variation. Hence, a broadening of the genetic basis of breeding material is necessary. We conclude that establishment of DNA fingerprint is feasible by means of SRAP markers.

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

    Science.gov (United States)

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

    2015-04-01

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

  2. A sequence-based genetic map of Medicago truncatula and comparison of marker colinearity with M. sativa

    NARCIS (Netherlands)

    Choi, H.K.; Kim, D.; Uhm, T.; Limpens, E.H.M.; Lim, H.; Mun, J.H.; Kalo, P.; Penmetsa, R.V.; Seres, A.; Kulikova, O.; Roe, B.A.; Bisseling, T.; Kiss, G.B.; Cook, D.R.

    2004-01-01

    A core genetic map of the legume Medicago truncatula has been established by analyzing the segregation of 288 sequence-characterized genetic markers in an E, population composed of 93 individuals. These molecular markers correspond to 141 ESTs, 80 BAC end sequence tags, and 67 resistance gene

  3. Genetic differentiation in Pyrenophora teres f. teres populations from Syria and Tunisia as assessed by AFLP markers.

    Science.gov (United States)

    Bouajila, A; Zoghlami, N; Murad, S; Baum, M; Ghorbel, A; Nazari, K

    2013-06-01

    To investigate the level of genetic differentiation and diversity among Pyrenophora teres isolate populations originating from different agro-ecological areas of Syria and Tunisia and to determine the potential of AFLP profiling in genotyping Pyrenophora teres f. teres. In this study, AFLP markers have been employed to identify patterns of population structure in 20 Pyrenophora teres f. teres populations from Syria and Tunisia. Ninety-four isolates were studied by the use of a protocol that involved stringent PCR amplification of fragments derived from digestion of genomic DNA with restriction enzymes EcoRI and MesI. Based on 401 amplified polymorphic DNA markers (AFLP), variance analyses indicated that most of the variation was partitioned within rather than between populations. Genotypic diversity (GD) was high for populations from Rihane, local landraces and different agro-ecological zones (GD = 0·75-0·86). There was high genetic differentiation among pathogen populations from different host populations in Syria (Gst  = 0·31, ht = 0·190) and Tunisia (Gst  = 0·39, ht = 0·263), which may be partly explained by the low gene flow around the areas sampled. A phenetic tree revealed three groups with high bootstrap values (55, 68, 76) and reflected the grouping of isolates based on host, or agro-ecological areas. AFLP profiling is an effective method for typing the genetically diverse pathogen Pyrenophora teres f. teres. The study represents a comparative analysis of the genetic diversity in P. teres isolates from two countries spanning two continents and also shows that several distinct P. teres genotypes may be found in a given environment. The implications of these findings for Pyrenophora teres f. teres evolutionary potential and net blotch-resistance breeding in Syria and Tunisia were also discussed. © 2012 The Society for Applied Microbiology.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-06-01

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

  5. Covariance Association Test (CVAT) Identifies Genetic Markers Associated with Schizophrenia in Functionally Associated Biological Processes

    DEFF Research Database (Denmark)

    Rohde, Palle Duun; Demontis, Ditte; Castro Dias Cuyabano, Beatriz

    2016-01-01

    was among the top performers. When extending CVAT to utilize a mixture of SNP effects, we found an increase in power to detect the causal sets. Applying the methods to a Danish schizophrenia case–control data set, we found genomic evidence for association of schizophrenia with vitamin A metabolism......Schizophrenia is a psychiatric disorder with large personal and social costs, and understanding the genetic etiology is important. Such knowledge can be obtained by testing the association between a disease phenotype and individual genetic markers; however, such single-marker methods have limited...... genomic best linear unbiased prediction (GBLUP), the covariance association test (CVAT). We compared the performance of CVAT to other commonly used set tests. The comparison was conducted using a simulated study population having the same genetic parameters as for schizophrenia. We found that CVAT...

  6. Alu repeats as markers for human population genetics

    Energy Technology Data Exchange (ETDEWEB)

    Batzer, M.A.; Alegria-Hartman, M. [Lawrence Livermore National Lab., CA (United States); Bazan, H. [Louisiana State Univ., New Orleans, LA (United States). Medical Center] [and others

    1993-09-01

    The Human-Specific (HS) subfamily of Alu sequences is comprised of a group of 500 nearly identical members which are almost exclusively restricted to the human genome. Individual subfamily members share an average of 97.9% nucleotide identity with each other and an average of 98.9% nucleotide identity with the HS subfamily consensus sequence. HS Alu family members are thought to be derived from a single source ``master`` gene, and have an average age of 2.8 million years. We have developed a Polymerase Chain Reaction (PCR) based assay using primers complementary to the 5 in. and 3 in. unique flanking DNA sequences from each HS Alu that allows the locus to be assayed for the presence or absence of an Alu repeat. Individual HS Alu sequences were found to be either monomorphic or dimorphic for the presence or absence of each repeat. The monomorphic HS Alu family members inserted in the human genome after the human/great ape divergence (which is thought to have occurred 4--6 million years ago), but before the radiation of modem man. The dimorphic HS Alu sequences inserted in the human genome after the radiation of modem man (within the last 200,000-one million years) and represent a unique source of information for human population genetics and forensic DNA analyses. These sites can be developed into Dimorphic Alu Sequence Tagged Sites (DASTS) for the Human Genome Project as well. HS Alu family member insertion dimorphism differs from other types of polymorphism (e.g. Variable Number of Tandem Repeat [VNTR] or Restriction Fragment Length Polymorphism [RFLP]) because individuals share HS Alu family member insertions based upon identity by descent from a common ancestor as a result of a single event which occurred one time within the human population. The VNTR and RFLP polymorphisms may arise multiple times within a population and are identical by state only.

  7. Markers

    Science.gov (United States)

    Healthy Schools Network, Inc., 2011

    2011-01-01

    Dry erase whiteboards come with toxic dry erase markers and toxic cleaning products. Dry erase markers labeled "nontoxic" are not free of toxic chemicals and can cause health problems. Children are especially vulnerable to environmental health hazards; moreover, schools commonly have problems with indoor air pollution, as they are more densely…

  8. Identifying genetic marker sets associated with phenotypes via an efficient adaptive score test

    KAUST Repository

    Cai, T.

    2012-06-25

    In recent years, genome-wide association studies (GWAS) and gene-expression profiling have generated a large number of valuable datasets for assessing how genetic variations are related to disease outcomes. With such datasets, it is often of interest to assess the overall effect of a set of genetic markers, assembled based on biological knowledge. Genetic marker-set analyses have been advocated as more reliable and powerful approaches compared with the traditional marginal approaches (Curtis and others, 2005. Pathways to the analysis of microarray data. TRENDS in Biotechnology 23, 429-435; Efroni and others, 2007. Identification of key processes underlying cancer phenotypes using biologic pathway analysis. PLoS One 2, 425). Procedures for testing the overall effect of a marker-set have been actively studied in recent years. For example, score tests derived under an Empirical Bayes (EB) framework (Liu and others, 2007. Semiparametric regression of multidimensional genetic pathway data: least-squares kernel machines and linear mixed models. Biometrics 63, 1079-1088; Liu and others, 2008. Estimation and testing for the effect of a genetic pathway on a disease outcome using logistic kernel machine regression via logistic mixed models. BMC bioinformatics 9, 292-2; Wu and others, 2010. Powerful SNP-set analysis for case-control genome-wide association studies. American Journal of Human Genetics 86, 929) have been proposed as powerful alternatives to the standard Rao score test (Rao, 1948. Large sample tests of statistical hypotheses concerning several parameters with applications to problems of estimation. Mathematical Proceedings of the Cambridge Philosophical Society, 44, 50-57). The advantages of these EB-based tests are most apparent when the markers are correlated, due to the reduction in the degrees of freedom. In this paper, we propose an adaptive score test which up- or down-weights the contributions from each member of the marker-set based on the Z-scores of

  9. Genetic Characterization of Five Hatchery Populations of the Pacific Abalone (Haliotis discus hannai Using Microsatellite Markers

    Directory of Open Access Journals (Sweden)

    Jeong-In Myeong

    2011-07-01

    Full Text Available The Pacific abalone, Haliotis discus hannai, is a popular food in Eastern Asia. Aquacultural production of this species has increased because of recent resource declines, the growing consumption, and ongoing government-operated stock release programs. Therefore, the genetic characterization of hatchery populations is necessary to maintain the genetic diversity of this species and to develop more effective aquaculture practices. We analyzed the genetic structures of five cultured populations in Korea using six microsatellite markers. The number of alleles per locus ranged from 15 to 64, with an average of 23.5. The mean observed and expected heterozygosities were 0.797 and 0.904, respectively. The inbreeding coefficient FIS ranged from 0.054 to 0.184 (mean FIS = 0.121 ± 0.056. The genetic differentiation across all populations was low but significant (overall FST = 0.009, P < 0.01. Pairwise multilocus FST tests, estimates of genetic distance, and phylogenetic and principal component analyses did not show a consistent relationship between geographic and genetic distances. These results could reflect extensive aquaculture, the exchange of breeds and eggs between hatcheries and/or genetic drift due to intensive breeding practices. Thus, for optimal resource management, the genetic variation of hatchery stocks should be monitored and inbreeding controlled within the abalone stocks that are being released every year. This genetic information will be useful for the management of both H. discus hannai fisheries and the aquaculture industry.

  10. Distinct subspecies or phenotypic plasticity? Genetic and morphological differentiation of mountain honey bees in East Africa.

    Science.gov (United States)

    Gruber, Karl; Schöning, Caspar; Otte, Marianne; Kinuthia, Wanja; Hasselmann, Martin

    2013-09-01

    Identifying the forces shaping intraspecific phenotypic and genotypic divergence are of key importance in evolutionary biology. Phenotypic divergence may result from local adaptation or, especially in species with strong gene flow, from pronounced phenotypic plasticity. Here, we examine morphological and genetic divergence among populations of the western honey bee Apis mellifera in the topographically heterogeneous East African region. The currently accepted "mountain refugia hypothesis" states that populations living in disjunct montane forests belong to a different lineage than those in savanna habitats surrounding these forests. We obtained microsatellite data, mitochondrial sequences, and morphometric data from worker honey bees collected from feral colonies in three montane forests and corresponding neighboring savanna regions in Kenya. Honey bee colonies from montane forests showed distinct worker morphology compared with colonies in savanna areas. Mitochondrial sequence data did not support the existence of the two currently accepted subspecies. Furthermore, analyses of the microsatellite data with a Bayesian clustering method did not support the existence of two source populations as it would be expected under the mountain refugia scenario. Our findings suggest that phenotypic plasticity rather than distinct ancestry is the leading cause behind the phenotypic divergence observed between montane forest and savanna honey bees. Our study thus corroborates the idea that high gene flow may select for increased plasticity.

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

    Science.gov (United States)

    Sakar, Ebru; Unver, Hulya; Ercisli, Sezai

    2016-12-01

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

  12. Genetic evolutionary taboo search for optimal marker placement in infrared patient setup

    International Nuclear Information System (INIS)

    Riboldi, M; Baroni, G; Spadea, M F; Tagaste, B; Garibaldi, C; Cambria, R; Orecchia, R; Pedotti, A

    2007-01-01

    In infrared patient setup adequate selection of the external fiducial configuration is required for compensating inner target displacements (target registration error, TRE). Genetic algorithms (GA) and taboo search (TS) were applied in a newly designed approach to optimal marker placement: the genetic evolutionary taboo search (GETS) algorithm. In the GETS paradigm, multiple solutions are simultaneously tested in a stochastic evolutionary scheme, where taboo-based decision making and adaptive memory guide the optimization process. The GETS algorithm was tested on a group of ten prostate patients, to be compared to standard optimization and to randomly selected configurations. The changes in the optimal marker configuration, when TRE is minimized for OARs, were specifically examined. Optimal GETS configurations ensured a 26.5% mean decrease in the TRE value, versus 19.4% for conventional quasi-Newton optimization. Common features in GETS marker configurations were highlighted in the dataset of ten patients, even when multiple runs of the stochastic algorithm were performed. Including OARs in TRE minimization did not considerably affect the spatial distribution of GETS marker configurations. In conclusion, the GETS algorithm proved to be highly effective in solving the optimal marker placement problem. Further work is needed to embed site-specific deformation models in the optimization process

  13. DEVELOPMENT OF EST-SSR MARKERS TO ASSESS GENETIC DIVERSITY OF BROCCOLI AND ITS RELATED SPECIES

    Directory of Open Access Journals (Sweden)

    Nur Kholilatul Izzah

    2017-01-01

    Full Text Available Development of Expressed Sequence Tag-Simple Sequence Repeat (EST-SSR markers derived from public database is known to be more efficient, faster and low cost. The objective of this study was to generate a new set of EST-SSR markers for broccoli and its related species and their usefulness for assessing their genetic diversity. A total of 202 Brassica oleracea ESTs were retrieved from NCBI and then assembled into 172 unigenes by means of CAP3 program. Identification of SSRs was carried out using web-based tool, RepeatMasker software. Afterwards, EST-SSR markers were developed using Primer3 program. Among the identified SSRs, trinucleotide repeats were the most common repeat types, which accounted for about 50%. A total of eight primer pairs were successfully designed and yielded amplification products. Among them, five markers were polymorphic and displayed a total of 30 alleles with an average number of six alleles per locus. The polymorphic markers were subsequently used for analyzing genetic diversity of 36 B. oleracea cultivars including 22 broccoli, five cauliflower and nine kohlrabi cultivars based on genetic similarity matrix as implemented in NTSYS program. At similarity coefficient of 61%, a UPGMA clustering dendrogram effectively separated 36 genotypes into three main groups, where 30 out of 36 genotypes were clearly discriminated. The result obtained in the present study would help breeders in selecting parental lines for crossing. Moreover, the novel EST-SSR markers developed in the study could be a valuable tool for differentiating cultivars of broccoli and related species.

  14. Two genetic loci produce distinct carbohydrate-rich structural components of the Pseudomonas aeruginosa biofilm matrix.

    Science.gov (United States)

    Friedman, Lisa; Kolter, Roberto

    2004-07-01

    Pseudomonas aeruginosa forms biofilms, which are cellular aggregates encased in an extracellular matrix. Molecular genetics studies of three common autoaggregative phenotypes, namely wrinkled colonies, pellicles, and solid-surface-associated biofilms, led to the identification of two loci, pel and psl, that are involved in the production of carbohydrate-rich components of the biofilm matrix. The pel gene cluster is involved in the production of a glucose-rich matrix material in P. aeruginosa strain PA14 (L. Friedman and R. Kolter, Mol. Microbiol. 51:675-690, 2004). Here we investigate the role of the pel gene cluster in P. aeruginosa strain ZK2870 and identify a second genetic locus, termed psl, involved in the production of a mannose-rich matrix material. The 11 predicted protein products of the psl genes are homologous to proteins involved in carbohydrate processing. P. aeruginosa is thus able to produce two distinct carbohydrate-rich matrix materials. Either carbohydrate-rich matrix component appears to be sufficient for mature biofilm formation, and at least one of them is required for mature biofilm formation in P. aeruginosa strains PA14 and ZK2870. Copyright 2004 American Society for Microbiology

  15. Distinct Mechanisms of Nuclease-Directed DNA-Structure-Induced Genetic Instability in Cancer Genomes.

    Science.gov (United States)

    Zhao, Junhua; Wang, Guliang; Del Mundo, Imee M; McKinney, Jennifer A; Lu, Xiuli; Bacolla, Albino; Boulware, Stephen B; Zhang, Changsheng; Zhang, Haihua; Ren, Pengyu; Freudenreich, Catherine H; Vasquez, Karen M

    2018-01-30

    Sequences with the capacity to adopt alternative DNA structures have been implicated in cancer etiology; however, the mechanisms are unclear. For example, H-DNA-forming sequences within oncogenes have been shown to stimulate genetic instability in mammals. Here, we report that H-DNA-forming sequences are enriched at translocation breakpoints in human cancer genomes, further implicating them in cancer etiology. H-DNA-induced mutations were suppressed in human cells deficient in the nucleotide excision repair nucleases, ERCC1-XPF and XPG, but were stimulated in cells deficient in FEN1, a replication-related endonuclease. Further, we found that these nucleases cleaved H-DNA conformations, and the interactions of modeled H-DNA with ERCC1-XPF, XPG, and FEN1 proteins were explored at the sub-molecular level. The results suggest mechanisms of genetic instability triggered by H-DNA through distinct structure-specific, cleavage-based replication-independent and replication-dependent pathways, providing critical evidence for a role of the DNA structure itself in the etiology of cancer and other human diseases. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

  16. Gene-based single nucleotide polymorphism markers for genetic and association mapping in common bean.

    Science.gov (United States)

    Galeano, Carlos H; Cortés, Andrés J; Fernández, Andrea C; Soler, Álvaro; Franco-Herrera, Natalia; Makunde, Godwill; Vanderleyden, Jos; Blair, Matthew W

    2012-06-26

    In common bean, expressed sequence tags (ESTs) are an underestimated source of gene-based markers such as insertion-deletions (Indels) or single-nucleotide polymorphisms (SNPs). However, due to the nature of these conserved sequences, detection of markers is difficult and portrays low levels of polymorphism. Therefore, development of intron-spanning EST-SNP markers can be a valuable resource for genetic experiments such as genetic mapping and association studies. In this study, a total of 313 new gene-based markers were developed at target genes. Intronic variation was deeply explored in order to capture more polymorphism. Introns were putatively identified after comparing the common bean ESTs with the soybean genome, and the primers were designed over intron-flanking regions. The intronic regions were evaluated for parental polymorphisms using the single strand conformational polymorphism (SSCP) technique and Sequenom MassARRAY system. A total of 53 new marker loci were placed on an integrated molecular map in the DOR364 × G19833 recombinant inbred line (RIL) population. The new linkage map was used to build a consensus map, merging the linkage maps of the BAT93 × JALO EEP558 and DOR364 × BAT477 populations. A total of 1,060 markers were mapped, with a total map length of 2,041 cM across 11 linkage groups. As a second application of the generated resource, a diversity panel with 93 genotypes was evaluated with 173 SNP markers using the MassARRAY-platform and KASPar technology. These results were coupled with previous SSR evaluations and drought tolerance assays carried out on the same individuals. This agglomerative dataset was examined, in order to discover marker-trait associations, using general linear model (GLM) and mixed linear model (MLM). Some significant associations with yield components were identified, and were consistent with previous findings. In short, this study illustrates the power of intron-based markers for linkage and association mapping in

  17. Genetic characterization of local Criollo pig breeds from the Americas using microsatellite markers.

    Science.gov (United States)

    Revidatti, M A; Delgado Bermejo, J V; Gama, L T; Landi Periati, V; Ginja, C; Alvarez, L A; Vega-Pla, J L; Martínez, A M

    2014-11-01

    Little is known about local Criollo pig genetic resources and relationships among the various populations. In this paper, genetic diversity and relationships among 17 Criollo pig populations from 11 American countries were assessed with 24 microsatellite markers. Heterozygosities, F-statistics, and genetic distances were estimated, and multivariate, genetic structure and admixture analyses were performed. The overall means for genetic variability parameters based on the 24 microsatellite markers were the following: mean number of alleles per locus of 6.25 ± 2.3; effective number of alleles per locus of 3.33 ± 1.56; allelic richness per locus of 4.61 ± 1.37; expected and observed heterozygosity of 0.62 ± 0.04 and 0.57 ± 0.02, respectively; within-population inbreeding coefficient of 0.089; and proportion of genetic variability accounted for by differences among breeds of 0.11 ± 0.01. Genetic differences were not significantly associated with the geographical location to which breeds were assigned or their country of origin. Still, the NeighborNet dendrogram depicted the clustering by geographic origin of several South American breeds (Criollo Boliviano, Criollo of northeastern Argentina wet, and Criollo of northeastern Argentina dry), but some unexpected results were also observed, such as the grouping of breeds from countries as distant as El Salvador, Mexico, Ecuador, and Cuba. The results of genetic structure and admixture analyses indicated that the most likely number of ancestral populations was 11, and most breeds clustered separately when this was the number of predefined populations, with the exception of some closely related breeds that shared the same cluster and others that were admixed. These results indicate that Criollo pigs represent important reservoirs of pig genetic diversity useful for local development as well as for the pig industry.

  18. 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.

  19. Molecular marker studies in riverine buffaloes, for characterization and diagnosis of genetic defects

    International Nuclear Information System (INIS)

    Yadav, B.R.

    2005-01-01

    The buffalo is probably the last livestock species to have been domesticated, with many genetic, physiological and behavioural traits not yet well understood. Molecular markers have been used for characterizing animals and breeds, diagnosing diseases and identifying anatomical and physiological anomalies. RFLP studies showed low heterozygosity, but genomic and oligonucleotide probes showed species-specific bands useful for identification of carcass or other unknown samples. Use of RAPD revealed band frequencies, band sharing frequencies, genetic distances, and genetic and identity indexes in different breeds. Bovine microsatellite primers indicate that 70.9% of bovine loci were conserved in buffalo. Allele numbers, sizes, frequencies, heterozygosity and polymorphism information content showed breed-specific patterns. Different marker types - genomic and oligonucleotide probes, RAPD and microsatellites - are useful in parent identification. Individual specific DNA fingerprinting techniques were applied with twin-born animal (XX/XY) chimerism, sex identification, anatomically defective and XO individuals. Molecular markers are a potential tool for geneticists and breeders to evaluate existing germplasm and to manipulate it to develop character-specific strains and to provide the basis for effective genetic conservation. (author)

  20. Genetic diversity and DNA fingerprinting in jute(Corchorus spp.) based on SSR markers

    Institute of Scientific and Technical Information of China (English)

    Liwu; Zhang; Rongrong; Cai; Minhang; Yuan; Aifen; Tao; Jiantang; Xu; Lihui; Lin; Pingping; Fang; Jianmin; Qi

    2015-01-01

    Genetic diversity analysis and DNA finger printing are very useful in breeding programs,seed conservation and management. Jute(Corchorus spp.) is the second most important natural fiber crop after cotton. DNA fingerprinting studies in jute using SSR markers are limited. In this study, 58 jute accessions, including two control varieties(Huangma 179 and Kuanyechangguo) from the official variety registry in China were evaluated with 28 pairs of SSR primers. A total of 184 polymorphic loci were identified. Each primer detected 3 to 15 polymorphic loci, with an average of 6.6. The 58 jute accessions were DNA-fingerprinted with 67 SSR markers from the 28 primer pairs. These markers differentiated the 58 jute accessions from one another, with Co SSR305-120 and Co SSR174-195 differentiating Huangma 179 and Kuanyechangguo, respectively. NTSYS-pc2.10 software was used to analyze the genetic diversity in the 58 jute accessions. Their genetic similarity coefficients ranged from 0.520 to 0.910 with an average of 0.749, indicating relatively great genetic diversity among them. The 58 jute accessions were divided into four groups with the coefficient 0.710 used as a value for classification, consistent with their species and pedigrees. All these results may be useful both for protection of intellectual property rights of jute accessions and for jute improvement.

  1. Genetic diversity and DNA fingerprinting in jute (Corchorus spp. based on SSR markers

    Directory of Open Access Journals (Sweden)

    Liwu Zhang

    2015-10-01

    Full Text Available Genetic diversity analysis and DNA finger printing are very useful in breeding programs, seed conservation and management. Jute (Corchorus spp. is the second most important natural fiber crop after cotton. DNA fingerprinting studies in jute using SSR markers are limited. In this study, 58 jute accessions, including two control varieties (Huangma 179 and Kuanyechangguo from the official variety registry in China were evaluated with 28 pairs of SSR primers. A total of 184 polymorphic loci were identified. Each primer detected 3 to 15 polymorphic loci, with an average of 6.6. The 58 jute accessions were DNA-fingerprinted with 67 SSR markers from the 28 primer pairs. These markers differentiated the 58 jute accessions from one another, with CoSSR305-120 and CoSSR174-195 differentiating Huangma 179 and Kuanyechangguo, respectively. NTSYS-pc2.10 software was used to analyze the genetic diversity in the 58 jute accessions. Their genetic similarity coefficients ranged from 0.520 to 0.910 with an average of 0.749, indicating relatively great genetic diversity among them. The 58 jute accessions were divided into four groups with the coefficient 0.710 used as a value for classification, consistent with their species and pedigrees. All these results may be useful both for protection of intellectual property rights of jute accessions and for jute improvement.

  2. A Multi-Marker Genetic Association Test Based on the Rasch Model Applied to Alzheimer's Disease.

    Directory of Open Access Journals (Sweden)

    Wenjia Wang

    Full Text Available Results from Genome-Wide Association Studies (GWAS have shown that the genetic basis of complex traits often include many genetic variants with small to moderate effects whose identification remains a challenging problem. In this context multi-marker analysis at the gene and pathway level can complement traditional point-wise approaches that treat the genetic markers individually. In this paper we propose a novel statistical approach for multi-marker analysis based on the Rasch model. The method summarizes the categorical genotypes of SNPs by a generalized logistic function into a genetic score that can be used for association analysis. Through different sets of simulations, the false-positive rate and power of the proposed approach are compared to a set of existing methods, and shows good performances. The application of the Rasch model on Alzheimer's Disease (AD ADNI GWAS dataset also allows a coherent interpretation of the results. Our analysis supports the idea that APOE is a major susceptibility gene for AD. In the top genes selected by proposed method, several could be functionally linked to AD. In particular, a pathway analysis of these genes also highlights the metabolism of cholesterol, that is known to play a key role in AD pathogenesis. Interestingly, many of these top genes can be integrated in a hypothetic signalling network.

  3. Genetic diversity in natural populations of Jacaranda decurrens Cham. determined using RAPD and AFLP markers

    Directory of Open Access Journals (Sweden)

    Bianca W. Bertoni

    2010-01-01

    Full Text Available Jacaranda decurrens (Bignoniaceae is an endemic species of the Cerrado with validated antitumoral activity. The genetic diversity of six populations of J. decurrens located in the State of São Paulo was determined in this study by using molecular markers for randomly amplified polymorphic DNA (RAPD and amplified fragment length polymorphism (AFLP. Following optimization of the amplification reaction, 10 selected primers generated 78 reproducible RAPD fragments that were mostly (69.2% polymorphic. Two hundred and five reproducible AFLP fragments were generated by using four selected primer combinations; 46.3% of these fragments were polymorphic, indicating a considerable level of genetic diversity. Analysis of molecular variance (AMOVA using these two groups of markers indicated that variability was strongly structured amongst populations. The unweighted pair group method with arithmatic mean (UPGMA and Pearson's correlation coefficient (RAPD -0.16, p = 0.2082; AFLP 0.37, p = 0.1006 between genetic matrices and geographic distances suggested that the population structure followed an island model in which a single population of infinite size gave rise to the current populations of J. decurrens, independently of their spatial position. The results of this study indicate that RAPD and AFLP markers were similarly efficient in measuring the genetic variability amongst natural populations of J. decurrens. These data may be useful for developing strategies for the preservation of this medicinal species in the Cerrado.

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

    OpenAIRE

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

    2012-01-01

    Diversity Arrays Technology (DArT) provides a high-throughput whole-genome genotyping platform for the detection and scoring of hundreds of polymorphic loci without any need for prior sequence information. The work presented here details the development and performance of a DArT genotyping array for apple. This is the first paper on DArT in horticultural trees. Genetic mapping of DArT markers in two mapping populations and their integration with other marker types showed that DArT is a powerf...

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

    OpenAIRE

    Schouten, Henk J.; van de Weg, W. Eric; Carling, Jason; Khan, Sabaz Ali; McKay, Steven J.; van Kaauwen, Martijn P. W.; Wittenberg, Alexander H. J.; Koehorst-van Putten, Herma J. J.; Noordijk, Yolanda; Gao, Zhongshan; Rees, D. Jasper G.; Van Dyk, Maria M.; Jaccoud, Damian; Considine, Michael J.; Kilian, Andrzej

    2011-01-01

    Diversity Arrays Technology (DArT) provides a high-throughput whole-genome genotyping platform for the detection and scoring of hundreds of polymorphic loci without any need for prior sequence information. The work presented here details the development and performance of a DArT genotyping array for apple. This is the first paper on DArT in horticultural trees. Genetic mapping of DArT markers in two mapping populations and their integration with other marker types showed that DArT is a powerf...

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

    Science.gov (United States)

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

    2011-11-17

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

  7. Genetic diversity and population structure in Physalis peruviana and related taxa based on InDels and SNPs derived from COSII and IRG markers

    Science.gov (United States)

    Garzón-Martínez, Gina A.; Osorio-Guarín, Jaime A.; Delgadillo-Durán, Paola; Mayorga, Franklin; Enciso-Rodríguez, Felix E.; Landsman, David

    2015-01-01

    The genus Physalis is common in the Americas and includes several economically important species, among them Physalis peruviana that produces appetizing edible fruits. We studied the genetic diversity and population structure of P. peruviana and characterized 47 accessions of this species along with 13 accessions of related taxa consisting of 222 individuals from the Colombian Corporation of Agricultural Research (CORPOICA) germplasm collection, using Conserved Orthologous Sequences (COSII) and Immunity Related Genes (IRGs). In addition, 642 Single Nucleotide Polymorphism (SNPs) markers were identified and used for the genetic diversity analysis. A total of 121 alleles were detected in 24 InDels loci ranging from 2 to 9 alleles per locus, with an average of 5.04 alleles per locus. The average number of alleles in the SNP markers was two. The observed heterozygosity for P. peruviana with InDel and SNP markers was higher (0.48 and 0.59) than the expected heterozygosity (0.30 and 0.41). Interestingly, the observed heterozygosity in related taxa (0.4 and 0.12) was lower than the expected heterozygosity (0.59 and 0.25). The coefficient of population differentiation FST was 0.143 (InDels) and 0.038 (SNPs), showing a relatively low level of genetic differentiation among P. peruviana and related taxa. Higher levels of genetic variation were instead observed within populations based on the AMOVA analysis. Population structure analysis supported the presence of two main groups and PCA analysis based on SNP markers revealed two distinct clusters in the P. peruviana accessions corresponding to their state of cultivation. In this study, we identified molecular markers useful to detect genetic variation in Physalis germplasm for assisting conservation and crossbreeding strategies. PMID:26550601

  8. Genetic diversity and population structure in Physalis peruviana and related taxa based on InDels and SNPs derived from COSII and IRG markers.

    Science.gov (United States)

    Garzón-Martínez, Gina A; Osorio-Guarín, Jaime A; Delgadillo-Durán, Paola; Mayorga, Franklin; Enciso-Rodríguez, Felix E; Landsman, David; Mariño-Ramírez, Leonardo; Barrero, Luz Stella

    2015-12-01

    The genus Physalis is common in the Americas and includes several economically important species, among them Physalis peruviana that produces appetizing edible fruits. We studied the genetic diversity and population structure of P. peruviana and characterized 47 accessions of this species along with 13 accessions of related taxa consisting of 222 individuals from the Colombian Corporation of Agricultural Research (CORPOICA) germplasm collection, using Conserved Orthologous Sequences (COSII) and Immunity Related Genes (IRGs). In addition, 642 Single Nucleotide Polymorphism (SNPs) markers were identified and used for the genetic diversity analysis. A total of 121 alleles were detected in 24 InDels loci ranging from 2 to 9 alleles per locus, with an average of 5.04 alleles per locus. The average number of alleles in the SNP markers was two. The observed heterozygosity for P. peruviana with InDel and SNP markers was higher (0.48 and 0.59) than the expected heterozygosity (0.30 and 0.41). Interestingly, the observed heterozygosity in related taxa (0.4 and 0.12) was lower than the expected heterozygosity (0.59 and 0.25). The coefficient of population differentiation F ST was 0.143 (InDels) and 0.038 (SNPs), showing a relatively low level of genetic differentiation among P. peruviana and related taxa. Higher levels of genetic variation were instead observed within populations based on the AMOVA analysis. Population structure analysis supported the presence of two main groups and PCA analysis based on SNP markers revealed two distinct clusters in the P. peruviana accessions corresponding to their state of cultivation. In this study, we identified molecular markers useful to detect genetic variation in Physalis germplasm for assisting conservation and crossbreeding strategies.

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

    Directory of Open Access Journals (Sweden)

    Lígia Regina Lima Gouvêa

    2010-01-01

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

  10. [Genetic diversity of wild Cynodon dactylon germplasm detected by SRAP markers].

    Science.gov (United States)

    Yi, Yang-Jie; Zhang, Xin-Quan; Huang, Lin-Kai; Ling, Yao; Ma, Xiao; Liu, Wei

    2008-01-01

    Sequence-related amplified polymorphism (SRAP) molecular markers were used to detect the genetic diversity of 32 wild accessions of Cynodon dactylon collected from Sichuan, Chongqing, Guizhou and Tibet, China. The following results were obtained. (1) Fourteen primer pairs produced 132 polymorphic bands, averaged 9.4 bands per primer pair. The percentage of polymorphic bands in average was 79.8%. The Nei's genetic similarity coefficient of the tested accessions ranged from 0.591 to 0.957, and the average Nei's coefficient was 0.759. These results suggested that there was rich genetic diversity among the wild resources of Cynodon dactylon tested. (2) Thirty two wild accessions were clustered into four groups. Moreover, the accessions from the same origin frequently clustered into one group. The findings implied that a correlation among the wild resources, geographical and ecological environment. (3) Genetic differentiation between and within six eco-geographical groups of C. dactylon was estimated by Shannon's diversity index, which showed that 65.56% genetic variance existed within group, and 34.44% genetic variance was among groups. (4) Based on Nei's unbiased measures of genetic identity, UPGMA cluster analysis measures of six eco-geographical groups of Cynodon dactylon, indicated that there was a correlation between genetic differentiation and eco-geographical habits among the groups.

  11. Analysis of the genetic diversity of physic nut, Jatropha curcas L. accessions using RAPD markers.

    Science.gov (United States)

    Rafii, M Y; Shabanimofrad, M; Puteri Edaroyati, M W; Latif, M A

    2012-06-01

    A sum of 48 accessions of physic nut, Jatropha curcas L. were analyzed to determine the genetic diversity and association between geographical origin using RAPD-PCR markers. Eight primers generated a total of 92 fragments with an average of 11.5 amplicons per primer. Polymorphism percentages of J. curcas accessions for Selangor, Kelantan, and Terengganu states were 80.4, 50.0, and 58.7%, respectively, with an average of 63.04%. Jaccard's genetic similarity co-efficient indicated the high level of genetic variation among the accessions which ranged between 0.06 and 0.81. According to UPGMA dendrogram, 48 J. curcas accessions were grouped into four major clusters at coefficient level 0.3 and accessions from same and near states or regions were found to be grouped together according to their geographical origin. Coefficient of genetic differentiation (G(st)) value of J. curcas revealed that it is an outcrossing species.

  12. Genetic diversity of different accessions of Thymus kotschyanus using RAPD marker

    Directory of Open Access Journals (Sweden)

    Ahmad Ismaili

    2014-11-01

    Full Text Available Analysis of genetic diversity is a major step for understanding evolution and breeding applications. Recent advances in the application of the polymerase chain reaction make it possible to score individuals at a large number of loci. The RAPD technique has been successfully used in a variety of taxonomic and genetic diversity studies. The genetic diversity of 18 accessions of Thymus kotschyanus collected from different districts of Iran has been reported in this study, using 30 random amplified polymorphic DNA primers. Multivariate statistical analyses including principal coordinate analysis (PCOA and cluster analysis were used to group the accessions. From 29 primers, 385 bands were scored corresponding to an average of 13.27 bands per primer with 298 bands showing polymorphism (77.40%. A dendrogram constructed based on the UPGMA clustering method revealed three major clusters. The obtained results from grouping 18 accessions of T. kotschyanus with two studied methods indicated that in the most cases the applied methods produced similar grouping results. This study revealed nearly rich genetic diversity among T. kotschyanus accessions from different regions of Iran. The results showed RAPD marker was a useful marker for genetic diversity studies of T. kotschyanus and it was indicative of geographica variations.

  13. Genetic characterization of natural populations of pineapple guava (Acca sellowiana, with heterologous microsatellites markers

    Directory of Open Access Journals (Sweden)

    Karine Louise dos Santos

    2011-12-01

    Full Text Available Pineapple guava (Acca sellowiana is a native species from south Brazil and northeast Uruguay, and due to the unique flavor of its fruits, it is an income-generating alternative to small farmers. Knowledge on genetic diversity is an important tool for genetic improvement and conservation. Aiming to increase the knowledge with regarde to the species genetic diversity, fi ve natural populations of A. sellowiana were analyzed through microsatellites markers developed from Eucalyptus grandis W. Hill ex Maiden x E. urophylla S.T. Blake complex. Using 10 pairs of selected markers, 122 plants were characterized. The mean values for expected and observed heterozigosity were 0.42 and 0.47, respectively. The fˆ estimates did not differ from zero to four out of the five populations evaluated, suggesting a small inbreeding effect. In addition, private alleles and high genetic divergence was observed. the average genetic divergence among the populations was st Fˆ = 0,13 e st Rˆ = 0,14, mostly due to the incidenceof rare or exclusive alleles among some populations.

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

    Science.gov (United States)

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

    2014-03-01

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

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

    Science.gov (United States)

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

    2017-09-21

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

  16. Genetic similarity among commercial oil palm materials based on microsatellite markers

    Directory of Open Access Journals (Sweden)

    Diana Arias

    2012-08-01

    Full Text Available Microsatellite markers are used to determine genetic similarities among individuals and might be used in various applications in breeding programs. For example, knowing the genetic similarity relationships of commercial planting materials helps to better understand their responses to environmental, agronomic and plant health factors. This study assessed 17 microsatellite markers in 9 crosses (D x P of Elaeis guineensis Jacq. from various commercial companies in Malaysia, France, Costa Rica and Colombia, in order to find possible genetic differences and/or similarities. Seventy-seven alleles were obtained, with an average of 4.5 alleles per primer and a range of 2-8 amplified alleles. The results show a significant reduction of alleles, compared to the number of alleles reported for wild oil palm populations. The obtained dendrogram shows the formation of two groups based on their genetic similarity. Group A, with ~76% similarity, contains the commercial material of 3 codes of Deli x La Mé crosses produced in France and Colombia, and group B, with ~66% genetic similarity, includes all the materials produced by commercial companies in Malaysia, France, Costa Rica and Colombia

  17. Genetic Diversity of Selected Mangifera Species Revealed by Inter Simple Sequence Repeats Markers

    Directory of Open Access Journals (Sweden)

    Zulhairil Ariffin

    2015-01-01

    Full Text Available 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=7.50. Analysis on 18 Mangifera indica accessions also showed high degree of polymorphism of 99% and mean Shannon index, H0=5.74. Dice index of genetic similarity ranged from 0.0938 to 0.8046 among the Mangifera species. The dendrogram showed that the Mangifera species were grouped into three main divergent clusters. Cluster 1 comprised 14 accessions from Kedah and Perak. Cluster II and cluster III comprised 14 accessions from Sarawak and Sabah. Meanwhile, the Dice index of genetic similarity for 18 accessions of Mangifera indica ranged from 0.2588 to 0.7742. The dendrogram also showed the 18 accessions of Mangifera indica were grouped into three main clusters. Cluster I comprised 10 landraces of Mangifera indica from Kedah. Cluster II comprised 7 landraces of Mangifera indica followed by Chokanan to form Cluster III.

  18. Genetic Diversity Analysis of Tagetes Species Using PCR Based Molecular Markers

    International Nuclear Information System (INIS)

    Shahzadi, I.; Ahmad, R.; Waheed, U.; Shah, M. F.

    2016-01-01

    Tagetes is a genus of medicinally important wild and cultivated plants containing several chemical compounds. Lack of information on variation at molecular level present in Tagetes species is paramount to understand the genetic basis of medicinally important compounds. Current study aims at finding genetic variability in Tagetes species using random and specific molecular markers. Two primer systems including 25 RAPD and 3 STS (limonene gene) were used to ascertain genetic diversity of 15 Tagetes genotypes belonging to different species. We found that 20 of the 25 tested RAPD primers generated stable band patterns with 167 loci of amplification products. The proportion of polymorphic bands was 95.21 percent for RAPD primers. Three STS primers generated a total of 29 amplification products, of which 96.55 percent were polymorphic. Homology of genotypes was 53.18 percent and 51.11 percent with RAPD and STS primers respectively. The dendrogram obtained revealed that the range of overall genetic distances estimated was 22 percent to 100 percent through RAPD and 9 percent to 100 percent through STS markers. The findings help to establish that PCR-based assay such as RAPD and STS could be used successfully for estimation of genetic diversity of different genotypes of Tagetes that can be used for selection of parents for improvement of the species. (author)

  19. Assessment of genetic diversity in okra (abelmoschus esculentus l.) using rapd markers

    International Nuclear Information System (INIS)

    Haq, I.; Khan, A.A.; Azmat, M.A.

    2013-01-01

    Thirty nine okra genotypes were assessed for genetic variability using Random Amplified Polymorphic DNA (RAPD) markers. Twenty polymorphic RAPD primers amplified 111 DNA fragments, with an average of 5.5 fragments per primer. Among 39 okra genotypes, 107 fragments (96%) were found to be polymorphic. The UPGMA cluster analysis placed okra genotypes into seven main clusters. Sabzpari 2001 and Acc. No. 019221 had shown maximum similarity (83%) while the minimum similarity (44.14%) was observed between the genotypes Punjab Selection and Acc. No. 019217. Thus, by using RAPD primers a considerable polymorphism appeared to exist, which showed genetic variability in the okra genotypes. (author)

  20. Outlier SNP markers reveal fine-scale genetic structuring across European hake populations (Merluccius merluccius)

    DEFF Research Database (Denmark)

    Milano, I.; Babbucci, M.; Cariani, A.

    2014-01-01

    fishery. Analysis of 850 individuals from 19 locations across the entire distribution range showed evidence for several outlier loci, with significantly higher resolving power. While 299 putatively neutral SNPs confirmed the genetic break between basins (FCT = 0.016) and weak differentiation within basins...... even when neutral markers provide genetic homogeneity across populations. Here, 381 SNPs located in transcribed regions were used to assess largeand fine-scale population structure in the European hake (Merluccius merluccius), a widely distributed demersal species of high priority for the European...

  1. Modeling of genetic gain for single traits from marker-assisted seedling selection in clonally propagated crops

    Science.gov (United States)

    Ru, Sushan; Hardner, Craig; Carter, Patrick A; Evans, Kate; Main, Dorrie; Peace, Cameron

    2016-01-01

    Seedling selection identifies superior seedlings as candidate cultivars based on predicted genetic potential for traits of interest. Traditionally, genetic potential is determined by phenotypic evaluation. With the availability of DNA tests for some agronomically important traits, breeders have the opportunity to include DNA information in their seedling selection operations—known as marker-assisted seedling selection. A major challenge in deploying marker-assisted seedling selection in clonally propagated crops is a lack of knowledge in genetic gain achievable from alternative strategies. Existing models based on additive effects considering seed-propagated crops are not directly relevant for seedling selection of clonally propagated crops, as clonal propagation captures all genetic effects, not just additive. This study modeled genetic gain from traditional and various marker-based seedling selection strategies on a single trait basis through analytical derivation and stochastic simulation, based on a generalized seedling selection scheme of clonally propagated crops. Various trait-test scenarios with a range of broad-sense heritability and proportion of genotypic variance explained by DNA markers were simulated for two populations with different segregation patterns. Both derived and simulated results indicated that marker-based strategies tended to achieve higher genetic gain than phenotypic seedling selection for a trait where the proportion of genotypic variance explained by marker information was greater than the broad-sense heritability. Results from this study provides guidance in optimizing genetic gain from seedling selection for single traits where DNA tests providing marker information are available. PMID:27148453

  2. Problems of genetic diagnosis: serological markers in the prognosis of the development of human speed abilities

    Directory of Open Access Journals (Sweden)

    Serhiyenko Leonid Prokopovich

    2011-10-01

    Full Text Available The article deals with the study of correlation between blood groups system AB0 and Rh with the peculiarities of the development of human speed abilities. Complex of genetic markers is defined. It is possible to use this complex in the individual prognosis of the development of human motor abilities. With 0(I and A(II blood groups and Rh+ have a high inclination to the physical development. Better identify trends in the phenotypic expression of high-speed abilities in people with 0(I and A(II blood groups in comparison with people with the AB(IV and B(III blood group. The pattern of decreasing susceptibility to the development of high-speed abilities as follows: 0(I>A(II>B(III>AB (IV. It is established that a complex system of genetic markers AB0 and Rh blood has no gender differences.

  3. GeMprospector--online design of cross-species genetic marker candidates in legumes and grasses.

    Science.gov (United States)

    Fredslund, Jakob; Madsen, Lene H; Hougaard, Birgit K; Sandal, Niels; Stougaard, Jens; Bertioli, David; Schauser, Leif

    2006-07-01

    The web program GeMprospector (URL: http://cgi-www.daimi.au.dk/cgi-chili/GeMprospector/main) allows users to automatically design large sets of cross-species genetic marker candidates targeting either legumes or grasses. The user uploads a collection of ESTs from one or more legume or grass species, and they are compared with a database of clusters of homologous EST and genomic sequences from other legumes or grasses, respectively. Multiple sequence alignments between submitted ESTs and their homologues in the appropriate database form the basis of automated PCR primer design in conserved exons such that each primer set amplifies an intron. The only user input is a collection of ESTs, not necessarily from more than one species, and GeMprospector can boost the potential of such an EST collection by combining it with a large database to produce cross-species genetic marker candidates for legumes or grasses.

  4. Isolation and characterization of microsatellite markers and analysis of genetic variability in Curculigo latifolia Dryand.

    Science.gov (United States)

    Babaei, Nahid; Abdullah, Nur Ashikin Psyquay; Saleh, Ghizan; Abdullah, Thohirah Lee

    2012-11-01

    Curculin, a sweet protein found in Curculigo latifolia fruit has great potential for the pharmaceutical industry. This protein interestingly has been found to have both sweet taste and taste-modifying capacities comparable with other natural sweeteners. According to our knowledge this is the first reported case on the isolation of microsatellite loci in this genus. Hence, the current development of microsatellite markers for C. latifolia will facilitate future population genetic studies and breeding programs for this valuable plant. In this study 11 microsatellite markers were developed using 3' and 5' ISSR markers. The primers were tested on 27 accessions from all states of Peninsular Malaysia. The number of alleles per locus ranged from three to seven, with allele size ranging from 141 to 306 bp. The observed and expected heterozygosity ranged between 0.00-0.65 and 0.38-0.79, respectively. The polymorphic information content ranged from 0.35 to 0.74 and the Shannon's information index ranged from 0.82 to 1.57. These developed polymorphic microsatellites were used for constructing a dendrogram by unweighted pair group method with arithmetic mean cluster analysis using the Dice's similarity coefficient. Accessions association according to their geographical origin was observed. Based on characteristics of isolated microsatellites for C. latifolia accessions all genotype can be distinguished using these 11 microsatellite markers. These polymorphic markers could also be applied to studies on uniformity determination and somaclonal variation of tissue culture plantlets, varieties identification, genetic diversity, analysis of phylogenetic relationship, genetic linkage maps and quantitative trait loci in C. latifolia.

  5. Genetic diversity of cucumber estimated by morpho-physiological and EST-SSR markers.

    Science.gov (United States)

    Pandey, Sudhakar; Ansari, Waquar Akhter; Pandey, Maneesh; Singh, Bijendra

    2018-02-01

    In the present study, genetic variation among 40 cucumber genotypes was analyzed by means of morpho-physiological traits and 21 EST-SSR markers. Diversity was observed for morpho-physiological characters like days to 50% female flowering (37-46.9, number of fruits/plant (1.33-5.80), average fruit weight (41-333), vine length (36-364), relative water content (58.5-92.7), electrolyte leakage (15.9-37.1), photosynthetic efficiency (0.40-0.75) and chlorophyll concentration index (11.1-28.6). The pair wise Jaccard similarity coefficient ranged from 0.00 to 0.27 for quantitative traits and 0.24 to 0.96 for EST-SSR markers indicating that the accessions represent genetically diverse populations. With twenty-one EST-SSR markers, polymorphism revealed among 40 cucumber genotypes, number of alleles varied 2-6 with an average 3.05. Polymorphism information content varied from 0.002 to 0.989 (mean = 0.308). The number of effective allele (Ne), expected heterozygosity (He) and unbiased expected heterozygosity (uHe) of these EST-SSRs were 1.079-1.753, 0.074-0.428 and 0.074-0.434, respectively. Same 21 EST-SSR markers transferability checked in four other Cucumis species: snapmelon ( Cucumis melo var. momordica ), muskmelon ( Cucumis melo L.), pickling melon ( Cucumis melo var. conomon ) and wild muskmelon ( Cucumis melo var. agrestis ) with frequency of 61.9, 95.2, 76.2, and 76.2%, respectively. Present study provides useful information on variability, which can assist geneticists with desirable traits for cucumber germplasm utilization. Observed physiological parameters may assists in selection of genotype for abiotic stress tolerance also, EST-SSR markers may be useful for genetic studies in related species.

  6. Development of marker vaccines for rinderpest virus using reverse genetics technology

    International Nuclear Information System (INIS)

    Parida, S.; Walsh, E.P.; Anderson, J.; Baron, M.D.; Barrett, T.

    2005-01-01

    Rinderpest is an economically devastating disease of cattle (cattle plague), but a live-attenuated vaccine has been very successfully used in a global rinderpest eradication campaign. As a consequence, the endemic focus of the virus has been reduced to an area in eastern Africa known as the Kenya-Somali ecosystem. Although the vaccine is highly effective, it has a drawback in that vaccinated animals are serologically indistinguishable from those that have recovered from natural infection. In the final stages of the eradication campaign, when vaccination to control the spread of disease will only be used in emergencies to contain an outbreak, a marker vaccine would be a very useful tool to monitor possible wild virus spread outside the vaccination area. Marker vaccines for rinderpest, and other viruses with negative-sense RNA genomes, can now be produced using reverse genetics, and the development of such marker vaccines for rinderpest virus is described. (author)

  7. Genetic linkage of mild pseudoachondroplasia (PSACH) to markers in the pericentromeric region of chromosome 19

    Energy Technology Data Exchange (ETDEWEB)

    Briggs, M.D.; Rasmussen, M.; Garber, P.; Rimoin, D.L.; Cohn, D.H. (Steven Spielberg Pediatric Research Center, Los Angeles, CA (United States)); Weber, J.L. (Marshfield Medical Research Foundation, WI (United States)); Yuen, J.; Reinker, K. (Univ. of Hawaii, Honolulu, HI (United States))

    1993-12-01

    Pseudoachondroplasia (PSACH) is a dominantly inherited form of short-limb dwarfism characterized by dysplastic changes in the spine, epiphyses, and metaphyses and early onset osteoarthropathy. Chondrocytes from affected individuals accumulate an unusual appearing material in the rough endoplasmic reticulum, which has led to the hypothesis that a structural abnormality in a cartilage-specific protein produces the phenotype. The authors recently identified a large family with a mild form of pseudoachondroplasia. By genetic linkage to a dinucleotide repeat polymorphic marker (D19S199), they have localized the disease gene to chromosome 19 (maximum lod score of 7.09 at a recombination fraction of 0.03). Analysis of additional markers and recombinations between the linked markers and the phenotype suggests that the disease gene resides within a 6.3-cM interval in the immediate pericentromeric region of the chromosome. 39 refs., 2 figs., 1 tab.

  8. Genetic Assessment of Moroccan Tomato (Solanum lycopersicum L. Genotypes by RAPD and SSR Markers

    Directory of Open Access Journals (Sweden)

    Rajae Amraoui

    2017-06-01

    Full Text Available For the first time eight local tomato cultivars collected from four different regions of Morocco were assessed with RAPD and SSR methods. Most of RAPD markers give monomorphic banding profiles. Only OPU03 marker showed a total of 4 polymorphic amplicons out of 8 recorded in FIGUIG2 cultivar. The analysis with SSR markers gives more polymorphism. The number of alleles amplified assessed from 2 to 5 alleles among cultivars. The similarity matrix subjected by the unweighted pairgroup arithmetic method (UPGMA clustering grouped the cultivars in four groups where FIGUIG2 cultivar formed a separate and more distant cluster. In addition this cultivar holds the very high percentage of uniformity (99% indicating that is an homogeneous traditional cultivar with high purity. This genotype can be conserved and used in breeding programs. More traditional Moroccan cultivars must be collected in order to determine their genetic structure.

  9. [The muzzle and biochemical genetic markers as supplementary breed characteristics in cattle].

    Science.gov (United States)

    Tarasiuk, S I; Glazko, V I; Trofimenko, A L

    1997-01-01

    The comparative analysis of characteristics of three different cattle breeds (Brown Carpathian, Pinzgauer, Red Polish) on the 5 molecular-genetic markers and 5 muzzle dermatoglyphic types was carried out. It was indicated, that one characteristic can not be use as a breed-specific one but only their complex. The main aspect of search of this complex is the use of characteristics which mark different structure-functional systems of whole organism.

  10. [Cloning goat producing human lactoferrin with genetically modified donor cells selected by single or dual markers].

    Science.gov (United States)

    An, Liyou; Yuan, Yuguo; Yu, Baoli; Yang, Tingjia; Cheng, Yong

    2012-12-01

    We compared the efficiency of cloning goat using human lactoferrin (hLF) with genetically modified donor cells marked by single (Neo(r)) or double (Neo(r)/GFP) markers. Single marker expression vector (pBLC14) or dual markers expression vector (pAPLM) was delivered to goat fetal fibroblasts (GFF), and then the transgenic GFF was used as donor cells to produce transgenic goats. Respectively, 58.8% (20/34) and 86.7% (26/30) resistant cell lines confirmed the transgenic integration by PCR. Moreover, pAPLM cells lines were subcultured with several passages, only 20% (6/30) cell lines was observed fluorescence from each cell during the cell passage. Somatic cell nuclear transfer using the donor cells harbouring pBLC14 or pAPLM construct, resulting in a total of 806 reconstructed embryos, a pregnancy rate at 35 d (53.8%, 39.1%) and 60 d (26.9%, 21.7%), and an offspring birth rate (1.9%, 1.4%) with 5 and 7 newborn cloned goats, respectively. Transgene was confirmed by PCR and southern-blot in all cloned offspring. There were no significant differences at the reconstructed embryo fusion rates, pregnancy rates and the birth rate (P > 0.05) between single and double markers groups. The Neo(r)/GFP double markers could improve the reliability for accurately and efficiently selecting the genetically modified donor cells. No adverse effect was observed on the efficiency of transgenic goat production by SCNT using somatic cells transfected with double (Neo(r)/GFP) markers vector.

  11. Cultivar identification and genetic relationship of pineapple (Ananas comosus) cultivars using SSR markers.

    Science.gov (United States)

    Lin, Y S; Kuan, C S; Weng, I S; Tsai, C C

    2015-11-25

    The genetic relationships among 27 pineapple [Ananas comosus (L.) Merr.] cultivars and lines were examined using 16 simple sequence repeat (SSR) markers. The number of alleles per locus of the SSR markers ranged from 2 to 6 (average 3.19), for a total of 51 alleles. Similarity coefficients were calculated on the basis of 51 amplified bands. A dendrogram was created according to the 16 SSR markers by the unweighted pair-group method. The banding patterns obtained from the SSR primers allowed most of the cultivars and lines to be distinguished, with the exception of vegetative clones. According to the dendrogram, the 27 pineapple cultivars and lines were clustered into three main clusters and four individual clusters. As expected, the dendrogram showed that derived cultivars and lines are closely related to their parental cultivars; the genetic relationships between pineapple cultivars agree with the genealogy of their breeding history. In addition, the analysis showed that there is no obvious correlation between SSR markers and morphological characters. In conclusion, SSR analysis is an efficient method for pineapple cultivar identification and can offer valuable informative characters to identify pineapple cultivars in Taiwan.

  12. Genetic diversity and genetic structure of consecutive breeding generations of golden mandarin fish (Siniperca scherzeri Steindachner) using microsatellite markers.

    Science.gov (United States)

    Luo, X N; Yang, M; Liang, X F; Jin, K; Lv, L Y; Tian, C X; Yuan, Y C; Sun, J

    2015-09-25

    In this study, 12 polymorphic microsatellites were inves-tigated to determine the genetic diversity and structure of 5 consecu-tive selected populations of golden mandarin fish (Siniperca scherzeri Steindachner). The total numbers of alleles, average heterozyosity, and average polymorphism information content showed that the genetic diversity of these breeding populations was decreasing. Additionally, pairwise fixation index FST values among populations and Da values in-creased from F1 generation to subsequent generations (FST values from 0.0221-0.1408; Da values from 0.0608-0.1951). Analysis of molecular variance indicated that most genetic variations arise from individuals within populations (about 92.05%), while variation among populations accounted for only 7.95%. The allele frequency of the loci SC75-220 and SC101-222 bp changed regularly in the 5 breeding generations. Their frequencies were gradually increased and showed an enrichment trend, indicating that there may be genetic correlations between these 2 loci and breeding traits. Our study indicated that microsatellite markers are effective for assessing the genetic variability in the golden mandarin fish breeding program.

  13. Estimates of epistatic and pleiotropic effects of casein alpha s1 (CSN1S1) and thyroglobulin (TG) genetic markers on beef heifer performance traits enhanced by selection

    Science.gov (United States)

    Genetic marker effects and type of inheritance are estimated with poor precision when minor marker allele frequencies are low. A stable composite population (MARC II) was subjected to marker assisted selection for two years to equalize CSN1S1 and TG genetic marker frequencies to evaluate the epista...

  14. Genetic relationship among nine Rhododendron species in Qinling mountains, China using amplified fragment length polymorphism markers

    International Nuclear Information System (INIS)

    Zhao, B.; Zheng, X.Z.

    2015-01-01

    Genetic relationships of nine species of Rhododendron in the Qinling Mountains were evaluated using amplified fragment length polymorphism (AFLP) markers. A total of 440 amplification products were obtained using nine selected AFLP markers, of which 421 (95.40%) showed polymorphism. With these polymorphic products, a dendrogram was constructed using the unweighted pair-group method with arithmetic mean (UPGMA). R. calophytum, R. hypoglaucum and R. clementinae, belonging to Subgen Hymenanthes, gathered together, and the species derived from Subgen Rhododendron and Subgen Tsutsusi formed another two groups. R. tsinlingense, R. purdomii, R. Taibaiense and R. capitatum (Subsect. Lapponica), and R. concinnum (Subsect. Triflora) were clustered as one group, but they belong to difference subsect. and R. purdomii and R. Taibaiense showed the closest genetic distance, but both species differed greatly in morphological characteristics.These results showed that the genetic relationships among nine Rhododendron species, determined by AFLP markers, were partially related to their taxonomic position, geography distribution and morphological classification. The present study will benefit the identification and conservation of Rhododendron, and the development of new Rhododendron cultivar. (author)

  15. Genetic Diversity in Jatropha curcas L. Assessed with SSR and SNP Markers

    Directory of Open Access Journals (Sweden)

    Juan M. Montes

    2014-08-01

    Full Text Available Jatropha curcas L. (jatropha is an undomesticated plant that has recently received great attention for its utilization in biofuel production, rehabilitation of wasteland, and rural development. Knowledge of genetic diversity and marker-trait associations is urgently needed for the design of breeding strategies. The main goal of this study was to assess the genetic structure and diversity in jatropha germplasm with co-dominant markers (Simple Sequence Repeats (SSR and Single Nucleotide Polymorphism (SNP in a diverse, worldwide, germplasm panel of 70 accessions. We found a high level of homozygosis in the germplasm that does not correspond to the purely outcrossing mating system assumed to be present in jatropha. We hypothesize that the prevalent mating system of jatropha comprise a high level of self-fertilization and that the outcrossing rate is low. Genetic diversity in accessions from Central America and Mexico was higher than in accession from Africa, Asia, and South America. We identified makers associated with the presence of phorbol esters. We think that the utilization of molecular markers in breeding of jatropha will significantly accelerate the development of improved cultivars.

  16. Transferability of STS markers in studying genetic relationships of marvel grass (Dichanthium annulatum).

    Science.gov (United States)

    Saxena, Raghvendra; Chandra, Amaresh

    2011-11-01

    Transferability of sequence-tagged-sites (STS) markers was assessed for genetic relationships study among accessions of marvel grass (Dichanthium annulatum Forsk.). In total, 17 STS primers of Stylosanthes origin were tested for their reactivity with thirty accessions of Dichanthium annulatum. Of these, 14 (82.4%) reacted and a total 106 (84 polymorphic) bands were scored. The number of bands generated by individual primer pairs ranged from 4 to 11 with an average of 7.57 bands, whereas polymorphic bands ranged from 4 to 9 with an average of 6.0 bands accounts to an average polymorphism of 80.1%. Polymorphic information content (PIC) ranged from 0.222 to 0.499 and marker index (MI) from 1.33 to 4.49. Utilizing Dice coefficient of genetic similarity dendrogram was generated through un-weighted pairgroup method with arithmetic mean (UPGMA) algorithm. Further, clustering through sequential agglomerative hierarchical and nested (SAHN) method resulted three main clusters constituted all accessions except IGBANG-D-2. Though there was intermixing of few accessions of one agro-climatic region to another, largely groupings of accessions were with their regions of collections. Bootstrap analysis at 1000 scale also showed large number of nodes (11 to 17) having strong clustering (> 50). Thus, results demonstrate the utility of STS markers of Stylosanthes in studying the genetic relationships among accessions of Dichanthium.

  17. Insight into the genetic variability analysis and cultivar identification of tall fescue by using SSR markers.

    Science.gov (United States)

    Fu, Kaixin; Guo, Zhihui; Zhang, Xinquan; Fan, Yan; Wu, Wendan; Li, Daxu; Peng, Yan; Huang, Linkai; Sun, Ming; Bai, Shiqie; Ma, Xiao

    2016-01-01

    Genetic diversity of 19 forage-type and 2 turf-type cultivars of tall fescue ( Festuca arundinacea Schreb.) was revealed using SSR markers in an attempt to explore the genetic relationships among them, and examine potential use of SSR markers to identify cultivars by bulked samples. A total of 227 clear band was scored with 14 SSR primers and out of which 201 (88.6 %) were found polymorphic. The percentage of polymorphic bands (PPB) per primer pair varied from 62.5 to 100 % with an average of 86.9 %. The polymorphism information content (PIC) value ranged from 0.116 to 0.347 with an average of 0.257 and the highest PIC value (0.347) was noticed for primer NFA040 followed by NFA113 (0.346) whereas the highest discriminating power (D) of 1 was shown in NFA037 and LMgSSR02-01C. A Neighbor-joining dendrogram and the principal component analysis identified six major clusters and grouped the cultivars in agreement with their breeding histories. STRUCTURE analysis divided these cultivars into 3 sub-clades which correspond to distance based groupings. These findings indicates that SSR markers by bulking strategy are a useful tool to measure genetic diversity among tall fescue cultivars and could be used to supplement morphological data for plant variety protection.

  18. Analysis of genetic diversity and differentiation of seven stocks of Litopenaeus vannamei using microsatellite markers

    Science.gov (United States)

    Zhang, Kai; Wang, Weiji; Li, Weiya; Zhang, Quanqi; Kong, Jie

    2014-08-01

    Seven microsatellite markers were used to evaluate the genetic diversity and differentiation of seven stocks of Litopenaeus vannamei, which were introduced from Central and South America to China. All seven microsatellite loci were polymorphic, with polymorphism information content ( PIC) values ranging from 0.593 to 0.952. Totally 92 alleles were identified, and the number of alleles ( Na) and effective alleles ( Ne) varied between 4 and 21 and 2.7 and 14.6, respectively. Observed heterozygosity ( H o) values were lower than the expected heterozygosity ( H e) values (0.526-0.754), which indicated that the seven stocks possessed a rich genetic diversity. Thirty-seven tests were detected for reasonable significant deviation from Hardy-Weinberg equilibrium. F is values were positive at five loci, suggesting that there was a relatively high degree of inbreeding within stocks. Pairwise F st values ranged from 0.0225 to 0.151, and most of the stock pairs were moderately differentiated. Genetic distance and cluster analysis using UPGMA revealed a close genetic relationship of L. vannamei between Pop2 and Pop3. AMOVA indicated that the genetic variation among stocks (11.3%) was much lower than that within stocks (88.7%). Although the seven stocks had a certain degree of genetic differentiation and a rich genetic diversity, there is an increasing risk of decreased performance due to inbreeding in subsequent generations.

  19. Tracking the Genetic Stability of a Honey Bee (Hymenoptera: Apidae) Breeding Program With Genetic Markers.

    Science.gov (United States)

    Bourgeois, Lelania; Beaman, Lorraine

    2017-08-01

    A genetic stock identification (GSI) assay was developed in 2008 to distinguish Russian honey bees from other honey bee stocks that are commercially produced in the United States. Probability of assignment (POA) values have been collected and maintained since the stock release in 2008 to the Russian Honey Bee Breeders Association. These data were used to assess stability of the breeding program and the diversity levels of the contemporary breeding stock through comparison of POA values and genetic diversity parameters from the initial release to current values. POA values fluctuated throughout 2010-2016, but have recovered to statistically similar levels in 2016 (POA(2010) = 0.82, POA(2016) = 0.74; P = 0.33). Genetic diversity parameters (i.e., allelic richness and gene diversity) in 2016 also remained at similar levels when compared to those in 2010. Estimates of genetic structure revealed stability (FST(2009/2016) = 0.0058) with a small increase in the estimate of the inbreeding coefficient (FIS(2010) = 0.078, FIS(2016) = 0.149). The relationship among breeding lines, based on genetic distance measurement, was similar in 2008 and 2016 populations, but with increased homogeneity among lines (i.e., decreased genetic distance). This was expected based on the closed breeding system used for Russian honey bees. The successful application of the GSI assay in a commercial breeding program demonstrates the utility and stability of such technology to contribute to and monitor the genetic integrity of a breeding stock of an insect species. Published by Oxford University Press on behalf of Entomological Society of America 2017. This work is written by US Government employees and is in the public domain in the US.

  20. Cross-packaging of genetically distinct mouse and primate retroviral RNAs

    Directory of Open Access Journals (Sweden)

    Jaballah Soumeya

    2009-07-01

    Full Text Available Abstract Background The mouse mammary tumor virus (MMTV is unique from other retroviruses in having multiple viral promoters, which can be regulated by hormones in a tissue specific manner. This unique property has lead to increased interest in studying MMTV replication with the hope of developing MMTV based vectors for human gene therapy. However, it has recently been reported that related as well as unrelated retroviruses can cross-package each other's genome raising safety concerns towards the use of candidate retroviral vectors for human gene therapy. Therefore, using a trans complementation assay, we looked at the ability of MMTV RNA to be cross-packaged and propagated by an unrelated primate Mason-Pfizer monkey virus (MPMV that has intracellular assembly process similar to that of MMTV. Results Our results revealed that MMTV and MPMV RNAs could be cross-packaged by the heterologous virus particles reciprocally suggesting that pseudotyping between two genetically distinct retroviruses can take place at the RNA level. However, the cross-packaged RNAs could not be propagated further indicating a block at post-packaging events in the retroviral life cycle. To further confirm that the specificity of cross-packaging was conferred by the packaging sequences (ψ, we cloned the packaging sequences of these viruses on expression plasmids that generated non-viral RNAs. Test of these non-viral RNAs confirmed that the reciprocal cross-packaging was primarily due to the recognition of ψ by the heterologous virus proteins. Conclusion The results presented in this study strongly argue that MPMV and MMTV are promiscuous in their ability to cross-package each other's genome suggesting potential RNA-protein interactions among divergent retroviral RNAs proposing that these interactions are more complicated than originally thought. Furthermore, these observations raise the possibility that MMTV and MPMV genomes could also co-package providing substrates for

  1. Genetic diversity of wild and cultivated genotypes of pigeonpea through RAPD and SSR markers.

    Science.gov (United States)

    Walunjkar, Babasaheb C; Parihar, Akarsh; Singh, Nirbhay Kumar; Parmar, L D

    2015-03-01

    Eight wild and four cultivated pigeonpea genotypes were subjected to RAPD and microsatellite analysis, with 40 primers each. Out of these, eight RAPD and five SSR primers were found polymorphic. RAPD primers showed 100% polymorphism and produced a total of 517 DNA fragments, whereas SSR primers produced 67 fragments and they too showed 100% polymorphism. The RAPD markers revealed highest similarity co-efficient of 0.93 (GT-100 and ICPL-87), whereas the highest similarity co-efficient obtained with SSR markers was 1.00 (GTH-1 and GT-100). Average PIC value obtained with RAPD and SSR were 0.90 and 0.18, respectively. The arithmetic mean heterozygosity and marker index were 0.90 and 22.47 respectively with RAPD marker, whereas the corresponding values for SSR markers were 0.18 and 33.66. Moreover; the four wild genotypes (Cajanus scarabaeoides, Rhyncosia rufescence, Cajanus cajanifolius and Rhyncosia canna) and the four cultivars (GTH-1, GT-100, ICPL-87 and GT-1) grouped distinctly in the same subgroups of the dendrograms obtained with both RAPD and SSR analysis. Therefore, the findings of SSR supplement and validate the results obtained with RAPD analysis.

  2. Genetic diversity and relationships among different tomato varieties revealed by EST-SSR markers.

    Science.gov (United States)

    Korir, N K; Diao, W; Tao, R; Li, X; Kayesh, E; Li, A; Zhen, W; Wang, S

    2014-01-08

    The genetic diversity and relationship of 42 tomato varieties sourced from different geographic regions was examined with EST-SSR markers. The genetic diversity was between 0.18 and 0.77, with a mean of 0.49; the polymorphic information content ranged from 0.17 to 0.74, with a mean of 0.45. This indicates a fairly high degree of diversity among these tomato varieties. Based on the cluster analysis using unweighted pair-group method with arithmetic average (UPGMA), all the tomato varieties fell into 5 groups, with no obvious geographical distribution characteristics despite their diverse sources. The principal component analysis (PCA) supported the clustering result; however, relationships among varieties were more complex in the PCA scatterplot than in the UPGMA dendrogram. This information about the genetic relationships between these tomato lines helps distinguish these 42 varieties and will be useful for tomato variety breeding and selection. We confirm that the EST-SSR marker system is useful for studying genetic diversity among tomato varieties. The high degree of polymorphism and the large number of bands obtained per assay shows that SSR is the most informative marker system for tomato genotyping for purposes of rights/protection and for the tomato industry in general. It is recommended that these varieties be subjected to identification using an SSR-based manual cultivar identification diagram strategy or other easy-to-use and referable methods so as to provide a complete set of information concerning genetic relationships and a readily usable means of identifying these varieties.

  3. Identification of genetic markers linked to anthracnose resistance in sorghum using association analysis.

    Science.gov (United States)

    Upadhyaya, Hari D; Wang, Yi-Hong; Sharma, Rajan; Sharma, Shivali

    2013-06-01

    Anthracnose in sorghum caused by Colletotrichum sublineolum is one of the most destructive diseases affecting sorghum production under warm and humid conditions. Markers and genes linked to resistance to the disease are important for plant breeding. Using 14,739 SNP markers, we have mapped eight loci linked to resistance in sorghum through association analysis of a sorghum mini-core collection consisting of 242 diverse accessions evaluated for anthracnose resistance for 2 years in the field. The mini-core was representative of the International Crops Research Institute for the Semi-Arid Tropics' world-wide sorghum landrace collection. Eight marker loci were associated with anthracnose resistance in both years. Except locus 8, disease resistance-related genes were found in all loci based on their physical distance from linked SNP markers. These include two NB-ARC class of R genes on chromosome 10 that were partially homologous to the rice blast resistance gene Pib, two hypersensitive response-related genes: autophagy-related protein 3 on chromosome 1 and 4 harpin-induced 1 (Hin1) homologs on chromosome 8, a RAV transcription factor that is also part of R gene pathway, an oxysterol-binding protein that functions in the non-specific host resistance, and homologs of menthone:neomenthol reductase (MNR) that catalyzes a menthone reduction to produce the antimicrobial neomenthol. These genes and markers may be developed into molecular tools for genetic improvement of anthracnose resistance in sorghum.

  4. Age of Jupiter inferred from the distinct genetics and formation times of meteorites.

    Science.gov (United States)

    Kruijer, Thomas S; Burkhardt, Christoph; Budde, Gerrit; Kleine, Thorsten

    2017-06-27

    The age of Jupiter, the largest planet in our Solar System, is still unknown. Gas-giant planet formation likely involved the growth of large solid cores, followed by the accumulation of gas onto these cores. Thus, the gas-giant cores must have formed before dissipation of the solar nebula, which likely occurred within less than 10 My after Solar System formation. Although such rapid accretion of the gas-giant cores has successfully been modeled, until now it has not been possible to date their formation. Here, using molybdenum and tungsten isotope measurements on iron meteorites, we demonstrate that meteorites derive from two genetically distinct nebular reservoirs that coexisted and remained spatially separated between ∼1 My and ∼3-4 My after Solar System formation. The most plausible mechanism for this efficient separation is the formation of Jupiter, opening a gap in the disk and preventing the exchange of material between the two reservoirs. As such, our results indicate that Jupiter's core grew to ∼20 Earth masses within Jupiter is the oldest planet of the Solar System, and its solid core formed well before the solar nebula gas dissipated, consistent with the core accretion model for giant planet formation.

  5. 'Faceness' and affectivity: evidence for genetic contributions to distinct components of electrocortical response to human faces.

    Science.gov (United States)

    Shannon, Robert W; Patrick, Christopher J; Venables, Noah C; He, Sheng

    2013-12-01

    The ability to recognize a variety of different human faces is undoubtedly one of the most important and impressive functions of the human perceptual system. Neuroimaging studies have revealed multiple brain regions (including the FFA, STS, OFA) and electrophysiological studies have identified differing brain event-related potential (ERP) components (e.g., N170, P200) possibly related to distinct types of face information processing. To evaluate the heritability of ERP components associated with face processing, including N170, P200, and LPP, we examined ERP responses to fearful and neutral face stimuli in monozygotic (MZ) and dizygotic (DZ) twins. Concordance levels for early brain response indices of face processing (N170, P200) were found to be stronger for MZ than DZ twins, providing evidence of a heritable basis to each. These findings support the idea that certain key neural mechanisms for face processing are genetically coded. Implications for understanding individual differences in recognition of facial identity and the emotional content of faces are discussed. Copyright © 2013 Elsevier Inc. All rights reserved.

  6. Genetic diversity, identification, and certification of Chilean rice varieties using molecular markers

    Directory of Open Access Journals (Sweden)

    Viviana Becerra

    2015-09-01

    Full Text Available It takes approximately 14 yr to produce a new rice (Oryza sativa L. variety, that is, from initial hybridization to its commercial release. Currently, new varieties are identified based on morphological descriptors, which have been efficient over time. However, due to the main constraints on seed type impose to other breeding objectives and the pressure of continuous release of varieties, high degree of parentage, and genetic and morphological uniformity has been observed in the breeding populations. The objectives of this study were: to determine the genetic variability of Chilean and foreign commercial rice varieties, and determine, identify, and certify the genetic relationships among varieties, using simple sequence repeat (SSR markers. A total of 16 commercial varieties, some of them closely related, were included in the study, which were genétically analyzed using 54 microsatellites. The 54 microsatellite loci allowed the discrimination among the 16 varieties. The number of alleles ranged between 2 and 8 with a mean of 3.54 alleles per locus, while the polymorphism information content (PIC presented a mean of 0.44. The genetic distance and diversity parameters between pairs of varieties indicate a limited diversity among these genotypes. The cluster analysis indicated that varieties were grouped according to their grain type and pedigree. Results demonstrate that the identification and certification of varieties using microsatellite markers could be a good complement to existing agro-morphological data when varieties are closed related.

  7. The study of genetic diversity of Daemonorops draco (Palmae using ISSR markers

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    REVIS ASRA

    2014-10-01

    Full Text Available Asra R, Syamsuardi, Mansyurdin, Witono JR. 2014. The study of genetic diversity of Daemonorops draco (Palmae using ISSR markers. Biodiversitas 15: 109-114. The genetic diversity in five populations of Daemonorops draco(Willd. Blume (Jernang: in Bahasa Indonesia was analyzed using Inter Simple Sequence Repeat (ISSR markers. The screening results from using 15 ISSR primers showed that only 5 of ISSR primers had clear and reproducible bands. Based on the data from the matrix binary analyzed using POPGENE version 3.2, the highest genetic diversity was found in the Sepintun population at 0.0969 average heterozygosis (H and 0.146 average Shannon Index (I. The heterozygosis calculation of the total population (HT was 0.2571. The heterozygosis value within a population (HS=0.0704 was smaller than that between populations (DST=0.1867. Using the clustering analysis program Past version 32 on 43 individuals of D. draco, we found that there were three groups of D. draco. Group A consisted of 8 individuals in the Bengayoan population, group B consisted of 9 units in the Nunusan population and group C consisted of three populations; Tebo, Sepintun and Mandiangin consisted of 10, 8 and 8 individuals. The genetic similarity varied among all populations withthe values between 0.07-0.93.

  8. The impact of mating systems and dispersal on fine-scale genetic structure at maternally, paternally and biparentally inherited markers.

    Science.gov (United States)

    Shaw, Robyn E; Banks, Sam C; Peakall, Rod

    2018-01-01

    For decades, studies have focused on how dispersal and mating systems influence genetic structure across populations or social groups. However, we still lack a thorough understanding of how these processes and their interaction shape spatial genetic patterns over a finer scale (tens-hundreds of metres). Using uniparentally inherited markers may help answer these questions, yet their potential has not been fully explored. Here, we use individual-level simulations to investigate the effects of dispersal and mating system on fine-scale genetic structure at autosomal, mitochondrial and Y chromosome markers. Using genetic spatial autocorrelation analysis, we found that dispersal was the major driver of fine-scale genetic structure across maternally, paternally and biparentally inherited markers. However, when dispersal was restricted (mean distance = 100 m), variation in mating behaviour created strong differences in the comparative level of structure detected at maternally and paternally inherited markers. Promiscuity reduced spatial genetic structure at Y chromosome loci (relative to monogamy), whereas structure increased under polygyny. In contrast, mitochondrial and autosomal markers were robust to differences in the specific mating system, although genetic structure increased across all markers when reproductive success was skewed towards fewer individuals. Comparing males and females at Y chromosome vs. mitochondrial markers, respectively, revealed that some mating systems can generate similar patterns to those expected under sex-biased dispersal. This demonstrates the need for caution when inferring ecological and behavioural processes from genetic results. Comparing patterns between the sexes, across a range of marker types, may help us tease apart the processes shaping fine-scale genetic structure. © 2017 John Wiley & Sons Ltd.

  9. Conceptus development and transcriptome at preimplantation stages in lactating dairy cows of distinct genetic groups and estrous cyclic statuses.

    Science.gov (United States)

    Ribeiro, E S; Monteiro, A P A; Bisinotto, R S; Lima, F S; Greco, L F; Ealy, A D; Thatcher, W W; Santos, J E P

    2016-06-01

    The objectives were to compare development and transcriptome of preimplantation conceptuses 15 d after synchronized ovulation and artificial insemination (AI) according to the genetic background of the cow and estrous cyclicity at the initiation of the synchronization program. On d 39±3 postpartum, Holstein cows that were anovular (HA; n=10), Holstein cows that were estrous cyclic (HC; n=25), and Jersey/Holstein crossbred cows that were estrous cyclic (CC; n=25) were randomly selected in a grazing herd and subjected to the Ovsynch protocol. All cows were inseminated on d 49±3 postpartum, which was considered study d 0. Blood was sampled and analyzed for concentrations of progesterone, estradiol, insulin, and insulin-like growth factor 1 (IGF-1) on study d -10, -3, -1, 7, and 15 relative to AI. On study d 15, uteri were flushed and recovered fluid had IFN-τ concentrations measured and subjected to metabolomic analysis. Morphology of the recovered conceptuses was evaluated, and mRNA was extracted and subjected to transcriptome microarray analysis. Compared with HC, CC presented greater concentrations of progesterone and estradiol in plasma, with corpora lutea and preovulatory follicles of similar size. Conceptuses from CC were larger, tended to secrete greater amounts of IFN-τ, and had greater transcript expression of peroxisome proliferator-activated receptor gamma (PPARγ), an important transcription factor that coordinates lipid metabolism and elongation at preimplantation development. In addition, pregnant CC had greater concentrations of anandamide in the uterine flush, which might be important for elongation of the conceptus and early implantation. Conceptuses from HA were also longer and secreted greater amounts of IFN-τ than conceptuses from HC, likely because of the distinct progesterone profiles before and after AI. Nonetheless, anovular cows had reduced concentrations of IGF-1 in plasma, and their conceptuses presented remarkable transcriptomic

  10. MONITORING OF GENETIC DIVERSITY IN FARMED DEER POPULATIONS USING MICROSATELLITE MARKERS

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    Pavol Bajzík

    2011-12-01

    Full Text Available Deer (Cervidaei belong to the most important species used as farmed animals. We focused on assesing the genetic diversity among five deer populations. Analysis has been performed on a total of 183 animals originating from Czech Republic, Hungary, New Zealand, Poland and Slovak Republic. Genetic variability were investigated using 8 microsatellite markers used in deer. Statistical data of all populations we obtained on the basis of Nei statistics, using by POWERMARKER 3.23 programme. Graphical view of relationships among populations and individuals in the populations was obtained using the Dendroscope software. Molecular genetic data combinated with evaluation in statistical programmes could lead to a complex view of populations and diffrences among them.doi:10.5219/172

  11. The genetic profiles of two salmonid populations from Romania obtained through nuclear markers analysis

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    Ramona Nechifor

    2017-05-01

    Full Text Available The Salmonidae fish family is well represented in Romanian fauna, with a total of six species in the wild and reared in fish farms. Among them, the brown trout (Salmo trutta fario can be found in all major Romanian river basins. However, anthropogenic activities might disrupt salmonids’ habitats, so that inbreeding and genetic isolation might easily occur in the wild populations. We analyzed two wild brown trout populations from rivers targeted by anthropogenic activities, by using nuclear markers and genotyping in order to observe their genetic structure. We analyzed nine microsatellites and we observed their alleles frequencies, number of private alleles, observed and expected heterozygosity, as well as their population structure. The two populations are not in Hardy-Weinberg equilibrium for most of the loci and the inbreeding coefficient for both populations suggests a heterozygote deficit. Further sequencing data are needed in order to have a better view upon their complete genetic structure.

  12. Genetic diversity in some tunisian barley land races based on raped markers

    International Nuclear Information System (INIS)

    Abdellaos, R.; Kadir, K.; Naceur, M.B.; Kaab, L.B.B.

    2010-01-01

    The genetic diversity analysis of 15 barley land races was carried out using RAPD markers.These land races were collected from various bio climatic Tunisian zones. The amplification products varied from 4 to 11 bands ranging between 250 pb and 3000 pb. On 698 fragments counted, 578 are polymorphic showing a high level of polymorphism (82.8%). The relationship between the studied land races was evaluated according to (UPGMA) method that classified barley land races in 4 homogeneous groups. Among which, the group D included the majority of the land races with the introduced variety 'Martin'. The genetic distance between these land races is reduced, may be because of the presence of a common ancestor which led to a narrow genetic diversity. (author)

  13. Genetic diversity in some tunisian barley land races based on raped markers

    Energy Technology Data Exchange (ETDEWEB)

    Abdellaos, R; Kadir, K; Naceur, M B; Kaab, L B.B.,

    2010-12-15

    The genetic diversity analysis of 15 barley land races was carried out using RAPD markers.These land races were collected from various bio climatic Tunisian zones. The amplification products varied from 4 to 11 bands ranging between 250 pb and 3000 pb. On 698 fragments counted, 578 are polymorphic showing a high level of polymorphism (82.8%). The relationship between the studied land races was evaluated according to (UPGMA) method that classified barley land races in 4 homogeneous groups. Among which, the group D included the majority of the land races with the introduced variety 'Martin'. The genetic distance between these land races is reduced, may be because of the presence of a common ancestor which led to a narrow genetic diversity. (author)

  14. Microsatellite markers to determine population genetic structure in the golden anchovy, Coilia dussumieri.

    Science.gov (United States)

    Kathirvelpandian, A; Gopalakrishnan, A; Lakra, W S; Krishna, Gopal; Sharma, Rupam; Musammilu, K K; Basheer, V S; Jena, J K

    2014-06-01

    Coilia dussumieri (Valenciennes, 1848) commonly called as golden anchovy, constitutes a considerable fishery in the northern part of both the west and east coasts of India. Despite its clear-cut geographic isolation, the species is treated as a unit stock for fishery management purposes. We evaluated 32 microsatellite primer pairs from three closely related species (resource species) belonging to the family Engraulidae through cross-species amplification in C. dussumieri. Successful cross-priming was obtained with 10 loci, which were sequenced for confirmation of repeats. Loci were tested for delineating the genetic stock structure of four populations of C. dussumieri from both the coasts of India. The number of alleles per locus ranged from 8 to 18, with a mean of 12.3. Results of pairwise F ST indicated genetic stock structuring between the east and west coast populations of India and also validated the utilization of identified microsatellite markers in population genetic structure analysis.

  15. Genetic progress in multistage dairy cattle breeding schemes using genetic markers.

    Science.gov (United States)

    Schrooten, C; Bovenhuis, H; van Arendonk, J A M; Bijma, P

    2005-04-01

    The aim of this paper was to explore general characteristics of multistage breeding schemes and to evaluate multistage dairy cattle breeding schemes that use information on quantitative trait loci (QTL). Evaluation was either for additional genetic response or for reduction in number of progeny-tested bulls while maintaining the same response. The reduction in response in multistage breeding schemes relative to comparable single-stage breeding schemes (i.e., with the same overall selection intensity and the same amount of information in the final stage of selection) depended on the overall selection intensity, the selection intensity in the various stages of the breeding scheme, and the ratio of the accuracies of selection in the various stages of the breeding scheme. When overall selection intensity was constant, reduction in response increased with increasing selection intensity in the first stage. The decrease in response was highest in schemes with lower overall selection intensity. Reduction in response was limited in schemes with low to average emphasis on first-stage selection, especially if the accuracy of selection in the first stage was relatively high compared with the accuracy in the final stage. Closed nucleus breeding schemes in dairy cattle that use information on QTL were evaluated by deterministic simulation. In the base scheme, the selection index consisted of pedigree information and own performance (dams), or pedigree information and performance of 100 daughters (sires). In alternative breeding schemes, information on a QTL was accounted for by simulating an additional index trait. The fraction of the variance explained by the QTL determined the correlation between the additional index trait and the breeding goal trait. Response in progeny test schemes relative to a base breeding scheme without QTL information ranged from +4.5% (QTL explaining 5% of the additive genetic variance) to +21.2% (QTL explaining 50% of the additive genetic variance). A

  16. Glacial vicariance in the Pacific Northwest: evidence from a lodgepole pine mitochondrial DNA minisatellite for multiple genetically distinct and widely separated refugia.

    Science.gov (United States)

    Godbout, Julie; Fazekas, Aron; Newton, Craig H; Yeh, Francis C; Bousquet, Jean

    2008-05-01

    The Canadian side of the Pacific Northwest was almost entirely covered by ice during the last glacial maximum, which has induced vicariance and genetic population structure for several plant and animal taxa. Lodgepole pine (Pinus contorta Dougl. ex. Loud.) has a wide latitudinal and longitudinal distribution in the Pacific Northwest. Our main objective was to identify relictual signatures of glacial vicariance in the population structure of the species and search for evidence of distinct glacial refugia in the Pacific Northwest. A maternally inherited mitochondrial DNA minisatellite-like marker was used to decipher haplotype diversity in 91 populations of lodgepole pine located across the natural range. Overall population differentiation was sizeable (G(ST) = 0.365 and R(ST) = 0.568). Four relatively homogeneous groups of populations, possibly representative of as many genetically distinct glacial populations, were identified for the two main subspecies, ssp. latifolia and ssp. contorta. For ssp. contorta, one glacial lineage is suggested to have been located at high latitudes and possibly off the coast of mainland British Columbia (BC), while the other is considered to have been located south of the ice sheet along the Pacific coast. For ssp. latifolia, two genetically distinct glacial populations probably occurred south of the ice sheet: in the area bounded by the Cascades and Rocky Mountains ranges, and on the eastern side of the Rockies. A possible fifth refugium located in the Yukon may have also been present for ssp. latifolia. Zones of contact between these ancestral lineages were also apparent in interior and northern BC. These results indicate the role of the Queen Charlotte Islands and the Alexander Archipelago as a refugial zone for some Pacific Northwest species and the vicariant role played by the Cascades and the American Rocky Mountains during glaciation.

  17. Understanding the genetic diversity and population structure of yam (Dioscorea alata L.) using microsatellite markers

    Science.gov (United States)

    Arnau, Gemma; MN, Sheela; Chair, Hana; Lebot, Vincent; K, Abraham; Perrier, Xavier; Petro, Dalila; Penet, Laurent; Pavis, Claudie

    2017-01-01

    Yams (Dioscorea sp.) are staple food crops for millions of people in tropical and subtropical regions. Dioscorea alata, also known as greater yam, is one of the major cultivated species and most widely distributed throughout the tropics. Despite its economic and cultural importance, very little is known about its origin, diversity and genetics. As a consequence, breeding efforts for resistance to its main disease, anthracnose, have been fairly limited. The objective of this study was to contribute to the understanding of D. alata genetic diversity by genotyping 384 accessions from different geographical regions (South Pacific, Asia, Africa and the Caribbean), using 24 microsatellite markers. Diversity structuration was assessed via Principal Coordinate Analysis, UPGMA analysis and the Bayesian approach implemented in STRUCTURE. Our results revealed the existence of a wide genetic diversity and a significant structuring associated with geographic origin, ploidy levels and morpho-agronomic characteristics. Seventeen major groups of genetically close cultivars have been identified, including eleven groups of diploid cultivars, four groups of triploids and two groups of tetraploids. STRUCTURE revealed the existence of six populations in the diploid genetic pool and a few admixed cultivars. These results will be very useful for rationalizing D. alata genetic resources in breeding programs across different regions and for improving germplasm conservation methods. PMID:28355293

  18. Estimation of the genetic diversity in tetraploid alfalfa populations based on RAPD markers for breeding purposes.

    Science.gov (United States)

    Nagl, Nevena; Taski-Ajdukovic, Ksenija; Barac, Goran; Baburski, Aleksandar; Seccareccia, Ivana; Milic, Dragan; Katic, Slobodan

    2011-01-01

    Alfalfa is an autotetraploid, allogamous and heterozygous forage legume, whose varieties are synthetic populations. Due to the complex nature of the species, information about genetic diversity of germplasm used in any alfalfa breeding program is most beneficial. The genetic diversity of five alfalfa varieties, involved in progeny tests at Institute of Field and Vegetable Crops, was characterized based on RAPD markers. A total of 60 primers were screened, out of which 17 were selected for the analysis of genetic diversity. A total of 156 polymorphic bands were generated, with 10.6 bands per primer. Number and percentage of polymorphic loci, effective number of alleles, expected heterozygosity and Shannon's information index were used to estimate genetic variation. Variety Zuzana had the highest values for all tested parameters, exhibiting the highest level of variation, whereas variety RSI 20 exhibited the lowest. Analysis of molecular variance (AMOVA) showed that 88.39% of the total genetic variation was attributed to intra-varietal variance. The cluster analysis for individual samples and varieties revealed differences in their population structures: variety Zuzana showed a very high level of genetic variation, Banat and Ghareh were divided in subpopulations, while Pecy and RSI 20 were relatively uniform. Ways of exploiting the investigated germplasm in the breeding programs are suggested in this paper, depending on their population structure and diversity. The RAPD analysis shows potential to be applied in analysis of parental populations in semi-hybrid alfalfa breeding program in both, development of new homogenous germplasm, and identification of promising, complementary germplasm.

  19. Assessment of genetic diversity in lettuce (Lactuca sativa L.) germplasm using RAPD markers.

    Science.gov (United States)

    Sharma, Shubhangi; Kumar, Pankaj; Gambhir, Geetika; Kumar, Ramesh; Srivastava, D K

    2018-01-01

    The importance of germplasm characterization is an important link between the conservation and utilization of plant genetic resources in various breeding programmes. In the present study, genetic variability and relationships among 25 Lactuca sativa L. genotypes were tested using random amplified polymorphic DNA (RAPD) molecular markers. A total of 45 random decamer oligonucleotide primers were examined to generate RAPD profiles, out of these reproducible patterns were obtained with 22 primers. A total of 87 amplicon were obtained, out of which all were polymorphic and 7 were unique bands. The level of polymorphism across genotypes was 100% as revealed by RAPD. Genetic similarity matrix, based on Jaccard's coefficients ranged from 13.7 to 84.10% indicating a wide genetic base. Dendrogram was constructed by unweighted pair group method with arithmetic averages method. RAPD technology could be useful for identification of different accessions as well as assessing the genetic similarity among different genotypes of lettuce. The study reveals the limited genetic base and the needs to diversify using new sources from the germplasm.

  20. Microsatellite marker-based genetic analysis of relatedness between commercial and heritage turkeys (Meleagris gallopavo).

    Science.gov (United States)

    Kamara, D; Gyenai, K B; Geng, T; Hammade, H; Smith, E J

    2007-01-01

    The turkey is second only to the chicken in importance as an agriculturally important poultry species. Unlike the chicken, however, genetic studies of the turkey continue to be limited. For example, to date, many genomic investigations have been conducted to characterize genetic relationships between commercial (CO) and non-CO chicken breeds, whereas the nature of the genetic relatedness between CO and heritage turkeys remains unknown. The objective of the current research was to use microsatellites to analyze the genetic relatedness between CO and heritage domestic turkeys including Narragansett, Bourbon Red, Blue Slate, Spanish Black, and Royal Palm. Primer pairs specific for 10 previously described turkey microsatellite markers were used. The phylogenetic analysis showed that the Blue Slate, Bourbon Red, and Narragansett were genetically closely related to the CO strain, with a Nei distance of 0.30, and the Royal Palm and Spanish Black were the least related to the CO strain, with Nei distances of 0.41 and 0.40, respectively. The present work provides a foundation for the basis of using heritage turkeys to genetically improve CO populations by introgression.

  1. An efficient method to find potentially universal population genetic markers, applied to metazoans

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    Chenuil Anne

    2010-09-01

    Full Text Available Abstract Background Despite the impressive growth of sequence databases, the limited availability of nuclear markers that are sufficiently polymorphic for population genetics and phylogeography and applicable across various phyla restricts many potential studies, particularly in non-model organisms. Numerous introns have invariant positions among kingdoms, providing a potential source for such markers. Unfortunately, most of the few known EPIC (Exon Primed Intron Crossing loci are restricted to vertebrates or belong to multigenic families. Results In order to develop markers with broad applicability, we designed a bioinformatic approach aimed at avoiding multigenic families while identifying intron positions conserved across metazoan phyla. We developed a program facilitating the identification of EPIC loci which allowed slight variation in intron position. From the Homolens databases we selected 29 gene families which contained 52 promising introns for which we designed 93 primer pairs. PCR tests were performed on several ascidians, echinoderms, bivalves and cnidarians. On average, 24 different introns per genus were amplified in bilaterians. Remarkably, five of the introns successfully amplified in all of the metazoan genera tested (a dozen genera, including cnidarians. The influence of several factors on amplification success was investigated. Success rate was not related to the phylogenetic relatedness of a taxon to the groups that most influenced primer design, showing that these EPIC markers are extremely conserved in animals. Conclusions Our new method now makes it possible to (i rapidly isolate a set of EPIC markers for any phylum, even outside the animal kingdom, and thus, (ii compare genetic diversity at potentially homologous polymorphic loci between divergent taxa.

  2. Determination of genetic structure of germplasm collections: are traditional hierarchical clustering methods appropriate for molecular marker data?

    NARCIS (Netherlands)

    Odong, T.L.; Heerwaarden, van J.; Jansen, J.; Hintum, van T.J.L.; Eeuwijk, van F.A.

    2011-01-01

    Despite the availability of newer approaches, traditional hierarchical clustering remains very popular in genetic diversity studies in plants. However, little is known about its suitability for molecular marker data. We studied the performance of traditional hierarchical clustering techniques using

  3. Biogeographical Variation and Population Genetic Structure of Sporisorium scitamineum in Mainland China: Insights from ISSR and SP-SRAP Markers

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    Liping Xu

    2014-01-01

    Full Text Available A total of 100 Sporisorium scitamineum isolates were investigated by inter simple sequence repeat (ISSR and single primer-sequence related amplified polymorphism (SP-SRAP markers. These isolates were clearly assorted into three distinct clusters regardless of method used: either cluster analysis or by principal component analysis (PCA of the ISSR, SP-SRAP, or ISSR + SP-SRAP data set. The total gene diversity (Ht and gene diversity between subpopulations (Hs were estimated to be 0.34 to 0.38 and 0.22 to 0.29, respectively, by analyzing separately the ISSR and SP-SRAP data sets, and to be 0.26–0.36 by analyzing ISSR + SP-SRAP data set. The gene diversity attributable to differentiation among populations (Gst was estimated to be 0.35 and 0.22, and the gene flow (Nm was 0.94 and 1.78, respectively, when analyzing separately ISSR and SP-SRAP data set, and was 0.27 and 1.33, respectively, when analyzing ISSR + SP-SRAP data set. Our study showed that there is considerable genetic variation in the analyzed 100 isolates, and the environmental heterogeneity has played an important role for this observed high degree of variation. The genetic differentiation of sugarcane smut fungus depends to a large extent on the heterogeneity of their habitats and is the result of long-term adaptations of pathogens to their ecological environments.

  4. Developing Exon-Primed Intron-Crossing (EPIC) markers for population genetic studies in three Aedes disease vectors.

    Science.gov (United States)

    White, Vanessa Linley; Endersby, Nancy Margaret; Chan, Janice; Hoffmann, Ary Anthony; Weeks, Andrew Raymond

    2015-03-01

    Aedes aegypti, Aedes notoscriptus, and Aedes albopictus are important vectors of many arboviruses implicated in human disease such as dengue fever. Genetic markers applied across vector species can provide important information on population structure, gene flow, insecticide resistance, and taxonomy, however, robust microsatellite markers have proven difficult to develop in these species and mosquitoes generally. Here we consider the utility and transferability of 15 Ribosome protein (Rp) Exon-Primed Intron-Crossing (EPIC) markers for population genetic studies in these 3 Aedes species. Rp EPIC markers designed for Ae. aegypti also successfully amplified populations of the sister species, Ae. albopictus, as well as the distantly related species, Ae. notoscriptus. High SNP and good indel diversity in sequenced alleles plus support for amplification of the same regions across populations and species were additional benefits of these markers. These findings point to the general value of EPIC markers in mosquito population studies. © 2014 Institute of Zoology, Chinese Academy of Sciences.

  5. Genome Target Evaluator (GTEvaluator: A workflow exploiting genome dataset to measure the sensitivity and specificity of genetic markers.

    Directory of Open Access Journals (Sweden)

    Arnaud Felten

    Full Text Available Most of the bacterial typing methods used to discriminate isolates in medical or food safety microbiology are based on genetic markers used as targets in PCR or hybridization experiments. These DNA typing methods are important tools for studying prevalence and epidemiology, for conducting surveillance, investigations and control of biological hazard sources. In that perspective, it is crucial to insure that the chosen genetic markers have the greatest specificity and sensitivity. The wealth of whole-genome sequences available for many bacterial species offers the opportunity to evaluate the performance of these genetic markers. In the present study, we have developed GTEvaluator, a bioinformatics workflow which ranks genetic markers depending on their sensitivity and specificity towards groups of well-defined genomes. GTEvaluator identifies the most performant genetic markers to target individuals among a population. The individuals (i.e. a group of genomes within a collection are defined by any kind of particular phenotypic or biological properties inside a related population (i.e. collection of genomes. The performance of the genetic markers is computed by a distance value which takes into account both sensitivity and specificity. In this study we report two examples of GTEvaluator application. In the first example Bacillus phenotypic markers were evaluated for their capacity to distinguish B. cereus from B. thuringiensis. In the second experiment, GTEvaluator measured the performance of genetic markers dedicated to the molecular serotyping of Salmonella enterica. In one in silico experiment it was possible to test 64 markers onto 134 genomes corresponding to 14 different serotypes.

  6. Molecular markers for analyses of intraspecific genetic diversity in the Asian Tiger mosquito, Aedes albopictus.

    Science.gov (United States)

    Manni, Mosè; Gomulski, Ludvik M; Aketarawong, Nidchaya; Tait, Gabriella; Scolari, Francesca; Somboon, Pradya; Guglielmino, Carmela R; Malacrida, Anna R; Gasperi, Giuliano

    2015-03-28

    The dramatic worldwide expansion of Aedes albopictus (the Asian tiger mosquito) and its vector competence for numerous arboviruses represent a growing threat to public health security. Molecular markers are crucially needed for tracking the rapid spread of this mosquito and to obtain a deeper knowledge of population structure. This is a fundamental requirement for the development of strict monitoring protocols and for the improvement of sustainable control measures. Wild population samples from putative source areas and from newly colonised regions were analysed for variability at the ribosomal DNA internal transcribed spacer 2 (ITS2). Moreover, a new set of 23 microsatellite markers (SSR) was developed. Sixteen of these SSRs were tested in an ancestral (Thailand) and two adventive Italian populations. Seventy-six ITS2 sequences representing 52 unique haplotypes were identified, and AMOVA indicated that most of their variation occurred within individuals (74.36%), while only about 8% was detected among populations. Spatial analyses of molecular variance revealed that haplotype genetic similarity was not related to the geographic proximity of populations and the haplotype phylogeny clearly indicated that highly related sequences were distributed across populations from different geographical regions. The SSR markers displayed a high level of polymorphism both in the ancestral and in adventive populations, and F ST estimates suggested the absence of great differentiation. The ancestral nature of the Thai population was corroborated by its higher level of variability. The two types of genetic markers here implemented revealed the distribution of genetic diversity within and between populations and provide clues on the dispersion dynamics of this species. It appears that the diffusion of this mosquito does not conform to a progressive expansion from the native Asian source area, but to a relatively recent and chaotic propagule distribution mediated by human activities

  7. Development of Genetic Markers in Eucalyptus Species by Target Enrichment and Exome Sequencing

    Science.gov (United States)

    Dasgupta, Modhumita Ghosh; Dharanishanthi, Veeramuthu; Agarwal, Ishangi; Krutovsky, Konstantin V.

    2015-01-01

    The advent of next-generation sequencing has facilitated large-scale discovery, validation and assessment of genetic markers for high density genotyping. The present study was undertaken to identify markers in genes supposedly related to wood property traits in three Eucalyptus species. Ninety four genes involved in xylogenesis were selected for hybridization probe based nuclear genomic DNA target enrichment and exome sequencing. Genomic DNA was isolated from the leaf tissues and used for on-array probe hybridization followed by Illumina sequencing. The raw sequence reads were trimmed and high-quality reads were mapped to the E. grandis reference sequence and the presence of single nucleotide variants (SNVs) and insertions/ deletions (InDels) were identified across the three species. The average read coverage was 216X and a total of 2294 SNVs and 479 InDels were discovered in E. camaldulensis, 2383 SNVs and 518 InDels in E. tereticornis, and 1228 SNVs and 409 InDels in E. grandis. Additionally, SNV calling and InDel detection were conducted in pair-wise comparisons of E. tereticornis vs. E. grandis, E. camaldulensis vs. E. tereticornis and E. camaldulensis vs. E. grandis. This study presents an efficient and high throughput method on development of genetic markers for family– based QTL and association analysis in Eucalyptus. PMID:25602379

  8. Genetic divergence in Tetragonisca angustula Latreille, 1811 (Hymenoptera, Meliponinae, Trigonini based on rapd markers

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    Rosana de Cássia Oliveira

    2004-01-01

    Full Text Available One of the commonest neotropical stingless bees is Tetragonisca angustula (Latreille, 1811, popularly known in Portuguese as jataí, which occurs in variable nesting sites from Mexico to Argentina. We used 18 primers to generate 218 RAPD markers which we used to determined the genetic distance between T. angustula populations from 25 localities in three different Latin America countries, using Tetragonisca weyrauchi from the Brazilian state of Acre and the common honey bee (Apis mellifera as outgroups. Genetic distance, calculated as the Percentage of Dissimilarity (14%, based on all markers divided the T. angustula population into eastern (group 1 and western (group 2 groups. However, we were able to separate the two groups by using only two primers that have generated five specific molecular markers. The eastern group consists of T. angustula angustula which occurs from Panama to the Brazilian states of Maranhão and northern Minas Gerais and has spread through the Brazilian Atlantic Forest as far as the southern Brazilian state of Santa Catarina. Group 2 is made up of T. angustula fiebrigi which has a more southerly and western distribution, occurring only in the western Brazilian states of Mato Grosso and Mato Grosso do Sul as well as the west of some other Brazilian states (Goiás, Minas Gerais, São Paulo, Paraná and Santa Catarina and northeastern Argentina.

  9. Development of genetic markers in Eucalyptus species by target enrichment and exome sequencing.

    Directory of Open Access Journals (Sweden)

    Modhumita Ghosh Dasgupta

    Full Text Available The advent of next-generation sequencing has facilitated large-scale discovery, validation and assessment of genetic markers for high density genotyping. The present study was undertaken to identify markers in genes supposedly related to wood property traits in three Eucalyptus species. Ninety four genes involved in xylogenesis were selected for hybridization probe based nuclear genomic DNA target enrichment and exome sequencing. Genomic DNA was isolated from the leaf tissues and used for on-array probe hybridization followed by Illumina sequencing. The raw sequence reads were trimmed and high-quality reads were mapped to the E. grandis reference sequence and the presence of single nucleotide variants (SNVs and insertions/ deletions (InDels were identified across the three species. The average read coverage was 216X and a total of 2294 SNVs and 479 InDels were discovered in E. camaldulensis, 2383 SNVs and 518 InDels in E. tereticornis, and 1228 SNVs and 409 InDels in E. grandis. Additionally, SNV calling and InDel detection were conducted in pair-wise comparisons of E. tereticornis vs. E. grandis, E. camaldulensis vs. E. tereticornis and E. camaldulensis vs. E. grandis. This study presents an efficient and high throughput method on development of genetic markers for family- based QTL and association analysis in Eucalyptus.

  10. Dispersal capacity and genetic structure of Arapaima gigas on different geographic scales using microsatellite markers.

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    Juliana Araripe

    Full Text Available Despite the ecological and economic importance of the Arapaima gigas (Cuvier 1817, few data about its dispersal capacity are available. The present study was based on the analysis of microsatellite markers in order to estimate the dispersal capacity of the species on fine, meso, and large geographic scales. For this, 561 specimens obtained from stocks separated by distances of up to 25 km (fine scale, 100 km (meso scale, and 1300-2300 km (large scale were analyzed. The fine scale analysis indicated a marked genetic similarity between lakes, with low genetic differentiation, and significant differences between only a few pairs of sites. Low to moderate genetic differentiation was observed between pairs of sites on a meso scale (100 km, which could be explained by the distances between sites. By contrast, major genetic differentiation was recorded in the large scale analysis, that is, between stocks separated by distances of over 1300 km, with the analysis indicating that differentiation was not related solely to distance. The genetic structuring analysis indicated the presence of two stocks, one represented by the arapaimas of the Mamirauá Reserve, and the other by those of Santarém and Tucuruí. The dispersal of arapaimas over short distances indicates a process of lateral migration within the várzea floodplains, which may be the principal factor determining the considerable homogeneity observed among the várzea lakes. The populations separated by distances of approximately 100 km were characterized by reduced genetic differentiation, which was associated with the geographic distances between sites. Populations separated by distances of over 1300 km were characterized by a high degree of genetic differentiation, which may be related primarily to historical bottlenecks in population size and the sedentary behavior of the species. Evidence was found of asymmetric gene flow, resulting in increasing genetic variability in the population of the

  11. Dispersal capacity and genetic structure of Arapaima gigas on different geographic scales using microsatellite markers.

    Science.gov (United States)

    Araripe, Juliana; do Rêgo, Péricles Sena; Queiroz, Helder; Sampaio, Iracilda; Schneider, Horacio

    2013-01-01

    Despite the ecological and economic importance of the Arapaima gigas (Cuvier 1817), few data about its dispersal capacity are available. The present study was based on the analysis of microsatellite markers in order to estimate the dispersal capacity of the species on fine, meso, and large geographic scales. For this, 561 specimens obtained from stocks separated by distances of up to 25 km (fine scale), 100 km (meso scale), and 1300-2300 km (large scale) were analyzed. The fine scale analysis indicated a marked genetic similarity between lakes, with low genetic differentiation, and significant differences between only a few pairs of sites. Low to moderate genetic differentiation was observed between pairs of sites on a meso scale (100 km), which could be explained by the distances between sites. By contrast, major genetic differentiation was recorded in the large scale analysis, that is, between stocks separated by distances of over 1300 km, with the analysis indicating that differentiation was not related solely to distance. The genetic structuring analysis indicated the presence of two stocks, one represented by the arapaimas of the Mamirauá Reserve, and the other by those of Santarém and Tucuruí. The dispersal of arapaimas over short distances indicates a process of lateral migration within the várzea floodplains, which may be the principal factor determining the considerable homogeneity observed among the várzea lakes. The populations separated by distances of approximately 100 km were characterized by reduced genetic differentiation, which was associated with the geographic distances between sites. Populations separated by distances of over 1300 km were characterized by a high degree of genetic differentiation, which may be related primarily to historical bottlenecks in population size and the sedentary behavior of the species. Evidence was found of asymmetric gene flow, resulting in increasing genetic variability in the population of the Mamirau

  12. Genetic variation of rs438601 marker in the Iranian Population: An informative marker for molecular diagnosis of hemophilia B

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    P Dorri

    2014-12-01

    Conclusion: The study findings demonstrated that rs438601 marker due to high heterozygosity could be suggested as an appropriate diagnostic marker in linkage analysis and carrier detection of hemophilia B in regard with a sample of Iranian population.

  13. Ovarian carcinomas with genetic and epigenetic BRCA1 loss have distinct molecular abnormalities

    International Nuclear Information System (INIS)

    Press, Joshua Z; Smith, Margaret; Spellman, Paul T; Wang, Yuker; Miller, Dianne M; Horsman, Doug; Faham, Malek; Gilks, C Blake; Gray, Joe; Huntsman, David G; De Luca, Alessandro; Boyd, Niki; Young, Sean; Troussard, Armelle; Ridge, Yolanda; Kaurah, Pardeep; Kalloger, Steve E; Blood, Katherine A

    2008-01-01

    Subclassification of ovarian carcinomas can be used to guide treatment and determine prognosis. Germline and somatic mutations, loss of heterozygosity (LOH), and epigenetic events such as promoter hypermethylation can lead to decreased expression of BRCA1/2 in ovarian cancers. The mechanism of BRCA1/2 loss is a potential method of subclassifying high grade serous carcinomas. A consecutive series of 49 ovarian cancers was assessed for mutations status of BRCA1 and BRCA2, LOH at the BRCA1 and BRCA2 loci, methylation of the BRCA1 promoter, BRCA1, BRCA2, PTEN, and PIK3CA transcript levels, PIK3CA gene copy number, and BRCA1, p21, p53, and WT-1 immunohistochemistry. Eighteen (37%) of the ovarian carcinomas had germline or somatic BRCA1 mutations, or epigenetic loss of BRCA1. All of these tumours were high-grade serous or undifferentiated type. None of the endometrioid (n = 5), clear cell (n = 4), or low grade serous (n = 2) carcinomas showed loss of BRCA1, whereas 47% of the 38 high-grade serous or undifferentiated carcinomas had loss of BRCA1. It was possible to distinguish high grade serous carcinomas with BRCA1 mutations from those with epigenetic BRCA1 loss: tumours with BRCA1 mutations typically had decreased PTEN mRNA levels while those with epigenetic loss of BRCA1 had copy number gain of PIK3CA. Overexpression of p53 with loss of p21 expression occurred significantly more frequently in high grade serous carcinomas with epigenetic loss of BRCA1, compared to high grade serous tumors without loss of BRCA1. High grade serous carcinomas can be subclassified into three groups: BRCA1 loss (genetic), BRCA1 loss (epigenetic), and no BRCA1 loss. Tumors in these groups show distinct molecular alterations involving the PI3K/AKT and p53 pathways

  14. Ovarian carcinomas with genetic and epigenetic BRCA1 loss have distinct molecular abnormalities

    Energy Technology Data Exchange (ETDEWEB)

    Gilks, C. Blake; Press, Joshua Z.; De Luca, Alessandro; Boyd, Niki; Young, Sean; Troussard, Armelle; Ridge, Yolanda; Kaurah, Pardeep; Kalloger, Steve E.; Blood, Katherine A.; Smith, Margaret; Spellman, Paul T.; Wang, Yuker; Miller, Dianne M.; Horsman, Doug; Faham, Malek; Gilks, C. Blake; Gray, Joe; Huntsman, David G.

    2008-05-02

    Subclassification of ovarian carcinomas can be used to guide treatment and determine prognosis. Germline and somatic mutations, loss of heterozygosity (LOH), and epigenetic events such as promoter hypermethylation can lead to decreased expression of BRCA1/2 in ovarian cancers. The mechanism of BRCA1/2 loss is a potential method of subclassifying high grade serous carcinomas. A consecutive series of 49 ovarian cancers was assessed for mutations status of BRCA1 and BRCA2, LOH at the BRCA1 and BRCA2 loci, methylation of the BRCA1 promoter, BRCA1, BRCA2, PTEN, and PIK3CA transcript levels, PIK3CA gene copy number, and BRCA1, p21, p53, and WT-1 immunohistochemistry. Eighteen (37%) of the ovarian carcinomas had germline or somatic BRCA1 mutations, or epigenetic loss of BRCA1. All of these tumors were high-grade serous or undifferentiated type. None of the endometrioid (n=5), clear cell (n=4), or low grade serous (n=2) carcinomas showed loss of BRCA1, whereas 47% of the 38 high-grade serous or undifferentiated carcinomas had loss of BRCA1. It was possible to distinguish high grade serous carcinomas with BRCA1 mutations from those with epigenetic BRCA1 loss: tumors with BRCA1 mutations typically had decreased PTEN mRNA levels while those with epigenetic loss of BRCA1 had copy number gain of PIK3CA. Overexpression of p53 with loss of p21 expression occurred significantly more frequently in high grade serous carcinomas with epigenetic loss of BRCA1, compared to high grade serous tumors without loss of BRCA1. High grade serous carcinomas can be subclassified into three groups: BRCA1 loss (genetic), BRCA1 loss (epigenetic), and no BRCA1 loss. Tumors in these groups show distinct molecular alterations involving the PI3K/AKT and p53 pathways.

  15. Assessment of genome origins and genetic diversity in the genus Eleusine with DNA markers.

    Science.gov (United States)

    Salimath, S S; de Oliveira, A C; Godwin, I D; Bennetzen, J L

    1995-08-01

    Finger millet (Eleusine coracana), an allotetraploid cereal, is widely cultivated in the arid and semiarid regions of the world. Three DNA marker techniques, restriction fragment length polymorphism (RFLP), randomly amplified polymorphic DNA (RAPD), and inter simple sequence repeat amplification (ISSR), were employed to analyze 22 accessions belonging to 5 species of Eleusine. An 8 probe--3 enzyme RFLP combination, 18 RAPD primers, and 6 ISSR primers, respectively, revealed 14, 10, and 26% polymorphism in 17 accessions of E. coracana from Africa and Asia. These results indicated a very low level of DNA sequence variability in the finger millets but did allow each line to be distinguished. The different Eleusine species could be easily identified by DNA marker technology and the 16% intraspecific polymorphism exhibited by the two analyzed accessions of E. floccifolia suggested a much higher level of diversity in this species than in E. coracana. Between species, E. coracana and E. indica shared the most markers, while E. indica and E. tristachya shared a considerable number of markers, indicating that these three species form a close genetic assemblage within the Eleusine. Eleusine floccifolia and E. compressa were found to be the most divergent among the species examined. Comparison of RFLP, RAPD, and ISSR technologies, in terms of the quantity and quality of data output, indicated that ISSRs are particularly promising for the analysis of plant genome diversity.

  16. Prediction of genetic values of quantitative traits in plant breeding using pedigree and molecular markers.

    Science.gov (United States)

    Crossa, José; Campos, Gustavo de Los; Pérez, Paulino; Gianola, Daniel; Burgueño, Juan; Araus, José Luis; Makumbi, Dan; Singh, Ravi P; Dreisigacker, Susanne; Yan, Jianbing; Arief, Vivi; Banziger, Marianne; Braun, Hans-Joachim

    2010-10-01

    The availability of dense molecular markers has made possible the use of genomic selection (GS) for plant breeding. However, the evaluation of models for GS in real plant populations is very limited. This article evaluates the performance of parametric and semiparametric models for GS using wheat (Triticum aestivum L.) and maize (Zea mays) data in which different traits were measured in several environmental conditions. The findings, based on extensive cross-validations, indicate that models including marker information had higher predictive ability than pedigree-based models. In the wheat data set, and relative to a pedigree model, gains in predictive ability due to inclusion of markers ranged from 7.7 to 35.7%. Correlation between observed and predictive values in the maize data set achieved values up to 0.79. Estimates of marker effects were different across environmental conditions, indicating that genotype × environment interaction is an important component of genetic variability. These results indicate that GS in plant breeding can be an effective strategy for selecting among lines whose phenotypes have yet to be observed.

  17. Assessment of genetic diversity and phylogenetic relationships of Korean native chicken breeds using microsatellite markers

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    Joo Hee Seo

    2017-10-01

    Full Text Available Objective This study was conducted to investigate the basic information on genetic structure and characteristics of Korean Native chickens (NC and foreign breeds through the analysis of the pure chicken populations and commercial chicken lines of the Hanhyup Company which are popular in the NC market, using the 20 microsatellite markers. Methods In this study, the genetic diversity and phylogenetic relationships of 445 NC from five different breeds (NC, Leghorn [LH], Cornish [CS], Rhode Island Red [RIR], and Hanhyup [HH] commercial line were investigated by performing genotyping using 20 microsatellite markers. Results The highest genetic distance was observed between RIR and LH (18.9%, whereas the lowest genetic distance was observed between HH and NC (2.7%. In the principal coordinates analysis (PCoA illustrated by the first component, LH was clearly separated from the other groups. The correspondence analysis showed close relationship among individuals belonging to the NC, CS, and HH lines. From the STRUCTURE program, the presence of 5 clusters was detected and it was found that the proportion of membership in the different clusters was almost comparable among the breeds with the exception of one breed (HH, although it was highest in LH (0.987 and lowest in CS (0.578. For the cluster 1 it was high in HH (0.582 and in CS (0.368, while for the cluster 4 it was relatively higher in HH (0.392 than other breeds. Conclusion Our study showed useful genetic diversity and phylogenetic relationship data that can be utilized for NC breeding and development by the commercial chicken industry to meet consumer demands.

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

    Directory of Open Access Journals (Sweden)

    YUYU SURYASARI POERBA

    2010-07-01

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

  19. RAPD markers on genetic diversity in three populations of pisifera type of oil palm (elaeis guineensis)

    Science.gov (United States)

    Basyuni, M.; Prayogi, H.; Putri, L. A. P.; Syahputra, I.; Siregar, E. S.; Risnasari, I.; Wati, R.; Arifiyanto, D.

    2018-03-01

    Palm oil (E. guineensis) is one of the major commodity and contributing largely to non-petroleum oil of Indonesian foreign exchange. E. guineensis has three fruit types, dura (female), pisifera (male), and tenera —a hybrid between dura and pisifera. Pisifera plays an important function in the production of seed oil palm. The purpose of this research is to analyze genetic diversity of pisifera type of E. guineensis from three populations, Yangambi, Lame and Lame further cross in Bangun Bandar, North Sumatra, Indonesia. Eighteen samples for each population were analyzed using six RAPD markers. Results showed that RAPD markers were low polymorphic with 1.49, 1.39, and 1.00 average number alleles detected for Yagambi, Lame, and Lame further cross, respectively. The level of genetic diversity detected for each population was 0.28, 0.22, and 0.21 for Yagambi, Lame, and Lame further cross, respectively, indicating that the populations had little genetic variation. The highest of polymorphic information content (PIC) was found on the P11 primer of Yangambi (0.49) and P10 primer for lame further cross (0.49). By contrast, the lowest PIC belongs to P21 for Lame population (0.01). This data is likely to contributing oil palm breeding.

  20. Assessment of genetic diversity of Bermudagrass (Cynodon dactylon) using ISSR markers.

    Science.gov (United States)

    Farsani, Tayebeh Mohammadi; Etemadi, Nematollah; Sayed-Tabatabaei, Badraldin Ebrahim; Talebi, Majid

    2012-01-01

    Bermudagrass (Cynodon spp.) is a major turfgrass for home lawns, public parks, golf courses and sport fields and is known to have originated in the Middle East. Morphological and physiological characteristics are not sufficient to differentiate some bermudagrass genotypes because the differences between them are often subtle and subjected to environmental influences. In this study, twenty seven bermudagrass accessions and introductions, mostly from different parts of Iran, were assayed by inter-simple sequence repeat (ISSR) markers to differentiate and explore their genetic relationships. Fourteen ISSR primers amplified 389 fragments of which 313 (80.5%) were polymorphic. The average polymorphism information content (PIC) was 0.328, which shows that the majority of primers are informative. Cluster analysis using the un-weighted paired group method with arithmetic average (UPGMA) method and Jaccard's similarity coefficient (r = 0.828) grouped the accessions into six main clusters according to some degree to geographical origin, their chromosome number and some morphological characteristics. It can be concluded that there exists a wide genetic base of bermudograss in Iran and that ISSR markers are effective in determining genetic diversity and relationships among them.

  1. Three Molecular Markers Show No Evidence of Population Genetic Structure in the Gouldian Finch (Erythrura gouldiae.

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    Peri E Bolton

    Full Text Available Assessment of genetic diversity and connectivity between regions can inform conservation managers about risk of inbreeding, potential for adaptation and where population boundaries lie. The Gouldian finch (Erythrura gouldiae is a threatened species in northern Australia, occupying the savannah woodlands of the biogeographically complex monsoon tropics. We present the most comprehensive population genetic analysis of diversity and structure the Gouldian finch using 16 microsatellite markers, mitochondrial control region and 3,389 SNPs from genotyping-by-sequencing. Mitochondrial diversity is compared across three related, co-distributed finches with different conservation threat-statuses. There was no evidence of genetic differentiation across the western part of the range in any of the molecular markers, and haplotype diversity but not richness was lower than a common co-distributed species. Individuals within the panmictic population in the west may be highly dispersive within this wide area, and we urge caution when interpreting anecdotal observations of changes to the distribution and/or flock sizes of Gouldian finch populations as evidence of overall changes to the population size of this species.

  2. Genetic Diversity of Hibiscus tiliaceus (Malvaceae) in China Assessed using AFLP Markers

    Science.gov (United States)

    TANG, TIAN; ZHONG, YANG; JIAN, SHUGUANG; SHI, SUHUA

    2003-01-01

    Amplified fragment length polymorphism (AFLP) markers were used to investigate the genetic variations within and among nine natural populations of Hibiscus tiliaceus in China. DNA from 145 individuals was amplified with eight primer pairs. No polymorphisms were found among the 20 samples of a marginal population of recent origin probably due to a founder effect. Across the other 125 individuals, 501 of 566 bands (88·5 %) were polymorphic, and 125 unique AFLP phenotypes were observed. Estimates of genetic diversity agreed with life history traits of H. tiliaceus and geographical distribution. AMOVA analysis revealed that most genetic diversity resided within populations (84·8 %), which corresponded to results reported for outcrossing plants. The indirect estimate of gene flow based on ϕST was moderate (Nm = 1·395). Long-distance dispersal of floating seeds and local environments may play an important role in shaping the genetic diversity of the population and the genetic structure of this species. PMID:12930729

  3. Estimation of genetic structure of a Mycosphaerella musicola population using inter-simple sequence repeat markers.

    Science.gov (United States)

    Peixouto, Y S; Dórea Bragança, C A; Andrade, W B; Ferreira, C F; Haddad, F; Oliveira, S A S; Darosci Brito, F S; Miller, R N G; Amorim, E P

    2015-07-17

    Among the diseases affecting banana (Musa sp), yellow Sigatoka, caused by the fungal pathogen Mycosphaerella musicola Leach, is considered one of the most important in Brazil, causing losses throughout the year. Understanding the genetic structure of pathogen populations will provide insight into the life history of pathogens, including the evolutionary processes occurring in agrosystems. Tools for estimating the possible emergence of pathogen variants with altered pathogenicity, virulence, or aggressiveness, as well as resistance to systemic fungicides, can also be developed from such data. The objective of this study was to analyze the genetic diversity and population genetics of M. musicola in the main banana-producing regions in Brazil. A total of 83 isolates collected from different banana cultivars in the Brazilian states of Bahia, Rio Grande do Norte, and Minas Gerais were evaluated using inter-simple sequence repeat markers. High variability was detected between the isolates, and 85.5% of the haplotypes were singletons in the populations. The highest source of genetic diversity (97.22%) was attributed to variations within populations. Bayesian cluster analysis revealed the presence of 2 probable ancestral groups, however, showed no relationship to population structure in terms of collection site, state of origin, or cultivar. Similarly, we detected noevidence of genetic recombination between individuals within different states, indicating that asexual cycles play a major role in M. musicola reproduction and that long-distance dispersal of the pathogen is the main factor contributing to the lack of population structure in the fungus.

  4. Genetic Diversity Analysis of Iranian Jujube Ecotypes (Ziziphus spp. Using RAPD Molecular Marker

    Directory of Open Access Journals (Sweden)

    S Abbasi

    2012-12-01

    Full Text Available Jujube (Ziziphus jujuba Mill. is a valuable medicinal plant which is important in Iranian traditional medicines. Although the regional plants such as jujube play an important role in our economy, but they are forgotten in research and technology. Considering the economic and medicinal importance of jujube, the first step in breeding programs is determination of the genetic diversity among the individuals. 34 ecotypes of jujube, which have been collected from eight provinces of Iran, were used in this study. The genetic relationships of Iranian jujube ecotypes were analyzed using Random Amplified Polymorphic DNA (RAPD marker. Six out of 15 random decamer primers applied for RAPD analysis, showed an informative polymorphism. According to clustering analysis using UPGMA's methods, the ecotypes were classified into two major groups at the 0.81 level of genetic similarity. The highest value of similarity coefficient (0.92 was detected between Mazandaran and Golestan ecotypes and the most genetic diversity was observed in ecotypes of Khorasan-Jonoubi. The affinity of Khorasan-Jonoubi and Esfahan ecotypes indicated a possible common origin for the variation in these areas. Results indicated that RAPD analysis could be successfully used for the estimation of genetic diversity among Ziziphus ecotypes and it can be useful for further investigations.

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

    Science.gov (United States)

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

    2008-10-01

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

  6. Evaluation of the genetic distinctiveness of Greater Sage-grouse in the Bi-State Planning Area

    Science.gov (United States)

    Oyler-McCance, Sara J.; Casazza, Michael L.

    2011-01-01

    The purpose of this study was to further characterize a distinct population of Greater Sage-grouse: the population located along the border between Nevada and California (Bi-State Planning Area) and centered around the Mono Basin. This population was previously determined to be genetically distinct from other Greater Sage-grouse populations across their range. Previous genetic work focused on characterizing genetic variation across the species' range and thereby used a coarse sampling approach for species characterization. The goal of this study was to investigate this population further by obtaining samples from breeding locations within the population and analyzing those samples with the same mitochondrial and microsatellite loci used in previous studies. Blood samples were collected in six locations within the Bi-State Planning Area. Genetic data from subpopulations were then compared with each other and also with two populations outside of the Bi-State Planning Area. Particular attention was paid to subpopulation boundaries and internal dynamics by drawing comparisons among particular regions within the Bi-State Planning Area and regions proximal to it. All newly sampled subpopulations contained mitochondrial haplotypes and allele frequencies that were consistent with the genetically unique Bi-State (Mono Basin) Greater Sage-grouse described previously. This reinforces the fact that this group of Greater Sage-grouse is genetically unique and warrants special attention. Maintaining the genetic integrity of this population could protect the evolutionary potential of this population of Greater Sage-grouse. Additionally, the White Mountains subpopulation was found to be significantly distinct from all other Bi-State subpopulations.

  7. Genetic diversity of wild and cultivated Rubus species in Colombia using AFLP and SSR markers

    Directory of Open Access Journals (Sweden)

    Sandra Bibiana Aguilar

    2007-01-01

    Full Text Available The Andean blackberry belongs to the genus Rubus, the largest of the Rosaceae family and one of the mostdiverse of the plant kingdom. In Colombia Rubus glaucus Benth, known as the Andean raspberry or blackberry, is one of thenine edible of the genus out of forty-four reported species. In this study wild and cultivated genotypes, collected in the CentralAndes of Colombia were analyzed by AFLP and SSR markers. Sexual reproduction seems to play an important role inmaintaining the genetic variability in R. glaucus, and the viability of using the SSR of Rubus alceifolius to characterizeColombian Rubus species was clearly demonstrated. All species evaluated produced very specific banding patterns,differentiating them from the others. Both AFLP and SSR produced bands exclusive to each of the following species: R.robustus, R. urticifolius, R. glaucus, and R. rosifolius. The SSR markers differentiated diploid and tetraploid genotypes of R.glaucus.

  8. An evaluation of sequence tagged microsatellite site markers for genetic analysis within Citrus and related species.

    Science.gov (United States)

    Kijas, J M; Fowler, J C; Thomas, M R

    1995-04-01

    Microsatellites, also called sequence tagged microsatellite sites (STMSs), have become important markers for genome analysis but are currently little studied in plants. To assess the value of STMSs for analysis within the Citrus plant species, two example STMSs were isolated from an intergeneric cross between rangpur lime (Citrus x limonia Osbeck) and trifoliate orange (Poncirus trifoliata (L.) Raf.). Unique flanking primers were constructed for polymerase chain reaction amplification both within the test cross and across a broad range of citrus and related species. Both loci showed length variation between test cross parents with alleles segregating in a Mendelian fashion to progeny. Amplification across species showed the STMS flanking primers to be conserved in every genome tested. The traits of polymorphism, inheritance, and conservation across species mean that STMS markers are ideal for genome mapping within Citrus, which contains high levels of genetic variability.

  9. Results for five sets of forensic genetic markers studied in a Greek population sample

    DEFF Research Database (Denmark)

    Tomas Mas, Carmen; Skitsa, I; Steinmeier, E

    2015-01-01

    A population sample of 223 Greek individuals was typed for five sets of forensic genetic markers with the kits NGM SElect™, SNPforID 49plex, DIPplex(®), Argus X-12 and PowerPlex(®) Y23. No significant deviation from Hardy-Weinberg expectations was observed for any of the studied markers after Holm...... origin. The Greek population grouped closely to the other European populations measured by FST(*) distances. The match probability ranged from a value of 1 in 2×10(7) males by using haplotype frequencies of four X-chromosome haplogroups in males to 1 in 1.73×10(21) individuals for 16 autosomal STRs....

  10. Genetic Markers Analyses and Bioinformatic Approaches to Distinguish Between Olive Tree (Olea europaea L.) Cultivars.

    Science.gov (United States)

    Ben Ayed, Rayda; Ben Hassen, Hanen; Ennouri, Karim; Rebai, Ahmed

    2016-12-01

    The genetic diversity of 22 olive tree cultivars (Olea europaea L.) sampled from different Mediterranean countries was assessed using 5 SNP markers (FAD2.1; FAD2.3; CALC; SOD and ANTHO3) located in four different genes. The genotyping analysis of the 22 cultivars with 5 SNP loci revealed 11 alleles (average 2.2 per allele). The dendrogram based on cultivar genotypes revealed three clusters consistent with the cultivars classification. Besides, the results obtained with the five SNPs were compared to those obtained with the SSR markers using bioinformatic analyses and by computing a cophenetic correlation coefficient, indicating the usefulness of the UPGMA method for clustering plant genotypes. Based on principal coordinate analysis using a similarity matrix, the first two coordinates, revealed 54.94 % of the total variance. This work provides a more comprehensive explanation of the diversity available in Tunisia olive cultivars, and an important contribution for olive breeding and olive oil authenticity.

  11. Genetic and environmental variances of bone microarchitecture and bone remodeling markers: a twin study.

    Science.gov (United States)

    Bjørnerem, Åshild; Bui, Minh; Wang, Xiaofang; Ghasem-Zadeh, Ali; Hopper, John L; Zebaze, Roger; Seeman, Ego

    2015-03-01

    All genetic and environmental factors contributing to differences in bone structure between individuals mediate their effects through the final common cellular pathway of bone modeling and remodeling. We hypothesized that genetic factors account for most of the population variance of cortical and trabecular microstructure, in particular intracortical porosity and medullary size - void volumes (porosity), which establish the internal bone surface areas or interfaces upon which modeling and remodeling deposit or remove bone to configure bone microarchitecture. Microarchitecture of the distal tibia and distal radius and remodeling markers were measured for 95 monozygotic (MZ) and 66 dizygotic (DZ) white female twin pairs aged 40 to 61 years. Images obtained using high-resolution peripheral quantitative computed tomography were analyzed using StrAx1.0, a nonthreshold-based software that quantifies cortical matrix and porosity. Genetic and environmental components of variance were estimated under the assumptions of the classic twin model. The data were consistent with the proportion of variance accounted for by genetic factors being: 72% to 81% (standard errors ∼18%) for the distal tibial total, cortical, and medullary cross-sectional area (CSA); 67% and 61% for total cortical porosity, before and after adjusting for total CSA, respectively; 51% for trabecular volumetric bone mineral density (vBMD; all p accounted for 47% to 68% of the variance (all p ≤ 0.001). Cross-twin cross-trait correlations between tibial cortical porosity and medullary CSA were higher for MZ (rMZ  = 0.49) than DZ (rDZ  = 0.27) pairs before (p = 0.024), but not after (p = 0.258), adjusting for total CSA. For the remodeling markers, the data were consistent with genetic factors accounting for 55% to 62% of the variance. We infer that middle-aged women differ in their bone microarchitecture and remodeling markers more because of differences in their genetic factors than

  12. Molecular genetic markers for thyroid FNAB. Established assays and future perspective.

    Science.gov (United States)

    Musholt, Thomas J; Musholt, P B

    2015-01-01

    Thyroid nodules > 1 cm are observed in about 12% of unselected adult employees aged 18-65 years screened by ultrasound scan (40). While intensive ultrasound screening leads to early detection of thyroid diseases, the determination of benign or malignant behaviour remains uncertain and may trigger anxieties in many patients and their physicians. A considerable number of thyroid resections are consecutively performed due to suspicion of malignancy in the detected nodes. Fine needle aspiration biopsy (FNAB) has been recommended for the assessment of thyroid nodules to facilitate detection of thyroid carcinomas but also to rule out malignancy and thereby avoid unnecessary thyroid resections. However, cytology results are dependent on experience of the respective cytologist and unfortunately inconclusive in many cases. Molecular genetic markers are already used nowadays to enhance sensitivity and specificity of FNAB cytology in some centers in Germany. The most clinically relevant molecular genetic markers as pre-operative diagnostic tools and the clinical implications for the intraoperative and postoperative management were reviewed. Molecular genetic markers predominantly focus on the preoperative detection of thyroid malignancies rather than the exclusion of thyroid carcinomas. While some centers routinely assess FNABs, other centers concentrate on FNABs with cytology results of follicular neoplasia or suspicion of thyroid carcinoma. Predominantly mutations of BRAF, RET/PTC, RAS, and PAX8/PPARγ or expression of miRNAs are analyzed. However, only the detection of BRAF mutations predicts the presence of (papillary) thyroid malignancy with almost 98% probability, indicating necessity of oncologic thyroid resections irrespective of the cytology result. Other genetic alterations are associated with thyroid malignancy with varying frequency and achieve less impact on the clinical management. Molecular genetic analysis of FNABs is increasingly performed in Germany

  13. Molecular markers for genetic diversity, gene flow and genetic population structure of freshwater mussel species

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    AB Choupina

    Full Text Available Freshwater mussel species are in global decline. Anthropogenic changes of river channels and the decrease of autochthonous fish population, the natural hosts of mussels larval stages (glochidia, are the main causes. Therefore, the conservation of mussel species depends not only on habitat conservation, but also on the availability of the fish host. In Portugal, information concerning most of the mussel species is remarkably scarce. One of the most known species, Unio pictorum is also in decline however, in the basins of the rivers Tua and Sabor (Northeast of Portugal, there is some indication of relatively large populations. The aforementioned rivers can be extremely important for this species conservation not only in Portugal, but also in the remaining Iberian Peninsula. Thus, it is important to obtain data concerning Unio pictorum bioecology (distribution, habitat requirements, population structure, genetic variability, reproductive cycle and recruitment rates, as well as the genetic variability and structure of the population. Concomitantly, information concerning fish population structure, the importance of the different fish species as “glochidia” hosts and their appropriate density to allow effective mussel recruitment, will also be assessed. The achieved data is crucial to obtain information to develop effective management measures in order to promote the conservation of this bivalve species, the conservation of autochthonous fish populations, and consequently the integrity of the river habitats.

  14. Is there a genetic contribution to cultural differences? Collectivism, individualism and genetic markers of social sensitivity.

    Science.gov (United States)

    Way, Baldwin M; Lieberman, Matthew D

    2010-06-01

    Genes and culture are often thought of as opposite ends of the nature-nurture spectrum, but here we examine possible interactions. Genetic association studies suggest that variation within the genes of central neurotransmitter systems, particularly the serotonin (5-HTTLPR, MAOA-uVNTR) and opioid (OPRM1 A118G), are associated with individual differences in social sensitivity, which reflects the degree of emotional responsivity to social events and experiences. Here, we review recent work that has demonstrated a robust cross-national correlation between the relative frequency of variants in these genes and the relative degree of individualism-collectivism in each population, suggesting that collectivism may have developed and persisted in populations with a high proportion of putative social sensitivity alleles because it was more compatible with such groups. Consistent with this notion, there was a correlation between the relative proportion of these alleles and lifetime prevalence of major depression across nations. The relationship between allele frequency and depression was partially mediated by individualism-collectivism, suggesting that reduced levels of depression in populations with a high proportion of social sensitivity alleles is due to greater collectivism. These results indicate that genetic variation may interact with ecological and social factors to influence psychocultural differences.

  15. Genetic molecular analysis of Coffea arabica (Rubiaceae hybrids using SRAP markers

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    Manoj Kumar Mishra

    2011-06-01

    Full Text Available In Coffea arabica (arabica coffee, the phenotypic as well as genetic variability has been found low because of the narrow genetic basis and self fertile nature of the species. Because of high similarity in phenotypic appearance among the majority of arabica collections, selection of parental lines for inter-varietals hybridization and identification of resultant hybrids at an early stage of plant growth is difficult. DNA markers are known to be reliable in identifying closely related cultivars and hybrids. Sequence Related Amplified Polymorphism (SRAP is a new molecular marker technology developed based on PCR. In this paper, sixty arabica-hybrid progenies belonging to six crosses were analyzed using 31 highly polymorphic SRAP markers. The analysis revealed seven types of SRAP marker profiles which are useful in discriminating the parents and hybrids. The number of bands amplified per primer pair ranges from 6.13 to 8.58 with average number of seven bands. Among six hybrid combinations, percentage of bands shared between hybrids and their parents ranged from 66.29% to 85.71% with polymorphic bands varied from 27.64% to 60.0%. Percentage of hybrid specific fragments obtained in various hybrid combinations ranged from 0.71% to 10.86% and ascribed to the consequence of meiotic recombination. Based on the similarity index calculation, it was observed that F1 hybrids share maximum number of bands with the female parent compared to male parent. The results obtained in the present study revealed the effectiveness of SRAP technique in cultivar identification and hybrid analysis in this coffee species. Rev. Biol. Trop. 59 (2: 607-617. Epub 2011 June 01.

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

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    Claudio Brondani

    2006-01-01

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

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

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    Martin Vivodík

    2017-01-01

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

  18. [THE SOMATIC MUTATIONS AND ABERRANT METHYLATION AS POTENTIAL GENETIC MARKERS OF URINARY BLADDER CANCER].

    Science.gov (United States)

    Mikhailenko, D S; Kushlinskii, N E

    2016-02-01

    All around the world, more than 330 thousands cases of bladder cancer are registered annually hence representing actual problem of modern oncology. Still in demand are search and characteristic of new molecular markers of bladder cancer detecting in tumor cells from urinary sediment and having high diagnostic accuracy. The studies of last decade, especially using methods of genome-wide sequencing, permitted to receive a large amount of experimental data concerning development and progression of bladder cancer The review presents systematic analysis of publications available in PubMed data base mainly of last five years. The original studies of molecular genetic disorders under bladder cancer and meta-analyzes were considered This approach permitted to detected the most common local alterations of DNA under bladder cancer which can be detected using routine genetic methods indifferent clinical material and present prospective interest for development of test-systems. The molecular genetic markers of disease can be activating missense mutations in 7 and 10 exons of gene of receptor of growth factor of fibroblasts 3 (FGFR3), 9 and 20 exons of gene of Phosphatidylinositol-4,5-bi-phosphate-3-kinase (PIK3CA) and mutation in -124 and -146 nucleotides in promoter of gene of catalytic subunit telomerase (TERT). The development of test-systems on the basis of aberrant methylation of CpG-islets of genes-suppressors still is seemed as a difficult task because of differences in pattern of methylation of different primary tumors at various stages of clonal evolution of bladder cancer though they can be considered as potential markers.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-07-01

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

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

    International Nuclear Information System (INIS)

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

    2009-01-01

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

  1. Genome sequencing elucidates Sardinian genetic architecture and augments association analyses for lipid and blood inflammatory markers

    Science.gov (United States)

    Zoledziewska, Magdalena; Mulas, Antonella; Pistis, Giorgio; Steri, Maristella; Danjou, Fabrice; Kwong, Alan; Ortega del Vecchyo, Vicente Diego; Chiang, Charleston W. K.; Bragg-Gresham, Jennifer; Pitzalis, Maristella; Nagaraja, Ramaiah; Tarrier, Brendan; Brennan, Christine; Uzzau, Sergio; Fuchsberger, Christian; Atzeni, Rossano; Reinier, Frederic; Berutti, Riccardo; Huang, Jie; Timpson, Nicholas J; Toniolo, Daniela; Gasparini, Paolo; Malerba, Giovanni; Dedoussis, George; Zeggini, Eleftheria; Soranzo, Nicole; Jones, Chris; Lyons, Robert; Angius, Andrea; Kang, Hyun M.; Novembre, John; Sanna, Serena; Schlessinger, David; Cucca, Francesco; Abecasis, Gonçalo R

    2015-01-01

    We report ~17.6M genetic variants from whole-genome sequencing of 2,120 Sardinians; 22% are absent from prior sequencing-based compilations and enriched for predicted functional consequence. Furthermore, ~76K variants common in our sample (frequency >5%) are rare elsewhere (Genomes Project). We assessed the impact of these variants on circulating lipid levels and five inflammatory biomarkers. Fourteen signals, including two major new loci, were observed for lipid levels, and 19, including two novel loci, for inflammatory markers. New associations would be missed in analyses based on 1000 Genomes data, underlining the advantages of large-scale sequencing in this founder population. PMID:26366554

  2. A study of genetic markers in the South African Blesbok (Damaliscus Dorcas Phillipsi

    Directory of Open Access Journals (Sweden)

    D. R Osterhoff

    1972-12-01

    Full Text Available During culling operations on blesbok from the Rietvlei Nature Reserve, 198 blood samples were obtained for study of genetic markers including haemoglobins, transferrins, amylases, albumins and carbonic anhydrases. All animals exhibited the same pattern. Blood typing was performed by using goat reagents. These reagents could possibly be used to establish the relationship between the blesbok and the bontebok. Immunoelectrophoresis was used to detect any immunological differences; 123 blesbok samples were tested against antibovine serum prepared in rabbits. The animals could be grouped into four distinguishable types according to the shape and presence of the alpha-2-macroglobulin and the "horizontal55 band.

  3. A DArT marker genetic map of perennial ryegrass (Lolium perenne L.) integrated with detailed comparative mapping information; comparison with existing DArT marker genetic maps of Lolium perenne, L. multiflorum and Festuca pratensis.

    Science.gov (United States)

    King, Julie; Thomas, Ann; James, Caron; King, Ian; Armstead, Ian

    2013-07-03

    Ryegrasses and fescues (genera, Lolium and Festuca) are species of forage and turf grasses which are used widely in agricultural and amenity situations. They are classified within the sub-family Pooideae and so are closely related to Brachypodium distachyon, wheat, barley, rye and oats. Recently, a DArT array has been developed which can be used in generating marker and mapping information for ryegrasses and fescues. This represents a potential common marker set for ryegrass and fescue researchers which can be linked through to comparative genomic information for the grasses. A F2 perennial ryegrass genetic map was developed consisting of 7 linkage groups defined by 1316 markers and deriving a total map length of 683 cM. The marker set included 866 DArT and 315 gene sequence-based markers. Comparison with previous DArT mapping studies in perennial and Italian ryegrass (L. multiflorum) identified 87 and 105 DArT markers in common, respectively, of which 94% and 87% mapped to homoeologous linkage groups. A similar comparison with meadow fescue (F. pratensis) identified only 28 DArT markers in common, of which c. 50% mapped to non-homoelogous linkage groups. In L. perenne, the genetic distance spanned by the DArT markers encompassed the majority of the regions that could be described in terms of comparative genomic relationships with rice, Brachypodium distachyon, and Sorghum bicolor. DArT markers are likely to be a useful common marker resource for ryegrasses and fescues, though the success in aligning different populations through the mapping of common markers will be influenced by degrees of population interrelatedness. The detailed mapping of DArT and gene-based markers in this study potentially allows comparative relationships to be derived in future mapping populations characterised using solely DArT markers.

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

    International Nuclear Information System (INIS)

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

    2012-01-01

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

  5. Genetic diversity of sesame (sesamum indicum L.) germplasm from Pakistan using RAPD markers

    Energy Technology Data Exchange (ETDEWEB)

    Akbar, F; Rabbani, M A; Masood, M S; Shinwari, Z.K., E-mail: shinwari@qau.edu.p

    2011-08-15

    Genetic diversity among 20 sesame (Sesamum indicum L.) accessions was examined at DNA level by means of random amplified polymorphic DNA (RAPD) analysis. Ten primers used produced a total of 93 RAPD fragments, of which 70 (75%) were polymorphic. Each primer generated 5 to 17 amplified fragments with an average of 9.3 bands per primer. Based on pair-wise comparisons of RAPD amplification products, Nei and Li's similarity coefficients were computed to assess the associations among the accessions. Pair-wise similarity indices varied from 0.65 to 0.91. A UPGMA cluster analysis based on these genetic similarities located most of the accessions far apart from one another, showing a high level of polymorphism. Genetically, all the genotypes were classified into two major groups and six subgroups or clusters. A single accession (22243) was relatively distinct from rest of the accessions and created independent cluster. In conclusion, even with the use of a limited set of primers, RAPD technique revealed a high level of genetic variation among sesame accessions collected from diverse ecologies of Pakistan. This high level of genetic diversity among the genotypes suggested that RAPD technique is valuable for sesame systematic, and can be helpful for the upholding of germplasm banks and the competent choice of parents in breeding programs. (author)

  6. Genetic diversity of sesame (sesamum indicum L.) germplasm from Pakistan using RAPD markers

    International Nuclear Information System (INIS)

    Akbar, F; Rabbani, M.A.; Masood, M.S.; Shinwari, Z.K.

    2011-01-01

    Genetic diversity among 20 sesame (Sesamum indicum L.) accessions was examined at DNA level by means of random amplified polymorphic DNA (RAPD) analysis. Ten primers used produced a total of 93 RAPD fragments, of which 70 (75%) were polymorphic. Each primer generated 5 to 17 amplified fragments with an average of 9.3 bands per primer. Based on pair-wise comparisons of RAPD amplification products, Nei and Li's similarity coefficients were computed to assess the associations among the accessions. Pair-wise similarity indices varied from 0.65 to 0.91. A UPGMA cluster analysis based on these genetic similarities located most of the accessions far apart from one another, showing a high level of polymorphism. Genetically, all the genotypes were classified into two major groups and six subgroups or clusters. A single accession (22243) was relatively distinct from rest of the accessions and created independent cluster. In conclusion, even with the use of a limited set of primers, RAPD technique revealed a high level of genetic variation among sesame accessions collected from diverse ecologies of Pakistan. This high level of genetic diversity among the genotypes suggested that RAPD technique is valuable for sesame systematic, and can be helpful for the upholding of germplasm banks and the competent choice of parents in breeding programs. (author)

  7. Genetic diversity analysis of brassica napus/brassica campestris progenies using microsatellite markers

    International Nuclear Information System (INIS)

    Fayyaz, L.; Farhatullah, A.; Iqbal, S.; Kanwal, M.; Nawaz, I.

    2014-01-01

    Genetic diversity and relationship of F2 segregating progenies of interspecific crosses between B. napus N-501/B. campestris C-118 were studied. A set of 90 genotypes (2 parental lines and their 88 F2 progenies) was characterized separately using 24 microsatellite or SSR markers to cover the diversity as broadly as possibly present in them. In initial screening only 12 out of 24 SSR primers combination amplified DNA fragments, while the remaining 12 SSR primers did not amplify DNA fragment therefore those 12 SSR molecular markers were not used for further analysis. The 12 SSR primer combinations generated a total of 33 alleles, of that 32 were polymorphic loci, whereas only one was monomorphic locus. Primers BRMS-19 and BRMS-40 were highly polymorphic producing 4 bands each. Primer Ra2-D04 was less polymorphic and it produced only one band. The proportion of polymorphic loci was 95.83% which indicates high genetic diversity among the progenies. The average number of polymorphic alleles per locus was 2.66. The PIC values ranged from 0.395 for primer Ra2-E03 to 0.726 for primer BRMS-019 with an average genetic diversity (PIC value) of 0.584 per locus. Seven primers showed PIC values above 0.5 (50%) indicating high genetic diversity in the studied plant materials. Pair-wise similarity indices among 90 genotypes ranged from 0.3 to 0.95. Dendrogram obtained through UPGMA clustering of F2 progenies depicted eight main groups using similarity coefficient of 0.70. The progenies could be similar to their parents if they have the same banding patterns as that of the parents and could be distinguished from each other by the combination of fragments which are repeatedly present in one progeny and absent in the other. Considerable genetic diversity has been found among the F2 segregating progenies and their parents using SSR markers thus, SSR analysis proved to be a useful tool. (author)

  8. Predicting risk in space: Genetic markers for differential vulnerability to sleep restriction

    Science.gov (United States)

    Goel, Namni; Dinges, David F.

    2012-08-01

    Several laboratories have found large, highly reliable individual differences in the magnitude of cognitive performance, fatigue and sleepiness, and sleep homeostatic vulnerability to acute total sleep deprivation and to chronic sleep restriction in healthy adults. Such individual differences in neurobehavioral performance are also observed in space flight as a result of sleep loss. The reasons for these stable phenotypic differential vulnerabilities are unknown: such differences are not yet accounted for by demographic factors, IQ or sleep need, and moreover, psychometric scales do not predict those individuals cognitively vulnerable to sleep loss. The stable, trait-like (phenotypic) inter-individual differences observed in response to sleep loss—with intraclass correlation coefficients accounting for 58-92% of the variance in neurobehavioral measures—point to an underlying genetic component. To this end, we utilized multi-day highly controlled laboratory studies to investigate the role of various common candidate gene variants—each independently—in relation to cumulative neurobehavioral and sleep homeostatic responses to sleep restriction. These data suggest that common genetic variations (polymorphisms) involved in sleep-wake, circadian, and cognitive regulation may serve as markers for prediction of inter-individual differences in sleep homeostatic and neurobehavioral vulnerability to sleep restriction in healthy adults. Identification of genetic predictors of differential vulnerability to sleep restriction—as determined from candidate gene studies—will help identify astronauts most in need of fatigue countermeasures in space flight and inform medical standards for obtaining adequate sleep in space. This review summarizes individual differences in neurobehavioral vulnerability to sleep deprivation and ongoing genetic efforts to identify markers of such differences.

  9. A genetic linkage map with 178 SSR and 1 901 SNP markers constructed using a RIL population in wheat (Triticum aestivum L.)

    Institute of Scientific and Technical Information of China (English)

    ZHAI Hui-jie; FENG Zhi-yu; LIU Xin-ye; CHENG Xue-jiao; PENG Hui-ru; YAO Ying-yin; SUN Qi-xin; NI Zhong-fu

    2015-01-01

    The construction of high density genetic linkage map provides a powerful tool to detect and map quantitative trait loci (QTLs) controlling agronomically important traits. In this study, simple sequence repeat (SSR) markers and Illumina 9K iSelect single nucleotide polymorphism (SNP) genechip were employed to construct one genetic linkage map of common wheat (Triticum aestivum L.) using 191 recombinant inbred lines (RILs) derived from cross Yu 8679xJing 411. This map included 1 901 SNP loci and 178 SSR loci, covering 1 659.9 cM and 1 000 marker bins, with an average interval distance of 1.66 cM. A, B and D genomes covered 719.1,703.5 and 237.3 cM, with an average interval distance of 1.66, 1.45 and 2.9 cM, respectively. Notably, the genetic linkage map covered 20 chromosomes, with the exception of chromosome 5D. Bioinformatics analysis revealed that 1 754 (92.27%) of 1 901 mapped SNP loci could be aligned to 1 215 distinct wheat unigenes, among which 1 184 (97.4%) were located on one single chromosome, and the rest 31 (2.6%) were located on 2 to 3 chromosomes. By performing in silico comparison, 214 chromosome deletion bin-mapped expressed sequence tags (ESTs), 1 043 Brachypodium genes and 1 033 rice genes were further added onto the genetic linkage map. This map not only integrated genetic and physical maps, SSR and SNP loci, respectively, but also provided the information of Brachypodium and rice genes corresponding to 1 754 SNP loci. Therefore, it will be a useful tool for comparative genomics analysis, fine mapping of QTL/gene controlling agronomically important traits and marker-assisted selection breeding in wheat.

  10. Genetic diversity of turmeric germplasm (Curcuma longa; Zingiberaceae) identified by microsatellite markers.

    Science.gov (United States)

    Sigrist, M S; Pinheiro, J B; Filho, J A Azevedo; Zucchi, M I

    2011-03-09

    Turmeric (Curcuma longa) is a triploid, vegetatively propagated crop introduced early during the colonization of Brazil. Turmeric rhizomes are ground into a powder used as a natural dye in the food industry, although recent research suggests a greater potential for the development of drugs and cosmetics. In Brazil, little is known about the genetic variability available for crop improvement. We examined the genetic diversity among turmeric accessions from a Brazilian germplasm collection comprising 39 accessions collected from the States of Goiás, Mato Grosso do Sul, Minas Gerais, São Paulo, and Pará. For comparison, 18 additional genotypes were analyzed, including samples from India and Puerto Rico. Total DNA was extracted from lyophilized leaf tissue and genetic analysis was performed using 17 microsatellite markers (single-sequence repeats). Shannon-Weiner indexes ranged from 0.017 (Minas Gerais) to 0.316 (São Paulo). Analyses of molecular variance (AMOVA) demonstrated major differences between countries (63.4%) and that most of the genetic diversity in Brazil is found within states (75.3%). Genotypes from São Paulo State were the most divergent and potentially useful for crop improvement. Structure analysis indicated two main groups of accessions. These results can help target future collecting efforts for introduction of new materials needed to develop more productive and better adapted cultivars.

  11. Assessment of genetic variability in rice (oryza sativa l.) germplasm from Pakistan using rapd markers

    International Nuclear Information System (INIS)

    Pervaiz, Z.H.; Rabbani, M.A.; Shinwar, Z.K.; Masood, M.S.; Malik, S.A.

    2010-01-01

    Information on genetic diversity and relationships among rice genotypes from Pakistan is currently very limited. Molecular marker analysis can truly be beneficial in analyzing the diversity of rice germplasm providing useful information to broaden the genetic base of modern rice cultivars. The objective of this study was to evaluate the genetic polymorphism of 75 rice accessions and improved cultivars using random amplified polymorphic DNA (RAPD) technique. Twenty-eight decamer-primers generated a total of 145 RAPD fragments, of which 116 (80%) were polymorphic. The number of amplification products produced by each primer varied from 3 to 9 with an average of 5.2 alleles primer-1. The size of amplified fragments ranged from 250 to 4000bp. A dendrogram was generated from minimal variance algorithm using Ward method. All the 75 genotypes were grouped into two main groups corresponding to aromatic and non-aromatic types of indica rice. Clustering of accessions did not show any significant pattern of association between the RAPD fingerprints and collection sites. This type of analysis grouping different rice accessions in relation to fragrance, a major rice quality determinant, and varietal group is extremely useful to develop a core collection and gene bank management. Further more, the information revealed by the RAPDs regarding genetic variation is helpful to the plant breeder in selecting diverse parents and for future orientation of rice breeding program. (author)

  12. Genetic variation of Anastrepha suspensa (Diptera: Tephritidae) in Florida and the Caribbean using microsatellite DNA markers.

    Science.gov (United States)

    Boykin, Laura M; Shatters, Robert G; Hall, David G; Dean, David; Beerli, Peter

    2010-12-01

    Anastrepha suspensa (Loew) (Diptera: Tephritidae), the Caribbean fruit fly, is indigenous to Florida and the Greater Antilles where it causes economic losses in fruit crops, including citrus. Because of the geographic separation of many of its native locations and anecdotal descriptions of regional differences in host preferences, there have been questions about the population structure of A. suspensa. Seven DNA microsatellite markers were used to characterize the population genetic structure of A. suspensa, in Florida and the Caribbean from a variety of hosts, including citrus. We genotyped 729 A. suspensa individuals from Florida, Puerto Rico, Cayman Island, Dominican Republic, and Jamaica. The investigated seven loci displayed from 5 to 19 alleles, with expected heterozygosities ranging from 0.05 to 0.83. There were five unique alleles in Florida and three unique alleles in the Caribbean samples; however, no microsatellite alleles were specific to a single host plant. Genetic diversity was analyzed using F(ST) and analysis of molecular variance and revealed low genetic diversity between Florida and Caribbean samples and also between citrus and noncitrus samples. Analyses using migrate revealed there is continuous gene flow between sampling sites in Florida and the Caribbean and among different hosts. These results support previous comparisons based on the mitochondrial cytochrome oxidase I locus indicating there is no genetic differentiation among locations in Florida and the Caribbean and that there is no separation into host races.

  13. Microsatellite markers from tea green leafhopper Empoasca (Matsumurasca) onukii: a powerful tool for studying genetic structure in tea plantations.

    Science.gov (United States)

    Zhang, Li; Dietrich, Christopher H; Qin, Daozheng

    2016-07-29

    Tea green leafhopper is one of the most dominant pests in Chinese tea plantations. Recent evidence, including morphological and molecular data, revealed that tea green leafhopper in China is the same species as in Japan, Empoasca (Matsumurasca) onukii Matsuda. Previous morphological study that revealed variation in the structure of the male genitalia within and among populations of this species suggested that there may be significant population-level genetic variation. To provide powerful molecular markers to explore the population genetic diversity and population genetic structure of this pest in China, microsatellite markers were obtained by AFLP of sequences containing repeats (FIASCO). Eighteen polymorphic markers were evaluated for five populations of E. (M.) onukii, Two related empoascine leafhopper species were selected to test the transferability of the markers. Population genetic structure of E. (M.) onukii was detected using Structure analysis, principal coordinate analysis (PCoA) and variance analysis. The identified markers were polymorphic with total number of alleles ranging from 6 to 24 per locus, observed and expected heterozygosity ranged from 0.133 to 0.9 and 0.183 to 0.926, respectively, and the polymorphic information content value over all populations varied from 0.429 to 0.911. This is the first study to demonstrate that microsatellite markers provide valuable information for genetic structure of E. (M.) onukii in Chinese tea plantations. There is obvious genetic differentiation between the two populations in the Southwest tea area. These microsatellite markers will be the powerful tools for genetic studies of E. (M.) onukii and improve understanding of the microevolution of this species.

  14. Teaching practice and experiences of verifying the three laws of genetics based on the SSLP marker analysis.

    Science.gov (United States)

    Huang, Xue-Ying; Fan, Kai; Ye, Yan-Fang; Wang, Bin; Wu, Wei-Ren; Lan, Tao

    2017-09-20

    We explored the practical effect of the genetic analysis of simple sequence length polymorphism (SSLP) molecular markers in rice in the genetics lab course. Two parents and their F 2 population were analyzed and detected with three SSLP molecular markers that located on two chromosomes of the rice genome. The markers' genotype data were used to verify the three laws of genetics, including segregation, independent assortment and linkage and crossing-over. Our practice has proved not only beneficial to deepen students' understandings about the three laws of genetics, but also conducive to cultivate students' interests in research and innovation and improve their skills and comprehensive analysis abilities. At the same time, the application scope of the experiment was discussed. This comprehensive experiment is also useful for the transformation of scientific research achievements into undergraduate experimental teaching.

  15. Population genetics of Sargassum horneri (Fucales, Phaeophyta) in China revealed by ISSR and SRAP markers

    Science.gov (United States)

    Yu, Shenhui; Chong, Zhuo; Zhao, Fengjuan; Yao, Jianting; Duan, Delin

    2013-05-01

    Sargassum horneri is a common brown macro-alga that is found in the inter-tidal ecosystems of China. To investigate the current status of seaweed resources and provide basic data for its sustainable development, ISSR (inter simple sequence repeat) and SRAP (sequence related amplified polymorphism) markers were used to analyze the population genetics among nine natural populations of S. horneri. The nine studied populations were distributed over 2 000 km from northeast to south China. The percentage of polymorphic loci P % (ISSR, 99.44%; SRAP, 100.00%), Nei's genetic diversity H (ISSR, 0.107-0.199; SRAP, 0.100-0.153), and Shannon's information index I (ISSR, 0.157-0.291; SRAP, 0.148-0.219) indicated a fair amount of genetic variability among the nine populations. Moreover, the high degree of gene differentiation G st (ISSR, 0.654; SRAP, 0.718) and low gene flow N m (ISSR, 0.265; SRAP, 0.196) implied that there was significant among-population differentiation, possibly as a result of habitat fragmentation. The matrices of genetic distances and fixation indices ( F st) among the populations correlated well with their geographical distribution (Mantel test R =0.541 5, 0.541 8; P =0.005 0, 0.002 0 and R =0.728 6, 0.641 2; P =0.001 0, 0.001 0, respectively); the Rongcheng population in the Shandong peninsula was the only exception. Overall, the genetic differentiation agreed with the geographic isolation. The fair amount of genetic diversity that was revealed in the S. horneri populations in China indicated that the seaweed resources had not been seriously affected by external factors.

  16. Estimation of the Genetic Diversity in Tetraploid Alfalfa Populations Based on RAPD Markers for Breeding Purposes

    Directory of Open Access Journals (Sweden)

    Slobodan Katic

    2011-08-01

    Full Text Available Alfalfa is an autotetraploid, allogamous and heterozygous forage legume, whose varieties are synthetic populations. Due to the complex nature of the species, information about genetic diversity of germplasm used in any alfalfa breeding program is most beneficial. The genetic diversity of five alfalfa varieties, involved in progeny tests at Institute of Field and Vegetable Crops, was characterized based on RAPD markers. A total of 60 primers were screened, out of which 17 were selected for the analysis of genetic diversity. A total of 156 polymorphic bands were generated, with 10.6 bands per primer. Number and percentage of polymorphic loci, effective number of alleles, expected heterozygosity and Shannon’s information index were used to estimate genetic variation. Variety Zuzana had the highest values for all tested parameters, exhibiting the highest level of variation, whereas variety RSI 20 exhibited the lowest. Analysis of molecular variance (AMOVA showed that 88.39% of the total genetic variation was attributed to intra-varietal variance. The cluster analysis for individual samples and varieties revealed differences in their population structures: variety Zuzana showed a very high level of genetic variation, Banat and Ghareh were divided in subpopulations, while Pecy and RSI 20 were relatively uniform. Ways of exploiting the investigated germplasm in the breeding programs are suggested in this paper, depending on their population structure and diversity. The RAPD analysis shows potential to be applied in analysis of parental populations in semi-hybrid alfalfa breeding program in both, development of new homogenous germplasm, and identification of promising, complementary germplasm.

  17. Genetic architecture of the Delis-Kaplan Executive Function System Trail Making Test: evidence for distinct genetic influences on executive function.

    Science.gov (United States)

    Vasilopoulos, Terrie; Franz, Carol E; Panizzon, Matthew S; Xian, Hong; Grant, Michael D; Lyons, Michael J; Toomey, Rosemary; Jacobson, Kristen C; Kremen, William S

    2012-03-01

    To examine how genes and environments contribute to relationships among Trail Making Test (TMT) conditions and the extent to which these conditions have unique genetic and environmental influences. Participants included 1,237 middle-aged male twins from the Vietnam Era Twin Study of Aging. The Delis-Kaplan Executive Function System TMT included visual searching, number and letter sequencing, and set-shifting components. Phenotypic correlations among TMT conditions ranged from 0.29 to 0.60, and genes accounted for the majority (58-84%) of each correlation. Overall heritability ranged from 0.34 to 0.62 across conditions. Phenotypic factor analysis suggested a single factor. In contrast, genetic models revealed a single common genetic factor but also unique genetic influences separate from the common factor. Genetic variance (i.e., heritability) of number and letter sequencing was completely explained by the common genetic factor while unique genetic influences separate from the common factor accounted for 57% and 21% of the heritabilities of visual search and set shifting, respectively. After accounting for general cognitive ability, unique genetic influences accounted for 64% and 31% of those heritabilities. A common genetic factor, most likely representing a combination of speed and sequencing, accounted for most of the correlation among TMT 1-4. Distinct genetic factors, however, accounted for a portion of variance in visual scanning and set shifting. Thus, although traditional phenotypic shared variance analysis techniques suggest only one general factor underlying different neuropsychological functions in nonpatient populations, examining the genetic underpinnings of cognitive processes with twin analysis can uncover more complex etiological processes.

  18. Population genetic study of 34 X-Chromosome markers in 5 main ethnic groups of China.

    Science.gov (United States)

    Zhang, Suhua; Bian, Yingnan; Li, Li; Sun, Kuan; Wang, Zheng; Zhao, Qi; Zha, Lagabaiyila; Cai, Jifeng; Gao, Yuzhen; Ji, Chaoneng; Li, Chengtao

    2015-12-04

    As a multi-ethnic country, China has some indigenous population groups which vary in culture and social customs, perhaps as a result of geographic isolation and different traditions. However, upon close interactions and intermarriage, admixture of different gene pools among these ethnic groups may occur. In order to gain more insight on the genetic background of X-Chromosome from these ethnic groups, a set of X-markers (18 X-STRs and 16 X-Indels) was genotyped in 5 main ethnic groups of China (HAN, HUI, Uygur, Mongolian, Tibetan). Twenty-three private alleles were detected in HAN, Uygur, Tibetan and Mongolian. Significant differences (p population differentiation of HUI and Uygur. However, the HAN, Tibetan and Mongolian ethnic groups were closely clustered. Eighteen X-Indels exhibited in general congruent phylogenetic signal and similar cluster among the 5 ethnic groups compared with 16 X-STRs. Aforementioned results proved the genetic polymorphism and potential of the 34 X-markers in the 5 ethnic groups.

  19. Genetic diversity of Iranian honey bee (Apis mellifera meda Skorikow, 1829) populations based on ISSR markers.

    Science.gov (United States)

    Rahimi, A; Mirmoayedi, A; Kahrizi, D; Zarei, L; Jamali, S

    2016-04-30

    Honey bee is one of the most important insects considering its role in agriculture,ecology and economy as a whole. In this study, the genetic diversity of different Iranian honey bee populations was evaluated using inter simple sequence repeat (ISSR) markers. During May to September 2014, 108 young worker honey bees were collected from six different populations in 30 different geoclimatic locations from Golestan, Mazendaran, Guilan, West Azerbaijan, East Azerbaijan, Ardebil provinces of Iran. DNA was extracted from the worker honey bees. The quality and quantity of extracted DNA were measured. A set of ten primers were screened with the laboratory populations of honey bees. The number of fragments produced in the different honey bee populations varied from 3 to 10, varying within 150 to 1500 bp. The used ten ISSR primers generated 40 polymorphic fragments, and the average heterozygosity for each primer was 0.266. Maximum numbers of bands were recorded for primer A1. A dendrogram based on the Unweighted Pair Group Method with Arithmetic mean (UPGMA) method generated two sub-clusters. Honey bee populations of Golestan, Mazendaran, Guilan provinces were located in the first group. The second group included honey bee populations of Ardebil, West Azerbaijan, East Azerbaijan provinces, but this group showed a close relationship with other populations. The results showed obviously the ability of the ISSR marker technique to detect the genetic diversity among the honey bee populations.

  20. Population Genetics and Drug Resistance Markers: An Essential for Malaria Surveillance in Pakistan

    International Nuclear Information System (INIS)

    Raza, A.; Beg, M.A.

    2013-01-01

    Plasmodium (P.) vivax is the prevalent malarial species accounting for 70% of malaria cases in Pakistan. However, baseline epidemiological data on P. vivax population structure and drug resistance are lacking from Pakistan. For population structure studies, molecular genetic markers, circumsporozoite protein (csp) and merozoite surface protein-1 (msp-1) are considered useful as these play an important role in P. vivax survival under immune and environmental pressure. Furthermore, these genes have also been identified as suitable candidates for vaccine development. While efforts for effective vaccine are underway, anti-malarial agents remain the mainstay for control. Evidence of resistance against commonly used anti-malarial agents, particularly Sulphadoxine-Pyrimethamine (SP) is threatening to make this form of control defunct. Therefore, studies on drug resistance are necessary so that anti-malarial treatment strategies can be structured and implemented accordingly by the Malaria Control Program, Pakistan. This review aims to provide information on genetic markers of P. vivax population structure and drug resistance and comment on their usefulness in molecular surveillance and control. (author)

  1. Genetic diversity and linkage disequilibrium in Chinese bread wheat (Triticum aestivum L.) revealed by SSR markers.

    Science.gov (United States)

    Hao, Chenyang; Wang, Lanfen; Ge, Hongmei; Dong, Yuchen; Zhang, Xueyong

    2011-02-18

    Two hundred and fifty bread wheat lines, mainly Chinese mini core accessions, were assayed for polymorphism and linkage disequilibrium (LD) based on 512 whole-genome microsatellite loci representing a mean marker density of 5.1 cM. A total of 6,724 alleles ranging from 1 to 49 per locus were identified in all collections. The mean PIC value was 0.650, ranging from 0 to 0.965. Population structure and principal coordinate analysis revealed that landraces and modern varieties were two relatively independent genetic sub-groups. Landraces had a higher allelic diversity than modern varieties with respect to both genomes and chromosomes in terms of total number of alleles and allelic richness. 3,833 (57.0%) and 2,788 (41.5%) rare alleles with frequencies of varieties displayed a wider average LD decay across the whole genome for locus pairs with r(2)>0.05 (Pvarieties. LD decay distances were also somewhat different for each of the 21 chromosomes, being higher for most of the chromosomes in modern varieties (<5 ∼ 25 cM) compared to landraces (<5 ∼ 15 cM), presumably indicating the influences of domestication and breeding. This study facilitates predicting the marker density required to effectively associate genotypes with traits in Chinese wheat genetic resources.

  2. SSR marker development and intraspecific genetic divergence exploration of Chrysanthemum indicum based on transcriptome analysis.

    Science.gov (United States)

    Han, Zhengzhou; Ma, Xinye; Wei, Min; Zhao, Tong; Zhan, Ruoting; Chen, Weiwen

    2018-04-25

    Chrysanthemum indicum L., an important ancestral species of the flowering plant chrysanthemum, can be used as medicine and for functional food development. Due to the lack of hereditary information for this species and the difficulty of germplasm identification, we herein provide new genetic insight from the perspective of intraspecific transcriptome comparison and present single sequence repeat (SSR) molecular marker recognition technology. Through the study of a diploid germplasm (DIWNT) and a tetraploid germplasm (DIWT), the following outcome were obtained. (1) A significant difference in Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations for specific homologous genes was observed using the OrthoMCL method for the identification of homologous gene families between the two cytotypes. Ka/Ks analysis of common, single-copy homologous family members also revealed a greater difference among genes that experienced positive selection than among those experiencing positive selection. (2) Of more practical value, 2575 SSR markers were predicted and partly verified. We used TaxonGap as a visual tool to inspect genotype uniqueness and screen for high-performance molecular loci; we recommend four primers of 65 randomly selected primers with a combined identification success rate of 88.6% as priorities for further development of DNA fingerprinting of C. indicum germplasm. The SSR technology based on next-generation sequencing was proved to be successful in the identification of C. indicum germplasms. And the information on the intraspecfic genetic divergence generated by transcriptome comparison deepened the understanding of this complex species' nature.

  3. Relative profile analysis of molecular markers for identification and genetic discrimination of loaches (Pisces, Nemacheilidae).

    Science.gov (United States)

    Patil, Tejas Suresh; Tamboli, Asif Shabodin; Patil, Swapnil Mahadeo; Bhosale, Amrut Ravindra; Govindwar, Sanjay Prabhu; Muley, Dipak Vishwanathrao

    2016-01-01

    Genus Nemacheilus, Nemachilichthys and Schistura belong to the family Nemacheilidae of the order Cypriniformes. The present investigation was undertaken to observe genetic diversity, phylogenetic relationship and to develop a molecular-based tool for taxonomic identification. For this purpose, four different types of molecular markers were utilized in which 29 random amplified polymorphic DNA (RAPD), 25 inter-simple sequence repeat (ISSR) markers, and 10 amplified fragment length polymorphism (AFLP) marker sets were screened and mitochondrial COI gene was sequenced. This study added COI barcodes for the identification of Nemacheilus anguilla, Nemachilichthys rueppelli and Schistura denisoni. RAPD showed higher polymorphism (100%) than the ISSR (93.75-100%) and AFLP (93.86-98.96%). The polymorphic information content (PIC), heterozygosity, multiplex ratio, and gene diversity was observed highest for AFLP primers, whereas the major allele frequency was observed higher for RAPD (0.5556) and lowest for AFLP (0.1667). The COI region of all individuals was successfully amplified and sequenced, which gave a 100% species resolution. Copyright © 2016 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  4. Genetic diversity of Bemisia tabaci (Genn. Populations in Brazil revealed by RAPD markers

    Directory of Open Access Journals (Sweden)

    L.H.C. Lima

    2002-01-01

    Full Text Available Bemisia tabaci (Genn. was considered a secondary pest in Brazil until 1990, despite being an efficient geminivirus vector in beans and soybean. In 1991, a new biotype, known as B. tabaci B biotype (=B. argentifolii was detected attacking weed plants and causing phytotoxic problems in Cucurbitaceae. Nowadays, B. tabaci is considered one of the most damaging whitefly pests in agricultural systems worldwide that transmits more than 60 different plant viruses. Little is known about the genetic variability of these populations in Brazil. Knowledge of the genetic variation within whitefly populations is necessary for their efficient control and management. The objectives of the present study were to use RAPD markers (1 to estimate the genetic diversity of B. tabaci populations, (2 to study the genetic relationships among B. tabaci biotypes and two other whitefly species and (3 to discriminate between B. tabaci biotypes. A sample of 109 B. tabaci female individuals obtained from 12 populations in Brazil were analyzed and compared to the A biotype from Arizona (USA and B biotype from California (USA and Paraguay. Trialeurodes vaporariorum and Aleurodicus cocois samples were also included. A total of 72 markers were generated by five RAPD primers and used in the analysis. All primers produced RAPD patterns that clearly distinguished the Bemisia biotypes and the two other whitefly species. Results also showed that populations of the B biotype have considerable genetic variability. An average Jaccard similarity of 0.73 was observed among the B biotype individuals analyzed. Cluster analysis demonstrated that, in general, Brazilian biotype B individuals are scattered independently in the localities where samples were collected. Nevertheless, some clusters were evident, joining individuals according to the host plants. AMOVA showed that most of the total genetic variation is found within populations (56.70%, but a significant portion of the variation is found

  5. ASD and schizophrenia show distinct developmental profiles in common genetic overlap with population-based social-communication difficulties

    OpenAIRE

    St Pourcain, B.; Robinson, E.; Anttila, V.; Sullivan, B.; Maller, J.; Golding, J.; Skuse, D.; Ring, S.; Evans, D.; Zammit, S.; Fisher, S.; Neale, B.; Anney, R.; Ripke, S.; Hollegaard, M.

    2017-01-01

    Difficulties in social communication are part of the phenotypic overlap between autism spectrum disorders (ASD) and\\ud schizophrenia. Both conditions follow, however, distinct developmental patterns. Symptoms of ASD typically occur during early\\ud childhood, whereas most symptoms characteristic of schizophrenia do not appear before early adulthood. We investigated whether\\ud overlap in common genetic influences between these clinical conditions and impairments in social communication depends ...

  6. Comparative assessment of genetic diversity in Sesamum indicum L. using RAPD and SSR markers.

    Science.gov (United States)

    Dar, Aejaz Ahmad; Mudigunda, Sushma; Mittal, Pramod Kumar; Arumugam, Neelakantan

    2017-05-01

    Sesame (Sesamum indicum L.) is an ancient oilseed crop known for its nutty seeds and high-quality edible oil. It is an unexplored crop with a great economic potential. The present study deals with assessment of genetic diversity in the crop. Twenty two RAPD and 18 SSR primers were used for analysis of the 47 different sesame accessions grown in different agroclimatic zones of India. A total of 256 bands were obtained with RAPD primers, of which 191 were polymorphic. SSR primers gave 64 DNA bands, of which all of were polymorphic. The Jaccard's similarity coefficient of RAPD, SSR, and pooled RAPD and SSR data ranged from 0.510 to 0.885, 0.167 to 0.867, and 0.505 to 0.853, respectively. Maximum polymorphic information content was reported with SSRs (0.194) compared to RAPDs (0.186). Higher marker index was observed with RAPDs (1.426) than with SSRs (0.621). Similarly, maximum resolving power was found with RAPD (4.012) primers than with SSRs (0.884). The RAPD primer RPI-B11 and SSR primer S16 were the most informative in terms of describing genetic variability among the varieties under study. At a molecular level, the seed coat colour was distinguishable by the presence and absence of a group of marker amplicon/s. White and brown seeded varieties clustered close to each other, while black seeded varieties remained distanced from the cluster. In the present study, we found higher variability in Sesamum indicum L. using RAPD and SSR markers and these could assist in DNA finger printing, conservation of germplasm, and crop improvement.

  7. Evaluation of Mungbean Mutant Lines to Drought Stress and Their Genetic Relationships Using SSR Markers

    Directory of Open Access Journals (Sweden)

    Yuliasti

    2015-12-01

    Full Text Available Development of mungbean cultivarstolerant to drought stress through mutation breeding approach would enable us to anticipate the crop yield-reducing effects of climate changes. The objective of this research was to evaluate the yield performance of mungbean mutant lines that showed tolerance to drought stress, and to analyze their genetic diversity and relationship among mutant lines using SSR markers. The study was conducted during the dry season of 2012 in the Muneng experimental farm, Probolinggo, East Java. The experiment was laid out in a randomized block design with four replications. Five mutant lines and two parental lines as control were tested for evaluation of yield and drought tolerance under twoenvironments of two irrigation systems as treatment. The two environmental conditions consisted of optimal irrigation (at least three times: at planting, flowering and during pod filling and suboptimal irrigation (two times at planting and flowering. To evaluate genetic variation among selected mutant lines and their discrimination from parental lines in molecular level, a cluster analysis was performed using Unweighted Pair Group Method with Arithmetic Mean (UPGMA in the NTSYS software. The results showed that three mutant lines, including PsJ30, PsJ31, PsJ32 produced the highest grain yields of 1.17, 1.01, and 1.04 ton/ha, respectively, compared to the other mutant lines and the parents Gelatik (0.85 ton/ha and Perkutut (0.87 ton/ha as control check. Of those mutant lines, PSJ31 was the most tolerant to drought with sensitivity index value of 0.47. The PSJ31 has now been officially released as a new variety ( 2013, named as Muri which was identified to have high yield and tolerant to drought. Based on 23 SSR markers used for clustering analysis of those 3 selected mutant lines,9SSR markers (MBSS R033; satt137; MBSSR008; MBSSR203; MBSSR013; MBSSR021; MBSSR016; MBSSR136; and DMBSSR013 were successfully identified the three mungbean mutant

  8. TriMEDB: A database to integrate transcribed markers and facilitate genetic studies of the tribe Triticeae

    Directory of Open Access Journals (Sweden)

    Yoshida Takuhiro

    2008-06-01

    Full Text Available Abstract Background The recent rapid accumulation of sequence resources of various crop species ensures an improvement in the genetics approach, including quantitative trait loci (QTL analysis as well as the holistic population analysis and association mapping of natural variations. Because the tribe Triticeae includes important cereals such as wheat and barley, integration of information on the genetic markers in these crops should effectively accelerate map-based genetic studies on Triticeae species and lead to the discovery of key loci involved in plant productivity, which can contribute to sustainable food production. Therefore, informatics applications and a semantic knowledgebase of genome-wide markers are required for the integration of information on and further development of genetic markers in wheat and barley in order to advance conventional marker-assisted genetic analyses and population genomics of Triticeae species. Description The Triticeae mapped expressed sequence tag (EST database (TriMEDB provides information, along with various annotations, regarding mapped cDNA markers that are related to barley and their homologues in wheat. The current version of TriMEDB provides map-location data for barley and wheat ESTs that were retrieved from 3 published barley linkage maps (the barley single nucleotide polymorphism database of the Scottish Crop Research Institute, the barley transcript map of Leibniz Institute of Plant Genetics and Crop Plant Research, and HarvEST barley ver. 1.63 and 1 diploid wheat map. These data were imported to CMap to allow the visualization of the map positions of the ESTs and interrelationships of these ESTs with public gene models and representative cDNA sequences. The retrieved cDNA sequences corresponding to each EST marker were assigned to the rice genome to predict an exon-intron structure. Furthermore, to generate a unique set of EST markers in Triticeae plants among the public domain, 3472 markers were

  9. Genetic Background and Population Genetics of Hungarian Brown Trout Populations Using PCR-RFLP and Microsatellite Markers

    Directory of Open Access Journals (Sweden)

    Ágnes Ősz

    2015-12-01

    4 University of West Hungary, Mosonmagyaróvár Vár 2., 9200 Mosonmagyaróvár, Hungary Based on the analyses of the mitochondrial DNA of several European brown trout populations, five evolutionary lineages of brown trout were indentified (Atlantic, Danubian, Mediterranean, Adriatic, Marble. The species is bred primarily for stock enhancement of natural waters, however the most hatchery-maintained broodstocks originate from the Atlantic lineage. Due to the hydrogeography of Hungary our stocks should theoretically belong to the Danubian lineage; however, this has not been investigated earlier by genetic studies. For our genetic analysis, 702 fin clips were collected from two brown trout broodstocks (Lillafüred and Szilvásvárad as well as populations of natural streams (Bán, Jósva, Kemence, Apátkút, Bittva and Kölöntés in Hungary. Sequencing of the control region in mitochondrial DNA, three PCR-RFLP (mitochondrial DNA control region, lactate dehydrogenase and somatolactin genes and five microsatellite markers were used to distinguish between Danubian and Atlantic lineages of brown trout. The proportion of the mitochondrial haplotype of the Danubian lineage was low, with the exception of the Apátkúti, Kölöntés streams and Szilvásvárad broodstock. Analyses of nuclear PCR-RFLP and microsatellites markers showed various distributions of alleles characteristic of the Atlantic or Danubian lineages, although the Atlantic genotype has dominated in all population. In case of the analyses of microsatellites the polymorphism varied greatly at all locations. In addition we found several alleles that were not described earlier in other populations. Those alleles probably would be typical of Hungarian brown trout populations. Overall the populations were effectively in Hardy-Weinberg equilibrium for both PCR-RFLP and microsatellite markers. The remarkably high proportion of allochthonous Atlantic alleles in the analyzed sites is a clear indicator of the import

  10. Limited genetic diversity among Sarcocystis neurona strains infecting southern sea otters precludes distinction between marine and terrestrial isolates.

    Science.gov (United States)

    Wendte, J M; Miller, M A; Nandra, A K; Peat, S M; Crosbie, P R; Conrad, P A; Grigg, M E

    2010-04-19

    Sarcocystis neurona is an apicomplexan parasite identified as a cause of fatal neurological disease in the threatened southern sea otter (Enhydra lutris nereis). In an effort to characterize virulent S. neurona strains circulating in the marine ecosystem, this study developed a range of markers relevant for molecular genotyping. Highly conserved sequences within the 18S ribosomal gene array, the plastid-encoded RNA polymerase (RPOb) and the cytochrome c oxidase subunit 1 mitochondrial gene (CO1) were assessed for their ability to distinguish isolates at the genus and species level. For within-species comparisons, five surface antigens (SnSAG1-SnSAG5) and one high resolution microsatellite marker (Sn9) were developed as genotyping markers to evaluate intra-strain diversity. Molecular analysis at multiple loci revealed insufficient genetic diversity to distinguish terrestrial isolates from strains infecting marine mammals. Furthermore, SnSAG specific primers applied against DNA from the closely related species, Sarcocystis falcatula, lead to the discovery of highly similar orthologs to SnSAG2, 3, and 4, calling into question the specificity of diagnostic tests based on these antigens. The results of this study suggest a population genetic structure for S. neurona similar to that reported for the related parasite, Toxoplasma gondii, dominated by a limited number of successful genotypes. Published by Elsevier B.V.

  11. Genetic diversity and population structure of Pisum sativum accessions for marker-trait association of lipid content

    Directory of Open Access Journals (Sweden)

    Sajjad Ahmad

    2015-06-01

    Full Text Available Field pea (Pisum sativum L. is an important protein-rich pulse crop produced globally. Increasing the lipid content of Pisum seeds through conventional and contemporary molecular breeding tools may bring added value to the crop. However, knowledge about genetic diversity and lipid content in field pea is limited. An understanding of genetic diversity and population structure in diverse germplasm is important and a prerequisite for genetic dissection of complex characteristics and marker-trait associations. Fifty polymorphic microsatellite markers detecting a total of 207 alleles were used to obtain information on genetic diversity, population structure and marker-trait associations. Cluster analysis was performed using UPGMA to construct a dendrogram from a pairwise similarity matrix. Pea genotypes were divided into five major clusters. A model-based population structure analysis divided the pea accessions into four groups. Percentage lipid content in 35 diverse pea accessions was used to find potential associations with the SSR markers. Markers AD73, D21, and AA5 were significantly associated with lipid content using a mixed linear model (MLM taking population structure (Q and relative kinship (K into account. The results of this preliminary study suggested that the population could be used for marker-trait association mapping studies.

  12. Genetic relationships among Vietnamese local pigs investigated using genome-wide SNP markers.

    Science.gov (United States)

    Ishihara, S; Arakawa, A; Taniguchi, M; Luu, Q M; Pham, D L; Nguyen, B V; Mikawa, S; Kikuchi, K

    2018-02-01

    Vietnam is one of the most important countries for pig domestication, and a total of 26 local breeds have been reported. In the present study, genetic relationships among the various pig breeds were investigated using 90 samples collected from local pigs (15 breeds) in 15 distantly separated, distinct areas of the country and six samples from Landrace pigs in Hanoi as an out-group of a common Western breed. All samples were genotyped using the Illumina Porcine SNP60 v2 Genotyping BeadChip. We used 15 160-15 217 SNPs that showed a high degree of polymorphism in the Vietnamese breeds for identifying genetic relationships among the Vietnamese breeds. Principal components analysis showed that most pigs indigenous to Vietnam formed clusters correlated with their original geographic locations. Some Vietnamese breeds formed a cluster that was genetically related to the Western breed Landrace, suggesting the possibility of crossbreeding. These findings will be useful for the conservation and management of Vietnamese local pig breeds. © 2018 Stichting International Foundation for Animal Genetics.

  13. Multiplex Polymerase Chain Reaction for Identification of Shigellae and Four Shigella Species Using Novel Genetic Markers Screened by Comparative Genomics.

    Science.gov (United States)

    Kim, Hyun-Joong; Ryu, Ji-Oh; Song, Ji-Yeon; Kim, Hae-Yeong

    2017-07-01

    In the detection of Shigella species using molecular biological methods, previously known genetic markers for Shigella species were not sufficient to discriminate between Shigella species and diarrheagenic Escherichia coli. The purposes of this study were to screen for genetic markers of the Shigella genus and four Shigella species through comparative genomics and develop a multiplex polymerase chain reaction (PCR) for the detection of shigellae and Shigella species. A total of seven genomic DNA sequences from Shigella species were subjected to comparative genomics for the screening of genetic markers of shigellae and each Shigella species. The primer sets were designed from the screened genetic markers and evaluated using PCR with genomic DNAs from Shigella and other bacterial strains in Enterobacteriaceae. A novel Shigella quintuplex PCR, designed for the detection of Shigella genus, S. dysenteriae, S. boydii, S. flexneri, and S. sonnei, was developed from the evaluated primer sets, and its performance was demonstrated with specifically amplified results from each Shigella species. This Shigella multiplex PCR is the first to be reported with novel genetic markers developed through comparative genomics and may be a useful tool for the accurate detection of the Shigella genus and species from closely related bacteria in clinical microbiology and food safety.

  14. Development of a set of SSR markers for genetic polymorphism detection and interspecific hybrid jute breeding

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    Dipnarayan Saha

    2017-10-01

    Full Text Available Corchorus capsularis (white jute and C. olitorius (dark jute are the two principal cultivated species of jute that produce natural bast fiber of commercial importance. We have identified 4509 simple sequence repeat (SSR loci from 34,163 unigene sequences of C. capsularis to develop a non-redundant set of 2079 flanking primer pairs. Among the SSRs, trinucleotide repeats were most frequent (60% followed by dinucleotide repeats (37.6%. Annotation of the SSR-containing unigenes revealed their putative functions in various biological and molecular processes, including responses to biotic and abiotic signals. Eighteen expressed gene-derived SSR (eSSR markers were successfully mapped to the existing single-nucleotide polymorphism (SNP linkage map of jute, providing additional anchor points. Amplification of 72% of the 74 randomly selected primer pairs was successful in a panel of 24 jute accessions, comprising five and twelve accessions of C. capsularis and C. olitorius, respectively, and seven wild jute species. Forty-three primer pairs produced an average of 2.7 alleles and 58.1% polymorphism in a panel of 24 jute accessions. The mean PIC value was 0.34 but some markers showed PIC values higher than 0.5, suggesting that these markers can efficiently measure genetic diversity and serve for mapping of quantitative trait loci (QTLs in jute. A primer polymorphism survey with parents of a wide-hybridized population between a cultivated jute and its wild relative revealed their efficacy for interspecific hybrid identification. For ready accessibility of jute eSSR primers, we compiled all information in a user-friendly web database, JuteMarkerdb (http://jutemarkerdb.icar.gov.in/ for the first time in jute. This eSSR resource in jute is expected to be of use in characterization of germplasm, interspecific hybrid and variety identification, and marker-assisted breeding of superior-quality jute.

  15. Genetic Diversity and Identification of Chinese-Grown Pecan Using ISSR and SSR Markers

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    Zhong-Ren Guo

    2011-12-01

    Full Text Available Pecan is an important horticultural nut crop originally from North America and now widely cultivated in China for its high ecological, ornamental and economic value. Currently, there are over one hundred cultivars grown in China, including introduced American cultivars and Chinese seedling breeding cultivars. Molecular markers were used to assess the genetic diversity of these cultivars and to identify the pedigrees of fine pecan plants with good characteristics and no cultivar-related data. A total of 77 samples grown in China were studied, including 14 introduced cultivars, 12 domestic seedling breeding cultivars, and 49 fine pecan plants with no cultivar data, together with Carya cathayensis and Juglans nigra. A total of 77 ISSR and 19 SSR primers were prescreened; 10 ISSR and eight SSR primers were selected, yielding a total of 94 amplified bands (100% polymorphic in the range of 140–1,950 bp for the ISSR and 70 amplified bands (100% polymorphic in the range of 50–350 bp for SSR markers. Genetic diversity analyses indicated Chinese-grown pecan cultivars and fine plants had significant diversity at the DNA level. The dengrograms constructed with ISSR, SSR or combined data were very similar, but showed very weak grouping association with morphological characters. However, the progeny were always grouped with the parents. The great diversity found among the Chinese cultivars and the interesting germplasm of the fine pecan plants analyzed in this study are very useful for increasing the diversity of the pecan gene pool. All 77 accessions in this study could be separated based on the ISSR and SSR fingerprints produced by one or more primers. The results of our study also showed that ISSR and SSR techniques were both suitable for genetic diversity analyses and the identification of pecan resources.

  16. Genetic diversity and identification of Chinese-grown pecan using ISSR and SSR markers.

    Science.gov (United States)

    Jia, Xiao-Dong; Wang, Tao; Zhai, Min; Li, Yong-Rong; Guo, Zhong-Ren

    2011-12-06

    Pecan is an important horticultural nut crop originally from North America and now widely cultivated in China for its high ecological, ornamental and economic value. Currently, there are over one hundred cultivars grown in China, including introduced American cultivars and Chinese seedling breeding cultivars. Molecular markers were used to assess the genetic diversity of these cultivars and to identify the pedigrees of fine pecan plants with good characteristics and no cultivar-related data. A total of 77 samples grown in China were studied, including 14 introduced cultivars, 12 domestic seedling breeding cultivars, and 49 fine pecan plants with no cultivar data, together with Carya cathayensis and Juglans nigra. A total of 77 ISSR and 19 SSR primers were prescreened; 10 ISSR and eight SSR primers were selected, yielding a total of 94 amplified bands (100% polymorphic) in the range of 140-1,950 bp for the ISSR and 70 amplified bands (100% polymorphic) in the range of 50-350 bp for SSR markers. Genetic diversity analyses indicated Chinese-grown pecan cultivars and fine plants had significant diversity at the DNA level. The dengrograms constructed with ISSR, SSR or combined data were very similar, but showed very weak grouping association with morphological characters. However, the progeny were always grouped with the parents. The great diversity found among the Chinese cultivars and the interesting germplasm of the fine pecan plants analyzed in this study are very useful for increasing the diversity of the pecan gene pool. All 77 accessions in this study could be separated based on the ISSR and SSR fingerprints produced by one or more primers. The results of our study also showed that ISSR and SSR techniques were both suitable for genetic diversity analyses and the identification of pecan resources.

  17. Genetic Marker Discovery in Complex Traits: A Field Example on Fat Content and Composition in Pigs

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    Ramona Natacha Pena

    2016-12-01

    Full Text Available Among the large number of attributes that define pork quality, fat content and composition have attracted the attention of breeders in the recent years due to their interaction with human health and technological and sensorial properties of meat. In livestock species, fat accumulates in different depots following a temporal pattern that is also recognized in humans. Intramuscular fat deposition rate and fatty acid composition change with life. Despite indication that it might be possible to select for intramuscular fat without affecting other fat depots, to date only one depot-specific genetic marker (PCK1 c.2456C>A has been reported. In contrast, identification of polymorphisms related to fat composition has been more successful. For instance, our group has described a variant in the stearoyl-coA desaturase (SCD gene that improves the desaturation index of fat without affecting overall fatness or growth. Identification of mutations in candidate genes can be a tedious and costly process. Genome-wide association studies can help in narrowing down the number of candidate genes by highlighting those which contribute most to the genetic variation of the trait. Results from our group and others indicate that fat content and composition are highly polygenic and that very few genes explain more than 5% of the variance of the trait. Moreover, as the complexity of the genome emerges, the role of non-coding genes and regulatory elements cannot be disregarded. Prediction of breeding values from genomic data is discussed in comparison with conventional best linear predictors of breeding values. An example based on real data is given, and the implications in phenotype prediction are discussed in detail. The benefits and limitations of using large SNP sets versus a few very informative markers as predictors of genetic merit of breeding candidates are evaluated using field data as an example.

  18. Development of microsatellite markers to genetically differentiate populations of Octopus minor from Korea and China.

    Science.gov (United States)

    Kang, Jung-Ha; Kim, Yi-Kyung; Park, Jung-Youn; An, Chel-Min; Jun, Je-Chun

    2012-08-01

    Of the more than 300 octopus species, Octopus minor is one of the most popular and economically important species in Eastern Asia, including Korea, along with O. vulgaris, O. ocellatus, and O. aegina. We developed 19 microsatellite markers from Octopus minor and eight polymorphic markers were developed to analyze the genetic diversity and relationships among four octopus populations from Korea and three from China. The number of alleles per locus varied from 10 to 49, and allelic richness per locus ranged from 2 to 16.4 across all populations. The average allele number among the populations was 11.1, with a minimum of 8.3 and a maximum of 13.6. The mean allelic richness was 8.7 in all populations. The Hardy-Weinberg equilibrium (HWE) test revealed significant deviation in 19 of the 56 single-locus sites, and null alleles were presumed in five of eight loci. The pairwise F ( ST ) values between populations from Korea and China differed significantly in all pairwise comparisons. The genetic distances between the China and Korea samples ranged from 0.161 to 0.454. The genetic distances among the populations from Korea ranged from 0.033 to 0.090, with an average of 0.062; those among populations from China ranged from 0.191 to 0.316, with an average of 0.254. The populations from Korea and China formed clearly separated into clusters via an unweighted pair group method with arithmetic mean dendrogram. Furthermore, a population from muddy flats on the western coast of the Korean Peninsula and one from a rocky area on Jeju Island formed clearly separated subclusters. An assignment test based on the allele distribution discriminated between the Korean and Chinese origins with 96.9 % accuracy.

  19. Genetic diversity of sago palm in Indonesia based on chloroplast DNA (cpDNA markers

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    MEMEN SURAHMAN

    2010-07-01

    Full Text Available Abbas B, Renwarin Y, Bintoro MH, Sudarsono, Surahman M, Ehara H (2010 Genetic diversity of sago palm in Indonesia based on chloroplast DNA (cpDNA markers. Biodiversitas 11: 112-117. Sago palm (Metroxylon sagu Rottb. was believed capable to accumulate high carbohydrate content in its trunk. The capability of sago palm producing high carbohydrate should be an appropriate criterion for defining alternative crops in anticipating food crisis. The objective of this research was to study genetic diversity of sago palm in Indonesia based on cpDNA markers. Total genome extraction was done following the Qiagen DNA isolation protocols 2003. Single Nucleotide Fragments (SNF analyses were performed by using ABI Prism GeneScanR 3.7. SNF analyses detected polymorphism revealing eleven alleles and ten haplotypes from total 97 individual samples of sago palm. Specific haplotypes were found in the population from Papua, Sulawesi, and Kalimantan. Therefore, the three islands will be considered as origin of sago palm diversities in Indonesia. The highest haplotype numbers and the highest specific haplotypes were found in the population from Papua suggesting this islands as the centre and the origin of sago palm diversities in Indonesia. The research had however no sufficient data yet to conclude the Papua origin of sago palm. Genetic hierarchies and differentiations of sago palm samples were observed significantly different within populations (P=0.04574, among populations (P=0.04772, and among populations within the island (P=0.03366, but among islands no significant differentiations were observed (P= 0.63069.

  20. Assessment of Genetic Diversity in Opuntia spp. Portuguese Populations Using SSR Molecular Markers

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    Carlos M. G. Reis

    2018-04-01

    Full Text Available The Opuntia spp., most likely few individuals, were introduced in the Iberian Peninsula in the beginning of the 16th century, after the discovery of America, spreading afterwards throughout the Mediterranean basin. We analysed, for the first time, the genetic diversity in a set of 19 Portuguese Opuntia spp. populations from the species O. ficus-indica, O. elata, O. dillenii and O. robusta using nuclear microsatellite (nuSSR markers. The Italian cultivars ‘Bianca’, ‘Gialla’ and ‘Rossa’ were included in the study for comparison purposes. The nuSSR amplifications produced from five to 16 alleles, with an average of 9.2 alleles per primer pair, and average polymorphism information content of 0.71. The estimated Dice coefficient among populations varied from 0.26 to 1.0, indicating high interspecific genetic diversity but low genetic diversity at the intraspecific level. The hierarchical clustering analysis revealed four major groups that clearly separated the four Opuntia species. Among the O. ficus-indica populations, two sub-clusters were found, one including the white pulp fruits (with cv. Bianca and the other with the orange pulp ones and including the cv. Gialla, the cv. Rossa, and one pale yellow pulp population. No genetic differences were found between the inermis form, O. ficus-indica f. ficus-indica, and the rewilded spiny one, O. ficus-indica f. amyclaea. The dendrogram indicated that the clustering pattern was unrelated to geographical origin. The results revealed a low level of genetic diversity among the Portuguese populations of O. ficus-indica.

  1. Genetic diversity and phylogenetic relationship of Indonesian Local goats using microsatellite DNA markers

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    M Syamsul Arifin Zein

    2012-03-01

    Full Text Available Genetic diversity is important information in the process of conservation and sustainable utilization of animal genetic resources. Thirteen microsatellite markers were used to estimate the degree of genetic diversity on five Indonesian local goats. Results showed the highest average allele diversity present in the locus MAF70 (5.6 ± 2.9, and the lowest was in the locus MAF035 (1.6 ± 0.6, the average number of alleles per locus was 6 ± 2.3. The lowest average alleles diversity present was in the Gembrong goat (2.2 ± 1.1 and the highest was in the Jawarandu goat (4.9 ± 2.2. There is a unique alleles at loci MCM527 and present in all Indonesian local goat with the highest allele frequency on Peranakan Etawa (37.2% and lowest in Gembrong goat (7.9%. H0 ranged from 0.372 ± 0.173 (Gembrong to 0.540 ± 0.204 (Peranakan Etawa, and HE ranging from 0.249 ± 0.196 (Gembrong to 0.540 ± 0.212 (Peranakan Etawa.The genetic differentiation for inbreeding among population (FIS, within population (FIT, and average genetic differention (FST were 0,0208 (2,08%, 0,1532 (15,32%, and 0,1352 (13,52%, respectively. Locus ILSTS029, BMS1494, MAF035 and INRA0132 had a low PIC value (PIC 0.5. Phylogenetic relationship was consistent with the history of its development based on Kacang goat except was for Gembrong Goat. This research information can be used for conservation strategies and breeding programs on each population of Indonesian local goat.

  2. Using microsatellite markers to analyze genetic diversity in 14 sheep types in Iran

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    M. T. Vajed Ebrahimi

    2017-07-01

    Full Text Available Investigation of genetic relationship among populations has been traditionally based on the analysis of allele frequencies at different loci. The prime objective of this research was to measure the genetic polymorphism of five microsatellite markers (McMA2, BM6444, McMA26, HSC, and OarHH35 and study genetic diversity of 14 sheep types in Iran. Genomic DNA was extracted from blood samples of 565 individuals using an optimized salting-out DNA extraction procedure. The polymerase chain reaction (PCR was successfully performed with the specific primers. Some locus–population combinations were not at Hardy–Weinberg equilibrium (P < 0. 05. The microsatellite analysis revealed high allelic and gene diversity in all 14 breeds. Pakistani and Arabi breeds showed the highest mean number of alleles (11.8 and 11 respectively, while the highest value for polymorphic information content was observed for the Arabi breed (0.88. A UPGMA (unweighted pair group method with arithmetic mean dendrogram based on the Nei's standard genetic distance among studied breeds showed a separate cluster for Arabi and Pakistani breeds and another cluster for other breeds. The Shannon index (H0 for McMA2, BM6444, McMA26, HSC, and OarHH35 was 2.31, 2.17, 2.27, 2.04 and 2.18, respectively, and polymorphic information content (PIC values were 0.88, 0.92, 0.87, 0.84, and 0.86 for McMA2, BM6444, McMA26, HSC, and OarHH35, respectively. The high degree of variability demonstrated within the studied sheep types implies that these populations are rich reservoirs of genetic diversity that must be preserved.

  3. Unraveling the genetic structure of Brazilian commercial sugarcane cultivars through microsatellite markers.

    Science.gov (United States)

    Manechini, João Ricardo Vieira; da Costa, Juliana Borges; Pereira, Bruna Turcatto; Carlini-Garcia, Luciana Aparecida; Xavier, Mauro Alexandre; Landell, Marcos Guimarães de Andrade; Pinto, Luciana Rossini

    2018-01-01

    The Brazilian sugarcane industry plays an important role in the worldwide supply of sugar and ethanol. Investigation into the genetic structure of current commercial cultivars and comparisons to the main ancestor species allow sugarcane breeding programs to better manage crosses and germplasm banks as well as to promote its rational use. In the present study, the genetic structure of a group of Brazilian cultivars currently grown by commercial producers was assessed through microsatellite markers and contrasted with a group of basic germplasm mainly composed of Saccharum officinarum and S. spontaneum accessions. A total of 285 alleles was obtained by a set of 12 SSRs primer pairs that taken together were able to efficiently distinguish and capture the genetic variability of sugarcane commercial cultivars and basic germplasm accessions allowing its application in a fast and cost-effective way for routine cultivar identification and management of sugarcane germplasm banks. Allelic distribution revealed that 97.6% of the cultivar alleles were found in the basic germplasm while 42% of the basic germplasm alleles were absent in cultivars. Of the absent alleles, 3% was exclusive to S. officinarum, 33% to S. spontaneum and 19% to other species/exotic hybrids. We found strong genetic differentiation between the Brazilian commercial cultivars and the two main species (S. officinarum: [Formula: see text] = 0.211 and S. spontaneum: [Formula: see text] = 0.216, Pcommercial cultivars. Average dissimilarity within cultivars was 1.2 and 1.4 times lower than that within S. officinarum and S. spontaneum. Genetic divergence found between cultivars and S. spontaneum accessions has practical applications for energy cane breeding programs as the choice of more divergent parents will maximize the frequency of transgressive individuals in the progeny.

  4. Comparative linkage meta-analysis reveals regionally-distinct, disparate genetic architectures: application to bipolar disorder and schizophrenia.

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    Brady Tang

    2011-04-01

    Full Text Available New high-throughput, population-based methods and next-generation sequencing capabilities hold great promise in the quest for common and rare variant discovery and in the search for "missing heritability." However, the optimal analytic strategies for approaching such data are still actively debated, representing the latest rate-limiting step in genetic progress. Since it is likely a majority of common variants of modest effect have been identified through the application of tagSNP-based microarray platforms (i.e., GWAS, alternative approaches robust to detection of low-frequency (1-5% MAF and rare (<1% variants are of great importance. Of direct relevance, we have available an accumulated wealth of linkage data collected through traditional genetic methods over several decades, the full value of which has not been exhausted. To that end, we compare results from two different linkage meta-analysis methods--GSMA and MSP--applied to the same set of 13 bipolar disorder and 16 schizophrenia GWLS datasets. Interestingly, we find that the two methods implicate distinct, largely non-overlapping, genomic regions. Furthermore, based on the statistical methods themselves and our contextualization of these results within the larger genetic literatures, our findings suggest, for each disorder, distinct genetic architectures may reside within disparate genomic regions. Thus, comparative linkage meta-analysis (CLMA may be used to optimize low-frequency and rare variant discovery in the modern genomic era.

  5. Estimating additive and non-additive genetic variances and predicting genetic merits using genome-wide dense single nucleotide polymorphism markers.

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    Guosheng Su

    Full Text Available Non-additive genetic variation is usually ignored when genome-wide markers are used to study the genetic architecture and genomic prediction of complex traits in human, wild life, model organisms or farm animals. However, non-additive genetic effects may have an important contribution to total genetic variation of complex traits. This study presented a genomic BLUP model including additive and non-additive genetic effects, in which additive and non-additive genetic relation matrices were constructed from information of genome-wide dense single nucleotide polymorphism (SNP markers. In addition, this study for the first time proposed a method to construct dominance relationship matrix using SNP markers and demonstrated it in detail. The proposed model was implemented to investigate the amounts of additive genetic, dominance and epistatic variations, and assessed the accuracy and unbiasedness of genomic predictions for daily gain in pigs. In the analysis of daily gain, four linear models were used: 1 a simple additive genetic model (MA, 2 a model including both additive and additive by additive epistatic genetic effects (MAE, 3 a model including both additive and dominance genetic effects (MAD, and 4 a full model including all three genetic components (MAED. Estimates of narrow-sense heritability were 0.397, 0.373, 0.379 and 0.357 for models MA, MAE, MAD and MAED, respectively. Estimated dominance variance and additive by additive epistatic variance accounted for 5.6% and 9.5% of the total phenotypic variance, respectively. Based on model MAED, the estimate of broad-sense heritability was 0.506. Reliabilities of genomic predicted breeding values for the animals without performance records were 28.5%, 28.8%, 29.2% and 29.5% for models MA, MAE, MAD and MAED, respectively. In addition, models including non-additive genetic effects improved unbiasedness of genomic predictions.

  6. Genetic diversity analyses of Lasiodiplodia theobromae on Morus alba and Agave sisalana based on RAPD and ISSR molecular markers

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    Hong-hui Xie

    2016-10-01

    Full Text Available Genetic diversity of 23 Lasiodiplodia theobromae isolates on Morus alba and 6 isolates on Agave sisalana in Guangxi province, China, was studied by using random amplified polymorphic DNA and inter-simple sequence repeat molecular markers. Results of two molecular markers showed that the average percentage of polymorphic loci of all isolates was more than 93%. Both dendrograms of two molecular markers showed obvious relationship between groups and the geographical locations where those strains were collected, among which, the 23 isolates on M. alba were divided into 4 populations and the 6 isolates on A. sisalana were separated as a independent population. The average genetic identity and genetic distance of 5 populations were 0.7215, 0.3284 and 0.7915, 0.2347, respectively, which indicated that the genetic identity was high and the genetic distance was short in the 5 populations. Average value of the gene diversity index (H and the Shannon’s information index (I of 29 isolates were significantly higher than 5 populations which showed that genetic diversity of those isolates was richer than the populations and the degree of genetic differentiation of the isolates was higher. The Gst and Nm of 29 isolates were 0.4411, 0.6335 and 0.4756, 0.5513, respectively, which showed that the genetic diversity was rich in those isolates.

  7. Identification of intra-accession genetic diversity in selfing crops using AFLP markers: implications for collection management

    NARCIS (Netherlands)

    Treuren, van R.; Hintum, van Th.J.L.

    2001-01-01

    Germplasm conserved as seeds in genebanks requires regular regeneration. In this process, selection and genetic drift may cause loss of genetic diversity from accessions. In the case of selfing crops, separation of distinct lines into different accessions may be an efficient strategy to avoid these

  8. Genetic architecture and bottleneck analyses of Salem Black goat breed based on microsatellite markers

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    A. K. Thiruvenkadan

    2014-09-01

    Full Text Available Aim: The present study was undertaken in Salem Black goat population for genetic analysis at molecular level to exploit the breed for planning sustainable improvement, conservation and utilization, which subsequently can improve the livelihood of its stakeholders. Materials and Methods: Genomic DNA was isolated from blood samples of 50 unrelated Salem Black goats with typical phenotypic features in several villages in the breeding tract and the genetic characterization and bottleneck analysis in Salem Black goat was done using 25 microsatellite markers as recommended by the Food and Agricultural Organization, Rome, Italy. The basic measures of genetic variation were computed using bioinformatic software. To evaluate the Salem Black goats for mutation drift equilibrium, three tests were performed under three different mutation models, viz., infinite allele model (IAM, stepwise mutation model (SMM and two-phase model (TPM and the observed gene diversity (He and expected equilibrium gene diversity (Heq were estimated under different models of microsatellite evolution. Results: The study revealed that the observed number of alleles ranged from 4 (ETH10, ILSTS008 to 17 (BM64444 with a total of 213 alleles and mean of 10.14±0.83 alleles across loci. The overall observed heterozygosity, expected heterozygosity, inbreeding estimate and polymorphism information content values were 0.631±0.041, 0.820±0.024, 0.233±0.044 and 0.786±0.023 respectively indicating high genetic diversity. The average observed gene diversities (He pooled over different markers was 0.829±0.024 and the average expected gene diversities under IAM, TPM and SMM models were 0.769±0.026, 0.808±0.024 and 0.837±0.020 respectively. The number of loci found to exhibit gene diversity excess under IAM, TPM and SMM models were 18, 17 and 12 respectively. Conclusion: All the three statistical tests, viz., sign test, standardized differences test and Wilcoxon sign rank test, revealed

  9. [Genetic polymorphism of flax Linum usitatissimum based on use of molecular cytogenetic markers].

    Science.gov (United States)

    Rachinskaia, O A; Lemesh, V A; Muravenko, O V; Iurkevich, O Iu; Guzenko, E V; Bol'sheva, N L; Bogdanova, M V; Samatadze, T E; Popov, K V; Malyshev, S V; Shostak, N G; Heller, K; Khotyleva, L V; Zelenin, A V

    2011-01-01

    Using a set of approaches based on the use of molecular cytogenetic markers (DAPI/C-banding, estimation of the total area of DAPI-positive regions in prophase nuclei, FISH with 26S and 5S rDNA probes) and the microsatellite (SSR-PCR) assay, we studied genomic polymorphism in 15 flax (Linum usitatissimum L.) varieties from different geographic regions belonging to three directions of selection (oil, fiber, and intermediate flaxes) and in the k-37 x Viking hybrid. All individual chromosomes have been identified in the karyotypes of these varieties on the basis of the patterns of differential DAPI/C-banding and the distribution of 26S and 5S rDNA, and idiograms of the chromosomes have been generated. Unlike the oil flax varieties, the chromosomes in the karyotypes of the fiber flax varieties have, as a rule, pericentromeric and telomeric DAPI-positive bands of smaller size, but contain larger intercalary regions. Two chromosomal rearrangements (chromosome 3 inversions) were discovered in the variety Luna and in the k-37 x Viking hybrid. In both these forms, no colocalization of 26S rDNA and 5S rDNA on the satellite chromosome was detected. The SSR assay with the use of 20 polymorphic pairs of primers revealed 22 polymorphic loci. Based on the SSR data, we analyzed genetic similarity of the flax forms studied and constructed a genetic similarity dendrogram. The genotypes studied here form three clusters. The oil varieties comprise an independent cluster. The genetically related fiber flax varieties Vita and Luna, as well as the landrace Lipinska XIII belonging to the intermediate type, proved to be closer to the oil varieties than the remaining fiber flax varieties. The results of the molecular chromosomal analysis in the fiber and oil flaxes confirm their very close genetic similarity. In spite of this, the combined use of the chromosomal and molecular markers has opened up unique possibilities for describing the genotypes of flax varieties and creating their genetic

  10. ASD and schizophrenia show distinct developmental profiles in common genetic overlap with population-based social communication difficulties.

    Science.gov (United States)

    St Pourcain, B; Robinson, E B; Anttila, V; Sullivan, B B; Maller, J; Golding, J; Skuse, D; Ring, S; Evans, D M; Zammit, S; Fisher, S E; Neale, B M; Anney, R J L; Ripke, S; Hollegaard, M V; Werge, T; Ronald, A; Grove, J; Hougaard, D M; Børglum, A D; Mortensen, P B; Daly, M J; Davey Smith, G

    2018-02-01

    Difficulties in social communication are part of the phenotypic overlap between autism spectrum disorders (ASD) and schizophrenia. Both conditions follow, however, distinct developmental patterns. Symptoms of ASD typically occur during early childhood, whereas most symptoms characteristic of schizophrenia do not appear before early adulthood. We investigated whether overlap in common genetic influences between these clinical conditions and impairments in social communication depends on the developmental stage of the assessed trait. Social communication difficulties were measured in typically-developing youth (Avon Longitudinal Study of Parents and Children, N⩽5553, longitudinal assessments at 8, 11, 14 and 17 years) using the Social Communication Disorder Checklist. Data on clinical ASD (PGC-ASD: 5305 cases, 5305 pseudo-controls; iPSYCH-ASD: 7783 cases, 11 359 controls) and schizophrenia (PGC-SCZ2: 34 241 cases, 45 604 controls, 1235 trios) were either obtained through the Psychiatric Genomics Consortium (PGC) or the Danish iPSYCH project. Overlap in genetic influences between ASD and social communication difficulties during development decreased with age, both in the PGC-ASD and the iPSYCH-ASD sample. Genetic overlap between schizophrenia and social communication difficulties, by contrast, persisted across age, as observed within two independent PGC-SCZ2 subsamples, and showed an increase in magnitude for traits assessed during later adolescence. ASD- and schizophrenia-related polygenic effects were unrelated to each other and changes in trait-disorder links reflect the heterogeneity of genetic factors influencing social communication difficulties during childhood versus later adolescence. Thus, both clinical ASD and schizophrenia share some genetic influences with impairments in social communication, but reveal distinct developmental profiles in their genetic links, consistent with the onset of clinical symptoms.

  11. DNA-based genetic markers for Rapid Cycling Brassica rapa (Fast Plants type designed for the teaching laboratory.

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    Eryn E. Slankster

    2012-06-01

    Full Text Available We have developed DNA-based genetic markers for rapid-cycling Brassica rapa (RCBr, also known as Fast Plants. Although markers for Brassica rapa already exist, ours were intentionally designed for use in a teaching laboratory environment. The qualities we selected for were robust amplification in PCR, polymorphism in RCBr strains, and alleles that can be easily resolved in simple agarose slab gels. We have developed two single nucleotide polymorphism (SNP based markers and 14 variable number tandem repeat (VNTR-type markers spread over four chromosomes. The DNA sequences of these markers represent variation in a wide range of genomic features. Among the VNTR-type markers, there are examples of variation in a nongenic region, variation within an intron, and variation in the coding sequence of a gene. Among the SNP-based markers there are examples of polymorphism in intronic DNA and synonymous substitution in a coding sequence. Thus these markers can serve laboratory exercises in both transmission genetics and molecular biology.

  12. Comparison of relative efficiency of genomic SSR and EST-SSR markers in estimating genetic diversity in sugarcane.

    Science.gov (United States)

    Parthiban, S; Govindaraj, P; Senthilkumar, S

    2018-03-01

    Twenty-five primer pairs developed from genomic simple sequence repeats (SSR) were compared with 25 expressed sequence tags (EST) SSRs to evaluate the efficiency of these two sets of primers using 59 sugarcane genetic stocks. The mean polymorphism information content (PIC) of genomic SSR was higher (0.72) compared to the PIC value recorded by EST-SSR marker (0.62). The relatively low level of polymorphism in EST-SSR markers may be due to the location of these markers in more conserved and expressed sequences compared to genomic sequences which are spread throughout the genome. Dendrogram based on the genomic SSR and EST-SSR marker data showed differences in grouping of genotypes. A total of 59 sugarcane accessions were grouped into 6 and 4 clusters using genomic SSR and EST-SSR, respectively. The highly efficient genomic SSR could subcluster the genotypes of some of the clusters formed by EST-SSR markers. The difference in dendrogram observed was probably due to the variation in number of markers produced by genomic SSR and EST-SSR and different portion of genome amplified by both the markers. The combined dendrogram (genomic SSR and EST-SSR) more clearly showed the genetic relationship among the sugarcane genotypes by forming four clusters. The mean genetic similarity (GS) value obtained using EST-SSR among 59 sugarcane accessions was 0.70, whereas the mean GS obtained using genomic SSR was 0.63. Although relatively lower level of polymorphism was displayed by the EST-SSR markers, genetic diversity shown by the EST-SSR was found to be promising as they were functional marker. High level of PIC and low genetic similarity values of genomic SSR may be more useful in DNA fingerprinting, selection of true hybrids, identification of variety specific markers and genetic diversity analysis. Identification of diverse parents based on cluster analysis can be effectively done with EST-SSR as the genetic similarity estimates are based on functional attributes related to

  13. Evaluation of genetic diversity in jackfruit (Artocarpus heterophyllus Lam.) based on amplified fragment length polymorphism markers.

    Science.gov (United States)

    Shyamalamma, S; Chandra, S B C; Hegde, M; Naryanswamy, P

    2008-07-22

    Artocarpus heterophyllus Lam., commonly called jackfruit, is a medium-sized evergreen tree that bears high yields of the largest known edible fruit. Yet, it has been little explored commercially due to wide variation in fruit quality. The genetic diversity and genetic relatedness of 50 jackfruit accessions were studied using amplified fragment length polymorphism markers. Of 16 primer pairs evaluated, eight were selected for screening of genotypes based on the number and quality of polymorphic fragments produced. These primer combinations produced 5976 bands, 1267 (22%) of which were polymorphic. Among the jackfruit accessions, the similarity coefficient ranged from 0.137 to 0.978; the accessions also shared a large number of monomorphic fragments (78%). Cluster analysis and principal component analysis grouped all jackfruit genotypes into three major clusters. Cluster I included the genotypes grown in a jackfruit region of Karnataka, called Tamaka, with very dry conditions; cluster II contained the genotypes collected from locations having medium to heavy rainfall in Karnataka; cluster III grouped the genotypes in distant locations with different environmental conditions. Strong coincidence of these amplified fragment length polymorphism-based groupings with geographical localities as well as morphological characters was observed. We found moderate genetic diversity in these jackfruit accessions. This information should be useful for tree breeding programs, as part of our effort to popularize jackfruit as a commercial crop.

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

    Science.gov (United States)

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

    2007-06-20

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

  15. Evaluation of Pulasan (Nephelium ramboutan-ake Genetic Diversity in Bogor, West Java, Using Microsatellite Markers

    Directory of Open Access Journals (Sweden)

    Amelia Luisyane Puhili

    2016-11-01

    Full Text Available Pulasan (Nephelium ramboutan-ake (Labill. Leenh fruit is highly similar to rambutan rapiah (Nephelium lappaceum fruit with ovate shape, sweet and sour fresh taste, but it has a thick rind. The diversity of pulasan is little informed including in Bogor. The objective of this study was to analyze the genetic diversity of pulasan from Bogor revealed by microsatellite marker. The DNA of 63 individuals from 10 populations of pulasan were extracted using CTAB method and amplified using two primer sets, LMLY6 (GA9(CA2(GA4 dan LMLY12 (CT11. DNA amplification product was visualized and arranged in a matrix of binary data then analyzed the value of the number of different alleles (Na, the number of effective alleles (Ne, Shannon information index (I, heterozygosity (He, and the percentage of polymorphism (PLP. The results of the analysis showed the highest genetic diversity was found in North Bogor (He=0.313. The genetic diversity within a population (61% was higher than that among populations (39%. A dendrogram was constructed using the Unweighted Pair Group Method with arithmetic Mean (UPGMA. The similarity index ranged from 52 to 100% that means there are close relationships among individuals. Cluster analyses grouped some individuals originated from different locations in the same group. The levels of heterozygosity within a population was determined by the history of each individual in a population.

  16. Genetic diversity and geographical dispersal in grapevine clones revealed by microsatellite markers.

    Science.gov (United States)

    Moncada, Ximena; Pelsy, Frédérique; Merdinoglu, Didier; Hinrichsen, Patricio

    2006-11-01

    Intravarietal genetic diversification associated with geographical dispersal of a vegetatively propagated species was studied using grapevine Vitis vinifera L. 'Cabernet Sauvignon' as a model. Fifty-nine clonal samples obtained from 7 countries (France, Chile, Spain, Australia, Hungary, USA, and Italy) were analyzed using 84 microsatellite markers. Eighteen polymorphic microsatellite loci (21.4%) were detected, finding 22 different genotypes in the population analyzed with a genetic similarity of over 97%. The presence of chimeric clones was evidenced at locus VMC5g7 by means of a segregation analysis of descendants by self-pollination of a triallelic Chilean clone and by somatic embryogenesis analysis, showing a mutation in L2 cell layer. Only 2 clones (obtained from France and Australia) presented the ancestral genotype, and the most divergent genotype was exhibited by another French clone, which had accumulated 5 somatic mutations. The 2 largest populations considered (from France and Chile) showed a clear divergency in the polymorphisms detected. These antecedents enabled the tracing of geographical dispersal with a phylogenetic hypothesis supporting France as the center of origin of diversification of Cabernet Sauvignon. The results obtained could help to explain diversification processes in other grapevine cultivars. The possibility that this kind of genetic variability occurs in other vegetatively propagated species is discussed, focusing on possible fingerprinting applications.

  17. Distinct genetic difference between the Duffy binding protein (PkDBPαII) of Plasmodium knowlesi clinical isolates from North Borneo and Peninsular Malaysia.

    Science.gov (United States)

    Fong, Mun-Yik; Rashdi, Sarah A A; Yusof, Ruhani; Lau, Yee-Ling

    2015-02-21

    Plasmodium knowlesi is one of the monkey malaria parasites that can cause human malaria. The Duffy binding protein of P. knowlesi (PkDBPαII) is essential for the parasite's invasion into human and monkey erythrocytes. A previous study on P. knowlesi clinical isolates from Peninsular Malaysia reported high level of genetic diversity in the PkDBPαII. Furthermore, 36 amino acid haplotypes were identified and these haplotypes could be separated into allele group I and allele group II. In the present study, the PkDBPαII of clinical isolates from the Malaysian states of Sarawak and Sabah in North Borneo was investigated, and compared with the PkDBPαII of Peninsular Malaysia isolates. Blood samples from 28 knowlesi malaria patients were used. These samples were collected between 2011 and 2013 from hospitals in North Borneo. The PkDBPαII region of the isolates was amplified by PCR, cloned into Escherichia coli, and sequenced. The genetic diversity, natural selection and phylogenetics of PkDBPαII haplotypes were analysed using MEGA5 and DnaSP ver. 5.10.00 programmes. Forty-nine PkDBPαII sequences were obtained. Comparison at the nucleotide level against P. knowlesi strain H as reference sequence revealed 58 synonymous and 102 non-synonymous mutations. Analysis on these mutations showed that PkDBPαII was under purifying (negative) selection. At the amino acid level, 38 different PkDBPαII haplotypes were identified. Twelve of the 28 blood samples had mixed haplotype infections. Phylogenetic analysis revealed that all the haplotypes were in allele group I, but they formed a sub-group that was distinct from those of Peninsular Malaysia. Wright's FST fixation index indicated high genetic differentiation between the North Borneo and Peninsular Malaysia haplotypes. This study is the first to report the genetic diversity and natural selection of PkDBPαII of P. knowlesi from Borneo Island. The PkDBPαII haplotypes found in this study were distinct from those from

  18. Pheno2Geno - High-throughput generation of genetic markers and maps from molecular phenotypes for crosses between inbred strains.

    Science.gov (United States)

    Zych, Konrad; Li, Yang; van der Velde, Joeri K; Joosen, Ronny V L; Ligterink, Wilco; Jansen, Ritsert C; Arends, Danny

    2015-02-19

    Genetic markers and maps are instrumental in quantitative trait locus (QTL) mapping in segregating populations. The resolution of QTL localization depends on the number of informative recombinations in the population and how well they are tagged by markers. Larger populations and denser marker maps are better for detecting and locating QTLs. Marker maps that are initially too sparse can be saturated or derived de novo from high-throughput omics data, (e.g. gene expression, protein or metabolite abundance). If these molecular phenotypes are affected by genetic variation due to a major QTL they will show a clear multimodal distribution. Using this information, phenotypes can be converted into genetic markers. The Pheno2Geno tool uses mixture modeling to select phenotypes and transform them into genetic markers suitable for construction and/or saturation of a genetic map. Pheno2Geno excludes candidate genetic markers that show evidence for multiple possibly epistatically interacting QTL and/or interaction with the environment, in order to provide a set of robust markers for follow-up QTL mapping. We demonstrate the use of Pheno2Geno on gene expression data of 370,000 probes in 148 A. thaliana recombinant inbred lines. Pheno2Geno is able to saturate the existing genetic map, decreasing the average distance between markers from 7.1 cM to 0.89 cM, close to the theoretical limit of 0.68 cM (with 148 individuals we expect a recombination every 100/148=0.68 cM); this pinpointed almost all of the informative recombinations in the population. The Pheno2Geno package makes use of genome-wide molecular profiling and provides a tool for high-throughput de novo map construction and saturation of existing genetic maps. Processing of the showcase dataset takes less than 30 minutes on an average desktop PC. Pheno2Geno improves QTL mapping results at no additional laboratory cost and with minimum computational effort. Its results are formatted for direct use in R/qtl, the leading R

  19. Chromosome 15q25.1 genetic markers associated with level of response to alcohol in humans.

    Science.gov (United States)

    Joslyn, Geoff; Brush, Gerry; Robertson, Margaret; Smith, Tom L; Kalmijn, Jelger; Schuckit, Marc; White, Raymond L

    2008-12-23

    As with other genetically complex common psychiatric and medical conditions, multiple genetic and environmental components contribute to alcohol use disorders (AUDs), which can confound attempts to identify genetic components. Intermediate phenotypes are often more closely correlated with underlying biology and have often proven invaluable in genetic studies. Level of response (LR) to alcohol is an intermediate phenotype for AUDs, and individuals with a low LR are at increased risk. A high rate of concurrent alcohol and nicotine use and dependence suggests that these conditions may share biochemical and genetic mechanisms. Genetic association studies indicate that a genetic locus, which includes the CHRNA5-CHRNA3-CHRNB4 gene cluster, plays a role in nicotine consumption and dependence. Genetic association with alcohol dependence was also recently shown. We show here that two of the markers from the nicotine studies also show an association (multiple testing corrected P a sample of 367 siblings. Additional markers in the region were analyzed and shown to be located in a 250-kb expanse of high linkage disequilibrium containing three additional genes. These findings indicate that LR intermediate phenotypes have utility in genetic approaches to AUDs and will prove valuable in the identification of other genetic loci conferring susceptibility to AUDs.

  20. Genetic Diversity of Alternaria alternata Causal Agent of Early Blight of Tomato in Khuzestan Province Using SSRs Marker

    Directory of Open Access Journals (Sweden)

    Khoshnood Nourollahi

    2017-03-01

    Full Text Available Introduction: The early blight of tomato caused by Alternaria alternata is one of the most important and destructive diseases in Khuzestan province. Study genetic structure of A. alternata populations provides different levels of information in the management of early blight disease in tomato farms. Short sequence repeat (SSR markers were used to determine the genetic structure and estimate genetic diversity in A. alternata isolates in Khuzestan province. Materials and Methods: In this study to evaluate the genetic diversity and genetic populations of A. alternata pathogen, sampling was randomly carried out on aerial parts of tomato plants with leaf brown lesions in farms and glasshouses from five different regions in Khuzestan province such as: Shoshtar, Omidiyeh, Dashte azadagan, Ahvaz, and Dezful. Each sample was cut into 2–5-mm long pieces, were surface-sterilized with 1% sodium hypochlorite for 3 min and rinsed three times with sterile distilled water and air-dried with sterile filter paper. The sterilized samples were placed onto a general medium potato dextrose agar (PDA. A total of 64 A. alternata isolates were obtained from infected samples. Pathogenicity test was carried out on local susceptible cultivar under an artificial condition in the greenhouse. For obtaining the mycelia mass, liquid cultures were initiated by adding 2–4 mm 2 pieces of filter paper to 250-mL Erlenmeyer flasks containing 100 mL PDB medium (potato dextrose broth. Mycelium was collected by filtration through sterile filter paper with a vacuum funnel. Mycelia were harvested, frozen and stored at -20°C. DNA was extracted using a modified hexadecyl trimethyl-ammonium bromide (CTAB procedure. A set of five paired sequence repeat primers (SSR were used to determine the genetic diversity of A. alternata isolates. PCR amplification was performed in a 25 μl reaction volume. The bands generated by SSR primers that were repeatable and clearly visible with a high

  1. The Distinct Genetics of Carbonaceous and Non-Carbonaceous Meteorites Inferred from Molybdenum Isotopes

    Science.gov (United States)

    Budde, G.; Burkhardt, C.; Kleine, T.

    2017-07-01

    Mo isotope systematics manifest a fundamental dichotomy in the genetic heritage of carbonaceous and non-carbonaceous meteorites. We discuss its implications in light of the most recent literature data and new isotope data for primitive achondrites.

  2. Development, cross-species/genera transferability of novel EST-SSR markers and their utility in revealing population structure and genetic diversity in sugarcane

    KAUST Repository

    Singh, Ram K.

    2013-07-01

    Sugarcane (Saccharum spp. hybrid) with complex polyploid genome requires a large number of informative DNA markers for various applications in genetics and breeding. Despite the great advances in genomic technology, it is observed in several crop species, especially in sugarcane, the availability of molecular tools such as microsatellite markers are limited. Now-a-days EST-SSR markers are preferred to genomic SSR (gSSR) as they represent only the functional part of the genome, which can be easily associated with desired trait. The present study was taken up with a new set of 351 EST-SSRs developed from the 4085 non redundant EST sequences of two Indian sugarcane cultivars. Among these EST-SSRs, TNR containing motifs were predominant with a frequency of 51.6%. Thirty percent EST-SSRs showed homology with annotated protein. A high frequency of SSRs was found in the 5\\'UTR and in the ORF (about 27%) and a low frequency was observed in the 3\\'UTR (about 8%). Two hundred twenty-seven EST-SSRs were evaluated, in sugarcane, allied genera of sugarcane and cereals, and 134 of these have revealed polymorphism with a range of PIC value 0.12 to 0.99. The cross transferability rate ranged from 87.0% to 93.4% in Saccharum complex, 80.0% to 87.0% in allied genera, and 76.0% to 80.0% in cereals. Cloning and sequencing of EST-SSR size variant amplicons revealed that the variation in the number of repeat-units was the main source of EST-SSR fragment polymorphism. When 124 sugarcane accessions were analyzed for population structure using model-based approach, seven genetically distinct groups or admixtures thereof were observed in sugarcane. Results of principal coordinate analysis or UPGMA to evaluate genetic relationships delineated also the 124 accessions into seven groups. Thus, a high level of polymorphism adequate genetic diversity and population structure assayed with the EST-SSR markers not only suggested their utility in various applications in genetics and genomics in

  3. Genetic distinction between contiguous urban and rural multimammate mice in Tanzania despite gene flow

    Czech Academy of Sciences Publication Activity Database

    Gryseels, S.; Goüy de Bellocq, Joëlle; Makundi, R.; Vanmechelen, K.; Broeckhove, J.; Mazoch, V.; Šumbera, R.; Zima Jr., Jan; Leirs, H.; Baird, Stuart J. E.

    2016-01-01

    Roč. 29, č. 10 (2016), s. 1952-1967 ISSN 1010-061X R&D Projects: GA ČR GCP502/11/J070; GA ČR GAP506/10/0983; GA MŠk EE2.3.20.0303 Institutional support: RVO:68081766 Keywords : Mastomys natalensis * urbanisation * synanthropy * population genetics * IMa2 * spatial genetics * Tanzania Subject RIV: EG - Zoology Impact factor: 2.792, year: 2016

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

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    Jorge Assis

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

  5. Genetic diversity in a Colombian bean (Phaseolus vulgaris L. collection as assessed by phaseolin patterns and isoenzymatic markers

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    Gustavo Ligarreto

    2012-08-01

    Full Text Available The knowledge of genetic diversity patterns increase the efficiency of the conservation and the enrichment of the genetic resourses. This study allowed the discrimination of the existing genetic variability in a Colombian collection of shrub bean by phaseolin patterns and isoenzymatic markers. Bean seed proteins revelated that the phaseolin patterns types T and C are predominant in the Andean pool, type S in the Meso-American pool and type B in Colombian and Central American accessions, with a predominance of 81% of phaseolin T in the Andean pool, and 78% of phaseolin B in the Meso-American pool. The accessions of cultivated and wild beans showed variation in 10 of the studied enzymatic systems: αβ-EST , GOT, αβ-ACP, DIA , PRX, AS D, 6-PGDH, MDH, IDH and ME; and monomorphism in the PGI and PGM systems. The isozyme systems presented 19 bands of activity, of which 74% were polymorphic loci. Both in the Andean and Meso-American genetic pools, the loci Mdh-1, Mdh-2, β-Est-1, Skdh and Me exhibited polymorphisms. Single alleles in the Meso-American pool were found in 6-Pgdh-2(103, Mdh-1(100, Idh100, α-Est-1(100, α-Est-2(100, and Dia-195; and in the Andean pool, in 6-Pgdh-1(100, and Acp-2(100. For degree of domestication, the wild and cultivated accessions presented polymorphisms in 58 and 47% of the lOCi, respectively. The enzymatic relationship cluster analysis of the studied bean collection revealed three distinct groups of accessions; namely the Meso-American pool, including its cultivated and wild accessions; the Andean pool, which is mainly comprised of cultivated accessions, plus the wild DGD-626; and finally, featured by a high degree of enzymatic polymorphism and by the presence of the type I phaseolin, a third group that contains only a wild accession from the northern, Peruvian Andes

  6. Inferring Genetic Variation and Demographic History of Michelia yunnanensis Franch. (Magnoliaceae from Chloroplast DNA Sequences and Microsatellite Markers

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    Shikang Shen

    2017-04-01

    Full Text Available Michelia yunnanensis Franch., is a traditional ornamental, aromatic, and medicinal shrub that endemic to Yunnan Province in southwest China. Although the species has a large distribution pattern and is abundant in Yunnan Province, the populations are dramatically declining because of overexploitation and habitat destruction. Studies on the genetic variation and demography of endemic species are necessary to develop effective conservation and management strategies. To generate such knowledge, we used 3 pairs of universal cpDNA markers and 10 pairs of microsatellite markers to assess the genetic diversity, genetic structure, and demographic history of 7 M. yunnanensis populations. We calculated a total of 88 alleles for 10 polymorphic loci and 10 haplotypes for a combined 2,089 bp of cpDNA. M. yunnanensis populations showed high genetic diversity (Ho = 0.551 for nuclear markers and Hd = 0.471 for cpDNA markers and low genetic differentiation (FST = 0.058. Geographical structure was not found among M. yunnanensis populations. Genetic distance and geographic distance were not correlated (P > 0.05, which indicated that geographic isolation is not the primary cause of the low genetic differentiation of M. yunnanensis. Additionally, M. yunnanensis populations contracted ~20,000–30,000 years ago, and no recent expansion occurred in current populations. Results indicated that the high genetic diversity of the species and within its populations holds promise for effective genetic resource management and sustainable utilization. Thus, we suggest that the conservation and management of M. yunnanensis should address exotic overexploitation and habitat destruction.

  7. Intra-specific genetic relationship analyses of Elaeagnus angustifolia based on RP-HPLC biochemical markers

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Elaeagnus angustifolia Linn. has various ecological, medicinal and economical uses. An approach was established using RP-HPLC (reversed-phase high-performance liquid chromatography) to classify and analyse the intra-specific genetic relationships of seventeen populations of E. angustifolia, collected from the Xinjiang areas of China. Chromatograms of alcohol-soluble proteins produced by seventeen populations ofE. angustifolia, were compared. Each chromatogram of alcohol-soluble proteins came from a single seed of one wild plant only. The results showed that when using a Waters Delta Pak. C18, 5 μm particle size reversed phase column (150 mm×3.9 mm), a linear gradient of 25%~60% solvent B with flow rate of 1 ml/min and run time of 67 min, the chromatography yielded optimum separation ofE. angustifolia alcohol-soluble proteins. Representative peaks in each population were chosen according to peak area and occurrence in every seed. The converted data on the elution peaks of each population were different and could be used to represent those populations. GSC (genetic similarity coefficients) of 41% to 62% showed a medium degree of genetic diversity among the populations in these eco-areas. Cluster analysis showed that the seventeen populations ofE. angustifolia could be divided into six clusters at the GSC=0.535 level and indicated the general and unique biochemical markers of these clusters. We suggest that E. angustifolia distribution in these eco-areas could be classified into six variable species. RP-HPLC was shown to be a rapid, repeatable and reliable method for E. angustifolia classification and identification and for analysis of genetic diversity.

  8. Genetic Diversity in Various Accessions of Pineapple [Ananas comosus (L.) Merr.] Using ISSR and SSR Markers.

    Science.gov (United States)

    Wang, Jian-Sheng; He, Jun-Hu; Chen, Hua-Rui; Chen, Ye-Yuan; Qiao, Fei

    2017-12-01

    Inter simple sequence repeat (ISSR) and simple sequence repeat (SSR) markers were used to assess the genetic diversity of 36 pineapple accessions that were introduced from 10 countries/regions. Thirteen ISSR primers amplified 96 bands, of which 91 (93.65%) were polymorphic, whereas 20 SSR primers amplified 73 bands, of which 70 (96.50%) were polymorphic. Nei's gene diversity (h = 0.28), Shannon's information index (I = 0.43), and polymorphism information content (PIC = 0.29) generated using the SSR primers were higher than that with ISSR primers (h =  0.23, I = 0.37, PIC = 0.24), thereby suggesting that the SSR system is more efficient than the ISSR system in assessing genetic diversity in various pineapple accessions. Mean genetic similarities were 0.74, 0.61, and 0.69, as determined using ISSR, SSR, and combined ISSR/SSR, respectively. These results suggest that the genetic diversity among pineapple accessions is very high. We clustered the 36 pineapple accessions into three or five groups on the basis of the phylogenetic trees constructed based on the results of ISSR, SSR, and combined ISSR/SSR analyses using the unweighted pair-group with arithmetic averaging (UPGMA) method. The results of principal components analysis (PCA) also supported the UPGMA clustering. These results will be useful not only for the scientific conservation and management of pineapple germplasm but also for the improvement of the current pineapple breeding strategies.

  9. Comparison of SSR and SNP markers in estimation of genetic diversity and population structure of Indian rice varieties.

    Directory of Open Access Journals (Sweden)

    Nivedita Singh

    Full Text Available Simple sequence repeat (SSR and Single Nucleotide Polymorphic (SNP, the two most robust markers for identifying rice varieties were compared for assessment of genetic diversity and population structure. Total 375 varieties of rice from various regions of India archived at the Indian National GeneBank, NBPGR, New Delhi, were analyzed using thirty six genetic markers, each of hypervariable SSR (HvSSR and SNP which were distributed across 12 rice chromosomes. A total of 80 alleles were amplified with the SSR markers with an average of 2.22 alleles per locus whereas, 72 alleles were amplified with SNP markers. Polymorphic information content (PIC values for HvSSR ranged from 0.04 to 0.5 with an average of 0.25. In the case of SNP markers, PIC values ranged from 0.03 to 0.37 with an average of 0.23. Genetic relatedness among the varieties was studied; utilizing an unrooted tree all the genotypes were grouped into three major clusters with both SSR and SNP markers. Analysis of molecular variance (AMOVA indicated that maximum diversity was partitioned between and within individual level but not between populations. Principal coordinate analysis (PCoA with SSR markers showed that genotypes were uniformly distributed across the two axes with 13.33% of cumulative variation whereas, in case of SNP markers varieties were grouped into three broad groups across two axes with 45.20% of cumulative variation. Population structure were tested using K values from 1 to 20, but there was no clear population structure, therefore Ln(PD derived Δk was plotted against the K to determine the number of populations. In case of SSR maximum Δk was at K=5 whereas, in case of SNP maximum Δk was found at K=15, suggesting that resolution of population was higher with SNP markers, but SSR were more efficient for diversity analysis.

  10. Comparison of SSR and SNP markers in estimation of genetic diversity and population structure of Indian rice varieties.

    Science.gov (United States)

    Singh, Nivedita; Choudhury, Debjani Roy; Singh, Amit Kumar; Kumar, Sundeep; Srinivasan, Kalyani; Tyagi, R K; Singh, N K; Singh, Rakesh

    2013-01-01

    Simple sequence repeat (SSR) and Single Nucleotide Polymorphic (SNP), the two most robust markers for identifying rice varieties were compared for assessment of genetic diversity and population structure. Total 375 varieties of rice from various regions of India archived at the Indian National GeneBank, NBPGR, New Delhi, were analyzed using thirty six genetic markers, each of hypervariable SSR (HvSSR) and SNP which were distributed across 12 rice chromosomes. A total of 80 alleles were amplified with the SSR markers with an average of 2.22 alleles per locus whereas, 72 alleles were amplified with SNP markers. Polymorphic information content (PIC) values for HvSSR ranged from 0.04 to 0.5 with an average of 0.25. In the case of SNP markers, PIC values ranged from 0.03 to 0.37 with an average of 0.23. Genetic relatedness among the varieties was studied; utilizing an unrooted tree all the genotypes were grouped into three major clusters with both SSR and SNP markers. Analysis of molecular variance (AMOVA) indicated that maximum diversity was partitioned between and within individual level but not between populations. Principal coordinate analysis (PCoA) with SSR markers showed that genotypes were uniformly distributed across the two axes with 13.33% of cumulative variation whereas, in case of SNP markers varieties were grouped into three broad groups across two axes with 45.20% of cumulative variation. Population structure were tested using K values from 1 to 20, but there was no clear population structure, therefore Ln(PD) derived Δk was plotted against the K to determine the number of populations. In case of SSR maximum Δk was at K=5 whereas, in case of SNP maximum Δk was found at K=15, suggesting that resolution of population was higher with SNP markers, but SSR were more efficient for diversity analysis.

  11. New STS molecular markers for assessment of genetic diversity and DNA fingerprinting in hop (Humulus lupulus L.).

    Science.gov (United States)

    Patzak, Josef; Vrba, Lukás; Matousek, Jaroslav

    2007-01-01

    Molecular markers have been increasingly used in genetic studies of crop species for their applicability in breeding programs. In this work, we report on the development of new sequence-tagged site (STS) markers based on sequence information from several identified hop (Humulus lupulus L.) genes. We demonstrate the usefulness of these STS markers and compare them to SSRs for identifying hop genotypes and estimating genetic diversity in a collection of 68 hop cultivars from around the world. We found 3 individual gene variants (A, B, C) of the chs_H1 gene in this collection. The most frequent gene variant, B (AJ304877), was not detected in Mt. Hood, Glacier, and Horizon (US) cultivars. Gene variant A came from an American germplasm through wild hops. We found length polymorphism in intron 1 of the chs2 gene, and 4 different amplified markers were detected in PCRs. The chs3 gene was found in only one third of the cultivars. None of the variants of the studied CHS genes were found in Humulus japonicus. We detected 5 major gene variants of DNA-binding protein in the collection of H. lupulus cultivars and 2 others in H. japonicus. We also found 3 individual gene variants of an endochitinase gene. The distribution of gene variants did not correlate with any resistance. We proved that developed STS markers can be successfully used for the analysis of genetic diversity and can substitute and supplement SSR markers in hop.

  12. Characterization and comparison of EST-SSR and TRAP markers for genetic analysis of the Japanese persimmon Diospyros kaki.

    Science.gov (United States)

    Luo, C; Zhang, F; Zhang, Q L; Guo, D Y; Luo, Z R

    2013-01-09

    We developed and characterized expressed sequence tags (ESTs)-simple sequence repeats (SSRs) and targeted region amplified polymorphism (TRAP) markers to examine genetic relationships in the persimmon genus Diospyros gene pool. In total, we characterized 14 EST-SSR primer pairs and 36 TRAP primer combinations, which were amplified across 20 germplasms of 4 species in the genus Diospyros. We used various genetic parameters, including effective multiplex ratio (EMR), diversity index (DI), and marker index (MI), to test the utility of these markers. TRAP markers gave higher EMR (24.85) but lower DI (0.33), compared to EST-SSRs (EMR = 3.65, DI = 0.34). TRAP gave a very high MI (8.08), which was about 8 times than the MI of EST-SSR (1.25). These markers were utilized for phylogenetic inference of 20 genotypes of Diospyros kaki Thunb. and allied species, with a result that all kaki genotypes clustered closely and 3 allied species formed an independent group. These markers could be further exploited for large-scale genetic relationship inference.

  13. Using SNP markers to estimate additive, dominance and imprinting genetic variance

    DEFF Research Database (Denmark)

    Lopes, M S; Bastiaansen, J W M; Janss, Luc

    The contributions of additive, dominance and imprinting effects to the variance of number of teats (NT) were evaluated in two purebred pig populations using SNP markers. Three different random regression models were evaluated, accounting for the mean and: 1) additive effects (MA), 2) additive...... and dominance effects (MAD) and 3) additive, dominance and imprinting effects (MADI). Additive heritability estimates were 0.30, 0.28 and 0.27-0.28 in both lines using MA, MAD and MADI, respectively. Dominance heritability ranged from 0.06 to 0.08 using MAD and MADI. Imprinting heritability ranged from 0.......01 to 0.02. Dominance effects make an important contribution to the genetic variation of NT in the two lines evaluated. Imprinting effects appeared less important for NT than additive and dominance effects. The SNP random regression model presented and evaluated in this study is a feasible approach...

  14. Characterisation of genetic markers in Mungbean using direct amplification of length polymorphisms (DALP)

    International Nuclear Information System (INIS)

    Kumar, S.V.; Tan, S.G.; Quah, S.C.

    2000-01-01

    A newly developed technique, Direct Amplification of Length Polymorphisms (DALP), developed by Desmarais and co-workers in 1998 was successfully used to identify and characterise new genetic markers in mungbean (Vigyia radiata). DALP uses an arbitrarily primed PCR (AP-PCR) to produce genomic fingerprints and is specifically designed to enable direct sequencing of polymorphic bands. In this study, an oligonucleotide pair DALP235 and DAPLR were tested on four varieties of mungbean (V3476, P4281, V5973 and V5784) and produced, through PCR, specific multibanded fingerprints which showed polymorphisms. These polymorphic bands are the result of length polymorphisms as well as absence and presence of bands. Some of the polymorphic zones may be codominantly inherited and may be potential microsatellites. The success of DALP in characterising new polymorphic loci and its ability to discover microsatellites without the use of priori knowledge of the mungbean genome is revolutionary. This would greatly facilitate the breeding and improvement of the crop. (author)

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

    International Nuclear Information System (INIS)

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

    2010-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-04-15

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

  17. Development of cleaved amplified polymorphic sequence markers and a CAPS-based genetic linkage map in watermelon (Citrullus lanatus [Thunb.] Matsum. and Nakai) constructed using whole-genome re-sequencing data.

    Science.gov (United States)

    Liu, Shi; Gao, Peng; Zhu, Qianglong; Luan, Feishi; Davis, Angela R; Wang, Xiaolu

    2016-03-01

    Cleaved amplified polymorphic sequence (CAPS) markers are useful tools for detecting single nucleotide polymorphisms (SNPs). This study detected and converted SNP sites into CAPS markers based on high-throughput re-sequencing data in watermelon, for linkage map construction and quantitative trait locus (QTL) analysis. Two inbred lines, Cream of Saskatchewan (COS) and LSW-177 had been re-sequenced and analyzed by Perl self-compiled script for CAPS marker development. 88.7% and 78.5% of the assembled sequences of the two parental materials could map to the reference watermelon genome, respectively. Comparative assembled genome data analysis provided 225,693 and 19,268 SNPs and indels between the two materials. 532 pairs of CAPS markers were designed with 16 restriction enzymes, among which 271 pairs of primers gave distinct bands of the expected length and polymorphic bands, via PCR and enzyme digestion, with a polymorphic rate of 50.94%. Using the new CAPS markers, an initial CAPS-based genetic linkage map was constructed with the F2 population, spanning 1836.51 cM with 11 linkage groups and 301 markers. 12 QTLs were detected related to fruit flesh color, length, width, shape index, and brix content. These newly CAPS markers will be a valuable resource for breeding programs and genetic studies of watermelon.

  18. Annotated genetic linkage maps of Pinus pinaster Ait. from a Central Spain population using microsatellite and gene based markers.

    Science.gov (United States)

    de Miguel, Marina; de Maria, Nuria; Guevara, M Angeles; Diaz, Luis; Sáez-Laguna, Enrique; Sánchez-Gómez, David; Chancerel, Emilie; Aranda, Ismael; Collada, Carmen; Plomion, Christophe; Cabezas, José-Antonio; Cervera, María-Teresa

    2012-10-04

    Pinus pinaster Ait. is a major resin producing species in Spain. Genetic linkage mapping can facilitate marker-assisted selection (MAS) through the identification of Quantitative Trait Loci and selection of allelic variants of interest in breeding populations. In this study, we report annotated genetic linkage maps for two individuals (C14 and C15) belonging to a breeding program aiming to increase resin production. We use different types of DNA markers, including last-generation molecular markers. We obtained 13 and 14 linkage groups for C14 and C15 maps, respectively. A total of 211 and 215 markers were positioned on each map and estimated genome length was between 1,870 and 2,166 cM respectively, which represents near 65% of genome coverage. Comparative mapping with previously developed genetic linkage maps for P. pinaster based on about 60 common markers enabled aligning linkage groups to this reference map. The comparison of our annotated linkage maps and linkage maps reporting QTL information revealed 11 annotated SNPs in candidate genes that co-localized with previously reported QTLs for wood properties and water use efficiency. This study provides genetic linkage maps from a Spanish population that shows high levels of genetic divergence with French populations from which segregating progenies have been previously mapped. These genetic maps will be of interest to construct a reliable consensus linkage map for the species. The importance of developing functional genetic linkage maps is highlighted, especially when working with breeding populations for its future application in MAS for traits of interest.

  19. Annotated genetic linkage maps of Pinus pinaster Ait. from a Central Spain population using microsatellite and gene based markers

    Directory of Open Access Journals (Sweden)

    de Miguel Marina

    2012-10-01

    Full Text Available Abstract Background Pinus pinaster Ait. is a major resin producing species in Spain. Genetic linkage mapping can facilitate marker-assisted selection (MAS through the identification of Quantitative Trait Loci and selection of allelic variants of interest in breeding populations. In this study, we report annotated genetic linkage maps for two individuals (C14 and C15 belonging to a breeding program aiming to increase resin production. We use different types of DNA markers, including last-generation molecular markers. Results We obtained 13 and 14 linkage groups for C14 and C15 maps, respectively. A total of 211 and 215 markers were positioned on each map and estimated genome length was between 1,870 and 2,166 cM respectively, which represents near 65% of genome coverage. Comparative mapping with previously developed genetic linkage maps for P. pinaster based on about 60 common markers enabled aligning linkage groups to this reference map. The comparison of our annotated linkage maps and linkage maps reporting QTL information revealed 11 annotated SNPs in candidate genes that co-localized with previously reported QTLs for wood properties and water use efficiency. Conclusions This study provides genetic linkage maps from a Spanish population that shows high levels of genetic divergence with French populations from which segregating progenies have been previously mapped. These genetic maps will be of interest to construct a reliable consensus linkage map for the species. The importance of developing functional genetic linkage maps is highlighted, especially when working with breeding populations for its future application in MAS for traits of interest.

  20. DOMINO: development of informative molecular markers for phylogenetic and genome-wide population genetic studies in non-model organisms.

    Science.gov (United States)

    Frías-López, Cristina; Sánchez-Herrero, José F; Guirao-Rico, Sara; Mora, Elisa; Arnedo, Miquel A; Sánchez-Gracia, Alejandro; Rozas, Julio

    2016-12-15

    The development of molecular markers is one of the most important challenges in phylogenetic and genome wide population genetics studies, especially in studies with non-model organisms. A highly promising approach for obtaining suitable markers is the utilization of genomic partitioning strategies for the simultaneous discovery and genotyping of a large number of markers. Unfortunately, not all markers obtained from these strategies provide enough information for solving multiple evolutionary questions at a reasonable taxonomic resolution. We have developed Development Of Molecular markers In Non-model Organisms (DOMINO), a bioinformatics tool for informative marker development from both next generation sequencing (NGS) data and pre-computed sequence alignments. The application implements popular NGS tools with new utilities in a highly versatile pipeline specifically designed to discover or select personalized markers at different levels of taxonomic resolution. These markers can be directly used to study the taxa surveyed for their design, utilized for further downstream PCR amplification in a broader set taxonomic scope, or exploited as suitable templates to bait design for target DNA enrichment techniques. We conducted an exhaustive evaluation of the performance of DOMINO via computer simulations and illustrate its utility to find informative markers in an empirical dataset. DOMINO is freely available from www.ub.edu/softevol/domino CONTACT: elsanchez@ub.edu or jrozas@ub.eduSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.